R3TS52 last accessed: 2022-11-04

reactome
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:48.431176

Other names: Reactome, a curated pathway database, reactome

REACTOME is an open-source, open access, manually curated and peer-reviewed pathway database.

Webpage:

http://reactome.org

Licence:

Name: Reactome-specific
URL: https://reactome.org/license

Publications: (11)

Publications
More detailed information about this field from each metasource.

The Reactome Pathway Knowledgebase
PMID: 29145629
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929

metasource: Fairsharing.org
version: FAIRsharing.org: Reactome; Reactome - a curated knowledgebase of biological pathways; DOI: https://doi.org/10.25504/FAIRsharing.tf6kj8; Last edited: March 12, 2021, 10:46 a.m.; Last accessed: Jan 03 2022 7:08 p.m.

The reactome pathway knowledgebase
PMID: 31691815
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929

metasource: Fairsharing.org
version: FAIRsharing.org: Reactome; Reactome - a curated knowledgebase of biological pathways; DOI: https://doi.org/10.25504/FAIRsharing.tf6kj8; Last edited: March 12, 2021, 10:46 a.m.; Last accessed: Jan 03 2022 7:08 p.m.

Reactome: a database of reactions, pathways and biological processes
PMID: 21067998
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:48.431176

Reactome: a knowledgebase of biological pathways
PMID: 15608231
metasource: Fairsharing.org
version: FAIRsharing.org: Reactome; Reactome - a curated knowledgebase of biological pathways; DOI: https://doi.org/10.25504/FAIRsharing.tf6kj8; Last edited: March 12, 2021, 10:46 a.m.; Last accessed: Jan 03 2022 7:08 p.m.

Reactome pathway analysis: a high-performance in-memory approach
PMID: 28249561
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929

Reactome graph database: Efficient access to complex pathway data
PMID: 29377902
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929

Reactome enhanced pathway visualization
PMID: 29077811
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929

Reactome diagram viewer: data structures and strategies to boost performance
PMID: 29186351
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929

Functional Interaction Network Construction and Analysis for Disease Discovery
PMID: 28150241
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929

The Reactome BioMart
PMID: 22012987
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:48.431176

http://dx.doi.org/10.1093/nar/gkt1102
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

The Reactome Pathway Knowledgebase PubMed citations: 1080.

1080 articles citing: The Reactome Pathway Knowledgebase

Breast cancer stage prediction: a computational approach guided by transcriptome analysis. PMID:35922530
CAF08 adjuvant enables single dose protection against respiratory syncytial virus infection in murine newborns. PMID:35918315
Challenges and Limitations of Biological Network Analysis. PMID:35892929
Getting Started with LINCS Datasets and Tools. PMID:35876555
The Culture Dish Surface Influences the Phenotype and Dissociation Strategy in Distinct Mouse Macrophage Populations. PMID:35874686
COVID-19 lung disease shares driver AT2 cytopathic features with Idiopathic pulmonary fibrosis. PMID:35870428
In-silico analysis of interacting pathways through KIM-1 protein interaction in diabetic nephropathy. PMID:35843953
Metabolite, protein, and tissue dysfunction associated with COVID-19 disease severity. PMID:35842456
Heparanase is a prognostic biomarker independent of tumor purity and hypoxia based on bioinformatics and immunohistochemistry analysis of esophageal squamous cell carcinoma. PMID:35840985
Multi-omics study identifies novel signatures of DNA/RNA, amino acid, peptide, and lipid metabolism by simulated diabetes on coronary endothelial cells. PMID:35835939
SARS-CoV-2 potential drugs, drug targets, and biomarkers: a viral-host interaction network-based analysis. PMID:35831333
A SOX17-PDGFB signaling axis regulates aortic root development. PMID:35831318
Inter- and intra-chromosomal modulators of the APOE ɛ2 and ɛ4 effects on the Alzheimer's disease risk. PMID:35809216
iPCD: A Comprehensive Data Resource of Regulatory Proteins in Programmed Cell Death. PMID:35805101
Recurrent somatic mutations as predictors of immunotherapy response. PMID:35803911
PolarMorphism enables discovery of shared genetic variants across multiple traits from GWAS summary statistics. PMID:35758773
Delayed Maturation of Oligodendrocyte Progenitors by Microgravity: Implications for Multiple Sclerosis and Space Flight. PMID:35743828
Polyphenols and IUGR Pregnancies: Effects of the Antioxidant Hydroxytyrosol on the Hippocampus Proteome in a Porcine Model. PMID:35740029
MLBioIGE: integration and interplay of machine learning and bioinformatics approach to identify the genetic effect of SARS-COV-2 on idiopathic pulmonary fibrosis patients. PMID:35734766
Exploration of the Nurse Shark (Ginglymostoma cirratum) Plasma Immunoproteome Using High-Resolution LC-MS/MS. PMID:35734164
Proteomic analysis reveals USP7 as a novel regulator of palmitic acid-induced hepatocellular carcinoma cell death. PMID:35732625
Time-resolved phosphoproteome and proteome analysis reveals kinase signaling on master transcription factors during myogenesis. PMID:35721465
Diagnostic value of abnormal chromosome 3p genes in small-cell lung cancer. PMID:35720498
Deriving time-concordant event cascades from gene expression data: A case study for Drug-Induced Liver Injury (DILI). PMID:35687583
Tissue Sampling and Homogenization with NIRL Enables Spatially Resolved Cell Layer Specific Proteomic Analysis of the Murine Intestine. PMID:35682811
An Integrated Multi-Omic Network Analysis Identifies Seizure-Associated Dysregulated Pathways in the GAERS Model of Absence Epilepsy. PMID:35682742
Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq data. PMID:35680885
Drug repositioning in non-small cell lung cancer (NSCLC) using gene co-expression and drug-gene interaction networks analysis. PMID:35676421
Seasonal and sex-dependent gene expression in emu (Dromaius novaehollandiae) fat tissues. PMID:35676317
Proteomic-based evidence for adult neurogenesis in birds and mammals as indicated from cerebrospinal fluid. PMID:35662184
Brain proteome profiling implicates the complement and coagulation cascade in multiple system atrophy brain pathology. PMID:35657417
Breaking the Immune Complexity of the Tumor Microenvironment Using Single-Cell Technologies. PMID:35651929
Identification of candidate biomarkers and pathways associated with type 1 diabetes mellitus using bioinformatics analysis. PMID:35650387
Small Molecule 20S Proteasome Enhancer Regulates MYC Protein Stability and Exhibits Antitumor Activity in Multiple Myeloma. PMID:35625675
An NF-κB- and Therapy-Related Regulatory Network in Glioma: A Potential Mechanism of Action for Natural Antiglioma Agents. PMID:35625673
Identification and Verification of m7G Modification Patterns and Characterization of Tumor Microenvironment Infiltration via Multi-Omics Analysis in Clear Cell Renal Cell Carcinoma. PMID:35592316
Human phospho-signaling networks of SARS-CoV-2 infection are rewired by population genetic variants. PMID:35579274
An Artificial Intelligence-guided signature reveals the shared host immune response in MIS-C and Kawasaki disease. PMID:35577777
Effects of age, amyloid, sex, and APOE ε4 on the CSF proteome in normal cognition. PMID:35571963
Small RNA sequencing and identification of papaya (Carica papaya L.) miRNAs with potential cross-kingdom human gene targets. PMID:35570207
Annotation and functional characterization of long noncoding RNAs deregulated in pancreatic adenocarcinoma. PMID:35567709
Cancer Metabolic Subtypes and Their Association with Molecular and Clinical Features. PMID:35565274
Skin Cancer-Associated S. aureus Strains Can Induce DNA Damage in Human Keratinocytes by Downregulating DNA Repair and Promoting Oxidative Stress. PMID:35565272
Identification of Potential Muscle Biomarkers in McArdle Disease: Insights from Muscle Proteome Analysis. PMID:35563042
Design and application of a knowledge network for automatic prioritization of drug mechanisms. PMID:35561182
A phase I trial of cyclosporine for hospitalized patients with COVID-19. PMID:35536669
Discovering Common Pathophysiological Processes between COVID-19 and Cystic Fibrosis by Differential Gene Expression Pattern Analysis. PMID:35528173
Identification of condition-specific regulatory mechanisms in normal and cancerous human lung tissue. PMID:35524179
A game changer for bipolar disorder diagnosis using RNA editing-based biomarkers. PMID:35504874
Synthetic lethality-based prediction of anti-SARS-CoV-2 targets. PMID:35502318
Mapping the epithelial-immune cell interactome upon infection in the gut and the upper airways. PMID:35501398
A systems genomics approach to uncover patient-specific pathogenic pathways and proteins in ulcerative colitis. PMID:35484353
Gene co-expression changes underlying the functional connectomic alterations in Alzheimer's disease. PMID:35461274
Darling: A Web Application for Detecting Disease-Related Biomedical Entity Associations with Literature Mining. PMID:35454109
On the influence of several factors on pathway enrichment analysis. PMID:35453140
De novo identification of maximally deregulated subnetworks based on multi-omics data with DeRegNet. PMID:35439941
SwissBioPics-an interactive library of cell images for the visualization of subcellular location data. PMID:35411389
Profiling Blood Serum Extracellular Vesicles in Plaque Psoriasis and Psoriatic Arthritis Patients Reveals Potential Disease Biomarkers. PMID:35409365
Physical and functional interactome atlas of human receptor tyrosine kinases. PMID:35384245
Non-linear archetypal analysis of single-cell RNA-seq data by deep autoencoders. PMID:35363784
Computational analyses of mechanism of action (MoA): data, methods and integration. PMID:35360890
Identifying and Validating Networks of Oncology Biomarkers Mined From the Scientific Literature. PMID:35342286
Reconstruction of a generic genome-scale metabolic network for chicken: Investigating network connectivity and finding potential biomarkers. PMID:35316277
scINSIGHT for interpreting single-cell gene expression from biologically heterogeneous data. PMID:35313930
BRCA1 mutations in high-grade serous ovarian cancer are associated with proteomic changes in DNA repair, splicing, transcription regulation and signaling. PMID:35292711
Artificial intelligence-rationalized balanced PPARα/γ dual agonism resets dysregulated macrophage processes in inflammatory bowel disease. PMID:35288651
Immune phenotype of the CD4+ T cells in the aged lymphoid organs and lacrimal glands. PMID:35279788
Identification of the shared gene signatures and pathways between sarcopenia and type 2 diabetes mellitus. PMID:35271662
Better Agreement of Human Transcriptomic and Proteomic Cancer Expression Data at the Molecular Pathway Activation Level. PMID:35269755
Network Approaches for Precision Oncology. PMID:35230690
A Transcriptomic Approach to Elucidate the Mechanisms of Gefitinib-Induced Toxicity in Healthy Human Intestinal Organoids. PMID:35216325
Integration of Transcriptome and Exome Genotyping Identifies Significant Variants with Autism Spectrum Disorder. PMID:35215271
DOTA: Deep Learning Optimal Transport Approach to Advance Drug Repositioning for Alzheimer's Disease. PMID:35204697
Chemerin Impact on Alternative mRNA Transcription in the Porcine Luteal Cells. PMID:35203364
The RD-Connect Genome-Phenome Analysis Platform: Accelerating diagnosis, research, and gene discovery for rare diseases. PMID:35178824
Single-Cell Analysis Uncovers Osteoblast Factor Growth Differentiation Factor 10 as Mediator of Vascular Smooth Muscle Cell Phenotypic Modulation Associated with Plaque Rupture in Human Carotid Artery Disease. PMID:35163719
Oxidative Stress Modulation by Carnosine in Scaffold Free Human Dermis Spheroids Model: A Proteomic Study. PMID:35163388
Unravelling Mechanisms of Doxorubicin-Induced Toxicity in 3D Human Intestinal Organoids. PMID:35163210
Single-Cell RNA-Seq Reveals a Crosstalk between Hyaluronan Receptor LYVE-1-Expressing Macrophages and Vascular Smooth Muscle Cells. PMID:35159221
HIF-1α Stabilization in Flagellin-Stimulated Human Bronchial Cells Impairs Barrier Function. PMID:35159204
A computational system for Bayesian benchmark dose estimation of genomic data in BBMD. PMID:35151117
Immune Infiltration of CD8+ T Cells in Patients With Diabetic Pancreatic Cancer Reduces the Malignancy of Cancer Tissues: An In Silico Study. PMID:35145483
Evolutionary rewiring of regulatory networks contributes to phenotypic differences between human and mouse orthologous genes. PMID:35137181
Multi-omic analysis reveals significantly mutated genes and DDX3X as a sex-specific tumor suppressor in cutaneous melanoma. PMID:35121978
RNF2 ablation reprograms the tumor-immune microenvironment and stimulates durable NK and CD4+ T-cell-dependent antitumor immunity. PMID:35121884
A new blood-based RNA signature (R9), for monitoring effectiveness of tuberculosis treatment in a South Indian longitudinal cohort. PMID:35118358
Comparison of confound adjustment methods in the construction of gene co-expression networks. PMID:35115012
Exploring the Contribution of (Poly)phenols to the Dietary Exposome Using High Resolution Mass Spectrometry Untargeted Metabolomics. PMID:35106906
Differences in thrombin and plasmin generation potential between East African and Western European adults: The role of genetic and non-genetic factors. PMID:35102686
Bromodomain Inhibition Reveals FGF15/19 As a Target of Epigenetic Regulation and Metabolic Control. PMID:35100352
Risk stratification of gastrointestinal stromal tumors by Nanostring gene expression profiling. PMID:35089395
Ubiquitous Aberration in Cholesterol Metabolism across Pancreatic Ductal Adenocarcinoma. PMID:35050168
Genome and transcriptome profiling of spontaneous preterm birth phenotypes. PMID:35046466
Identification of hub genes associated with COVID-19 and idiopathic pulmonary fibrosis by integrated bioinformatics analysis. PMID:35045126
The Highly Expressed IFIT1 in Nasopharyngeal Carcinoma Enhances Proliferation, Migration, and Invasion of Nasopharyngeal Carcinoma Cells. PMID:35038119
Assigning protein function from domain-function associations using DomFun. PMID:35033002
BATF promotes group 2 innate lymphoid cell-mediated lung tissue protection during acute respiratory virus infection. PMID:35030033
The breast pre-cancer atlas illustrates the molecular and micro-environmental diversity of ductal carcinoma in situ. PMID:35027560
Predicting sepsis severity at first clinical presentation: The role of endotypes and mechanistic signatures. PMID:35027333
Functional analysis of the stable phosphoproteome reveals cancer vulnerabilities. PMID:35015814
Potential biomarkers and signaling pathways associated with the pathogenesis of primary salivary gland carcinoma: a bioinformatics study. PMID:35012286
Temporal Quantitative Phosphoproteomics Profiling of Interleukin-33 Signaling Network Reveals Unique Modulators of Monocyte Activation. PMID:35011700
Potential Molecular Mechanisms and Remdesivir Treatment for Acute Respiratory Syndrome Corona Virus 2 Infection/COVID 19 Through RNA Sequencing and Bioinformatics Analysis. PMID:34992355
Genome-wide analysis of genetic predisposition to common polygenic cancers. PMID:34981446
Systems Biology and Bioinformatics approach to Identify blood based signatures molecules and drug targets of patient with COVID-19. PMID:34981034
Intermittent compressive force induces cell cycling and reduces apoptosis in embryoid bodies of mouse induced pluripotent stem cells. PMID:34980892
Multiplex-Heterogeneous Network-Based Capturing Potential SNP "Switches" of Pathways Associating With Diverse Disease Characteristics of Asthma. PMID:34970542
Different Glucose Metabolic Features According to Cancer and Immune Cells in the Tumor Microenvironment. PMID:34966676
Junctional instability in neuroepithelium and network hyperexcitability in a focal cortical dysplasia human model. PMID:34957478
GeneTonic: an R/Bioconductor package for streamlining the interpretation of RNA-seq data. PMID:34949163
Escherichia coli and Staphylococcus aureus Differentially Regulate Nrf2 Pathway in Bovine Mammary Epithelial Cells: Relation to Distinct Innate Immune Response. PMID:34943933
Elevated temperature inhibits SARS-CoV-2 replication in respiratory epithelium independently of IFN-mediated innate immune defenses. PMID:34932557
Deep learning tackles single-cell analysis-a survey of deep learning for scRNA-seq analysis. PMID:34929734
Altered microRNAs in C3H10T1/2 cells induced by p.E95K mutant IHH signaling. PMID:34922634
Exploring Pathway-Based Group Lasso for Cancer Survival Analysis: A Special Case of Multi-Task Learning. PMID:34912376
MRE11-dependent instability in mitochondrial DNA fork protection activates a cGAS immune signaling pathway. PMID:34910513
Single cell analysis of spondyloarthritis regulatory T cells identifies distinct synovial gene expression patterns and clonal fates. PMID:34907325
XDeathDB: a visualization platform for cell death molecular interactions. PMID:34907160
Multipopulational transcriptome analysis of post-weaned beef cattle at arrival further validates candidate biomarkers for predicting clinical bovine respiratory disease. PMID:34903778
Candida tropicalis Infection Modulates the Gut Microbiome and Confers Enhanced Susceptibility to Colitis in Mice. PMID:34890843
Meta-analyses identify DNA methylation associated with kidney function and damage. PMID:34887417
Epigenome-wide association study of serum urate reveals insights into urate co-regulation and the SLC2A9 locus. PMID:34887389
Proteomic Analysis Identifies FNDC1, A1BG, and Antigen Processing Proteins Associated with Tumor Heterogeneity and Malignancy in a Canine Model of Breast Cancer. PMID:34885011
Identification of KLF6/PSGs and NPY-Related USF2/CEACAM Transcriptional Regulatory Networks via Spinal Cord Bulk and Single-Cell RNA-Seq Analysis. PMID:34880956
A computational approach for the discovery of significant cancer genes by weighted mutation and asymmetric spreading strength in networks. PMID:34876593
Multi-omic machine learning predictor of breast cancer therapy response. PMID:34875674
Systems biology and machine learning approaches identify drug targets in diabetic nephropathy. PMID:34873190
Sparse Regression in Cancer Genomics: Comparing Variable Selection and Predictions in Real World Data. PMID:34866896
Functional enrichment of alternative splicing events with NEASE reveals insights into tissue identity and diseases. PMID:34857024
Gene regulatory network analysis defines transcriptome landscape with alternative splicing of human umbilical vein endothelial cells during replicative senescence. PMID:34856941
Exploring cell-specific miRNA regulation with single-cell miRNA-mRNA co-sequencing data. PMID:34856921
Expression of transport proteins in the rete mirabile of european silver and yellow eel. PMID:34856920
Molecular Signature and Immune Landscape of HCV-Associated Hepatocellular Carcinoma (HCC): Differences and Similarities with HBV-HCC. PMID:34849372
Genes and regulatory mechanisms associated with experimentally-induced bovine respiratory disease identified using supervised machine learning methodology. PMID:34824337
p300 or CBP is required for insulin-stimulated glucose uptake in skeletal muscle and adipocytes. PMID:34813504
Molecular Subclassification Based on Crosstalk Analysis Improves Prediction of Prognosis in Colorectal Cancer. PMID:34804112
Discriminative feature of cells characterizes cell populations of interest by a small subset of genes. PMID:34797848
HFIP: an integrated multi-omics data and knowledge platform for the precision medicine of heart failure. PMID:34791105
CyFi-MAP: an interactive pathway-based resource for cystic fibrosis. PMID:34782688
Deletion of GPR21 improves glucose homeostasis and inhibits the CCL2-CCR2 axis by divergent mechanisms. PMID:34782333
Tackling the Biological Meaning of the Human Olfactory Bulb Dyshomeostatic Proteome across Neurological Disorders: An Integrative Bioinformatic Approach. PMID:34768771
Transcriptomic Response of Primary Human Bronchial Cells to Repeated Exposures of Cigarette and ENDS Preparations. PMID:34767151
Severe types of fetopathy are associated with changes in the serological proteome of diabetic mothers. PMID:34766598
Identification of Pathway-Based Biomarkers with Crosstalk Analysis for Overall Survival Risk Prediction in Breast Cancer. PMID:34745202
International Prognostic Index-Based Immune Prognostic Model for Diffuse Large B-Cell Lymphoma. PMID:34745101
Genomic and Epigenomic Evaluation of Electrically Induced Exercise in People With Spinal Cord Injury: Application to Precision Rehabilitation. PMID:34718779
The unfolded protein response links tumor aneuploidy to local immune dysregulation. PMID:34698427
PIM1 phosphorylation of the androgen receptor and 14-3-3 ζ regulates gene transcription in prostate cancer. PMID:34697370
Machine learning applications for therapeutic tasks with genomics data. PMID:34693370
TPSC: a module detection method based on topology potential and spectral clustering in weighted networks and its application in gene co-expression module discovery. PMID:34689740
Regulatory insights into progression of cancer and Alzheimer's disorder from autophagy perspective. PMID:34665401
Association of peripheral blood DNA methylation level with Alzheimer's disease progression. PMID:34654479
Metabolic gene regulation by Drosophila GATA transcription factor Grain. PMID:34634038
SPT6 loss permits the transdifferentiation of keratinocytes into an intestinal fate that resembles Barrett's metaplasia. PMID:34622168
A protocol for dynamic model calibration. PMID:34619769
Bioinformatics and system biology approaches to identify pathophysiological impact of COVID-19 to the progression and severity of neurological diseases. PMID:34601390
Repurposing haloperidol for the treatment of rheumatoid arthritis: an integrative approach using data mining techniques. PMID:34589142
Integrative proteome analysis implicates aberrant RNA splicing in impaired developmental potential of aged mouse oocytes. PMID:34582091
Deep learning in cancer diagnosis, prognosis and treatment selection. PMID:34579788
Spatial variation in gene expression of Tasmanian devil facial tumors despite minimal host transcriptomic response to infection. PMID:34579650
Lepidium sativum Secondary Metabolites (Essential Oils): In Vitro and In Silico Studies on Human Hepatocellular Carcinoma Cell Lines. PMID:34579396
Synergistic Interactions of Cannabidiol with Chemotherapeutic Drugs in MCF7 Cells: Mode of Interaction and Proteomics Analysis of Mechanisms. PMID:34576262
Whole-Genome Profiles of Malay Colorectal Cancer Patients with Intact MMR Proteins. PMID:34573430
Comparative Transcriptome Analysis of the Expression of Antioxidant and Immunity Genes in the Spleen of a Cyanidin 3-O-Glucoside-Treated Alzheimer's Mouse Model. PMID:34573067
Platelet miRNA Biosignature Discriminates between Dementia with Lewy Bodies and Alzheimer's Disease. PMID:34572457
Meta-analysis and Consolidation of Farnesoid X Receptor Chromatin Immunoprecipitation Sequencing Data Across Different Species and Conditions. PMID:34558825
Metabolite patterns link diet, obesity, and type 2 diabetes in a Hispanic population. PMID:34553271
The role of metadata in reproducible computational research. PMID:34553169
Biologically informed deep neural network for prostate cancer discovery. PMID:34552244
Deep GONet: self-explainable deep neural network based on Gene Ontology for phenotype prediction from gene expression data. PMID:34551707
Molecular diversity of diencephalic astrocytes reveals adult astrogenesis regulated by Smad4. PMID:34549820
Synthetic lethality-based prediction of anti-SARS-CoV-2 targets. PMID:34545363
Proteogenomic characterization of pancreatic ductal adenocarcinoma. PMID:34534465
Mechanism of Radix Rhei Et Rhizome Intervention in Cerebral Infarction: A Research Based on Chemoinformatics and Systematic Pharmacology. PMID:34531920
Identifying digenic disease genes via machine learning in the Undiagnosed Diseases Network. PMID:34529933
Computational drug repositioning of atorvastatin for ulcerative colitis. PMID:34529084
LPCAT1 reprogramming cholesterol metabolism promotes the progression of esophageal squamous cell carcinoma. PMID:34518524
Investigating the Molecular Processes behind the Cell-Specific Toxicity Response to Titanium Dioxide Nanobelts. PMID:34502343
A lymphocyte-microglia-astrocyte axis in chronic active multiple sclerosis. PMID:34497421
Integrative transcriptomic profiling of a mouse model of hypertension-accelerated diabetic kidney disease. PMID:34494644
The association of immunosurveillance and distant metastases in colorectal cancer. PMID:34476575
18F-FDG PET/CT metabolic parameters correlate with EIF2S2 expression status in colorectal cancer. PMID:34475997
A machine learning framework for predicting drug-drug interactions. PMID:34475500
Small RNA sequencing evaluation of renal microRNA biomarkers in dogs with X-linked hereditary nephropathy. PMID:34465843
Adult stem cell-derived complete lung organoid models emulate lung disease in COVID-19. PMID:34463615
Effect of ciglitazone on adipogenic transdifferentiation of bovine skeletal muscle satellite cells. PMID:34447968
A Novel Approach for the Discovery of Biomarkers of Radiotherapy Response in Breast Cancer. PMID:34442440
A Mediation Approach to Discovering Causal Relationships between the Metabolome and DNA Methylation in Type 1 Diabetes. PMID:34436483
PathExNET: A tool for extracting pathway expression networks from gene expression statistics. PMID:34429851
Dietary omega-3 fatty acid intake impacts peripheral blood DNA methylation -anti-inflammatory effects and individual variability in a pilot study. PMID:34411715
Genome-scale metabolic modelling of SARS-CoV-2 in cancer cells reveals an increased shift to glycolytic energy production. PMID:34409594
NGF-TrkA signaling dictates neural ingrowth and aberrant osteochondral differentiation after soft tissue trauma. PMID:34400627
Altered regulation of DPF3, a member of the SWI/SNF complexes, underlies the 14q24 renal cancer susceptibility locus. PMID:34390653
Patients with PWS and related syndromes display differentially methylated regions involved in neurodevelopmental and nutritional trajectory. PMID:34389046
Safety and feasibility of an in situ vaccination and immunomodulatory targeted radionuclide combination immuno-radiotherapy approach in a comparative (companion dog) setting. PMID:34383787
A Multi-omics Longitudinal Study Reveals Alteration of the Leukocyte Activation Pathway in COVID-19 Patients. PMID:34379420
Metabolomic Identification of Anticancer Metabolites of Australian Propolis and Proteomic Elucidation of Its Synergistic Mechanisms with Doxorubicin in the MCF7 Cells. PMID:34360606
Functional Analysis of Non-Genetic Resistance to Platinum in Epithelial Ovarian Cancer Reveals a Role for the MBD3-NuRD Complex in Resistance Development. PMID:34359703
A proteogenomic portrait of lung squamous cell carcinoma. PMID:34358469
FLAME: A Web Tool for Functional and Literature Enrichment Analysis of Multiple Gene Lists. PMID:34356520
DNA and RNA Sequencing Recapitulated Aberrant Tumor Metabolism in Liver Cancer Cell Lines. PMID:34350138
Differentially Expressed Gene Pathways in the Conjunctiva of Sjögren Syndrome Keratoconjunctivitis Sicca. PMID:34349764
Identifying molecular insight of synergistic complexities for SARS-CoV-2 infection with pre-existing type 2 diabetes. PMID:34340124
TMEM180 contributes to SW480 human colorectal cancer cell proliferation through intra-cellular metabolic pathways. PMID:34332338
Stress-primed secretory autophagy promotes extracellular BDNF maturation by enhancing MMP9 secretion. PMID:34330919
Transcriptome features of striated muscle aging and predictability of protein level changes. PMID:34328155
RNA sequencing identifies global transcriptional changes in peripheral CD4+ cells during active oesophagitis and following epicutaneous immunotherapy in eosinophilic oesophagitis. PMID:34322233
VarSAn: associating pathways with a set of genomic variants using network analysis. PMID:34313777
A new strategy to uncover fragile X proteomic biomarkers using the nascent proteome of peripheral blood mononuclear cells (PBMCs). PMID:34312401
HSP90 inhibition downregulates DNA replication and repair genes via E2F1 repression. PMID:34302809
Genetic mapping of novel modifiers for ApcMin induced intestinal polyps' development using the genetic architecture power of the collaborative cross mice. PMID:34294033
Development of a Novel Immune Infiltration-Related ceRNA Network and Prognostic Model for Sarcoma. PMID:34277600
Predicting mechanism of action of novel compounds using compound structure and transcriptomic signature coembedding. PMID:34252937
Chronic cerebral lipocalin 2 exposure elicits hippocampal neuronal dysfunction and cognitive impairment. PMID:34245812
Identification of anticancer drug target genes using an outside competitive dynamics model on cancer signaling networks. PMID:34238960
Upregulating KTN1 promotes Hepatocellular Carcinoma progression. PMID:34234850
A comprehensive review of integrative pharmacology-based investigation: A paradigm shift in traditional Chinese medicine. PMID:34221858
Identification of candidate biomarkers and therapeutic agents for heart failure by bioinformatics analysis. PMID:34218797
Applications and analytical tools of cell communication based on ligand-receptor interactions at single cell level. PMID:34217372
Parkinson's disease patient-specific neuronal networks carrying the LRRK2 G2019S mutation unveil early functional alterations that predate neurodegeneration. PMID:34215735
The Genome-Wide Binding Profile for Human RE1 Silencing Transcription Factor Unveils a Unique Genetic Circuitry in Hippocampus. PMID:34210779
Clinical characteristics and genetic spectrum of 26 individuals of Chinese origin with primary ciliary dyskinesia. PMID:34210339
Toward a Coronavirus Knowledge Graph. PMID:34209818
OmiEmbed: A Unified Multi-Task Deep Learning Framework for Multi-Omics Data. PMID:34207255
Acetyl Coenzyme A Synthase 2 Acts as a Prognostic Biomarker Associated with Immune Infiltration in Cervical Squamous Cell Carcinoma. PMID:34206705
A Comprehensive Bioinformatics Analysis of Notch Pathways in Bladder Cancer. PMID:34205690
Orthosiphon stamineus Proteins Alleviate Hydrogen Peroxide Stress in SH-SY5Y Cells. PMID:34202937
Global Proteomic Profiling of Pediatric AML: A Pilot Study. PMID:34202615
CROssBAR: comprehensive resource of biomedical relations with knowledge graph representations. PMID:34181736
Molecular determinants of response to PD-L1 blockade across tumor types. PMID:34172722
Evolution of fibroblasts in the lung metastatic microenvironment is driven by stage-specific transcriptional plasticity. PMID:34169837
Environmental enrichment preserves a young DNA methylation landscape in the aged mouse hippocampus. PMID:34162876
Microbial and genetic-based framework identifies drug targets in inflammatory bowel disease. PMID:34158863
New insights into the mechanisms underlying 5-fluorouracil-induced intestinal toxicity based on transcriptomic and metabolomic responses in human intestinal organoids. PMID:34151400
Low CLOCK and CRY2 in 2nd trimester human maternal blood and risk of preterm birth: a nested case-control study†. PMID:34142702
Somatic mutation subtypes of lung adenocarcinoma in East Asian reveal divergent biological characteristics and therapeutic vulnerabilities. PMID:34142036
Transcriptomic analyses of gastrulation-stage mouse embryos with differential susceptibility to alcohol. PMID:34137816
Genome-scale mechanistic modeling of signaling pathways made easy: A bioconductor/cytoscape/web server framework for the analysis of omic data. PMID:34136096
AI-guided discovery of the invariant host response to viral pandemics. PMID:34127431
Predicting biological pathways of chemical compounds with a profile-inspired approach. PMID:34118870
netgsa: Fast computation and interactive visualization for topology-based pathway enrichment analysis. PMID:34115744
Macropinocytosis requires Gal-3 in a subset of patient-derived glioblastoma stem cells. PMID:34112916
Metagenomic Next-Generation Sequencing for Pathogen Detection and Transcriptomic Analysis in Pediatric Central Nervous System Infections. PMID:34104666
Acyl-CoA synthetase 6 is required for brain docosahexaenoic acid retention and neuroprotection during aging. PMID:34100386
Molecular omics resources should require sex annotation: a call for action. PMID:34099934
Drug repurposing screens identify chemical entities for the development of COVID-19 interventions. PMID:34083527
Immunological and hematological outcomes following protracted low dose/low dose rate ionizing radiation and simulated microgravity. PMID:34075076
Revisiting Ehrlichia ruminantium Replication Cycle Using Proteomics: The Host and the Bacterium Perspectives. PMID:34073568
Modulation of Early Neutrophil Granulation: The Circulating Tumor Cell-Extravesicular Connection in Pancreatic Ductal Adenocarcinoma. PMID:34072942
Genome-Wide Analysis of Sex Disparities in the Genetic Architecture of Lung and Colorectal Cancers. PMID:34062886
Multi-Dimensional Transcriptome Analysis Reveals Modulation of Cholesterol Metabolism as Highly Integrated Response to Brain Injury. PMID:34054419
Rapid evolution of mammalian APLP1 as a synaptic adhesion molecule. PMID:34050225
Pooled CRISPR screening in pancreatic cancer cells implicates co-repressor complexes as a cause of multiple drug resistance via regulation of epithelial-to-mesenchymal transition. PMID:34049503
Mergeomics 2.0: a web server for multi-omics data integration to elucidate disease networks and predict therapeutics. PMID:34048577
Computational Biology and Machine Learning Approaches to Understand Mechanistic Microbiome-Host Interactions. PMID:34046017
Using Interpretable Deep Learning to Model Cancer Dependencies. PMID:34042953
Loss of 15-lipoxygenase disrupts Treg differentiation altering their pro-resolving functions. PMID:34040168
The Drosophila brain on cocaine at single-cell resolution. PMID:34035044
Pan-cancer characterization of metabolism-related biomarkers identifies potential therapeutic targets. PMID:34030708
KEA3: improved kinase enrichment analysis via data integration. PMID:34019655
Utilizing graph machine learning within drug discovery and development. PMID:34013350
An overview of graph databases and their applications in the biomedical domain. PMID:34003247
A miR-375/YAP axis regulates neuroendocrine differentiation and tumorigenesis in lung carcinoid cells. PMID:34001972
Transcriptome Analyses Reveal IL6/Stat3 Signaling Involvement in Radial Glia Proliferation After Stab Wound Injury in the Adult Zebrafish Optic Tectum. PMID:33996824
ProteoMill: Efficient network-based functional analysis portal for proteomics data. PMID:33978717
A detailed map of coupled circadian clock and cell cycle with qualitative dynamics validation. PMID:33975535
The transcriptional landscape analysis of basal cell carcinomas reveals novel signalling pathways and actionable targets. PMID:33972406
Integrative-omics for discovery of network-level disease biomarkers: a case study in Alzheimer's disease. PMID:33971669
Pharmacological Mechanisms Underlying the Anti-asthmatic Effects of Modified Guomin Decoction Determined by Network Pharmacology and Molecular Docking. PMID:33968984
Integration of peripheral transcriptomics, genomics, and interactomics following trauma identifies causal genes for symptoms of post-traumatic stress and major depression. PMID:33963278
EARN: an ensemble machine learning algorithm to predict driver genes in metastatic breast cancer. PMID:33962648
Dual proteome-scale networks reveal cell-specific remodeling of the human interactome. PMID:33961781
Knowledge-Based Biomedical Data Science. PMID:33954284
The genomic basis of evolutionary differentiation among honey bees. PMID:33947700
Spatial Distribution of Private Gene Mutations in Clear Cell Renal Cell Carcinoma. PMID:33946379
Schema: metric learning enables interpretable synthesis of heterogeneous single-cell modalities. PMID:33941239
Functional and genetic determinants of mutation rate variability in regulatory elements of cancer genomes. PMID:33941236
RNA-seq analysis of ageing human retinal pigment epithelium: Unexpected up-regulation of visual cycle gene transcription. PMID:33934486
Caveolin-1-driven membrane remodelling regulates hnRNPK-mediated exosomal microRNA sorting in cancer. PMID:33931969
A clinical transcriptome approach to patient stratification and therapy selection in acute myeloid leukemia. PMID:33931648
Impairment of the neurotrophic signaling hub B-Raf contributes to motoneuron degeneration in spinal muscular atrophy. PMID:33931501
Potential impact of celiac disease genetic risk factors on T cell receptor signaling in gluten-specific CD4+ T cells. PMID:33927210
RNA-Seq Reveals Function of Bta-miR-149-5p in the Regulation of Bovine Adipocyte Differentiation. PMID:33922274
Identification of Novel Biomarkers and Candidate Drug in Ovarian Cancer. PMID:33921660
Multi-Omics Approaches to Define Calcific Aortic Valve Disease Pathogenesis. PMID:33914608
The microRNA analysis portal is a next-generation tool for exploring and analyzing miRNA-focused data in the literature. PMID:33903708
Gene network and biological pathways associated with susceptibility to differentiated thyroid carcinoma. PMID:33903625
Investigation of candidate genes and mechanisms underlying obesity associated type 2 diabetes mellitus using bioinformatics analysis and screening of small drug molecules. PMID:33902539
Comprehensive at-arrival transcriptomic analysis of post-weaned beef cattle uncovers type I interferon and antiviral mechanisms associated with bovine respiratory disease mortality. PMID:33901263
An integrated landscape of protein expression in human cancer. PMID:33893311
Finding associations in a heterogeneous setting: statistical test for aberration enrichment. PMID:33892787
Integrated bioinformatics analysis reveals novel key biomarkers and potential candidate small molecule drugs in gestational diabetes mellitus. PMID:33890634
Transcriptional profile in rat muscle: down-regulation networks in acute strenuous exercise. PMID:33859869
Crop breeding for a changing climate: integrating phenomics and genomics with bioinformatics. PMID:33852055
PNOC Expressed by B Cells in Cholangiocarcinoma Was Survival Related and LAIR2 Could Be a T Cell Exhaustion Biomarker in Tumor Microenvironment: Characterization of Immune Microenvironment Combining Single-Cell and Bulk Sequencing Technology. PMID:33841428
MendelVar: gene prioritization at GWAS loci using phenotypic enrichment of Mendelian disease genes. PMID:33836063
Peptide location fingerprinting reveals modification-associated biomarker candidates of ageing in human tissue proteomes. PMID:33830638
Selected Clostridia Strains from The Human Microbiota and their Metabolite, Butyrate, Improve Experimental Autoimmune Encephalomyelitis. PMID:33829410
Identification of hub genes related to the progression of type 1 diabetes by computational analysis. PMID:33827531
MicroRNA-29 is an essential regulator of brain maturation through regulation of CH methylation. PMID:33826889
In Vitro Radiosensitivity of Murine Marrow Stromal Cells Varies Across Donor Strains. PMID:33826738
A NOVEL NOX/PHOX-CD38-NAADP-TFEB AXIS IMPORTANT FOR MACROPHAGE ACTIVATION DURING BACTERIAL PHAGOCYTOSIS. PMID:33818279
Network bioinformatics analysis provides insight into drug repurposing for COVID-19. PMID:33817623
Identification of Breast Cancer Subtype-Specific Biomarkers by Integrating Copy Number Alterations and Gene Expression Profiles. PMID:33809336
Harnessing the IL-21-BATF Pathway in the CD8+ T Cell Anti-Tumor Response. PMID:33809259
Distinct miRNA Signatures and Networks Discern Fetal from Adult Erythroid Differentiation and Primary from Immortalized Erythroid Cells. PMID:33807258
A Streamlined Approach to Pathway Analysis from RNA-Sequencing Data. PMID:33802642
A Detailed Catalogue of Multi-Omics Methodologies for Identification of Putative Biomarkers and Causal Molecular Networks in Translational Cancer Research. PMID:33802234
Dissection of the Genetic Association between Anorexia Nervosa and Obsessive-Compulsive Disorder at the Network and Cellular Levels. PMID:33801746
Integrative Data Analytic Framework to Enhance Cancer Precision Medicine. PMID:33796878
An energy metabolism-based eight-gene signature correlates with the clinical outcome of esophagus carcinoma. PMID:33794814
Aconiti lateralis Radix Praeparata inhibits Alzheimer's disease by regulating the complex regulation network with the core of GRIN1 and MAPK1. PMID:33784489
Ceratothoa oestroides Infection in European Sea Bass: Revealing a Long Misunderstood Relationship. PMID:33777043
Regulatory Function of Sympathetic Innervation on the Endo/Lysosomal Trafficking of Acetylcholine Receptor. PMID:33776791
Immune modulation underpins the anti-cancer activity of HDAC inhibitors. PMID:33773029
Genome-wide transcriptome study in skin biopsies reveals an association of E2F4 with cadasil and cognitive impairment. PMID:33767277
Elevated glucose represses lysosomal and mTOR-related genes in renal epithelial cells composed of progenitor CD133+ cells. PMID:33764985
Deep learning assisted multi-omics integration for survival and drug-response prediction in breast cancer. PMID:33761889
SBGN Bricks Ontology as a tool to describe recurring concepts in molecular networks. PMID:33758926
Radium-223 Treatment Increases Immune Checkpoint Expression in Extracellular Vesicles from the Metastatic Prostate Cancer Bone Microenvironment. PMID:33753455
Appyters: Turning Jupyter Notebooks into data-driven web apps. PMID:33748796
Noise regularization removes correlation artifacts in single-cell RNA-seq data preprocessing. PMID:33748795
FunHoP: Enhanced Visualization and Analysis of Functionally Homologous Proteins in Complex Metabolic Networks. PMID:33741524
Pathway size matters: the influence of pathway granularity on over-representation (enrichment analysis) statistics. PMID:33726670
Integration of summary data from GWAS and eQTL studies identified novel risk genes for coronary artery disease. PMID:33725943
COVID-19 patient transcriptomic and genomic profiling reveals comorbidity interactions with psychiatric disorders. PMID:33723208
How to Get Started with Single Cell RNA Sequencing Data Analysis. PMID:33722930
Comprehensive Integration of Genome-Wide Association and Gene Expression Studies Reveals Novel Gene Signatures and Potential Therapeutic Targets for Helicobacter pylori-Induced Gastric Disease. PMID:33717131
Integrated cross-study datasets of genetic dependencies in cancer. PMID:33712601
Identification of potential and novel target genes in pituitary prolactinoma by bioinformatics analysis. PMID:33709028
An RNA tagging approach for system-wide RNA-binding proteome profiling and dynamics investigation upon transcription inhibition. PMID:33693821
Integrative network analyses of transcriptomics data reveal potential drug targets for acute radiation syndrome. PMID:33692493
Frequent Subgraph Mining of Functional Interaction Patterns Across Multiple Cancers. PMID:33691023
Discovery of novel candidates for anti-liposarcoma therapies by medium-scale high-throughput drug screening. PMID:33690666
IFN signaling and neutrophil degranulation transcriptional signatures are induced during SARS-CoV-2 infection. PMID:33674719
Comparison of plasma and cerebrospinal fluid proteomes identifies gene products guiding adult neurogenesis and neural differentiation in birds. PMID:33674647
Colocalization analysis of polycystic ovary syndrome to identify potential disease-mediating genes and proteins. PMID:33664499
Impact of obesity on day-night differences in cardiac metabolism. PMID:33660366
Identification of candidate genes and pathways in retinopathy of prematurity by whole exome sequencing of preterm infants enriched in phenotypic extremes. PMID:33654115
Calf Diarrhea Caused by Prolonged Expansion of Autochthonous Gut Enterobacteriaceae and Their Lytic Bacteriophages. PMID:33653940
The angiogenic potential of CD271+ human adipose tissue-derived mesenchymal stem cells. PMID:33653407
Dual DNA and protein tagging of open chromatin unveils dynamics of epigenomic landscapes in leukemia. PMID:33649590
Transcriptome analysis of ciliary-dependent MCH signaling in differentiating 3T3-L1 pre-adipocytes. PMID:33649390
Differential regulation of β-catenin-mediated transcription via N- and C-terminal co-factors governs identity of murine intestinal epithelial stem cells. PMID:33649334
The Peripheral Blood Transcriptome Is Correlated With PET Measures of Lung Inflammation During Successful Tuberculosis Treatment. PMID:33643286
Linking clinotypes to phenotypes and genotypes from laboratory test results in comprehensive physical exams. PMID:33627109
Automating parameter selection to avoid implausible biological pathway models. PMID:33623016
Comparative Genomics and Integrated Network Approach Unveiled Undirected Phylogeny Patterns, Co-mutational Hot Spots, Functional Cross Talk, and Regulatory Interactions in SARS-CoV-2. PMID:33622851
Identification of key pathways and genes in polycystic ovary syndrome via integrated bioinformatics analysis and prediction of small therapeutic molecules. PMID:33622336
Intraductal xenografts show lobular carcinoma cells rely on their own extracellular matrix and LOXL1. PMID:33616307
Elavl1 Impacts Osteogenic Differentiation and mRNA Levels of Genes Involved in ECM Organization. PMID:33614643
Identification of biomarkers and pathways for the SARS-CoV-2 infections that make complexities in pulmonary arterial hypertension patients. PMID:33611340
Public data sources to support systems toxicology applications. PMID:33604492
Enrichment analyses of diseases and pathways associated with precocious puberty using PrecocityDB. PMID:33602974
Virus infection of the CNS disrupts the immune-neural-synaptic axis via induction of pleiotropic gene regulation of host responses. PMID:33599611
Dissection of intercellular communication using the transcriptome-based framework ICELLNET. PMID:33597528
Relaxed initiation pausing of ribosomes drives oncogenic translation. PMID:33597240
Converting disease maps into heavyweight ontologies: general methodology and application to Alzheimer's disease. PMID:33590873
Searching for a Putative Mechanism of RIZ2 Tumor-Promoting Function in Cancer Models. PMID:33585202
Proteogenomic and metabolomic characterization of human glioblastoma. PMID:33577785
UniProt-Related Documents (UniReD): assisting wet lab biologists in their quest on finding novel counterparts in a protein network. PMID:33575553
Improved cancer biomarkers identification using network-constrained infinite latent feature selection. PMID:33571282
Bioinformatics analyses of significant genes, related pathways, and candidate diagnostic biomarkers and molecular targets in SARS-CoV-2/COVID-19. PMID:33553808
Genetic and functional interaction network analysis reveals global enrichment of regulatory T cell genes influencing basal cell carcinoma susceptibility. PMID:33549134
A Meta-Analysis of the Effects of High-LET Ionizing Radiations in Human Gene Expression. PMID:33546472
TP53 Mutations as a Driver of Metastasis Signaling in Advanced Cancer Patients. PMID:33546249
The Genetics of Sudden Infant Death Syndrome-Towards a Gene Reference Resource. PMID:33540853
Clinical, histopathologic and molecular features of idiopathic and diabetic nodular mesangial sclerosis in humans. PMID:33537765
Differential DNA methylation in recovery from shift work disorder. PMID:33536559
Identification of 38 novel loci for systemic lupus erythematosus and genetic heterogeneity between ancestral groups. PMID:33536424
A comprehensive evaluation of skin aging-related circular RNA expression profiles. PMID:33534927
ViralLink: An integrated workflow to investigate the effect of SARS-CoV-2 on intracellular signalling and regulatory pathways. PMID:33534793
Atherosclerosis Regression and Cholesterol Efflux in Hypertriglyceridemic Mice. PMID:33530703
Single-Cell Gene Network Analysis and Transcriptional Landscape of MYCN-Amplified Neuroblastoma Cell Lines. PMID:33525507
Human pathways in animal models: possibilities and limitations. PMID:33524155
Gene expression signatures of target tissues in type 1 diabetes, lupus erythematosus, multiple sclerosis, and rheumatoid arthritis. PMID:33523973
Synthetic lethality across normal tissues is strongly associated with cancer risk, onset, and tumor suppressor specificity. PMID:33523837
Pathway-Based Drug-Repurposing Schemes in Cancer: The Role of Translational Bioinformatics. PMID:33520715
ICN: Extracting interconnected communities in gene Co-expression networks. PMID:33508087
Differential DNA Methylation Landscape in Skin Fibroblasts from African Americans with Systemic Sclerosis. PMID:33498390
Evaluation of Computationally Designed Peptides against TWEAK, a Cytokine of the Tumour Necrosis Factor Ligand Family. PMID:33494438
Loss of Parkinson's susceptibility gene LRRK2 promotes carcinogen-induced lung tumorigenesis. PMID:33483550
Integrative computational approach identifies drug targets in CD4+ T-cell-mediated immune disorders. PMID:33483502
MicroExonator enables systematic discovery and quantification of microexons across mouse embryonic development. PMID:33482885
Likelihood ratio statistics for gene set enrichment in Alzheimer's disease pathways. PMID:33480182
Selective antisense oligonucleotide inhibition of human IRF4 prevents malignant myeloma regeneration via cell cycle disruption. PMID:33476575
Tumour inflammation signature and expression of S100A12 and HLA class I improve survival in HPV-negative hypopharyngeal cancer. PMID:33469045
Relationship between CD4 T cell turnover, cellular differentiation and HIV persistence during ART. PMID:33465157
Prediction and mechanistic analysis of drug-induced liver injury (DILI) based on chemical structure. PMID:33461600
Diverse Taxonomies for Diverse Chemistries: Enhanced Representation of Natural Product Metabolism in UniProtKB. PMID:33445429
Disease severity-specific neutrophil signatures in blood transcriptomes stratify COVID-19 patients. PMID:33441124
Post-transcriptional circadian regulation in macrophages organizes temporally distinct immunometabolic states. PMID:33436377
Evaluating accessibility, usability and interoperability of genome-scale metabolic models for diverse yeasts species. PMID:33428734
Deferoxamine mesylate improves splicing and GAA activity of the common c.-32-13T>G allele in late-onset PD patient fibroblasts. PMID:33426149
An Integrated Platform for Skin Cancer Heterogenous and Multilayered Data Management. PMID:33404959
Somatostatin receptor 2 expression in nasopharyngeal cancer is induced by Epstein Barr virus infection: impact on prognosis, imaging and therapy. PMID:33402692
Analysis of the TCGA Dataset Reveals that Subsites of Laryngeal Squamous Cell Carcinoma are Molecularly Distinct. PMID:33396315
Network- and systems-based re-engineering of dendritic cells with non-coding RNAs for cancer immunotherapy. PMID:33391542
The Large Scale Structure of Human Metabolism Reveals Resilience via Extensive Signaling Crosstalk. PMID:33391012
Upregulation of peroxisome proliferator-activated receptor-α and the lipid metabolism pathway promotes carcinogenesis of ampullary cancer. PMID:33390794
The Proteomic Landscape of Resting and Activated CD4+ T Cells Reveal Insights into Cell Differentiation and Function. PMID:33383959
The Interactome of Cancer-Related Lysyl Oxidase and Lysyl Oxidase-Like Proteins. PMID:33383846
Functional Genomic Analysis of a RUNX3 Polymorphism Associated With Ankylosing Spondylitis. PMID:33369221
MultiPaths: a python framework for analyzing multi-layer biological networks using diffusion algorithms. PMID:33367476
scLM: Automatic Detection of Consensus Gene Clusters Across Multiple Single-cell Datasets. PMID:33359676
Does tetanus vaccination contribute to reduced severity of the COVID-19 infection? PMID:33341328
Roundup causes embryonic development failure and alters metabolic pathways and gut microbiota functionality in non-target species. PMID:33339542
Gene expression profiling of SARS-CoV-2 infections reveal distinct primary lung cell and systemic immune infection responses that identify pathways relevant in COVID-19 disease. PMID:33333559
Exercise during pregnancy mitigates negative effects of parental obesity on metabolic function in adult mouse offspring. PMID:33332990
The miR-23a∼27a∼24-2 microRNA Cluster Promotes Inflammatory Polarization of Macrophages. PMID:33328213
Characterisation of gene and pathway expression in stabilised blood from children with coeliac disease. PMID:33323471
NF-κB Signaling Is Regulated by Fucosylation in Metastatic Breast Cancer Cells. PMID:33322811
Postnatal Growth Restriction in Mice Alters Cardiac Protein Composition and Leads to Functional Impairment in Adulthood. PMID:33322681
DriveWays: a method for identifying possibly overlapping driver pathways in cancer. PMID:33319839
Hearing impairment due to Mir183/96/182 mutations suggests both loss and gain of function effects. PMID:33318051
Rho-GTPase pathways may differentiate treatment response to TNF-alpha and IL-17A inhibitors in psoriatic arthritis. PMID:33303908
Comprehensive gene expression profiling of human astrocytes treated with a hepatic encephalopathy-inducible factor, alpha 1-antichymotripsin. PMID:33299931
Multi-Omics Analysis Identifying Key Biomarkers in Ovarian Cancer. PMID:33297760
Identification of Dysregulated Genes for Late-Onset Alzheimer's Disease Using Gene Expression Data in Brain. PMID:33282526
Informatics Inference of Exercise-Induced Modulation of Brain Pathways Based on Cerebrospinal Fluid Micro-RNAs in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome. PMID:33274349
Deep Learning in LncRNAome: Contribution, Challenges, and Perspectives. PMID:33266128
Improvement of Disease Resistance in Livestock: Application of Immunogenomics and CRISPR/Cas9 Technology. PMID:33260762
Differential gene expression analysis reveals pathways important in early post-traumatic osteoarthritis in an equine model. PMID:33256611
Mining GWAS and eQTL data for CF lung disease modifiers by gene expression imputation. PMID:33253230
Chemocentric Informatics Analysis: Dexamethasone Versus Combination Therapy for COVID-19. PMID:33251412
Identification of potential mRNA panels for severe acute respiratory syndrome coronavirus 2 (COVID-19) diagnosis and treatment using microarray dataset and bioinformatics methods. PMID:33251083
Multi-omics integration in biomedical research - A metabolomics-centric review. PMID:33248648
Comparative analysis of transcriptomic profile, histology, and IDH mutation for classification of gliomas. PMID:33244057
Integrated Proteogenomic Characterization across Major Histological Types of Pediatric Brain Cancer. PMID:33242424
Genetic profiling for diffuse type and genomically stable subtypes in gastric cancer. PMID:33240471
Cortical morphology at birth reflects spatiotemporal patterns of gene expression in the fetal human brain. PMID:33226978
Endocrine disrupting chemicals and COVID-19 relationships: A computational systems biology approach. PMID:33223326
Deep sequencing reveals a DAP1 regulatory haplotype that potentiates autoimmunity in systemic lupus erythematosus. PMID:33213505
Proteogenomic Landscape of Breast Cancer Tumorigenesis and Targeted Therapy. PMID:33212010
A Middle-Out Modeling Strategy to Extend a Colon Cancer Logical Model Improves Drug Synergy Predictions in Epithelial-Derived Cancer Cell Lines. PMID:33195403
Integrated transcriptome meta-analysis of pancreatic ductal adenocarcinoma and matched adjacent pancreatic tissues. PMID:33194391
Exome Sequencing Identifies Abnormalities in Glycosylation and ANKRD36C in Patients with Immune-Mediated Thrombotic Thrombocytopenic Purpura. PMID:33184803
Molecular pathophysiology of diabetes mellitus during pregnancy with antenatal complications. PMID:33184417
Quantitative Structure-Mutation-Activity Relationship Tests (QSMART) model for protein kinase inhibitor response prediction. PMID:33183223
Comparative Transcriptome Analysis of the Regenerating Zebrafish Telencephalon Unravels a Resource With Key Pathways During Two Early Stages and Activation of Wnt/β-Catenin Signaling at the Early Wound Healing Stage. PMID:33163496
Molecular Subsets in Renal Cancer Determine Outcome to Checkpoint and Angiogenesis Blockade. PMID:33157048
Drug sensitivity prediction with normal inverse Gaussian shrinkage informed by external data. PMID:33155717
Cholesterol-Rich Microdomains Contribute to PAR1 Signaling in Platelets Despite a Weak Localization of the Receptor in These Microdomains. PMID:33138025
Cross-resistance of cisplatin selected cells to anti-microtubule agents: Role of general survival mechanisms. PMID:33129114
Replication stress conferred by POT1 dysfunction promotes telomere relocalization to the nuclear pore. PMID:33122293
Comprehensive Gene Analysis of IgG4-Related Ophthalmic Disease Using RNA Sequencing. PMID:33121169
DNA methylation in canine brains is related to domestication and dog-breed formation. PMID:33119634
Proteomic signatures of acute oxidative stress response to paraquat in the mouse heart. PMID:33116222
Nuclear gene proximity and protein interactions shape transcript covariations in mammalian single cells. PMID:33116115
Genes and Pathways Implicated in Tetralogy of Fallot Revealed by Ultra-Rare Variant Burden Analysis in 231 Genome Sequences. PMID:33110418
Involvement of NEK2 and its interaction with NDC80 and CEP250 in hepatocellular carcinoma. PMID:33109182
Data on chemical-gene interactions and biological categories enriched with genes sensitive to chemical exposures. PMID:33102660
VARAdb: a comprehensive variation annotation database for human. PMID:33095866
Mir-30d Regulates Cardiac Remodeling by Intracellular and Paracrine Signaling. PMID:33092465
Plasma proteomic profile of age, health span, and all-cause mortality in older adults. PMID:33089916
Differences in maternal gene expression in Cesarean section delivery compared with vaginal delivery. PMID:33082495
Organophosphorus flame retardants are developmental neurotoxicants in a rat primary brainsphere in vitro model. PMID:33078273
Epigenome-wide association study of Alzheimer's disease replicates 22 differentially methylated positions and 30 differentially methylated regions. PMID:33069246
A practical guide to mechanistic systems modeling in biology using a logic-based approach. PMID:33064138
Meta-analysis of gene expression profiling reveals novel basal gene signatures in MCF-10A cells transformed with cadmium. PMID:33062196
Host gene expression modulated by Zika virus infection of human-293 cells. PMID:33059318
A strategy to incorporate prior knowledge into correlation network cutoff selection. PMID:33056991
smORFunction: a tool for predicting functions of small open reading frames and microproteins. PMID:33054771
SWATH-MS based proteomic profiling of pancreatic ductal adenocarcinoma tumours reveals the interplay between the extracellular matrix and related intracellular pathways. PMID:33048956
Myf6/MRF4 is a myogenic niche regulator required for the maintenance of the muscle stem cell pool. PMID:33047485
Bioinformatic Identification of Potential Hub Genes in Muscle-Invasive Bladder Urothelial Carcinoma. PMID:33035117
Network-based identification genetic effect of SARS-CoV-2 infections to Idiopathic pulmonary fibrosis (IPF) patients. PMID:33024988
Genomic Study of Babesia bovis Infection Level and Its Association With Tick Count in Hereford and Braford Cattle. PMID:33013839
Discovering lethal alleles across the turkey genome using a transmission ratio distortion approach. PMID:33006154
Investigating Radiotherapy Response in a Novel Syngeneic Model of Prostate Cancer. PMID:33003551
Metabolic pathway inference using multi-label classification with rich pathway features. PMID:33001968
Swimming under elevated hydrostatic pressure increases glycolytic activity in gas gland cells of the European eel. PMID:32997701
Finding New Molecular Targets of Familiar Natural Products Using In Silico Target Prediction. PMID:32993084
Protein Translation Inhibition is Involved in the Activity of the Pan-PIM Kinase Inhibitor PIM447 in Combination with Pomalidomide-Dexamethasone in Multiple Myeloma. PMID:32987735
ERAD deficiency promotes mitochondrial dysfunction and transcriptional rewiring in human hepatic cells. PMID:32978261
Systems pharmacological study illustrates the immune regulation, anti-infection, anti-inflammation, and multi-organ protection mechanism of Qing-Fei-Pai-Du decoction in the treatment of COVID-19. PMID:32978039
Molecular Characterization of the Coproduced Extracellular Vesicles in HEK293 during Virus-Like Particle Production. PMID:32975947
Comprehending Meningioma Signaling Cascades Using Multipronged Proteomics Approaches & Targeted Validation of Potential Markers. PMID:32974197
Single-Cell RNA Sequencing Analysis Reveals a Crucial Role for CTHRC1 (Collagen Triple Helix Repeat Containing 1) Cardiac Fibroblasts After Myocardial Infarction. PMID:32972203
Review on the Computational Genome Annotation of Sequences Obtained by Next-Generation Sequencing. PMID:32962098
Trem2 promotes anti-inflammatory responses in microglia and is suppressed under pro-inflammatory conditions. PMID:32959884
An unanticipated tumor-suppressive role of the SUMO pathway in the intestine unveiled by Ubc9 haploinsufficiency. PMID:32948837
PAWER: protein array web exploreR. PMID:32942983
The CRISPR-Cas9 crATIC HeLa transcriptome: Characterization of a novel cellular model of ATIC deficiency and ZMP accumulation. PMID:32939338
Dose and Dose-Rate Effects in a Mouse Model of Internal Exposure to 137Cs. Part 1: Global Transcriptomic Responses in Blood. PMID:32931585
The mutational landscape of the SCAN-B real-world primary breast cancer transcriptome. PMID:32926574
Overexpression of α-Synuclein Reorganises Growth Factor Profile of Human Astrocytes. PMID:32914394
Transcriptome Analysis of Early Defenses in Rice against Fusarium fujikuroi. PMID:32910281
Polygenic architecture informs potential vulnerability to drug-induced liver injury. PMID:32895570
PCOSKBR2: a database of genes, diseases, pathways, and networks associated with polycystic ovary syndrome. PMID:32895427
Transcriptomic analysis links diverse hypothalamic cell types to fibroblast growth factor 1-induced sustained diabetes remission. PMID:32895383
Mass spectrometry-based analysis of formalin-fixed, paraffin-embedded distal cholangiocarcinoma identifies stromal thrombospondin-2 as a potential prognostic marker. PMID:32887625
A porcine ligated loop model reveals new insight into the host immune response against Campylobacter jejuni. PMID:32887530
Single-Cell NGS-Based Analysis of Copy Number Alterations Reveals New Insights in Circulating Tumor Cells Persistence in Early-Stage Breast Cancer. PMID:32887501
Comparative proteomic analysis of osteogenic differentiated human adipose tissue and bone marrow-derived stromal cells. PMID:32885592
Type I IFNs and CD8 T cells increase intestinal barrier permeability after chronic viral infection. PMID:32880630
The genomic landscape of Mongolian hepatocellular carcinoma. PMID:32873799
High expression of MKK3 is associated with worse clinical outcomes in African American breast cancer patients. PMID:32873298
Evolutionary and Functional Analysis of Korean Native Pig Using Single Nucleotide Polymorphisms. PMID:32868490
Anatabine ameliorates intestinal inflammation and reduces the production of pro-inflammatory factors in a dextran sulfate sodium mouse model of colitis. PMID:32855621
Identifying the Potential Mechanism of Action of SNPs Associated With Breast Cancer Susceptibility With GVITamIN. PMID:32850701
Integrated Bioinformatics Analysis Reveals Key Candidate Genes and Pathways Associated With Clinical Outcome in Hepatocellular Carcinoma. PMID:32849813
Differential Regulation of miRNA Profiles of Human Cells Experimentally Infected by Leishmania donovani Isolated From Indian Visceral Leishmaniasis and Post-Kala-Azar Dermal Leishmaniasis. PMID:32849363
Longitudinal Stroke Recovery Associated With Dysregulation of Complement System-A Proteomics Pathway Analysis. PMID:32849183
Strategies to Enhance Logic Modeling-Based Cell Line-Specific Drug Synergy Prediction. PMID:32848834
SBML Level 3: an extensible format for the exchange and reuse of biological models. PMID:32845085
Genome-wide association meta-analysis for early age-related macular degeneration highlights novel loci and insights for advanced disease. PMID:32843070
Ageing compromises mouse thymus function and remodels epithelial cell differentiation. PMID:32840480
Transcriptional and functional insights into the host immune response against the emerging fungal pathogen Candida auris. PMID:32839538
Single-cell RNA-seq reveals ectopic and aberrant lung-resident cell populations in idiopathic pulmonary fibrosis. PMID:32832599
Phenotype stability under dynamic brain-tumor environment stimuli maps glioblastoma progression in patients. PMID:32832595
Sex differences in circulating proteins in heart failure with preserved ejection fraction. PMID:32831121
G protein-coupled estrogen receptor 1 (GPER-1) and agonist G-1 inhibit growth of ovarian cancer cells by activation of anti-tumoral transcriptome responses: impact of GPER-1 mRNA on survival. PMID:32813115
Exploring the mechanism of Radix Rhei Et Rhizome intervention in intracerebral hemorrhage based on systematic pharmacology and proteomics strategy. PMID:32803256
Genetic analyses identify GSDMB associated with asthma severity, exacerbations, and antiviral pathways. PMID:32795586
IFN signaling and neutrophil degranulation transcriptional signatures are induced during SARS-CoV-2 infection. PMID:32793903
Pathway-specific model estimation for improved pathway annotation by network crosstalk. PMID:32788619
Respiratory Effects of Exposure to Aerosol From the Candidate Modified-Risk Tobacco Product THS 2.2 in an 18-Month Systems Toxicology Study With A/J Mice. PMID:32780831
Identification of key genes in atrial fibrillation using bioinformatics analysis. PMID:32778054
A biochemical network modeling of a whole-cell. PMID:32764598
Plasma proteomic profile of frailty. PMID:32762010
FLUTE: Fast and reliable knowledge retrieval from biomedical literature. PMID:32761077
Modeling Pathway Dynamics of the Skeletal Muscle Response to Intravenous Methylprednisolone (MPL) Administration in Rats: Dosing and Tissue Effects. PMID:32760706
Application of Transcriptional Gene Modules to Analysis of Caenorhabditis elegans' Gene Expression Data. PMID:32759329
Inducers of the endothelial cell barrier identified through chemogenomic screening in genome-edited hPSC-endothelial cells. PMID:32759214
Glycosaminoglycan-Protein Interactions: The First Draft of the Glycosaminoglycan Interactome. PMID:32757871
Pharmacoproteomics Identifies Kinase Pathways that Drive the Epithelial-Mesenchymal Transition and Drug Resistance in Hepatocellular Carcinoma. PMID:32755597
Genome-Wide Screen for Context-Dependent Tumor Suppressors Identified Using in Vivo Models for Neoplasia in Drosophila. PMID:32737065
Protamine-2 Deficiency Initiates a Reactive Oxygen Species (ROS)-Mediated Destruction Cascade during Epididymal Sperm Maturation in Mice. PMID:32727081
Wide-ranging analysis of survival-related alternative splicing events in invasive breast carcinoma. PMID:32724430
Ubiquitin-proteasome system, lipid metabolism and DNA damage repair are triggered by antipsychotic medication in human oligodendrocytes: implications in schizophrenia. PMID:32724114
Comparative Genomic Analysis of Rapidly Evolving SARS-CoV-2 Reveals Mosaic Pattern of Phylogeographical Distribution. PMID:32723797
Autoimmunity gene IRGM suppresses cGAS-STING and RIG-I-MAVS signaling to control interferon response. PMID:32715615
Proteome of Glioblastoma-Derived Exosomes as a Source of Biomarkers. PMID:32708613
Expanded Phenotypic Definition Identifies Hundreds of Potential Causative Genes for Leukodystrophies and Leukoencephalopathies. PMID:32704519
BiPOm: a rule-based ontology to represent and infer molecule knowledge from a biological process-centered viewpoint. PMID:32703160
Endocrine disrupting chemicals and COVID-19 relationships: a computational systems biology approach. PMID:32699854
Somatic Evolution in Non-neoplastic IBD-Affected Colon. PMID:32697969
Noncanonical STAT3 activity sustains pathogenic Th17 proliferation and cytokine response to antigen. PMID:32697822
How to Annotate and Submit a Short Linear Motif to the Eukaryotic Linear Motif Resource. PMID:32696353
Meta-analysis of gene expression profiles of lean and obese PCOS to identify differentially regulated pathways and risk of comorbidities. PMID:32695266
A telescope GWAS analysis strategy, based on SNPs-genes-pathways ensamble and on multivariate algorithms, to characterize late onset Alzheimer's disease. PMID:32694537
Monocyte-derived APCs are central to the response of PD1 checkpoint blockade and provide a therapeutic target for combination therapy. PMID:32690667
Footprint-based functional analysis of multiomic data. PMID:32685770
The power and limitations of gene expression pathway analyses toward predicting population response to environmental stressors. PMID:32684953
UXT in Sertoli cells is required for blood-testis barrier integrity†. PMID:32678429
Unified inference of missense variant effects and gene constraints in the human genome. PMID:32667917
Leveraging the Comparative Toxicogenomics Database to Fill in Knowledge Gaps for Environmental Health: A Test Case for Air Pollution-induced Cardiovascular Disease. PMID:32663284
Mapping signalling perturbations in myocardial fibrosis via the integrative phosphoproteomic profiling of tissue from diverse sources. PMID:32661320
Adenovirus-mediated ubiquitination alters protein-RNA binding and aids viral RNA processing. PMID:32661314
Sex- and Region-Specific Differences in the Transcriptomes of Rat Microglia from the Brainstem and Cervical Spinal Cord. PMID:32661056
Chromatin network markers of leukemia. PMID:32657405
Proteogenomic Characterization Reveals Therapeutic Vulnerabilities in Lung Adenocarcinoma. PMID:32649874
A three-tiered integrative analysis of transcriptional data reveals the shared pathways related to heart failure from different aetiologies. PMID:32638546
The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST). PMID:32637990
DNA methylation patterns from peripheral blood separate coronary artery disease patients with and without heart failure. PMID:32618141
Identifying persistent structures in multiscale 'omics data. PMID:32587977
Epigenome-450K-wide methylation signatures of active cigarette smoking: The Young Finns Study. PMID:32583859
The Immunomodulatory Signature of Extracellular Vesicles From Cardiosphere-Derived Cells: A Proteomic and miRNA Profiling. PMID:32582685
CD200 promotes immunosuppression in the pancreatic tumor microenvironment. PMID:32581043
Vaccination of koalas during antibiotic treatment for Chlamydia-induced cystitis induces an improved antibody response to Chlamydia pecorum. PMID:32576914
BioModels Parameters: a treasure trove of parameter values from published systems biology models. PMID:32573648
Lysosomal degradation ensures accurate chromosomal segregation to prevent chromosomal instability. PMID:32573315
SPANX Control of Lamin A/C Modulates Nuclear Architecture and Promotes Melanoma Growth. PMID:32571981
Selection of established tumour cells through narrow diameter micropores enriches for elevated Ras/Raf/MEK/ERK MAPK signalling and enhanced tumour growth. PMID:32569510
Expression profiling of microRNAs and isomiRs in conventional central chondrosarcoma. PMID:32566253
Laser capture microdissection coupled mass spectrometry (LCM-MS) for spatially resolved analysis of formalin-fixed and stained human lung tissues. PMID:32565759
Transcriptome-Wide Regulation of Key Developmental Pathways in the Mouse Neural Tube by Prenatal Alcohol Exposure. PMID:32557641
Identification of functionally connected multi-omic biomarkers for Alzheimer's disease using modularity-constrained Lasso. PMID:32555747
Multi-omics network analysis reveals distinct stages in the human aging progression in epidermal tissue. PMID:32554863
Alzheimer's disease-related dysregulation of mRNA translation causes key pathological features with ageing. PMID:32546772
Epstein-Barr Virus LMP1 Promotes Syntenin-1- and Hrs-Induced Extracellular Vesicle Formation for Its Own Secretion To Increase Cell Proliferation and Migration. PMID:32546618
Transcription Analysis of the Chemerin Impact on Gene Expression Profile in the Luteal Cells of Gilts. PMID:32545672
Dynamic rewiring of the human interactome by interferon signaling. PMID:32539747
A kinase-deficient NTRK2 splice variant predominates in glioma and amplifies several oncogenic signaling pathways. PMID:32532995
Feature selection strategies for drug sensitivity prediction. PMID:32523056
IRE1α regulates macrophage polarization, PD-L1 expression, and tumor survival. PMID:32520957
Collapsing the list of myocardial infarction-related differentially expressed genes into a diagnostic signature. PMID:32517814
Studies of human twins reveal genetic variation that affects dietary fat perception. PMID:32516399
The Prediction of miRNAs in SARS-CoV-2 Genomes: hsa-miR Databases Identify 7 Key miRs Linked to Host Responses and Virus Pathogenicity-Related KEGG Pathways Significant for Comorbidities. PMID:32512929
Mining the Prognostic Value of HNRNPAB and Its Function in Breast Carcinoma. PMID:32509843
Dual Transcriptomic and Molecular Machine Learning Predicts all Major Clinical Forms of Drug Cardiotoxicity. PMID:32508633
Interpreting molecular similarity between patients as a determinant of disease comorbidity relationships. PMID:32504002
Identifying genetic variants and pathways associated with extreme levels of fetal hemoglobin in sickle cell disease in Tanzania. PMID:32503527
PS4DR: a multimodal workflow for identification and prioritization of drugs based on pathway signatures. PMID:32503412
Entinostat augments NK cell functions via epigenetic upregulation of IFIT1-STING-STAT4 pathway. PMID:32499867
LncRNA UCA1 Induces Acquired Resistance to Gefitinib by Epigenetically Silencing CDKN1A Expression in Non-small-Cell Lung Cancer. PMID:32477939
Potential dual functional roles of the Y-linked RBMY in hepatocarcinogenesis. PMID:32473614
Dysregulation of the MMP/TIMP Proteolytic System in Subependymal Giant Cell Astrocytomas in Patients With Tuberous Sclerosis Complex: Modulation of MMP by MicroRNA-320d In Vitro. PMID:32472129
Pulmonary and systemic responses to aerosolized lysate of Staphylococcus aureus and Escherichia coli in calves. PMID:32471444
Molecular characterisation of TP53 mutated squamous cell carcinomas of the lung to identify putative targets for therapy. PMID:32468587
Overcoming Genetically Based Resistance Mechanisms to PD-1 Blockade. PMID:32467343
Urinary proteomics links keratan sulfate degradation and lysosomal enzymes to early type 1 diabetes. PMID:32453760
Activin-mediated alterations of the fibroblast transcriptome and matrisome control the biomechanical properties of skin wounds. PMID:32451392
Transcriptional profiling of lung macrophages identifies a predictive signature for inflammatory lung disease in preterm infants. PMID:32444859
Discrete populations of isotype-switched memory B lymphocytes are maintained in murine spleen and bone marrow. PMID:32444631
Extending the small-molecule similarity principle to all levels of biology with the Chemical Checker. PMID:32440005
Genetic regulators of mineral amount in Nelore cattle muscle predicted by a new co-expression and regulatory impact factor approach. PMID:32439843
ThETA: transcriptome-driven efficacy estimates for gene-based TArget discovery. PMID:32437556
Summary-Based Methylome-Wide Association Analyses Suggest Potential Genetically Driven Epigenetic Heterogeneity of Alzheimer's Disease. PMID:32429084
Quantifying genetic effects on disease mediated by assayed gene expression levels. PMID:32424349
Identification of Prognostic Immune Genes in Bladder Urothelial Carcinoma. PMID:32420368
Multi-omics systems toxicology study of mouse lung assessing the effects of aerosols from two heat-not-burn tobacco products and cigarette smoke. PMID:32419906
The sensitivity of transcriptomics BMD modeling to the methods used for microarray data normalization. PMID:32413060
Mutation severity spectrum of rare alleles in the human genome is predictive of disease type. PMID:32413045
Ellagic acid and human cancers: a systems pharmacology and docking study to identify principal hub genes and main mechanisms of action. PMID:32410114
Mitochondrial DNA alterations may influence the cisplatin responsiveness of oral squamous cell carcinoma. PMID:32398775
Circulating myeloid cells invade the central nervous system to mediate cachexia during pancreatic cancer. PMID:32391790
Applying knowledge-driven mechanistic inference to toxicogenomics. PMID:32387679
Proteomic Profiling of Small Extracellular Vesicles Secreted by Human Pancreatic Cancer Cells Implicated in Cellular Transformation. PMID:32382024
GeneTrail 3: advanced high-throughput enrichment analysis. PMID:32379325
Single-cell RNA-seq with spike-in cells enables accurate quantification of cell-specific drug effects in pancreatic islets. PMID:32375897
Metabonomic Profile and Signaling Pathway Prediction of Depression-Associated Suicidal Behavior. PMID:32372980
A Genome-scale CRISPR Screen Identifies the ERBB and mTOR Signaling Networks as Key Determinants of Response to PI3K Inhibition in Pancreatic Cancer. PMID:32371585
Mitral valve leaflet response to ischaemic mitral regurgitation: from gene expression to tissue remodelling. PMID:32370692
Plasma metabolite biomarkers predictive of radiation induced cardiotoxicity. PMID:32360032
Comprehensive Molecular Characterization Identifies Distinct Genomic and Immune Hallmarks of Renal Medullary Carcinoma. PMID:32359397
Single-cell expression and Mendelian randomization analyses identify blood genes associated with lifespan and chronic diseases. PMID:32358504
Extracellular Vesicles Secreted by Corneal Epithelial Cells Promote Myofibroblast Differentiation. PMID:32357574
Site-Dependent Lineage Preference of Adipose Stem Cells. PMID:32351957
Identification of Hub Genes Related to Carcinogenesis and Prognosis in Colorectal Cancer Based on Integrated Bioinformatics. PMID:32351322
Ly6cLo non-classical monocytes promote resolution of rhesus rotavirus-mediated perinatal hepatic inflammation. PMID:32346042
Shared genetic architecture and casual relationship between leptin levels and type 2 diabetes: large-scale cross-trait meta-analysis and Mendelian randomization analysis. PMID:32341051
Differential Effects of the Hormonal and Copper Intrauterine Device on the Endometrial Transcriptome. PMID:32327684
Whole Exome Sequencing reveals NOTCH1 mutations in anaplastic large cell lymphoma and points to Notch both as a key pathway and a potential therapeutic target. PMID:32327503
Association of Proteins Modulating Immune Response and Insulin Clearance During Gestation with Antenatal Complications in Patients with Gestational or Type 2 Diabetes Mellitus. PMID:32326243
Transcriptional Signatures That Define Ulcerative Colitis in Remission. PMID:32322884
A high definition picture of somatic mutations in chronic lymphoproliferative disorder of natural killer cells. PMID:32321919
The Computational Diet: A Review of Computational Methods Across Diet, Microbiome, and Health. PMID:32318028
Efficient differentiation and polarization of primary cultured neurons on poly(lactic acid) scaffolds with microgrooved structures. PMID:32317746
Prognostic significance of an invasive leader cell-derived mutation cluster on chromosome 16q. PMID:32315457
Setting the basis of best practices and standards for curation and annotation of logical models in biology-highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop. PMID:32313939
PDZ Domains as Drug Targets. PMID:32313833
RA-map: building a state-of-the-art interactive knowledge base for rheumatoid arthritis. PMID:32311035
Ceramide launches an acute anti-adhesion pro-migration cell signaling program in response to chemotherapy. PMID:32307766
Pooled Knockin Targeting for Genome Engineering of Cellular Immunotherapies. PMID:32302591
The European Research Network on Signal Transduction (ERNEST): Toward a Multidimensional Holistic Understanding of G Protein-Coupled Receptor Signaling. PMID:32296774
Stromal Cells Covering Omental Fat-Associated Lymphoid Clusters Trigger Formation of Neutrophil Aggregates to Capture Peritoneal Contaminants. PMID:32294409
Lymphovascular invasion in breast cancer is associated with gene expression signatures of cell proliferation but not lymphangiogenesis or immune response. PMID:32285241
Structured reviews for data and knowledge-driven research. PMID:32283553
Bioinformatic identification of hub genes and key pathways in neutrophils of patients with acute respiratory distress syndrome. PMID:32282748
A Next-Generation Risk Assessment Case Study for Coumarin in Cosmetic Products. PMID:32275751
GOMCL: a toolkit to cluster, evaluate, and extract non-redundant associations of Gene Ontology-based functions. PMID:32272889
Test of Arabidopsis Space Transcriptome: A Discovery Environment to Explore Multiple Plant Biology Spaceflight Experiments. PMID:32265943
Expression profile analysis identifies key genes as prognostic markers for metastasis of osteosarcoma. PMID:32256213
Unveiling new disease, pathway, and gene associations via multi-scale neural network. PMID:32251458
Cell Type-Specific Intralocus Interactions Reveal Oligodendrocyte Mechanisms in MS. PMID:32246942
Adaptive Shifts in Gene Regulation Underlie a Developmental Delay in Thermogenesis in High-Altitude Deer Mice. PMID:32243546
The Brain-Skin Connection and the Pathogenesis of Psoriasis: A Review with a Focus on the Serotonergic System. PMID:32224981
Vesicles Shed by Pathological Murine Adipocytes Spread Pathology: Characterization and Functional Role of Insulin Resistant/Hypertrophied Adiposomes. PMID:32214011
A Computational Approach for Mapping Heme Biology in the Context of Hemolytic Disorders. PMID:32211383
OncoOmics approaches to reveal essential genes in breast cancer: a panoramic view from pathogenesis to precision medicine. PMID:32210335
Standard machine learning approaches outperform deep representation learning on phenotype prediction from transcriptomics data. PMID:32197580
SingleCellSignalR: inference of intercellular networks from single-cell transcriptomics. PMID:32196115
Network-based identification of signature genes KLF6 and SPOCK1 associated with oral submucous fibrosis. PMID:32190310
Identification of an energy metabolism‑related gene signature in ovarian cancer prognosis. PMID:32186777
AllEnricher: a comprehensive gene set function enrichment tool for both model and non-model species. PMID:32183716
Cyclosporine a directly affects human and mouse b cell migration in vitro by disrupting a hIF-1 αdependent, o2 sensing, molecular switch. PMID:32183695
Comparative Molecular Analysis of Cancer Behavior Cultured In Vitro, In Vivo, and Ex Vivo. PMID:32183351
Suppression of a Subset of Interferon-Induced Genes by Human Papillomavirus Type 16 E7 via a Cyclin Dependent Kinase 8-Dependent Mechanism. PMID:32183180
Integrative Analysis of MicroRNA and Gene Interactions for Revealing Candidate Signatures in Prostate Cancer. PMID:32180804
Wikidata as a knowledge graph for the life sciences. PMID:32180547
Circulating anti-geronic factors from heterochonic parabionts promote vascular rejuvenation in aged mice: transcriptional footprint of mitochondrial protection, attenuation of oxidative stress, and rescue of endothelial function by young blood. PMID:32172434
Genetic Pathways in Nonalcoholic Fatty Liver Disease: Insights From Systems Biology. PMID:32170962
Subcellular localization of FANCD2 is associated with survival in ovarian carcinoma. PMID:32165999
Forecasting risk gene discovery in autism with machine learning and genome-scale data. PMID:32165711
Outcome-Related Signatures Identified by Whole Transcriptome Sequencing of Resectable Stage III/IV Melanoma Evaluated after Starting Hu14.18-IL2. PMID:32152202
The influence of rare variants in circulating metabolic biomarkers. PMID:32150548
Blood DNA Methylation and Aging: A Cross-Sectional Analysis and Longitudinal Validation in the InCHIANTI Study. PMID:32147700
OncoMX: A Knowledgebase for Exploring Cancer Biomarkers in the Context of Related Cancer and Healthy Data. PMID:32142370
De novo transcriptome of the diatom Cylindrotheca closterium identifies genes involved in the metabolism of anti-inflammatory compounds. PMID:32139778
Temporal changes in the gene expression heterogeneity during brain development and aging. PMID:32139741
miR-221-3p Regulates VEGFR2 Expression in High-Risk Prostate Cancer and Represents an Escape Mechanism from Sunitinib In Vitro. PMID:32131507
Germline Features Associated with Immune Infiltration in Solid Tumors. PMID:32130895
The reduction of DSS-induced colitis severity in mice exposed to cigarette smoke is linked to immune modulation and microbial shifts. PMID:32123204
Eosinophil accumulation predicts response to melanoma treatment with immune checkpoint inhibitors. PMID:32117594
Metabolic effects of bezafibrate in mitochondrial disease. PMID:32107855
Genetic Modifiers and Rare Mendelian Disease. PMID:32106447
TIFAB Regulates USP15-Mediated p53 Signaling during Stressed and Malignant Hematopoiesis. PMID:32101751
Exploring Integrative Analysis Using the BioMedical Evidence Graph. PMID:32097025
Tumour heterogeneity and the evolutionary trade-offs of cancer. PMID:32094544
Equivalent change enrichment analysis: assessing equivalent and inverse change in biological pathways between diverse experiments. PMID:32093613
Secretome Analysis of Mouse Dendritic Cells Interacting with a Probiotic Strain of Lactobacillus gasseri. PMID:32093322
A Guide to Conquer the Biological Network Era Using Graph Theory. PMID:32083072
FibroAtlas: A Database for the Exploration of Fibrotic Diseases and Their Genes. PMID:32082621
Pan-cancer analysis reveals cooperativity of both strands of microRNA that regulate tumorigenesis and patient survival. PMID:32080184
CUX1 and IκBζ (NFKBIZ) mediate the synergistic inflammatory response to TNF and IL-17A in stromal fibroblasts. PMID:32079724
Endogenous Retrovirus Activation as a Key Mechanism of Anti-Tumor Immune Response in Radiotherapy. PMID:32074012
Single-cell analysis of olfactory neurogenesis and differentiation in adult humans. PMID:32066986
Proteogenomic Characterization of Endometrial Carcinoma. PMID:32059776
RBP EIF2S2 Promotes Tumorigenesis and Progression by Regulating MYC-Mediated Inhibition via FHIT-Related Enhancers. PMID:32059763
Enhancing reproducibility of gene expression analysis with known protein functional relationships: The concept of well-associated protein. PMID:32058996
Exploration of databases and methods supporting drug repurposing: a comprehensive survey. PMID:32055842
In-silico simulated prototype-patients using TPMS technology to study a potential adverse effect of sacubitril and valsartan. PMID:32053711
Poly-Enrich: count-based methods for gene set enrichment testing with genomic regions. PMID:32051932
Rapid and site-specific deep phosphoproteome profiling by data-independent acquisition without the need for spectral libraries. PMID:32034161
Comparison of the Transcriptome Response within the Swine Tracheobronchial Lymphnode Following Infection with PRRSV, PCV-2 or IAV-S. PMID:32033425
Genetic screens in isogenic mammalian cell lines without single cell cloning. PMID:32029722
Integrative pathway enrichment analysis of multivariate omics data. PMID:32024846
From reads to insight: a hitchhiker's guide to ATAC-seq data analysis. PMID:32014034
Human and mouse essentiality screens as a resource for disease gene discovery. PMID:32005800
In silico approach to predict pancreatic β-cells classically secreted proteins. PMID:32003782
Immune correlates of tuberculosis disease and risk translate across species. PMID:31996462
Zika virus targets the human thymic epithelium. PMID:31992777
ADAPT identifies an ESCRT complex composition that discriminates VCaP from LNCaP prostate cancer cell exosomes. PMID:31989173
Genetic architecture study of rheumatoid arthritis and juvenile idiopathic arthritis. PMID:31988799
Highly multiplexed proteomic assessment of human bone marrow in acute myeloid leukemia. PMID:31985806
Multi-omics characterization of a diet-induced obese model of non-alcoholic steatohepatitis. PMID:31980690
A graph-based algorithm for RNA-seq data normalization. PMID:31978105
Compartment and hub definitions tune metabolic networks for metabolomic interpretations. PMID:31972021
Knowledge-guided analysis of "omics" data using the KnowEnG cloud platform. PMID:31971940
Transcriptomic profiles reveal differences between the right and left ventricle in normoxia and hypoxia. PMID:31960631
Comparative proteomic analysis of different stages of breast cancer tissues using ultra high performance liquid chromatography tandem mass spectrometer. PMID:31945087
Transcriptome meta-analysis reveals differences of immune profile between eutopic endometrium from stage I-II and III-IV endometriosis independently of hormonal milieu. PMID:31941945
Characterization of Human Induced Pluripotent Stem Cell-Derived Hepatocytes with Mature Features and Potential for Modeling Metabolic Diseases. PMID:31940797
Metabolomic networks and pathways associated with feed efficiency and related-traits in Duroc and Landrace pigs. PMID:31937890
A pipeline to create predictive functional networks: application to the tumor progression of hepatocellular carcinoma. PMID:31937236
Analysis of Low Molecular Weight Substances and Related Processes Influencing Cellular Cholesterol Efflux. PMID:31933239
Whole blood transcriptomic analysis of beef cattle at arrival identifies potential predictive molecules and mechanisms that indicate animals that naturally resist bovine respiratory disease. PMID:31929561
Construction of asthma related competing endogenous RNA network revealed novel long non-coding RNAs and potential new drugs. PMID:31924195
Perturbation of Ephrin Receptor Signaling and Glutamatergic Transmission in the Hypothalamus in Depression Using Proteomics Integrated With Metabolomics. PMID:31920518
Mechanisms of tissue and cell-type specificity in heritable traits and diseases. PMID:31913361
Frameshift mutations at the C-terminus of HIST1H1E result in a specific DNA hypomethylation signature. PMID:31910894
Leveraging complementary computational models for prioritizing chemicals of developmental and reproductive toxicity concern: an example of food contact materials. PMID:31897520
Developing preliminary blood metabolomics-based biomarkers of insufficient sleep in humans. PMID:31894238
A systems approach identifies Enhancer of Zeste Homolog 2 (EZH2) as a protective factor in epilepsy. PMID:31891591
Heat-induced hyperthermia impacts the follicular fluid proteome of the periovulatory follicle in lactating dairy cows. PMID:31887207
BRD4-Regulated Molecular Targets in Mantle Cell Lymphoma: Insights into Targeted Therapeutic Approach. PMID:31882553
Label-Free Quantitative Proteomics Distinguishes General and Site-Specific Host Responses to Pseudomonas aeruginosa Infection at the Ocular Surface. PMID:31874121
Human cytomegalovirus interactome analysis identifies degradation hubs, domain associations and viral protein functions. PMID:31873071
Novel TMEM173 Mutation and the Role of Disease Modifying Alleles. PMID:31866997
HPOAnnotator: improving large-scale prediction of HPO annotations by low-rank approximation with HPO semantic similarities and multiple PPI networks. PMID:31865916
Depolarization-Associated CircRNA Regulate Neural Gene Expression and in Some Cases May Function as Templates for Translation. PMID:31861825
Single-Cell Expression Variability Implies Cell Function. PMID:31861624
FMRP has a cell-type-specific role in CA1 pyramidal neurons to regulate autism-related transcripts and circadian memory. PMID:31860442
Human Cerebral Organoids and Fetal Brain Tissue Share Proteomic Similarities. PMID:31850342
Menagerie: A text-mining tool to support animal-human translation in neurodegeneration research. PMID:31846471
Multi-omics analysis of multiple missions to space reveal a theme of lipid dysregulation in mouse liver. PMID:31844325
The human DEPhOsphorylation Database DEPOD: 2019 update. PMID:31836896
The coding and non-coding transcriptional landscape of subependymal giant cell astrocytomas. PMID:31834371
An Annotated Draft Genome of the Mountain Hare (Lepus timidus). PMID:31834364
Mycobacterium tuberculosis HN878 Infection Induces Human-Like B-Cell Follicles in Mice. PMID:31832640
Next-generation hypomethylating agent SGI-110 primes acute myeloid leukemia cells to IAP antagonist by activating extrinsic and intrinsic apoptosis pathways. PMID:31831875
Using mechanistic models for the clinical interpretation of complex genomic variation. PMID:31831811
Abundance of ethnically biased microsatellites in human gene regions. PMID:31830051
Impacts of NRF2 activation in non-small-cell lung cancer cell lines on extracellular metabolites. PMID:31828882
miR-221 Augments TRAIL-Mediated Apoptosis in Prostate Cancer Cells by Inducing Endogenous TRAIL Expression and Targeting the Functional Repressors SOCS3 and PIK3R1. PMID:31828111
The Impact of Pathway Database Choice on Statistical Enrichment Analysis and Predictive Modeling. PMID:31824580
Deep learning for inferring gene relationships from single-cell expression data. PMID:31822622
Proteogenomics of Colorectal Cancer Liver Metastases: Complementing Precision Oncology with Phenotypic Data. PMID:31805664
Deregulation of the Histone Lysine-Specific Demethylase 1 Is Involved in Human Hepatocellular Carcinoma. PMID:31805626
Constitutive Activation of Natural Killer Cells in Primary Biliary Cholangitis. PMID:31803181
Reactome and ORCID-fine-grained credit attribution for community curation. PMID:31802127
Graph-based information diffusion method for prioritizing functionally related genes in protein-protein interaction networks. PMID:31797617
Cisplatin treatment of testicular cancer patients introduces long-term changes in the epigenome. PMID:31796056
Characterization of NCC-RbC-51, an RB cell line isolated from a metastatic site. PMID:31781967
Meta-Analysis of HTLV-1-Infected Patients Identifies CD40LG and GBP2 as Markers of ATLL and HAM/TSP Clinical Status: Two Genes Beat as One. PMID:31781157
Mechanisms of different response to ionizing irradiation in isogenic head and neck cancer cell lines. PMID:31775835
Targeted exon sequencing in deceased schizophrenia patients in Denmark. PMID:31773318
Brief Normothermic Machine Perfusion Rejuvenates Discarded Human Kidneys. PMID:31773055
Identifying Cancer genes by combining two-rounds RWR based on multiple biological data. PMID:31760937
The role of haematological traits in risk of ischaemic stroke and its subtypes. PMID:31755939
High-resolution genome-wide expression analysis of single myofibers using SMART-Seq. PMID:31753917
A single factor dominates the behavior of rhythmic genes in mouse organs. PMID:31747875
A nutritional memory effect counteracts benefits of dietary restriction in old mice. PMID:31742247
Discovery of disease- and drug-specific pathways through community structures of a literature network. PMID:31738408
Representing glycophenotypes: semantic unification of glycobiology resources for disease discovery. PMID:31735951
pathDIP 4: an extended pathway annotations and enrichment analysis resource for human, model organisms and domesticated species. PMID:31733064
Profiling the microRNA signature of the peripheral sensory ganglia in experimental autoimmune encephalomyelitis (EAE). PMID:31729981
Identification of the key differentially expressed genes and pathways involved in neutrophilia. PMID:31726910
Proteomic profiling of the thrombin-activated canine platelet secretome (CAPS). PMID:31721811
Predicting the Probability that a Chemical Causes Steatosis Using Adverse Outcome Pathway Bayesian Networks (AOPBNs). PMID:31721239
Serum Exosome MicroRNAs Predict Multiple Sclerosis Disease Activity after Fingolimod Treatment. PMID:31721043
Dynamics of Non-Canonical Amino Acid-Labeled Intra- and Extracellular Proteins in the Developing Mouse. PMID:31719929
Identification of loci associated with conception rate in primiparous Holstein cows. PMID:31718557
A pan-inflammatory microRNA-cluster is associated with orbital non-Hodgkin lymphoma and idiopathic orbital inflammation. PMID:31713839
RPGeNet v2.0: expanding the universe of retinal disease gene interactions network. PMID:31712826
The Cytoscape BioGateway App: explorative network building from the BioGateway triple store. PMID:31710663
Gene expression analysis of the cerebellar cortex in essential tremor. PMID:31707044
Integrated transcriptomic analysis reveals hub genes involved in diagnosis and prognosis of pancreatic cancer. PMID:31706267
Body fluid from the parasitic worm Ascaris suum inhibits broad-acting pro-inflammatory programs in dendritic cells. PMID:31705653
PathTracer: High-sensitivity detection of differential pathway activity in tumours. PMID:31704995
Targeting Epithelial Mesenchymal Plasticity in Pancreatic Cancer: A Compendium of Preclinical Discovery in a Heterogeneous Disease. PMID:31703358
The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species. PMID:31701156
Causal Inference Engine: a platform for directional gene set enrichment analysis and inference of active transcriptional regulators. PMID:31701125
GREM1 is associated with metastasis and predicts poor prognosis in ER-negative breast cancer patients. PMID:31694641
Understanding allergic multimorbidity within the non-eosinophilic interactome. PMID:31693680
PDBe: improved findability of macromolecular structure data in the PDB. PMID:31691821
miRPathDB 2.0: a novel release of the miRNA Pathway Dictionary Database. PMID:31691816
The reactome pathway knowledgebase. PMID:31691815
Enzyme annotation in UniProtKB using Rhea. PMID:31688925
'One DB to rule them all'-the RING: a Regulatory INteraction Graph combining TFs, genes/proteins, SNPs, diseases and drugs. PMID:31682269
Plant Reactome: a knowledgebase and resource for comparative pathway analysis. PMID:31680153
Astrovirus replication in human intestinal enteroids reveals multi-cellular tropism and an intricate host innate immune landscape. PMID:31671153
Expression Atlas update: from tissues to single cells. PMID:31665515
CRISPR-Cas9-mediated knockout of SPRY2 in human hepatocytes leads to increased glucose uptake and lipid droplet accumulation. PMID:31664995
Phenome-wide association study of TTR and RBP4 genes in 361,194 individuals reveals novel insights in the genetics of hereditary and wildtype transthyretin amyloidoses. PMID:31659433
Atypical KRASG12R Mutant Is Impaired in PI3K Signaling and Macropinocytosis in Pancreatic Cancer. PMID:31649109
Bovine Genome Database: new annotation tools for a new reference genome. PMID:31647100
Pathway Commons 2019 Update: integration, analysis and exploration of pathway data. PMID:31647099
Modeling cancer drug response through drug-specific informative genes. PMID:31645597
Luteal Lipids Regulate Progesterone Production and May Modulate Immune Cell Function During the Estrous Cycle and Pregnancy. PMID:31636603
Two Distinct Subtypes Revealed in Blood Transcriptome of Breast Cancer Patients With an Unsupervised Analysis. PMID:31632916
De novo and recessive forms of congenital heart disease have distinct genetic and phenotypic landscapes. PMID:31624253
LnCeVar: a comprehensive database of genomic variations that disturb ceRNA network regulation. PMID:31617563
Neglog: Homology-Based Negative Data Sampling Method for Genome-Scale Reconstruction of Human Protein-Protein Interaction Networks. PMID:31614890
Biological Network Approaches and Applications in Rare Disease Studies. PMID:31614842
Bioinformatics for Marine Products: An Overview of Resources, Bottlenecks, and Perspectives. PMID:31614509
Integration of Large-Scale Genomic Data Sources With Evolutionary History Reveals Novel Genetic Loci for Congenital Heart Disease. PMID:31613678
Elimination of Reference Mapping Bias Reveals Robust Immune Related Allele-Specific Expression in Crossbred Sheep. PMID:31608110
pathfindR: An R Package for Comprehensive Identification of Enriched Pathways in Omics Data Through Active Subnetworks. PMID:31608109
A Network Pharmacology Study of the Multi-Targeting Profile of an Antiarrhythmic Chinese Medicine Xin Su Ning. PMID:31607935
VarSite: Disease variants and protein structure. PMID:31606900
Integrated molecular characterization of chondrosarcoma reveals critical determinants of disease progression. PMID:31604924
CancerGeneNet: linking driver genes to cancer hallmarks. PMID:31598703
Intermittent compressive force promotes osteogenic differentiation in human periodontal ligament cells by regulating the transforming growth factor-β pathway. PMID:31591384
Down-regulation of the islet-specific zinc transporter-8 (ZnT8) protects human insulinoma cells against inflammatory stress. PMID:31591269
A tailored approach to fusion transcript identification increases diagnosis of rare inherited disease. PMID:31577830
5-Hydroxymethylcytosines in Circulating Cell-Free DNA Reveal Vascular Complications of Type 2 Diabetes. PMID:31575611
Systematically Analyzing the Pathogenic Variations for Acute Intermittent Porphyria. PMID:31572191
Prognostic implications of 5-hydroxymethylcytosines from circulating cell-free DNA in diffuse large B-cell lymphoma. PMID:31570490
Metabolic Diversity in Human Non-Small Cell Lung Cancer Cells. PMID:31564558
Differential Gene Expression in Articular Cartilage and Subchondral Bone of Neonatal and Adult Horses. PMID:31557843
Role of NF-kappaB2-p100 in regulatory T cell homeostasis and activation. PMID:31554891
The metaRbolomics Toolbox in Bioconductor and beyond. PMID:31548506
Rethinking Lupus Nephritis Classification on a Molecular Level. PMID:31547518
Towards a standard diet-induced and biopsy-confirmed mouse model of non-alcoholic steatohepatitis: Impact of dietary fat source. PMID:31543682
Extracellular vesicles from endometriosis patients are characterized by a unique miRNA-lncRNA signature. PMID:31534048
Activation and In Vivo Evolution of the MAIT Cell Transcriptome in Mice and Humans Reveals Tissue Repair Functionality. PMID:31533045
Spaceflight influences gene expression, photoreceptor integrity, and oxidative stress-related damage in the murine retina. PMID:31527661
Synergistic Cytotoxicity of Renieramycin M and Doxorubicin in MCF-7 Breast Cancer Cells. PMID:31527453
The CRISPR-Cas9 crADSL HeLa transcriptome: A first step in establishing a model for ADSL deficiency and SAICAR accumulation. PMID:31516833
Nuclear decoupling is part of a rapid protein-level cellular response to high-intensity mechanical loading. PMID:31515493
Accelerating Medicines Partnership: Organizational Structure and Preliminary Data From the Phase 1 Studies of Lupus Nephritis. PMID:31502417
Probabilistic cell-type assignment of single-cell RNA-seq for tumor microenvironment profiling. PMID:31501550
Functional profiling of nucleotide Excision repair in breast cancer. PMID:31499327
hypeR: an R package for geneset enrichment workflows. PMID:31498385
A Survey of Gene Prioritization Tools for Mendelian and Complex Human Diseases. PMID:31494632
H3K4me3, H3K9ac, H3K27ac, H3K27me3 and H3K9me3 Histone Tags Suggest Distinct Regulatory Evolution of Open and Condensed Chromatin Landmarks. PMID:31491936
Altered gating of Kv1.4 in the nucleus accumbens suppresses motivation for reward. PMID:31487241
The Spectrinome: The Interactome of a Scaffold Protein Creating Nuclear and Cytoplasmic Connectivity and Function. PMID:31483159
Macrophage spatial heterogeneity in gastric cancer defined by multiplex immunohistochemistry. PMID:31477692
Integration analysis for novel lncRNA markers predicting tumor recurrence in human colon adenocarcinoma. PMID:31470869
Significance of circulating microRNAs in diabetes mellitus type 2 and platelet reactivity: bioinformatic analysis and review. PMID:31470851
Gene Expression Predicts Histological Severity and Reveals Distinct Molecular Profiles of Nonalcoholic Fatty Liver Disease. PMID:31467298
Multidimensional Predictors of Susceptibility and Resilience to Social Defeat Stress. PMID:31466563
Leveraging protein dynamics to identify cancer mutational hotspots using 3D structures. PMID:31462496
Metabolomic, transcriptomic and genetic integrative analysis reveals important roles of adenosine diphosphate in haemostasis and platelet activation in non-small-cell lung cancer. PMID:31461552
Neonatal T Follicular Helper Cells Are Lodged in a Pre-T Follicular Helper Stage Favoring Innate Over Adaptive Germinal Center Responses. PMID:31456798
Priming mobilization of hair follicle stem cells triggers permanent loss of regeneration after alkylating chemotherapy. PMID:31455775
Chronic Low Dose Oral Exposure to Microcystin-LR Exacerbates Hepatic Injury in a Murine Model of Non-Alcoholic Fatty Liver Disease. PMID:31450746
Mice Exposed to Combined Chronic Low-Dose Irradiation and Modeled Microgravity Develop Long-Term Neurological Sequelae. PMID:31443374
Differential gene expression and gene-set enrichment analysis in Caco-2 monolayers during a 30-day timeline with Dexamethasone exposure. PMID:31438773
Administration of a Postbiotic Causes Immunomodulatory Responses in Broiler Gut and Reduces Disease Pathogenesis Following Challenge. PMID:31426502
Adult and iPS-derived non-parenchymal cells regulate liver organoid development through differential modulation of Wnt and TGF-β. PMID:31416480
Therapeutic Targeting of RNA Splicing Catalysis through Inhibition of Protein Arginine Methylation. PMID:31408619
A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism. PMID:31395883
Long Non-Coding RNA Expression Levels Modulate Cell-Type-Specific Splicing Patterns by Altering Their Interaction Landscape with RNA-Binding Proteins. PMID:31390792
Quantifying the impact of public omics data. PMID:31383865
Phosphoproteomics reveals conserved exercise-stimulated signaling and AMPK regulation of store-operated calcium entry. PMID:31381180
Innate Immune Response to Influenza Virus at Single-Cell Resolution in Human Epithelial Cells Revealed Paracrine Induction of Interferon Lambda 1. PMID:31375585
A Comprehensive Study of Vesicular and Non-Vesicular miRNAs from a Volume of Cerebrospinal Fluid Compatible with Clinical Practice. PMID:31367240
PathwayMatcher: proteoform-centric network construction enables fine-granularity multiomics pathway mapping. PMID:31363752
Genome of the Komodo dragon reveals adaptations in the cardiovascular and chemosensory systems of monitor lizards. PMID:31358948
RNA sequencing profiling of the retina in C57BL/6J and DBA/2J mice: Enhancing the retinal microarray data sets from GeneNetwork. PMID:31354228
Genetic variation across RNA metabolism and cell death gene networks is implicated in the semantic variant of primary progressive aphasia. PMID:31350420
Analysis of gene expression in rheumatoid arthritis and related conditions offers insights into sex-bias, gene biotypes and co-expression patterns. PMID:31344123
A meta-analysis of multiple matched aCGH/expression cancer datasets reveals regulatory relationships and pathway enrichment of potential oncogenes. PMID:31335867
Inactivation of Prostaglandin E2 as a Mechanism for UGT2B17-Mediated Adverse Effects in Chronic Lymphocytic Leukemia. PMID:31334126
Functional genomics identifies predictive markers and clinically actionable resistance mechanisms to CDK4/6 inhibition in bladder cancer. PMID:31331377
Aberrant DNA methylation defines isoform usage in cancer, with functional implications. PMID:31329578
Spatiotemporal Gene Coexpression and Regulation in Mouse Cardiomyocytes of Early Cardiac Morphogenesis. PMID:31322043
Functional DNA variations associated with Saudi female with low VO2max: a pilot microarray study. PMID:31312377
Association of imputed prostate cancer transcriptome with disease risk reveals novel mechanisms. PMID:31308362
PhenPath: a tool for characterizing biological functions underlying different phenotypes. PMID:31307376
Truncating Variant in Myof Gene Is Associated With Limb-Girdle Type Muscular Dystrophy and Cardiomyopathy. PMID:31297131
Single-Cell Signature Explorer for comprehensive visualization of single cell signatures across scRNA-seq datasets. PMID:31294801
Epimutations in Developmental Genes Underlie the Onset of Domestication in Farmed European Sea Bass. PMID:31289822
Genome-wide functional association networks: background, data & state-of-the-art resources. PMID:31281921
Effect of Linearization in a WNT Signaling Model. PMID:31281412
Uncovering biomarker genes with enriched classification potential from Hallmark gene sets. PMID:31278367
Cancer classification and pathway discovery using non-negative matrix factorization. PMID:31271844
Deep evolutionary origin of limb and fin regeneration. PMID:31270239
Synthetic modeling reveals HOXB genes are critical for the initiation and maintenance of human leukemia. PMID:31266935
Proteomic Analysis of Plasma Reveals Fat Mass Influences Cancer-Related Pathways in Healthy Humans Fed Controlled Diets Differing in Glycemic Load. PMID:31266826
HIV and HCV augments inflammatory responses through increased TREM-1 expression and signaling in Kupffer and Myeloid cells. PMID:31260499
Proteomics INTegrator (PINT): An Online Tool To Store, Query, and Visualize Large Proteomics Experiment Results. PMID:31260318
Improving the diagnostic yield of exome- sequencing by predicting gene-phenotype associations using large-scale gene expression analysis. PMID:31253775
Estimation of allele-specific fitness effects across human protein-coding sequences and implications for disease. PMID:31249063
Prioritization of metabolic genes as novel therapeutic targets in estrogen-receptor negative breast tumors using multi-omics data and text mining. PMID:31231467
Gene Information eXtension (GIX): effortless retrieval of gene product information on any website. PMID:31217594
De Novo Assembly and Annotation of the Larval Transcriptome of Two Spadefoot Toads Widely Divergent in Developmental Rate. PMID:31217263
Current best practices in single-cell RNA-seq analysis: a tutorial. PMID:31217225
Circulating tumor cell and cell-free RNA capture and expression analysis identify platelet-associated genes in metastatic lung cancer. PMID:31215484
The transcriptome landscape associated with Disrupted-in-Schizophrenia-1 locus impairment in early development and adulthood. PMID:31204062
Altered Levels of Proteins and Phosphoproteins, in the Absence of Early Causative Transcriptional Changes, Shape the Molecular Pathogenesis in the Brain of Young Presymptomatic Ki91 SCA3/MJD Mouse. PMID:31201651
Large-scale gene expression analysis reveals robust gene signatures for prognosis prediction in lung adenocarcinoma. PMID:31198635
An integrative cross-omics analysis of DNA methylation sites of glucose and insulin homeostasis. PMID:31197173
Identification of critical connectors in the directed reaction-centric graphs of microbial metabolic networks. PMID:31195955
Investigating the Protein Signature of Adamantinomatous Craniopharyngioma Pediatric Brain Tumor Tissue: Towards the Comprehension of Its Aggressive Behavior. PMID:31191748
DNA methylation profiling allows for characterization of atrial and ventricular cardiac tissues and hiPSC-CMs. PMID:31186048
ANASTASIA: An Automated Metagenomic Analysis Pipeline for Novel Enzyme Discovery Exploiting Next Generation Sequencing Data. PMID:31178894
Identification of key modules and hub genes for small-cell lung carcinoma and large-cell neuroendocrine lung carcinoma by weighted gene co-expression network analysis of clinical tissue-proteomes. PMID:31166966
ORVAL: a novel platform for the prediction and exploration of disease-causing oligogenic variant combinations. PMID:31147699
Single-Cell Analysis of the Normal Mouse Aorta Reveals Functionally Distinct Endothelial Cell Populations. PMID:31146585
Graph Algorithms for Condensing and Consolidating Gene Set Analysis Results. PMID:31142576
Map and model-moving from observation to prediction in toxicogenomics. PMID:31140561
Mitochondria function associated genes contribute to Parkinson's Disease risk and later age at onset. PMID:31123700
Loss of TLE3 promotes the mitochondrial program in beige adipocytes and improves glucose metabolism. PMID:31123067
MultiPLIER: A Transfer Learning Framework for Transcriptomics Reveals Systemic Features of Rare Disease. PMID:31121115
Assessment of Novel Genome-Wide Significant Gene Loci and Lesion Growth in Geographic Atrophy Secondary to Age-Related Macular Degeneration. PMID:31120506
ALS blood expression profiling identifies new biomarkers, patient subgroups, and evidence for neutrophilia and hypoxia. PMID:31118040
Senescence Signature in Skin Biopsies From Systemic Sclerosis Patients Treated With Senolytic Therapy: Potential Predictor of Clinical Response? PMID:31112009
Tubular cell and keratinocyte single-cell transcriptomics applied to lupus nephritis reveal type I IFN and fibrosis relevant pathways. PMID:31110316
MutationDistiller: user-driven identification of pathogenic DNA variants. PMID:31106342
The Placental Atlas Tool (PAT): A collaborative research and discovery platform for the placental research community. PMID:31103066
Securing the future of research computing in the biosciences. PMID:31095554
PathMe: merging and exploring mechanistic pathway knowledge. PMID:31092193
Unbiased Boolean analysis of public gene expression data for cell cycle gene identification. PMID:31091168
In silico prediction of housekeeping long intergenic non-coding RNAs reveals HKlincR1 as an essential player in lung cancer cell survival. PMID:31089191
Differential Effects of Influenza Virus NA, HA Head, and HA Stalk Antibodies on Peripheral Blood Leukocyte Gene Expression during Human Infection. PMID:31088926
Data-Driven Analysis of Age, Sex, and Tissue Effects on Gene Expression Variability in Alzheimer's Disease. PMID:31068785
g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update). PMID:31066453
Comparison of Proteome Composition of Serum Enriched in Extracellular Vesicles Isolated from Polycythemia Vera Patients and Healthy Controls. PMID:31064135
Plasma protein biomarkers and their association with mutually exclusive cardiovascular phenotypes: the FIBRO-TARGETS case-control analyses. PMID:31062082
Integrative proteomics reveals an increase in non-degradative ubiquitylation in activated CD4+ T cells. PMID:31061531
Repeated Changes to the Gravitational Field Negatively Affect the Serum Concentration of Select Growth Factors and Cytokines. PMID:31057415
Genetic heterogeneity of Alzheimer's disease in subjects with and without hypertension. PMID:31055733
Genes with High Network Connectivity Are Enriched for Disease Heritability. PMID:31051114
An Integrated Chemical Proteomics Approach for Quantitative Profiling of Intracellular ADP-Ribosylation. PMID:31040352
Molecular dissection of box jellyfish venom cytotoxicity highlights an effective venom antidote. PMID:31040274
Dynamics of Dual Specificity Phosphatases and Their Interplay with Protein Kinases in Immune Signaling. PMID:31035605
Dissecting intratumoral myeloid cell plasticity by single cell RNA-seq. PMID:31033233
The MACADAM database: a MetAboliC pAthways DAtabase for Microbial taxonomic groups for mining potential metabolic capacities of archaeal and bacterial taxonomic groups. PMID:31032842
The Transcriptomic Toolbox: Resources for Interpreting Large Gene Expression Data within a Precision Medicine Context for Metabolic Disease Atherosclerosis. PMID:31032818
Unique RNA signature of different lesion types in the brain white matter in progressive multiple sclerosis. PMID:31023379
Systems Biology and Multi-Omics Integration: Viewpoints from the Metabolomics Research Community. PMID:31003499
Exploring the cross-phenotype network region of disease modules reveals concordant and discordant pathways between chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis. PMID:30997486
Studying alcohol use disorder using Drosophila melanogaster in the era of 'Big Data'. PMID:30992041
Identification of Important Invasion-Related Genes in Non-functional Pituitary Adenomas. PMID:30982163
Combinatorial Detection of Conserved Alteration Patterns for Identifying Cancer Subnetworks. PMID:30978274
Using NGS-methylation profiling to understand the molecular pathogenesis of young MI patients who have subsequent cardiac events. PMID:30971167
isoTar: Consensus Target Prediction with Enrichment Analysis for MicroRNAs Harboring Editing Sites and Other Variations. PMID:30963495
Evaluating measures of association for single-cell transcriptomics. PMID:30962620
IgE re-programs alternatively-activated human macrophages towards pro-inflammatory anti-tumoural states. PMID:30956175
Metabolic reaction network-based recursive metabolite annotation for untargeted metabolomics. PMID:30944337
Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. PMID:30944313
Integrating gene regulatory pathways into differential network analysis of gene expression data. PMID:30940863
PyCellBase, an efficient python package for easy retrieval of biological data from heterogeneous sources. PMID:30922213
Combined Transcriptome and Proteome Analysis of Immortalized Human Keratinocytes Expressing Human Papillomavirus 16 (HPV16) Oncogenes Reveals Novel Key Factors and Networks in HPV-Induced Carcinogenesis. PMID:30918060
Integrative Bioinformatics Analysis Reveals Potential Gene Biomarkers and Analysis of Function in Human Degenerative Disc Annulus Fibrosus Cells. PMID:30915367
Encircling the regions of the pharmacogenomic landscape that determine drug response. PMID:30914058
Genome-wide association study of blood lipids in Indians confirms universality of established variants. PMID:30911093
A Genome-Wide Analysis of the Penumbral Volume in Inbred Mice following Middle Cerebral Artery Occlusion. PMID:30911049
Exercise-Induced Activated Platelets Increase Adult Hippocampal Precursor Proliferation and Promote Neuronal Differentiation. PMID:30905740
The histone chaperone HIRA promotes the induction of host innate immune defences in response to HSV-1 infection. PMID:30901352
O-GlcNAcylation Enhances Double-Strand Break Repair, Promotes Cancer Cell Proliferation, and Prevents Therapy-Induced Senescence in Irradiated Tumors. PMID:30885991
A new approach to identifying hypertension-associated genes in the mesenteric artery of spontaneously hypertensive rats and stroke-prone spontaneously hypertensive rats. PMID:30882592
Identification of Important Effector Proteins in the FOXJ1 Transcriptional Network Associated With Ciliogenesis and Ciliary Function. PMID:30881373
Quantitative proteomic changes in LPS-activated monocyte-derived dendritic cells: A SWATH-MS study. PMID:30867486
Acting locally - affecting globally: RNA sequencing of gilthead sea bream with a mild Sparicotyle chrysophrii infection reveals effects on apoptosis, immune and hypoxia related genes. PMID:30866816
Repeated clinical malaria episodes are associated with modification of the immune system in children. PMID:30862316
PIMKL: Pathway-Induced Multiple Kernel Learning. PMID:30854223
Unsupervised classification of multi-omics data during cardiac remodeling using deep learning. PMID:30853547
Beyond Pathway Analysis: Identification of Active Subnetworks in Rett Syndrome. PMID:30847002
Physiological Expression of Ion Channel Receptors in Human Periodontal Ligament Stem Cells. PMID:30845727
SGLT2 inhibition reprograms systemic metabolism via FGF21-dependent and -independent mechanisms. PMID:30843877
Development of a multicellular pancreatic tumor microenvironment system using patient-derived tumor cells. PMID:30839006
Functional geometry of protein interactomes. PMID:30821317
The analysis of a time-course transcriptome profile by systems biology approaches reveals key molecular processes in acute kidney injury. PMID:30815016
Identification of bioactive metabolites using activity metabolomics. PMID:30814649
Protocol Update for large-scale genome and gene function analysis with the PANTHER classification system (v.14.0). PMID:30804569
White shark genome reveals ancient elasmobranch adaptations associated with wound healing and the maintenance of genome stability. PMID:30782839
Towards a data-integrated cell. PMID:30778056
Necroptosis in primate luteolysis: a role for ceramide. PMID:30774995
FunMappOne: a tool to hierarchically organize and visually navigate functional gene annotations in multiple experiments. PMID:30767762
Hypersensitive IFN Responses in Lupus Keratinocytes Reveal Key Mechanistic Determinants in Cutaneous Lupus. PMID:30745462
Chronic Inflammation Permanently Reshapes Tissue-Resident Immunity in Celiac Disease. PMID:30739797
A genetic variant associated with multiple sclerosis inversely affects the expression of CD58 and microRNA-548ac from the same gene. PMID:30730892
Comparison of RNA-Seq and Microarray Gene Expression Platforms for the Toxicogenomic Evaluation of Liver From Short-Term Rat Toxicity Studies. PMID:30723492
Ulcerative colitis: functional analysis of the in-depth proteome. PMID:30718987
Integration of macromolecular complex data into the Saccharomyces Genome Database. PMID:30715277
Serotonin inhibits axonal regeneration of identifiable descending neurons after a complete spinal cord injury in lampreys. PMID:30709851
Combining CDKN1A gene expression and genome-wide SNPs in a twin cohort to gain insight into the heritability of individual radiosensitivity. PMID:30706161
Cell cycle, energy metabolism and DNA repair pathways in cancer cells are suppressed by Compound Kushen Injection. PMID:30678652
From Genotype to Phenotype: Through Chromatin. PMID:30678090
Integrative analysis of gene expression profiles reveals distinct molecular characteristics in oral tongue squamous cell carcinoma. PMID:30675303
Circ-ZNF609 regulates G1-S progression in rhabdomyosarcoma. PMID:30670781
Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap. PMID:30664679
Microglial nodules provide the environment for pathogenic T cells in human encephalitis. PMID:30663001
FURIN Inhibition Reduces Vascular Remodeling and Atherosclerotic Lesion Progression in Mice. PMID:30651003
Gene Expression Pathways across Multiple Tissues in Antineutrophil Cytoplasmic Antibody-associated Vasculitis Reveal Core Pathways of Disease Pathology. PMID:30647166
Region-resolved proteomics profiling of monkey heart. PMID:30644093
Proteogenomics Uncovers Critical Elements of Host Response in Bovine Soft Palate Epithelial Cells Following In Vitro Infection with Foot-And-Mouth Disease Virus. PMID:30642035
Genome-wide analysis of genetic predisposition to Alzheimer's disease and related sex disparities. PMID:30636644
Mutational analysis of head and neck squamous cell carcinoma stratified by smoking status. PMID:30626742
Introducing WikiPathways as a Data-Source to Support Adverse Outcome Pathways for Regulatory Risk Assessment of Chemicals and Nanomaterials. PMID:30622555
A Computational Approach Identifies Immunogenic Features of Prognosis in Human Cancers. PMID:30622534
The Network of Cancer Genes (NCG): a comprehensive catalogue of known and candidate cancer genes from cancer sequencing screens. PMID:30606230
UbiHub: a data hub for the explorers of ubiquitination pathways. PMID:30601939
The Role of Nerve Growth Factor in Maintaining Proliferative Capacity, Colony-Forming Efficiency, and the Limbal Stem Cell Phenotype. PMID:30599086
Time-lagged Ordered Lasso for network inference. PMID:30594121
The RTK Interactome: Overview and Perspective on RTK Heterointeractions. PMID:30589534
Improvement in Outcomes After Cardiac Arrest and Resuscitation by Inhibition of S-Nitrosoglutathione Reductase. PMID:30586713
Identifying Potential Ageing-Modulating Drugs In Silico. PMID:30581056
Transcriptomes of microglia in experimental cerebral malaria in mice in the presence and absence of Type I Interferon signaling. PMID:30572937
An integrative approach for building personalized gene regulatory networks for precision medicine. PMID:30567569
ComPath: an ecosystem for exploring, analyzing, and curating mappings across pathway databases. PMID:30564458
Identification of Common and Rare Genetic Variation Associated With Plasma Protein Levels Using Whole-Exome Sequencing and Mass Spectrometry. PMID:30562114
Integrating molecular networks with genetic variant interpretation for precision medicine. PMID:30548534
Connecting nutrition composition measures to biomedical research. PMID:30541615
Comparative Analysis of Oomycete Genome Evolution Using the Oomycete Gene Order Browser (OGOB). PMID:30535146
LCE: an open web portal to explore gene expression and clinical associations in lung cancer. PMID:30532070
GM604 regulates developmental neurogenesis pathways and the expression of genes associated with amyotrophic lateral sclerosis. PMID:30524706
Type 1 Diabetes Mellitus-Associated Genetic Variants Contribute to Overlapping Immune Regulatory Networks. PMID:30524468
Cardiovascular Effects and Molecular Mechanisms of Bisphenol A and Its Metabolite MBP in Zebrafish. PMID:30520632
Solving for X: Evidence for sex-specific autism biomarkers across multiple transcriptomic studies. PMID:30520558
Multi-Study Proteomic and Bioinformatic Identification of Molecular Overlap between Amyotrophic Lateral Sclerosis (ALS) and Spinal Muscular Atrophy (SMA). PMID:30518112
Embracing the Dark Side: Computational Approaches to Unveil the Functionality of Genes Lacking Biological Annotation in Drug-Induced Liver Injury. PMID:30515189
LncACTdb 2.0: an updated database of experimentally supported ceRNA interactions curated from low- and high-throughput experiments. PMID:30476305
Negative Regulation of BOK Expression by Recruitment of TRIM28 to Regulatory Elements in Its 3' Untranslated Region. PMID:30471638
A reference set of curated biomedical data and metadata from clinical case reports. PMID:30457569
Genome-wide CRISPR Screens in Primary Human T Cells Reveal Key Regulators of Immune Function. PMID:30449619
SIFTS: updated Structure Integration with Function, Taxonomy and Sequences resource allows 40-fold increase in coverage of structure-based annotations for proteins. PMID:30445541
Regulatory Genomic Data Cubism. PMID:30428322
Prioritising candidate genes causing QTL using hierarchical orthologous groups. PMID:30423067
HumanNet v2: human gene networks for disease research. PMID:30418591
Potential widespread denitrosylation of brain proteins following prolonged restraint: proposed links between stress and central nervous system disease. PMID:30414012
Oestrogen receptor α AF-1 and AF-2 domains have cell population-specific functions in the mammary epithelium. PMID:30413705
PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools. PMID:30407594
Cancer cells exploit an orphan RNA to drive metastatic progression. PMID:30397354
The Gene Ontology Resource: 20 years and still GOing strong. PMID:30395331
Plasmodium-specific atypical memory B cells are short-lived activated B cells. PMID:30387712
Disease networks identify specific conditions and pleiotropy influencing multimorbidity in the general population. PMID:30374096
Feature related multi-view nonnegative matrix factorization for identifying conserved functional modules in multiple biological networks. PMID:30373534
Application of Proteomics Technologies in Oil Palm Research. PMID:30367348
Clust: automatic extraction of optimal co-expressed gene clusters from gene expression data. PMID:30359297
Complex Portal 2018: extended content and enhanced visualization tools for macromolecular complexes. PMID:30357405
CancerSEA: a cancer single-cell state atlas. PMID:30329142
BMDExpress 2: enhanced transcriptomic dose-response analysis workflow. PMID:30329029
Neuropsychiatric Systemic Lupus Erythematosus Is Dependent on Sphingosine-1-Phosphate Signaling. PMID:30319641
Aptamer-based proteomics of serum and plasma in acquired aplastic anemia. PMID:30312735
Adipocyte proteome and secretome influence inflammatory and hormone pathways in glioma. PMID:30302719
In Search of Biomarkers for Pathogenesis and Control of Leishmaniasis by Global Analyses of Leishmania-Infected Macrophages. PMID:30283744
Updates in Rhea: SPARQLing biochemical reaction data. PMID:30272209
The Comparative Toxicogenomics Database: update 2019. PMID:30247620
A genome-wide association study for natural antibodies measured in blood of Canadian Holstein cows. PMID:30241501
Prognostic modeling of the immune-centric transcriptome reveals interleukin signaling candidates contributing to differential patient outcomes. PMID:30202894
PRMT5 inhibition promotes osteogenic differentiation of mesenchymal stromal cells and represses basal interferon stimulated gene expression. PMID:30189247
Evaluation of potential effects of Plastin 3 overexpression and low-dose SMN-antisense oligonucleotides on putative biomarkers in spinal muscular atrophy mice. PMID:30188931
Phylo-PFP: improved automated protein function prediction using phylogenetic distance of distantly related sequences. PMID:30165572
Turning omics data into therapeutic insights. PMID:30149217
Integrated Dissection of Cysteine Oxidative Post-translational Modification Proteome During Cardiac Hypertrophy. PMID:30141336
Setting the stage for a role of the postsynaptic proteome in inherited neurometabolic disorders. PMID:30132229
Proteomic Analysis of Urine from California Sea Lions ( Zalophus californianus): A Resource for Urinary Biomarker Discovery. PMID:30113852
Identification of novel immune-relevant drug target genes for Alzheimer's Disease by combining ontology inference with network analysis. PMID:30106219
Proteomics: Clinical and research applications in respiratory diseases. PMID:30105802
Dysfunction of Sister Chromatids Separation Promotes Progression of Hepatocellular Carcinoma According to Analysis of Gene Expression Profiling. PMID:30100882
Towards FAIRer Biological Knowledge Networks Using a Hybrid Linked Data and Graph Database Approach. PMID:30085931
TLR-3 Stimulation Skews M2 Macrophages to M1 Through IFN-αβ Signaling and Restricts Tumor Progression. PMID:30072995
Reconstructing phosphorylation signalling networks from quantitative phosphoproteomic data. PMID:30072490
Proteomic interaction profiling reveals KIFC1 as a factor involved in early targeting of F508del-CFTR to degradation. PMID:30066085
Characterizing functional consequences of DNA copy number alterations in breast and ovarian tumors by spaceMap. PMID:30057342
Transcriptional Alterations in the Trigeminal Ganglia, Nucleus and Peripheral Blood Mononuclear Cells in a Rat Orofacial Pain Model. PMID:29997476
Genetic predisposition to B-cell acute lymphoblastic leukemia at 14q11.2 is mediated by a CEBPE promoter polymorphism. PMID:29977016
Pirfenidone decreases mesothelioma cell proliferation and migration via inhibition of ERK and AKT and regulates mesothelioma tumor microenvironment in vivo. PMID:29968778
More than fishing for a cure: The promises and pitfalls of high throughput cancer cell line screens. PMID:29953899
OmicsNet: a web-based tool for creation and visual analysis of biological networks in 3D space. PMID:29878180
Genome-wide association study identifies loci associated with milk leukocyte phenotypes following experimental challenge with Streptococcus uberis. PMID:29862454
CoNVaQ: a web tool for copy number variation-based association studies. PMID:29776329
MetExplore: collaborative edition and exploration of metabolic networks. PMID:29718355
Systematic evaluation of RNA quality, microarray data reliability and pathway analysis in fresh, fresh frozen and formalin-fixed paraffin-embedded tissue samples. PMID:29679021
Implications of publicly available genomic data resources in searching for therapeutic targets of obesity and type 2 diabetes. PMID:29674722
Intact interleukin-10 receptor signaling protects from hippocampal damage elicited by experimental neurotropic virus infection of SJL mice. PMID:29666403
In silico cancer research towards 3R. PMID:29649981
Radiation-Induced Gene Expression Changes in High and Low Grade Breast Cancer Cell Types. PMID:29617354
Gene microarray analysis of lncRNA and mRNA expression profiles in patients with high‑grade ovarian serous cancer. PMID:29577163
Profound Tissue Specificity in Proliferation Control Underlies Cancer Drivers and Aneuploidy Patterns. PMID:29576454
Proteomic identification and characterization of hepatic glyoxalase 1 dysregulation in non-alcoholic fatty liver disease. PMID:29456458
Integration of multiple networks and pathways identifies cancer driver genes in pan-cancer analysis. PMID:29304754
The reactome pathway knowledgebase PubMed citations: 852.

852 articles citing: The reactome pathway knowledgebase

Metabolomic and proteomic profiling in bipolar disorder patients revealed potential molecular signatures related to hemostasis. PMID:35922643
Methods to capture proteomic and metabolomic signatures from cerebrospinal fluid and serum of healthy individuals. PMID:35922450
The Utility of Small Fishes for the Genetic Study of Human Age-Related Disorders. PMID:35910227
Identification of immune-related and autophagy-related genes for the prediction of survival in bladder cancer. PMID:35909123
Metabolomic predictors of phenotypic traits can replace and complement measured clinical variables in population-scale expression profiling studies. PMID:35907790
Multi-Omics Interdisciplinary Research Integration to Accelerate Dementia Biomarker Development (MIRIADE). PMID:35903119
Selective targeting BMP2 and 4 in SMAD4 negative esophageal adenocarcinoma inhibits tumor growth and aggressiveness in preclinical models. PMID:35902550
Lipid metabolism-related genes as biomarkers and therapeutic targets reveal endometrial receptivity and immune microenvironment in women with reproductive dysfunction. PMID:35895215
Proteomic Assessment of C57BL/6 Hippocampi after Non-Selective Pharmacological Inhibition of Nitric Oxide Synthase Activity: Implications of Seizure-like Neuronal Hyperexcitability Followed by Tauopathy. PMID:35892672
Multi-Level Biological Network Analysis and Drug Repurposing Based on Leukocyte Transcriptomics in Severe COVID-19: In Silico Systems Biology to Precision Medicine. PMID:35887528
An Integrated Bioinformatics Analysis towards the Identification of Diagnostic, Prognostic, and Predictive Key Biomarkers for Urinary Bladder Cancer. PMID:35884419
Shared mechanisms across the major psychiatric and neurodegenerative diseases. PMID:35882878
ContactPFP: Protein function prediction using predicted contact information. PMID:35875419
orsum: a Python package for filtering and comparing enrichment analyses using a simple principle. PMID:35870894
Cardiomyocyte Cell-Cycle Regulation in Neonatal Large Mammals: Single Nucleus RNA-Sequencing Data Analysis via an Artificial-Intelligence-Based Pipeline. PMID:35860330
SARS-CoV-2 infection produces chronic pulmonary epithelial and immune cell dysfunction with fibrosis in mice. PMID:35857635
Single-Cell RNA Sequencing Reveals Cellular and Transcriptional Changes Associated With Traumatic Brain Injury. PMID:35846152
Genetic Factors and Their Role in the Pathogenesis of Biliary Atresia. PMID:35844731
A Metabolism-Related Gene Prognostic Index Bridging Metabolic Signatures and Antitumor Immune Cycling in Head and Neck Squamous Cell Carcinoma. PMID:35844514
Pan-sarcoma characterization of lncRNAs in the crosstalk of EMT and tumour immunity identifies distinct clinical outcomes and potential implications for immunotherapy. PMID:35842562
Time and phenotype-dependent transcriptome analysis in AAV-TGFβ1 and Bleomycin-induced lung fibrosis models. PMID:35842487
Tumor treating fields affect mesothelioma cell proliferation by exerting histotype-dependent cell cycle checkpoint activations and transcriptional modulations. PMID:35840560
Identification of Therapeutic Targets for Amyotrophic Lateral Sclerosis Using PandaOmics - An AI-Enabled Biological Target Discovery Platform. PMID:35837482
Genome-wide analyses of 200,453 individuals yield new insights into the causes and consequences of clonal hematopoiesis. PMID:35835912
Microglia coordinate cellular interactions during spinal cord repair in mice. PMID:35835751
Scalable multiplex co-fractionation/mass spectrometry platform for accelerated protein interactome discovery. PMID:35831314
The heterogeneous pharmacological medical biochemical network PharMeBINet. PMID:35821017
Most Pathways Can Be Related to the Pathogenesis of Alzheimer's Disease. PMID:35813951
A Divergent Selection on Breast Meat Ultimate pH, a Key Factor for Chicken Meat Quality, is Associated With Different Circulating Lipid Profiles. PMID:35812337
Transcriptome Profiling of the Dorsomedial Prefrontal Cortex in Suicide Victims. PMID:35806070
Proteomic profiling of serum small extracellular vesicles reveals immune signatures of children with pneumonia. PMID:35800266
Potential Application of Pyroptosis in Kidney Renal Clear Cell Carcinoma Immunotherapy and Targeted Therapy. PMID:35795559
Comparison of tissue tropism and host response to enteric and respiratory enteroviruses. PMID:35789345
Demystifying the long noncoding RNA landscape of small EVs derived from human mesenchymal stromal cells. PMID:35777918
A Role of the TEX101 Interactome in the Common Aetiology Behind Male Subfertility and Testicular Germ Cell Tumor. PMID:35774118
The close interaction between hypoxia-related proteins and metastasis in pancarcinomas. PMID:35773405
Editome landscape of CCM-derived endothelial cells. PMID:35771000
An automatic integrative method for learning interpretable communities of biological pathways. PMID:35769343
Network-based machine learning approach to predict immunotherapy response in cancer patients. PMID:35764641
Pathway importance by graph convolutional network and Shapley additive explanations in gene expression phenotype of diffuse large B-cell lymphoma. PMID:35749395
Differences and Similarities between the Lung Transcriptomic Profiles of COVID-19, COPD, and IPF Patients: A Meta-Analysis Study of Pathophysiological Signaling Pathways. PMID:35743918
An Overview of the Importance and Value of Porcine Species in Sialic Acid Research. PMID:35741423
Glutamine antagonist JHU083 improves psychosocial behavior and sleep deficits in EcoHIV-infected mice. PMID:35734753
Zika Virus Strains and Dengue Virus Induce Distinct Proteomic Changes in Neural Stem Cells and Neurospheres. PMID:35732867
Single-nucleus profiling of human dilated and hypertrophic cardiomyopathy. PMID:35732739
DNA Methylation Analysis of Turner Syndrome BAV. PMID:35711915
A hexa-species transcriptome atlas of mammalian embryogenesis delineates metabolic regulation across three different implantation modes. PMID:35710749
Elucidating gene expression patterns across multiple biological contexts through a large-scale investigation of transcriptomic datasets. PMID:35705903
cGAS-STING drives the IL-6-dependent survival of chromosomally instable cancers. PMID:35705809
Network approaches for modeling the effect of drugs and diseases. PMID:35704883
OMA1 mediates local and global stress responses against protein misfolding in CHCHD10 mitochondrial myopathy. PMID:35700042
Gene expression profiling and protein-protein interaction analysis reveals the dynamic role of MCM7 in Alzheimer's disorder and breast cancer. PMID:35698583
Estimation of tumor cell total mRNA expression in 15 cancer types predicts disease progression. PMID:35697807
Screening membraneless organelle participants with machine-learning models that integrate multimodal features. PMID:35687670
An Integrated Multi-Omic Network Analysis Identifies Seizure-Associated Dysregulated Pathways in the GAERS Model of Absence Epilepsy. PMID:35682742
Sedoheptulose Kinase SHPK Expression in Glioblastoma: Emerging Role of the Nonoxidative Pentose Phosphate Pathway in Tumor Proliferation. PMID:35682658
Ptpn1 deletion protects oval cells against lipoapoptosis by favoring lipid droplet formation and dynamics. PMID:35681014
Drug repositioning in non-small cell lung cancer (NSCLC) using gene co-expression and drug-gene interaction networks analysis. PMID:35676421
Data-dependent visualization of biological networks in the web-browser with NDExEdit. PMID:35675360
Patient-level proteomic network prediction by explainable artificial intelligence. PMID:35672443
An approach to cellular tropism of SARS-CoV-2 through protein-protein interaction and enrichment analysis. PMID:35672403
A Resource to Infer Molecular Paths Linking Cancer Mutations to Perturbation of Cell Metabolism. PMID:35664677
Early and Late Transcriptional Changes in Blood, Neural, and Colon Tissues in Rat Models of Stress-Induced and Comorbid Pain Hypersensitivity Reveal Regulatory Roles in Neurological Disease. PMID:35655748
A stromal Integrated Stress Response activates perivascular cancer-associated fibroblasts to drive angiogenesis and tumour progression. PMID:35654839
Baseline Elevations of Leukotriene Metabolites and Altered Plasmalogens Are Prognostic Biomarkers of Plaque Progression in Systemic Lupus Erythematosus. PMID:35651909
Deep Learning-Based Protein Features Predict Overall Survival and Chemotherapy Benefit in Gastric Cancer. PMID:35651795
Mapping the cardiac vascular niche in heart failure. PMID:35641541
Annotation Query (AnnoQ): an integrated and interactive platform for large-scale genetic variant annotation. PMID:35640593
Target and drug predictions for SARS-CoV-2 infection in hepatocellular carcinoma patients. PMID:35639708
Epithelioid Pleural Mesothelioma Is Characterized by Tertiary Lymphoid Structures in Long Survivors: Results from the MATCH Study. PMID:35628597
A Nine-Strain Bacterial Consortium Improves Portal Hypertension and Insulin Signaling and Delays NAFLD Progression In Vivo. PMID:35625927
Immune-Related Protein Interaction Network in Severe COVID-19 Patients toward the Identification of Key Proteins and Drug Repurposing. PMID:35625619
Transmembrane Protein 170B is a Prognostic Biomarker and Associated With Immune Infiltrates in Pancreatic Adenocarcinoma. PMID:35601487
Transcriptome-wide prediction of prostate cancer gene expression from histopathology images using co-expression based convolutional neural networks. PMID:35595235
Human liver single nucleus and single cell RNA sequencing identify a hepatocellular carcinoma-associated cell-type affecting survival. PMID:35581624
Cardioprotection by selective SGLT-2 inhibitors in a non-diabetic mouse model of myocardial ischemia/reperfusion injury: a class or a drug effect? PMID:35581445
Mapping and Validation of scRNA-Seq-Derived Cell-Cell Communication Networks in the Tumor Microenvironment. PMID:35572582
Inwardly rectifying potassium channels mediate polymyxin-induced nephrotoxicity. PMID:35570209
Identifying Protein Features and Pathways Responsible for Toxicity Using Machine Learning and Tox21: Implications for Predictive Toxicology. PMID:35566372
A Data Science Approach for the Identification of Molecular Signatures of Aggressive Cancers. PMID:35565454
Metastatic Transition of Pancreatic Ductal Cell Adenocarcinoma Is Accompanied by the Emergence of Pro-Invasive Cancer-Associated Fibroblasts. PMID:35565326
Multiomic Profiling Identified EGF Receptor Signaling as a Potential Inhibitor of Type I Interferon Response in Models of Oncolytic Therapy by Vesicular Stomatitis Virus. PMID:35563635
Sample-Specific Perturbation of Gene Interactions Identifies Pancreatic Cancer Subtypes. PMID:35563183
Implication of genetic variants in primary microRNA processing sites in the risk of multiple sclerosis. PMID:35561450
CBNplot: Bayesian network plots for enrichment analysis. PMID:35561164
A Community-Driven, Openly Accessible Molecular Pathway Integrating Knowledge on Malignant Pleural Mesothelioma. PMID:35558518
Exome sequencing of hepatocellular carcinoma in lemurs identifies potential cancer drivers: A pilot study. PMID:35557512
DNA methylation signatures of childhood trauma predict psychiatric disorders and other adverse outcomes 17 years after exposure. PMID:35546634
Proteomic profiling of lung diffusion impairment in the recovery stage of SARS-CoV-2-induced ARDS. PMID:35538880
Transcriptome Architecture of Osteoblastic Cells Infected With Staphylococcus aureus Reveals Strong Inflammatory Responses and Signatures of Metabolic and Epigenetic Dysregulation. PMID:35531332
A Review and Meta-Analysis of Influenza Interactome Studies. PMID:35531276
Single-cell genomics identifies distinct B1 cell developmental pathways and reveals aging-related changes in the B-cell receptor repertoire. PMID:35526067
TNFRSF13B is a potential contributor to prostate cancer. PMID:35524261
Identification of Key Pathways Associated With Residual Feed Intake of Beef Cattle Based on Whole Blood Transcriptome Data Analyzed Using Gene Set Enrichment Analysis. PMID:35518641
Dissecting the Role of Immune Checkpoint Regulation Patterns in Tumor Microenvironment and Prognosis of Gastric Cancer. PMID:35518357
miRNA-199a-5p/SLC2A1 axis regulates glucose metabolism in non-small cell lung cancer. PMID:35517408
Interactome and Ubiquitinome Analyses Identify Functional Targets of Herpes Simplex Virus 1 Infected Cell Protein 0. PMID:35516420
Germline predisposition to pediatric Ewing sarcoma is characterized by inherited pathogenic variants in DNA damage repair genes. PMID:35512711
A hybrid approach unveils drug repurposing candidates targeting an Alzheimer pathophysiology mechanism. PMID:35510183
An eIF3d-dependent switch regulates HCMV replication by remodeling the infected cell translation landscape to mimic chronic ER stress. PMID:35508137
IMEx Databases: Displaying Molecular Interactions into a Single, Standards-Compliant Dataset. PMID:35507258
Interleukin-6 inhibition in ST-elevation myocardial infarction: Immune cell profile in the randomised ASSAIL-MI trial. PMID:35504178
Identifying novel SMYD3 interactors on the trail of cancer hallmarks. PMID:35495117
Rare coding variants in DNA damage repair genes associated with timing of natural menopause. PMID:35493704
Genome evolution of a nonparasitic secondary heterotroph, the diatom Nitzschia putrida. PMID:35486731
A systems genomics approach to uncover patient-specific pathogenic pathways and proteins in ulcerative colitis. PMID:35484353
Membranome 3.0: Database of single-pass membrane proteins with AlphaFold models. PMID:35481632
Cancer Progression Gene Expression Profiling Identifies the Urokinase Plasminogen Activator Receptor as a Biomarker of Metastasis in Cutaneous Squamous Cell Carcinoma. PMID:35480116
A Cancer Associated Fibroblasts-Related Six-Gene Panel for Anti-PD-1 Therapy in Melanoma Driven by Weighted Correlation Network Analysis and Supervised Machine Learning. PMID:35479936
Extracting functional insights from loss-of-function screens using deep link prediction. PMID:35474966
Capillary Electrophoresis Mass Spectrometry for Scalable Single-Cell Proteomics. PMID:35464213
Artificial Intelligence Uncovers Natural MMP Inhibitor Crocin as a Potential Treatment of Thoracic Aortic Aneurysm and Dissection. PMID:35463768
Assessing proteolytic events in bioinformatic reanalysis of public secretome data from melanoma cell lines. PMID:35462751
Recognition of a Novel Gene Signature for Human Glioblastoma. PMID:35456975
Molecular Evolutionary Rate Predicts Intraspecific Genetic Polymorphism and Species-Specific Selection. PMID:35456514
Single-cell transcriptomics identifies Mcl-1 as a target for senolytic therapy in cancer. PMID:35449130
Bacillus Calmette-Guérin-induced trained immunity protects against SARS-CoV-2 challenge in K18-hACE2 mice. PMID:35446790
Multi-omics integration and interactomics reveals molecular networks and regulators of the beneficial effect of yoga and exercise. PMID:35444372
Generation of human islet cell type-specific identity genesets. PMID:35440614
Identification of Common and Distinct Pathways in Inflammatory Bowel Disease and Colorectal Cancer: A Hypothesis Based on Weighted Gene Co-Expression Network Analysis. PMID:35432477
Pulmonary Inflammatory Response in Lethal COVID-19 Reveals Potential Therapeutic Targets and Drugs in Phases III/IV Clinical Trials. PMID:35422702
Population-scale long-read sequencing uncovers transposable elements associated with gene expression variation and adaptive signatures in Drosophila. PMID:35413957
Urinary Proteomic Profile of Arterial Stiffness Is Associated With Mortality and Cardiovascular Outcomes. PMID:35411793
Scaling up oligogenic diseases research with OLIDA: the Oligogenic Diseases Database. PMID:35411390
E-Cadherin-Deficient Cells Are Sensitive to the Multikinase Inhibitor Dasatinib. PMID:35406381
Cardiovascular signatures of COVID-19 predict mortality and identify barrier stabilizing therapies. PMID:35405523
Extracellular Matrix-Based Gene Expression Signature Defines Two Prognostic Subtypes of Hepatocellular Carcinoma With Different Immune Microenvironment Characteristics. PMID:35402515
Genomic Evidence Supports the Recognition of Endometriosis as an Inflammatory Systemic Disease and Reveals Disease-Specific Therapeutic Potentials of Targeting Neutrophil Degranulation. PMID:35401535
Expansion of Schizophrenia Gene Network Knowledge Using Machine Learning Selected Signals From Dorsolateral Prefrontal Cortex and Amygdala RNA-seq Data. PMID:35386517
SuperDendrix algorithm integrates genetic dependencies and genomic alterations across pathways and cancer types. PMID:35382456
SPCS: a spatial and pattern combined smoothing method for spatial transcriptomic expression. PMID:35380614
Bioinformatical analysis identifies PDLIM3 as a potential biomarker associated with immune infiltration in patients with endometriosis. PMID:35378934
Loss of Claudin-4 Reduces DNA Damage Repair and Increases Sensitivity to PARP Inhibitors. PMID:35373300
Insight Into the Long Noncoding RNA and mRNA Coexpression Profile in the Human Blood Transcriptome Upon Leishmania infantum Infection. PMID:35370994
Soluble TGFBI aggravates the malignancy of cholangiocarcinoma through activation of the ITGB1 dependent PPARγ signalling pathway. PMID:35357655
Evaluating the predictive accuracy of curated biological pathways in a public knowledgebase. PMID:35348650
Bioinformatics analysis of potential therapeutic targets for COVID-19 infection in patients with carotid atherosclerosis. PMID:35344771
Multi-Omics Characterization of Type 2 Diabetes Mellitus-Induced Cognitive Impairment in the db/db Mouse Model. PMID:35335269
Latent Variables Capture Pathway-Level Points of Departure in High-Throughput Toxicogenomic Data. PMID:35333521
Functional Enrichment Analysis of Regulatory Elements. PMID:35327392
Cerebrospinal Fluid Proteome Alterations Associated with Neuropsychiatric Symptoms in Cognitive Decline and Alzheimer's Disease. PMID:35326481
A regulator of G protein signaling 5 marked subpopulation of vascular smooth muscle cells is lost during vascular disease. PMID:35320283
Characterization of the genetic architecture of infant and early childhood body mass index. PMID:35315439
Novel prevention insights into depletion of oxidative stress status through regular exercise and grape seed effective substance in heart ischemia rat model. PMID:35311161
Understanding the activating mechanism of the immune system against COVID-19 by Traditional Indian Medicine: Network pharmacology approach. PMID:35305722
Biomimetic hydrogel supports initiation and growth of patient-derived breast tumor organoids. PMID:35304464
Antifungals influence the immune-related transcriptomic landscape of human monocytes after Aspergillus fumigatus infection. PMID:35301416
Oncogenic gene expression and epigenetic remodeling of cis-regulatory elements in ASXL1-mutant chronic myelomonocytic leukemia. PMID:35301312
From Causal Networks to Adverse Outcome Pathways: A Developmental Neurotoxicity Case Study. PMID:35295214
The AOP-DB RDF: Applying FAIR Principles to the Semantic Integration of AOP Data Using the Research Description Framework. PMID:35295213
Beyond AOPs: A Mechanistic Evaluation of NAMs in DART Testing. PMID:35295212
Whole genome sequencing delineates regulatory, copy number, and cryptic splice variants in early onset cardiomyopathy. PMID:35288587
Inhibition of miR-128 Enhances Vocal Sequence Organization in Juvenile Songbirds. PMID:35283744
Streptococcus pneumoniae and Influenza A Virus Co-Infection Induces Altered Polyubiquitination in A549 Cells. PMID:35281454
Distinct Epileptogenic Mechanisms Associated with Seizures in Wolf-Hirschhorn Syndrome. PMID:35278209
Transcriptomics of Parental Care in the Hypothalamic-Septal Region of Female Zebra Finch Brain. PMID:35269661
Chicory: Understanding the Effects and Effectors of This Functional Food. PMID:35267932
Broad Transcriptomic Impact of Sorafenib and Its Relation to the Antitumoral Properties in Liver Cancer Cells. PMID:35267509
The Non-pregnant and Pregnant Human Cervix: a Systematic Proteomic Analysis. PMID:35266109
Selective pressure of endocrine therapy activates the integrated stress response through NFκB signaling in a subpopulation of ER positive breast cancer cells. PMID:35264224
Urgent need for consistent standards in functional enrichment analysis. PMID:35263338
A novel single-cell RNA-sequencing approach and its applicability connecting genotype to phenotype in ageing disease. PMID:35260714
Computing microRNA-gene interaction networks in pan-cancer using miRDriver. PMID:35260634
Cure of syngeneic carcinomas with targeted IL-12 through obligate reprogramming of lymphoid and myeloid immunity. PMID:35260537
Whole-genome sequencing reveals host factors underlying critical COVID-19. PMID:35255492
Synergistic action of WDR5 and HDM2 inhibitors in SMARCB1-deficient cancer cells. PMID:35252869
Fusobacterium nucleatum is associated with inflammation and poor survival in early-stage HPV-negative tongue cancer. PMID:35252868
Mining RNAseq data reveals dynamic metaboloepigenetic profiles in human, mouse and bovine pre-implantation embryos. PMID:35252810
A network-based computational and experimental framework for repurposing compounds toward the treatment of non-alcoholic fatty liver disease. PMID:35252807
Genome-Wide Methylation Profiling in the Thalamus of Scrapie Sheep. PMID:35252421
An omic and multidimensional spatial atlas from serial biopsies of an evolving metastatic breast cancer. PMID:35243422
Dynamic Control Balancing Cell Proliferation and Inflammation is Crucial for an Effective Immune Response to Malaria. PMID:35242812
System-wide transcriptome damage and tissue identity loss in COVID-19 patients. PMID:35233546
Pathway Analysis for Cancer Research and Precision Oncology Applications. PMID:35230687
Neuronal-glial communication perturbations in murine SOD1G93A spinal cord. PMID:35228715
PubChem Protein, Gene, Pathway, and Taxonomy Data Collections: Bridging Biology and Chemistry through Target-Centric Views of PubChem Data. PMID:35227770
Potential biomarkers in the fibrosis progression of nonalcoholic steatohepatitis (NASH). PMID:35226336
Developmental Regulation and Functional Prediction of microRNAs in an Expanded Fasciola hepatica miRNome. PMID:35223544
Multiple Myeloma Patient Tumors With High Levels of Cereblon Exon-10 Deletion Splice Variant Upregulate Clinically Targetable Pro-Inflammatory Cytokine Pathways. PMID:35222546
Identification of Molecular Signatures and Candidate Drugs in Vascular Dementia by Bioinformatics Analyses. PMID:35221911
Student biocuration projects as a learning environment. PMID:35211294
Functional Analysis of Autoantibody Signatures in Rheumatoid Arthritis. PMID:35209238
Computational Models for Clinical Applications in Personalized Medicine-Guidelines and Recommendations for Data Integration and Model Validation. PMID:35207655
Molecular Composition of Serum Exosomes Could Discriminate Rectal Cancer Patients with Different Responses to Neoadjuvant Radiotherapy. PMID:35205741
Impact of Maternal Obesity on Liver Disease in the Offspring: A Comprehensive Transcriptomic Analysis and Confirmation of Results in a Murine Model. PMID:35203502
Single-Cell RNA-Seq Analysis of Olfactory Mucosal Cells of Alzheimer's Disease Patients. PMID:35203328
Serological profiling reveals hsa-miR-451a as a possible biomarker of anaphylaxis. PMID:35202004
Identification of Potential Immune Checkpoint Inhibitor Targets in Gliomas via Bioinformatic Analyses. PMID:35198632
Effective drug combinations in breast, colon and pancreatic cancer cells. PMID:35197630
Identification of phenotype-specific networks from paired gene expression-cell shape imaging data. PMID:35197309
A model of persistent post SARS-CoV-2 induced lung disease for target identification and testing of therapeutic strategies. PMID:35194605
Rare disorders have many faces: in silico characterization of rare disorder spectrum. PMID:35193637
TLR2 and TLR7 mediate distinct immunopathological and antiviral plasmacytoid dendritic cell responses to SARS-CoV-2 infection. PMID:35178710
Modeling Progression of Single Cell Populations Through the Cell Cycle as a Sequence of Switches. PMID:35178429
CPEB1 directs muscle stem cell activation by reprogramming the translational landscape. PMID:35177647
A Proximal-to-Distal Survey of Healthy Adult Human Small Intestine and Colon Epithelium by Single-Cell Transcriptomics. PMID:35176508
TLR4 is a regulator of trained immunity in a murine model of Duchenne muscular dystrophy. PMID:35169163
LINE-1 expression in cancer correlates with p53 mutation, copy number alteration, and S phase checkpoint. PMID:35169076
Hyaluronidase-1-mediated glycocalyx impairment underlies endothelial abnormalities in polypoidal choroidal vasculopathy. PMID:35164755
Insights into the Steps of Breast Cancer-Brain Metastases Development: Tumor Cell Interactions with the Blood-Brain Barrier. PMID:35163822
SPDL1 Is an Independent Predictor of Patient Outcome in Colorectal Cancer. PMID:35163739
Differential Expression of Serum Extracellular Vesicle miRNAs in Multiple Sclerosis: Disease-Stage Specificity and Relevance to Pathophysiology. PMID:35163583
Unravelling Mechanisms of Doxorubicin-Induced Toxicity in 3D Human Intestinal Organoids. PMID:35163210
Whole Blood Transcriptional Fingerprints of High-Grade Glioma and Longitudinal Tumor Evolution under Carbon Ion Radiotherapy. PMID:35158950
T-SIGn tumor reengineering therapy and CAR T cells synergize in combination therapy to clear human lung tumor xenografts and lung metastases in NSG mice. PMID:35154906
Skeletal muscle undergoes fiber type metabolic switch without myosin heavy chain switch in response to defective fatty acid oxidation. PMID:35150906
Machine learning prediction and tau-based screening identifies potential Alzheimer's disease genes relevant to immunity. PMID:35149761
Advancing drug safety science by integrating molecular knowledge with post-marketing adverse event reports. PMID:35143713
In silico prediction of HIV-1-host molecular interactions and their directionality. PMID:35134057
Placental proteins with predicted roles in fetal development decrease in premature infants. PMID:35132128
Plasma miRNA profile at COVID-19 onset predicts severity status and mortality. PMID:35130828
Shared Genetic Architecture and Causal Relationship Between Asthma and Cardiovascular Diseases: A Large-Scale Cross-Trait Analysis. PMID:35126453
Do Genetic Polymorphisms Affect Fetal Hemoglobin (HbF) Levels in Patients With Sickle Cell Anemia Treated With Hydroxyurea? A Systematic Review and Pathway Analysis. PMID:35126118
Artificial intelligence analysis to explore synchronize exercise, cobalamin, and magnesium as new actors to therapeutic of migraine symptoms: a randomized, placebo-controlled trial. PMID:35112219
Proteomics Study Reveals the Anti-Depressive Mechanisms and the Compatibility Advantage of Chaihu-Shugan-San in a Rat Model of Chronic Unpredictable Mild Stress. PMID:35111057
miR-182 targeting reprograms tumor-associated macrophages and limits breast cancer progression. PMID:35105806
Genomic prediction of growth in a commercially, recreationally, and culturally important marine resource, the Australian snapper (Chrysophrys auratus). PMID:35100370
A novel variant in SMG9 causes intellectual disability, confirming a role for nonsense-mediated decay components in neurocognitive development. PMID:35087184
Bioactive peptides from broccoli stems strongly enhance regenerative keratinocytes by stimulating controlled proliferation. PMID:35086428
A cluster of blood-based protein biomarkers reflecting coagulation relates to the burden of cerebral small vessel disease. PMID:35086368
Impact of high platelet turnover on the platelet transcriptome: Results from platelet RNA-sequencing in patients with sepsis. PMID:35085240
Gene and metabolite expression dependence on body mass index in human myocardium. PMID:35082386
Comparative assessment of genes driving cancer and somatic evolution in non-cancer tissues: an update of the Network of Cancer Genes (NCG) resource. PMID:35078504
A simple guide to de novo transcriptome assembly and annotation. PMID:35076693
Kidney organoids recapitulate human basement membrane assembly in health and disease. PMID:35076391
Pre-transplant Transcriptional Signature in Peripheral Blood Mononuclear Cells of Acute Renal Allograft Rejection. PMID:35071278
BioInfograph: An Online Tool to Design and Display Multi-Panel Scientific Figure Interactively. PMID:35069687
Circadian Regulation Patterns With Distinct Immune Landscapes in Gliomas Aid in the Development of a Risk Model to Predict Prognosis and Therapeutic Response. PMID:35069579
RadSigBench: a framework for benchmarking functional genomics signatures of cancer cell radiosensitivity. PMID:35066588
Extracellular vesicles produced by the human commensal gut bacterium Bacteroides thetaiotaomicron affect host immune pathways in a cell-type specific manner that are altered in inflammatory bowel disease. PMID:35064769
Searching for New Z-DNA/Z-RNA Binding Proteins Based on Structural Similarity to Experimentally Validated Zα Domain. PMID:35054954
Proteomic Analysis of Retinal Tissue in an S100B Autoimmune Glaucoma Model. PMID:35053014
WNT/beta-catenin signalling interrupts a senescence-induction cascade in human mesenchymal stem cells that restricts their expansion. PMID:35048158
Plant Reactome and PubChem: The Plant Pathway and (Bio)Chemical Entity Knowledgebases. PMID:35037224
Gramene: A Resource for Comparative Analysis of Plants Genomes and Pathways. PMID:35037202
Analysis of the circRNA and T-UCR populations identifies convergent pathways in mouse and human models of Rett syndrome. PMID:35036070
Identification of long non-coding RNAs and RNA binding proteins in breast cancer subtypes. PMID:35027621
Tubastatin A maintains adult skeletal muscle stem cells in a quiescent state ex vivo and improves their engraftment ability in vivo. PMID:35021050
InterCellar enables interactive analysis and exploration of cell-cell communication in single-cell transcriptomic data. PMID:35017628
Expression of type I interferon-associated genes at antiretroviral therapy interruption predicts HIV virological rebound. PMID:35013427
Overexpression of microRNAs miR-25-3p, miR-185-5p and miR-132-3p in Late Onset Fetal Growth Restriction, Validation of Results and Study of the Biochemical Pathways Involved. PMID:35008715
Hyperinflammatory environment drives dysfunctional myeloid cell effector response to bacterial challenge in COVID-19. PMID:35007290
The novel proteomic signature for cardiac allograft vasculopathy. PMID:35005846
BIRC2-BIRC3 amplification: a potentially druggable feature of a subset of head and neck cancers in patients with Fanconi anemia. PMID:34997070
Identification of an at-risk subpopulation with high immune infiltration based on the peroxisome pathway and TIM3 in colorectal cancer. PMID:34996408
Deep learning-based brain transcriptomic signatures associated with the neuropathological and clinical severity of Alzheimer's disease. PMID:34993477
Glutaminase 2 knockdown reduces hyperammonemia and associated lethality of urea cycle disorder mouse model. PMID:34988999
Interpretable generative deep learning: an illustration with single cell gene expression data. PMID:34988661
Transcriptional Analysis of Nuclear-Encoded Mitochondrial Genes in Eight Neurodegenerative Disorders: The Analysis of Seven Diseases in Reference to Friedreich's Ataxia. PMID:34987545
HMDB 5.0: the Human Metabolome Database for 2022. PMID:34986597
CREB1K292 and HINFPK330 as Putative Common Therapeutic Targets in Alzheimer's and Parkinson's Disease. PMID:34984308
Capturing the transcription factor interactome in response to sub-lethal insecticide exposure. PMID:34977825
The Mouse Gastrointestinal Bacteria Catalogue enables translation between the mouse and human gut microbiotas via functional mapping. PMID:34971560
GDPLichi: a DNA Damage Repair-Related Gene Classifier for Predicting Lung Adenocarcinoma Immune Checkpoint Inhibitors Response. PMID:34970479
Trojan horse treatment based on PEG-coated extracellular vesicles to deliver doxorubicin to melanoma in vitro and in vivo. PMID:34964693
Hepatic MIR20B promotes nonalcoholic fatty liver disease by suppressing PPARA. PMID:34964438
Urine proteomics identifies biomarkers for diabetic kidney disease at different stages. PMID:34963468
Combining Human Genetics of Multiple Sclerosis with Oxidative Stress Phenotype for Drug Repositioning. PMID:34959343
9-ING-41, a Small Molecule Inhibitor of GSK-3β, Potentiates the Effects of Chemotherapy on Colorectal Cancer Cells. PMID:34955846
A high-resolution mass spectrometry based proteomic dataset of human regulatory T cells. PMID:34950757
MiRNA-Regulated Pathways for Hypertrophic Cardiomyopathy: Network-Based Approach to Insight into Pathogenesis. PMID:34946964
Thalidomide Exerts Anti-Inflammatory Effects in Cutaneous Lupus by Inhibiting the IRF4/NF-ҡB and AMPK1/mTOR Pathways. PMID:34944673
Deepening into Intracellular Signaling Landscape through Integrative Spatial Proteomics and Transcriptomics in a Lymphoma Model. PMID:34944421
Genome-Wide RNAi Screening Identifies Novel Pathways/Genes Involved in Oxidative Stress and Repurposable Drugs to Preserve Cystic Fibrosis Airway Epithelial Cell Integrity. PMID:34943039
UDP-glucose dehydrogenase expression is upregulated following EMT and differentially affects intracellular glycerophosphocholine and acetylaspartate levels in breast mesenchymal cell lines. PMID:34942055
Crypt and Villus Transcriptomic Responses in Mouse Small Intestine Following Oral Exposure to Hexavalent Chromium. PMID:34935971
Elevated temperature inhibits SARS-CoV-2 replication in respiratory epithelium independently of IFN-mediated innate immune defenses. PMID:34932557
A Pan-respiratory Antiviral Chemotype Targeting a Transient Host Multiprotein Complex. PMID:34931190
Genome-wide association and functional interrogation identified a variant at 3p26.1 modulating ovarian cancer survival among Chinese women. PMID:34930913
Targeting CK2 mediated signaling to impair/tackle SARS-CoV-2 infection: a computational biology approach. PMID:34930105
Co-exposure of sodium arsenite and uranyl acetate differentially alters gene expression in CD3/CD28 activated CD4+ T-cells. PMID:34926170
exoRBase 2.0: an atlas of mRNA, lncRNA and circRNA in extracellular vesicles from human biofluids. PMID:34918744
Transcriptome Analysis of Large to Giant Congenital Melanocytic Nevus Reveals Cell Cycle Arrest and Immune Evasion: Identifying Potential Targets for Treatment. PMID:34912899
DNA methylation of ARHGAP30 is negatively associated with ARHGAP30 expression in lung adenocarcinoma, which reduces tumor immunity and is detrimental to patient survival. PMID:34910688
Association of Complement and MAPK Activation With SARS-CoV-2-Associated Myocardial Inflammation. PMID:34910083
Worldwide Protein Data Bank (wwPDB): A virtual treasure for research in biotechnology. PMID:34908533
The mining and construction of a knowledge base for gene-disease association in mitochondrial diseases. PMID:34903783
Network Analysis of Microarray Data. PMID:34902128
Pathway Enrichment Analysis of Microarray Data. PMID:34902127
Regulatory modules of human thermogenic adipocytes: functional genomics of large cohort and Meta-analysis derived marker-genes. PMID:34895148
Integrative analysis of immune-related multi-omics profiles identifies distinct prognosis and tumor microenvironment patterns in osteosarcoma. PMID:34894177
Deep Proteomic Analysis on Biobanked Paraffine-Archived Melanoma with Prognostic/Predictive Biomarker Read-Out. PMID:34885218
Palm Oil-Rich Diet Affects Murine Liver Proteome and S-Palmitoylome. PMID:34884899
Genes and Pathways Associated with Skeletal Sagittal Malocclusions: A Systematic Review. PMID:34884839
Structural Predictive Model of Presenilin-2 Protein and Analysis of Structural Effects of Familial Alzheimer's Disease Mutations. PMID:34881055
A computational approach for the discovery of significant cancer genes by weighted mutation and asymmetric spreading strength in networks. PMID:34876593
Multi-omics approach to COVID-19: a domain-based literature review. PMID:34876157
reString: an open-source Python software to perform automatic functional enrichment retrieval, results aggregation and data visualization. PMID:34873191
Cilium Expression Score Predicts Glioma Survival. PMID:34868236
SBGNview: towards data analysis, integration and visualization on all pathways. PMID:34864890
Isoform-level Quantification for Single-Cell RNA Sequencing. PMID:34864849
Higher order genetic interactions switch cancer genes from two-hit to one-hit drivers. PMID:34862370
Author-sourced capture of pathway knowledge in computable form using Biofactoid. PMID:34860157
Stable Isotopes for Tracing Cardiac Metabolism in Diseases. PMID:34859064
A Transcriptional Signature of IL-2 Expanded Natural Killer Cells Predicts More Favorable Prognosis in Bladder Cancer. PMID:34858395
Isocitrate dehydrogenase mutations are associated with altered IL-1β responses in acute myeloid leukemia. PMID:34857894
Development of a custom next-generation sequencing panel for the determination of bladder cancer risk in a Tunisian cohort. PMID:34854013
Cross-species analysis of viral nucleic acid interacting proteins identifies TAOKs as innate immune regulators. PMID:34853303
PharmacoDB 2.0: improving scalability and transparency of in vitro pharmacogenomics analysis. PMID:34850112
ConsensusPathDB 2022: molecular interactions update as a resource for network biology. PMID:34850110
Chronic cortisol differentially impacts stem cell-derived astrocytes from major depressive disorder patients. PMID:34848679
Large-Scale Plasma Protein Profiling of Incident Myocardial Infarction, Ischemic Stroke, and Heart Failure. PMID:34845919
T cell landscape and dynamics in immunoglobulin light chain amyloidosis before and after daratumumab-based therapy. PMID:34845849
Knowledge-guided artificial intelligence technologies for decoding complex multiomics interactions in cells. PMID:34844399
Repurposing hyperpolarization-activated cyclic nucleotide-gated channels as a novel therapy for breast cancer. PMID:34841695
Deletion of pancreas-specific miR-216a reduces beta-cell mass and inhibits pancreatic cancer progression in mice. PMID:34841287
Identification of copy number variation-driven molecular subtypes informative for prognosis and treatment in pancreatic adenocarcinoma of a Chinese cohort. PMID:34839264
Pathway Enrichment Analysis of Microarray Data Fom Human Penis of Diabetic and Peyronie's Patients, in Comparison With Diabetic Rat Erectile Dysfunction Models. PMID:34838480
Brain-Restricted Inhibition of IL-6 Trans-Signaling Mildly Affects Metabolic Consequences of Maternal Obesity in Male Offspring. PMID:34835991
Heterogeneity in the Response of Different Subtypes of Drosophila melanogaster Midgut Cells to Viral Infections. PMID:34835089
Identification of Differentially Expressed Genes in Different Glioblastoma Regions and Their Association with Cancer Stem Cell Development and Temozolomide Response. PMID:34834399
Integrative Analyses Reveal Tstd1 as a Potential Modulator of HDL Cholesterol and Mitochondrial Function in Mice. PMID:34831199
Impacts of p97 on Proteome Changes in Human Cells during Coronaviral Replication. PMID:34831176
Enhancer RNA Profiling in Smoking and HPV Associated HNSCC Reveals Associations to Key Oncogenes. PMID:34830428
Integration and Visualization of Regulatory Elements and Variations of the EPAS1 Gene in Human. PMID:34828399
Network medicine for disease module identification and drug repurposing with the NeDRex platform. PMID:34824199
The Hitchhiker's Guide to Untargeted Lipidomics Analysis: Practical Guidelines. PMID:34822371
Effects of photodeoxygenation on cell biology using dibenzothiophene S-oxide derivatives as O(3P)-precursors. PMID:34822125
ORAI1 Limits SARS-CoV-2 Infection by Regulating Tonic Type I IFN Signaling. PMID:34819389
Comprehensive Study of Human FBXW7 Deleterious nsSNP's Functional Inference and Susceptibility to Gynaecological Cancer. PMID:34817806
Genetic alterations associated with malignant transformation of sporadic vestibular schwannoma. PMID:34816314
A 3D primary human cell-based in vitro model of non-alcoholic steatohepatitis for efficacy testing of clinical drug candidates. PMID:34815444
Metabolic Imbalance Effect on Retinal Müller Glial Cells Reprogramming Capacity: Involvement of Histone Deacetylase SIRT6. PMID:34804128
Targeted Next-Generation Sequencing Indicates a Frequent Oligogenic Involvement in Primary Ovarian Insufficiency Onset. PMID:34803902
The metabolic growth limitations of petite cells lacking the mitochondrial genome. PMID:34799698
Disease modeling of pulmonary fibrosis using human pluripotent stem cell-derived alveolar organoids. PMID:34798066
Convergent molecular mechanisms underlying cognitive impairment in mucopolysaccharidosis type II. PMID:34797484
Homeostatic IL-13 in healthy skin directs dendritic cell differentiation to promote TH2 and inhibit TH17 cell polarization. PMID:34795444
DeepPhospho accelerates DIA phosphoproteome profiling through in silico library generation. PMID:34795227
Metatranscriptomics to characterize respiratory virome, microbiome, and host response directly from clinical samples. PMID:34790908
The reactome pathway knowledgebase 2022. PMID:34788843
Muscle transcriptome provides the first insight into the dynamics of gene expression with progression of age in sheep. PMID:34785720
Toward modeling metabolic state from single-cell transcriptomics. PMID:34785394
Metabolic resistance to the inhibition of mitochondrial transcription revealed by CRISPR-Cas9 screen. PMID:34779571
Aberrant Extrafollicular B Cells, Immune Dysfunction, Myeloid Inflammation, and MyD88-Mutant Progenitors Precede Waldenstrom Macroglobulinemia. PMID:34778800
Integrative Multi-omics Landscape of Non-structural Protein 3 of Severe Acute Respiratory Syndrome Coronaviruses. PMID:34774773
Identification of DNA Damage Repair-Associated Prognostic Biomarkers for Prostate Cancer Using Transcriptomic Data Analysis. PMID:34769200
Bromodomain Containing Protein 4 (BRD4) Regulates Expression of its Interacting Coactivators in the Innate Response to Respiratory Syncytial Virus. PMID:34765643
Breast Cancer Antiestrogen Resistance 3 (BCAR3) promotes tumor growth and progression in triple-negative breast cancer. PMID:34765292
TopoFun: a machine learning method to improve the functional similarity of gene co-expression modules. PMID:34761220
Besca, a single-cell transcriptomics analysis toolkit to accelerate translational research. PMID:34761219
Circulating Plasma Biomarkers in Biopsy-Confirmed Kidney Disease. PMID:34759008
Web-based transcriptome analysis determines a sixteen-gene signature and associated drugs on hearing loss patients: A bioinformatics approach. PMID:34758154
Rhea, the reaction knowledgebase in 2022. PMID:34755880
IID 2021: towards context-specific protein interaction analyses by increased coverage, enhanced annotation and enrichment analysis. PMID:34755877
HumanNet v3: an improved database of human gene networks for disease research. PMID:34747468
Hymenoptera Genome Database: new genomes and annotation datasets for improved go enrichment and orthologue analyses. PMID:34747465
Network Biology Approaches to Achieve Precision Medicine in Inflammatory Bowel Disease. PMID:34745229
Cross-platform transcriptomic profiling of the response to recombinant human erythropoietin. PMID:34737331
Longitudinal single-cell analysis of a myeloma mouse model identifies subclonal molecular programs associated with progression. PMID:34732728
Transcriptome and Exome Analyses of Hepatocellular Carcinoma Reveal Patterns to Predict Cancer Recurrence in Liver Transplant Patients. PMID:34725972
Identification of a Putative Enhancer RNA for EGFR in Hyper-Accessible Regions in Esophageal Squamous Cell Carcinoma Cells by Analysis of Chromatin Accessibility Landscapes. PMID:34722266
Using Genomic and Transcriptome Analyses to Identify the Role of the Oxidative Stress Pathway in Renal Clear Cell Carcinoma and Its Potential Therapeutic Significance. PMID:34721758
Defining the Role of Nuclear Factor (NF)-κB p105 Subunit in Human Macrophage by Transcriptomic Analysis of NFKB1 Knockout THP1 Cells. PMID:34721373
Path4Drug: Data Science Workflow for Identification of Tissue-Specific Biological Pathways Modulated by Toxic Drugs. PMID:34721010
TcoFBase: a comprehensive database for decoding the regulatory transcription co-factors in human and mouse. PMID:34718747
The IUPHAR/BPS guide to PHARMACOLOGY in 2022: curating pharmacology for COVID-19, malaria and antibacterials. PMID:34718737
Complex Portal 2022: new curation frontiers. PMID:34718729
Importance-Penalized Joint Graphical Lasso (IPJGL): differential network inference via GGMs. PMID:34718410
Maternal methionine supplementation during gestation alters alternative splicing and DNA methylation in bovine skeletal muscle. PMID:34717556
PANTHER: Making genome-scale phylogenetics accessible to all. PMID:34717010
Centrality of drug targets in protein networks. PMID:34715787
Pathway-targeting gene matrix for Drosophila gene set enrichment analysis. PMID:34710184
Genome-scale metabolic modeling reveals SARS-CoV-2-induced metabolic changes and antiviral targets. PMID:34709707
Using predictive machine learning models for drug response simulation by calibrating patient-specific pathway signatures. PMID:34707117
Multilayer omics analysis reveals a non-classical retinoic acid signaling axis that regulates hematopoietic stem cell identity. PMID:34706256
Comparative genomics reveals molecular mechanisms underlying health and reproduction in cryptorchid mammals. PMID:34702182
The unfolded protein response links tumor aneuploidy to local immune dysregulation. PMID:34698427
Gene Ontology curation of the blood-brain barrier to improve the analysis of Alzheimer's and other neurological diseases. PMID:34697638
Recent innovations and in-depth aspects of post-genome wide association study (Post-GWAS) to understand the genetic basis of complex phenotypes. PMID:34689168
ARID1A deficiency weakens BRG1-RAD21 interaction that jeopardizes chromatin compactness and drives liver cancer cell metastasis. PMID:34689165
Characterization, isolation, and in vitro culture of leptomeningeal fibroblasts. PMID:34688068
Transcriptome changes in maternal peripheral blood during term parturition mimic perturbations preceding spontaneous preterm birth†. PMID:34686873
Differential regulation of transposable elements (TEs) during the murine submandibular gland development. PMID:34686213
A Unified Transcriptional, Pharmacogenomic, and Gene Dependency Approach to Decipher the Biology, Diagnostic Markers, and Therapeutic Targets Associated with Prostate Cancer Metastasis. PMID:34680307
Platelet proteome dynamics in hibernating 13-lined ground squirrels. PMID:34677084
Performance Assessment of the Network Reconstruction Approaches on Various Interactomes. PMID:34676243
Prediction of severe adverse events, modes of action and drug treatments for COVID-19's complications. PMID:34675303
A Complex Proteomic Response of the Parasitic Nematode Anisakis simplex s.s. to Escherichia coliLipopolysaccharide. PMID:34673282
Proteomic Signatures of Human Visceral and Subcutaneous Adipocytes. PMID:34669916
Disrupted circadian oscillations in type 2 diabetes are linked to altered rhythmic mitochondrial metabolism in skeletal muscle. PMID:34669477
Network-Based Approaches Reveal Potential Therapeutic Targets for Host-Directed Antileishmanial Therapy Driving Drug Repurposing. PMID:34668739
Characterization and miRNA Profiling of Extracellular Vesicles from Human Osteoarthritic Subchondral Bone Multipotential Stromal Cells (MSCs). PMID:34667479
NPCDR: natural product-based drug combination and its disease-specific molecular regulation. PMID:34664659
COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms. PMID:34664389
Gene correlation network analysis to identify regulatory factors in sciatic nerve injury. PMID:34663380
Detection of Neanderthal Adaptively Introgressed Genetic Variants That Modulate Reporter Gene Expression in Human Immune Cells. PMID:34662402
Genetic and epigenetic characterization of posterior pituitary tumors. PMID:34661724
Comprehensive landscape and interference of clonal haematopoiesis mutations for liquid biopsy: A Chinese pan-cancer cohort. PMID:34658138
Text mining-based word representations for biomedical data analysis and protein-protein interaction networks in machine learning tasks. PMID:34653224
Serum Fetuin-B Levels Are Elevated in Women with Metabolic Syndrome and Associated with Increased Oxidative Stress. PMID:34646426
TIGER: The gene expression regulatory variation landscape of human pancreatic islets. PMID:34644572
Neutrophil Pathways of Inflammation Characterize the Blood Transcriptomic Signature of Patients with Psoriasis and Cardiovascular Disease. PMID:34639156
Cilostazol Induces eNOS and TM Expression via Activation with Sirtuin 1/Krüppel-like Factor 2 Pathway in Endothelial Cells. PMID:34638626
Regulation of ER Composition and Extent, and Putative Action in Protein Networks by ER/NE Protein TMEM147. PMID:34638576
OnTheFly2.0: a text-mining web application for automated biomedical entity recognition, document annotation, network and functional enrichment analysis. PMID:34632381
Circulating MicroRNAs in the Second Trimester From Pregnant Women Who Subsequently Developed Preeclampsia: Potential Candidates as Predictive Biomarkers and Pathway Analysis for Target Genes of miR-204-5p. PMID:34630130
Genome-wide analysis of DNA methylation in 106 schizophrenia family trios in Han Chinese. PMID:34628353
rPAC: Route based pathway analysis for cohorts of gene expression data sets. PMID:34628030
A systematic review of common genetic variation and biological pathways in autism spectrum disorder. PMID:34627165
Novel chemotherapeutic agent FX-9 activates NF-κB signaling and induces G1 phase arrest by activating CDKN1A in a human prostate cancer cell line. PMID:34625047
Component of oligomeric Golgi complex 1 deficiency leads to hypoglycemia: a case report and literature review. PMID:34625039
Differential expression profile of gluten-specific T cells identified by single-cell RNA-seq. PMID:34618841
SARS-CoV-2 Coronavirus Spike Protein-Induced Apoptosis, Inflammatory, and Oxidative Stress Responses in THP-1-Like-Macrophages: Potential Role of Angiotensin-Converting Enzyme Inhibitor (Perindopril). PMID:34616396
Genetic effects on longitudinal cognitive decline during the early stages of Alzheimer's disease. PMID:34615922
The Big Picture of Glioblastoma Malignancy: A Meta-Analysis of Glioblastoma Proteomics to Identify Altered Biological Pathways. PMID:34604635
GeneTrail: A Framework for the Analysis of High-Throughput Profiles. PMID:34604304
Dissecting Genomic Determinants of Positive Selection with an Evolution-Guided Regression Model. PMID:34597406
The role of pumpkin pulp extract carotenoids against mycotoxin damage in the blood brain barrier in vitro. PMID:34587668
VEGA is an interpretable generative model for inferring biological network activity in single-cell transcriptomics. PMID:34584103
Short-term transcriptomic response to plasma membrane injury. PMID:34580330
Association of miR-499 Polymorphism and Its Regulatory Networks with Hashimoto Thyroiditis Susceptibility: A Population-Based Case-Control Study. PMID:34576267
Prognostic Impact and Functional Annotations of KIF11 and KIF14 Expression in Patients with Colorectal Cancer. PMID:34575892
Molecular Classification Models for Triple Negative Breast Cancer Subtype Using Machine Learning. PMID:34575658
miR-27b-3p a Negative Regulator of DSB-DNA Repair. PMID:34573315
Modelling Nonalcoholic Steatohepatitis In Vivo-A Close Transcriptomic Similarity Supports the Guinea Pig Disease Model. PMID:34572384
Transcriptomic Analysis of HCN-2 Cells Suggests Connection among Oxidative Stress, Senescence, and Neuron Death after SARS-CoV-2 Infection. PMID:34571838
Distinct gene-set burden patterns underlie common generalized and focal epilepsies. PMID:34571366
A biallelic SNIP1 Amish founder variant causes a recognizable neurodevelopmental disorder. PMID:34570759
CTR-DB, an omnibus for patient-derived gene expression signatures correlated with cancer drug response. PMID:34570230
A highly multiplexed quantitative phosphosite assay for biology and preclinical studies. PMID:34569154
Construction of Interferon-Gamma-Related Gene Signature to Characterize the Immune-Inflamed Phenotype of Glioblastoma and Predict Prognosis, Efficacy of Immunotherapy and Radiotherapy. PMID:34566988
Systems-Level Proteomics Evaluation of Microglia Response to Tumor-Supportive Anti-Inflammatory Cytokines. PMID:34566949
PncsHub: a platform for annotating and analyzing non-classically secreted proteins in Gram-positive bacteria. PMID:34551435
Caveolin-1 and Sox-2 are predictive biomarkers of cetuximab response in head and neck cancer. PMID:34546978
Investigation of pharmacological mechanism of natural product using pathway fingerprints similarity based on "drug-target-pathway" heterogenous network. PMID:34544480
Oxidative stress in retinal pigment epithelium impairs stem cells: a vicious cycle in age-related macular degeneration. PMID:34535868
TISMO: syngeneic mouse tumor database to model tumor immunity and immunotherapy response. PMID:34534350
Differential Abundance of Brain Mitochondrial Proteins in Yak and Cattle: A Proteomics-Based Study. PMID:34532350
TFTenricher: a python toolbox for annotation enrichment analysis of transcription factor target genes. PMID:34530727
Identification of immune correlates of fatal outcomes in critically ill COVID-19 patients. PMID:34529726
Synergistic PIM kinase and proteasome inhibition as a therapeutic strategy for MYC-overexpressing triple-negative breast cancer. PMID:34525344
Activation of Hippo signaling pathway mediates mitochondria dysfunction and dilated cardiomyopathy in mice. PMID:34522223
Bioinformatics analysis identified shared differentially expressed genes as potential biomarkers for Hashimoto's thyroiditis-related papillary thyroid cancer. PMID:34522174
Functional human genes typically exhibit epigenetic conservation. PMID:34520456
Bottom-up assembly of biomedical relevant fully synthetic extracellular vesicles. PMID:34516902
Bioinformatic analysis for potential biological processes and key targets of heart failure-related stroke. PMID:34514752
Towards Building a Quantitative Proteomics Toolbox in Precision Medicine: A Mini-Review. PMID:34512391
Unified AI framework to uncover deep interrelationships between gene expression and Alzheimer's disease neuropathologies. PMID:34508095
CancerMIRNome: an interactive analysis and visualization database for miRNome profiles of human cancer. PMID:34500460
Transcriptomics Profiling Identifies Cisplatin-Inducible Death Receptor 5 Antisense Long Non-coding RNA as a Modulator of Proliferation and Metastasis in HeLa Cells. PMID:34497804
A Novel Intercellular Communication-Associated Gene Signature for Prognostic Prediction and Clinical Value in Patients With Lung Adenocarcinoma. PMID:34497634
The Analysis of Gene Expression Data Incorporating Tumor Purity Information. PMID:34497631
General Caspase Inhibition in Primary Chondrogenic Cultures Impacts Their Transcription Profile Including Osteoarthritis-Related Factors. PMID:34496641
Pathway analysis in metabolomics: Recommendations for the use of over-representation analysis. PMID:34492007
A 14-Marker Multiplexed Imaging Panel for Prognostic Biomarkers and Tumor Heterogeneity in Head and Neck Squamous Cell Carcinoma. PMID:34490110
Genetic Prioritization, Therapeutic Repositioning and Cross-Disease Comparisons Reveal Inflammatory Targets Tractable for Kidney Stone Disease. PMID:34489936
Reproducible immortalization of erythroblasts from multiple stem cell sources provides approach for sustainable RBC therapeutics. PMID:34485592
Prospects and challenges of cancer systems medicine: from genes to disease networks. PMID:34471925
Leveraging the Mendelian disorders of the epigenetic machinery to systematically map functional epigenetic variation. PMID:34463256
Computational analysis of sense-antisense chimeric transcripts reveals their potential regulatory features and the landscape of expression in human cells. PMID:34458728
Comprehensive Analysis of the Systemic Transcriptomic Alternations and Inflammatory Response during the Occurrence and Progress of COVID-19. PMID:34457122
In silico identification of MicroRNAs targeting the key nucleator of stress granules, G3BP: Promising therapeutics for SARS-CoV-2 infection. PMID:34456603
Integrated analysis of cell cycle-related genes in HR+/HER2- breast cancer. PMID:34449047
Multi-Omics Analysis of SOX4, SOX11, and SOX12 Expression and the Associated Pathways in Human Cancers. PMID:34442467
Workflows for Rapid Functional Annotation of Diverse Arthropod Genomes. PMID:34442314
Adenine Nucleotide Translocase 1 Expression Modulates the Immune Response in Ischemic Hearts. PMID:34440901
Molecular Pathways Involved in the Development of Congenital Erythrocytosis. PMID:34440324
Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review. PMID:34439912
Absent from DNA and protein: genomic characterization of nullomers and nullpeptides across functional categories and evolution. PMID:34433494
The RNA binding protein Quaking represses splicing of the Fibronectin EDA exon and downregulates the interferon response. PMID:34428287
Ten simple rules for creating reusable pathway models for computational analysis and visualization. PMID:34411100
Mechanism-Centric Approaches for Biomarker Detection and Precision Therapeutics in Cancer. PMID:34408770
Th1 polarization defines the synovial fluid T cell compartment in oligoarticular juvenile idiopathic arthritis. PMID:34403374
A systematic comparison of data- and knowledge-driven approaches to disease subtype discovery. PMID:34396389
Diffusion enables integration of heterogeneous data and user-driven learning in a desktop knowledge-base. PMID:34379637
The molecular basis, genetic control and pleiotropic effects of local gene co-expression. PMID:34376650
TIPS: trajectory inference of pathway significance through pseudotime comparison for functional assessment of single-cell RNAseq data. PMID:34370020
A systems-based framework to computationally describe putative transcription factors and signaling pathways regulating glycan biosynthesis. PMID:34367349
Males and Females Have Distinct Molecular Events in the Articular Cartilage during Knee Osteoarthritis. PMID:34360640
Two-Pore Channels Regulate Expression of Various Receptors and Their Pathway-Related Proteins in Multiple Ways. PMID:34359976
Genome-Wide Association Studies of Conotruncal Heart Defects with Normally Related Great Vessels in the United States. PMID:34356046
Expanding the MECP2 network using comparative genomics reveals potential therapeutic targets for Rett syndrome. PMID:34355696
miRNome and Functional Network Analysis of PGRMC1 Regulated miRNA Target Genes Identify Pathways and Biological Functions Associated With Triple Negative Breast Cancer. PMID:34350123
A Computational Exploration of the Molecular Network Associated to Neuroinflammation in Alzheimer's Disease. PMID:34335238
Placental miR-3940-3p Is Associated With Maternal Insulin Resistance in Late Pregnancy. PMID:34333643
CellCall: integrating paired ligand-receptor and transcription factor activities for cell-cell communication. PMID:34331449
Clinical Genetic Risk Variants Inform a Functional Protein Interaction Network for Tetralogy of Fallot. PMID:34328347
Loss of the mitochondrial phosphate carrier SLC25A3 induces remodeling of the cardiac mitochondrial protein acylome. PMID:34319827
Enhancing the interoperability of glycan data flow between ChEBI, PubChem and GlyGen. PMID:34314492
VarSAn: associating pathways with a set of genomic variants using network analysis. PMID:34313777
Genomic signatures of the unjamming transition in compressed human bronchial epithelial cells. PMID:34301595
Pseudoexfoliation and Cataract Syndrome Associated with Genetic and Epidemiological Factors in a Mayan Cohort of Guatemala. PMID:34299682
CFTR Lifecycle Map-A Systems Medicine Model of CFTR Maturation to Predict Possible Active Compound Combinations. PMID:34299207
Compatibility of Distinct Label-Free Proteomic Workflows in Absolute Quantification of Proteins Linked to the Oocyte Quality in Human Follicular Fluid. PMID:34299044
Effect of the Electromagnetic Field (EMF) Radiation on Transcriptomic Profile of Pig Myometrium during the Peri-Implantation Period-An In Vitro Study. PMID:34298942
Proteomics of Primary Uveal Melanoma: Insights into Metastasis and Protein Biomarkers. PMID:34298739
Expression dynamics of HAND1/2 in in vitro human cardiomyocyte differentiation. PMID:34297940
Systematic review of human post-mortem immunohistochemical studies and bioinformatics analyses unveil the complexity of astrocyte reaction in Alzheimer's disease. PMID:34297416
Metabolic landscapes in sarcomas. PMID:34294128
Type 2 immunity is maintained during cancer-associated adipose tissue wasting. PMID:34291232
Exome sequencing identifies novel somatic variants in African American esophageal squamous cell carcinoma. PMID:34285259
Chronic complement dysregulation drives neuroinflammation after traumatic brain injury: a transcriptomic study. PMID:34281628
MTA2 sensitizes gastric cancer cells to PARP inhibition by induction of DNA replication stress. PMID:34280886
Integrative resource for network-based investigation of COVID-19 combinatorial drug repositioning and mechanism of action. PMID:34278363
The 2021 update of the EPA's adverse outcome pathway database. PMID:34253739
Genes involved in immune, gene translation and chromatin organization pathways associated with Mycoplasma ovipneumoniae presence in nasal secretions of domestic sheep. PMID:34252097
Bioinformatics Analysis Reveals Crosstalk Among Platelets, Immune Cells, and the Glomerulus That May Play an Important Role in the Development of Diabetic Nephropathy. PMID:34249963
Altered skeletal muscle metabolic pathways, age, systemic inflammation, and low cardiorespiratory fitness associate with improvements in disease activity following high-intensity interval training in persons with rheumatoid arthritis. PMID:34246305
TIDB: a comprehensive database of trained immunity. PMID:34244719
Identification of viral-mediated pathogenic mechanisms in neurodegenerative diseases using network-based approaches. PMID:34237135
ORA , FCS , and PT Strategies in Functional Enrichment Analysis. PMID:34236661
Systematic analysis of SARS-CoV-2 infection of an ACE2-negative human airway cell. PMID:34214467
IGFBP2 Is a Potential Master Regulator Driving the Dysregulated Gene Network Responsible for Short Survival in Glioblastoma Multiforme. PMID:34211498
Molecular Insights into the Oxygen-Sensing Pathway and Erythropoietin Expression Regulation in Erythropoiesis. PMID:34209205
Prognostic Significance of KIF11 and KIF14 Expression in Pancreatic Adenocarcinoma. PMID:34208606
HGF/c-Met Inhibition as Adjuvant Therapy Improves Outcomes in an Orthotopic Mouse Model of Pancreatic Cancer. PMID:34199452
Towards a global investigation of transcriptomic signatures through co-expression networks and pathway knowledge for the identification of disease mechanisms. PMID:34197603
Crowdsourcing assessment of maternal blood multi-omics for predicting gestational age and preterm birth. PMID:34195686
Curating and comparing 114 strain-specific genome-scale metabolic models of Staphylococcus aureus. PMID:34188046
Assembling Disease Networks From Causal Interaction Resources. PMID:34178043
Acute Effects on the Human Peripheral Blood Transcriptome of Decompression Sickness Secondary to Scuba Diving. PMID:34177613
The AML microenvironment catalyzes a stepwise evolution to gilteritinib resistance. PMID:34171263
Rare Modifier Variants Alter the Severity of Cardiovascular Disease in Pseudoxanthoma Elasticum: Identification of Novel Candidate Modifier Genes and Disease Pathways Through Mixture of Effects Analysis. PMID:34169069
Low-density lipoprotein receptor-related protein 1 (LRP1) is a novel receptor for apolipoprotein A4 (APOA4) in adipose tissue. PMID:34168225
Accurate prediction of cis-regulatory modules reveals a prevalent regulatory genome of humans. PMID:34159315
Transcriptional Profiles Reveal Deregulation of Lipid Metabolism and Inflammatory Pathways in Neurons Exposed to Palmitic Acid. PMID:34155583
Low Energy Electron Irradiation Is a Potent Alternative to Gamma Irradiation for the Inactivation of (CAR-)NK-92 Cells in ATMP Manufacturing. PMID:34149724
Predicting the probability of death using proteomics. PMID:34145379
Transcriptomic analyses of gastrulation-stage mouse embryos with differential susceptibility to alcohol. PMID:34137816
Transcriptomic Signature Differences Between SARS-CoV-2 and Influenza Virus Infected Patients. PMID:34135895
Proteomics and Epidemiological Models of Human Aging. PMID:34135771
Machine learning-based prediction of survival prognosis in cervical cancer. PMID:34134623
Matrix-screening reveals a vast potential for direct protein-protein interactions among RNA binding proteins. PMID:34133714
Cancer Grade Model: a multi-gene machine learning-based risk classification for improving prognosis in breast cancer. PMID:34131308
Genome-wide CRISPR screen identifies protein pathways modulating tau protein levels in neurons. PMID:34127790
DGLinker: flexible knowledge-graph prediction of disease-gene associations. PMID:34125897
Sphingomyelin and Medullary Sponge Kidney Disease: A Biological Link Identified by Omics Approach. PMID:34124100
Small Intestinal Tuft Cell Activity Associates With Energy Metabolism in Diet-Induced Obesity. PMID:34122403
Assessment of a complete and classified platelet proteome from genome-wide transcripts of human platelets and megakaryocytes covering platelet functions. PMID:34117303
Efficient representations of tumor diversity with paired DNA-RNA aberrations. PMID:34115745
Integrating protein networks and machine learning for disease stratification in the Hereditary Spastic Paraplegias. PMID:34113825
Multifaceted regulation of hepatic lipid metabolism by YY1. PMID:34099540
Interpreting the lipidome: bioinformatic approaches to embrace the complexity. PMID:34091802
Chamber-enriched gene expression profiles in failing human hearts with reduced ejection fraction. PMID:34088950
Mapping Proximity Associations of Core Spindle Assembly Checkpoint Proteins. PMID:34087075
KOBAS-i: intelligent prioritization and exploratory visualization of biological functions for gene enrichment analysis. PMID:34086934
Different epigenetic signatures of newborn telomere length and telomere attrition rate in early life. PMID:34086604
Secreted gelsolin inhibits DNGR-1-dependent cross-presentation and cancer immunity. PMID:34081922
Mechnetor: a web server for exploring protein mechanism and the functional context of genetic variants. PMID:34076240
CovidExpress: an interactive portal for intuitive investigation on SARS-CoV-2 related transcriptomes. PMID:34075382
A Novel Method for Creating a Synthetic L-DOPA Proteome and In Vitro Evidence of Incorporation. PMID:34073856
The Moringin/α-CD Pretreatment Induces Neuroprotection in an In Vitro Model of Alzheimer's Disease: A Transcriptomic Study. PMID:34073287
Characteristics of the Urinary Proteome in Women with Overactive Bladder Syndrome: A Case-Control Study. PMID:34072980
TrkA Interacts with and Phosphorylates STAT3 to Enhance Gene Transcription and Promote Breast Cancer Stem Cells in Triple-Negative and HER2-Enriched Breast Cancers. PMID:34066153
Diet-Induced Obesity Impairs Outcomes and Induces Multi-Factorial Deficiencies in Effector T Cell Responses Following Anti-CTLA-4 Combinatorial Immunotherapy in Renal Tumor-Bearing Mice. PMID:34064933
High-Throughput Proteomic Profiling of Nipple Aspirate Fluid from Breast Cancer Patients Compared with Non-Cancer Controls: A Step Closer to Clinical Feasibility. PMID:34064148
Proteotyping of knockout mouse strains reveals sex- and strain-specific signatures in blood plasma. PMID:34050187
Proteomic and transcriptional changes associated with MeCP2 dysfunction reveal nodes for therapeutic intervention in Rett syndrome. PMID:34048843
The COVID-19 Data Portal: accelerating SARS-CoV-2 and COVID-19 research through rapid open access data sharing. PMID:34048576
snpXplorer: a web application to explore human SNP-associations and annotate SNP-sets. PMID:34048563
BENviewer: a gene interaction network visualization server based on graph embedding model. PMID:34048546
Toxoplasma gondii secreted effectors co-opt host repressor complexes to inhibit necroptosis. PMID:34043960
CPA: a web-based platform for consensus pathway analysis and interactive visualization. PMID:34037798
The Potential Genes Mediate the Pathogenicity of Allogeneic CD4+T Cell in aGVHD Mouse Model. PMID:34036106
A 3D system to model human pancreas development and its reference single-cell transcriptome atlas identify signaling pathways required for progenitor expansion. PMID:34035279
LSD1 and Aberrant DNA Methylation Mediate Persistence of Enteroendocrine Progenitors That Support BRAF-Mutant Colorectal Cancer. PMID:34035083
Transcriptomic and metabolomic characterization of post-hatch metabolic reprogramming during hepatic development in the chicken. PMID:34030631
Disease-specific interactome alterations via epichaperomics: the case for Alzheimer's disease. PMID:34028172
Toxicogenomic Profiling of 28 Nanomaterials in Mouse Airways. PMID:34026454
TIGIT and PD-1 Immune Checkpoint Pathways Are Associated With Patient Outcome and Anti-Tumor Immunity in Glioblastoma. PMID:34025646
Network-based analysis of key regulatory genes implicated in Type 2 Diabetes Mellitus and Recurrent Miscarriages in Turner Syndrome. PMID:34021221
eVITTA: a web-based visualization and inference toolbox for transcriptome analysis. PMID:34019643
A computational approach for detecting physiological homogeneity in the midst of genetic heterogeneity. PMID:34015270
Characterization and comparison of gene-centered human interactomes. PMID:34010955
Novel cell types and developmental lineages revealed by single-cell RNA-seq analysis of the mouse crista ampullaris. PMID:34003106
Molecular Evolution of Ecological Specialisation: Genomic Insights from the Diversification of Murine Rodents. PMID:33988699
Drug Repurposing: A Network-based Approach to Amyotrophic Lateral Sclerosis. PMID:33987813
Ultraviolet light-induced collagen degradation inhibits melanoma invasion. PMID:33980846
Deciphering the Efficacy and Mechanisms of Chinese Herbal Medicine for Diabetic Kidney Disease by Integrating Web-Based Biochemical Databases and Real-World Clinical Data: Retrospective Cohort Study. PMID:33973855
ORAI1 establishes resistance to SARS-CoV-2 infection by regulating tonic type I interferon signaling. PMID:33972946
Identification of Long Non-coding RNA Isolated From Naturally Infected Macrophages and Associated With Bovine Johne's Disease in Canadian Holstein Using a Combination of Neural Networks and Logistic Regression. PMID:33969037
Reactome and the Gene Ontology: Digital convergence of data resources. PMID:33964129
CLEP: A Hybrid Data- and Knowledge- Driven Framework for Generating Patient Representations. PMID:33964127
The differences in SARS-CoV and SARS-CoV-2 specific co-expression network mediated biological process in human gut enterocytes. PMID:33957338
Functional and tissue enrichment analyses suggest that SARS-CoV-2 infection affects host metabolism and catabolism mediated by interference on host proteins. PMID:33956332
Comparison of sparse biclustering algorithms for gene expression datasets. PMID:33951731
Transcriptomic meta-analysis of disuse muscle atrophy vs. resistance exercise-induced hypertrophy in young and older humans. PMID:33951310
Functional Specificity of the Members of the Sos Family of Ras-GEF Activators: Novel Role of Sos2 in Control of Epidermal Stem Cell Homeostasis. PMID:33946974
Experimental and natural evidence of SARS-CoV-2-infection-induced activation of type I interferon responses. PMID:33937724
Assessment of differentially methylated loci in individuals with end-stage kidney disease attributed to diabetic kidney disease: an exploratory study. PMID:33933144
Combined VEGFR and MAPK pathway inhibition in angiosarcoma. PMID:33931674
FMRP attenuates activity dependent modifications in the mitochondrial proteome. PMID:33931071
Gene signature extraction and cell identity recognition at the single-cell level with Cell-ID. PMID:33927417
Comorbidities and Susceptibility to COVID-19: A Generalized Gene Set Data Mining Approach. PMID:33924631
Proteomic and Bioinformatic Investigation of Altered Pathways in Neuroglobin-Deficient Breast Cancer Cells. PMID:33924212
Targeting Methylglyoxal in Diabetic Kidney Disease Using the Mitochondria-Targeted Compound MitoGamide. PMID:33922959
Identification of Expression Patterns and Potential Prognostic Significance of m5C-Related Regulators in Head and Neck Squamous Cell Carcinoma. PMID:33912441
Comprehensive at-arrival transcriptomic analysis of post-weaned beef cattle uncovers type I interferon and antiviral mechanisms associated with bovine respiratory disease mortality. PMID:33901263
The VRNetzer platform enables interactive network analysis in Virtual Reality. PMID:33893283
Effect of HPV 16 E6 Oncoprotein Variants on the Alterations of the Proteome of C33A Cells. PMID:33893080
MitopatHs: a new logically-framed tool for visualizing multiple mitochondrial pathways. PMID:33889820
System-Level Analysis of Alzheimer's Disease Prioritizes Candidate Genes for Neurodegeneration. PMID:33889174
The BioCyc Metabolic Network Explorer. PMID:33882841
APICURON: a database to credit and acknowledge the work of biocurators. PMID:33882120
Brain proteomic changes by histone deacetylase inhibition after traumatic brain injury. PMID:33880414
An EPIC predictor of gestational age and its application to newborns conceived by assisted reproductive technologies. PMID:33875015
Nuclear Dishevelled targets gene regulatory regions and promotes tumor growth. PMID:33860601
CytoTalk: De novo construction of signal transduction networks using single-cell transcriptomic data. PMID:33853780
Comparison of tear proteomic and neuromediator profiles changes between small incision lenticule extraction (SMILE) and femtosecond laser-assisted in-situ keratomileusis (LASIK). PMID:33842006
Endogenous neuroprotective mechanism of ATP2B1 in transcriptional regulation of ischemic preconditioning. PMID:33841647
Artificial Intelligence and Early Detection of Pancreatic Cancer: 2020 Summative Review. PMID:33835956
Summarizing RNA-Seq Data or Differentially Expressed Genes Using Gene Set, Network, or Pathway Analysis. PMID:33835442
Reusability and composability in process description maps: RAS-RAF-MEK-ERK signalling. PMID:33834185
A Survey of Compound Heterozygous Variants in Pediatric Cancers and Structural Birth Defects. PMID:33828584
Intratumoral CD103+ CD8+ T cells predict response to PD-L1 blockade. PMID:33827905
miRSM: an R package to infer and analyse miRNA sponge modules in heterogeneous data. PMID:33822666
Gene expression evaluation of antioxidant enzymes in patients with hepatocellular carcinoma: RT-qPCR and bioinformatic analyses. PMID:33821873
A Resource for the Network Representation of Cell Perturbations Caused by SARS-CoV-2 Infection. PMID:33809949
Quantitative Proteomic Approach Reveals Altered Metabolic Pathways in Response to the Inhibition of Lysine Deacetylases in A549 Cells under Normoxia and Hypoxia. PMID:33806075
A Detailed Catalogue of Multi-Omics Methodologies for Identification of Putative Biomarkers and Causal Molecular Networks in Translational Cancer Research. PMID:33802234
Heterogeneous Off-Target Effects of Ultra-Low Dose Dimethyl Sulfoxide (DMSO) on Targetable Signaling Events in Lung Cancer In Vitro Models. PMID:33802212
The Role of Autophagy and lncRNAs in the Maintenance of Cancer Stem Cells. PMID:33799834
Interactome Mapping of eIF3A in a Colon Cancer and an Immortalized Embryonic Cell Line Using Proximity-Dependent Biotin Identification. PMID:33799492
An integrative multi-omics approach reveals new central nervous system pathway alterations in Alzheimer's disease. PMID:33794997
An Integrative in silico Drug Repurposing Approach for Identification of Potential Inhibitors of SARS-CoV-2 Main Protease. PMID:33787066
Upregulation of the pathogenic transcription factor SPI1/PU.1 in tuberous sclerosis complex and focal cortical dysplasia by oxidative stress. PMID:33786950
VaximmutorDB: A Web-Based Vaccine Immune Factor Database and Its Application for Understanding Vaccine-Induced Immune Mechanisms. PMID:33777032
Regulatory Function of Sympathetic Innervation on the Endo/Lysosomal Trafficking of Acetylcholine Receptor. PMID:33776791
FOXD1 regulates cell division in clear cell renal cell carcinoma. PMID:33761914
Deep learning assisted multi-omics integration for survival and drug-response prediction in breast cancer. PMID:33761889
Cardiovascular informatics: building a bridge to data harmony. PMID:33751044
Integrated intra- and intercellular signaling knowledge for multicellular omics analysis. PMID:33749993
Boosting GWAS using biological networks: A study on susceptibility to familial breast cancer. PMID:33735170
Global proteomic analysis of extracellular matrix in mouse and human brain highlights relevance to cerebrovascular disease. PMID:33730931
Bacteria-host transcriptional response during endothelial invasion by Staphylococcus aureus. PMID:33727596
In silico Analyses of Immune System Protein Interactome Network, Single-Cell RNA Sequencing of Human Tissues, and Artificial Neural Networks Reveal Potential Therapeutic Targets for Drug Repurposing Against COVID-19. PMID:33716737
Identification of Natural Antisense Transcripts in Mouse Brain and Their Association With Autism Spectrum Disorder Risk Genes. PMID:33716665
Transcriptional analysis of islets of Langerhans from organ donors of different ages. PMID:33711030
Systematic analysis of SARS-CoV-2 infection of an ACE2-negative human airway cell. PMID:33688646
Analysing the yeast complexome-the Complex Portal rising to the challenge. PMID:33677561
Germline and Somatic Whole-Exome Sequencing Identifies New Candidate Genes Involved in Familial Predisposition to Serrated Polyposis Syndrome. PMID:33672345
Why Do Muse Stem Cells Present an Enduring Stress Capacity? Hints from a Comparative Proteome Analysis. PMID:33669748
Cannabis Use Induces Distinctive Proteomic Alterations in Olfactory Neuroepithelial Cells of Schizophrenia Patients. PMID:33668817
Genome-wide association meta-analysis identifies pleiotropic risk loci for aerodigestive squamous cell cancers. PMID:33667223
OmicLoupe: facilitating biological discovery by interactive exploration of multiple omic datasets and statistical comparisons. PMID:33663372
Network pharmacology and RNA-sequencing reveal the molecular mechanism of Xuebijing injection on COVID-19-induced cardiac dysfunction. PMID:33662681
The overexpression of DNA repair genes in invasive ductal and lobular breast carcinomas: Insights on individual variations and precision medicine. PMID:33662042
Melanoma-associated glycosyltransferase GCNT2 as an emerging biomarker and therapeutic target. PMID:33660254
SARS-CoV-2 genomic surveillance identifies naturally occurring truncations of ORF7a that limit immune suppression. PMID:33655280
Novel gene signatures for stage classification of the squamous cell carcinoma of the lung. PMID:33649335
Interspecies chimeric conditions affect the developmental rate of human pluripotent stem cells. PMID:33647016
Gene Size Matters: An Analysis of Gene Length in the Human Genome. PMID:33643374
Benchmarking network-based gene prioritization methods for cerebral small vessel disease. PMID:33634312
Biallelic variants in COPB1 cause a novel, severe intellectual disability syndrome with cataracts and variable microcephaly. PMID:33632302
Identification of candidate repurposable drugs to combat COVID-19 using a signature-based approach. PMID:33627767
Proteomic profile of melanoma cell-derived small extracellular vesicles in patients' plasma: a potential correlate of melanoma progression. PMID:33613873
Systemic delivery of antagomirs during blood-brain barrier disruption is disease-modifying in experimental epilepsy. PMID:33609732
The expression characteristics and prognostic roles of autophagy-related genes in gastric cancer. PMID:33604190
Plasma microRNA signature associated with retinopathy in patients with type 2 diabetes. PMID:33602976
Longitudinal Changes of Circulating miRNAs During Bisphosphonate and Teriparatide Treatment in an Animal Model of Postmenopausal Osteoporosis. PMID:33598975
Genome-wide analysis suggests the importance of vascular processes and neuroinflammation in late-life antidepressant response. PMID:33589590
Protein Phosphorylation in Depolarized Synaptosomes: Dissecting Primary Effects of Calcium from Synaptic Vesicle Cycling. PMID:33582301
Integration of single-cell datasets reveals novel transcriptomic signatures of β-cells in human type 2 diabetes. PMID:33575641
Alternative mRNA Processing of Innate Response Pathways in Respiratory Syncytial Virus (RSV) Infection. PMID:33572560
The kinetic landscape of an RNA-binding protein in cells. PMID:33568810
Variation of DNA Methylation in Newborns Associated with Exhaled Carbon Monoxide during Pregnancy. PMID:33567599
SUMO pathway, blood coagulation and oxidative stress in SARS-CoV-2 infection. PMID:33558851
miR-31 Displays Subtype Specificity in Lung Cancer. PMID:33558335
Chronic Hyperglycemia Drives Functional Impairment of Lymphocytes in Diabetic INS C94Y Transgenic Pigs. PMID:33552065
Integrative molecular characterization of sarcomatoid and rhabdoid renal cell carcinoma. PMID:33547292
Distinct DNA Methylation Patterns of Rheumatoid Arthritis Peripheral Blood and Synovial Tissue T Cells. PMID:33544432
Transcriptomic Analysis of Right Ventricular Remodeling in Two Rat Models of Pulmonary Hypertension: Identification and Validation of Epithelial-to-Mesenchymal Transition in Human Right Ventricular Failure. PMID:33541093
Genome-scale metabolic modeling reveals SARS-CoV-2-induced metabolic changes and antiviral targets. PMID:33532779
Broad Kinase Inhibition Mitigates Early Neuronal Dysfunction in Tauopathy. PMID:33530349
Host transcriptional response to TB preventive therapy differentiates two sub-groups of IGRA-positive individuals. PMID:33524936
LAPTM5 Plays a Key Role in the Diagnosis and Prognosis of Testicular Germ Cell Tumors. PMID:33521125
Pervasive duplication of tumor suppressors in Afrotherians during the evolution of large bodies and reduced cancer risk. PMID:33513090
Screening for potential targets to reduce stenosis in bioprosthetic heart valves. PMID:33510256
Inflammatory Leptomeningeal Cytokines Mediate COVID-19 Neurologic Symptoms in Cancer Patients. PMID:33508216
A regularized functional regression model enabling transcriptome-wide dosage-dependent association study of cancer drug response. PMID:33493149
Synthetic Organic Compounds From Paper Industry Wastes: Integrated Biotechnological Interventions. PMID:33490048
PDGFRβ is an essential therapeutic target for BRCA1-deficient mammary tumors. PMID:33478572
Common Transcriptional Program of Liver Fibrosis in Mouse Genetic Models and Humans. PMID:33467660
Is gene expression among women with rheumatoid arthritis dysregulated during a postpartum flare? PMID:33461591
Serial co-expression analysis of host factors from SARS-CoV viruses highly converges with former high-throughput screenings and proposes key regulators. PMID:33458747
Methylarginine metabolites are associated with attenuated muscle protein synthesis in cancer-associated muscle wasting. PMID:33453990
Bone Marrow Failure Syndromes, Overlapping Diseases with a Common Cytokine Signature. PMID:33445786
Platelet Proteomes, Pathways, and Phenotypes as Informants of Vascular Wellness and Disease. PMID:33441027
Transcriptomic Analysis of Respiratory Tissue and Cell Line Models to Examine Glycosylation Machinery during SARS-CoV-2 Infection. PMID:33435561
Transcriptome profiling of insulin sensitive tissues from GH deficient mice following GH treatment. PMID:33433889
Comprehensive assessments of germline deletion structural variants reveal the association between prognostic MUC4 and CEP72 deletions and immune response gene expression in colorectal cancer patients. PMID:33431054
Computational Identification of Master Regulators Influencing Trypanotolerance in Cattle. PMID:33429951
Role of Multiomics Data to Understand Host-Pathogen Interactions in COVID-19 Pathogenesis. PMID:33426872
Absence of NLRP3 Inflammasome in Hematopoietic Cells Reduces Adverse Remodeling After Experimental Myocardial Infarction. PMID:33426377
Mammalian cell proliferation requires noncatalytic functions of O-GlcNAc transferase. PMID:33419956
The iPPI-DB initiative: A Community-centered database of Protein-Protein Interaction modulators. PMID:33416858
Transcriptome of nasopharyngeal samples from COVID-19 patients and a comparative analysis with other SARS-CoV-2 infection models reveal disparate host responses against SARS-CoV-2. PMID:33413422
Sex differences in expression of immune elements emerge in children, young adults and mice with osteosarcoma. PMID:33407928
Single-cell transcriptome analysis revealed the heterogeneity and microenvironment of gastrointestinal stromal tumors. PMID:33393143
The Large Scale Structure of Human Metabolism Reveals Resilience via Extensive Signaling Crosstalk. PMID:33391012
Identification of Driver Genes Regulating the T-Cell-Infiltrating Levels in Hepatocellular Carcinoma. PMID:33381145
The status of causality in biological databases: data resources and data retrieval possibilities to support logical modeling. PMID:33378765
Conditional Generative Adversarial Networks for Individualized Treatment Effect Estimation and Treatment Selection. PMID:33362849
Obesity induced by high-fat diet is associated with critical changes in biological and molecular functions of mesenchymal stromal cells present in visceral adipose tissue. PMID:33361524
From miRNA Target Gene Network to miRNA Function: miR-375 Might Regulate Apoptosis and Actin Dynamics in the Heart Muscle via Rho-GTPases-Dependent Pathways. PMID:33352947
Genetic Variants behind Cardiovascular Diseases and Dementia. PMID:33352859
CHOmics: A web-based tool for multi-omics data analysis and interactive visualization in CHO cell lines. PMID:33351794
Systematic review and meta-analysis of human transcriptomics reveals neuroinflammation, deficient energy metabolism, and proteostasis failure across neurodegeneration. PMID:33347974
Recognition of plausible therapeutic agents to combat COVID-19: An omics data based combined approach. PMID:33346100
MicroRNA-1291 Is Associated With Locoregional Metastases in Patients With Early-Stage Breast Cancer. PMID:33343622
Rasa3 regulates stage-specific cell cycle progression in murine erythropoiesis. PMID:33341069
The dysregulation of metabolic pathways and induction of the pentose phosphate pathway in renal ischaemia-reperfusion injury. PMID:33338266
SECAT: Quantifying Protein Complex Dynamics across Cell States by Network-Centric Analysis of SEC-SWATH-MS Profiles. PMID:33333029
Ulcerative Colitis-Derived Colonoid Culture: A Multi-Mineral-Approach to Improve Barrier Protein Expression. PMID:33330453
Frameshift Variant in Novel Adenosine-A1-Receptor Homolog Associated With Bovine Spastic Syndrome/Late-Onset Bovine Spastic Paresis in Holstein Sires. PMID:33329738
NF-κB Signaling Is Regulated by Fucosylation in Metastatic Breast Cancer Cells. PMID:33322811
PEREGRINE: A genome-wide prediction of enhancer to gene relationships supported by experimental evidence. PMID:33320871
Effect of EZH2 on pulmonary artery smooth muscle cell migration in pulmonary hypertension. PMID:33313943
Improved risk stratification in younger IDH wild-type glioblastoma patients by combining a 4-miRNA signature with MGMT promoter methylation status. PMID:33305269
A blood transcriptome-based analysis of disease progression, immune regulation, and symptoms in coronavirus-infected patients. PMID:33293514
Proteomic Study Identifies Glycolytic and Inflammation Pathways Involved in Recurrent Otitis Media. PMID:33291465
PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API. PMID:33290554
SFRP4 drives invasion in gastric cancer and is an early predictor of recurrence. PMID:33277667
Personalized B cell response to the Lactobacillus rhamnosus GG probiotic in healthy human subjects: a randomized trial. PMID:33274667
Spatially Targeted Proteomics of the Host-Pathogen Interface during Staphylococcal Abscess Formation. PMID:33270421
Drug2ways: Reasoning over causal paths in biological networks for drug discovery. PMID:33264280
Integrative proteomics reveals principles of dynamic phosphosignaling networks in human erythropoiesis. PMID:33259127
Investigation of COVID-19 comorbidities reveals genes and pathways coincident with the SARS-CoV-2 viral disease. PMID:33257774
Highly diversified core promoters in the human genome and their effects on gene expression and disease predisposition. PMID:33256598
The European Bioinformatics Institute: empowering cooperation in response to a global health crisis. PMID:33245775
Unraveling the Role of Epicardial Adipose Tissue in Coronary Artery Disease: Partners in Crime? PMID:33238643
The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets. PMID:33237311
Expression of Pro-Angiogenic Markers Is Enhanced by Blue Light in Human RPE Cells. PMID:33233546
Spatial profiling of gastric cancer patient-matched primary and locoregional metastases reveals principles of tumour dissemination. PMID:33229445
FlyBase: updates to the Drosophila melanogaster knowledge base. PMID:33219682
canSAR: update to the cancer translational research and drug discovery knowledgebase. PMID:33219674
Comprehensive analysis of the prognosis for chromobox family in gastric cancer. PMID:33209489
Whole exome sequencing and trio analysis to broaden the variant spectrum of genes in idiopathic hypogonadotropic hypogonadism. PMID:33208564
The IMEx coronavirus interactome: an evolving map of Coronaviridae-host molecular interactions. PMID:33206959
Epigenetic profiling of Italian patients identified methylation sites associated with hereditary transthyretin amyloidosis. PMID:33203445
Open Targets Platform: supporting systematic drug-target identification and prioritisation. PMID:33196847
Plant miRNAs Reduce Cancer Cell Proliferation by Targeting MALAT1 and NEAT1: A Beneficial Cross-Kingdom Interaction. PMID:33193626
Inference of Diagnostic Markers and Therapeutic Targets From CSF Proteomics for the Treatment of Hydrocephalus. PMID:33192320
Analysis of miR-9-5p, miR-124-3p, miR-21-5p, miR-138-5p, and miR-1-3p in Glioblastoma Cell Lines and Extracellular Vesicles. PMID:33187334
Impact of Porcine Arterivirus, Influenza B, and Their Coinfection on Antiviral Response in the Porcine Lung. PMID:33187194
FunRes: resolving tissue-specific functional cell states based on a cell-cell communication network model. PMID:33179736
Mesenchymal stem cells negatively regulate CD4<sup>+</sup> T cell activation in patients with primary Sjögren syndrome through the miRNA‑125b and miRNA‑155 TCR pathway. PMID:33179091
Tear proteomics of orbital decompression for disfiguring exophthalmos in inactive thyroid-associated ophthalmopathy. PMID:33178351
Datanator: an integrated database of molecular data for quantitatively modeling cellular behavior. PMID:33174603
MitoCarta3.0: an updated mitochondrial proteome now with sub-organelle localization and pathway annotations. PMID:33174596
The translational landscape of SARS-CoV-2 and infected cells. PMID:33173862
Lung transcriptome of a COVID-19 patient and systems biology predictions suggest impaired surfactant production which may be druggable by surfactant therapy. PMID:33173052
Gramene 2021: harnessing the power of comparative genomics and pathways for plant research. PMID:33170273
Pathway information extracted from 25 years of pathway figures. PMID:33168034
EpiGraphDB: a database and data mining platform for health data science. PMID:33165574
Molecular characterization of breast cancer: a potential novel immune-related lncRNAs signature. PMID:33160384
TCRD and Pharos 2021: mining the human proteome for disease biology. PMID:33156327
MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models. PMID:33156326
PubChem in 2021: new data content and improved web interfaces. PMID:33151290
The interactome of multifunctional HAX1 protein suggests its role in the regulation of energy metabolism, de-aggregation, cytoskeleton organization and RNA-processing. PMID:33146709
Whole egg consumption increases gene expression within the glutathione pathway in the liver of Zucker Diabetic Fatty rats. PMID:33141822
The risk of COVID-19 for pregnant women: Evidences of molecular alterations associated with preeclampsia in SARS-CoV-2 infection. PMID:33137411
Genome-scale metabolic reconstruction of the non-model yeast Issatchenkia orientalis SD108 and its application to organic acids production. PMID:33134082
Upregulation of miR-9 and miR-193b over human Th17 cell differentiation. PMID:33128433
Virus-Host Protein-Protein Interactions between Human Papillomavirus 16 E6 A1 and D2/D3 Sub-Lineages: Variances and Similarities. PMID:33121134
Biomarker Prioritisation and Power Estimation Using Ensemble Gene Regulatory Network Inference. PMID:33114263
Identification of Molecular Network Associated with Neuroprotective Effects of Yashtimadhu (Glycyrrhiza glabra L.) by Quantitative Proteomics of Rotenone-Induced Parkinson's Disease Model. PMID:33110989
Soluble Compounds Released by Hypoxic Stroma Confer Invasive Properties to Pancreatic Ductal Adenocarcinoma. PMID:33105540
The adenoviral protein E4orf4: a probing tool to decipher mechanical stress-induced nuclear envelope remodeling in tumor cells. PMID:33103553
Data on chemical-gene interactions and biological categories enriched with genes sensitive to chemical exposures. PMID:33102660
Mechanisms of interleukin 4 mediated increase in efficacy of vaccines against opioid use disorders. PMID:33101712
Small interfering RNA-mediated knockdown of KRT80 suppresses colorectal cancer proliferation. PMID:33101466
Systematic Identification of Hub Genes in Placenta Accreta Spectrum Based on Integrated Transcriptomic and Proteomic Analysis. PMID:33101378
System biological investigations of hydroxychloroquine and azithromycin targets and their implications in QT interval prolongation. PMID:33098839
Keap1 inhibition sensitizes head and neck squamous cell carcinoma cells to ionizing radiation via impaired non-homologous end joining and induced autophagy. PMID:33087706
The Dark Kinase Knowledgebase: an online compendium of knowledge and experimental results of understudied kinases. PMID:33079988
Effect of Dietary Sodium Modulation on Pig Adrenal Steroidogenesis and Transcriptome Profiles. PMID:33070662
Comparative Toxicogenomics Database (CTD): update 2021. PMID:33068428
ABC Exporters in Pathogenesis: Role of Synthetic Anti-Microbial Peptides. PMID:33068233
Cell-free DNA in plasma as an essential immune system regulator. PMID:33060738
Using whole-exome sequencing and protein interaction networks to prioritize candidate genes for germline cutaneous melanoma susceptibility. PMID:33057211
Tumor genotype, location, and malignant potential shape the immunogenicity of primary untreated gastrointestinal stromal tumors. PMID:33048845
Protein ontology on the semantic web for knowledge discovery. PMID:33046717
INTEDE: interactome of drug-metabolizing enzymes. PMID:33045737
Genomic, proteomic, and systems biology approaches in biomarker discovery for multiple sclerosis. PMID:33039896
Lupus serum induces inflammatory interaction with neutrophils in human glomerular endothelial cells. PMID:33037079
Data mining of human plasma proteins generates a multitude of highly predictive aging clocks that reflect different aspects of aging. PMID:33031577
MiR-29 coordinates age-dependent plasticity brakes in the adult visual cortex. PMID:33026181
Rewiring of B cell receptor signaling by Epstein-Barr virus LMP2A. PMID:33020271
Screening and Identification of Key Biomarkers in Acquired Lapatinib-Resistant Breast Cancer. PMID:33013420
Differential network analysis of bovine muscle reveals changes in gene coexpression patterns in response to changes in maternal nutrition. PMID:33008289
In-silico drug repurposing study predicts the combination of pirfenidone and melatonin as a promising candidate therapy to reduce SARS-CoV-2 infection progression and respiratory distress caused by cytokine storm. PMID:33006999
Body mass index-associated molecular characteristics involved in tumor immune and metabolic pathways. PMID:32999719
Investigation of COVID-19 comorbidities reveals genes and pathways coincident with the SARS-CoV-2 viral disease. PMID:32995795
Anti-PD-1 Immunotherapy and Radiotherapy for Stage IV Intrahepatic Cholangiocarcinoma: A Case Report. PMID:32984358
Favorable Immune Microenvironment in Patients with EGFR and MAPK Co-Mutations. PMID:32982525
Systems Biology: A Multi-Omics Integration Approach to Metabolism and the Microbiome. PMID:32981293
Review on the Computational Genome Annotation of Sequences Obtained by Next-Generation Sequencing. PMID:32962098
Predicting gene regulatory networks from cell atlases. PMID:32958603
Network and Systems Medicine: Position Paper of the European Collaboration on Science and Technology Action on Open Multiscale Systems Medicine. PMID:32954378
Extracellular vesicles from human iPSC-derived neural stem cells: miRNA and protein signatures, and anti-inflammatory and neurogenic properties. PMID:32944193
Role of GATA3 exon 6 germline mutations in breast cancer progression in Egyptian female patients. PMID:32938228
The mutational landscape of the SCAN-B real-world primary breast cancer transcriptome. PMID:32926574
Overexpression of α-Synuclein Reorganises Growth Factor Profile of Human Astrocytes. PMID:32914394
Meningeal lymphatic dysfunction exacerbates traumatic brain injury pathogenesis. PMID:32913280
ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis. PMID:32907876
Panomicon: A web-based environment for interactive, visual analysis of multi-omics data. PMID:32904262
Radiation induces dynamic changes to the T cell repertoire in renal cell carcinoma patients. PMID:32900949
Extracellular Matrix Injury of Kidney Allografts in Antibody-Mediated Rejection: A Proteomics Study. PMID:32900843
Proteostasis and Proteotoxicity in the Network Medicine Era. PMID:32899160
Ontological approach to the knowledge systematization of a toxic process and toxic course representation framework for early drug risk management. PMID:32883995
Actomyosin contractility confers mechanoprotection against TNFα-induced disruption of the intervertebral disc. PMID:32875103
Computational Methods and Software Tools for Functional Analysis of miRNA Data. PMID:32872205
Multidimensional Proteome Profiling of Blood-Brain Barrier Perturbation by Group B Streptococcus. PMID:32843537
Identification of Novel Targets of Knee Osteoarthritis Shared by Cartilage and Synovial Tissue. PMID:32842604
Genetic deletion of microRNA-22 blunts the inflammatory transcriptional response to status epilepticus and exacerbates epilepsy in mice. PMID:32825833
The Oncogenic Roles of PTTG1 and PTTG2 Genes and Pseudogene PTTG3P in Head and Neck Squamous Cell Carcinomas. PMID:32824814
MicroRNAs isolated from peripheral blood in the first trimester predict spontaneous preterm birth. PMID:32790689
Orchestration of Intracellular Circuits by G Protein-Coupled Receptor 39 for Hepatitis B Virus Proliferation. PMID:32784555
MicroRNA Profiling in Paired Left and Right Eyes, Lungs, and Testes of Normal Mice. PMID:32769059
Glycosaminoglycan-Protein Interactions: The First Draft of the Glycosaminoglycan Interactome. PMID:32757871
Metastasis of Uveal Melanoma with Monosomy-3 Is Associated with a Less Glycogenetic Gene Expression Profile and the Dysregulation of Glycogen Storage. PMID:32751097
The enzymology of human eicosanoid pathways: the lipoxygenase branches. PMID:32748021
An Activity-Guided Map of Electrophile-Cysteine Interactions in Primary Human T Cells. PMID:32730809
A comparative study on normal and obese mice indicates that the secretome of mesenchymal stromal cells is influenced by tissue environment and physiopathological conditions. PMID:32727501
The Roles of Imprinted SLC22A18 and SLC22A18AS Gene Overexpression Caused by Promoter CpG Island Hypomethylation as Diagnostic and Prognostic Biomarkers for Non-Small Cell Lung Cancer Patients. PMID:32726996
PertInInt: An Integrative, Analytical Approach to Rapidly Uncover Cancer Driver Genes with Perturbed Interactions and Functionalities. PMID:32711844
Infiltrative tumour growth pattern correlates with poor outcome in oesophageal cancer. PMID:32675198
Metabolic networks of the Nicotiana genus in the spotlight: content, progress and outlook. PMID:32662816
PEDL: extracting protein-protein associations using deep language models and distant supervision. PMID:32657389
The Global Phosphorylation Landscape of SARS-CoV-2 Infection. PMID:32645325
Comparative proteomic analysis of human mesenchymal stromal cell behavior on calcium phosphate ceramics with different osteoinductive potential. PMID:32642640
Phosphoproteomic quantitation and causal analysis reveal pathways in GPVI/ITAM-mediated platelet activation programs. PMID:32640021
Characterization of Glycolysis-Associated Molecules in the Tumor Microenvironment Revealed by Pan-Cancer Tissues and Lung Cancer Single Cell Data. PMID:32635458
Vascular Homeostasis and Inflammation in Health and Disease-Lessons from Single Cell Technologies. PMID:32630148
The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE). PMID:32598315
The IMEx Coronavirus interactome: an evolving map of Coronaviridae-Host molecular interactions. PMID:32587962
Transcriptome-Wide Regulation of Key Developmental Pathways in the Mouse Neural Tube by Prenatal Alcohol Exposure. PMID:32557641
A kinase-deficient NTRK2 splice variant predominates in glioma and amplifies several oncogenic signaling pathways. PMID:32532995
Analysis of the molecular mechanism of Pudilan (PDL) treatment for COVID-19 by network pharmacology tools. PMID:32505821
Identifying temporal molecular signatures underlying cardiovascular diseases: A data science platform. PMID:32504647
An Anti-Cancer Peptide LVTX-8 Inhibits the Proliferation and Migration of Lung Tumor Cells by Regulating Causal Genes' Expression in p53-Related Pathways. PMID:32498425
SNPnexus: a web server for functional annotation of human genome sequence variation (2020 update). PMID:32496546
Using Reactome to build an autophagy mechanism knowledgebase. PMID:32486891
Potential dual functional roles of the Y-linked RBMY in hepatocarcinogenesis. PMID:32473614
Integrative analysis of large-scale loss-of-function screens identifies robust cancer-associated genetic interactions. PMID:32463358
Urinary proteomics links keratan sulfate degradation and lysosomal enzymes to early type 1 diabetes. PMID:32453760
Phosphoproteomics identifies dual-site phosphorylation in an extended basophilic motif regulating FILIP1-mediated degradation of filamin-C. PMID:32444788
Maternal Protein Restriction in Rats Alters the Expression of Genes Involved in Mitochondrial Metabolism and Epitranscriptomics in Fetal Hypothalamus. PMID:32438566
ThETA: transcriptome-driven efficacy estimates for gene-based TArget discovery. PMID:32437556
The Ratiometric Transcript Signature MX2/GPR183 Is Consistently Associated With RTS,S-Mediated Protection Against Controlled Human Malaria Infection. PMID:32411130
COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms. PMID:32371892
SVF-derived extracellular vesicles carry characteristic miRNAs in lipedema. PMID:32350368
Drug Research Meets Network Science: Where Are We? PMID:32338900
Genetics and Epigenetics of Atopic Dermatitis: An Updated Systematic Review. PMID:32325630
Is Low Alveolar Type II Cell SOD3 in the Lungs of Elderly Linked to the Observed Severity of COVID-19? PMID:32323565
SPEED2: inferring upstream pathway activity from differential gene expression. PMID:32313938
Green Tea Polyphenol EGCG Attenuates MDSCs-mediated Immunosuppression through Canonical and Non-Canonical Pathways in a 4T1 Murine Breast Cancer Model. PMID:32290071
The Effect of 3'-Hydroxy-3,4,5,4'-Tetramethoxy -stilbene, the Metabolite of the Resveratrol Analogue DMU-212, on the Motility and Proliferation of Ovarian Cancer Cells. PMID:32046103
The 27th annual Nucleic Acids Research database issue and molecular biology database collection. PMID:31906604
Glucocorticoids counteract hypertrophic effects of myostatin inhibition in dystrophic muscle. PMID:31830002
Reactome: a database of reactions, pathways and biological processes PubMed citations: 718.

718 articles citing: Reactome: a database of reactions, pathways and biological processes

Pan-Src kinase inhibitor treatment attenuates diabetic kidney injury via inhibition of Fyn kinase-mediated endoplasmic reticulum stress. PMID:35918533
The Landscape of Virus-Host Protein-Protein Interaction Databases. PMID:35910656
Repurposing Drugs via Network Analysis: Opportunities for Psychiatric Disorders. PMID:35890359
Analyzing the Systems Biology Effects of COVID-19 mRNA Vaccines to Assess Their Safety and Putative Side Effects. PMID:35889989
Integrated Transcriptome and Metabolomic Analysis Reveal Anti-Angiogenic Properties of Disarib, a Novel Bcl2-Specific Inhibitor. PMID:35885991
The Time Sequence of Gene Expression Changes after Spinal Cord Injury. PMID:35883679
Aggregative trans-eQTL analysis detects trait-specific target gene sets in whole blood. PMID:35882830
The Culture Dish Surface Influences the Phenotype and Dissociation Strategy in Distinct Mouse Macrophage Populations. PMID:35874686
Temporal response characterization across individual multiomics profiles of prediabetic and diabetic subjects. PMID:35840765
Systems biology models to identify the influence of SARS-CoV-2 infections to the progression of human autoimmune diseases. PMID:35818398
N(6)-methyladenosine methylation-regulated polo-like kinase 1 cell cycle homeostasis as a potential target of radiotherapy in pancreatic adenocarcinoma. PMID:35773310
Metabolomic and Transcriptomic Profiling Identified Significant Genes in Thymic Epithelial Tumor. PMID:35736499
An Interaction-Based Method for Refining Results From Gene Set Enrichment Analysis. PMID:35706447
Cooperation between KDM6B overexpression and TET2 deficiency in the pathogenesis of chronic myelomonocytic leukemia. PMID:35697791
Network Pharmacology Approach for Medicinal Plants: Review and Assessment. PMID:35631398
Rapid Molecular Diagnosis of Genetically Inherited Neuromuscular Disorders Using Next-Generation Sequencing Technologies. PMID:35628876
Whole-Genome Sequencing Identifies PPARGC1A as a Putative Modifier of Cancer Risk in BRCA1/2 Mutation Carriers. PMID:35625955
BioTAGME: A Comprehensive Platform for Biological Knowledge Network Analysis. PMID:35571058
Gene Expression Profiling of Glioblastoma to Recognize Potential Biomarker Candidates. PMID:35571016
Bone Progenitors Pull the Strings on the Early Metabolic Rewiring Occurring in Prostate Cancer Cells. PMID:35565211
Driver gene detection through Bayesian network integration of mutation and expression profiles. PMID:35561191
Transcriptional Profiling and Deriving a Seven-Gene Signature That Discriminates Active and Latent Tuberculosis: An Integrative Bioinformatics Approach. PMID:35456421
Expanding biochemical knowledge and illuminating metabolic dark matter with ATLASx. PMID:35322036
MHC-II Signature Correlates With Anti-Tumor Immunity and Predicts anti-PD-L1 Response of Bladder Cancer. PMID:35223828
Methods to Improve Molecular Diagnosis in Genomic Cold Cases in Pediatric Neurology. PMID:35205378
Transcriptome-wide association study of coronary artery disease identifies novel susceptibility genes. PMID:35175464
An Integrative Network Approach to Identify Common Genes for the Therapeutics in Tuberculosis and Its Overlapping Non-Communicable Diseases. PMID:35153741
A Systematic Analysis on the Genes and Their Interaction Underlying the Comorbidity of Alzheimer's Disease and Major Depressive Disorder. PMID:35126089
Multimodal analysis suggests differential immuno-metabolic crosstalk in lung squamous cell carcinoma and adenocarcinoma. PMID:35087143
Identification of Molecular Biomarkers and Key Pathways for Esophageal Carcinoma (EsC): A Bioinformatics Approach. PMID:35071597
Early-life viral infections are associated with disadvantageous immune and microbiota profiles and recurrent respiratory infections. PMID:35058634
NETME: on-the-fly knowledge network construction from biomedical literature. PMID:35013714
IL-17 Pathway Members as Potential Biomarkers of Effective Systemic Treatment and Cardiovascular Disease in Patients with Moderate-to-Severe Psoriasis. PMID:35008981
Meta-Analysis and Bioinformatics Detection of Susceptibility Genes in Diabetic Nephropathy. PMID:35008447
Network analysis of host-pathogen protein interactions in microbe induced cardiovascular diseases. PMID:35001887
A Novel Homozygous TTC7A Missense Mutation Results in Familial Multiple Intestinal Atresia and Combined Immunodeficiency. PMID:34975848
Surgical resection of glioblastomas induces pleiotrophin-mediated self-renewal of glioblastoma stem cells in recurrent tumors. PMID:34964899
High-Quality Genome-Scale Reconstruction of Corynebacterium glutamicum ATCC 13032. PMID:34867870
Pharmacological inhibition of LSD1 triggers myeloid differentiation by targeting GSE1 oncogenic functions in AML. PMID:34862459
Gene Expression Profiling of Skeletal Muscles. PMID:34828324
Development of a bioinformatics platform for analysis of quantitative transcriptomics and proteomics data: the OMnalysis. PMID:34820180
Establishment and characterization of prostate organoids from treatment-naïve patients with prostate cancer. PMID:34820005
Comprehensive Mapping of the Cell Response to Borrelia bavariensis in the Brain Microvascular Endothelial Cells in vitro Using RNA-Seq. PMID:34819924
Integrative Omics Analysis Unravels Microvascular Inflammation-Related Pathways in Kidney Allograft Biopsies. PMID:34795664
Co-evolution based machine-learning for predicting functional interactions between human genes. PMID:34753957
Network analysis reveals rare disease signatures across multiple levels of biological organization. PMID:34753928
Tumor relevant protein functional interactions identified using bipartite graph analyses. PMID:34728699
Distinct DNA Methylation Patterns of Subependymal Giant Cell Astrocytomas in Tuberous Sclerosis Complex. PMID:34709498
Network-driven analysis of human-Plasmodium falciparum interactome: processes for malaria drug discovery and extracting in silico targets. PMID:34702263
PaIRKAT: A pathway integrated regression-based kernel association test with applications to metabolomics and COPD phenotypes. PMID:34679079
Proteomics: Concepts and applications in human medicine. PMID:34630910
Role of HRTPT in kidney proximal epithelial cell regeneration: Integrative differential expression and pathway analyses using microarray and scRNA-seq. PMID:34626063
A Computational Framework to Identify Transcriptional and Network Differences between Hepatocellular Carcinoma and Normal Liver Tissue and Their Applications in Repositioning Drugs. PMID:34604388
RNA-RNA interactions between SARS-CoV-2 and host benefit viral development and evolution during COVID-19 infection. PMID:34585235
Alternative Splicing Regulation of Low-Frequency Genetic Variants in Exon 2 of TREM2 in Alzheimer's Disease by Splicing-Based Aggregation. PMID:34576031
A Novel Approach for the Discovery of Biomarkers of Radiotherapy Response in Breast Cancer. PMID:34442440
Identifying causal models between genetically regulated methylation patterns and gene expression in healthy colon tissue. PMID:34419169
m6A-express: uncovering complex and condition-specific m6A regulation of gene expression. PMID:34417605
Mapping gene and gene pathways associated with coronary artery disease: a CARDIoGRAM exome and multi-ancestry UK biobank analysis. PMID:34385509
Studying the effect of alpha-synuclein and Parkinson's disease linked mutants on inter pathway connectivities. PMID:34381149
Regulatory Network Analysis in Estradiol-Treated Human Endothelial Cells. PMID:34360960
Transcriptomic analyses of livers from mice exposed to 1,4-dioxane for up to 90 days to assess potential mode(s) of action underlying liver tumor development. PMID:34345848
NICEdrug.ch, a workflow for rational drug design and systems-level analysis of drug metabolism. PMID:34340747
An integrative study of genetic variants with brain tissue expression identifies viral etiology and potential drug targets of multiple sclerosis. PMID:34284104
Bioinformatic Analysis of Temporal and Spatial Proteome Alternations During Infections. PMID:34276775
Systems Biomedicine of Primary and Metastatic Colorectal Cancer Reveals Potential Therapeutic Targets. PMID:34249670
Identification and Characterization of Robust Hepatocellular Carcinoma Prognostic Subtypes Based on an Integrative Metabolite-Protein Interaction Network. PMID:34247449
Identification of Diagnostic Markers for Major Depressive Disorder Using Machine Learning Methods. PMID:34220416
Control of tissue development and cell diversity by cell cycle-dependent transcriptional filtering. PMID:34212855
Clinicopathological-Associated Regulatory Network of Deregulated circRNAs in Hepatocellular Carcinoma. PMID:34199580
StrongestPath: a Cytoscape application for protein-protein interaction analysis. PMID:34187355
Identification of Dysregulated Complement Activation Pathways Driven by N-Glycosylation Alterations in T2D Patients. PMID:34178943
Evolving scenario of big data and Artificial Intelligence (AI) in drug discovery. PMID:34159484
Genetic and behavioral adaptation of Candida parapsilosis to the microbiome of hospitalized infants revealed by in situ genomics, transcriptomics, and proteomics. PMID:34154658
Whole-Exome Sequencing Analysis of Oral Squamous Cell Carcinoma Delineated by Tobacco Usage Habits. PMID:34136393
Proteomic Analyses of Vitreous in Proliferative Diabetic Retinopathy: Prior Studies and Future Outlook. PMID:34070658
An Immunometabolic Shift Modulates Cytotoxic Lymphocyte Activation During Melanoma Progression in TRPA1 Channel Null Mice. PMID:34041030
Transcriptional analysis of muscle tissue and isolated satellite cells in spastic cerebral palsy. PMID:33987836
Highly deregulated lncRNA LOC is associated with overall worse prognosis in Hepatocellular Carcinoma patients. PMID:33976720
A Population-Specific Major Allele Reference Genome From The United Arab Emirates Population. PMID:33968136
Performance assessment of sample-specific network control methods for bulk and single-cell biological data analysis. PMID:33956788
Predicting Tumor Cell Response to Synergistic Drug Combinations Using a Novel Simplified Deep Learning Model. PMID:33936513
CladeOScope: functional interactions through the prism of clade-wise co-evolution. PMID:33928243
RNA-Seq Reveals Function of Bta-miR-149-5p in the Regulation of Bovine Adipocyte Differentiation. PMID:33922274
Targeting the tumor stroma: integrative analysis reveal GATA2 and TORYAIP1 as novel prognostic targets in breast and ovarian cancer. PMID:33907495
Identification of IFN-Induced Transmembrane Protein 1 With Prognostic Value in Pancreatic Cancer Using Network Module-Based Analysis. PMID:33869009
Epigenetic alteration contributes to the transcriptional reprogramming in T-cell prolymphocytic leukemia. PMID:33859327
Destination Amyotrophic Lateral Sclerosis. PMID:33854469
Artificial Intelligence and Early Detection of Pancreatic Cancer: 2020 Summative Review. PMID:33835956
Machine Learning Reduced Gene/Non-Coding RNA Features That Classify Schizophrenia Patients Accurately and Highlight Insightful Gene Clusters. PMID:33805976
Microbial Metabolomics: From Methods to Translational Applications. PMID:33791977
Identification of theranostic factors for patients developing metastasis after surgery for early-stage lung adenocarcinoma. PMID:33664854
Genetic architectures of proximal and distal colorectal cancer are partly distinct. PMID:33632709
Spatiotemporal dissection of the cell cycle with single-cell proteogenomics. PMID:33627808
Linking clinotypes to phenotypes and genotypes from laboratory test results in comprehensive physical exams. PMID:33627109
RIP-seq reveals LINE-1 ORF1p association with p-body enriched mRNAs. PMID:33563338
Modeling drug response using network-based personalized treatment prediction (NetPTP) with applications to inflammatory bowel disease. PMID:33544718
ViralLink: An integrated workflow to investigate the effect of SARS-CoV-2 on intracellular signalling and regulatory pathways. PMID:33534793
Pathway-Based Drug-Repurposing Schemes in Cancer: The Role of Translational Bioinformatics. PMID:33520715
An Efficient and Easy-to-Use Network-Based Integrative Method of Multi-Omics Data for Cancer Genes Discovery. PMID:33488678
Longitudinal saliva omics responses to immune perturbation: a case study. PMID:33436912
Network controllability-based algorithm to target personalized driver genes for discovering combinatorial drugs of individual patients. PMID:33434272
An Integrative Computational Approach for the Prediction of Human-Plasmodium Protein-Protein Interactions. PMID:33426052
Computational analysis to repurpose drugs for COVID-19 based on transcriptional response of host cells to SARS-CoV-2. PMID:33413329
Three hematologic/immune system-specific expressed genes are considered as the potential biomarkers for the diagnosis of early rheumatoid arthritis through bioinformatics analysis. PMID:33407587
Development and Validation of a Five-Gene Signature to Predict Relapse-Free Survival in Multiple Sclerosis. PMID:33343487
A biomimetic engineered bone platform for advanced testing of prosthetic implants. PMID:33335113
Co-expression of cancer driver genes: IDH-wildtype glioblastoma-derived tumorspheres. PMID:33317554
Understanding the Molecular Drivers of Disease Heterogeneity in Crohn's Disease Using Multi-omic Data Integration and Network Analysis. PMID:33313682
GWAS and Beyond: Using Omics Approaches to Interpret SNP Associations. PMID:33312764
iDMer: an integrative and mechanism-driven response system for identifying compound interventions for sudden virus outbreak. PMID:33302292
COPD patients with chronic bronchitis and higher sputum eosinophil counts show increased type-2 and PDE4 gene expression in sputum. PMID:33295083
Putative Epigenetic Biomarkers of Stress in Red Blood Cells of Chickens Reared Across Different Biomes. PMID:33240310
Discovering novel driver mutations from pan-cancer analysis of mutational and gene expression profiles. PMID:33232371
nSARS-Cov-2, pulmonary edema and thrombosis: possible molecular insights using miRNA-gene circuits in regulatory networks. PMID:33209992
Epidermal Growth Factor Is Essential for the Maintenance of Novel Prostate Epithelial Cells Isolated From Patient-Derived Organoids. PMID:33195205
Dedifferentiation and neuronal repression define familial Alzheimer's disease. PMID:33188013
A Workflow of Integrated Resources to Catalyze Network Pharmacology Driven COVID-19 Research. PMID:33173863
Revealing Prognosis-Related Pathways at the Individual Level by a Comprehensive Analysis of Different Cancer Transcription Data. PMID:33138076
Functional in vivo and in vitro effects of 20q11.21 genetic aberrations on hPSC differentiation. PMID:33122739
Single-cell patterning and axis characterization in the murine and human definitive endoderm. PMID:33106598
Computational Identification of Human Biological Processes and Protein Sequence Motifs Putatively Targeted by SARS-CoV-2 Proteins Using Protein-Protein Interaction Networks. PMID:33103435
A genome-wide association study of severe asthma exacerbations in Latino children and adolescents. PMID:33093117
ROS production and mitochondrial dysfunction driven by PU.1-regulated NOX4-p22phox activation in Aβ-induced retinal pigment epithelial cell injury. PMID:33052238
Tumor Microenvironment-Associated Immune-Related Genes for the Prognosis of Malignant Pleural Mesothelioma. PMID:33042835
Unveiling COVID-19-associated organ-specific cell types and cell-specific pathway cascade. PMID:32968798
Multi-layered Spatial Transcriptomics Identify Secretory Factors Promoting Human Hematopoietic Stem Cell Development. PMID:32946788
Unveiling the Physical and Functional Niches of FAM26F by Analyzing Its Subcellular Localization and Novel Interacting Partners. PMID:32923759
Drug Repositioning for P-Glycoprotein Mediated Co-Expression Networks in Colorectal Cancer. PMID:32903699
Comprehensive functional annotation of susceptibility variants identifies genetic heterogeneity between lung adenocarcinoma and squamous cell carcinoma. PMID:32889700
Integrated genomic analysis reveals mutated ELF3 as a potential gallbladder cancer vaccine candidate. PMID:32839463
Integrated Bioinformatic Analysis Identifies Networks and Promising Biomarkers for Hepatitis B Virus-Related Hepatocellular Carcinoma. PMID:32775402
Comprehensive Network Analysis Reveals Alternative Splicing-Related lncRNAs in Hepatocellular Carcinoma. PMID:32760422
OmicsON - Integration of omics data with molecular networks and statistical procedures. PMID:32726348
ClusterMine: A knowledge-integrated clustering approach based on expression profiles of gene sets. PMID:32698720
ProtExA: A tool for post-processing proteomics data providing differential expression metrics, co-expression networks and functional analytics. PMID:32670509
Transcriptomic analysis by RNA sequencing characterises malignant progression of canine insulinoma from normal tissue to metastatic disease. PMID:32665562
Advancing computer-aided drug discovery (CADD) by big data and data-driven machine learning modeling. PMID:32663517
Identification of Differentially Expressed Hematopoiesis-associated Genes in Term Low Birth Weight Newborns by Systems Genomics Approach. PMID:32655286
RAGE impairs murine diabetic atherosclerosis regression and implicates IRF7 in macrophage inflammation and cholesterol metabolism. PMID:32641587
Network of clinically-relevant lncRNAs-mRNAs associated with prognosis of hepatocellular carcinoma patients. PMID:32636408
Multi-tissue epigenetic analysis of the osteoarthritis susceptibility locus mapping to the plectin gene PLEC. PMID:32580029
Composition of Caenorhabditis elegans extracellular vesicles suggests roles in metabolism, immunity, and aging. PMID:32578074
Macrophage correlates with immunophenotype and predicts anti-PD-L1 response of urothelial cancer. PMID:32550918
Protein Network Studies on PCOS Biomarkers With S100A8, Druggability Assessment, and RNA Aptamer Designing to Control Its Cyst Migration Effect. PMID:32478041
Dysregulation of the MMP/TIMP Proteolytic System in Subependymal Giant Cell Astrocytomas in Patients With Tuberous Sclerosis Complex: Modulation of MMP by MicroRNA-320d In Vitro. PMID:32472129
Transcript expression-aware annotation improves rare variant interpretation. PMID:32461655
Effects of B cell-activating factor on tumor immunity. PMID:32434989
Identification of differentially expressed genes in actinic keratosis samples treated with ingenol mebutate gel. PMID:32413042
Prioritizing Cancer Genes Based on an Improved Random Walk Method. PMID:32411180
Increased expression of plakoglobin is associated with upregulated MAPK and PI3K/AKT signalling pathways in early resectable pancreatic ductal adenocarcinoma. PMID:32382352
Human adipose-derived mesenchymal stem cell-conditioned medium ameliorates polyneuropathy and foot ulceration in diabetic BKS db/db mice. PMID:32357914
Bioinformatics Methods for Mass Spectrometry-Based Proteomics Data Analysis. PMID:32326049
Viral status, immune microenvironment and immunological response to checkpoint inhibitors in hepatocellular carcinoma. PMID:32303615
Deconvolution of diffuse gastric cancer and the suppression of CD34 on the BALB/c nude mice model. PMID:32293340
Virtual screening web servers: designing chemical probes and drug candidates in the cyberspace. PMID:32187356
Downregulation of histone methyltransferase SET8 inhibits progression of hepatocellular carcinoma. PMID:32161353
Multi-omics analysis of ten carbon nanomaterials effects highlights cell type specific patterns of molecular regulation and adaptation. PMID:32140619
Assessment of the Mode of Action Underlying the Effects of GenX in Mouse Liver and Implications for Assessing Human Health Risks. PMID:32138627
Model-based analysis of response and resistance factors of cetuximab treatment in gastric cancer cell lines. PMID:32119655
Genome-wide Association Analysis in Humans Links Nucleotide Metabolism to Leukocyte Telomere Length. PMID:32109421
Passenger Mutations in More Than 2,500 Cancer Genomes: Overall Molecular Functional Impact and Consequences. PMID:32084333
A Network-Based Bioinformatics Approach to Identify Molecular Biomarkers for Type 2 Diabetes that Are Linked to the Progression of Neurological Diseases. PMID:32041280
EHMT2 Inhibition Induces Cell Death in Human Non-Small Cell Lung Cancer by Altering the Cholesterol Biosynthesis Pathway. PMID:32028644
Toward a gold standard for benchmarking gene set enrichment analysis. PMID:32026945
Pathway and network analysis of more than 2500 whole cancer genomes. PMID:32024854
Dysregulated lncRNA-miRNA-mRNA Network Reveals Patient Survival-Associated Modules and RNA Binding Proteins in Invasive Breast Carcinoma. PMID:32010179
Transcriptional analysis of THP-1 cells infected with Leishmania infantum indicates no activation of the inflammasome platform. PMID:31961876
Eighty-eight variants highlight the role of T cell regulation and airway remodeling in asthma pathogenesis. PMID:31959851
Persistent Exposure to Fusobacterium nucleatum Triggers Chemokine/Cytokine Release and Inhibits the Proliferation and Osteogenic Differentiation Capabilities of Human Gingiva-Derived Mesenchymal Stem Cells. PMID:31921705
Analysis of Differentially Expressed Genes in Coronary Artery Disease by Integrated Microarray Analysis. PMID:31881747
The coding and non-coding transcriptional landscape of subependymal giant cell astrocytomas. PMID:31834371
Transcriptome analysis of human brain microvascular endothelial cells response to Neisseria meningitidis and its antigen MafA using RNA-seq. PMID:31822804
Early Transcriptional Landscapes of Chlamydia trachomatis-Infected Epithelial Cells at Single Cell Resolution. PMID:31803632
Meglumine acridone acetate, the ionic salt of CMA and N-methylglucamine, induces apoptosis in human PBMCs via the mitochondrial pathway. PMID:31796757
Qualitative transcriptional signature for predicting pathological response of colorectal cancer to FOLFOX therapy. PMID:31785020
Ovarian cancer detection by DNA methylation in cervical scrapings. PMID:31775891
A novel network control model for identifying personalized driver genes in cancer. PMID:31765387
Measurement of Conditional Relatedness Between Genes Using Fully Convolutional Neural Network. PMID:31695723
Sequence variants with large effects on cardiac electrophysiology and disease. PMID:31641117
Hepatic PKA inhibition accelerates the lipid accumulation in liver. PMID:31632452
MicroRNAs: Fine Tuners of Monocyte Heterogeneity. PMID:31608049
The MTH1 inhibitor TH588 is a microtubule-modulating agent that eliminates cancer cells by activating the mitotic surveillance pathway. PMID:31604991
Keratin 19 regulates cell cycle pathway and sensitivity of breast cancer cells to CDK inhibitors. PMID:31601969
Diesel exhaust particles dysregulate multiple immunological pathways in murine macrophages: Lessons from microarray and scRNA-seq technologies. PMID:31568751
Comparison of Gene Expression Responses in the Small Intestine of Mice Following Exposure to 3 Carcinogens Using the S1500+ Gene Set Informs a Potential Common Adverse Outcome Pathway. PMID:31558096
Drug repurposing for breast cancer therapy: Old weapon for new battle. PMID:31550502
Genome-wide association studies identify polygenic effects for completed suicide in the Japanese population. PMID:31476763
Genomic Prediction Including SNP-Specific Variance Predictors. PMID:31467030
Identifying chemogenetic interactions from CRISPR screens with drugZ. PMID:31439014
Cancer-associated mutations in DICER1 RNase IIIa and IIIb domains exert similar effects on miRNA biogenesis. PMID:31417090
Stoichiometric gene-to-reaction associations enhance model-driven analysis performance: Metabolic response to chronic exposure to Aldrin in prostate cancer. PMID:31416420
Effects of long-term feeding of rapeseed meal on skeletal muscle transcriptome, production efficiency and meat quality traits in Norwegian Landrace growing-finishing pigs. PMID:31390356
Differential network analysis and protein-protein interaction study reveals active protein modules in glucocorticoid resistance for infant acute lymphoblastic leukemia. PMID:31370801
RITAN: rapid integration of term annotation and network resources. PMID:31355053
Stromal integrin α11 regulates PDGFR-β signaling and promotes breast cancer progression. PMID:31287804
Fibril-induced glutamine-/asparagine-rich prions recruit stress granule proteins in mammalian cells. PMID:31266883
In Silico Toxicology Data Resources to Support Read-Across and (Q)SAR. PMID:31244651
A Systematic Review of MicroRNA Expression as Biomarker of Late-Onset Alzheimer's Disease. PMID:31240600
Astrocyte-specific transcriptome analysis using the ALDH1L1 bacTRAP mouse reveals novel biomarkers of astrogliosis in response to neurotoxicity. PMID:31222732
IgG based immunome analyses of breast cancer patients reveal underlying signaling pathways. PMID:31191821
Multi-domain semantic similarity in biomedical research. PMID:31138117
Identification of Crucial Candidate Genes and Pathways in Glioblastoma Multiform by Bioinformatics Analysis. PMID:31137733
BioUML: an integrated environment for systems biology and collaborative analysis of biomedical data. PMID:31131402
Identification of LIFR, PIK3R1, and MMP12 as Novel Prognostic Signatures in Gallbladder Cancer Using Network-Based Module Analysis. PMID:31119098
Overlapping and unique roles played by ROCK1 and 2 in the modulation of coding and long noncoding RNA expression. PMID:31117934
anamiR: integrated analysis of MicroRNA and gene expression profiling. PMID:31088348
Sex differences in gene expression related to antipsychotic induced weight gain. PMID:30986260
Altered gene expression in antipsychotic-induced weight gain. PMID:30971689
Integrated Somatic and Germline Whole-Exome Sequencing Analysis in Women with Lung Cancer after a Previous Breast Cancer. PMID:30925779
RNAi-based small molecule repositioning reveals clinically approved urea-based kinase inhibitors as broadly active antivirals. PMID:30883607
Identifying miRNA-mRNA regulatory relationships in breast cancer with invariant causal prediction. PMID:30876399
DeepTACT: predicting 3D chromatin contacts via bootstrapping deep learning. PMID:30869141
Using Machine Learning to Measure Relatedness Between Genes: A Multi-Features Model. PMID:30862804
MorCVD: A Unified Database for Host-Pathogen Protein-Protein Interactions of Cardiovascular Diseases Related to Microbes. PMID:30858555
Automated exploration of gene ontology term and pathway networks with ClueGO-REST. PMID:30847467
Genetic meta-analysis of diagnosed Alzheimer's disease identifies new risk loci and implicates Aβ, tau, immunity and lipid processing. PMID:30820047
A novel approach to modelling transcriptional heterogeneity identifies the oncogene candidate CBX2 in invasive breast carcinoma. PMID:30820027
Analysis of Predicted Host-Parasite Interactomes Reveals Commonalities and Specificities Related to Parasitic Lifestyle and Tissues Tropism. PMID:30815000
FoPA: identifying perturbed signaling pathways in clinical conditions using formal methods. PMID:30808299
Genetic variants differentially associated with rheumatoid arthritis and systemic lupus erythematosus reveal the disease-specific biology. PMID:30804378
Bioinformatic gene analysis for potential biomarkers and therapeutic targets of atrial fibrillation-related stroke. PMID:30760287
Prolonged Cold Ischemia Induces Necroptotic Cell Death in Ischemia-Reperfusion Injury and Contributes to Primary Graft Dysfunction after Lung Transplantation. PMID:30742487
Plasma Proteome Signature of Sepsis: a Functionally Connected Protein Network. PMID:30706660
High-throughput RNAi screening reveals cancer-selective lethal targets in the RNA spliceosome. PMID:30705407
Network Analysis Reveals TNF as a Major Hub of Reactive Inflammation Following Spinal Cord Injury. PMID:30700814
Assessing the public landscape of clinical-stage pharmaceuticals through freely available online databases. PMID:30690196
Leveraging Multilayered "Omics" Data for Atopic Dermatitis: A Road Map to Precision Medicine. PMID:30631320
The Importance of Biologic Knowledge and Gene Expression Context for Genomic Data Interpretation. PMID:30619486
Network spectra for drug-target identification in complex diseases: new guns against old foes. PMID:30596144
Drug repositioning using drug-disease vectors based on an integrated network. PMID:30463505
BioGraph: a web application and a graph database for querying and analyzing bioinformatics resources. PMID:30458802
Pathway-based subnetworks enable cross-disease biomarker discovery. PMID:30420699
Ensembl 2019. PMID:30407521
From Single Level Analysis to Multi-Omics Integrative Approaches: A Powerful Strategy towards the Precision Oncology. PMID:30373182
Application of Proteomics Technologies in Oil Palm Research. PMID:30367348
Transcriptome profiling of rubber tree (Hevea brasiliensis) discovers candidate regulators of the cold stress response. PMID:30315521
First Degree Relatives of Patients with Celiac Disease Harbour an Intestinal Transcriptomic Signature that Might Protect them from Enterocyte Damage. PMID:30293993
Integration of genome-wide mRNA and miRNA expression, and DNA methylation data of three cell lines exposed to ten carbon nanomaterials. PMID:30228994
Using predicate and provenance information from a knowledge graph for drug efficacy screening. PMID:30189889
Short term optical defocus perturbs normal developmental shifts in retina/RPE protein abundance. PMID:30157773
Biobank-driven genomic discovery yields new insight into atrial fibrillation biology. PMID:30061737
Transcriptomic Analysis of Hepatic Cells in Multicellular Organotypic Liver Models. PMID:30054499
A Component Formula of Chinese Medicine for Hypercholesterolemia Based on Virtual Screening and Biology Network. PMID:30050582
Mitochondrial double-stranded RNA triggers antiviral signalling in humans. PMID:30046113
Expression of the Circadian Clock Gene BMAL1 Positively Correlates With Antitumor Immunity and Patient Survival in Metastatic Melanoma. PMID:29946530
Systems-Based Interactome Analysis for Hematopoiesis Effect of Angelicae sinensis Radix: Regulated Network of Cell Proliferation towards Hemopoiesis. PMID:29943236
DeCoST: A New Approach in Drug Repurposing From Control System Theory. PMID:29922160
REDESIGN: RDF-based Differential Signaling Framework for Precision Medicine Analytics. PMID:29888036
Proteomics Versus Clinical Data and Stochastic Local Search Based Feature Selection for Acute Myeloid Leukemia Patients' Classification. PMID:29869179
Distinct sperm nucleus behaviors between genotypic and temperature-dependent sex determination males are associated with replication and expression-related pathways in a gynogenetic fish. PMID:29866041
Differential but Complementary HIF1α and HIF2α Transcriptional Regulation. PMID:29843956
RnaSeqSampleSize: real data based sample size estimation for RNA sequencing. PMID:29843589
Transcriptome based individualized therapy of refractory pediatric sarcomas: feasibility, tolerability and efficacy. PMID:29755686
Core signaling pathways in ovarian cancer stem cell revealed by integrative analysis of multi-marker genomics data. PMID:29723215
LiverSex Computational Model: Sexual Aspects in Hepatic Metabolism and Abnormalities. PMID:29706895
Biomedical Informatics on the Cloud: A Treasure Hunt for Advancing Cardiovascular Medicine. PMID:29700073
New perspectives: systems medicine in cardiovascular disease. PMID:29699591
YummyData: providing high-quality open life science data. PMID:29688370
Systematic Evaluation of Molecular Networks for Discovery of Disease Genes. PMID:29605183
System-wide coordinates of higher order functions in host-pathogen environment upon Mycobacterium tuberculosis infection. PMID:29567998
Efficient pathway enrichment and network analysis of GWAS summary data using GSA-SNP2. PMID:29562348
The Pathway Coexpression Network: Revealing pathway relationships. PMID:29554099
Network-based integration of multi-omics data for prioritizing cancer genes. PMID:29547932
An integrated approach to infer cross-talks between intracellular protein transport and signaling pathways. PMID:29536825
Discriminate the response of Acute Myeloid Leukemia patients to treatment by using proteomics data and Answer Set Programming. PMID:29536824
SMILE: a novel procedure for subcellular module identification with localisation expansion. PMID:29533218
CD40 ligand deficiency causes functional defects of peripheral neutrophils that are improved by exogenous IFN-γ. PMID:29518426
Isoform-level gene expression patterns in single-cell RNA-sequencing data. PMID:29490015
A global network of biomedical relationships derived from text. PMID:29490008
Transcription factor PU.1 is involved in the progression of glioma. PMID:29467892
CEMiTool: a Bioconductor package for performing comprehensive modular co-expression analyses. PMID:29458351
Quick tips for creating effective and impactful biological pathways using the Systems Biology Graphical Notation. PMID:29447151
Immune activation underlies a sustained clinical response to Yttrium-90 radioembolisation in hepatocellular carcinoma. PMID:29440463
Gene expression profile analysis of the progression of carotid atherosclerotic plaques. PMID:29436628
Overexpression of PGC-1α in aging muscle enhances a subset of young-like molecular patterns. PMID:29427317
RNA-seq transcriptome analysis of breast cancer cell lines under shikonin treatment. PMID:29422643
Proteome Profiling of Diabetic Mellitus Patient Urine for Discovery of Biomarkers by Comprehensive MS-Based Proteomics. PMID:29415455
MeCP2 interacts with chromosomal microRNAs in brain. PMID:29412786
Assessing the Role of Muscle Protein Breakdown in Response to Nutrition and Exercise in Humans. PMID:29368185
Semi-supervised identification of cancer subgroups using survival outcomes and overlapping grouping information. PMID:29336210
Perturbation-response genes reveal signaling footprints in cancer gene expression. PMID:29295995
Genome-wide Study of Atrial Fibrillation Identifies Seven Risk Loci and Highlights Biological Pathways and Regulatory Elements Involved in Cardiac Development. PMID:29290336
Zinc Detoxification: A Functional Genomics and Transcriptomics Analysis in Drosophila melanogaster Cultured Cells. PMID:29223976
Construction of an miRNA-Regulated Pathway Network Reveals Candidate Biomarkers for Postmenopausal Osteoporosis. PMID:29158773
Host immune response index in gastric cancer identified by comprehensive analyses of tumor immunity. PMID:29147610
PAGER 2.0: an update to the pathway, annotated-list and gene-signature electronic repository for Human Network Biology. PMID:29126216
Predicting age by mining electronic medical records with deep learning characterizes differences between chronological and physiological age. PMID:29113935
Ubiquitin Conjugation Probed by Inflammation in Myeloid-Derived Suppressor Cell Extracellular Vesicles. PMID:29061044
Diverse type 2 diabetes genetic risk factors functionally converge in a phenotype-focused gene network. PMID:29059180
A High-Resolution Genome-Wide CRISPR/Cas9 Viability Screen Reveals Structural Features and Contextual Diversity of the Human Cell-Essential Proteome. PMID:29038160
Mutational landscape of RNA-binding proteins in human cancers. PMID:29023197
Pathway Analysis with Signaling Hypergraphs. PMID:28991726
Systems approach to the pharmacological actions of HDAC inhibitors reveals EP300 activities and convergent mechanisms of regulation in diabetes. PMID:28886276
Basal-A Triple-Negative Breast Cancer Cells Selectively Rely on RNA Splicing for Survival. PMID:28878028
CytoCluster: A Cytoscape Plugin for Cluster Analysis and Visualization of Biological Networks. PMID:28858211
Personalized analysis of pathway aberrance induced by sevoflurane and propofol. PMID:28849088
Perturbed human sub-networks by Fusobacterium nucleatum candidate virulence proteins. PMID:28793925
Identification of altered pathways in breast cancer based on individualized pathway aberrance score. PMID:28789343
Network reconstruction and validation of the Snf1/AMPK pathway in baker's yeast based on a comprehensive literature review. PMID:28725459
A novel method to identify hub pathways of rheumatoid arthritis based on differential pathway networks. PMID:28713940
Gramene Database: Navigating Plant Comparative Genomics Resources. PMID:28713666
HDNetDB: A Molecular Interaction Database for Network-Oriented Investigations into Huntington's Disease. PMID:28701700
Improving the detection of pathways in genome-wide association studies by combined effects of SNPs from Linkage Disequilibrium blocks. PMID:28615668
Across-proteome modeling of dimer structures for the bottom-up assembly of protein-protein interaction networks. PMID:28499419
Pathview Web: user friendly pathway visualization and data integration. PMID:28482075
A Novel Method to Identify Differential Pathways in Hippocampus Alzheimer's Disease. PMID:28479591
WebGIVI: a web-based gene enrichment analysis and visualization tool. PMID:28472919
Gene set selection via LASSO penalized regression (SLPR). PMID:28472344
1000 Genomes-based meta-analysis identifies 10 novel loci for kidney function. PMID:28452372
LncRNAs2Pathways: Identifying the pathways influenced by a set of lncRNAs of interest based on a global network propagation method. PMID:28425476
Model-based unsupervised learning informs metformin-induced cell-migration inhibition through an AMPK-independent mechanism in breast cancer. PMID:28423712
Proof-of-Concept Workflow for Establishing Reference Intervals of Human Urine Proteome for Monitoring Physiological and Pathological Changes. PMID:28396014
Benchmarking pathway interaction network for colorectal cancer to identify dysregulated pathways. PMID:28380197
Human enterovirus 71 protein interaction network prompts antiviral drug repositioning. PMID:28220872
Expression Quantitative Trait loci (QTL) in tumor adjacent normal breast tissue and breast tumor tissue. PMID:28152060
Epigenetic profiling of human brain differential DNA methylation networks in schizophrenia. PMID:28117656
Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks. PMID:28114351
A genome-wide scan for genes under balancing selection in Drosophila melanogaster. PMID:28086750
RAIN: RNA-protein Association and Interaction Networks. PMID:28077569
Non-Coding RNAs in Lung Cancer: Contribution of Bioinformatics Analysis to the Development of Non-Invasive Diagnostic Tools. PMID:28035947
Gene-based analyses reveal novel genetic overlap and allelic heterogeneity across five major psychiatric disorders. PMID:28035465
Transcriptomic analysis displays the effect of (-)-roemerine on the motility and nutrient uptake in Escherichia coli. PMID:28013396
Prediction of Possible Biomarkers and Novel Pathways Conferring Risk to Post-Traumatic Stress Disorder. PMID:27997584
miRTar2GO: a novel rule-based model learning method for cell line specific microRNA target prediction that integrates Ago2 CLIP-Seq and validated microRNA-target interaction data. PMID:27903911
LPA receptor activity is basal specific and coincident with early pregnancy and involution during mammary gland postnatal development. PMID:27808166
Pathway Analysis Based on Attractor and Cross Talk in Colon Cancer. PMID:27746583
Identify potential drugs for cardiovascular diseases caused by stress-induced genes in vascular smooth muscle cells. PMID:27703845
Bioinformatics analysis of the molecular mechanism of diffuse intrinsic pontine glioma. PMID:27698822
Biochemical Foundations of Health and Energy Conservation in Hibernating Free-ranging Subadult Brown Bear Ursus arctos. PMID:27609515
The Robustness of Pathway Analysis in Identifying Potential Drug Targets in Non-Small Cell Lung Carcinoma. PMID:27600345
STAMS: STRING-assisted module search for genome wide association studies and application to autism. PMID:27542772
Genome-Wide Prediction and Analysis of 3D-Domain Swapped Proteins in the Human Genome from Sequence Information. PMID:27467780
Ontology-based Vaccine and Drug Adverse Event Representation and Theory-guided Systematic Causal Network Analysis toward Integrative Pharmacovigilance Research. PMID:27458549
Community-Reviewed Biological Network Models for Toxicology and Drug Discovery Applications. PMID:27429547
Multi-omics landscapes of colorectal cancer subtypes discriminated by an individualized prognostic signature for 5-fluorouracil-based chemotherapy. PMID:27429074
Integrating Transcriptomic and Proteomic Data Using Predictive Regulatory Network Models of Host Response to Pathogens. PMID:27403523
Systems Genetic Analyses Highlight a TGFβ-FOXO3 Dependent Striatal Astrocyte Network Conserved across Species and Associated with Stress, Sleep, and Huntington's Disease. PMID:27390852
Clinical significance of mitofusin-2 and its signaling pathways in hepatocellular carcinoma. PMID:27389277
BcCluster: A Bladder Cancer Database at the Molecular Level. PMID:27376128
Cholesterol Metabolism and Prostate Cancer Lethality. PMID:27325648
Prediction of cancer drug sensitivity using high-dimensional omic features. PMID:27324412
System Review about Function Role of ESCC Driver Gene KDM6A by Network Biology Approach. PMID:27294188
GCGene: a gene resource for gastric cancer with literature evidence. PMID:27127885
Network-driven plasma proteomics expose molecular changes in the Alzheimer's brain. PMID:27112350
Analysis of microRNA expression during the torpor-arousal cycle of a mammalian hibernator, the 13-lined ground squirrel. PMID:27084747
Comprehensive Transcriptome Meta-analysis to Characterize Host Immune Responses in Helminth Infections. PMID:27058578
Transcriptome sequencing reveals e-cigarette vapor and mainstream-smoke from tobacco cigarettes activate different gene expression profiles in human bronchial epithelial cells. PMID:27041137
miTALOS v2: Analyzing Tissue Specific microRNA Function. PMID:26998997
Functional genetics-directed identification of novel pharmacological inhibitors of FAS- and TNF-dependent apoptosis that protect mice from acute liver failure. PMID:26986512
REGene: a literature-based knowledgebase of animal regeneration that bridge tissue regeneration and cancer. PMID:26975833
Rationalising the role of Keratin 9 as a biomarker for Alzheimer's disease. PMID:26973255
Comprehensive genomic analysis of malignant pleural mesothelioma identifies recurrent mutations, gene fusions and splicing alterations. PMID:26928227
Complementary Post Transcriptional Regulatory Information is Detected by PUNCH-P and Ribosome Profiling. PMID:26898226
Identification of Molecular Targets for Predicting Colon Adenocarcinoma. PMID:26868022
Recruitment of the Mammalian Histone-modifying EMSY Complex to Target Genes Is Regulated by ZNF131. PMID:26841866
Network-based in silico drug efficacy screening. PMID:26831545
Drug repositioning for non-small cell lung cancer by using machine learning algorithms and topological graph theory. PMID:26817825
Cascade: an RNA-seq visualization tool for cancer genomics. PMID:26810393
Fast and Rigorous Computation of Gene and Pathway Scores from SNP-Based Summary Statistics. PMID:26808494
Multi-task consensus clustering of genome-wide transcriptomes from related biological conditions. PMID:26801959
Compendium of Immune Signatures Identifies Conserved and Species-Specific Biology in Response to Inflammation. PMID:26795250
CSGene: a literature-based database for cell senescence genes and its application to identify critical cell aging pathways and associated diseases. PMID:26775705
Comprehensive analysis of schizophrenia-associated loci highlights ion channel pathways and biologically plausible candidate causal genes. PMID:26755824
Pathway Analysis: State of the Art. PMID:26733877
ECGene: A Literature-Based Knowledgebase of Endometrial Cancer Genes. PMID:26699919
Constructing a molecular interaction network for thyroid cancer via large-scale text mining of gene and pathway events. PMID:26679379
Current dichotomy between traditional molecular biological and omic research in cancer biology and pharmacology. PMID:26677427
Genome-wide identification of Wig-1 mRNA targets by RIP-Seq analysis. PMID:26672765
Frequent alterations in cytoskeleton remodelling genes in primary and metastatic lung adenocarcinomas. PMID:26647728
Newly Constructed Network Models of Different WNT Signaling Cascades Applied to Breast Cancer Expression Data. PMID:26632845
Integrated genomic characterization of IDH1-mutant glioma malignant progression. PMID:26618343
Therapeutic target database update 2016: enriched resource for bench to clinical drug target and targeted pathway information. PMID:26578601
Sphingosine kinase 2 is a chikungunya virus host factor co-localized with the viral replication complex. PMID:26576339
Psychiatric gene discoveries shape evidence on ADHD's biology. PMID:26573769
Argonaute 2 and nasopharyngeal carcinoma: a genetic association study and functional analysis. PMID:26545861
Comparative study on gene set and pathway topology-based enrichment methods. PMID:26489510
An evidence-based knowledgebase of metastasis suppressors to identify key pathways relevant to cancer metastasis. PMID:26486520
Integrative Genomics-Based Discovery of Novel Regulators of the Innate Antiviral Response. PMID:26485378
Personalised pathway analysis reveals association between DNA repair pathway dysregulation and chromosomal instability in sporadic breast cancer. PMID:26456802
Bioinformatics analyses of differentially expressed genes associated with bisphosphonate-related osteonecrosis of the jaw in patients with multiple myeloma. PMID:26445550
Association of glutathione S-transferase T1 and M1 polymorphisms with prostate cancer susceptibility in populations of Asian descent: a meta-analysis. PMID:26416453
Integrative analysis of human protein, function and disease networks. PMID:26399914
The role of breast-feeding in infant immune system: a systems perspective on the intestinal microbiome. PMID:26399409
Protein networks in induced sputum from smokers and COPD patients. PMID:26396508
mapDIA: Preprocessing and statistical analysis of quantitative proteomics data from data independent acquisition mass spectrometry. PMID:26381204
Dissecting Germ Cell Metabolism through Network Modeling. PMID:26367011
Interactive Big Data Resource to Elucidate Human Immune Pathways and Diseases. PMID:26362267
Longitudinal omics modeling and integration in clinical metabonomics research: challenges in childhood metabolic health research. PMID:26301225
Comparative analysis of anti-viral transcriptomics reveals novel effects of influenza immune antagonism. PMID:26272204
DeDaL: Cytoscape 3 app for producing and morphing data-driven and structure-driven network layouts. PMID:26271256
Integrated analysis of numerous heterogeneous gene expression profiles for detecting robust disease-specific biomarkers and proposing drug targets. PMID:26261215
Optimal Threshold Determination for Interpreting Semantic Similarity and Particularity: Application to the Comparison of Gene Sets and Metabolic Pathways Using GO and ChEBI. PMID:26230274
Representing virus-host interactions and other multi-organism processes in the Gene Ontology. PMID:26215368
Cross-cancer profiling of molecular alterations within the human autophagy interaction network. PMID:26208877
Novel structural co-expression analysis linking the NPM1-associated ribosomal biogenesis network to chronic myelogenous leukemia. PMID:26205693
The gastrin and cholecystokinin receptors mediated signaling network: a scaffold for data analysis and new hypotheses on regulatory mechanisms. PMID:26205660
Atlas of Cancer Signalling Network: a systems biology resource for integrative analysis of cancer data with Google Maps. PMID:26192618
A Frame-Shift Mutation in CAV1 Is Associated with a Severe Neonatal Progeroid and Lipodystrophy Syndrome. PMID:26176221
Pathway Graphical Lasso. PMID:26167394
Pathway and network analysis of cancer genomes. PMID:26125594
dbEMT: an epithelial-mesenchymal transition associated gene resource. PMID:26099468
Cross-organism analysis using InterMine. PMID:26097192
PrOnto database : GO term functional dissimilarity inferred from biological data. PMID:26089836
Proteins interaction network and modeling of IGVH mutational status in chronic lymphocytic leukemia. PMID:26088082
Revealing Pathway Dynamics in Heart Diseases by Analyzing Multiple Differential Networks. PMID:26083688
Association of Protein Translation and Extracellular Matrix Gene Sets with Breast Cancer Metastasis: Findings Uncovered on Analysis of Multiple Publicly Available Datasets Using Individual Patient Data Approach. PMID:26080057
Lysoplex: An efficient toolkit to detect DNA sequence variations in the autophagy-lysosomal pathway. PMID:26075876
Pedican: an online gene resource for pediatric cancers with literature evidence. PMID:26073932
PAGER: constructing PAGs and new PAG-PAG relationships for network biology. PMID:26072489
Tumor Necrosis Factor Receptor 2 Restricts the Pathogenicity of CD8(+) T Cells in Mice With Colitis. PMID:26072395
Gene expression changes reflect clinical response in a placebo-controlled randomized trial of abatacept in patients with diffuse cutaneous systemic sclerosis. PMID:26071192
kpath: integration of metabolic pathway linked data. PMID:26055101
Extreme multifunctional proteins identified from a human protein interaction network. PMID:26054620
ONION: Functional Approach for Integration of Lipidomics and Transcriptomics Data. PMID:26053255
DECODE: an integrated differential co-expression and differential expression analysis of gene expression data. PMID:26026612
PathRings: a web-based tool for exploration of ortholog and expression data in biological pathways. PMID:25982732
Pathway-based Biomarkers for Breast Cancer in Proteomics. PMID:25972728
Improving the Understanding of Pathogenesis of Human Papillomavirus 16 via Mapping Protein-Protein Interaction Network. PMID:25961044
MIMP: predicting the impact of mutations on kinase-substrate phosphorylation. PMID:25938373
Genome-wide methylation study on depression: differential methylation and variable methylation in monozygotic twins. PMID:25918994
Computational algorithms to predict Gene Ontology annotations. PMID:25916950
The genetic basis of peripheral arterial disease: current knowledge, challenges, and future directions. PMID:25908728
Bioinformatics analyses of significant prognostic risk markers for thyroid papillary carcinoma. PMID:25908172
Linking gene expression to phenotypes via pathway information. PMID:25901272
The BioMart community portal: an innovative alternative to large, centralized data repositories. PMID:25897122
Prediction of host - pathogen protein interactions between Mycobacterium tuberculosis and Homo sapiens using sequence motifs. PMID:25887594
Genome-wide Analysis of Body Proportion Classifies Height-Associated Variants by Mechanism of Action and Implicates Genes Important for Skeletal Development. PMID:25865494
Identification of stage-specific biomarkers in lung adenocarcinoma based on RNA-seq data. PMID:25861020
Harnessing the heart of big data. PMID:25814682
Personal genomes, quantitative dynamic omics and personalized medicine. PMID:25798291
Performance of case-control rare copy number variation annotation in classification of autism. PMID:25783485
Time since onset of disease and individual clinical markers associate with transcriptional changes in uncomplicated dengue. PMID:25768297
A statistical framework for revealing signaling pathways perturbed by DNA variants. PMID:25765646
PathCards: multi-source consolidation of human biological pathways. PMID:25725062
Are there genetic paths common to obesity, cardiovascular disease outcomes, and cardiovascular risk factors? PMID:25722444
Therapeutic opportunities within the DNA damage response. PMID:25709118
New genetic loci link adipose and insulin biology to body fat distribution. PMID:25673412
CSAX: Characterizing Systematic Anomalies in eXpression Data. PMID:25651392
A global microRNA screen identifies regulators of the ErbB receptor signaling network. PMID:25630670
Inferring biological tasks using Pareto analysis of high-dimensional data. PMID:25622107
Biological interpretation of genome-wide association studies using predicted gene functions. PMID:25597830
Protein interactome of muscle invasive bladder cancer. PMID:25569276
Pathway mapping and development of disease-specific biomarkers: protein-based network biomarkers. PMID:25560835
Proteomic analysis of the response to cell cycle arrests in human myeloid leukemia cells. PMID:25555159
ReNE: a cytoscape plugin for regulatory network enhancement. PMID:25541727
Pathway analysis and transcriptomics improve protein identification by shotgun proteomics from samples comprising small number of cells--a benchmarking study. PMID:25521637
In silico analysis of autoimmune diseases and genetic relationships to vaccination against infectious diseases. PMID:25486901
Crosstalk between signaling pathways provided by single and multiple protein phosphorylation sites. PMID:25451034
Spectrum of diverse genomic alterations define non-clear cell renal carcinoma subtypes. PMID:25401301
Splicing mutation analysis reveals previously unrecognized pathways in lymph node-invasive breast cancer. PMID:25394353
iPathCons and iPathDB: an improved insect pathway construction tool and the database. PMID:25388589
Proteomics for systems toxicology. PMID:25379146
A pan-cancer modular regulatory network analysis to identify common and cancer-specific network components. PMID:25374456
A method for gene-based pathway analysis using genomewide association study summary statistics reveals nine new type 1 diabetes associations. PMID:25371288
Systems analysis reveals down-regulation of a network of pro-survival miRNAs drives the apoptotic response in dilated cardiomyopathy. PMID:25361207
Computational approaches for microalgal biofuel optimization: a review. PMID:25309916
Transcriptome analysis elucidates key developmental components of bryozoan lophophore development. PMID:25300304
Functional phylogenomics analysis of bacteria and archaea using consistent genome annotation with UniFam. PMID:25293379
SCL/TAL1-mediated transcriptional network enhances megakaryocytic specification of human embryonic stem cells. PMID:25292191
Defining the role of common variation in the genomic and biological architecture of adult human height. PMID:25282103
A novel common variant in DCST2 is associated with length in early life and height in adulthood. PMID:25281659
Formal modelling of toll like receptor 4 and JAK/STAT signalling pathways: insight into the roles of SOCS-1, interferon-β and proinflammatory cytokines in sepsis. PMID:25255432
Network medicine analysis of COPD multimorbidities. PMID:25248857
Using drug response data to identify molecular effectors, and molecular "omic" data to identify candidate drugs in cancer. PMID:25213708
Drug repositioning discovery for early- and late-stage non-small-cell lung cancer. PMID:25210704
Network signatures link hepatic effects of anti-diabetic interventions with systemic disease parameters. PMID:25204982
Data mining of atherosclerotic plaque transcriptomes predicts STAT1-dependent inflammatory signal integration in vascular disease. PMID:25196434
FSim: a novel functional similarity search algorithm and tool for discovering functionally related gene products. PMID:25184141
DawnRank: discovering personalized driver genes in cancer. PMID:25177370
Unbiased functional clustering of gene variants with a phenotypic-linkage network. PMID:25166029
Personalized identification of altered pathways in cancer using accumulated normal tissue data. PMID:25161229
Evidence for functional convergence in genes upregulated by herbivores ingesting plant secondary compounds. PMID:25123454
Pathway analysis approaches for rare and common variants: insights from Genetic Analysis Workshop 18. PMID:25112195
Genome-wide association analyses identify variants in developmental genes associated with hypospadias. PMID:25108383
BioJS: an open source standard for biological visualisation - its status in 2014. PMID:25075290
Text-mining-assisted biocuration workflows in Argo. PMID:25037308
Bioinformatic analysis of proteomics data. PMID:25033288
Gene network-based analysis identifies two potential subtypes of small intestinal neuroendocrine tumors. PMID:25023465
In silico identification of potential targets and drugs for non-small cell lung cancer. PMID:25014226
Expanding the computational toolbox for mining cancer genomes. PMID:25001846
Proteogenomic convergence for understanding cancer pathways and networks. PMID:24994965
Tools and databases of the KOMICS web portal for preprocessing, mining, and dissemination of metabolomics data. PMID:24949426
Lynx web services for annotations and systems analysis of multi-gene disorders. PMID:24948611
On the crucial cerebellar wound healing-related pathways and their cross-talks after traumatic brain injury in Danio rerio. PMID:24926785
Protein conservation and variation suggest mechanisms of cell type-specific modulation of signaling pathways. PMID:24922536
dbCerEx: a web-based database for the analysis of cervical cancer transcriptomes. PMID:24918550
Ontology-supported research on vaccine efficacy, safety and integrative biological networks. PMID:24909153
Genome-wide association studies of refractive error and myopia, lessons learned, and implications for the future. PMID:24876304
Transduction motif analysis of gastric cancer based on a human signaling network. PMID:24838641
R-based software for the integration of pathway data into bioinformatic algorithms. PMID:24833336
Analysis pipeline for the epistasis search - statistical versus biological filtering. PMID:24817878
Identification of functional modules by integration of multiple data sources using a Bayesian network classifier. PMID:24736851
A rule-based ontological framework for the classification of molecules. PMID:24735706
No large-effect low-frequency coding variation found for myocardial infarction. PMID:24728188
Novel skin phenotypes revealed by a genome-wide mouse reverse genetic screen. PMID:24721909
Identifying biological pathways that underlie primordial short stature using network analysis. PMID:24711643
The palmitoyl acyltransferase HIP14 shares a high proportion of interactors with huntingtin: implications for a role in the pathogenesis of Huntington's disease. PMID:24705354
Identification of odorant-receptor interactions by global mapping of the human odorome. PMID:24695519
Computational tools for the secondary analysis of metabolomics experiments. PMID:24688685
Prediction of individualized therapeutic vulnerabilities in cancer from genomic profiles. PMID:24665131
Systems-level analysis of innate immunity. PMID:24655298
An integrative modeling framework reveals plasticity of TGF-β signaling. PMID:24618419
Modulation of neuronal proteome profile in response to Japanese encephalitis virus infection. PMID:24599148
Digital cell quantification identifies global immune cell dynamics during influenza infection. PMID:24586061
Increased interaction with insulin receptor substrate 1, a novel abnormality in insulin resistance and type 2 diabetes. PMID:24584551
A systems biology analysis of the unique and overlapping transcriptional responses to caloric restriction and dietary methionine restriction in rats. PMID:24571921
Detection of type 2 diabetes related modules and genes based on epigenetic networks. PMID:24565181
PathNER: a tool for systematic identification of biological pathway mentions in the literature. PMID:24555844
Importance of collection in gene set enrichment analysis of drug response in cancer cell lines. PMID:24522610
Whole-genome pathway analysis on 132,497 individuals identifies novel gene-sets associated with body mass index. PMID:24497910
BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains. PMID:24495517
A network-assisted co-clustering algorithm to discover cancer subtypes based on gene expression. PMID:24491042
Integrated mRNA and microRNA transcriptome sequencing characterizes sequence variants and mRNA-microRNA regulatory network in nasopharyngeal carcinoma model systems. PMID:24490137
Semantic particularity measure for functional characterization of gene sets using gene ontology. PMID:24489737
An evidence-based knowledgebase of pulmonary arterial hypertension to identify genes and pathways relevant to pathogenesis. PMID:24448676
Comprehensive genomic analysis of rhabdomyosarcoma reveals a landscape of alterations affecting a common genetic axis in fusion-positive and fusion-negative tumors. PMID:24436047
ISAAC - InterSpecies Analysing Application using Containers. PMID:24428905
Systematic nucleo-cytoplasmic trafficking of proteins following exposure of MCF7 breast cancer cells to estradiol. PMID:24422525
MicroRNAs Implicated in Dysregulation of Gene Expression Following Human Lung Transplantation. PMID:24416715
Methylome-wide association study of schizophrenia: identifying blood biomarker signatures of environmental insults. PMID:24402055
Low frequency variants, collapsed based on biological knowledge, uncover complexity of population stratification in 1000 genomes project data. PMID:24385916
MOPED enables discoveries through consistently processed proteomics data. PMID:24350770
A systems' biology approach to study microRNA-mediated gene regulatory networks. PMID:24350286
CyTargetLinker: a cytoscape app to integrate regulatory interactions in network analysis. PMID:24340000
Functional interpretation of non-coding sequence variation: concepts and challenges. PMID:24311363
STITCH 4: integration of protein-chemical interactions with user data. PMID:24293645
Network analysis of GWAS data. PMID:24287332
Lynx: a database and knowledge extraction engine for integrative medicine. PMID:24270788
SASD: the Synthetic Alternative Splicing Database for identifying novel isoform from proteomics. PMID:24267658
Modulation of epidermal transcription circuits in psoriasis: new links between inflammation and hyperproliferation. PMID:24260178
The Reactome pathway knowledgebase. PMID:24243840
Integrating in silico resources to map a signaling network. PMID:24233784
Gramene 2013: comparative plant genomics resources. PMID:24217918
UniHI 7: an enhanced database for retrieval and interactive analysis of human molecular interaction networks. PMID:24214987
DriverDB: an exome sequencing database for cancer driver gene identification. PMID:24214964
Annotating cancer variants and anti-cancer therapeutics in reactome. PMID:24213504
SMPDB 2.0: big improvements to the Small Molecule Pathway Database. PMID:24203708
The pancreatic expression database: recent extensions and updates. PMID:24163255
MEROPS: the database of proteolytic enzymes, their substrates and inhibitors. PMID:24157837
Pathways of Toxicity. PMID:24127042
Integrated enrichment analysis of variants and pathways in genome-wide association studies indicates central role for IL-2 signaling genes in type 1 diabetes, and cytokine signaling genes in Crohn's disease. PMID:24098138
Novel modeling of cancer cell signaling pathways enables systematic drug repositioning for distinct breast cancer metastases. PMID:24097821
Using biological pathway data with paxtools. PMID:24068901
Capturing cooperative interactions with the PSI-MI format. PMID:24067240
QSSPN: dynamic simulation of molecular interaction networks describing gene regulation, signalling and whole-cell metabolism in human cells. PMID:24064420
A computational approach to chemical etiologies of diabetes. PMID:24048418
PICT1 regulates TP53 via RPL11 and is involved in gastric cancer progression. PMID:24045667
Manteia, a predictive data mining system for vertebrate genes and its applications to human genetic diseases. PMID:24038354
PainNetworks: a web-based resource for the visualisation of pain-related genes in the context of their network associations. PMID:24036287
IQdb: an intelligence quotient score-associated gene resource for human intelligence. PMID:24030781
NetWeAvers: an R package for integrative biological network analysis with mass spectrometry data. PMID:24008417
Principles of self-organization in biological pathways: a hypothesis on the autogenous association of alpha-synuclein. PMID:24003031
Web Apollo: a web-based genomic annotation editing platform. PMID:24000942
Early innate immunity determines outcome of Mycobacterium tuberculosis pulmonary infection in rabbits. PMID:23958185
Conversion of KEGG metabolic pathways to SBGN maps including automatic layout. PMID:23953132
Pathway analysis using genome-wide association study data for coronary restenosis--a potential role for the PARVB gene. PMID:23950981
A genome-wide siRNA screen identifies proteasome addiction as a vulnerability of basal-like triple-negative breast cancer cells. PMID:23948298
Human growth is associated with distinct patterns of gene expression in evolutionarily conserved networks. PMID:23941278
ETV4 promotes metastasis in response to activation of PI3-kinase and Ras signaling in a mouse model of advanced prostate cancer. PMID:23918374
Pathprinting: An integrative approach to understand the functional basis of disease. PMID:23890051
TIMP1 overexpression mediates resistance of MCF-7 human breast cancer cells to fulvestrant and down-regulates progesterone receptor expression. PMID:23881388
Analysis of the genomic response of human prostate cancer cells to histone deacetylase inhibitors. PMID:23880963
Genes dysregulated to different extent or oppositely in estrogen receptor-positive and estrogen receptor-negative breast cancers. PMID:23875016
High-throughput miRNA and mRNA sequencing of paired colorectal normal, tumor and metastasis tissues and bioinformatic modeling of miRNA-1 therapeutic applications. PMID:23874421
Predicting and analyzing interactions between Mycobacterium tuberculosis and its human host. PMID:23844013
Integrating pathways of Parkinson's disease in a molecular interaction map. PMID:23832570
BioBin: a bioinformatics tool for automating the binning of rare variants using publicly available biological knowledge. PMID:23819467
A nutrigenomic framework to identify time-resolving responses of hepatic genes in diet-induced obese mice. PMID:23813319
Consensus and conflict cards for metabolic pathway databases. PMID:23803311
Cancer missense mutations alter binding properties of proteins and their interaction networks. PMID:23799087
PosMed: Ranking genes and bioresources based on Semantic Web Association Study. PMID:23761449
Integrative analysis of cancer-related signaling pathways. PMID:23760067
Differential network analysis for the identification of condition-specific pathway activity and regulation. PMID:23749957
Construction of protein phosphorylation networks by data mining, text mining and ontology integration: analysis of the spindle checkpoint. PMID:23749465
Genome Maps, a new generation genome browser. PMID:23748955
Pathview: an R/Bioconductor package for pathway-based data integration and visualization. PMID:23740750
Pathway databases: making chemical and biological sense of the genomic data flood. PMID:23706629
Integrating murine gene expression studies to understand obstructive lung disease due to chronic inhaled endotoxin. PMID:23675439
LipidHome: a database of theoretical lipids optimized for high throughput mass spectrometry lipidomics. PMID:23667450
Candidate gene association studies: a comprehensive guide to useful in silico tools. PMID:23656885
InterMOD: integrated data and tools for the unification of model organism research. PMID:23652793
GeneSetDB: A comprehensive meta-database, statistical and visualisation framework for gene set analysis. PMID:23650583
MicroRNA profiling in lymphocytes and serum of tyrosinemia type-I patients. PMID:23649765
Use of the protein ontology for multi-faceted analysis of biological processes: a case study of the spindle checkpoint. PMID:23637705
The role of structural bioinformatics resources in the era of integrative structural biology. PMID:23633580
Computational solutions for omics data. PMID:23594911
Towards the collaborative curation of the registry underlying Identifiers.org. PMID:23584831
Label-free quantitative proteomics of the lysine acetylome in mitochondria identifies substrates of SIRT3 in metabolic pathways. PMID:23576753
Pharmacogenomics of insulin-like growth factor-I generation during GH treatment in children with GH deficiency or Turner syndrome. PMID:23567489
Insights into the increasing virulence of the swine-origin pandemic H1N1/2009 influenza virus. PMID:23549303
Discovery-2: an interactive resource for the rational selection and comparison of putative drug target proteins in malaria. PMID:23537208
The Enzyme Portal: a case study in applying user-centred design methods in bioinformatics. PMID:23514033
Integration of clinical data with a genome-scale metabolic model of the human adipocyte. PMID:23511207
Systems biology approaches for discovering biomarkers for traumatic brain injury. PMID:23510232
Functional site plasticity in domain superfamilies. PMID:23499848
In silico discovery of mitosis regulation networks associated with early distant metastases in estrogen receptor positive breast cancers. PMID:23470717
Protein complex-based analysis framework for high-throughput data sets. PMID:23443684
Lineage analysis of basal epithelial cells reveals their unexpected plasticity and supports a cell-of-origin model for prostate cancer heterogeneity. PMID:23434823
Comparative transcriptomics of early dipteran development. PMID:23432914
A de novo assembly of the newt transcriptome combined with proteomic validation identifies new protein families expressed during tissue regeneration. PMID:23425577
Using BioBin to explore rare variant population stratification. PMID:23424138
Are predicted protein structures of any value for binding site prediction and virtual ligand screening? PMID:23415854
The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies. PMID:23398680
Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review. PMID:23384594
Whole genome gene expression analysis reveals casiopeína-induced apoptosis pathways. PMID:23382936
Evidence for postinitiation regulation of mRNA biogenesis in tuberculosis. PMID:23378427
Important miRs of pathways in different tumor types. PMID:23358700
Network models of genome-wide association studies uncover the topological centrality of protein interactions in complex diseases. PMID:23355459
CluePedia Cytoscape plugin: pathway insights using integrated experimental and in silico data. PMID:23325622
Subcellular proteomics reveals a role for nucleo-cytoplasmic trafficking at the DNA replication origin activation checkpoint. PMID:23320540
NeuroDNet - an open source platform for constructing and analyzing neurodegenerative disease networks. PMID:23286825
Docking studies and network analyses reveal capacity of compounds from Kandelia rheedii to strengthen cellular immunity by interacting with host proteins during tuberculosis infection. PMID:23275699
Genes involved in host-parasite interactions can be revealed by their correlated expression. PMID:23275547
Identification of HYPK-interacting proteins reveals involvement of HYPK in regulating cell growth, cell cycle, unfolded protein response and cell death. PMID:23272104
Systems biology, bioinformatics, and biomarkers in neuropsychiatry. PMID:23269912
TEAK: topology enrichment analysis framework for detecting activated biological subpathways. PMID:23268448
Time-lapse imaging of neuroblastoma cells to determine cell fate upon gene knockdown. PMID:23251412
Gene family matters: expanding the HGNC resource. PMID:23245209
A network module-based method for identifying cancer prognostic signatures. PMID:23228031
The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013. PMID:23203882
STRING v9.1: protein-protein interaction networks, with increased coverage and integration. PMID:23203871
PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees. PMID:23193289
Systems biology of pathogen-host interaction: networks of protein-protein interaction within pathogens and pathogen-human interactions in the post-genomic era. PMID:23193100
BioGPS and MyGene.info: organizing online, gene-centric information. PMID:23175613
Reconciliation of metabolites and biochemical reactions for metabolic networks. PMID:23172809
Visual analysis of transcriptome data in the context of anatomical structures and biological networks. PMID:23162564
Gene expression analysis of a murine model with pulmonary vascular remodeling compared to end-stage IPAH lungs. PMID:23157700
RNApathwaysDB--a database of RNA maturation and decay pathways. PMID:23155061
The ConsensusPathDB interaction database: 2013 update. PMID:23143270
α-Linolenic acid suppresses cholesterol and triacylglycerol biosynthesis pathway by suppressing SREBP-2, SREBP-1a and -1c expression. PMID:23138267
MODOMICS: a database of RNA modification pathways--2013 update. PMID:23118484
Enzyme informatics. PMID:23116471
Knowledge building insights on biomarkers of arsenic toxicity to keratinocytes and melanocytes. PMID:23115478
Bio-crude transcriptomics: gene discovery and metabolic network reconstruction for the biosynthesis of the terpenome of the hydrocarbon oil-producing green alga, Botryococcus braunii race B (Showa). PMID:23110428
ECMDB: the E. coli Metabolome Database. PMID:23109553
The Comparative Toxicogenomics Database: update 2013. PMID:23093600
TSGene: a web resource for tumor suppressor genes. PMID:23066107
Ten challenges for systems medicine. PMID:23060899
IPAD: the Integrated Pathway Analysis Database for Systematic Enrichment Analysis. PMID:23046449
Coordinating GWAS results with gene expression in a systems immunologic paradigm in autoimmunity. PMID:23040211
Tissue-specific functional networks for prioritizing phenotype and disease genes. PMID:23028291
Reactome - a curated knowledgebase of biological pathways: megakaryocytes and platelets. PMID:22985186
Online tools for bioinformatics analyses in nutrition sciences. PMID:22983844
A Systems Biology Approach to Deciphering the Etiology of Steatosis Employing Patient-Derived Dermal Fibroblasts and iPS Cells. PMID:22969728
Evidence of abundant purifying selection in humans for recently acquired regulatory functions. PMID:22956687
Proteomic analysis of lysine acetylation sites in rat tissues reveals organ specificity and subcellular patterns. PMID:22902405
The Notch signalling system: recent insights into the complexity of a conserved pathway. PMID:22868267
Comparison of methods for competitive tests of pathway analysis. PMID:22859961
Getting personalized cancer genome analysis into the clinic: the challenges in bioinformatics. PMID:22839973
Integrating gene expression and protein-protein interaction network to prioritize cancer-associated genes. PMID:22838965
B-Raf activation cooperates with PTEN loss to drive c-Myc expression in advanced prostate cancer. PMID:22836754
Parasites, proteomes and systems: has Descartes' clock run out of time? PMID:22828391
Dual targeting of the Akt/mTOR signaling pathway inhibits castration-resistant prostate cancer in a genetically engineered mouse model. PMID:22815528
CIDeR: multifactorial interaction networks in human diseases. PMID:22809392
Endosomal crosstalk: meeting points for signaling pathways. PMID:22796207
Combinatorial drug therapy for cancer in the post-genomic era. PMID:22781697
Genomics and bioinformatics of Parkinson's disease. PMID:22762024
Involvement of microRNA families in cancer. PMID:22743268
Fungal genome resources at NCBI. PMID:22737589
Prognostic PET 18F-FDG uptake imaging features are associated with major oncogenomic alterations in patients with resected non-small cell lung cancer. PMID:22710433
DEFOG: discrete enrichment of functionally organized genes. PMID:22706384
Using the reactome database. PMID:22700314
CellBase, a comprehensive collection of RESTful web services for retrieving relevant biological information from heterogeneous sources. PMID:22693220
Inferring the regulatory network behind a gene expression experiment. PMID:22693210
Computational tools for metabolic engineering. PMID:22629572
Evolutionary conservation and network structure characterize genes of phenotypic relevance for mitosis in human. PMID:22577488
Characterization of breast cancer interstitial fluids by TmT labeling, LTQ-Orbitrap Velos mass spectrometry, and pathway analysis. PMID:22563702
Linking proteins to signaling pathways for experiment design and evaluation. PMID:22558382
OREMPdb: a semantic dictionary of computational pathway models. PMID:22536973
A framework for mapping, visualisation and automatic model creation of signal-transduction networks. PMID:22531118
Context-specific protein network miner--an online system for exploring context-specific protein interaction networks from the literature. PMID:22493694
Integrated inference and analysis of regulatory networks from multi-level measurements. PMID:22482944
Personal omics profiling reveals dynamic molecular and medical phenotypes. PMID:22424236
Gene expression profiling of peripheral blood mononuclear cells in the setting of peripheral arterial disease. PMID:22409835
Infection Strategies of Bacterial and Viral Pathogens through Pathogen-Human Protein-Protein Interactions. PMID:22347880
TranscriptomeBrowser 3.0: introducing a new compendium of molecular interactions and a new visualization tool for the study of gene regulatory networks. PMID:22292669
Identification of aberrant pathways and network activities from high-throughput data. PMID:22287794
Large-scale mapping of human protein interactome using structural complexes. PMID:22261719
Network systems biology for targeted cancer therapies. PMID:22176777
Phosphorylation in protein-protein binding: effect on stability and function. PMID:22153503
The 2012 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection. PMID:22144685
Gene expression and pathway analysis of ovarian cancer cells selected for resistance to cisplatin, paclitaxel, or doxorubicin. PMID:22141344
IPAVS: Integrated Pathway Resources, Analysis and Visualization System. PMID:22140115
MMMDB: Mouse Multiple Tissue Metabolome Database. PMID:22139941
AutismKB: an evidence-based knowledgebase of autism genetics. PMID:22139918
MOPED: Model Organism Protein Expression Database. PMID:22139914
hiPathDB: a human-integrated pathway database with facile visualization. PMID:22123737
GeneSigDB: a manually curated database and resource for analysis of gene expression signatures. PMID:22110038
DNAtraffic--a new database for systems biology of DNA dynamics during the cell life. PMID:22110027
WikiPathways: building research communities on biological pathways. PMID:22096230
modMine: flexible access to modENCODE data. PMID:22080565
STITCH 3: zooming in on protein-chemical interactions. PMID:22075997
SuperTarget goes quantitative: update on drug-target interactions. PMID:22067455
Critical amino acid residues in proteins: a BioMart integration of Reactome protein annotations with PRIDE mass spectrometry data and COSMIC somatic mutations. PMID:22025670
BioPAX support in CellDesigner. PMID:22021903
The Reactome BioMart. PMID:22012987
Critical assessment of human metabolic pathway databases: a stepping stone for future integration. PMID:21999653
Systems-biology approaches to discover anti-viral effectors of the human innate immune response. PMID:21994773
The curation paradigm and application tool used for manual curation of the scientific literature at the Comparative Toxicogenomics Database. PMID:21933848
The representation of protein complexes in the Protein Ontology (PRO). PMID:21929785
Minimum information about a bioactive entity (MIABE). PMID:21878981
ppiTrim: constructing non-redundant and up-to-date interactomes. PMID:21873645
Exploring pathway interactions in insulin resistant mouse liver. PMID:21843341
Tutorial videos of bioinformatics resources: online distribution trial in Japan named TogoTV. PMID:21803786
The InterPro BioMart: federated query and web service access to the InterPro Resource. PMID:21785143
Ensembl BioMarts: a hub for data retrieval across taxonomic space. PMID:21785142
Reactome pathway analysis to enrich biological discovery in proteomics data sets. PMID:21751369
Maps of open chromatin guide the functional follow-up of genome-wide association signals: application to hematological traits. PMID:21738486
KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases. PMID:21715386
Multi-institutional prostate cancer study of genetic susceptibility in populations of African descent. PMID:21705483
Published and perished? The influence of the searched protein database on the long-term storage of proteomics data. PMID:21700957
Gene-class analysis of expression patterns induced by psychoactive pharmaceutical exposure in fathead minnow (Pimephales promelas) indicates induction of neuronal systems. PMID:21684349
Unraveling molecular signatures of immunostimulatory adjuvants in the female genital tract through systems biology. PMID:21666746
GLAMM: Genome-Linked Application for Metabolic Maps. PMID:21624891
Data mining using the Catalogue of Somatic Mutations in Cancer BioMart. PMID:21609966
A survey of metabolic databases emphasizing the MetaCyc family. PMID:21523460
The annotation of the asparagine N-linked glycosylation pathway in the Reactome database. PMID:21199820
Reactome: a knowledgebase of biological pathways PubMed citations: 561.

561 articles citing: Reactome: a knowledgebase of biological pathways

Analysis on the desert adaptability of indigenous sheep in the southern edge of Taklimakan Desert. PMID:35851076
Transcriptional regulatory networks of circulating immune cells in type 1 diabetes: A community knowledgebase. PMID:35832893
Computing optimal factories in metabolic networks with negative regulation. PMID:35758789
mirTarRnaSeq: An R/Bioconductor Statistical Package for miRNA-mRNA Target Identification and Interaction Analysis. PMID:35698050
SARS-CoV-2 infection impairs the insulin/IGF signaling pathway in the lung, liver, adipose tissue, and pancreatic cells via IRF1. PMID:35688210
Reprogramming of Plant Central Metabolism in Response to Abiotic Stresses: A Metabolomics View. PMID:35628526
Heuristic shortest hyperpaths in cell signaling hypergraphs. PMID:35619179
Alanine-specific appetite in slow growing chickens is associated with impaired glucose transport and TCA cycle. PMID:35606689
Integrative clustering methods for multi-omics data. PMID:35573155
Enhancing Data Integration, Interoperability, and Reuse to Address Complex and Emerging Environmental Health Problems. PMID:35549252
Individualized pathway activity algorithm identifies oncogenic pathways in pan-cancer analysis. PMID:35487057
Integrative analysis of mutated genes and mutational processes reveals novel mutational biomarkers in colorectal cancer. PMID:35439935
Predicting causal genes from psychiatric genome-wide association studies using high-level etiological knowledge. PMID:35411039
TBGA: a large-scale Gene-Disease Association dataset for Biomedical Relation Extraction. PMID:35361129
Evaluating the predictive accuracy of curated biological pathways in a public knowledgebase. PMID:35348650
Survival analysis of pathway activity as a prognostic determinant in breast cancer. PMID:35344554
Network Preservation Analysis Reveals Dysregulated Synaptic Modules and Regulatory Hubs Shared Between Alzheimer's Disease and Temporal Lobe Epilepsy. PMID:35309145
Pathway Analysis for Cancer Research and Precision Oncology Applications. PMID:35230687
An analysis of genetically regulated gene expression and the role of co-expression networks across 16 psychiatric and substance use phenotypes. PMID:35217801
Unlocking the Memory Component of Alzheimer's Disease: Biological Processes and Pathways across Brain Regions. PMID:35204764
Knowledge-Driven Approaches to Create the MTox700+ Metabolite Panel for Predicting Toxicity. PMID:35094093
Association between Arsenic Level, Gene Expression in Asian Population, and In Vitro Carcinogenic Bladder Tumor. PMID:35039759
NETME: on-the-fly knowledge network construction from biomedical literature. PMID:35013714
COVID-19 Specific Immune Markers Revealed by Single Cell Phenotypic Profiling. PMID:34944610
Gene set analysis with graph embedded kernel association test. PMID:34935928
Analysis of Mutations and Dysregulated Pathways Unravels Carcinogenic Effect and Clinical Actionability of Mutational Processes. PMID:34901014
RDFizing the biosynthetic pathway of E.coli O-antigen to enable semantic sharing of microbiology data. PMID:34809564
Transmission distortion and genetic incompatibilities between alleles in a multigenerational mouse advanced intercross line. PMID:34791189
Short-term treatment with multi-drug regimens combining BRAF/MEK-targeted therapy and immunotherapy results in durable responses in Braf-mutated melanoma. PMID:34777916
Lamellipodin-RICTOR Signaling Mediates Glioblastoma Cell Invasion and Radiosensitivity Downstream of EGFR. PMID:34771501
A linked data graph approach to integration of immunological data. PMID:34707915
MPA_Pathway_Tool: User-Friendly, Automatic Assignment of Microbial Community Data on Metabolic Pathways. PMID:34681649
Global Transcriptome Characterization and Assembly of the Thermophilic Ascomycete Chaetomium thermophilum. PMID:34680944
Comparison of Two Experimental Mouse Dry Eye Models through Inflammatory Gene Set Enrichment Analysis Based on a Multiplexed Transcriptomic Approach. PMID:34639111
A Chinese host genetic study discovered IFNs and causality of laboratory traits on COVID-19 severity. PMID:34608450
Using BioPAX-Parser (BiP) to enrich lists of genes or proteins with pathway data. PMID:34592927
Alternative Splicing Regulation of Low-Frequency Genetic Variants in Exon 2 of TREM2 in Alzheimer's Disease by Splicing-Based Aggregation. PMID:34576031
Molecular Biology Networks and Key Gene Regulators for Inflammatory Biomarkers Shared by Breast Cancer Development: Multi-Omics Systems Analysis. PMID:34572592
A 14-Marker Multiplexed Imaging Panel for Prognostic Biomarkers and Tumor Heterogeneity in Head and Neck Squamous Cell Carcinoma. PMID:34490110
LinkedImm: a linked data graph database for integrating immunological data. PMID:34433410
RNA sequencing and functional studies of patient-derived cells reveal that neurexin-1 and regulators of this pathway are associated with poor outcomes in Ewing sarcoma. PMID:34403115
Adenosine deaminase modulates metabolic remodeling and orchestrates joint destruction in rheumatoid arthritis. PMID:34301999
DIVIS: Integrated and Customizable Pipeline for Cancer Genome Sequencing Analysis and Interpretation. PMID:34168993
WormPaths: Caenorhabditis elegans metabolic pathway annotation and visualization. PMID:34117752
Measuring pathway database coverage of the phosphoproteome. PMID:34113485
DeepOmix: A scalable and interpretable multi-omics deep learning framework and application in cancer survival analysis. PMID:34093987
Skeletal Muscle Gene Expression Profile in Response to Caloric Restriction and Aging: A Role for SirT1. PMID:34063079
PhenCards: a data resource linking human phenotype information to biomedical knowledge. PMID:34034817
Destination Amyotrophic Lateral Sclerosis. PMID:33854469
The transcriptomic responses of Atlantic salmon (Salmo salar) to high temperature stress alone, and in combination with moderate hypoxia. PMID:33845767
Multi-Staged Data-Integrated Multi-Omics Analysis for Symptom Science Research. PMID:33827270
Multi-Omics Data Analysis Uncovers Molecular Networks and Gene Regulators for Metabolic Biomarkers. PMID:33801830
Bayesian network-driven clustering analysis with feature selection for high-dimensional multi-modal molecular data. PMID:33664338
Kmt2c mutations enhance HSC self-renewal capacity and convey a selective advantage after chemotherapy. PMID:33596429
Gene networks and pathways for plasma lipid traits via multitissue multiomics systems analysis. PMID:33561811
Longitudinal saliva omics responses to immune perturbation: a case study. PMID:33436912
Induced organoids derived from patients with ulcerative colitis recapitulate colitic reactivity. PMID:33431859
Identifying the miRNA Signature Association with Aging-Related Senescence in Glioblastoma. PMID:33419230
lncRNA NEAT1 ameliorates LPS‑induced inflammation in MG63 cells by activating autophagy and suppressing the NLRP3 inflammasome. PMID:33416115
WormPaths: Caenorhabditis elegans metabolic pathway annotation and visualization. PMID:33398287
Multi-omics integration in biomedical research - A metabolomics-centric review. PMID:33248648
Plasma Proteome Responses in Salmonid Fish Following Immunization. PMID:33133099
Identification of New Therapeutic Targets for Gastric Cancer With Bioinformatics. PMID:33014013
Influence of species and processing parameters on recovery and content of brain tissue-derived extracellular vesicles. PMID:32944174
Identifying disease-associated signaling pathways through a novel effector gene analysis. PMID:32864216
Single-Cell Analysis of Neonatal HSC Ontogeny Reveals Gradual and Uncoordinated Transcriptional Reprogramming that Begins before Birth. PMID:32822583
Six-Gene Signature Associated with Immune Cells in the Progression of Atherosclerosis Discovered by Comprehensive Bioinformatics Analyses. PMID:32821283
FLUTE: Fast and reliable knowledge retrieval from biomedical literature. PMID:32761077
Impact of vaccine type on HIV-1 vaccine elicited antibody durability and B cell gene signature. PMID:32747654
Large-scale Multi-omic Analysis of COVID-19 Severity. PMID:32743614
Genetic Markers for Later Remission in Response to Early Improvement of Antidepressants. PMID:32664413
Integration of genomics, metagenomics, and metabolomics to identify interplay between susceptibility alleles and microbiota in adenoma initiation. PMID:32600361
Differential methylation and expression of genes in the hypoxia-inducible factor 1 signaling pathway are associated with paclitaxel-induced peripheral neuropathy in breast cancer survivors and with preclinical models of chemotherapy-induced neuropathic pain. PMID:32586194
Revisiting the use of graph centrality models in biological pathway analysis. PMID:32549913
Curation of cancer hallmark-based genes and pathways for in silico characterization of chemical carcinogenesis. PMID:32539087
Nucleic Acid Quantitation with Log-Linear Response Hybridization Probe Sets. PMID:32475109
HyperQuant-A Computational Pipeline for Higher Order Multiplexed Quantitative Proteomics. PMID:32455206
Applying knowledge-driven mechanistic inference to toxicogenomics. PMID:32387679
Transcriptomics in cancer revealed by Positron Emission Tomography radiomics. PMID:32221360
Integrative differential expression and gene set enrichment analysis using summary statistics for scRNA-seq studies. PMID:32221292
Association of functional variants and protein-to-protein physical interactions of human MutY homolog linked with familial adenomatous polyposis and colorectal cancer syndrome. PMID:32072083
Identification of 34 genes conferring genetic and pharmacological risk for the comorbidity of schizophrenia and smoking behaviors. PMID:32012119
Prediction of blood-based biomarkers and subsequent design of bisulfite PCR-LDR-qPCR assay for breast cancer detection. PMID:32005108
A network analysis to identify mediators of germline-driven differences in breast cancer prognosis. PMID:31949161
De novo variants in exomes of congenital heart disease patients identify risk genes and pathways. PMID:31941532
The Cellular Transcriptome in the Maternal Circulation During Normal Pregnancy: A Longitudinal Study. PMID:31921132
Temporal analysis of mRNA expression profiles in Orientia infected C3HeB/FeJ mouse. PMID:31906849
Systems Vaccinology for a Live Attenuated Tularemia Vaccine Reveals Unique Transcriptional Signatures That Predict Humoral and Cellular Immune Responses. PMID:31878161
Terminal neuron localization to the upper cortical plate is controlled by the transcription factor NEUROD2. PMID:31873146
Integrative genomic analysis identified common regulatory networks underlying the correlation between coronary artery disease and plasma lipid levels. PMID:31870308
Competing endogenous network analysis identifies lncRNA Meg3 activates inflammatory damage in UVB induced murine skin lesion by sponging miR-93-5p/epiregulin axis. PMID:31761787
Association of metabolic and genetic heterogeneity in head and neck squamous cell carcinoma with prognostic implications: integration of FDG PET and genomic analysis. PMID:31754877
A single factor dominates the behavior of rhythmic genes in mouse organs. PMID:31747875
Single-Cell RNA Sequencing of Plant-Associated Bacterial Communities. PMID:31736899
Whole-cortex mapping of common genetic influences on depression and a social deficits dimension. PMID:31727881
Graphene quantum dots rescue protein dysregulation of pancreatic β-cells exposed to human islet amyloid polypeptide. PMID:31695851
Measurement of Conditional Relatedness Between Genes Using Fully Convolutional Neural Network. PMID:31695723
PRODIGY: personalized prioritization of driver genes. PMID:31681944
Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma. PMID:31675502
Discovering genetic interactions bridging pathways in genome-wide association studies. PMID:31537791
Signaling pathways and gene co-expression modules associated with cytoskeleton and axon morphology in breast cancer survivors with chronic paclitaxel-induced peripheral neuropathy. PMID:31486345
DNA methylation profiling identifies potentially significant epigenetically-regulated genes in glioblastoma multiforme. PMID:31423235
Moving from Empirical to Rational Vaccine Design in the 'Omics' Era. PMID:31416125
Artificial Intelligence for Drug Toxicity and Safety. PMID:31383376
A gene co-expression network-based analysis of multiple brain tissues reveals novel genes and molecular pathways underlying major depression. PMID:31306407
Predictive Analysis Using Chemical-Gene Interaction Networks Consistent with Observed Endocrine Activity and Mutagenicity of U.S. Streams. PMID:31287672
Human Systems Biology and Metabolic Modelling: A Review-From Disease Metabolism to Precision Medicine. PMID:31281846
IAMBEE: a web-service for the identification of adaptive pathways from parallel evolved clonal populations. PMID:31127271
Plasticity of intestinal gene expression profile signatures reflected by nutritional interventions in piglets. PMID:31122193
GREIN: An Interactive Web Platform for Re-analyzing GEO RNA-seq Data. PMID:31110304
MOSClip: multi-omic and survival pathway analysis for the identification of survival associated gene and modules. PMID:31049575
The TP53 Apoptotic Network Is a Primary Mediator of Resistance to BCL2 Inhibition in AML Cells. PMID:31048320
Systems biology in inflammatory bowel diseases: on the way to precision medicine. PMID:31040620
Transcriptional changes in response to ketamine ester-analogs SN 35210 and SN 35563 in the rat brain. PMID:30971208
Integrative Genomics Analysis Unravels Tissue-Specific Pathways, Networks, and Key Regulators of Blood Pressure Regulation. PMID:30931314
FAIRness and Usability for Open-access Omics Data Systems. PMID:30815061
Functional Heatmap: an automated and interactive pattern recognition tool to integrate time with multi-omics assays. PMID:30770734
Consistency, Inconsistency, and Ambiguity of Metabolite Names in Biochemical Databases Used for Genome-Scale Metabolic Modelling. PMID:30736318
GLIS Rearrangement is a Genomic Hallmark of Hyalinizing Trabecular Tumor of the Thyroid Gland. PMID:30648929
Multi-omics integration reveals molecular networks and regulators of psoriasis. PMID:30642337
RNA sequencing identifies common pathways between cigarette smoke exposure and replicative senescence in human airway epithelia. PMID:30626320
Plasma Protein Biomarkers for the Prediction of CSF Amyloid and Tau and [18F]-Flutemetamol PET Scan Result. PMID:30618716
AS03-Adjuvanted H5N1 Avian Influenza Vaccine Modulates Early Innate Immune Signatures in Human Peripheral Blood Mononuclear Cells. PMID:30566602
Let it RE:IN: integrating experimental observations to predict pluripotency network behaviour. PMID:30545825
Variant information systems for precision oncology. PMID:30463544
Strategies for Pathway Analysis Using GWAS and WGS Data. PMID:30387919
Complex Portal 2018: extended content and enhanced visualization tools for macromolecular complexes. PMID:30357405
A novel pathway analysis approach based on the unexplained disregulation of genes. PMID:30337764
In Search of Biomarkers for Pathogenesis and Control of Leishmaniasis by Global Analyses of Leishmania-Infected Macrophages. PMID:30283744
Pathogenic variants in glutamyl-tRNAGln amidotransferase subunits cause a lethal mitochondrial cardiomyopathy disorder. PMID:30283131
Identification of key pathways and genes in lung carcinogenesis. PMID:30250533
Alpha kinase 1 controls intestinal inflammation by suppressing the IL-12/Th1 axis. PMID:30228258
Using Supervised Learning Methods for Gene Selection in RNA-Seq Case-Control Studies. PMID:30123241
Identification of pathways and genes associated with cerebral palsy. PMID:30109564
Integrative analysis of the inter-tumoral heterogeneity of triple-negative breast cancer. PMID:30087365
Manzamine A Exerts Anticancer Activity against Human Colorectal Cancer Cells. PMID:30060617
An integrative approach to develop computational pipeline for drug-target interaction network analysis. PMID:29980766
Identification of Antifungal Targets Based on Computer Modeling. PMID:29973534
Association analyses of more than 140,000 men identify 63 new prostate cancer susceptibility loci. PMID:29892016
Using Regularization to Infer Cell Line Specificity in Logical Network Models of Signaling Pathways. PMID:29872402
p53 Mediates Vast Gene Expression Changes That Contribute to Poor Chemotherapeutic Response in a Mouse Model of Breast Cancer. PMID:29852458
Abnormally high expression of POLD1, MCM2, and PLK4 promotes relapse of acute lymphoblastic leukemia. PMID:29768346
Navigating the disease landscape: knowledge representations for contextualizing molecular signatures. PMID:29684165
IRS2 mutations linked to invasion in pleomorphic invasive lobular carcinoma. PMID:29669935
Transcriptome-wide discovery of coding and noncoding RNA-binding proteins. PMID:29636419
Oncogenic Signaling Pathways in The Cancer Genome Atlas. PMID:29625050
Systematic Evaluation of Molecular Networks for Discovery of Disease Genes. PMID:29605183
Integrative analysis of imaging and transcriptomic data of the immune landscape associated with tumor metabolism in lung adenocarcinoma: Clinical and prognostic implications. PMID:29556367
BIOPYDB: A Dynamic Human Cell Specific Biochemical Pathway Database with Advanced Computational Analyses Platform. PMID:29547394
A graphical and computational modeling platform for biological pathways. PMID:29543794
SMILE: a novel procedure for subcellular module identification with localisation expansion. PMID:29533218
Identification of a gene expression signature predicting survival in oral cavity squamous cell carcinoma using Monte Carlo cross validation. PMID:29496061
Systematic target function annotation of human transcription factors. PMID:29325558
Boolean network modeling in systems pharmacology. PMID:29307099
The node-weighted Steiner tree approach to identify elements of cancer-related signaling pathways. PMID:29297291
Coxsackievirus-Induced Proteomic Alterations in Primary Human Islets Provide Insights for the Etiology of Diabetes. PMID:29264452
Evaluation of epidermal growth factor receptor signaling effects in gastric cancer cell lines by detailed motility-focused phenotypic characterization linked with molecular analysis. PMID:29237412
Functional network community detection can disaggregate and filter multiple underlying pathways in enrichment analyses. PMID:29218878
Differential prioritization of therapies to subtypes of triple negative breast cancer using a systems medicine method. PMID:29190967
Computational systems biology approaches for Parkinson's disease. PMID:29185073
Statistical Contributions to Bioinformatics: Design, Modeling, Structure Learning, and Integration. PMID:29129969
Urinary peptidomics analysis reveals proteases involved in diabetic nephropathy. PMID:29123184
Association analysis identifies 65 new breast cancer risk loci. PMID:29059683
Inferring gene and protein interactions using PubMed citations and consensus Bayesian networks. PMID:29049295
Post-Processing Partitions to Identify Domains of Modularity Optimization. PMID:29046743
Non-canonical reader modules of BAZ1A promote recovery from DNA damage. PMID:29021563
A novel network analysis approach reveals DNA damage, oxidative stress and calcium/cAMP homeostasis-associated biomarkers in frontotemporal dementia. PMID:29020091
The Encyclopedia of Proteome Dynamics: a big data ecosystem for (prote)omics. PMID:28981707
Pathway-based discovery of genetic interactions in breast cancer. PMID:28957314
Pathway and network-based analysis of genome-wide association studies and RT-PCR validation in polycystic ovary syndrome. PMID:28949383
Protein-Protein Interactions in Virus-Host Systems. PMID:28861068
Thirty Minutes of Hypobaric Hypoxia Provokes Alterations of Immune Response, Haemostasis, and Metabolism Proteins in Human Serum. PMID:28858246
ePlant: Visualizing and Exploring Multiple Levels of Data for Hypothesis Generation in Plant Biology. PMID:28808136
Mitotic Vulnerability in Triple-Negative Breast Cancer Associated with LIN9 Is Targetable with BET Inhibitors. PMID:28807940
Defining the biological basis of radiomic phenotypes in lung cancer. PMID:28731408
Two microRNA signatures for malignancy and immune infiltration predict overall survival in advanced epithelial ovarian cancer. PMID:28716985
Differential regulation of miRNA and mRNA expression in the myocardium of Nrf2 knockout mice. PMID:28673258
Functional dissection of human targets for KSHV-encoded miRNAs using network analysis. PMID:28600495
Genetic wiring maps of single-cell protein states reveal an off-switch for GPCR signalling. PMID:28562590
Gene Set Enrichment Analyses: lessons learned from the heart failure phenotype. PMID:28559929
Annotating function to differentially expressed LincRNAs in myelodysplastic syndrome using a network-based method. PMID:28472271
Improving data workflow systems with cloud services and use of open data for bioinformatics research. PMID:28419324
Integrated network analysis reveals potentially novel molecular mechanisms and therapeutic targets of refractory epilepsies. PMID:28388656
Transcriptome analysis of endometrial tissues following GnRH agonist treatment in a mouse adenomyosis model. PMID:28331289
Network reconstruction of the mouse secretory pathway applied on CHO cell transcriptome data. PMID:28298216
NFP: An R Package for Characterizing and Comparing of Annotated Biological Networks. PMID:28280740
Pathway Cross-Talk Analysis in Detecting Significant Pathways in Barrett's Esophagus Patients. PMID:28263955
Estimation of Directed Acyclic Graphs Through Two-stage Adaptive Lasso for Gene Network Inference. PMID:28239216
An approach to infer putative disease-specific mechanisms using neighboring gene networks. PMID:28200075
Annotating Mutational Effects on Proteins and Protein Interactions: Designing Novel and Revisiting Existing Protocols. PMID:28188534
Var2GO: a web-based tool for gene variants selection. PMID:28185576
The PeptideAtlas of the Domestic Laying Hen. PMID:28166638
Prioritizing biological pathways by recognizing context in time-series gene expression data. PMID:28155707
A network-based pathway-expanding approach for pathway analysis. PMID:28155638
Meta-analytic support vector machine for integrating multiple omics data. PMID:28149325
Cell-Based Systems Biology Analysis of Human AS03-Adjuvanted H5N1 Avian Influenza Vaccine Responses: A Phase I Randomized Controlled Trial. PMID:28099485
Global open data management in metabolomics. PMID:28092796
Is the average shortest path length of gene set a reflection of their biological relatedness? PMID:28073302
Microarray analysis of differentially-expressed genes and linker genes associated with the molecular mechanism of colorectal cancer. PMID:27899990
Time-course microarray analysis for identifying candidate genes involved in obesity-associated pathological changes in the mouse colon. PMID:27895803
Biomolecular Network-Based Synergistic Drug Combination Discovery. PMID:27891522
MinePath: Mining for Phenotype Differential Sub-paths in Molecular Pathways. PMID:27832067
Impact of neonatal iron deficiency on hippocampal DNA methylation and gene transcription in a porcine biomedical model of cognitive development. PMID:27809765
Systems biology analysis reveals role of MDM2 in diabetic nephropathy. PMID:27777973
The promises of quantitative systems pharmacology modelling for drug development. PMID:27761201
ApoptomiRs of Breast Cancer: Basics to Clinics. PMID:27746811
Self-Contained Statistical Analysis of Gene Sets. PMID:27711232
Subpathway-CorSP: Identification of metabolic subpathways via integrating expression correlations and topological features between metabolites and genes of interest within pathways. PMID:27625019
VEGF-A/VEGFR2 signaling network in endothelial cells relevant to angiogenesis. PMID:27619687
Combination therapy with BPTES nanoparticles and metformin targets the metabolic heterogeneity of pancreatic cancer. PMID:27559084
Modelling the Structure and Dynamics of Biological Pathways. PMID:27509052
Pathway-Informed Classification System (PICS) for Cancer Analysis Using Gene Expression Data. PMID:27486299
Parallel or convergent evolution in human population genomic data revealed by genotype networks. PMID:27484992
Deep genome sequencing and variation analysis of 13 inbred mouse strains defines candidate phenotypic alleles, private variation and homozygous truncating mutations. PMID:27480531
Gene-Disease Interaction Retrieval from Multiple Sources: A Network Based Method. PMID:27478829
The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. PMID:27374120
Integrative analysis of cancer genes in a functional interactome. PMID:27356765
Comprehensive analysis of high-throughput screens with HiTSeekR. PMID:27330136
Integrated gene set analysis for microRNA studies. PMID:27324197
Post hoc Analysis for Detecting Individual Rare Variant Risk Associations Using Probit Regression Bayesian Variable Selection Methods in Case-Control Sequencing Studies. PMID:27312771
Qualitative dynamics semantics for SBGN process description. PMID:27306057
SPATIAL: A System-level PAThway Impact AnaLysis approach. PMID:27193997
Successful establishment of patient-derived tumor xenografts from gastrointestinal stromal tumor-a single center experience. PMID:27186422
Network-driven plasma proteomics expose molecular changes in the Alzheimer's brain. PMID:27112350
A Network of Splice Isoforms for the Mouse. PMID:27079421
Evidence for embryonic stem-like signature and epithelial-mesenchymal transition features in the spheroid cells derived from lung adenocarcinoma. PMID:27048287
Characterization of visceral and subcutaneous adipose tissue transcriptome in pregnant women with and without spontaneous labor at term: implication of alternative splicing in the metabolic adaptations of adipose tissue to parturition. PMID:26994472
Transcriptional profiling of dendritic cells matured in different osmolarities. PMID:26981363
E2F7 regulates transcription and maturation of multiple microRNAs to restrain cell proliferation. PMID:26961310
Protein functional analysis data in support of comparative proteomics of the pathogenic black yeast Exophiala dermatitidis under different temperature conditions. PMID:26958594
TransOmic analysis of forebrain sections in Sp2 conditional knockout embryonic mice using IR-MALDESI imaging of lipids and LC-MS/MS label-free proteomics. PMID:26942738
Genetic overlap between multiple sclerosis and several cardiovascular disease risk factors. PMID:26920376
Novel loci and pathways significantly associated with longevity. PMID:26912274
The "Majority Illusion" in Social Networks. PMID:26886112
Estimation of sparse directed acyclic graphs for multivariate counts data. PMID:26849781
SEPARATING THE CAUSES AND CONSEQUENCES IN DISEASE TRANSCRIPTOME. PMID:26776202
Transcriptional profiling revealed the anti-proliferative effect of MFN2 deficiency and identified risk factors in lung adenocarcinoma. PMID:26733181
Multi-label multi-instance transfer learning for simultaneous reconstruction and cross-talk modeling of multiple human signaling pathways. PMID:26718335
Exome-wide association analysis reveals novel coding sequence variants associated with lipid traits in Chinese. PMID:26690388
CARFMAP: A Curated Pathway Map of Cardiac Fibroblasts. PMID:26673252
1α,25-Dihydroxyvitamin D3 Regulates Mitochondrial Oxygen Consumption and Dynamics in Human Skeletal Muscle Cells. PMID:26601949
A comparison of human and mouse gene co-expression networks reveals conservation and divergence at the tissue, pathway and disease levels. PMID:26589719
Improved detection of disease-associated variation by sex-specific characterization and prediction of genes required for fertility. PMID:26473511
Estimating cumulative pathway effects on risk for age-related macular degeneration using mixed linear models. PMID:26467978
Virtual pathway explorer (viPEr) and pathway enrichment analysis tool (PEANuT): creating and analyzing focus networks to identify cross-talk between molecules and pathways. PMID:26467653
Diversity in Compartmental Dynamics of Gene Regulatory Networks: The Immune Response in Primary Influenza A Infection in Mice. PMID:26413862
PathwaysWeb: a gene pathways API with directional interactions, expanded gene ontology, and versioning. PMID:26400039
The PFP and ESG protein function prediction methods in 2014: effect of database updates and ensemble approaches. PMID:26380077
Identification of Gene-Expression Signatures and Protein Markers for Breast Cancer Grading and Staging. PMID:26375396
Extended LineSets: a visualization technique for the interactive inspection of biological pathways. PMID:26361500
A legion of potential regulatory sRNAs exists beyond the typical microRNAs microcosm. PMID:26354861
RNA sequencing provides exquisite insight into the manipulation of the alveolar macrophage by tubercle bacilli. PMID:26346536
Cross-tissue and cross-species analysis of gene expression in skeletal muscle and electric organ of African weakly-electric fish (Teleostei; Mormyridae). PMID:26335922
An integrated network platform for contextual prioritization of drugs and pathways. PMID:26315485
Network Modules of the Cross-Species Genotype-Phenotype Map Reflect the Clinical Severity of Human Diseases. PMID:26301634
MESSI: metabolic engineering target selection and best strain identification tool. PMID:26255308
Algorithms for modeling global and context-specific functional relationship networks. PMID:26254431
Evidence of perturbations of the cytokine network in preterm labor. PMID:26232508
Knowledge transfer via classification rules using functional mapping for integrative modeling of gene expression data. PMID:26202217
Time-course gene profiling and networks in demethylated retinoblastoma cell line. PMID:26143641
Using prior knowledge from cellular pathways and molecular networks for diagnostic specimen classification. PMID:26141830
Transcriptional response of Atlantic salmon families to Piscirickettsia salmonis infection highlights the relevance of the iron-deprivation defence system. PMID:26141111
NET-GE: a novel NETwork-based Gene Enrichment for detecting biological processes associated to Mendelian diseases. PMID:26110971
A random forest approach to capture genetic effects in the presence of population structure. PMID:26109276
An integrated approach to reveal miRNAs' impacts on the functional consequence of copy number alterations in cancer. PMID:26099552
Examination of Epigenetic and other Molecular Factors Associated with mda-9/Syntenin Dysregulation in Cancer Through Integrated Analyses of Public Genomic Datasets. PMID:26093898
Tools for visualization and analysis of molecular networks, pathways, and -omics data. PMID:26082651
Discrete Logic Modelling Optimization to Contextualize Prior Knowledge Networks Using PRUNET. PMID:26058016
Temporal gene expression profiling of the rat knee joint capsule during immobilization-induced joint contractures. PMID:26006773
Pan-phylum Comparison of Nematode Metabolic Potential. PMID:26000881
Dissection of the style's response to pollination using transcriptome profiling in self-compatible (Solanum pimpinellifolium) and self-incompatible (Solanum chilense) tomato species. PMID:25976872
ClustVis: a web tool for visualizing clustering of multivariate data using Principal Component Analysis and heatmap. PMID:25969447
Analysis of Cynandione A's Anti-Ischemic Stroke Effects from Pathways and Protein-Protein Interactome. PMID:25955557
Multiset Statistics for Gene Set Analysis. PMID:25914887
Personal genomes, quantitative dynamic omics and personalized medicine. PMID:25798291
YPED: an integrated bioinformatics suite and database for mass spectrometry-based proteomics research. PMID:25712262
Protein complex discovery by interaction filtering from protein interaction networks using mutual rank coexpression and sequence similarity. PMID:25692131
Comparison of human cell signaling pathway databases--evolution, drawbacks and challenges. PMID:25632107
Network analysis of gene expression in peripheral blood identifies mTOR and NF-κB pathways involved in antipsychotic-induced extrapyramidal symptoms. PMID:25623440
Amyloid precursor protein interaction network in human testis: sentinel proteins for male reproduction. PMID:25591988
Assessment of subnetwork detection methods for breast cancer. PMID:25520555
PROGgeneV2: enhancements on the existing database. PMID:25518851
Pathway activity inference for multiclass disease classification through a mathematical programming optimisation framework. PMID:25475756
The COPD Knowledge Base: enabling data analysis and computational simulation in translational COPD research. PMID:25471253
A set-based association test identifies sex-specific gene sets associated with type 2 diabetes. PMID:25429300
Text mining in cancer gene and pathway prioritization. PMID:25392685
17β-estradiol modulates gene expression in the female mouse cerebral cortex. PMID:25372139
MitProNet: A knowledgebase and analysis platform of proteome, interactome and diseases for mammalian mitochondria. PMID:25347823
Network-based analysis of comorbidities risk during an infection: SARS and HIV case studies. PMID:25344230
Large-scale integration of small molecule-induced genome-wide transcriptional responses, Kinome-wide binding affinities and cell-growth inhibition profiles reveal global trends characterizing systems-level drug action. PMID:25324859
Systematic identification of transcriptional and post-transcriptional regulations in human respiratory epithelial cells during influenza A virus infection. PMID:25281301
Biological network exploration with Cytoscape 3. PMID:25199793
Inter-species pathway perturbation prediction via data-driven detection of functional homology. PMID:25150249
SPARQLGraph: a web-based platform for graphically querying biological Semantic Web databases. PMID:25127889
Global transcriptome-wide analysis of CIK cells identify distinct roles of IL-2 and IL-15 in acquisition of cytotoxic capacity against tumor. PMID:25108500
Identification of a novel luminal molecular subtype of breast cancer. PMID:25076125
MPINet: metabolite pathway identification via coupling of global metabolite network structure and metabolomic profile. PMID:25057481
Bioinformatic prediction of WSSV-host protein-protein interaction. PMID:24982879
IIS--Integrated Interactome System: a web-based platform for the annotation, analysis and visualization of protein-metabolite-gene-drug interactions by integrating a variety of data sources and tools. PMID:24949626
LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures. PMID:24906883
Wiring miRNAs to pathways: a topological approach to integrate miRNA and mRNA expression profiles. PMID:24803669
Clinical proteomic biomarkers: relevant issues on study design & technical considerations in biomarker development. PMID:24679154
Plant systems biology: insights, advances and challenges. PMID:24671625
Resources for functional genomics studies in Drosophila melanogaster. PMID:24653003
Detection of 1α,25-dihydroxyvitamin D-regulated miRNAs in zebrafish by whole transcriptome sequencing. PMID:24650217
Immunomic, genomic and transcriptomic characterization of CT26 colorectal carcinoma. PMID:24621249
Thematic series on biomedical ontologies in JBMS: challenges and new directions. PMID:24602198
Navigating the multilayered organization of eukaryotic signaling: a new trend in data integration. PMID:24550716
Review of biological network data and its applications. PMID:24465231
A primer for disease gene prioritization using next-generation sequencing data. PMID:24465230
Genetic interaction networks: better understand to better predict. PMID:24381582
Gene-gene interaction network analysis of ovarian cancer using TCGA data. PMID:24314048
Towards pathway curation through literature mining--a case study using PharmGKB. PMID:24297561
Systems biology approach to the dissection of the complexity of regulatory networks in the S. scrofa cardiocirculatory system. PMID:24284405
A comparison of gene set analysis methods in terms of sensitivity, prioritization and specificity. PMID:24260172
Integrating in silico resources to map a signaling network. PMID:24233784
Annotating cancer variants and anti-cancer therapeutics in reactome. PMID:24213504
Proteomic changes during B cell maturation: 2D-DIGE approach. PMID:24205016
Path2Models: large-scale generation of computational models from biochemical pathway maps. PMID:24180668
High-throughput RNA interference screens integrative analysis: Towards a comprehensive understanding of the virus-host interplay. PMID:24175227
Alterations of immune response of Non-Small Cell Lung Cancer with Azacytidine. PMID:24162015
Methods and approaches in the topology-based analysis of biological pathways. PMID:24133454
NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps. PMID:24099179
Selective anticancer agents suppress aging in Drosophila. PMID:24096697
Peripheral blood mononuclear cell gene expression profiles predict poor outcome in idiopathic pulmonary fibrosis. PMID:24089408
A comprehensive map of the influenza A virus replication cycle. PMID:24088197
Detecting and removing inconsistencies between experimental data and signaling network topologies using integer linear programming on interaction graphs. PMID:24039561
An online model composition tool for system biology models. PMID:24006914
Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE). PMID:23986566
A systematic analysis of host factors reveals a Med23-interferon-λ regulatory axis against herpes simplex virus type 1 replication. PMID:23950709
An integrative characterization of recurrent molecular aberrations in glioblastoma genomes. PMID:23907387
Module-based breast cancer classification. PMID:23819260
Modeling approaches for qualitative and semi-quantitative analysis of cellular signaling networks. PMID:23803171
The UCSC Interaction Browser: multidimensional data views in pathway context. PMID:23748957
Proteome-wide discovery of mislocated proteins in cancer. PMID:23674306
INCORPORATING BIOLOGICAL INFORMATION INTO LINEAR MODELS: A BAYESIAN APPROACH TO THE SELECTION OF PATHWAYS AND GENES. PMID:23667412
Platelet aggregation pathway network-based approach for evaluating compounds efficacy. PMID:23662134
Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. PMID:23586463
An integrated approach to uncover driver genes in breast cancer methylation genomes. PMID:23579546
Biographer: web-based editing and rendering of SBGN compliant biochemical networks. PMID:23574737
Differential expression analysis for pathways. PMID:23516350
Interpretation of genomic variants using a unified biological network approach. PMID:23505346
BiNoM 2.0, a Cytoscape plugin for accessing and analyzing pathways using standard systems biology formats. PMID:23453054
Functional-network-based gene set analysis using gene-ontology. PMID:23418449
Increased expression of endoplasmic reticulum stress and unfolded protein response genes in peripheral blood mononuclear cells from patients with limited cutaneous systemic sclerosis and pulmonary arterial hypertension. PMID:23400395
Evidence for postinitiation regulation of mRNA biogenesis in tuberculosis. PMID:23378427
Visualizing multidimensional cancer genomics data. PMID:23363777
SignaLink 2 - a signaling pathway resource with multi-layered regulatory networks. PMID:23331499
Mining disease fingerprints from within genetic pathways. PMID:23304411
Functional characterization of motif sequences under purifying selection. PMID:23303791
Chapter 3: Small molecules and disease. PMID:23300405
Pathway correlation profile of gene-gene co-expression for identifying pathway perturbation. PMID:23284898
A vertex similarity-based framework to discover and rank orphan disease-related genes. PMID:23281592
Non Linear Programming (NLP) formulation for quantitative modeling of protein signal transduction pathways. PMID:23226239
Pathway Distiller - multisource biological pathway consolidation. PMID:23134636
CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms. PMID:23079107
MetNet Online: a novel integrated resource for plant systems biology. PMID:23066841
Annotate-it: a Swiss-knife approach to annotation, analysis and interpretation of single nucleotide variation in human disease. PMID:23013645
EnrichNet: network-based gene set enrichment analysis. PMID:22962466
A chain reaction approach to modelling gene pathways. PMID:22943042
Role of aldo-keto reductases and other doxorubicin pharmacokinetic genes in doxorubicin resistance, DNA binding, and subcellular localization. PMID:22938713
Genome-wide association study identifies eight new risk loci for polycystic ovary syndrome. PMID:22885925
The glucose-deprivation network counteracts lapatinib-induced toxicity in resistant ErbB2-positive breast cancer cells. PMID:22864381
Embryonic stem cell interactomics: the beginning of a long road to biological function. PMID:22847281
State of the art in silico tools for the study of signaling pathways in cancer. PMID:22837650
Subnetwork-based analysis of chronic lymphocytic leukemia identifies pathways that associate with disease progression. PMID:22837534
A text-mining system for extracting metabolic reactions from full-text articles. PMID:22823282
Whole transcriptome RNA-Seq analysis of breast cancer recurrence risk using formalin-fixed paraffin-embedded tumor tissue. PMID:22808097
Differentially co-expressed interacting protein pairs discriminate samples under distinct stages of HIV type 1 infection. PMID:22784566
MuSiC: identifying mutational significance in cancer genomes. PMID:22759861
Research resource: whole transcriptome RNA sequencing detects multiple 1α,25-dihydroxyvitamin D(3)-sensitive metabolic pathways in developing zebrafish. PMID:22734042
Integrating literature-constrained and data-driven inference of signalling networks. PMID:22734019
NetWalker: a contextual network analysis tool for functional genomics. PMID:22732065
Public domain databases for medicinal chemistry. PMID:22731701
Down-weighting overlapping genes improves gene set analysis. PMID:22713124
WikiCell: a unified resource platform for human transcriptomics research. PMID:22702248
Transcriptional profiling of human brain endothelial cells reveals key properties crucial for predictive in vitro blood-brain barrier models. PMID:22675443
NF-E2-related factor 1 (Nrf1) serves as a novel regulator of hepatic lipid metabolism through regulation of the Lipin1 and PGC-1β genes. PMID:22586274
THINK Back: KNowledge-based Interpretation of High Throughput data. PMID:22536867
Functional organization and its implication in evolution of the human protein-protein interaction network. PMID:22530615
Genome-wide gene expression analysis implicates the immune response and lymphangiogenesis in the pathogenesis of fetal chylothorax. PMID:22529953
Network-based functional enrichment. PMID:22479706
Exploring and challenging the network of angiogenesis. PMID:22355580
A systemic network triggered by human cytomegalovirus entry. PMID:22312338
When one and one gives more than two: challenges and opportunities of integrative omics. PMID:22303399
Recovering protein-protein and domain-domain interactions from aggregation of IP-MS proteomics of coregulator complexes. PMID:22219718
Modeling community-wide molecular networks of multicellular systems. PMID:22210865
Network systems biology for targeted cancer therapies. PMID:22176777
PathVar: analysis of gene and protein expression variance in cellular pathways using microarray data. PMID:22123829
YMDB: the Yeast Metabolome Database. PMID:22064855
Deciphering causal and statistical relations of molecular aberrations and gene expressions in NCI-60 cell lines. PMID:22051105
Software for systems biology: from tools to integrated platforms. PMID:22048662
The Reactome BioMart. PMID:22012987
Network-based prediction and analysis of HIV dependency factors. PMID:21966263
Multi-membership gene regulation in pathway based microarray analysis. PMID:21939531
Application of computational systems biology to explore environmental toxicity hazards. PMID:21846611
The contrasting roles of PPARδ and PPARγ in regulating the metabolic switch between oxidation and storage of fats in white adipose tissue. PMID:21843327
Transcriptional gene network inference from a massive dataset elucidates transcriptome organization and gene function. PMID:21785136
Reactome pathway analysis to enrich biological discovery in proteomics data sets. PMID:21751369
Simulating quantitative cellular responses using asynchronous threshold Boolean network ensembles. PMID:21745399
An organogenesis network-based comparative transcriptome analysis for understanding early human development in vivo and in vitro. PMID:21733158
The orphan disease networks. PMID:21664998
Web-based metabolic network visualization with a zooming user interface. PMID:21595965
Signalogs: orthology-based identification of novel signaling pathway components in three metazoans. PMID:21559328
Signaling gateway molecule pages--a data model perspective. PMID:21505029
PathScan: a tool for discerning mutational significance in groups of putative cancer genes. PMID:21498403
Consensus-phenotype integration of transcriptomic and metabolomic data implies a role for metabolism in the chemosensitivity of tumour cells. PMID:21483477
The Rat Genome Database pathway portal. PMID:21478484
The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods. PMID:21472436
A network-based multi-target computational estimation scheme for anticoagulant activities of compounds. PMID:21445339
Supervised learning and prediction of physical interactions between human and HIV proteins. PMID:21382517
Identification of differential protein interactors of lamin A and progerin. PMID:21327095
Landscape mapping of functional proteins in insulin signal transduction and insulin resistance: a network-based protein-protein interaction analysis. PMID:21305025
SIDEKICK: Genomic data driven analysis and decision-making framework. PMID:21192813
Extending pathways and processes using molecular interaction networks to analyse cancer genome data. PMID:21144022
A comparative study of cancer proteins in the human protein-protein interaction network. PMID:21143787
GOAPhAR: An Integrative Discovery Tool for Annotation, Pathway Analysis. PMID:21132056
Enrichment map: a network-based method for gene-set enrichment visualization and interpretation. PMID:21085593
Multi-level reproducibility of signature hubs in human interactome for breast cancer metastasis. PMID:21059271
A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity. PMID:20953172
The early whole-blood transcriptional signature of dengue virus and features associated with progression to dengue shock syndrome in Vietnamese children and young adults. PMID:20943967
Gene regulatory network reveals oxidative stress as the underlying molecular mechanism of type 2 diabetes and hypertension. PMID:20942928
ChemProt: a disease chemical biology database. PMID:20935044
The G protein-coupled receptor T-cell death-associated gene 8 (TDAG8) facilitates tumor development by serving as an extracellular pH sensor. PMID:20855608
Investigating the validity of current network analysis on static conglomerate networks by protein network stratification. PMID:20846443
The BioPAX community standard for pathway data sharing. PMID:20829833
Viral organization of human proteins. PMID:20827298
Consistency, comprehensiveness, and compatibility of pathway databases. PMID:20819233
The human-bacterial pathogen protein interaction networks of Bacillus anthracis, Francisella tularensis, and Yersinia pestis. PMID:20711500
A genome-wide siRNA screen reveals multiple mTORC1 independent signaling pathways regulating autophagy under normal nutritional conditions. PMID:20627085
Somatic polyploidy promotes cell function under stress and energy depletion: evidence from tissue-specific mammal transcriptome. PMID:20625914
Flexible network reconstruction from relational databases with Cytoscape and CytoSQL. PMID:20594316
Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM. PMID:20529912
A systems biology approach to dissection of the effects of small bicyclic peptidomimetics on a panel of saccharomyces cerevisiae mutants. PMID:20501664
Functional features, biological pathways, and protein interaction networks of addiction-related genes. PMID:20491072
The mEPN scheme: an intuitive and flexible graphical system for rendering biological pathways. PMID:20478018
Networks inferred from biochemical data reveal profound differences in toll-like receptor and inflammatory signaling between normal and transformed hepatocytes. PMID:20460255
BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions. PMID:20426874
Reconstruction of gene regulatory modules in cancer cell cycle by multi-source data integration. PMID:20422009
Different sets of QTLs influence fitness variation in yeast. PMID:20160707
Genome-wide RNAi screen identifies human host factors crucial for influenza virus replication. PMID:20081832
NetPath: a public resource of curated signal transduction pathways. PMID:20067622
Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology. PMID:19955237
SMPDB: The Small Molecule Pathway Database. PMID:19948758
STITCH 2: an interaction network database for small molecules and proteins. PMID:19897548
Elucidation of functional consequences of signalling pathway interactions. PMID:19895694
Evolution of biomolecular networks: lessons from metabolic and protein interactions. PMID:19851337
Towards a systems biology approach to mammalian cell cycle: modeling the entrance into S phase of quiescent fibroblasts after serum stimulation. PMID:19828076
An integrated systems analysis implicates EGR1 downregulation in simian immunodeficiency virus encephalitis-induced neural dysfunction. PMID:19812322
Discovering cancer genes by integrating network and functional properties. PMID:19765316
MouseCyc: a curated biochemical pathways database for the laboratory mouse. PMID:19682380
Pathway databases and tools for their exploitation: benefits, current limitations and challenges. PMID:19638971
PANTHER pathway: an ontology-based pathway database coupled with data analysis tools. PMID:19597783
Word-based characterization of promoters involved in human DNA repair pathways. PMID:19594877
Pirfenidone is renoprotective in diabetic kidney disease. PMID:19578007
Inferring novel disease indications for known drugs by semantically linking drug action and disease mechanism relationships. PMID:19426461
Database resources in metabolomics: an overview. PMID:19418229
Rich can get poor: conversion of hub to non-hub proteins. PMID:19399641
The transferome of metabolic genes explored: analysis of the horizontal transfer of enzyme encoding genes in unicellular eukaryotes. PMID:19368726
Comparison of automated candidate gene prediction systems using genes implicated in type 2 diabetes by genome-wide association studies. PMID:19208173
A factor graph nested effects model to identify networks from genetic perturbations. PMID:19180177
Network integration and graph analysis in mammalian molecular systems biology. PMID:19045817
A survey of visualization tools for biological network analysis. PMID:19040716
A novel signaling pathway impact analysis. PMID:18990722
UniHI 4: new tools for query, analysis and visualization of the human protein-protein interactome. PMID:18984619
PIG--the pathogen interaction gateway. PMID:18984614
VirHostNet: a knowledge base for the management and the analysis of proteome-wide virus-host interaction networks. PMID:18984613
Michigan molecular interactions r2: from interacting proteins to pathways. PMID:18978014
Update of KDBI: Kinetic Data of Bio-molecular Interaction database. PMID:18971255
metaTIGER: a metabolic evolution resource. PMID:18953037
HMDB: a knowledgebase for the human metabolome. PMID:18953024
Overview of the protein-protein interaction annotation extraction task of BioCreative II. PMID:18834495
Mining tissue specificity, gene connectivity and disease association to reveal a set of genes that modify the action of disease causing genes. PMID:18822114
PharmGKB: an integrated resource of pharmacogenomic data and knowledge. PMID:18819074
InnateDB: facilitating systems-level analyses of the mammalian innate immune response. PMID:18766178
Network-based model weighting to detect multiple loci influencing complex diseases. PMID:18719944
Using multiple ontologies to integrate complex biological data. PMID:18629202
Arabidopsis reactome: a foundation knowledgebase for plant systems biology. PMID:18591350
Meta-analysis approach identifies candidate genes and associated molecular networks for type-2 diabetes mellitus. PMID:18590522
Targeting the human cancer pathway protein interaction network by structural genomics. PMID:18487680
Design logic of a cannabinoid receptor signaling network that triggers neurite outgrowth. PMID:18487186
PaLS: filtering common literature, biological terms and pathway information. PMID:18467422
Getting started in biological pathway construction and analysis. PMID:18463709
A map of human protein interactions derived from co-expression of human mRNAs and their orthologs. PMID:18414481
Predicting cancer involvement of genes from heterogeneous data. PMID:18371197
A comprehensive modular map of molecular interactions in RB/E2F pathway. PMID:18319725
SPIKE--a database, visualization and analysis tool of cellular signaling pathways. PMID:18289391
The landscape of human proteins interacting with viruses and other pathogens. PMID:18282095
STITCH: interaction networks of chemicals and proteins. PMID:18084021
Broad network-based predictability of Saccharomyces cerevisiae gene loss-of-function phenotypes. PMID:18053250
Framework for a protein ontology. PMID:18047702
EndoNet: an information resource about regulatory networks of cell-to-cell communication. PMID:18045786
Integrative analysis for finding genes and networks involved in diabetes and other complex diseases. PMID:18045462
PRIDE: new developments and new datasets. PMID:18033805
e-Fungi: a data resource for comparative analysis of fungal genomes. PMID:18028535
Discovery of protein interaction networks shared by diseases. PMID:17992746
BioHealthBase: informatics support in the elucidation of influenza virus host pathogen interactions and virulence. PMID:17965094
Integration of biological networks and gene expression data using Cytoscape. PMID:17947979
Network-based classification of breast cancer metastasis. PMID:17940530
Improved human disease candidate gene prioritization using mouse phenotype. PMID:17939863
Gallus GBrowse: a unified genomic database for the chicken. PMID:17933775
Graphs in molecular biology. PMID:17903289
Linking microarray reporters with protein functions. PMID:17897448
A systems biology approach for pathway level analysis. PMID:17785539
FlyMine: an integrated database for Drosophila and Anopheles genomics. PMID:17615057
Metabolic network visualization eliminating node redundance and preserving metabolic pathways. PMID:17608928
GenMAPP 2: new features and resources for pathway analysis. PMID:17588266
VisANT 3.0: new modules for pathway visualization, editing, prediction and construction. PMID:17586824
Onto-Tools: new additions and improvements in 2006. PMID:17584796
DEEP--a tool for differential expression effector prediction. PMID:17584786
BioPP: a tool for web-publication of biological networks. PMID:17519033
Advancing translational research with the Semantic Web. PMID:17493285
g:Profiler--a web-based toolset for functional profiling of gene lists from large-scale experiments. PMID:17478515
Formal TCA cycle description based on elementary actions. PMID:17426387
National Institute of Allergy and Infectious Diseases bioinformatics resource centers: new assets for pathogen informatics. PMID:17420237
METANNOGEN: compiling features of biochemical reactions needed for the reconstruction of metabolic networks. PMID:17408512
Patterns of somatic mutation in human cancer genomes. PMID:17344846
From bytes to bedside: data integration and computational biology for translational cancer research. PMID:17319736
Classification of microarray data using gene networks. PMID:17270037
Refinement and expansion of signaling pathways: the osmotic response network in yeast. PMID:17267811
An evaluation of human protein-protein interaction data in the public domain. PMID:17254303
IDconverter and IDClight: conversion and annotation of gene and protein IDs. PMID:17214880
HMDB: the Human Metabolome Database. PMID:17202168
Bringing metabolic networks to life: integration of kinetic, metabolic, and proteomic data. PMID:17173670
Bringing metabolic networks to life: convenience rate law and thermodynamic constraints. PMID:17173669
T1DBase: integration and presentation of complex data for type 1 diabetes research. PMID:17169983
UniHI: an entry gate to the human protein interactome. PMID:17158159
How complete are current yeast and human protein-interaction networks? PMID:17147767
IntAct--open source resource for molecular interaction data. PMID:17145710
PolyDoms: a whole genome database for the identification of non-synonymous coding SNPs with the potential to impact disease. PMID:17142238
CellCircuits: a database of protein network models. PMID:17135207
Michigan Molecular Interactions (MiMI): putting the jigsaw puzzle together. PMID:17130145
PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways. PMID:17130144
Parameter estimate of signal transduction pathways. PMID:17118160
cPath: open source software for collecting, storing, and querying biological pathways. PMID:17101041
STRING 7--recent developments in the integration and prediction of protein interactions. PMID:17098935
Patome: a database server for biological sequence annotation and analysis in issued patents and published patent applications. PMID:17085479
'Genome design' model and multicellular complexity: golden middle. PMID:17062620
Meta-All: a system for managing metabolic pathway information. PMID:17059592
AgBase: a functional genomics resource for agriculture. PMID:16961921
The Pathway Tools cellular overview diagram and Omics Viewer. PMID:16893960
A multivariate approach for integrating genome-wide expression data and biological knowledge. PMID:16877751
metaSHARK: a WWW platform for interactive exploration of metabolic networks. PMID:16845107
Dry work in a wet world: computation in systems biology. PMID:16820781
Heterozygous carriers of Nijmegen Breakage Syndrome have a distinct gene expression phenotype. PMID:16809669
Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae. PMID:16762047
Reconstruction of a functional human gene network, with an application for prioritizing positional candidate genes. PMID:16685651
A case study in pathway knowledgebase verification. PMID:16603083
Preliminary evidence of mitochondrial dysfunction associated with post-infective fatigue after acute infection with Epstein Barr virus. PMID:16448567
The UCSC Genome Browser Database: update 2006. PMID:16381938
TRANSPATH: an information resource for storing and visualizing signaling pathways and their pathological aberrations. PMID:16381929
pSTIING: a 'systems' approach towards integrating signalling pathways, interaction and transcriptional regulatory networks in inflammation and cancer. PMID:16381926
The Gene Ontology (GO) project in 2006. PMID:16381878
SMART 5: domains in the context of genomes and networks. PMID:16381859
The Universal Protein Resource (UniProt): an expanding universe of protein information. PMID:16381842
MachineProse: an ontological framework for scientific assertions. PMID:16357355
HomoMINT: an inferred human network based on orthology mapping of protein interactions discovered in model organisms. PMID:16351748
Platelet genomics and proteomics in human health and disease. PMID:16322782
FACT--a framework for the functional interpretation of high-throughput experiments. PMID:15985174
Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome. PMID:15892868
The European Bioinformatics Institute's data resources: towards systems biology. PMID:15608238
Reactome pathway analysis: a high-performance in-memory approach PubMed citations: 198.

198 articles citing: Reactome pathway analysis: a high-performance in-memory approach

Whole genome sequencing reveals the independent clonal origin of multifocal ileal neuroendocrine tumors. PMID:35922826
The Potential Complementary Role of Using Chinese Herbal Medicine with Western Medicine in Treating COVID-19 Patients: Pharmacology Network Analysis. PMID:35890093
Transcriptomic Evidence That Switching from Tobacco to Electronic Cigarettes Does Not Reverse Damage to the Respiratory Epithelium. PMID:35878275
Molecular Evolution of the Activating Transcription Factors Shapes the Adaptive Cellular Responses to Oxidative Stress. PMID:35873797
Increasing reproducibility, robustness, and generalizability of biomarker selection from meta-analysis using Bayesian methodology. PMID:35759523
Compartmentalization of Intrarenal Programmed Cell Death Protein 1-Ligand 1 and Its Receptor in Kidney Injury Related to Immune Checkpoint Inhibitor Nephrotoxicity. PMID:35755033
Cell-Cell Contact Mediates Gene Expression and Fate Choice of Human Neural Stem/Progenitor Cells. PMID:35681435
Time-Series Clustering of lncRNA-mRNA Expression during the Adipogenic Transdifferentiation of Porcine Skeletal Muscle Satellite Cells. PMID:35678667
BioTAGME: A Comprehensive Platform for Biological Knowledge Network Analysis. PMID:35571058
Proteomic analysis of autoimmune retinopathy implicates NrCAM as a potential biomarker. PMID:35529077
Pathophysiological pathway differences in children who present with COVID-19 ARDS compared to COVID -19 induced MIS-C. PMID:35501302
Potential Pleiotropic Genes and Shared Biological Pathways in Epilepsy and Depression Based on GWAS Summary Statistics. PMID:35463244
Targeting the EGFR-ERK axis using the compatible solute ectoine to stabilize CFTR mutant F508del. PMID:35412656
Investigation and Validation of Molecular Characteristics of Endometrium in Recurrent Miscarriage and Unexplained Infertility from a Transcriptomic Perspective. PMID:35370464
Cell-Matrix Interactions Contribute to Barrier Function in Human Colon Organoids. PMID:35360746
Pan-cancer analysis identifies BIRC5 as a prognostic biomarker. PMID:35331169
Identification of a Steroid Hormone-Associated Gene Signature Predicting the Prognosis of Prostate Cancer through an Integrative Bioinformatics Analysis. PMID:35326723
GIRK3 deletion facilitates kappa opioid signaling in chondrocytes, delays vascularization and promotes bone lengthening in mice. PMID:35314385
Impact of Maternal Obesity on Liver Disease in the Offspring: A Comprehensive Transcriptomic Analysis and Confirmation of Results in a Murine Model. PMID:35203502
Quantitative Proteomic Study Unmasks Fibrinogen Pathway in Polycystic Liver Disease. PMID:35203500
Evaluating the detection ability of a range of epistasis detection methods on simulated data for pure and impure epistatic models. PMID:35180244
eNAMPT Is a Novel Damage-associated Molecular Pattern Protein That Contributes to the Severity of Radiation-induced Lung Fibrosis. PMID:35167418
First genome-wide association study investigating blood pressure and renal traits in domestic cats. PMID:35115544
Hidradenitis Suppurativa and Comorbid Disorder Biomarkers, Druggable Genes, New Drugs and Drug Repurposing-A Molecular Meta-Analysis. PMID:35056940
Genome and transcriptome profiling of spontaneous preterm birth phenotypes. PMID:35046466
Transcriptomic analysis of choroidal neovascularization reveals dysregulation of immune and fibrosis pathways that are attenuated by a novel anti-fibrotic treatment. PMID:35039609
NETME: on-the-fly knowledge network construction from biomedical literature. PMID:35013714
Hyperinflammatory environment drives dysfunctional myeloid cell effector response to bacterial challenge in COVID-19. PMID:35007290
Antigen presentation and interferon signatures in B cells driven by localized ablative cancer immunotherapy correlate with extended survival. PMID:34976205
Co-exposure of sodium arsenite and uranyl acetate differentially alters gene expression in CD3/CD28 activated CD4+ T-cells. PMID:34926170
GraphOmics: an interactive platform to explore and integrate multi-omics data. PMID:34922446
Structural Predictive Model of Presenilin-2 Protein and Analysis of Structural Effects of Familial Alzheimer's Disease Mutations. PMID:34881055
Significant transcriptomic changes are associated with the inhibitory effects of 5-aza-2-deoxycytidine during adipogenic differentiation of MG-63 cells. PMID:34867036
NEIL1 and NEIL2 DNA glycosylases modulate anxiety and learning in a cooperative manner in mice. PMID:34857879
Latency-associated DNA methylation patterns among HIV-1 infected individuals with distinct disease progression courses or antiretroviral virologic response. PMID:34837007
Effects of photodeoxygenation on cell biology using dibenzothiophene S-oxide derivatives as O(3P)-precursors. PMID:34822125
A database on differentially expressed microRNAs during rodent bladder healing. PMID:34750474
Development of a Blood-based Transcriptional Risk Score for Chronic Obstructive Pulmonary Disease. PMID:34739356
Network-based protein-protein interaction prediction method maps perturbations of cancer interactome. PMID:34727106
Path4Drug: Data Science Workflow for Identification of Tissue-Specific Biological Pathways Modulated by Toxic Drugs. PMID:34721010
SARS-CoV-2-host proteome interactions for antiviral drug discovery. PMID:34709727
A Unified Transcriptional, Pharmacogenomic, and Gene Dependency Approach to Decipher the Biology, Diagnostic Markers, and Therapeutic Targets Associated with Prostate Cancer Metastasis. PMID:34680307
Music of metagenomics-a review of its applications, analysis pipeline, and associated tools. PMID:34657989
Alterations in HLA Class I-Presented Immunopeptidome and Class I-Interactome upon Osimertinib Resistance in EGFR Mutant Lung Adenocarcinoma. PMID:34638461
Genome-wide associations for immune traits in two maternal pig lines. PMID:34610786
Repurposing haloperidol for the treatment of rheumatoid arthritis: an integrative approach using data mining techniques. PMID:34589142
Biological Significance of the Protein Changes Occurring in the Cerebrospinal Fluid of Alzheimer's Disease Patients: Getting Clues from Proteomic Studies. PMID:34573996
Construction of Interferon-Gamma-Related Gene Signature to Characterize the Immune-Inflamed Phenotype of Glioblastoma and Predict Prognosis, Efficacy of Immunotherapy and Radiotherapy. PMID:34566988
Identification of Key Candidate Genes and Chemical Perturbagens in Diabetic Kidney Disease Using Integrated Bioinformatics Analysis. PMID:34557161
Deorphanizing Caspase-3 and Caspase-9 Substrates In and Out of Apoptosis with Deep Substrate Profiling. PMID:34553588
Podocyte-specific KLF4 is required to maintain parietal epithelial cell quiescence in the kidney. PMID:34516901
Air pollution-induced epigenetic changes: disease development and a possible link with hypersensitivity pneumonitis. PMID:34498177
Upregulated glycolysis correlates with tumor progression and immune evasion in head and neck squamous cell carcinoma. PMID:34493792
Drug Discovery of Spinal Muscular Atrophy (SMA) from the Computational Perspective: A Comprehensive Review. PMID:34445667
Dynamic Network Biomarker of Pre-Exhausted CD8+ T Cells Contributed to T Cell Exhaustion in Colorectal Cancer. PMID:34434188
Estimating the predictive power of silent mutations on cancer classification and prognosis. PMID:34385450
Minor Allele Frequencies and Molecular Pathways Differences for SNPs Associated with Amyotrophic Lateral Sclerosis in Subjects Participating in the UKBB and 1000 Genomes Project. PMID:34362180
miRNome and Functional Network Analysis of PGRMC1 Regulated miRNA Target Genes Identify Pathways and Biological Functions Associated With Triple Negative Breast Cancer. PMID:34350123
A Computational Exploration of the Molecular Network Associated to Neuroinflammation in Alzheimer's Disease. PMID:34335238
Gene expression analysis method integration and co-expression module detection applied to rare glucide metabolism disorders using ExpHunterSuite. PMID:34301987
Microbiota Modulates Cardiac Transcriptional Responses to Intermittent Hypoxia and Hypercapnia. PMID:34248668
RNA-seq analysis reveals significant transcriptome changes in huntingtin-null human neuroblastoma cells. PMID:34215255
Serine-Threonine Kinase Receptor-Associated Protein (STRAP) Knockout Decreases the Malignant Phenotype in Neuroblastoma Cell Lines. PMID:34206917
In Vitro Characterization of the Innate Immune Pathways Engaged by Live and Inactivated Tick-Borne Encephalitis Virus. PMID:34204532
Orthosiphon stamineus Proteins Alleviate Hydrogen Peroxide Stress in SH-SY5Y Cells. PMID:34202937
A systems pharmacology approach based on oncogenic signalling pathways to determine the mechanisms of action of natural products in breast cancer from transcriptome data. PMID:34193143
Involvement of eNAMPT/TLR4 signaling in murine radiation pneumonitis: protection by eNAMPT neutralization. PMID:34139379
Manipulation of the unfolded protein response: A pharmacological strategy against coronavirus infection. PMID:34138976
Revisiting the Characteristics of Testicular Germ Cell Lines GC-1(spg) and GC-2(spd)ts. PMID:34125394
A new molecular classification to drive precision treatment strategies in primary Sjögren's syndrome. PMID:34112769
PIGNON: a protein-protein interaction-guided functional enrichment analysis for quantitative proteomics. PMID:34088263
Fe-S cofactors in the SARS-CoV-2 RNA-dependent RNA polymerase are potential antiviral targets. PMID:34083449
Characteristics of the Urinary Proteome in Women with Overactive Bladder Syndrome: A Case-Control Study. PMID:34072980
Pro-inflammatory Monocyte Phenotype During Acute Progression of Cerebral Small Vessel Disease. PMID:34055930
Telomere damage promotes vascular smooth muscle cell senescence and immune cell recruitment after vessel injury. PMID:34021256
The chemical defensome of five model teleost fish. PMID:34006915
Deciphering the Efficacy and Mechanisms of Chinese Herbal Medicine for Diabetic Kidney Disease by Integrating Web-Based Biochemical Databases and Real-World Clinical Data: Retrospective Cohort Study. PMID:33973855
EARN: an ensemble machine learning algorithm to predict driver genes in metastatic breast cancer. PMID:33962648
Transcriptional signatures of synaptic vesicle genes define myotonic dystrophy type I neurodegeneration. PMID:33955002
Comparison of sparse biclustering algorithms for gene expression datasets. PMID:33951731
Characterization and Safety Profile of Transfer Factors Peptides, a Nutritional Supplement for Immune System Regulation. PMID:33947143
A systematic analysis of protein-altering exonic variants in chronic obstructive pulmonary disease. PMID:33909500
VB10, a new blood biomarker for differential diagnosis and recovery monitoring of acute viral and bacterial infections. PMID:33906069
Multi-omics integration strategies for animal epigenetic studies - A review. PMID:33902167
Proteoglycans contribute to the functional integrity of the glomerular endothelial cell surface layer and are regulated in diabetic kidney disease. PMID:33875683
Nuclear Dishevelled targets gene regulatory regions and promotes tumor growth. PMID:33860601
USP7 limits CDK1 activity throughout the cell cycle. PMID:33856059
A Systems Biology Approach Identifies B Cell Maturation Antigen (BCMA) as a Biomarker Reflecting Oral Vaccine Induced IgA Antibody Responses in Humans. PMID:33828557
In Vitro Radiosensitivity of Murine Marrow Stromal Cells Varies Across Donor Strains. PMID:33826738
Distinct Age-Specific miRegulome Profiling of Isolated Small and Large Intestinal Epithelial Cells in Mice. PMID:33805523
Demographic History, Adaptation, and NRAP Convergent Evolution at Amino Acid Residue 100 in the World Northernmost Cattle from Siberia. PMID:33784744
Drug ranking using machine learning systematically predicts the efficacy of anti-cancer drugs. PMID:33767176
Gene Set Enrichment Analysis of Interaction Networks Weighted by Node Centrality. PMID:33719329
Linking bacterial enterotoxins and alpha defensin 5 expansion in the Crohn's colitis: A new insight into the etiopathogenetic and differentiation triggers driving colonic inflammatory bowel disease. PMID:33690604
Reproducing diabetic retinopathy features using newly developed human induced-pluripotent stem cell-derived retinal Müller glial cells. PMID:33683746
Differential blood DNA methylation across Lewy body dementias. PMID:33665346
The kinetic landscape of an RNA-binding protein in cells. PMID:33568810
Bcl9 Depletion Modulates Endothelial Cell in Tumor Immune Microenvironment in Colorectal Cancer Tumor. PMID:33552975
In-silico network-based analysis of drugs used against COVID-19: Human well-being study. PMID:33519272
Gene expressions in cerebral palsy subjects reveal structural and functional changes in the gastrocnemius muscle that are closely associated with passive muscle stiffness. PMID:33515289
Structural similarity-based prediction of host factors associated with SARS-CoV-2 infection and pathogenesis. PMID:33506741
IDH1 mutations induce organelle defects via dysregulated phospholipids. PMID:33504762
Single-Cell RNA Sequencing of Tocilizumab-Treated Peripheral Blood Mononuclear Cells as an in vitro Model of Inflammation. PMID:33469465
A subset of liver resident natural killer cells is expanded in hepatitis C-infected patients with better liver function. PMID:33452360
USP15 Deubiquitinase Safeguards Hematopoiesis and Genome Integrity in Hematopoietic Stem Cells and Leukemia Cells. PMID:33378683
Glioblastoma CUSA Fluid Protein Profiling: A Comparative Investigation of the Core and Peripheral Tumor Zones. PMID:33374813
MNK Inhibition Sensitizes KRAS-Mutant Colorectal Cancer to mTORC1 Inhibition by Reducing eIF4E Phosphorylation and c-MYC Expression. PMID:33328217
Comprehensive Transcriptomic Analysis Reveals Dysregulated Competing Endogenous RNA Network in Endocrine Resistant Breast Cancer Cells. PMID:33324567
A long noncoding RNA, LncMyoD, modulates chromatin accessibility to regulate muscle stem cell myogenic lineage progression. PMID:33293420
Effects of Sphingosine-1-Phosphate on Cell Viability, Differentiation, and Gene Expression of Adipocytes. PMID:33291440
An integrated approach to biomarker discovery reveals gene signatures highly predictive of cancer progression. PMID:33277589
Identifying the Chinese Herbal Medicine Network and Core Formula for Allergic Rhinitis on a Real-World Database. PMID:33204289
In silico and in vitro studies reveal complement system drives coagulation cascade in SARS-CoV-2 pathogenesis. PMID:33200027
Divergent organ-specific isogenic metastatic cell lines identified using multi-omics exhibit differential drug sensitivity. PMID:33196681
Zinc Modulates Several Transcription-Factor Regulated Pathways in Mouse Skeletal Muscle Cells. PMID:33153045
Significant transcriptomic changes are associated with differentiation of bone marrow-derived mesenchymal stem cells into neural progenitor-like cells in the presence of bFGF and EGF. PMID:33133516
Virus-Host Protein-Protein Interactions between Human Papillomavirus 16 E6 A1 and D2/D3 Sub-Lineages: Variances and Similarities. PMID:33121134
The adenoviral protein E4orf4: a probing tool to decipher mechanical stress-induced nuclear envelope remodeling in tumor cells. PMID:33103553
Investigating the Transition of Pre-Symptomatic to Symptomatic Huntington's Disease Status Based on Omics Data. PMID:33049985
Implication of ZNF217 in Accelerating Tumor Development and Therapeutically Targeting ZNF217-Induced PI3K-AKT Signaling for the Treatment of Metastatic Osteosarcoma. PMID:32999043
pS421 huntingtin modulates mitochondrial phenotypes and confers neuroprotection in an HD hiPSC model. PMID:32978366
Can Scoliotic Discs Be Controls for Molecular Studies in Intervertebral Disc Research? Insights From Proteomics. PMID:32945197
Extracellular vesicles from human iPSC-derived neural stem cells: miRNA and protein signatures, and anti-inflammatory and neurogenic properties. PMID:32944193
Warmth Prevents Bone Loss Through the Gut Microbiota. PMID:32916104
ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis. PMID:32907876
Cocaine-mediated circadian reprogramming in the striatum through dopamine D2R and PPARγ activation. PMID:32895370
Deciphering the secretome of leukocyte-platelet rich fibrin: towards a better understanding of its wound healing properties. PMID:32884030
Game theoretic centrality: a novel approach to prioritize disease candidate genes by combining biological networks with the Shapley value. PMID:32787845
Identification of a five-gene signature for predicting the progression and prognosis of stage I endometrial carcinoma. PMID:32782557
Identification of key genes in atrial fibrillation using bioinformatics analysis. PMID:32778054
Genetic heterogeneity and prognostic impact of recurrent ANK2 and TP53 mutations in mantle cell lymphoma: a multi-centre cohort study. PMID:32770099
Single-Sample Node Entropy for Molecular Transition in Pre-deterioration Stage of Cancer. PMID:32766227
Variants in SCAF4 Cause a Neurodevelopmental Disorder and Are Associated with Impaired mRNA Processing. PMID:32730804
Glycogen accumulation, central carbon metabolism, and aging of hematopoietic stem and progenitor cells. PMID:32665666
Proteogenomic Characterization Reveals Therapeutic Vulnerabilities in Lung Adenocarcinoma. PMID:32649874
Characterization of Glycolysis-Associated Molecules in the Tumor Microenvironment Revealed by Pan-Cancer Tissues and Lung Cancer Single Cell Data. PMID:32635458
Inflammatory pathway analytes predicting rapid cognitive decline in MCI stage of Alzheimer's disease. PMID:32634865
Seq-ing answers: Current data integration approaches to uncover mechanisms of transcriptional regulation. PMID:32612756
Alterations in the chondrocyte surfaceome in response to pro-inflammatory cytokines. PMID:32586320
Human ZKSCAN3 and Drosophila M1BP are functionally homologous transcription factors in autophagy regulation. PMID:32541927
Feature selection strategies for drug sensitivity prediction. PMID:32523056
Chromatin Trapping of Factors Involved in DNA Replication and Repair Underlies Heat-Induced Radio- and Chemosensitization. PMID:32521766
Studies of human twins reveal genetic variation that affects dietary fat perception. PMID:32516399
Molecular characterisation of TP53 mutated squamous cell carcinomas of the lung to identify putative targets for therapy. PMID:32468587
Proteomic Characterization of Colorectal Cancer Cells versus Normal-Derived Colon Mucosa Cells: Approaching Identification of Novel Diagnostic Protein Biomarkers in Colorectal Cancer. PMID:32422974
Pathway Analysis of Genes Identified through Post-GWAS to Underpin Prostate Cancer Aetiology. PMID:32397189
Proteomic Profiling of Small Extracellular Vesicles Secreted by Human Pancreatic Cancer Cells Implicated in Cellular Transformation. PMID:32382024
Metabonomic Profile and Signaling Pathway Prediction of Depression-Associated Suicidal Behavior. PMID:32372980
Extracellular Vesicles Secreted by Corneal Epithelial Cells Promote Myofibroblast Differentiation. PMID:32357574
In Silico Analysis of a Highly Mutated Gene in Cancer Provides Insight into Abnormal mRNA Splicing: Splicing Factor 3B Subunit 1K700E Mutant. PMID:32354150
Investigating the epithelial barrier and immune signatures in the pathogenesis of equine insect bite hypersensitivity. PMID:32343720
RA-map: building a state-of-the-art interactive knowledge base for rheumatoid arthritis. PMID:32311035
Suppression of a Subset of Interferon-Induced Genes by Human Papillomavirus Type 16 E7 via a Cyclin Dependent Kinase 8-Dependent Mechanism. PMID:32183180
Integrative Analysis of MicroRNA and Gene Interactions for Revealing Candidate Signatures in Prostate Cancer. PMID:32180804
Type 1 Interferon Responses Underlie Tumor-Selective Replication of Oncolytic Measles Virus. PMID:32087150
Activated FGF2 signaling pathway in tumor vasculature is essential for acquired resistance to anti-VEGF therapy. PMID:32076044
Endogenous Retrovirus Activation as a Key Mechanism of Anti-Tumor Immune Response in Radiotherapy. PMID:32074012
Machine Learning and Bioinformatics Models to Identify Pathways that Mediate Influences of Welding Fumes on Cancer Progression. PMID:32066756
Comparison of the Transcriptome Response within the Swine Tracheobronchial Lymphnode Following Infection with PRRSV, PCV-2 or IAV-S. PMID:32033425
Reconstructing kinase network topologies from phosphoproteomics data reveals cancer-associated rewiring. PMID:31959955
Characterization of Human Induced Pluripotent Stem Cell-Derived Hepatocytes with Mature Features and Potential for Modeling Metabolic Diseases. PMID:31940797
miRNAs as radio-response biomarkers for breast cancer stem cells. PMID:31930680
Machine learning for the detection of early immunological markers as predictors of multi-organ dysfunction. PMID:31857590
miR-221 Augments TRAIL-Mediated Apoptosis in Prostate Cancer Cells by Inducing Endogenous TRAIL Expression and Targeting the Functional Repressors SOCS3 and PIK3R1. PMID:31828111
Deregulation of the Histone Lysine-Specific Demethylase 1 Is Involved in Human Hepatocellular Carcinoma. PMID:31805626
Reactome and ORCID-fine-grained credit attribution for community curation. PMID:31802127
A single factor dominates the behavior of rhythmic genes in mouse organs. PMID:31747875
Characterisation of the developing heart in a pressure overloaded model utilising RNA sequencing to direct functional analysis. PMID:31724174
A Network Pharmacology Study of the Multi-Targeting Profile of an Antiarrhythmic Chinese Medicine Xin Su Ning. PMID:31607935
Chemical Genomic Profiling Unveils the in Vitro and in Vivo Antiplasmodial Mechanism of Açaí (Euterpe oleracea Mart.) Polyphenols. PMID:31572864
Terminal Effector CD8 T Cells Defined by an IKZF2+IL-7R- Transcriptional Signature Express FcγRIIIA, Expand in HIV Infection, and Mediate Potent HIV-Specific Antibody-Dependent Cellular Cytotoxicity. PMID:31519862
Newly isolated marine bacterial exopolysaccharides enhance antitumor activity in HepG2 cells via affecting key apoptotic factors and activating toll like receptors. PMID:31493282
Macrophage spatial heterogeneity in gastric cancer defined by multiplex immunohistochemistry. PMID:31477692
Gene expression association study in feline mammary carcinomas. PMID:31461477
Target Genes of Autism Risk Loci in Brain Frontal Cortex. PMID:31447881
Exploring the Mitochondrial Degradome by the TAILS Proteomics Approach in a Cellular Model of Parkinson's Disease. PMID:31417398
Genome of the Komodo dragon reveals adaptations in the cardiovascular and chemosensory systems of monitor lizards. PMID:31358948
Integrated identification of key genes and pathways in Alzheimer's disease via comprehensive bioinformatical analyses. PMID:31346329
HIV and HCV augments inflammatory responses through increased TREM-1 expression and signaling in Kupffer and Myeloid cells. PMID:31260499
Proteomic insight into the pathogenesis of CAPN5-vitreoretinopathy. PMID:31110225
Panoramic Visualization of Circulating MicroRNAs Across Neurodegenerative Diseases in Humans. PMID:31037649
Identification of pathways associated with chemosensitivity through network embedding. PMID:30893303
Unsupervised classification of multi-omics data during cardiac remodeling using deep learning. PMID:30853547
Phase I clinical trial of an intranodally administered mRNA-based therapeutic vaccine against HIV-1 infection. PMID:30289805
Genome-wide DNA methylation encodes cardiac transcriptional reprogramming in human ischemic heart failure. PMID:30089854
Rare variants in SOX17 are associated with pulmonary arterial hypertension with congenital heart disease. PMID:30029678
Distinct sperm nucleus behaviors between genotypic and temperature-dependent sex determination males are associated with replication and expression-related pathways in a gynogenetic fish. PMID:29866041
Biomedical Informatics on the Cloud: A Treasure Hunt for Advancing Cardiovascular Medicine. PMID:29700073
Constraints on signaling network logic reveal functional subgraphs on Multiple Myeloma OMIC data. PMID:29589566
Worldwide Protein Data Bank validation information: usage and trends. PMID:29533231
Troponin through the looking-glass: emerging roles beyond regulation of striated muscle contraction. PMID:29416706
Interleukins and their signaling pathways in the Reactome biological pathway database. PMID:29378288
Developing a 'personalome' for precision medicine: emerging methods that compute interpretable effect sizes from single-subject transcriptomes. PMID:29272327
Reactome diagram viewer: data structures and strategies to boost performance. PMID:29186351
The Reactome Pathway Knowledgebase. PMID:29145629
A GLO10 score for the prediction of prognosis in high grade gliomas. PMID:29050331
'Multi-omic' data analysis using O-miner. PMID:28981577
Molecular mechanisms underlying gliomas and glioblastoma pathogenesis revealed by bioinformatics analysis of microarray data. PMID:28952134