FAIRsharing.9d5f5r; Last edited: March 9, 2021, 4:07 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929

The BioGRID Interaction Database
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:34.038241

biogrid
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:34.038241

Other names: BioGRID, The BioGRID Interaction Database, biogrid

The Biological General Repository for Interaction Datasets (BioGRID) is a curated biological database of protein-protein interactions, genetic interactions, chemical interactions, and post-translational modifications.

Webpage:

https://thebiogrid.org

Licence:

Name: MIT
URL: https://downloads.thebiogrid.org/BioGRID

Publications: (10)

Publications
More detailed information about this field from each metasource.

BioGRID: a general repository for interaction datasets
PMID: 16381927
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929

metasource: Fairsharing.org
version: FAIRsharing.org: BioGRID; Biological General Repository for Interaction Datasets; DOI: https://doi.org/10.25504/FAIRsharing.9d5f5r; Last edited: March 9, 2021, 4:07 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

The BioGRID interaction database: 2015 update
PMID: 25428363
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929

The BioGRID interaction database: 2019 update
PMID: 30476227
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929

metasource: Fairsharing.org
version: FAIRsharing.org: BioGRID; Biological General Repository for Interaction Datasets; DOI: https://doi.org/10.25504/FAIRsharing.9d5f5r; Last edited: March 9, 2021, 4:07 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

The BioGRID interaction database: 2017 update
PMID: 27980099
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929

The BioGRID Interaction Database: 2011 update
PMID: 21071413
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929

metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:34.038241

The BioGRID interaction database: 2013 update
PMID: 23203989
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929

The BioGRID Interaction Database: 2008 update
PMID: 18000002
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929

The BioGRID database: A comprehensive biomedical resource of curated protein, genetic, and chemical interactions
PMID: 33070389
metasource: Fairsharing.org
version: FAIRsharing.org: BioGRID; Biological General Repository for Interaction Datasets; DOI: https://doi.org/10.25504/FAIRsharing.9d5f5r; Last edited: March 9, 2021, 4:07 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

The GRID: the General Repository for Interaction Datasets
PMID: 12620108
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929

metasource: Fairsharing.org
version: FAIRsharing.org: BioGRID; Biological General Repository for Interaction Datasets; DOI: https://doi.org/10.25504/FAIRsharing.9d5f5r; Last edited: March 9, 2021, 4:07 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

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

BioGRID: a general repository for interaction datasets PubMed citations: 1602.

1602 articles citing: BioGRID: a general repository for interaction datasets

BioAlign: An Accurate Global PPI Network Alignment Algorithm. PMID:35898232
Challenges and Limitations of Biological Network Analysis. PMID:35892929
Analyzing the Systems Biology Effects of COVID-19 mRNA Vaccines to Assess Their Safety and Putative Side Effects. PMID:35889989
Drug-Target Network Study Reveals the Core Target-Protein Interactions of Various COVID-19 Treatments. PMID:35885993
Network Proximity-Based Drug Repurposing Strategy for Early and Late Stages of Primary Biliary Cholangitis. PMID:35884999
Integration of probabilistic functional networks without an external Gold Standard. PMID:35879662
Consensus clustering for Bayesian mixture models. PMID:35864476
DeepND: Deep multitask learning of gene risk for comorbid neurodevelopmental disorders. PMID:35845835
Deep learning frameworks for protein-protein interaction prediction. PMID:35832624
A functional reference map of the RNF8 interactome in cancer. PMID:35831895
Bioinformatics-Driven Identification of p62 as A Crucial Oncogene in Liver Cancer. PMID:35814476
Conserved recombination patterns across coronavirus subgenera. PMID:35814334
In-silico screening and in-vitro assay show the antiviral effect of Indomethacin against SARS-CoV-2. PMID:35809412
PHILM2Web: A high-throughput database of macromolecular host-pathogen interactions on the Web. PMID:35776535
N(6)-methyladenosine methylation-regulated polo-like kinase 1 cell cycle homeostasis as a potential target of radiotherapy in pancreatic adenocarcinoma. PMID:35773310
Molecular characterization of low-grade serous ovarian carcinoma identifies genomic aberrations according to hormone receptor expression. PMID:35768582
Unique SMYD5 Structure Revealed by AlphaFold Correlates with Its Functional Divergence. PMID:35740908
Identification of the Potential Molecular Mechanisms Linking RUNX1 Activity with Nonalcoholic Fatty Liver Disease, by Means of Systems Biology. PMID:35740337
Integrating multi-omics data reveals function and therapeutic potential of deubiquitinating enzymes. PMID:35737447
A Conserved Long Intergenic Non-coding RNA Containing snoRNA Sequences, lncCOBRA1, Affects Arabidopsis Germination and Development. PMID:35693169
Computational identification of protein complexes from network interactions: Present state, challenges, and the way forward. PMID:35685359
Transcriptomic analysis reveals pathophysiological relationship between chronic obstructive pulmonary disease (COPD) and periodontitis. PMID:35676670
Complementary omics strategies to dissect p53 signaling networks under nutrient stress. PMID:35635656
Network Pharmacology Approach for Medicinal Plants: Review and Assessment. PMID:35631398
The R Language: An Engine for Bioinformatics and Data Science. PMID:35629316
Targeting HIF-1α Function in Cancer through the Chaperone Action of NQO1: Implications of Genetic Diversity of NQO1. PMID:35629169
Proteome-wide prediction and analysis of the Cryptosporidium parvum protein-protein interaction network through integrative methods. PMID:35615014
FAM198B promotes colorectal cancer progression by regulating the polarization of tumor-associated macrophages via the SMAD2 signaling pathway. PMID:35587159
GenePlexus: a web-server for gene discovery using network-based machine learning. PMID:35580053
Bioinformatics-Based Approaches to Study Virus-Host Interactions During SARS-CoV-2 Infection. PMID:35554909
Transcriptome analysis of clock disrupted cancer cells reveals differential alternative splicing of cancer hallmarks genes. PMID:35552415
Long-read sequencing unveils high-resolution HPV integration and its oncogenic progression in cervical cancer. PMID:35538075
Small RNA sequencing and bioinformatics analysis of RAW264.7-derived exosomes after Mycobacterium Bovis Bacillus Calmette-Guérin infection. PMID:35525953
Dynamic and widespread control of poly(A) tail length during macrophage activation. PMID:35512831
ImitateDB: A database for domain and motif mimicry incorporating host and pathogen protein interactions. PMID:35487995
Cyclin-Dependent Kinase 6 Identified as the Target Protein in the Antitumor Activity of Tetrastigma hemsleyanum. PMID:35480115
Identification of dynamic driver sets controlling phenotypical landscapes. PMID:35465155
Novel Protein-Protein Interactions Highlighting the Crosstalk between Hypoplastic Left Heart Syndrome, Ciliopathies and Neurodevelopmental Delays. PMID:35456433
The cargo adapter protein CLINT1 is phosphorylated by the Numb-associated kinase BIKE and mediates dengue virus infection. PMID:35452674
An interolog-based barley interactome as an integration framework for immune signaling. PMID:35435213
Transcriptome Analysis in Hippocampus of Rats Prenatally Exposed to Valproic Acid and Effects of Intranasal Treatment of Oxytocin. PMID:35432011
Phylogenetic profiling in eukaryotes: The effect of species, orthologous group, and interactome selection on protein interaction prediction. PMID:35421089
Repurposing Multiple-Molecule Drugs for COVID-19-Associated Acute Respiratory Distress Syndrome and Non-Viral Acute Respiratory Distress Syndrome via a Systems Biology Approach and a DNN-DTI Model Based on Five Drug Design Specifications. PMID:35409008
Expansion of Schizophrenia Gene Network Knowledge Using Machine Learning Selected Signals From Dorsolateral Prefrontal Cortex and Amygdala RNA-seq Data. PMID:35386517
The Prognostic Significance and Gene Expression Characteristics of Gastric Signet-Ring Cell Carcinoma: A Study Based on the SEER and TCGA Databases. PMID:35372476
The D2R-DISC1 protein complex and associated proteins are altered in schizophrenia and normalized with antipsychotic treatment. PMID:35361701
Computational methods, databases and tools for synthetic lethality prediction. PMID:35352098
Predicting protein-protein interactions between banana and Fusarium oxysporum f. sp. cubense race 4 integrating sequence and domain homologous alignment and neural network verification. PMID:35351140
Discrete Logic Modeling of Cell Signaling Pathways. PMID:35347689
Transposon insertional mutagenesis of diverse yeast strains suggests coordinated gene essentiality polymorphisms. PMID:35314699
Finding New Ways How to Control BACE1. PMID:35305135
Reconstructing codependent cellular cross-talk in lung adenocarcinoma using REMI. PMID:35302849
Eucalyptus grandis AUX/INDOLE-3-ACETIC ACID 13 (EgrIAA13) is a novel transcriptional regulator of xylogenesis. PMID:35292886
HAUS5 Is A Potential Prognostic Biomarker With Functional Significance in Breast Cancer. PMID:35280773
A pan-cancer analysis of the oncogenic role of Holliday junction recognition protein in human tumors. PMID:35274047
MESH1 knockdown triggers proliferation arrest through TAZ repression. PMID:35273140
Proximity Profiling of the CFTR Interaction Landscape in Response to Orkambi. PMID:35269585
The long-term effects of genomic selection: 1. Response to selection, additive genetic variance, and genetic architecture. PMID:35255802
Modeling multi-scale data via a network of networks. PMID:35238343
Methods to Improve Molecular Diagnosis in Genomic Cold Cases in Pediatric Neurology. PMID:35205378
Gene Ontology Groups and Signaling Pathways Regulating the Process of Avian Satellite Cell Differentiation. PMID:35205287
p53-mediated neurodegeneration in the absence of the nuclear protein Akirin2. PMID:35198879
PARK2 regulates eIF4B-driven lymphomagenesis. PMID:35191952
Tcf12 and NeuroD1 cooperatively drive neuronal migration during cortical development. PMID:35147187
Barcode fusion genetics-protein-fragment complementation assay (BFG-PCA): tools and resources that expand the potential for binary protein interaction discovery. PMID:35137167
A systematic study of motif pairs that may facilitate enhancer-promoter interactions. PMID:35130376
Polygenic networks in peripheral leukocytes indicate patterns associated with HIV infection and context-dependent effects of cannabis use. PMID:35128491
Chemoproteomic-enabled characterization of small GTPase Rab1a as a target of an N-arylbenzimidazole ligand's rescue of Parkinson's-associated cell toxicity. PMID:35128413
Profiling of RNA-binding Proteins Interacting With Glucagon and Adipokinetic Hormone mRNAs. PMID:35118022
Probabilistic Graphical Models Applied to Biological Networks. PMID:35113399
Visualization of a curated Oryza sativa L. CDPKs Protein-Protein Interaction Network (CDPK-OsPPIN). PMID:35098050
Phosphopeptide enrichment using Phos-tag technology reveals functional phosphorylation of the nucleocapsid protein of SARS-CoV-2. PMID:35093569
MED12 is overexpressed in glioblastoma patients and serves as an oncogene by targeting the VDR/BCL6/p53 axis. PMID:35091793
From communities to protein complexes: A local community detection algorithm on PPI networks. PMID:35085263
Graphlet eigencentralities capture novel central roles of genes in pathways. PMID:35077468
β-Synuclein: An Enigmatic Protein with Diverse Functionality. PMID:35053291
Gene Network of Susceptibility to Atypical Femoral Fractures Related to Bisphosphonate Treatment. PMID:35052486
Single-cell transcriptomics of human iPSC differentiation dynamics reveal a core molecular network of Parkinson's disease. PMID:35027645
Benchmark Evaluation of Protein-Protein Interaction Prediction Algorithms. PMID:35011283
Prognostic Significance of CCNB2 Expression in Triple-Negative Breast Cancer. PMID:35002325
Cytochrome b561 Serves as a Potential Prognostic Biomarker and Target for Breast Cancer. PMID:35002301
Network analysis of host-pathogen protein interactions in microbe induced cardiovascular diseases. PMID:35001887
Machine learning-based predictions of dietary restriction associations across ageing-related genes. PMID:34983372
Understanding Gene Expression and Transcriptome Profiling of COVID-19: An Initiative Towards the Mapping of Protective Immunity Genes Against SARS-CoV-2 Infection. PMID:34975833
Integrative analysis of the molecular mechanisms, immunological features and immunotherapy response of ferroptosis regulators across 33 cancer types. PMID:34975326
A novel circRNA-miRNA-mRNA network reveals hsa-circ-0040039 as a biomarker for intervertebral disc degeneration. PMID:34939437
Targeting CK2 mediated signaling to impair/tackle SARS-CoV-2 infection: a computational biology approach. PMID:34930105
Characterization of the AGR2 Interactome Uncovers New Players of Protein Disulfide Isomerase Network in Cancer Cells. PMID:34929376
Protein network analysis to prioritize key genes in amyotrophic lateral sclerosis. PMID:34918006
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
XDeathDB: a visualization platform for cell death molecular interactions. PMID:34907160
MultiCapsNet: A General Framework for Data Integration and Interpretable Classification. PMID:34899854
Histone Chaperone Nucleophosmin Regulates Transcription of Key Genes Involved in Oral Tumorigenesis. PMID:34898280
MYC assembles and stimulates topoisomerases 1 and 2 in a "topoisome". PMID:34890565
Prolyl endopeptidase-like is a (thio)esterase involved in mitochondrial respiratory chain function. PMID:34888501
Study of Neuronal Apoptosis ceRNA Network in Hippocampal Sclerosis of Human Temporal Lobe Epilepsy by RNA-Seq. PMID:34867172
Predicting Bone Metastasis Using Gene Expression-Based Machine Learning Models. PMID:34858485
Loss of full-length hnRNP R isoform impairs DNA damage response in motoneurons by inhibiting Yb1 recruitment to chromatin. PMID:34850154
ConsensusPathDB 2022: molecular interactions update as a resource for network biology. PMID:34850110
Knowledge-guided artificial intelligence technologies for decoding complex multiomics interactions in cells. PMID:34844399
Therapeutic targeting of SPIB/SPI1-facilitated interplay of cancer cells and neutrophils inhibits aerobic glycolysis and cancer progression. PMID:34841706
Chromatin Accessibility and Transcriptomic Alterations in Murine Ovarian Granulosa Cells upon Deoxynivalenol Exposure. PMID:34831041
Immune Infiltration-Related Signature Predicts Risk Stratification and Immunotherapy Efficacy in Grade II and III Gliomas. PMID:34805164
Transcriptomic taxonomy and neurogenic trajectories of adult human, macaque, and pig hippocampal and entorhinal cells. PMID:34798047
Trends in biological data integration for the selection of enzymes and transcription factors related to cellulose and hemicellulose degradation in fungi. PMID:34777932
Bioinformatics approach to identify common gene signatures of patients with coronavirus 2019 and lung adenocarcinoma. PMID:34775559
Computationally Reconstructed Interactome of Bradyrhizobium diazoefficiens USDA110 Reveals Novel Functional Modules and Protein Hubs for Symbiotic Nitrogen Fixation. PMID:34769335
Computed structures of core eukaryotic protein complexes. PMID:34762488
The titin N2B and N2A regions: biomechanical and metabolic signaling hubs in cross-striated muscles. PMID:34745373
Network Biology Approaches to Achieve Precision Medicine in Inflammatory Bowel Disease. PMID:34745229
Network-based protein-protein interaction prediction method maps perturbations of cancer interactome. PMID:34727106
Hsp90 interaction networks in fungi-tools and techniques. PMID:34718512
Importance-Penalized Joint Graphical Lasso (IPJGL): differential network inference via GGMs. PMID:34718410
Centrality of drug targets in protein networks. PMID:34715787
AKIRIN2 controls the nuclear import of proteasomes in vertebrates. PMID:34711951
Improved supervised prediction of aging-related genes via weighted dynamic network analysis. PMID:34696741
DeepTrio: a ternary prediction system for protein-protein interaction using mask multiple parallel convolutional neural networks. PMID:34694333
Convergent genomic signatures of high-altitude adaptation among domestic mammals. PMID:34692117
Alternative Splicing Mechanisms Underlying Opioid-Induced Hyperalgesia. PMID:34680965
GAK and PRKCD are positive regulators of PRKN-independent mitophagy. PMID:34671015
Transcriptome profiling of pepper leaves by RNA-Seq during an incompatible and a compatible pepper-tobamovirus interaction. PMID:34667194
Identifying disease-gene associations using a convolutional neural network-based model by embedding a biological knowledge graph with entity descriptions. PMID:34653225
Predicting PY motif-mediated protein-protein interactions in the Nedd4 family of ubiquitin ligases. PMID:34637467
Efficient and accurate identification of protein complexes from protein-protein interaction networks based on the clustering coefficient. PMID:34630943
A survey on computational methods in discovering protein inhibitors of SARS-CoV-2. PMID:34623382
Pan-Cancer Analysis Reveals That E1A Binding Protein p300 Mutations Increase Genome Instability and Antitumor Immunity. PMID:34616736
Prediction of Protein-Protein Interactions in Arabidopsis, Maize, and Rice by Combining Deep Neural Network With Discrete Hilbert Transform. PMID:34616437
Proteomic analysis identifies novel binding partners of BAP1. PMID:34591877
Molecular Characterization of NDL1-AGB1 Mediated Salt Stress Signaling: Further Exploration of the Role of NDL1 Interacting Partners. PMID:34571915
Selectivity of Lewy body protein interactions along the aggregation pathway of α-synuclein. PMID:34556785
Identification of Novel Choroidal Neovascularization-Related Genes Using Laplacian Heat Diffusion Algorithm. PMID:34532497
Generalized and social anxiety disorder interactomes show distinctive overlaps with striosome and matrix interactomes. PMID:34526518
Towards Building a Quantitative Proteomics Toolbox in Precision Medicine: A Mini-Review. PMID:34512391
Exosomes Secreted by Adipose-Derived Stem Cells Following FK506 Stimulation Reduce Autophagy of Macrophages in Spine after Nerve Crush Injury. PMID:34502537
Inflammatory gene expression profiling in peripheral blood from patients with Alzheimer's disease reveals key pathways and hub genes with potential diagnostic utility: a preliminary study. PMID:34484988
Prospects and challenges of cancer systems medicine: from genes to disease networks. PMID:34471925
The chemical biology of coronavirus host-cell interactions. PMID:34458775
Drug Discovery of Spinal Muscular Atrophy (SMA) from the Computational Perspective: A Comprehensive Review. PMID:34445667
Proteomics of Mouse Heart Ventricles Reveals Mitochondria and Metabolism as Major Targets of a Post-Infarction Short-Acting GLP1Ra-Therapy. PMID:34445425
Bioinformatics analysis of the transcriptional expression of minichromosome maintenance proteins as potential indicators of survival in patients with cervical cancer. PMID:34404366
Machine learning approaches for drug combination therapies. PMID:34368832
Application and Perspectives of MALDI-TOF Mass Spectrometry in Clinical Microbiology Laboratories. PMID:34361974
TMEM135 is a Novel Regulator of Mitochondrial Dynamics and Physiology with Implications for Human Health Conditions. PMID:34359920
Revealing protein-protein interactions at the transcriptome scale by sequencing. PMID:34348091
Functional Roles of Bromodomain Proteins in Cancer. PMID:34298819
Integrating ensemble systems biology feature selection and bimodal deep neural network for breast cancer prognosis prediction. PMID:34290286
New approaches to predict the effect of co-occurring variants on protein characteristics. PMID:34256028
In silico-driven analysis of the Glossina morsitans morsitans antennae transcriptome in response to repellent or attractant compounds. PMID:34249514
Single-nucleus chromatin accessibility and transcriptomic characterization of Alzheimer's disease. PMID:34239132
E-type prostanoid receptor 4 drives resolution of intestinal inflammation by blocking epithelial necroptosis. PMID:34239062
GABA-receptive microglia selectively sculpt developing inhibitory circuits. PMID:34233165
Molecular Mechanisms Regulating the DNA Repair Protein APE1: A Focus on Its Flexible N-Terminal Tail Domain. PMID:34208390
Aurora Kinase A proximity map reveals centriolar satellites as regulators of its ciliary function. PMID:34169630
An information theoretic approach to link prediction in multiplex networks. PMID:34168194
LSTM-PHV: prediction of human-virus protein-protein interactions by LSTM with word2vec. PMID:34160596
Novel loci and potential mechanisms of major depressive disorder, bipolar disorder, and schizophrenia. PMID:34159505
Evolving scenario of big data and Artificial Intelligence (AI) in drug discovery. PMID:34159484
Genomes reveal selective sweeps in kiang and donkey for high-altitude adaptation. PMID:34156172
Side effect prediction based on drug-induced gene expression profiles and random forest with iterative feature selection. PMID:34155353
Mapping the multiscale structure of biological systems. PMID:34139169
Overexpression of human BAG3P209L in mice causes restrictive cardiomyopathy. PMID:34117258
Measuring pathway database coverage of the phosphoproteome. PMID:34113485
Proteomimetic surface fragments distinguish targets by function. PMID:34094300
Construction of Condition-Specific Gene Regulatory Network Using Kernel Canonical Correlation Analysis. PMID:34093651
PIGNON: a protein-protein interaction-guided functional enrichment analysis for quantitative proteomics. PMID:34088263
Mapping Proximity Associations of Core Spindle Assembly Checkpoint Proteins. PMID:34087075
A proximity-dependent biotinylation map of a human cell. PMID:34079125
Proteomic Analyses of Vitreous in Proliferative Diabetic Retinopathy: Prior Studies and Future Outlook. PMID:34070658
driveR: a novel method for prioritizing cancer driver genes using somatic genomics data. PMID:34030627
Up-regulated RFC2 predicts unfavorable progression in hepatocellular carcinoma. PMID:34022962
Utilizing graph machine learning within drug discovery and development. PMID:34013350
ERG transcription factors have a splicing regulatory function involving RBFOX2 that is altered in the EWS-FLI1 oncogenic fusion. PMID:34009296
Analyzing host-viral interactome of SARS-CoV-2 for identifying vulnerable host proteins during COVID-19 pathogenesis. PMID:34004362
SynLeGG: analysis and visualization of multiomics data for discovery of cancer 'Achilles Heels' and gene function relationships. PMID:33997893
The SARS-CoV-2 RNA interactome. PMID:33989516
Crinet: A computational tool to infer genome-wide competing endogenous RNA (ceRNA) interactions. PMID:33983999
Capturing dynamic relevance in Boolean networks using graph theoretical measures. PMID:33983406
Simultaneous learning of individual microRNA-gene interactions and regulatory comodules. PMID:33971820
A scheme for inferring viral-host associations based on codon usage patterns identifies the most affected signaling pathways during COVID-19. PMID:33965637
Integration of peripheral transcriptomics, genomics, and interactomics following trauma identifies causal genes for symptoms of post-traumatic stress and major depression. PMID:33963278
Muscle Glycogen Phosphorylase and Its Functional Partners in Health and Disease. PMID:33924466
Intrinsically Disordered Proteins as Regulators of Transient Biological Processes and as Untapped Drug Targets. PMID:33917117
Malignant Pleural Mesothelioma Interactome with 364 Novel Protein-Protein Interactions. PMID:33916178
Identification of the Key Role of NF-κB Signaling Pathway in the Treatment of Osteoarthritis With Bushen Zhuangjin Decoction, a Verification Based on Network Pharmacology Approach. PMID:33912052
Spatially resolved cell polarity proteomics of a human epiblast model. PMID:33893097
MultiVERSE: a multiplex and multiplex-heterogeneous network embedding approach. PMID:33888761
Algorithm-Based Meta-Analysis Reveals the Mechanistic Interaction of the Tumor Suppressor LIMD1 With Non-Small-Cell Lung Carcinoma. PMID:33869018
DUSP7 regulates the activity of ERK2 to promote proper chromosome alignment during cell division. PMID:33865857
Bioinformatic Analysis of Key Genes and Pathways Related to Keloids. PMID:33860039
Elucidating transcriptomic profiles from single-cell RNA sequencing data using nature-inspired compressed sensing. PMID:33855366
Persona2vec: a flexible multi-role representations learning framework for graphs. PMID:33834106
Predicting Protein-Protein Interactions Using Symmetric Logistic Matrix Factorization. PMID:33831302
Quantifying evolutionary importance of protein sites: A Tale of two measures. PMID:33826605
Detection of H3K4me3 Identifies NeuroHIV Signatures, Genomic Effects of Methamphetamine and Addiction Pathways in Postmortem HIV+ Brain Specimens that Are Not Amenable to Transcriptome Analysis. PMID:33805201
Next-generation yeast-two-hybrid analysis with Y2H-SCORES identifies novel interactors of the MLA immune receptor. PMID:33798202
A lysosomal enigma CLN5 and its significance in understanding neuronal ceroid lipofuscinosis. PMID:33792748
Gene Tracer: A smart, interactive, voice-controlled Alexa skill for gene information retrieval and browsing, mutation annotation, and network visualization. PMID:33792640
Structural and Drug Screening Analysis of the Non-structural Proteins of Severe Acute Respiratory Syndrome Coronavirus 2 Virus Extracted From Indian Coronavirus Disease 2019 Patients. PMID:33767730
PecanPy: a fast, efficient, and parallelized Python implementation of node2vec. PMID:33760066
Removing auto-activators from yeast-two-hybrid assays by conditional negative selection. PMID:33750818
Logical modeling of thymus and natural killer lymphocyte differentiation. PMID:33735399
Prioritization of schizophrenia risk genes from GWAS results by integrating multi-omics data. PMID:33731678
Gene variants of coagulation related proteins that interact with SARS-CoV-2. PMID:33730015
Protein context shapes the specificity of SH3 domain-mediated interactions in vivo. PMID:33712617
Repurposing novel therapeutic candidate drugs for coronavirus disease-19 based on protein-protein interaction network analysis. PMID:33711981
B7-H6 is a new potential biomarker and therapeutic target of T-lymphoblastic lymphoma. PMID:33708955
Identification of novel prognostic genes of triple-negative breast cancer using meta-analysis and weighted gene co-expressed network analysis. PMID:33708832
A Molecular Interaction Map of Klebsiella pneumoniae and Its Human Host Reveals Potential Mechanisms of Host Cell Subversion. PMID:33679637
Integrative Analysis Identified Key Schizophrenia Risk Factors from an Abnormal Behavior Mouse Gene Set. PMID:33672431
A weakened interface in the P182L variant of HSP27 associated with severe Charcot-Marie-Tooth neuropathy causes aberrant binding to interacting proteins. PMID:33644875
Gene Size Matters: An Analysis of Gene Length in the Human Genome. PMID:33643374
Enhanced Understanding of Molecular Interactions and Function Underlying Pain Processes Through Networks of Transcript Isoforms, Genes, and Gene Families. PMID:33633454
The Fate of Speckled Protein 100 (Sp100) During Herpesviruses Infection. PMID:33598438
Drug repurposing for COVID-19 via knowledge graph completion. PMID:33571675
Genetic control of the human brain proteome. PMID:33571421
RNA Sequencing Reveals Distinct Immune Responses in the Chorioamniotic Membranes of Women with Preterm Labor and Microbial or Sterile Intra-amniotic Inflammation. PMID:33558326
Protein-protein interaction analysis reveals a novel cancer stem cell related target TMEM17 in colorectal cancer. PMID:33549114
Role of Antizyme Inhibitor Proteins in Cancers and Beyond. PMID:33531815
Integrative analysis of transcriptomic data for identification of T-cell activation-related mRNA signatures indicative of preterm birth. PMID:33504832
Comparative analysis on the anti-inflammatory/immune effect of mesenchymal stem cell therapy for the treatment of pulmonary arterial hypertension. PMID:33479312
An empirical meta-analysis of the life sciences linked open data on the web. PMID:33479214
System-Wide Pollution of Biomedical Data: Consequence of the Search for Hub Genes of Hepatocellular Carcinoma Without Spatiotemporal Consideration. PMID:33475988
DeORFanizing Candida albicans Genes using Coexpression. PMID:33472984
Insights into the Mechanism of Bovine Spermiogenesis Based on Comparative Transcriptomic Studies. PMID:33466297
Devil in the details: Mechanistic variations impact information transfer across models of transcriptional cascades. PMID:33439904
Complementary and divergent functions of zebrafish Tango1 and Ctage5 in tissue development and homeostasis. PMID:33439675
Transcriptome analysis of cepharanthine against a SARS-CoV-2-related coronavirus. PMID:33423067
Biotin Proximity Labeling for Protein-Protein Interaction Discovery: The BioID Method. PMID:33421001
Elucidating the network features and evolutionary attributes of intra- and interspecific protein-protein interactions between human and pathogenic bacteria. PMID:33420198
PC2P: Parameter-free network-based prediction of protein complexes. PMID:33416831
Chemical Decorations of "MARs" Residents in Orchestrating Eukaryotic Gene Regulation. PMID:33409278
Bioinformatics analysis of common key genes and pathways of intracranial, abdominal, and thoracic aneurysms. PMID:33407182
Novel RB1 and MET Gene Mutations in a Case with Bilateral Retinoblastoma Followed by Multiple Metastatic Osteosarcoma. PMID:33375764
Systems Approach to Pathogenic Mechanism of Type 2 Diabetes and Drug Discovery Design Based on Deep Learning and Drug Design Specifications. PMID:33375269
Multi-task learning for the simultaneous reconstruction of the human and mouse gene regulatory networks. PMID:33339842
Identification of Interleukin-9 Producing Immune Cells in Endometrial Carcinoma and Establishment of a Prognostic Nomogram. PMID:33329510
Identifying Influencers in Social Networks. PMID:33286224
Growth of pancreatic cancers with hemizygous chromosomal 17p loss of MYBBP1A can be preferentially targeted by PARP inhibitors. PMID:33277249
A Novel Proximity Biotinylation Assay Based on the Self-Associating Split GFP1-10/11. PMID:33276494
CovMulNet19, Integrating Proteins, Diseases, Drugs, and Symptoms: A Network Medicine Approach to COVID-19. PMID:33274348
Tgfb3 and Mmp13 regulated the initiation of liver fibrosis progression as dynamic network biomarkers. PMID:33269546
BPI and KIR6.1 as significant hub genes for vein graft restenosis. PMID:33259239
The Path towards Predicting Evolution as Illustrated in Yeast Cell Polarity. PMID:33255231
EffectorK, a comprehensive resource to mine for Ralstonia, Xanthomonas, and other published effector interactors in the Arabidopsis proteome. PMID:33245626
Perversely expressed long noncoding RNAs can alter host response and viral proliferation in SARS-CoV-2 infection. PMID:33224264
ClusterM: a scalable algorithm for computational prediction of conserved protein complexes across multiple protein interaction networks. PMID:33208103
Tau Pathology Drives Dementia Risk-Associated Gene Networks toward Chronic Inflammatory States and Immunosuppression. PMID:33207193
The Landscape of Coronavirus Disease 2019 (COVID-19) and Integrated Analysis SARS-CoV-2 Receptors and Potential Inhibitors in Lung Adenocarcinoma Patients. PMID:33195212
H-RACS: a handy tool to rank anti-cancer synergistic drugs. PMID:33173014
Deciphering cell-cell interactions and communication from gene expression. PMID:33168968
SAlign-a structure aware method for global PPI network alignment. PMID:33148180
Functional module detection through integration of single-cell RNA sequencing data with protein-protein interaction networks. PMID:33138772
Extraction and Integration of Genetic Networks from Short-Profile Omic Data Sets. PMID:33137869
BIKE regulates dengue virus infection and is a cellular target for broad-spectrum antivirals. PMID:33137362
Genome-Wide Search for SNP Interactions in GWAS Data: Algorithm, Feasibility, Replication Using Schizophrenia Datasets. PMID:33133133
LAMP: disease classification derived from layered assessment on modules and pathways in the human gene network. PMID:33126852
Preclinical validation of therapeutic targets predicted by tensor factorization on heterogeneous graphs. PMID:33106501
Determinants of correlated expression of transcription factors and their target genes. PMID:33104784
Plasmatic Membrane Expression of Adhesion Molecules in Human Cardiac Progenitor/Stem Cells Might Explain Their Superior Cell Engraftment after Cell Transplantation. PMID:33101423
Discover novel disease-associated genes based on regulatory networks of long-range chromatin interactions. PMID:33096239
PyGNA: a unified framework for geneset network analysis. PMID:33092528
Implementation of homology based and non-homology based computational methods for the identification and annotation of orphan enzymes: using Mycobacterium tuberculosis H37Rv as a case study. PMID:33076816
The BioGRID database: A comprehensive biomedical resource of curated protein, genetic, and chemical interactions. PMID:33070389
LRRK2 mediates microglial neurotoxicity via NFATc2 in rodent models of synucleinopathies. PMID:33055242
Identification of Latent Oncogenes with a Network Embedding Method and Random Forest. PMID:33029511
Nano-ellagic acid: inhibitory actions on aldose reductase and α-glucosidase in secondary complications of diabetes, strengthened by in silico docking studies. PMID:32999815
Identification of potential gene drivers of cutaneous squamous cell carcinoma: Analysis of microarray data. PMID:32991423
Yeast Ppz1 protein phosphatase toxicity involves the alteration of multiple cellular targets. PMID:32973189
Cilia interactome with predicted protein-protein interactions reveals connections to Alzheimer's disease, aging and other neuropsychiatric processes. PMID:32973177
Graph embedding-based novel protein interaction prediction via higher-order graph convolutional network. PMID:32970681
Mining genetic and transcriptomic data using machine learning approaches in Parkinson's disease. PMID:32964109
DeepHE: Accurately predicting human essential genes based on deep learning. PMID:32936825
Potential impact on coagulopathy of gene variants of coagulation related proteins that interact with SARS-CoV-2. PMID:32935103
MasterPATH: network analysis of functional genomics screening data. PMID:32928103
Genome-Wide Identification of RNA Editing Sites Affecting Intramuscular Fat in Pigs. PMID:32927662
A large accessory protein interactome is rewired across environments. PMID:32924934
A functionally defined high-density NRF2 interactome reveals new conditional regulators of ARE transactivation. PMID:32911434
Investigating the Role of Telomere and Telomerase Associated Genes and Proteins in Endometrial Cancer. PMID:32899298
Investigating Core Signaling Pathways of Hepatitis B Virus Pathogenesis for Biomarkers Identification and Drug Discovery via Systems Biology and Deep Learning Method. PMID:32878239
Link prediction in real-world multiplex networks via layer reconstruction method. PMID:32874603
Systems Analysis of Biliary Atresia Through Integration of High-Throughput Biological Data. PMID:32848883
Lasting and Sex-Dependent Impact of Maternal Immune Activation on Molecular Pathways of the Amygdala. PMID:32848554
Hypoxia Predicts Poor Prognosis in Neuroblastoma Patients and Associates with Biological Mechanisms Involved in Telomerase Activation and Tumor Microenvironment Reprogramming. PMID:32825087
Analytical Guidelines for co-fractionation Mass Spectrometry Obtained through Global Profiling of Gold Standard Saccharomyces cerevisiae Protein Complexes. PMID:32817346
Integrative genomics approach identifies conserved transcriptomic networks in Alzheimer's disease. PMID:32803238
Mycoplasma hyopneumoniae J elicits an antioxidant response and decreases the expression of ciliary genes in infected swine epithelial cells. PMID:32792522
Computational Methods for Predicting Functions at the mRNA Isoform Level. PMID:32784445
The REGγ inhibitor NIP30 increases sensitivity to chemotherapy in p53-deficient tumor cells. PMID:32764536
Global Analysis of Cereal microProteins Suggests Diverse Roles in Crop Development and Environmental Adaptation. PMID:32763954
Regulation of Trpm activation and calcium wave initiation during Drosophila egg activation. PMID:32735035
Network Approaches for Dissecting the Immune System. PMID:32717640
Kinase Interaction Network Expands Functional and Disease Roles of Human Kinases. PMID:32707033
Interactome of SARS-CoV-2 / nCoV19 modulated host proteins with computationally predicted PPIs. PMID:32702714
Proteinarium: Multi-sample protein-protein interaction analysis and visualization tool. PMID:32702417
Identification of COVID-19 Infection-Related Human Genes Based on a Random Walk Model in a Virus-Human Protein Interaction Network. PMID:32685484
uKIN Combines New and Prior Information with Guided Network Propagation to Accurately Identify Disease Genes. PMID:32684276
Phylogenetic analysis of the Tc1/mariner superfamily reveals the unexplored diversity of pogo-like elements. PMID:32612713
Extensive signal integration by the phytohormone protein network. PMID:32612234
Selective Neuronal Vulnerability in Alzheimer's Disease: A Network-Based Analysis. PMID:32603655
Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses. PMID:32597660
Expansions of chemosensory gene orthologs among selected tsetse fly species and their expressions in Glossina morsitans morsitans tsetse fly. PMID:32589659
Symmetries and cluster synchronization in multilayer networks. PMID:32576813
Genome-wide Enrichment of De Novo Coding Mutations in Orofacial Cleft Trios. PMID:32574564
Comprehensive Analysis of Prognostic Alternative Splicing Signatures in Endometrial Cancer. PMID:32547595
A flexible network-based imputing-and-fusing approach towards the identification of cell types from single-cell RNA-seq data. PMID:32527285
Proteomic profiling of the monothiol glutaredoxin Grx3 reveals its global role in the regulation of iron dependent processes. PMID:32525871
MIPPIE: the mouse integrated protein-protein interaction reference. PMID:32496562
MeCP2 facilitates breast cancer growth via promoting ubiquitination-mediated P53 degradation by inhibiting RPL5/RPL11 transcription. PMID:32483207
Updating dual-specificity tyrosine-phosphorylation-regulated kinase 2 (DYRK2): molecular basis, functions and role in diseases. PMID:32462403
Structural and Functional Analyses of the FAM46C/Plk4 Complex. PMID:32433990
Humanization of yeast genes with multiple human orthologs reveals functional divergence between paralogs. PMID:32421706
G2G: A web-server for the prediction of human synthetic lethal interactions. PMID:32419903
Neural networks for open and closed Literature-based Discovery. PMID:32413059
Mutation severity spectrum of rare alleles in the human genome is predictive of disease type. PMID:32413045
Molecular determinants underlying functional innovations of TBP and their impact on transcription initiation. PMID:32404905
A massively parallel barcoded sequencing pipeline enables generation of the first ORFeome and interactome map for rice. PMID:32398372
RESTful API for iPTMnet: a resource for protein post-translational modification network discovery. PMID:32395768
The tapeworm interactome: inferring confidence scored protein-protein interactions from the proteome of Hymenolepis microstoma. PMID:32380953
PDZ Domains as Drug Targets. PMID:32313833
Predicting Protein Functions Based on Differential Co-expression and Neighborhood Analysis. PMID:32302512
Modulation of stress and immune response by Amblyomin-X results in tumor cell death in a horse melanoma model. PMID:32286411
Systems Biology Analysis of the Antagonizing Effects of HIV-1 Tat Expression in the Brain over Transcriptional Changes Caused by Methamphetamine Sensitization. PMID:32283831
HIPPIE2: a method for fine-scale identification of physically interacting chromatin regions. PMID:32270138
Whole-Genome and RNA Sequencing Reveal Variation and Transcriptomic Coordination in the Developing Human Prefrontal Cortex. PMID:32268104
Proximity mapping of the microtubule plus-end tracking protein SLAIN2 using the BioID approach. PMID:32256142
A network analysis to identify pathophysiological pathways distinguishing ischaemic from non-ischaemic heart failure. PMID:32243695
Loss-of-function tolerance of enhancers in the human genome. PMID:32243438
Sex-specific and shared expression profiles of vulnerability and resilience to trauma in brain and blood. PMID:32228684
HNF4A-AS1/hnRNPU/CTCF axis as a therapeutic target for aerobic glycolysis and neuroblastoma progression. PMID:32216806
Coupled matrix-matrix and coupled tensor-matrix completion methods for predicting drug-target interactions. PMID:32186716
A homozygous missense variant in CACNB4 encoding the auxiliary calcium channel beta4 subunit causes a severe neurodevelopmental disorder and impairs channel and non-channel functions. PMID:32176688
Overexpression of the Selective Autophagy Cargo Receptor NBR1 Modifies Plant Response to Sulfur Deficit. PMID:32164165
Supervised learning is an accurate method for network-based gene classification. PMID:32129827
Stitching the synapse: Cross-linking mass spectrometry into resolving synaptic protein interactions. PMID:32128395
Exploring Integrative Analysis Using the BioMedical Evidence Graph. PMID:32097025
Hierarchy and levels: analysing networks to study mechanisms in molecular biology. PMID:32089112
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
Long-term survivors of early breast cancer treated with chemotherapy are characterized by a pro-inflammatory biomarker profile compared to matched controls. PMID:32078215
Collective intelligence defines biological functions in Wikipedia as communities in the hidden protein connection network. PMID:32069277
Integrated analysis and knockdown of RAB23 indicate the role of RAB23 in gastric adenocarcinoma. PMID:32042761
Genetic screens in isogenic mammalian cell lines without single cell cloning. PMID:32029722
Pathway and network analysis of more than 2500 whole cancer genomes. PMID:32024854
Identification of cancer driver genes based on nucleotide context. PMID:32015527
Genomic Features and Clinical Characteristics of Adolescents and Young Adults With Cholangiocarcinoma. PMID:32010606
Developing a virus-microRNA interactome using cytoscape. PMID:31993337
Comparative Genomic Mapping Implicates LRRK2 for Intellectual Disability and Autism at 12q12, and HDHD1, as Well as PNPLA4, for X-Linked Intellectual Disability at Xp22.31. PMID:31963867
TMEM98 is a negative regulator of FRAT mediated Wnt/ß-catenin signalling. PMID:31961879
Mmi1, the Yeast Ortholog of Mammalian Translationally Controlled Tumor Protein (TCTP), Negatively Affects Rapamycin-Induced Autophagy in Post-Diauxic Growth Phase. PMID:31936125
BCOR-coupled H2A monoubiquitination represses a subset of androgen receptor target genes regulating prostate cancer proliferation. PMID:31925334
Puupehenone, a Marine-Sponge-Derived Sesquiterpene Quinone, Potentiates the Antifungal Drug Caspofungin by Disrupting Hsp90 Activity and the Cell Wall Integrity Pathway. PMID:31915228
Casein Kinase 1δ Stabilizes Mature Axons by Inhibiting Transcription Termination of Ankyrin. PMID:31910362
Interpreting pathways to discover cancer driver genes with Moonlight. PMID:31900418
Substrate specificity of thioredoxins and glutaredoxins - towards a functional classification. PMID:31890941
Human protein-RNA interaction network is highly stable across mammals. PMID:31888461
Matrisome-Associated Gene Expression Patterns Correlating with TIMP2 in Cancer. PMID:31882975
Transcription factor regulatory modules provide the molecular mechanisms for functional redundancy observed among transcription factors in yeast. PMID:31881824
Refining modules to determine functionally significant clusters in molecular networks. PMID:31874644
HPOAnnotator: improving large-scale prediction of HPO annotations by low-rank approximation with HPO semantic similarities and multiple PPI networks. PMID:31865916
LRRK2 Biology from structure to dysfunction: research progresses, but the themes remain the same. PMID:31864390
Nuclear factor erythroid 2 - related factor 2 and its relationship with cellular response in nickel exposure: a systems biology analysis. PMID:31852525
Improving drug response prediction by integrating multiple data sources: matrix factorization, kernel and network-based approaches. PMID:31838491
The human DEPhOsphorylation Database DEPOD: 2019 update. PMID:31836896
An Integrated Pan-Cancer Analysis and Structure-Based Virtual Screening of GPR15. PMID:31835584
Defined factors to reactivate cell cycle activity in adult mouse cardiomyocytes. PMID:31827131
Transcriptome Meta-Analysis Deciphers a Dysregulation in Immune Response-Associated Gene Signatures during Sepsis. PMID:31817302
The oncogenic potential of small nuclear ribonucleoprotein polypeptide G: a comprehensive and perspective view. PMID:31814883
Impact of negative lymph nodes on colon cancer survival and exploring relevant transcriptomics differences through real-world data analyses. PMID:31807507
Leveraging User-Friendly Network Approaches to Extract Knowledge From High-Throughput Omics Datasets. PMID:31798629
CERENKOV3: Clustering and molecular network-derived features improve computational prediction of functional noncoding SNPs. PMID:31797625
DeepEP: a deep learning framework for identifying essential proteins. PMID:31787076
Glycogen branching enzyme controls cellular iron homeostasis via Iron Regulatory Protein 1 and mitoNEET. PMID:31784520
Network Modeling Approaches and Applications to Unravelling Non-Alcoholic Fatty Liver Disease. PMID:31771247
Identifying gene function and module connections by the integration of multispecies expression compendia. PMID:31754022
Estimating network changes from lifespan measurements using a parsimonious gene network model of cellular aging. PMID:31747877
Is MYND Domain-Mediated Assembly of SMYD3 Complexes Involved in Calcium Dependent Signaling? PMID:31737645
Investigation of Proteomic and Phosphoproteomic Responses to Signaling Network Perturbations Reveals Functional Pathway Organizations in Yeast. PMID:31722220
Genetic Loci Associated with Early Salt Stress Responses of Roots. PMID:31707259
Sudden unexpected death in asymptomatic infants due to PPA2 variants. PMID:31705601
Co-regulation map of the human proteome enables identification of protein functions. PMID:31690884
Oxoglutarate dehydrogenase and acetyl-CoA acyltransferase 2 selectively associate with H2A.Z-occupied promoters and are required for histone modifications. PMID:31682939
UBASH3A Regulates the Synthesis and Dynamics of TCR-CD3 Complexes. PMID:31659016
Pathway Commons 2019 Update: integration, analysis and exploration of pathway data. PMID:31647099
Common Nodes of Virus-Host Interaction Revealed Through an Integrated Network Analysis. PMID:31636628
Gene Repositioning Is Under Constraints After Evolutionary Conserved Gene Neighborhood Separate. PMID:31632448
Experimental evolution reveals a general role for the methyltransferase Hmt1 in noise buffering. PMID:31613873
pathfindR: An R Package for Comprehensive Identification of Enriched Pathways in Omics Data Through Active Subnetworks. PMID:31608109
Filaments and phenotypes: cellular roles and orphan effects associated with mutations in cytoplasmic intermediate filament proteins. PMID:31602295
Patterns and Constraints in the Evolution of Sperm Individualization Genes in Insects, with an Emphasis on Beetles. PMID:31590243
Conserved Central Intraviral Protein Interactome of the Herpesviridae Family. PMID:31575665
Pyk2-dependent phosphorylation of LSR enhances localization of LSR and tricellulin at tricellular tight junctions. PMID:31574128
Broad Phenotypes of Disorders/Differences of Sex Development in MAMLD1 Patients Through Oligogenic Disease. PMID:31555317
Single-cell transcriptomic profiling of the aging mouse brain. PMID:31551601
Enabling Web-scale data integration in biomedicine through Linked Open Data. PMID:31531395
Identifying Protein Complexes from Dynamic Temporal Interval Protein-Protein Interaction Networks. PMID:31531351
Identifying protein complexes based on an edge weight algorithm and core-attachment structure. PMID:31521132
miR-486 is modulated by stretch and increases ventricular growth. PMID:31513548
In vivo epigenetic editing of Sema6a promoter reverses transcallosal dysconnectivity caused by C11orf46/Arl14ep risk gene. PMID:31511512
CSF1R inhibitor JNJ-40346527 attenuates microglial proliferation and neurodegeneration in P301S mice. PMID:31504240
Gene Cascade Finder: A tool for identification of gene cascades and its application in Caenorhabditis elegans. PMID:31504044
Chromobox homolog 8 (CBX8) Interacts with Y-Box binding protein 1 (YBX1) to promote cellular proliferation in hepatocellular carcinoma cells. PMID:31495785
The MyMOMA domain of MYO19 encodes for distinct Miro-dependent and Miro-independent mechanisms of interaction with mitochondrial membranes. PMID:31479585
Application of hyperbolic geometry in link prediction of multiplex networks. PMID:31471541
The role of structural pleiotropy and regulatory evolution in the retention of heteromers of paralogs. PMID:31454312
Transcriptome and Network Dissection of Microsatellite Stable and Highly Instable Colorectal Cancer. PMID:31450919
Hamiltonian energy as an efficient approach to identify the significant key regulators in biological networks. PMID:31442253
Machine learning empowers phosphoproteome prediction in cancers. PMID:31410451
The interactome of KRAB zinc finger proteins reveals the evolutionary history of their functional diversification. PMID:31403225
A seed-extended algorithm for detecting protein complexes based on density and modularity with topological structure and GO annotations. PMID:31390979
Nuclear envelope deformation controls cell cycle progression in response to mechanical force. PMID:31368207
Detection of dynamic protein complexes through Markov Clustering based on Elephant Herd Optimization Approach. PMID:31366992
A comprehensive study on genome-wide coexpression network of KHDRBS1/Sam68 reveals its cancer and patient-specific association. PMID:31366900
Endogenous IQGAP1 and IQGAP3 do not functionally interact with Ras. PMID:31363101
Identification of Upregulated HNRNPs Associated with Poor Prognosis in Pancreatic Cancer. PMID:31355266
Rad5 dysregulation drives hyperactive recombination at replication forks resulting in cisplatin sensitivity and genome instability. PMID:31350889
Identification of differentially expressed genes in small and non-small cell lung cancer based on meta-analysis of mRNA. PMID:31338439
Tunicamycin Sensitivity-Suppression by High Gene Dosage Reveals New Functions of the Yeast Hog1 MAP Kinase. PMID:31336877
Contrasting Gene Expression Profiles of Monocytes and Lymphocytes From Peste-Des-Petits-Ruminants Virus Infected Goats. PMID:31333643
CAGI5: Objective performance assessments of predictions based on the Evolutionary Action equation. PMID:31317604
A systematic approach to orient the human protein-protein interaction network. PMID:31289271
Uncovering biomarker genes with enriched classification potential from Hallmark gene sets. PMID:31278367
Cancer driver genes: a guilty by resemblance doctrine. PMID:31275738
Fibril-induced glutamine-/asparagine-rich prions recruit stress granule proteins in mammalian cells. PMID:31266883
Inferring Interaction Networks From Multi-Omics Data. PMID:31249591
Augmenting subnetwork inference with information extracted from the scientific literature. PMID:31246951
Multi-omics Characterization of Interaction-mediated Control of Human Protein Abundance levels. PMID:31239291
Computational analysis of single-cell transcriptomics data elucidates the stabilization of Oct4 expression in the E3.25 mouse preimplantation embryo. PMID:31222057
Protein interactions and consensus clustering analysis uncover insights into herpesvirus virion structure and function relationships. PMID:31199794
Using genetics to understand biology. PMID:31189902
Rapid Evolution of Gained Essential Developmental Functions of a Young Gene via Interactions with Other Essential Genes. PMID:31187122
Differential gene expression analysis of human cumulus cells. PMID:31181875
Boolean gene regulatory network model of centromere function in Saccharomyces cerevisiae. PMID:31175490
Identification of Endogenous Adenomatous Polyposis Coli Interaction Partners and β-Catenin-Independent Targets by Proteomics. PMID:31160382
Opioid-Induced Hyperalgesia Is Associated with Dysregulation of Circadian Rhythm and Adaptive Immune Pathways in the Mouse Trigeminal Ganglia and Nucleus Accumbens. PMID:31129808
Identification of genes underlying phenotypic plasticity of wing size via insulin signaling pathway by network-based analysis in Sogatella furcifera. PMID:31113376
Murine obscurin and Obsl1 have functionally redundant roles in sarcolemmal integrity, sarcoplasmic reticulum organization, and muscle metabolism. PMID:31098411
Optimized Cross-Linking Mass Spectrometry for in Situ Interaction Proteomics. PMID:31083951
A White-Box Machine Learning Approach for Revealing Antibiotic Mechanisms of Action. PMID:31080069
Associating expression and genomic data using co-occurrence measures. PMID:31072345
modEnrichr: a suite of gene set enrichment analysis tools for model organisms. PMID:31069376
Automated assessment of biological database assertions using the scientific literature. PMID:31035936
Topological and functional comparison of community detection algorithms in biological networks. PMID:31029085
Deciphering the three-domain architecture in schlafens and the structures and roles of human schlafen12 and serpinB12 in transcriptional regulation. PMID:31026779
A context-based ABC model for literature-based discovery. PMID:31017923
Predicting synthetic lethal interactions using conserved patterns in protein interaction networks. PMID:30995217
Cullin-3 dependent deregulation of ACTN1 represents a new pathogenic mechanism in nemaline myopathy. PMID:30990797
Pathway centrality in protein interaction networks identifies putative functional mediating pathways in pulmonary disease. PMID:30971743
Downregulation of CENPF Remodels Prostate Cancer Cells and Alters Cellular Metabolism. PMID:30957416
GNE: a deep learning framework for gene network inference by aggregating biological information. PMID:30953525
Disease association of human tumor suppressor genes. PMID:30945018
Cx43-Associated Secretome and Interactome Reveal Synergistic Mechanisms for Glioma Migration and MMP3 Activation. PMID:30941001
Meta-path Based Prioritization of Functional Drug Actions with Multi-Level Biological Networks. PMID:30940832
A Genome-Wide Analysis of the Penumbral Volume in Inbred Mice following Middle Cerebral Artery Occlusion. PMID:30911049
Expression, purification and crystallization of the novel Xenopus tropicalis ALDH16B1, a homologue of human ALDH16A1. PMID:30894314
Identification of Important Effector Proteins in the FOXJ1 Transcriptional Network Associated With Ciliogenesis and Ciliary Function. PMID:30881373
DDOT: A Swiss Army Knife for Investigating Data-Driven Biological Ontologies. PMID:30878356
Prioritization of genes involved in endothelial cell apoptosis by their implication in lymphedema using an analysis of associative gene networks with ANDSystem. PMID:30871556
AIControl: replacing matched control experiments with machine learning improves ChIP-seq peak identification. PMID:30869146
MorCVD: A Unified Database for Host-Pathogen Protein-Protein Interactions of Cardiovascular Diseases Related to Microbes. PMID:30858555
Expression and Characterization of Human Fragile X Mental Retardation Protein Isoforms and Interacting Proteins in Human Cells. PMID:30853789
Deciphering the complex role of thrombospondin-1 in glioblastoma development. PMID:30850588
Environment-dependent fitness gains can be driven by horizontal gene transfer of transporter-encoding genes. PMID:30842288
Compendium of synovial signatures identifies pathologic characteristics for predicting treatment response in rheumatoid arthritis patients. PMID:30831253
Magic roundabout is an endothelial-specific ohnolog of ROBO1 which neo-functionalized to an essential new role in angiogenesis. PMID:30802244
Reduced mitochondrial fusion and Huntingtin levels contribute to impaired dendritic maturation and behavioral deficits in Fmr1-mutant mice. PMID:30742117
Data mining for mutation-specific targets in acute myeloid leukemia. PMID:30728456
Ubiquinol-cytochrome C reductase core protein II promotes tumorigenesis by facilitating p53 degradation. PMID:30674441
A De Novo Shape Motif Discovery Algorithm Reveals Preferences of Transcription Factors for DNA Shape Beyond Sequence Motifs. PMID:30660610
Translational control mechanisms in cutaneous malignant melanoma: the role of eIF2α. PMID:30634982
UbiHub: a data hub for the explorers of ubiquitination pathways. PMID:30601939
Time-lagged Ordered Lasso for network inference. PMID:30594121
Identification of genes required for eye development by high-throughput screening of mouse knockouts. PMID:30588515
Protein complexes identification based on go attributed network embedding. PMID:30572820
Systems biology analysis reveals new insights into invasive lung cancer. PMID:30547817
Aberrantly expressed long noncoding RNAs and genes in Parkinson's disease. PMID:30538480
Genomic identification and functional analysis of essential genes in Caenorhabditis elegans. PMID:30514206
Subgrouping breast cancer patients based on immune evasion mechanisms unravels a high involvement of transforming growth factor-beta and decoy receptor 3. PMID:30513096
Identification of evolutionarily conserved gene networks mediating neurodegenerative dementia. PMID:30510257
Genome-wide identification of RETINOBLASTOMA RELATED 1 binding sites in Arabidopsis reveals novel DNA damage regulators. PMID:30500810
ERRα promotes breast cancer cell dissemination to bone by increasing RANK expression in primary breast tumors. PMID:30478447
Heterologous Hsp90 promotes phenotypic diversity through network evolution. PMID:30439936
An E2-ubiquitin thioester-driven approach to identify substrates modified with ubiquitin and ubiquitin-like molecules. PMID:30429481
Integration of Tumor Genomic Data with Cell Lines Using Multi-dimensional Network Modules Improves Cancer Pharmacogenomics. PMID:30414925
The protein interaction networks of mucolipins and two-pore channels. PMID:30395881
Characterization of Squamous Cell Lung Cancers from Appalachian Kentucky. PMID:30377206
Computational discovery of dynamic cell line specific Boolean networks from multiplex time-course data. PMID:30372442
Antiviral activity of the mineralocorticoid receptor NR3C2 against Herpes simplex virus Type 1 (HSV-1) infection. PMID:30367157
Transcriptomic and functional network features of lung squamous cell carcinoma through integrative analysis of GEO and TCGA data. PMID:30367091
Establishment of stably expandable induced myogenic stem cells by four transcription factors. PMID:30361642
Modelling Self-Organization in Complex Networks Via a Brain-Inspired Network Automata Theory Improves Link Reliability in Protein Interactomes. PMID:30361555
Defining Essentiality Score of Protein-Coding Genes and Long Noncoding RNAs. PMID:30356729
Use of Laplacian Heat Diffusion Algorithm to Infer Novel Genes With Functions Related to Uveitis. PMID:30349554
Affinity capture of polyribosomes followed by RNAseq (ACAPseq), a discovery platform for protein-protein interactions. PMID:30345971
The 7q11.23 Protein DNAJC30 Interacts with ATP Synthase and Links Mitochondria to Brain Development. PMID:30318146
Discovering Genetic Factors for psoriasis through exhaustively searching for significant second order SNP-SNP interactions. PMID:30315195
Domain architecture of BAF250a reveals the ARID and ARM-repeat domains with implication in function and assembly of the BAF remodeling complex. PMID:30307988
Fyn Regulates Binding Partners of Cyclic-AMP Dependent Protein Kinase A. PMID:30274258
Launching the C-HPP neXt-CP50 Pilot Project for Functional Characterization of Identified Proteins with No Known Function. PMID:30269496
The Systems Biology of Single-Cell Aging. PMID:30267677
A mitochondrial proteome profile indicative of type 2 diabetes mellitus in skeletal muscles. PMID:30266947
Deubiquitinase Usp12 functions noncatalytically to induce autophagy and confer neuroprotection in models of Huntington's disease. PMID:30266909
WEADE: A workflow for enrichment analysis and data exploration. PMID:30265728
Identifying Drivers of Parallel Evolution: A Regression Model Approach. PMID:30252076
Bioinformatics Analysis Identifies p53 as a Candidate Prognostic Biomarker for Neuropathic Pain. PMID:30233637
Exploring transcription factors reveals crucial members and regulatory networks involved in different abiotic stresses in Brassica napus L. PMID:30231862
Quantifying layer similarity in multiplex networks: a systematic study. PMID:30224981
Insights into archaeal chaperone machinery: a network-based approach. PMID:30178307
Loss of the E3 ubiquitin ligase MKRN1 represses diet-induced metabolic syndrome through AMPK activation. PMID:30143610
Multi-omic Directed Networks Describe Features of Gene Regulation in Aged Brains and Expand the Set of Genes Driving Cognitive Decline. PMID:30140277
Targeting Focal Adhesion Kinase Using Inhibitors of Protein-Protein Interactions. PMID:30134553
Bioinformatics analysis to screen for critical genes between survived and non‑survived patients with sepsis. PMID:30132542
Genome-wide Identification and Characterization of Enhancers Across 10 Human Tissues. PMID:30123079
Dynamical Analysis of the Regulatory Network Controlling Natural Killer Cells Differentiation. PMID:30116200
Synstable Fusion: A Network-Based Algorithm for Estimating Driver Genes in Fusion Structures. PMID:30115851
Convex skeletons of complex networks. PMID:30111666
A Methodological Assessment and Characterization of Genetically-Driven Variation in Three Human Phosphoproteomes. PMID:30108239
Reconstruction of the Protein-Protein Interaction Network for Protein Complexes Identification by Walking on the Protein Pair Fingerprints Similarity Network. PMID:30087694
Evolution of In Silico Strategies for Protein-Protein Interaction Drug Discovery. PMID:30082644
Brain region-dependent gene networks associated with selective breeding for increased voluntary wheel-running behavior. PMID:30071007
Automatic extraction of protein-protein interactions using grammatical relationship graph. PMID:30066644
Cross-species systems analysis identifies gene networks differentially altered by sleep loss and depression. PMID:30050989
From systems to biology: A computational analysis of the research articles on systems biology from 1992 to 2013. PMID:30044828
ProfPPIdb: Pairs of physical protein-protein interactions predicted for entire proteomes. PMID:30020956
Cancerin: A computational pipeline to infer cancer-associated ceRNA interaction networks. PMID:30011266
Leveraging prior knowledge for protein-protein interaction extraction with memory network. PMID:30010731
Loss of tumor suppressor IGFBP4 drives epigenetic reprogramming in hepatic carcinogenesis. PMID:29992318
Genome-wide SWAp-Tag yeast libraries for proteome exploration. PMID:29988094
Time-resolved transcriptomics in neural stem cells identifies a v-ATPase/Notch regulatory loop. PMID:29959232
Systems-Based Interactome Analysis for Hematopoiesis Effect of Angelicae sinensis Radix: Regulated Network of Cell Proliferation towards Hemopoiesis. PMID:29943236
Chromatin That Guides Dosage Compensation Is Modulated by the siRNA Pathway in Drosophila melanogaster. PMID:29921620
A new method for predicting essential proteins based on participation degree in protein complex and subgraph density. PMID:29894517
Exploring Landscape of Drug-Target-Pathway-Side Effect Associations. PMID:29888057
Network-based machine learning and graph theory algorithms for precision oncology. PMID:29872707
Identification of MOSPD2, a novel scaffold for endoplasmic reticulum membrane contact sites. PMID:29858488
PhosContext2vec: a distributed representation of residue-level sequence contexts and its application to general and kinase-specific phosphorylation site prediction. PMID:29844483
Evidence for interaction between Hsp90 and the ER membrane complex. PMID:29808299
eXpression2Kinases (X2K) Web: linking expression signatures to upstream cell signaling networks. PMID:29800326
A website to identify shared genes in Saccharomyces cerevisiae homozygous deletion library screens. PMID:29792161
Neural networks for link prediction in realistic biomedical graphs: a multi-dimensional evaluation of graph embedding-based approaches. PMID:29783926
Discovering novel SNPs that are correlated with patient outcome in a Singaporean cancer patient cohort treated with gemcitabine-based chemotherapy. PMID:29751792
INTERSPIA: a web application for exploring the dynamics of protein-protein interactions among multiple species. PMID:29746660
PPI network analyses of human WD40 protein family systematically reveal their tendency to assemble complexes and facilitate the complex predictions. PMID:29745845
Network inference reveals novel connections in pathways regulating growth and defense in the yeast salt response. PMID:29738528
LncRNA OIP5-AS1 is overexpressed in undifferentiated oral tumors and integrated analysis identifies as a downstream effector of stemness-associated transcription factors. PMID:29728583
Core signaling pathways in ovarian cancer stem cell revealed by integrative analysis of multi-marker genomics data. PMID:29723215
Role of duplicate genes in determining the tissue-selectivity of hereditary diseases. PMID:29723191
Delineating the HMGB1 and HMGB2 interactome in prostate and ovary epithelial cells and its relationship with cancer. PMID:29721183
An RNAi-mediated screen identifies novel targets for next-generation antiepileptic drugs based on increased expression of the homeostatic regulator pumilio. PMID:29718742
New perspectives: systems medicine in cardiovascular disease. PMID:29699591
Determining the minimum number of protein-protein interactions required to support known protein complexes. PMID:29698482
An epistatic effect of KRT25 on SP6 is involved in curly coat in horses. PMID:29686323
Integrative bioinformatics analysis characterizing the role of EDC3 in mRNA decay and its association to intellectual disability. PMID:29685133
The Interactomic Analysis Reveals Pathogenic Protein Networks in Phomopsis longicolla Underlying Seed Decay of Soybean. PMID:29666630
Functional Analysis of Hif1 Histone Chaperone in Saccharomyces cerevisiae. PMID:29661843
Massive mining of publicly available RNA-seq data from human and mouse. PMID:29636450
Predicting essential proteins by integrating orthology, gene expressions, and PPI networks. PMID:29634727
MTGO: PPI Network Analysis Via Topological and Functional Module Identification. PMID:29615773
Systematic Evaluation of Molecular Networks for Discovery of Disease Genes. PMID:29605183
Promoter architecture determines cotranslational regulation of mRNA. PMID:29567675
Predicting protein complexes using a supervised learning method combined with local structural information. PMID:29554120
Integrated analysis of microarray data to identify the genes critical for the rupture of intracranial aneurysm. PMID:29552131
BIOPYDB: A Dynamic Human Cell Specific Biochemical Pathway Database with Advanced Computational Analyses Platform. PMID:29547394
Expression of reactive species related genes is associated with patient survival in luminal B breast cancer. PMID:29545070
Formation of chimeric genes with essential functions at the origin of eukaryotes. PMID:29534719
Predicted Arabidopsis Interactome Resource and Gene Set Linkage Analysis: A Transcriptomic Analysis Resource. PMID:29530937
Combined use of protein biomarkers and network analysis unveils deregulated regulatory circuits in Duchenne muscular dystrophy. PMID:29529088
Analysis of Gene Regulatory Networks of Maize in Response to Nitrogen. PMID:29518046
A peripheral blood transcriptomic signature predicts autoantibody development in infants at risk of type 1 diabetes. PMID:29515040
Multi-chaperone function modulation and association with cytoskeletal proteins are key features of the function of AIP in the pituitary gland. PMID:29507682
Improving prediction of heterodimeric protein complexes using combination with pairwise kernel. PMID:29504897
Yersinia pestis Targets the Host Endosome Recycling Pathway during the Biogenesis of the Yersinia-Containing Vacuole To Avoid Killing by Macrophages. PMID:29463656
Combinatorial CRISPR-Cas9 Metabolic Screens Reveal Critical Redox Control Points Dependent on the KEAP1-NRF2 Regulatory Axis. PMID:29452643
Distinct methylation profile of mucinous ovarian carcinoma reveals susceptibility to proteasome inhibitors. PMID:29451304
Dynamic network biomarker indicates pulmonary metastasis at the tipping point of hepatocellular carcinoma. PMID:29445139
The rolB plant oncogene affects multiple signaling protein modules related to hormone signaling and plant defense. PMID:29396465
Binding and entry of peste des petits ruminants virus into caprine endometrial epithelial cells profoundly affect early cellular gene expression. PMID:29368634
Three-dimensional spatial analysis of missense variants in RTEL1 identifies pathogenic variants in patients with Familial Interstitial Pneumonia. PMID:29361909
Using Yeast Synthetic Lethality To Inform Drug Combination for Malaria. PMID:29358287
Morphological inversion of complex diffusion. PMID:29346889
Discovering Altered Regulation and Signaling Through Network-based Integration of Transcriptomic, Epigenomic, and Proteomic Tumor Data. PMID:29344883
Using genetic buffering relationships identified in fission yeast to reveal susceptibilities in cells lacking hamartin or tuberin function. PMID:29343513
Genomic Identification and Functional Characterization of Essential Genes in Caenorhabditis elegans. PMID:29339407
MicroRNA-200a confers chemoresistance by antagonizing TP53INP1 and YAP1 in human breast cancer. PMID:29329575
Integrating transcriptional activity in genome-scale models of metabolism. PMID:29322933
Inferring ontology graph structures using OWL reasoning. PMID:29304741
The phosphatidylinositide 3-kinase (PI3K) signaling pathway is a determinant of zileuton response in adults with asthma. PMID:29298996
The node-weighted Steiner tree approach to identify elements of cancer-related signaling pathways. PMID:29297291
A Seed Expansion Graph Clustering Method for Protein Complexes Detection in Protein Interaction Networks. PMID:29292776
Identification of genes highly downregulated in pancreatic cancer through a meta-analysis of microarray datasets: implications for discovery of novel tumor-suppressor genes and therapeutic targets. PMID:29288362
The integration of weighted gene association networks based on information entropy. PMID:29272314
Germline TTN variants are enriched in PTEN-wildtype Bannayan-Riley-Ruvalcaba syndrome. PMID:29263846
Deciphering the Relationship between Obesity and Various Diseases from a Network Perspective. PMID:29258237
Evaluating the associations between human circadian rhythms and dysregulated genes in liver cancer cells. PMID:29250165
Multi-Objective Optimization Algorithm to Discover Condition-Specific Modules in Multiple Networks. PMID:29240706
LeishDB: a database of coding gene annotation and non-coding RNAs in Leishmania braziliensis. PMID:29220437
Prediction of essential proteins based on subcellular localization and gene expression correlation. PMID:29219067
Annotating gene sets by mining large literature collections with protein networks. PMID:29218918
HIDEEP: a systems approach to predict hormone impacts on drug efficacy based on effect paths. PMID:29192270
PlanNET: homology-based predicted interactome for multiple planarian transcriptomes. PMID:29186384
Systems Bioinformatics: increasing precision of computational diagnostics and therapeutics through network-based approaches. PMID:29186305
Optimal percolation on multiplex networks. PMID:29147014
CommWalker: correctly evaluating modules in molecular networks in light of annotation bias. PMID:29112702
Inferring gene and protein interactions using PubMed citations and consensus Bayesian networks. PMID:29049295
A nonparametric significance test for sampled networks. PMID:29036452
Native KCC2 interactome reveals PACSIN1 as a critical regulator of synaptic inhibition. PMID:29028184
PICKLE 2.0: A human protein-protein interaction meta-database employing data integration via genetic information ontology. PMID:29023571
Mutational landscape of RNA-binding proteins in human cancers. PMID:29023197
A novel network analysis approach reveals DNA damage, oxidative stress and calcium/cAMP homeostasis-associated biomarkers in frontotemporal dementia. PMID:29020091
MD-Miner: a network-based approach for personalized drug repositioning. PMID:28984195
A Comprehensive Analysis of Transcript-Supported De Novo Genes in Saccharomyces sensu stricto Yeasts. PMID:28981695
Functional 5' UTR motif discovery with LESMoN: Local Enrichment of Sequence Motifs in biological Networks. PMID:28977652
MAPPIN: a method for annotating, predicting pathogenicity and mode of inheritance for nonsynonymous variants. PMID:28977528
Multi-dimensional histone methylations for coordinated regulation of gene expression under hypoxia. PMID:28977425
Network-Based Method for Identifying Co- Regeneration Genes in Bone, Dentin, Nerve and Vessel Tissues. PMID:28974058
Using neural networks for reducing the dimensions of single-cell RNA-Seq data. PMID:28973464
Network-Based Coverage of Mutational Profiles Reveals Cancer Genes. PMID:28957656
Conjecture Regarding Posttranslational Modifications to the Arabidopsis Type I Proton-Pumping Pyrophosphatase (AVP1). PMID:28955362
Stable Gene Regulatory Network Modeling From Steady-State Data. PMID:28952574
Computational Approaches to Identify Genetic Interactions for Cancer Therapeutics. PMID:28941356
A computational method using the random walk with restart algorithm for identifying novel epigenetic factors. PMID:28932904
P-body proteins regulate transcriptional rewiring to promote DNA replication stress resistance. PMID:28916784
MPZL1 forms a signalling complex with GRB2 adaptor and PTPN11 phosphatase in HER2-positive breast cancer cells. PMID:28912526
MCbiclust: a novel algorithm to discover large-scale functionally related gene sets from massive transcriptomics data collections. PMID:28911113
Identification of high-confidence RNA regulatory elements by combinatorial classification of RNA-protein binding sites. PMID:28886744
Evolutionary analysis and interaction prediction for protein-protein interaction network in geometric space. PMID:28886027
Chronic obstructive pulmonary disease candidate gene prioritization based on metabolic networks and functional information. PMID:28873096
Vertebrate GAF/ThPOK: emerging functions in chromatin architecture and transcriptional regulation. PMID:28856379
Using ALoFT to determine the impact of putative loss-of-function variants in protein-coding genes. PMID:28851873
The effect of Bu Zhong Yi Qi decoction on simulated weightlessness‑induced muscle atrophy and its mechanisms. PMID:28849026
Domain-based prediction of the human isoform interactome provides insights into the functional impact of alternative splicing. PMID:28846689
Taxonomically Restricted Genes with Essential Functions Frequently Play Roles in Chromosome Segregation in Caenorhabditis elegans and Saccharomyces cerevisiae. PMID:28839119
Construction of an integrated gene regulatory network link to stress-related immune system in cattle. PMID:28825201
Integrative network and transcriptomics-based approach predicts genotype- specific drug combinations for melanoma. PMID:28815138
ODG: Omics database generator - a tool for generating, querying, and analyzing multi-omics comparative databases to facilitate biological understanding. PMID:28797229
CODA: Integrating multi-level context-oriented directed associations for analysis of drug effects. PMID:28790372
Interchromosomal Transfer of Immune Regulation During Infection of Barley with the Powdery Mildew Pathogen. PMID:28790145
Identification of essential genes for cancer immunotherapy. PMID:28783722
Global Gene Expression Analysis Reveals Crosstalk between Response Mechanisms to Cold and Drought Stresses in Cassava Seedlings. PMID:28769962
CrossCheck: an open-source web tool for high-throughput screen data analysis. PMID:28724888
Development of an in silico method for the identification of subcomplexes involved in the biogenesis of multiprotein complexes in Saccharomyces cerevisiae. PMID:28693620
Metabolic modeling to identify engineering targets for Komagataella phaffii: The effect of biomass composition on gene target identification. PMID:28691262
Drug Target Protein-Protein Interaction Networks: A Systematic Perspective. PMID:28691014
Strength of functional signature correlates with effect size in autism. PMID:28687074
Prognostic cancer gene signatures share common regulatory motifs. PMID:28684851
Global gene expression profiling and senescence biomarker analysis of hESC exposed to H2O2 induced non-cytotoxic oxidative stress. PMID:28676096
Spatiotemporal profile of postsynaptic interactomes integrates components of complex brain disorders. PMID:28671696
Systematic bacterialization of yeast genes identifies a near-universally swappable pathway. PMID:28661399
CrY2H-seq: a massively multiplexed assay for deep-coverage interactome mapping. PMID:28650476
APPL1 is a multifunctional endosomal signaling adaptor protein. PMID:28620038
Contextualization of drug-mediator relations using evidence networks. PMID:28617226
Agonist-specific Protein Interactomes of Glucocorticoid and Androgen Receptor as Revealed by Proximity Mapping. PMID:28611094
Neighbours of cancer-related proteins have key influence on pathogenesis and could increase the drug target space for anticancer therapies. PMID:28603644
A methodology for elucidating regulatory mechanisms leading to changes in lipid profiles. PMID:28596719
Integration of over 9,000 mass spectrometry experiments builds a global map of human protein complexes. PMID:28596423
Characterization of developmental defects in the forebrain resulting from hyperactivated mTOR signaling by integrative analysis of transcriptomic and proteomic data. PMID:28588230
Network-assisted target identification for haploinsufficiency and homozygous profiling screens. PMID:28574983
Genetic wiring maps of single-cell protein states reveal an off-switch for GPCR signalling. PMID:28562590
Generating testable hypotheses for schizophrenia and rheumatoid arthritis pathogenesis by integrating epidemiological, genomic, and protein interaction data. PMID:28560257
A scalable double-barcode sequencing platform for characterization of dynamic protein-protein interactions. PMID:28541284
Methylation of human eukaryotic elongation factor alpha (eEF1A) by a member of a novel protein lysine methyltransferase family modulates mRNA translation. PMID:28520920
Combining inferred regulatory and reconstructed metabolic networks enhances phenotype prediction in yeast. PMID:28520713
Network-aided Bi-Clustering for discovering cancer subtypes. PMID:28432308
Use of Graph Database for the Integration of Heterogeneous Biological Data. PMID:28416946
Drebrin restricts rotavirus entry by inhibiting dynamin-mediated endocytosis. PMID:28416666
Transcriptional regulatory networks underlying the reprogramming of spermatogonial stem cells to multipotent stem cells. PMID:28408750
Inferring modulators of genetic interactions with epistatic nested effects models. PMID:28406896
Knockdown of Broad-Complex Gene Expression of Bombyx mori by Oligopyrrole Carboxamides Enhances Silk Production. PMID:28400559
Finding low-conductance sets with dense interactions (FLCD) for better protein complex prediction. PMID:28361714
Comparison of tissue/disease specific integrated networks using directed graphlet signatures. PMID:28361704
Net2Align: An Algorithm For Pairwise Global Alignment of Biological Networks. PMID:28356678
Computational identifying and characterizing circular RNAs and their associated genes in hepatocellular carcinoma. PMID:28346469
Bacterial Carriers for Glioblastoma Therapy. PMID:28345020
A Comprehensive View of the β-Arrestinome. PMID:28321204
NaviGO: interactive tool for visualization and functional similarity and coherence analysis with gene ontology. PMID:28320317
Predicting drug-drug interactions through drug structural similarities and interaction networks incorporating pharmacokinetics and pharmacodynamics knowledge. PMID:28316654
Systematic morphological profiling of human gene and allele function via Cell Painting. PMID:28315521
Delineating functional principles of the bow tie structure of a kinase-phosphatase network in the budding yeast. PMID:28298210
Modeling anorexia nervosa: transcriptional insights from human iPSC-derived neurons. PMID:28291261
Ornithine Aminotransferase, an Important Glutamate-Metabolizing Enzyme at the Crossroads of Multiple Metabolic Pathways. PMID:28272331
Pathway Cross-Talk Analysis in Detecting Significant Pathways in Barrett's Esophagus Patients. PMID:28263955
Integrated systems biology analysis of KSHV latent infection reveals viral induction and reliance on peroxisome mediated lipid metabolism. PMID:28257516
The amyloid interactome: Exploring protein aggregation. PMID:28249044
CLK-dependent exon recognition and conjoined gene formation revealed with a novel small molecule inhibitor. PMID:28232751
HAPPI-2: a Comprehensive and High-quality Map of Human Annotated and Predicted Protein Interactions. PMID:28212602
A Comprehensive Gene Expression Meta-analysis Identifies Novel Immune Signatures in Rheumatoid Arthritis Patients. PMID:28210261
An approach to infer putative disease-specific mechanisms using neighboring gene networks. PMID:28200075
Evaluating the effect of annotation size on measures of semantic similarity. PMID:28193260
Incorporating prior biological knowledge for network-based differential gene expression analysis using differentially weighted graphical LASSO. PMID:28187708
Protein complex prediction for large protein protein interaction networks with the Core&Peel method. PMID:28185552
How can functional annotations be derived from profiles of phenotypic annotations? PMID:28183267
Nestedness across biological scales. PMID:28166284
Accurate prediction of human essential genes using only nucleotide composition and association information. PMID:28158612
Skewing in Arabidopsis roots involves disparate environmental signaling pathways. PMID:28143395
Epigenetic profiling of human brain differential DNA methylation networks in schizophrenia. PMID:28117656
GSNFS: Gene subnetwork biomarker identification of lung cancer expression data. PMID:28117655
Methyl-CpG-Binding Protein MBD1 Regulates Neuronal Lineage Commitment through Maintaining Adult Neural Stem Cell Identity. PMID:28100736
Is the average shortest path length of gene set a reflection of their biological relatedness? PMID:28073302
Drug Response Prediction as a Link Prediction Problem. PMID:28067293
Non-Coding RNAs in Lung Cancer: Contribution of Bioinformatics Analysis to the Development of Non-Invasive Diagnostic Tools. PMID:28035947
The role of prostate tumor overexpressed 1 in cancer progression. PMID:28029646
Predictability of Genetic Interactions from Functional Gene Modules. PMID:28007839
Transcriptome analyses identify key cellular factors associated with HIV-1-associated neuropathogenesis in infected men. PMID:28005686
Improved method for prioritization of disease associated lncRNAs based on ceRNA theory and functional genomics data. PMID:27992375
Brassinosteroid signaling converges with SUPPRESSOR OF PHYTOCHROME B4-#3 to influence the expression of SMALL AUXIN UP RNA genes and hypocotyl growth. PMID:27984677
HOXA repression is mediated by nucleoporin Nup93 assisted by its interactors Nup188 and Nup205. PMID:27980680
Integrating Information in Biological Ontologies and Molecular Networks to Infer Novel Terms. PMID:27976738
Investigating the human Calcineurin Interaction Network using the πɸLxVP SLiM. PMID:27974827
PlaMoM: a comprehensive database compiles plant mobile macromolecules. PMID:27924044
Rheumatoid arthritis: Modelling cytokine signalling networks. PMID:27904145
Role of Hepatic-Specific Transcription Factors and Polycomb Repressive Complex 2 during Induction of Fibroblasts to Hepatic Fate. PMID:27902735
A genome wide dosage suppressor network reveals genomic robustness. PMID:27899637
A scored human protein-protein interaction network to catalyze genomic interpretation. PMID:27892958
Biomolecular Network-Based Synergistic Drug Combination Discovery. PMID:27891522
PLK1, A Potential Target for Cancer Therapy. PMID:27888710
Mitochondrial Sirtuin Network Reveals Dynamic SIRT3-Dependent Deacetylation in Response to Membrane Depolarization. PMID:27881304
Computational approaches for the identification of cancer genes and pathways. PMID:27863091
Increasing Role of Titin Mutations in Neuromuscular Disorders. PMID:27854229
DGCA: A comprehensive R package for Differential Gene Correlation Analysis. PMID:27846853
iSeq: A New Double-Barcode Method for Detecting Dynamic Genetic Interactions in Yeast. PMID:27821633
Asc1p/RACK1 Connects Ribosomes to Eukaryotic Phosphosignaling. PMID:27821475
Exploring genetic suppression interactions on a global scale. PMID:27811238
Genetic-and-Epigenetic Interspecies Networks for Cross-Talk Mechanisms in Human Macrophages and Dendritic Cells during MTB Infection. PMID:27803888
An Integrative Analysis of Preeclampsia Based on the Construction of an Extended Composite Network Featuring Protein-Protein Physical Interactions and Transcriptional Relationships. PMID:27802351
yMap: an automated method to map yeast variants to protein modifications and functional regions. PMID:27797766
A prior-based integrative framework for functional transcriptional regulatory network inference. PMID:27794550
A Systems Biology Comparison of Ovarian Cancers Implicates Putative Somatic Driver Mutations through Protein-Protein Interaction Models. PMID:27788148
Systems biology analysis reveals role of MDM2 in diabetic nephropathy. PMID:27777973
Genome-Wide Gene/Genome Dosage Imbalance Regulates Gene Expressions in Synthetic Brassica napus and Derivatives (AC, AAC, CCA, CCAA). PMID:27721820
SONAR Discovers RNA-Binding Proteins from Analysis of Large-Scale Protein-Protein Interactomes. PMID:27720645
Intrinsic noise and deviations from criticality in Boolean gene-regulatory networks. PMID:27713479
DBSecSys 2.0: a database of Burkholderia mallei and Burkholderia pseudomallei secretion systems. PMID:27650316
Reduction strategies for hierarchical multi-label classification in protein function prediction. PMID:27627880
inFRank: a ranking-based identification of influential genes in biological networks. PMID:27623074
Structural and mechanistic insights into human splicing factor SF3b complex derived using an integrated approach guided by the cryo-EM density maps. PMID:27618338
Exploring Quantitative Yeast Phenomics with Single-Cell Analysis of DNA Damage Foci. PMID:27617677
Positive Selection Linked with Generation of Novel Mammalian Dentition Patterns. PMID:27613398
Comprehensive Proteome Profiling of Platelet Identified a Protein Profile Predictive of Responses to An Antiplatelet Agent Sarpogrelate. PMID:27601597
Fast Inference for the Latent Space Network Model Using a Case-Control Approximate Likelihood. PMID:27570438
An ensemble framework for identifying essential proteins. PMID:27557880
Functional characterization of EI24-induced autophagy in the degradation of RING-domain E3 ligases. PMID:27541728
Nuclear autophagy: An evolutionarily conserved mechanism of nuclear degradation in the cytoplasm. PMID:27541589
Predicting diabetes mellitus genes via protein-protein interaction and protein subcellular localization information. PMID:27535125
Interaction Between Peroxisome Proliferator Activated Receptor δ and Epithelial Membrane Protein 2 Polymorphisms Influences HDL-C Levels in the Chinese Population. PMID:27530449
The Role of Node Heterogeneity in the Coupled Spreading of Epidemics and Awareness. PMID:27517715
VHLdb: A database of von Hippel-Lindau protein interactors and mutations. PMID:27511743
Systems Analysis of the Complement-Induced Priming Phase of Liver Regeneration. PMID:27511733
ARN: analysis and prediction by adipogenic professional database. PMID:27503118
Whole Exome Sequencing Identifies TSC1/TSC2 Biallelic Loss as the Primary and Sufficient Driver Event for Renal Angiomyolipoma Development. PMID:27494029
Evaluating the impact of single nucleotide variants on transcription factor binding. PMID:27492288
Context-specific functional module based drug efficacy prediction. PMID:27490093
Ligand Similarity Complements Sequence, Physical Interaction, and Co-Expression for Gene Function Prediction. PMID:27467773
Small-molecule binding sites to explore protein-protein interactions in the cancer proteome. PMID:27452673
Investigating the Combinatory Effects of Biological Networks on Gene Co-expression. PMID:27445830
TSSC1 is novel component of the endosomal retrieval machinery. PMID:27440922
The nonessentiality of essential genes in yeast provides therapeutic insights into a human disease. PMID:27440870
Defining the Protein-Protein Interaction Network of the Human Protein Tyrosine Phosphatase Family. PMID:27432908
Valosin-containing protein (VCP)-Adaptor Interactions are Exceptionally Dynamic and Subject to Differential Modulation by a VCP Inhibitor. PMID:27406709
Transcriptomic response of yeast cells to ATX1 deletion under different copper levels. PMID:27401861
Systems view of adipogenesis via novel omics-driven and tissue-specific activity scoring of network functional modules. PMID:27385551
The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. PMID:27374120
Intrinsic protein disorder in histone lysine methylation. PMID:27356874
SorghumFDB: sorghum functional genomics database with multidimensional network analysis. PMID:27352859
FOXR2 Interacts with MYC to Promote Its Transcriptional Activities and Tumorigenesis. PMID:27346356
A noncatalytic function of the topoisomerase II CTD in Aurora B recruitment to inner centromeres during mitosis. PMID:27325791
Reconstructing the temporal progression of HIV-1 immune response pathways. PMID:27307624
Computational approaches in target identification and drug discovery. PMID:27293534
The Drosophila ETV5 Homologue Ets96B: Molecular Link between Obesity and Bipolar Disorder. PMID:27280443
ELAVL2-regulated transcriptional and splicing networks in human neurons link neurodevelopment and autism. PMID:27260404
Review on Graph Clustering and Subgraph Similarity Based Analysis of Neurological Disorders. PMID:27258269
Data set of interactomes and metabolic pathways of proteins differentially expressed in brains with Alzheimer׳s disease. PMID:27257613
Ribosome recycling defects modify the balance between the synthesis and assembly of specific subunits of the oxidative phosphorylation complexes in yeast mitochondria. PMID:27257059
The Use of Protein-Protein Interactions for the Analysis of the Associations between PM2.5 and Some Diseases. PMID:27243032
Future paradigms for precision oncology. PMID:27223079
The probability of speciation on an interaction network with unequal substitution rates. PMID:27177943
Dissecting the expression relationships between RNA-binding proteins and their cognate targets in eukaryotic post-transcriptional regulatory networks. PMID:27161996
Genome-scale prediction of moonlighting proteins using diverse protein association information. PMID:27153604
Building a glaucoma interaction network using a text mining approach. PMID:27152122
ChromNet: Learning the human chromatin network from all ENCODE ChIP-seq data. PMID:27139377
Network-Based Protein Biomarker Discovery Platforms. PMID:27103885
Quantitative Tagless Copurification: A Method to Validate and Identify Protein-Protein Interactions. PMID:27099342
Synthetic protein interactions reveal a functional map of the cell. PMID:27098839
APP Is a Context-Sensitive Regulator of the Hippocampal Presynaptic Active Zone. PMID:27092780
AuPairWise: A Method to Estimate RNA-Seq Replicability through Co-expression. PMID:27082953
Visualization of Metabolic Interaction Networks in Microbial Communities Using VisANT 5.0. PMID:27081850
Uncovering disease mechanisms through network biology in the era of Next Generation Sequencing. PMID:27080396
Pharmacometabolomics-aided Pharmacogenomics in Autoimmune Disease. PMID:27077110
Biomolecular Relationships Discovered from Biological Labyrinth and Lost in Ocean of Literature: Community Efforts Can Rescue Until Automated Artificial Intelligence Takes Over. PMID:27066067
FAM46 proteins are novel eukaryotic non-canonical poly(A) polymerases. PMID:27060136
Protein Interaction Networks Link Schizophrenia Risk Loci to Synaptic Function. PMID:27056717
A Consensus Network of Gene Regulatory Factors in the Human Frontal Lobe. PMID:27014338
Thermodynamic measures of cancer: Gibbs free energy and entropy of protein-protein interactions. PMID:27012959
A graph theoretical approach to data fusion. PMID:26992203
An integrative data analysis platform for gene set analysis and knowledge discovery in a data warehouse framework. PMID:26989145
Constitutive Negative Regulation of R Proteins in Arabidopsis also via Autophagy Related Pathway? PMID:26973696
PIPINO: A Software Package to Facilitate the Identification of Protein-Protein Interactions from Affinity Purification Mass Spectrometry Data. PMID:26966684
Trifunctional cross-linker for mapping protein-protein interaction networks and comparing protein conformational states. PMID:26952210
Involvement of Polycomb Repressive Complex 2 in Maturation of Induced Pluripotent Stem Cells during Reprogramming of Mouse and Human Fibroblasts. PMID:26938987
Key Immune Events of the Pathomechanisms of Early Cardioembolic Stroke: Multi-Database Mining and Systems Biology Approach. PMID:26927091
The human DNA ends proteome uncovers an unexpected entanglement of functional pathways. PMID:26921407
Functional Evaluations of Genes Disrupted in Patients with Tourette's Disorder. PMID:26903887
An interactive web-based application for Comprehensive Analysis of RNAi-screen Data. PMID:26902267
Comparative analysis of housekeeping and tissue-selective genes in human based on network topologies and biological properties. PMID:26897376
Constructing an integrated genetic and epigenetic cellular network for whole cellular mechanism using high-throughput next-generation sequencing data. PMID:26897165
A high definition look at the NF-Y regulome reveals genome-wide associations with selected transcription factors. PMID:26896797
Investigating the specific core genetic-and-epigenetic networks of cellular mechanisms involved in human aging in peripheral blood mononuclear cells. PMID:26895224
Binding interface change and cryptic variation in the evolution of protein-protein interactions. PMID:26892785
Protection or resection: BOD1L as a novel replication fork protection factor. PMID:26889944
Comprehensive Expression Profiling and Functional Network Analysis of p53-Regulated MicroRNAs in HepG2 Cells Treated with Doxorubicin. PMID:26886852
Using contrast patterns between true complexes and random subgraphs in PPI networks to predict unknown protein complexes. PMID:26868667
Topological characteristics of target genes regulated by abiotic-stress-responsible miRNAs in a rice interactome network. PMID:26830287
Accelerating Adverse Outcome Pathway Development Using Publicly Available Data Sources. PMID:26809562
A multiple kernel learning algorithm for drug-target interaction prediction. PMID:26801218
Lamina Associated Polypeptide 1 (LAP1) Interactome and Its Functional Features. PMID:26784240
Prediction and characterization of protein-protein interaction network in Bacillus licheniformis WX-02. PMID:26782814
Multi-omic measurement of mutually exclusive loss-of-function enriches for candidate synthetic lethal gene pairs. PMID:26781748
A Factor Graph Approach to Automated GO Annotation. PMID:26771463
Focused Analysis of Exome Sequencing Data for Rare Germline Mutations in Familial and Sporadic Lung Cancer. PMID:26762739
Systematic Phenomics Analysis Deconvolutes Genes Mutated in Intellectual Disability into Biologically Coherent Modules. PMID:26748517
Differential Occurrence of Interactions and Interaction Domains in Proteins Containing Homopolymeric Amino Acid Repeats. PMID:26734058
BioGRID: A Resource for Studying Biological Interactions in Yeast. PMID:26729913
Use of the BioGRID Database for Analysis of Yeast Protein and Genetic Interactions. PMID:26729909
Identifying novel protein phenotype annotations by hybridizing protein-protein interactions and protein sequence similarities. PMID:26728152
Scope and limitations of yeast as a model organism for studying human tissue-specific pathways. PMID:26714768
JMJD5 (Jumonji Domain-containing 5) Associates with Spindle Microtubules and Is Required for Proper Mitosis. PMID:26710852
Forward Individualized Medicine from Personal Genomes to Interactomes. PMID:26696898
Transcriptome analysis in calorie-restricted rats implicates epigenetic and post-translational mechanisms in neuroprotection and aging. PMID:26694192
Genome-Wide Analysis of the TORC1 and Osmotic Stress Signaling Network in Saccharomyces cerevisiae. PMID:26681516
A computational method for drug repositioning using publicly available gene expression data. PMID:26679199
Disentangling the multigenic and pleiotropic nature of molecular function. PMID:26678917
A deep proteomics perspective on CRM1-mediated nuclear export and nucleocytoplasmic partitioning. PMID:26673895
Integrated analysis of global proteome, phosphoproteome, and glycoproteome enables complementary interpretation of disease-related protein networks. PMID:26657352
Analysis of COPII Vesicles Indicates a Role for the Emp47-Ssp120 Complex in Transport of Cell Surface Glycoproteins. PMID:26650540
AnGeLi: A Tool for the Analysis of Gene Lists from Fission Yeast. PMID:26635866
PPIM: A Protein-Protein Interaction Database for Maize. PMID:26620522
Dominance from the perspective of gene-gene and gene-chemical interactions. PMID:26613610
The cytoplasmic peptide:N-glycanase (NGLY1) - Structure, expression and cellular functions. PMID:26611529
Evolution of disorder in Mediator complex and its functional relevance. PMID:26590257
Re-analysis of protein data reveals the germination pathway and up accumulation mechanism of cell wall hydrolases during the radicle protrusion step of seed germination in Podophyllum hexandrum- a high altitude plant. PMID:26579141
Investigation of Pathogenic Genes in Chinese sporadic Hypertrophic Cardiomyopathy Patients by Whole Exome Sequencing. PMID:26573135
Transposable elements at the center of the crossroads between embryogenesis, embryonic stem cells, reprogramming, and long non-coding RNAs. PMID:26543668
Getting the most out of RNA-seq data analysis. PMID:26539333
Inferring plant microRNA functional similarity using a weighted protein-protein interaction network. PMID:26538106
Multiple SNP Set Analysis for Genome-Wide Association Studies Through Bayesian Latent Variable Selection. PMID:26515609
A Glimpse to Background and Characteristics of Major Molecular Biological Networks. PMID:26491677
Characterization of the Cardiac Overexpression of HSPB2 Reveals Mitochondrial and Myogenic Roles Supported by a Cardiac HspB2 Interactome. PMID:26465331
Connectivity Homology Enables Inter-Species Network Models of Synthetic Lethality. PMID:26451775
PPCheck: A Webserver for the Quantitative Analysis of Protein-Protein Interfaces and Prediction of Residue Hotspots. PMID:26448684
Condition-specific genetic interaction maps reveal crosstalk between the cAMP/PKA and the HOG MAPK pathways in the activation of the general stress response. PMID:26446933
Integrated analysis of gene expression and genomic aberration data in osteosarcoma (OS). PMID:26427513
Global multiple protein-protein interaction network alignment by combining pairwise network alignments. PMID:26423128
A fast and high performance multiple data integration algorithm for identifying human disease genes. PMID:26399620
Genome-wide prediction of prokaryotic two-component system networks using a sequence-based meta-predictor. PMID:26384938
The Role of ARF6 in Biliary Atresia. PMID:26379158
Interactive Big Data Resource to Elucidate Human Immune Pathways and Diseases. PMID:26362267
Panorama of ancient metazoan macromolecular complexes. PMID:26344197
Targeting SOD1 induces synthetic lethal killing in BLM- and CHEK2-deficient colorectal cancer cells. PMID:26318585
Novel Application of Junction Trees to the Interpretation of Epigenetic Differences among Lung Cancer Subtypes. PMID:26306226
Network Modules of the Cross-Species Genotype-Phenotype Map Reflect the Clinical Severity of Human Diseases. PMID:26301634
Gene Function Prediction from Functional Association Networks Using Kernel Partial Least Squares Regression. PMID:26288239
Functional Analysis and Characterization of Differential Coexpression Networks. PMID:26282208
Distilling a Visual Network of Retinitis Pigmentosa Gene-Protein Interactions to Uncover New Disease Candidates. PMID:26267445
Computational analysis of protein interaction networks for infectious diseases. PMID:26261187
Algorithms for modeling global and context-specific functional relationship networks. PMID:26254431
Environmental Interactions and Epistasis Are Revealed in the Proteomic Responses to Complex Stimuli. PMID:26247773
Revisiting topological properties and models of protein-protein interaction networks from the perspective of dataset evolution. PMID:26243826
An Integrative Approach for Mapping Differentially Expressed Genes and Network Components Using Novel Parameters to Elucidate Key Regulatory Genes in Colorectal Cancer. PMID:26222778
Isoform-specific interactions of the von Hippel-Lindau tumor suppressor protein. PMID:26211615
Network-Based Logistic Classification with an Enhanced L 1/2 Solver Reveals Biomarker and Subnetwork Signatures for Diagnosing Lung Cancer. PMID:26185761
Acquisition of estrogen independence induces TOB1-related mechanisms supporting breast cancer cell proliferation. PMID:26165839
Transcriptomic-Wide Discovery of Direct and Indirect HuR RNA Targets in Activated CD4+ T Cells. PMID:26162078
Computational Inferences of the Functions of Alternative/Noncanonical Splice Isoforms Specific to HER2+/ER-/PR- Breast Cancers, a Chromosome 17 C-HPP Study. PMID:26147891
Arabidopsis MAS2, an Essential Gene That Encodes a Homolog of Animal NF-κ B Activating Protein, Is Involved in 45S Ribosomal DNA Silencing. PMID:26139346
α2-Macroglobulin Can Crosslink Multiple Plasmodium falciparum Erythrocyte Membrane Protein 1 (PfEMP1) Molecules and May Facilitate Adhesion of Parasitized Erythrocytes. PMID:26134405
Inference of Low and High-Grade Glioma Gene Regulatory Networks Delineates the Role of Rnd3 in Establishing Multiple Hallmarks of Cancer. PMID:26132659
Rechecking the Centrality-Lethality Rule in the Scope of Protein Subcellular Localization Interaction Networks. PMID:26115027
Self-Organizing Feature Maps Identify Proteins Critical to Learning in a Mouse Model of Down Syndrome. PMID:26111164
A computational method for clinically relevant cancer stratification and driver mutation module discovery using personal genomics profiles. PMID:26099165
Gene Expression Associated with Early and Late Chronotypes in Drosophila melanogaster. PMID:26097463
A predicted protein interactome identifies conserved global networks and disease resistance subnetworks in maize. PMID:26089837
By the company they keep: interaction networks define the binding ability of transcription factors. PMID:26089389
Biallelic Mutations in NBAS Cause Recurrent Acute Liver Failure with Onset in Infancy. PMID:26073778
Inferring orthologous gene regulatory networks using interspecies data fusion. PMID:26072515
Dietary MicroRNA Database (DMD): An Archive Database and Analytic Tool for Food-Borne microRNAs. PMID:26030752
A functional biological network centered on XRCC3: a new possible marker of chemoradiotherapy resistance in rectal cancer patients. PMID:26023803
Causal Modeling of Cancer-Stromal Communication Identifies PAPPA as a Novel Stroma-Secreted Factor Activating NFκB Signaling in Hepatocellular Carcinoma. PMID:26020769
A density-based clustering approach for identifying overlapping protein complexes with functional preferences. PMID:26013799
SPECTRA: An Integrated Knowledge Base for Comparing Tissue and Tumor-Specific PPI Networks in Human. PMID:26005672
From raw data to biological discoveries: a computational analysis pipeline for mass spectrometry-based proteomics. PMID:26002791
Evolution. Systematic humanization of yeast genes reveals conserved functions and genetic modularity. PMID:25999509
Proteomic analysis of three gonad types of swamp eel reveals genes differentially expressed during sex reversal. PMID:25985063
Reverse enGENEering of Regulatory Networks from Big Data: A Roadmap for Biologists. PMID:25983554
Dynamic network-based relevance score reveals essential proteins and functional modules in directed differentiation. PMID:25977693
NetworkAnalyst for statistical, visual and network-based meta-analysis of gene expression data. PMID:25950236
Predicting peptide-mediated interactions on a genome-wide scale. PMID:25938916
Hierarchical ensemble methods for protein function prediction. PMID:25937954
Lineage-specific sequence evolution and exon edge conservation partially explain the relationship between evolutionary rate and expression level in A. thaliana. PMID:25930165
Genetic similarity between cancers and comorbid Mendelian diseases identifies candidate driver genes. PMID:25926297
Predicting involvement of polycomb repressive complex 2 in direct conversion of mouse fibroblasts into induced neural stem cells. PMID:25890371
Identifying module biomarker in type 2 diabetes mellitus by discriminative area of functional activity. PMID:25888350
Probabilistic inference of biological networks via data integration. PMID:25874225
Genome-wide protein-protein interaction screening by protein-fragment complementation assay (PCA) in living cells. PMID:25867901
cDREM: inferring dynamic combinatorial gene regulation. PMID:25844671
Combinatorial proteomic analysis of intercellular signaling applied to the CD28 T-cell costimulatory receptor. PMID:25829543
Uncovering RNA binding proteins associated with age and gender during liver maturation. PMID:25824884
Comprehensive data resources and analytical tools for pathological association of aminoacyl tRNA synthetases with cancer. PMID:25824651
Control of cell-cell forces and collective cell dynamics by the intercellular adhesome. PMID:25812522
Proper evaluation of alignment-free network comparison methods. PMID:25810431
A hybrid computational method for the discovery of novel reproduction-related genes. PMID:25768094
Scoring Large-Scale Affinity Purification Mass Spectrometry Datasets with MiST. PMID:25754993
Characterization of the interaction between Rfa1 and Rad24 in Saccharomyces cerevisiae. PMID:25719602
Spatiotemporal 16p11.2 protein network implicates cortical late mid-fetal brain development and KCTD13-Cul3-RhoA pathway in psychiatric diseases. PMID:25695269
Data Imputation in Epistatic MAPs by Network-Guided Matrix Completion. PMID:25658751
A Comprehensive Membrane Interactome Mapping of Sho1p Reveals Fps1p as a Novel Key Player in the Regulation of the HOG Pathway in S. cerevisiae. PMID:25644660
Comparison of human cell signaling pathway databases--evolution, drawbacks and challenges. PMID:25632107
Database of Gene Co-Regulation (dGCR): A Web Tool for Analysing Patterns of Gene Co-regulation across Publicly Available Expression Data. PMID:25628763
Protein folding and binding can emerge as evolutionary spandrels through structural coupling. PMID:25624494
Computational deconvolution of genome wide expression data from Parkinson's and Huntington's disease brain tissues using population-specific expression analysis. PMID:25620908
Ror2 as a therapeutic target in cancer. PMID:25614331
Topology-function conservation in protein-protein interaction networks. PMID:25609797
Proteomic analyses reveal distinct chromatin-associated and soluble transcription factor complexes. PMID:25609649
Robustness analysis on interspecies interaction network for iron and glucose competition between Candida albicans and zebrafish during infection. PMID:25603810
Properties of sparse penalties on inferring gene regulatory networks from time-course gene expression data. PMID:25569860
Application of quantitative trait locus mapping and transcriptomics to studies of the senescence-accelerated phenotype in rats. PMID:25563673
Pathway mapping and development of disease-specific biomarkers: protein-based network biomarkers. PMID:25560835
Identifying cooperative transcription factors in yeast using multiple data sources. PMID:25559499
Altered Transcriptional Control Networks with Trans-Differentiation of Isogenic Mutant-KRas NSCLC Models. PMID:25538889
Locus heterogeneity disease genes encode proteins with high interconnectivity in the human protein interaction network. PMID:25538735
Multitask learning of signaling and regulatory networks with application to studying human response to flu. PMID:25522349
MicroRNA Dysregulation, Gene Networks, and Risk for Schizophrenia in 22q11.2 Deletion Syndrome. PMID:25484875
Dynamics of re-constitution of the human nuclear proteome after cell division is regulated by NLS-adjacent phosphorylation. PMID:25483092
OntoGene web services for biomedical text mining. PMID:25472638
ModuleBlast: identifying activated sub-networks within and across species. PMID:25428368
Community structure detection for overlapping modules through mathematical programming in protein interaction networks. PMID:25412367
Pathway connectivity and signaling coordination in the yeast stress-activated signaling network. PMID:25411400
Protein interaction networks reveal novel autism risk genes within GWAS statistical noise. PMID:25409314
A least square method based model for identifying protein complexes in protein-protein interaction network. PMID:25405206
A systems biology strategy to identify molecular mechanisms of action and protein indicators of traumatic brain injury. PMID:25399920
β-CateninC429S mice exhibit sterility consequent to spatiotemporally sustained Wnt signalling in the internal genitalia. PMID:25376241
Identification of SUMO-2/3-modified proteins associated with mitotic chromosomes. PMID:25367092
From molecular signatures to predictive biomarkers: modeling disease pathophysiology and drug mechanism of action. PMID:25364744
Prediction of disease-related genes based on weighted tissue-specific networks by using DNA methylation. PMID:25350763
A group LASSO-based method for robustly inferring gene regulatory networks from multiple time-course datasets. PMID:25350697
Integrating PPI datasets with the PPI data from biomedical literature for protein complex detection. PMID:25350598
Identifying disease genes by integrating multiple data sources. PMID:25350511
MitProNet: A knowledgebase and analysis platform of proteome, interactome and diseases for mammalian mitochondria. PMID:25347823
Identifying roles of "Jun-Chen-Zuo-Shi" component herbs of QiShenYiQi formula in treating acute myocardial ischemia by network pharmacology. PMID:25342960
The role of TGF-β signaling and apoptosis in innate and adaptive immunity in zebrafish: a systems biology approach. PMID:25341656
GroupRank: rank candidate genes in PPI network by differentially expressed gene groups. PMID:25330105
Yeast systems biology: our best shot at modeling a cell. PMID:25316779
The Hsp90-dependent proteome is conserved and enriched for hub proteins with high levels of protein-protein connectivity. PMID:25316598
Enhancing the functional content of eukaryotic protein interaction networks. PMID:25275489
Hope for GWAS: relevant risk genes uncovered from GWAS statistical noise. PMID:25268625
Collaborative mining and interpretation of large-scale data for biomedical research insights. PMID:25268270
Interactions Among Plant Transcription Factors Regulating Expression of Stress-responsive Genes. PMID:25249757
Predicting disease associations via biological network analysis. PMID:25228247
Systems cell biology. PMID:25225336
Pulsatile dynamics in the yeast proteome. PMID:25220054
Global analysis of protein aggregation in yeast during physiological conditions and arsenite stress. PMID:25217615
Human Tra2 proteins jointly control a CHEK1 splicing switch among alternative and constitutive target exons. PMID:25208576
Pvr expression regulators in equilibrium signal control and maintenance of Drosophila blood progenitors. PMID:25201876
Transcriptome sequencing of a large human family identifies the impact of rare noncoding variants. PMID:25192044
Controlled sumoylation of the mevalonate pathway enzyme HMGS-1 regulates metabolism during aging. PMID:25187565
Construction and analysis of the protein-protein interaction networks based on gene expression profiles of Parkinson's disease. PMID:25170921
TEMPI: probabilistic modeling time-evolving differential PPI networks with multiPle information. PMID:25161233
The genomic landscape of compensatory evolution. PMID:25157590
The exocyst and regulatory GTPases in urinary exosomes. PMID:25138791
From pathways to networks: connecting dots by establishing protein-protein interaction networks in signaling pathways using affinity purification and mass spectrometry. PMID:25137225
A novel mutation in VCP causes Charcot-Marie-Tooth Type 2 disease. PMID:25125609
A systems biology approach identified different regulatory networks targeted by KSHV miR-K12-11 in B cells and endothelial cells. PMID:25106478
A system based network approach to ethanol tolerance in Saccharomyces cerevisiae. PMID:25103914
Phen-Gen: combining phenotype and genotype to analyze rare disorders. PMID:25086502
Integration of proteomic and transcriptomic profiles identifies a novel PDGF-MYC network in human smooth muscle cells. PMID:25080971
Integrative analysis reveals disease-associated genes and biomarkers for prostate cancer progression. PMID:25080090
Finding pathway-modulating genes from a novel Ontology Fingerprint-derived gene network. PMID:25063300
Proteome-wide analysis of human disease mutations in short linear motifs: neglected players in cancer? PMID:25057855
Bioinformatic analysis of proteomics data. PMID:25033288
DBSecSys: a database of Burkholderia mallei secretion systems. PMID:25030112
Gene network-based analysis identifies two potential subtypes of small intestinal neuroendocrine tumors. PMID:25023465
Network-based analysis identifies epigenetic biomarkers of esophageal squamous cell carcinoma progression. PMID:25015989
Brefeldin A-inhibited guanine nucleotide-exchange protein 3 (BIG3) is predicted to interact with its partner through an ARM-type α-helical structure. PMID:24997568
Proteogenomic convergence for understanding cancer pathways and networks. PMID:24994965
Minimal metabolic pathway structure is consistent with associated biomolecular interactions. PMID:24987116
Systems biology in the context of big data and networks. PMID:24982882
Correlating information contents of gene ontology terms to infer semantic similarity of gene products. PMID:24963342
Homology-based prediction of interactions between proteins using Averaged One-Dependence Estimators. PMID:24953126
Proteomics analysis of the non-muscle myosin heavy chain IIa-enriched actin-myosin complex reveals multiple functions within the podocyte. PMID:24949636
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
Detecting protein complexes in protein interaction networks using a ranking algorithm with a refined merging procedure. PMID:24944073
Scale-space measures for graph topology link protein network architecture to function. PMID:24931989
DrugComboRanker: drug combination discovery based on target network analysis. PMID:24931988
New directions for diffusion-based network prediction of protein function: incorporating pathways with confidence. PMID:24931987
Network-dosage compensation topologies as recurrent network motifs in natural gene networks. PMID:24929807
On the crucial cerebellar wound healing-related pathways and their cross-talks after traumatic brain injury in Danio rerio. PMID:24926785
Alterations in the cerebellar (Phospho)proteome of a cyclic guanosine monophosphate (cGMP)-dependent protein kinase knockout mouse. PMID:24925903
GASOLINE: a Greedy And Stochastic algorithm for optimal Local multiple alignment of Interaction NEtworks. PMID:24911103
Genome-wide survey of tissue-specific microRNA and transcription factor regulatory networks in 12 tissues. PMID:24889152
TGF-β stimulation in human and murine cells reveals commonly affected biological processes and pathways at transcription level. PMID:24886091
The Index-based Subgraph Matching Algorithm with General Symmetries (ISMAGS): exploiting symmetry for faster subgraph enumeration. PMID:24879305
Poly (ADP-ribose) in the pathogenesis of Parkinson's disease. PMID:24874851
Inferring host gene subnetworks involved in viral replication. PMID:24874113
Insights from cerebellar transcriptomic analysis into the pathogenesis of ataxia. PMID:24862029
Analysis pipeline for the epistasis search - statistical versus biological filtering. PMID:24817878
Controllability in protein interaction networks. PMID:24778220
Prediction and experimental characterization of nsSNPs altering human PDZ-binding motifs. PMID:24722214
Systems biology as an integrated platform for bioinformatics, systems synthetic biology, and systems metabolic engineering. PMID:24709875
Protein-protein interaction detection: methods and analysis. PMID:24693427
Global quantitative modeling of chromatin factor interactions. PMID:24675896
Plant systems biology: insights, advances and challenges. PMID:24671625
Improving protein function prediction using domain and protein complexes in PPI networks. PMID:24655481
Synthetic cytotoxicity: digenic interactions with TEL1/ATM mutations reveal sensitivity to low doses of camptothecin. PMID:24653001
Detecting overlapping protein complexes by rough-fuzzy clustering in protein-protein interaction networks. PMID:24642838
REIL proteins of Arabidopsis thaliana interact in yeast-2-hybrid assays with homologs of the yeast Rlp24, Rpl24A, Rlp24B, Arx1, and Jjj1 proteins. PMID:24603461
DAWN: a framework to identify autism genes and subnetworks using gene expression and genetics. PMID:24602502
Family-based analysis identified CD2 as a susceptibility gene for primary open angle glaucoma in Chinese Han population. PMID:24597656
Inferring regulatory networks by combining perturbation screens and steady state gene expression profiles. PMID:24586224
Integrative analysis of many RNA-seq datasets to study alternative splicing. PMID:24583115
Computational prediction of the human-microbial oral interactome. PMID:24576332
Inferring functional transcription factor-gene binding pairs by integrating transcription factor binding data with transcription factor knockout data. PMID:24565265
Corbi: a new R package for biological network alignment and querying. PMID:24565104
Conceptualization of molecular findings by mining gene annotations. PMID:24564884
Prediction of heterotrimeric protein complexes by two-phase learning using neighboring kernels. PMID:24564744
Molecular pathway identification using biological network-regularized logistic models. PMID:24564637
PLW: Probabilistic Local Walks for detecting protein complexes from protein interaction networks. PMID:24564427
Modulation of gene expression regulated by the transcription factor NF-κB/RelA. PMID:24523406
Computational developments in microRNA-regulated protein-protein interactions. PMID:24507415
Increased expression of c-Jun in nonalcoholic fatty liver disease. PMID:24492282
Identifying driver mutations in sequenced cancer genomes: computational approaches to enable precision medicine. PMID:24479672
A comparative study of Whi5 and retinoblastoma proteins: from sequence and structure analysis to intracellular networks. PMID:24478706
Identification of human disease genes from interactome network using graphlet interaction. PMID:24465923
Review of biological network data and its applications. PMID:24465231
Characterizing and controlling the inflammatory network during influenza A virus infection. PMID:24445954
A protein profile of visceral adipose tissues linked to early pathogenesis of type 2 diabetes mellitus. PMID:24403596
Computational Prediction of Protein-Protein Interaction Networks: Algo-rithms and Resources. PMID:24396273
Protein interaction network for Alzheimer's disease using computational approach. PMID:24391359
Protein complex identification by integrating protein-protein interaction evidence from multiple sources. PMID:24386289
Systems biology approach to stage-wise characterization of epigenetic genes in lung adenocarcinoma. PMID:24369052
Chemical genetics of rapamycin-insensitive TORC2 in S. cerevisiae. PMID:24360963
Discovering implicit entity relation with the gene-citation-gene network. PMID:24358368
Predicting protein-protein interaction by the mirrortree method: possibilities and limitations. PMID:24349035
Identification of unstable network modules reveals disease modules associated with the progression of Alzheimer's disease. PMID:24348898
Establishing an osteosarcoma associated protein-protein interaction network to explore the pathogenesis of osteosarcoma. PMID:24330838
Network analysis of GWAS data. PMID:24287332
Integrative functional genomic analyses implicate specific molecular pathways and circuits in autism. PMID:24267887
Dynamic trans-acting factor colocalization in human cells. PMID:24243024
Evolutionary rate patterns of genes involved in the Drosophila Toll and Imd signaling pathway. PMID:24209511
Synthetic genetic targeting of genome instability in cancer. PMID:24202319
Network cluster analysis of protein-protein interaction network identified biomarker for early onset colorectal cancer. PMID:24197691
Going the distance for protein function prediction: a new distance metric for protein interaction networks. PMID:24194834
Mutations in the gene encoding IFT dynein complex component WDR34 cause Jeune asphyxiating thoracic dystrophy. PMID:24183451
Cumulative haploinsufficiency and triplosensitivity drive aneuploidy patterns and shape the cancer genome. PMID:24183448
Methods and approaches in the topology-based analysis of biological pathways. PMID:24133454
Mass spectrometry coupled experiments and protein structure modeling methods. PMID:24132151
Intrinsically disordered regions in autophagy proteins. PMID:24115198
A sampling framework for incorporating quantitative mass spectrometry data in protein interaction analysis. PMID:24093595
Reconstruction of the experimentally supported human protein interactome: what can we learn? PMID:24088582
Functional module identification in protein interaction networks by interaction patterns. PMID:24085567
Using PPI network autocorrelation in hierarchical multi-label classification trees for gene function prediction. PMID:24070402
Clustering based on multiple biological information: approach for predicting protein complexes. PMID:24067423
JunD/AP1 regulatory network analysis during macrophage activation in a rat model of crescentic glomerulonephritis. PMID:24053712
Evolution after whole-genome duplication: a network perspective. PMID:24048644
Characterization and prediction of haploinsufficiency using systems-level gene properties in yeast. PMID:24048642
Integrative approaches for finding modular structure in biological networks. PMID:24045689
Horizontal gene transfer in osmotrophs: playing with public goods. PMID:24018383
Inferring the effective TOR-dependent network: a computational study in yeast. PMID:24005029
Interspecies protein-protein interaction network construction for characterization of host-pathogen interactions: a Candida albicans-zebrafish interaction study. PMID:23947337
Discovery of cell-type specific regulatory elements in the human genome using differential chromatin modification analysis. PMID:23945931
A miniaturized chemical proteomic approach for target profiling of clinical kinase inhibitors in tumor biopsies. PMID:23901793
Identification of yeast cell cycle regulated genes based on genomic features. PMID:23895232
Inferring potential microRNA-microRNA associations based on targeting propensity and connectivity in the context of protein interaction network. PMID:23874989
Mining differential top-k co-expression patterns from time course comparative gene expression datasets. PMID:23870110
Identification of Novel Stress Granule Components That Are Involved in Nuclear Transport. PMID:23826389
Genome-Wide Responses of Female Fruit Flies Subjected to Divergent Mating Regimes. PMID:23826372
Towards systematic discovery of signaling networks in budding yeast filamentous growth stress response using interventional phosphorylation data. PMID:23825934
CHD@ZJU: a knowledgebase providing network-based research platform on coronary heart disease. PMID:23818526
Identifying proteins controlling key disease signaling pathways. PMID:23812988
PIMiner: a web tool for extraction of protein interactions from biomedical literature. PMID:23798227
Prediction of heterodimeric protein complexes from weighted protein-protein interaction networks using novel features and kernel functions. PMID:23776458
The functional interactome landscape of the human histone deacetylase family. PMID:23752268
Passing messages between biological networks to refine predicted interactions. PMID:23741402
A network pharmacology approach to evaluating the efficacy of chinese medicine using genome-wide transcriptional expression data. PMID:23737854
Protein complex detection using interaction reliability assessment and weighted clustering coefficient. PMID:23688127
Structure and non-structure of centrosomal proteins. PMID:23671615
Interfacing cellular networks of S. cerevisiae and E. coli: connecting dynamic and genetic information. PMID:23663484
Modular biological function is most effectively captured by combining molecular interaction data types. PMID:23658761
Protein complex detection via weighted ensemble clustering based on Bayesian nonnegative matrix factorization. PMID:23658709
The role of protein interactions in mediating essentiality and synthetic lethality. PMID:23638160
Bioinformatics analysis identify novel OB fold protein coding genes in C. elegans. PMID:23638006
Systematic analysis of experimental phenotype data reveals gene functions. PMID:23626672
The index-based subgraph matching algorithm (ISMA): fast subgraph enumeration in large networks using optimized search trees. PMID:23620730
Evolutionary capacitance and control of protein stability in protein-protein interaction networks. PMID:23592969
Function relaxation followed by diversifying selection after whole-genome duplication in flowering plants. PMID:23580595
Improved method for protein complex detection using bottleneck proteins. PMID:23566214
t-LSE: a novel robust geometric approach for modeling protein-protein interaction networks. PMID:23560036
The potential of text mining in data integration and network biology for plant research: a case study on Arabidopsis. PMID:23532071
Copy-number variation of cancer-gene orthologs is sufficient to induce cancer-like symptoms in Saccharomyces cerevisiae. PMID:23531409
Parametric Bayesian priors and better choice of negative examples improve protein function prediction. PMID:23511543
Interpretation of genomic variants using a unified biological network approach. PMID:23505346
Novel semantic similarity measure improves an integrative approach to predicting gene functional associations. PMID:23497449
A role for the nucleoporin Nup170p in chromatin structure and gene silencing. PMID:23452847
Neurodevelopmental and neuropsychiatric disorders represent an interconnected molecular system. PMID:23439483
From hub proteins to hub modules: the relationship between essentiality and centrality in the yeast interactome at different scales of organization. PMID:23436988
Proteome-wide prediction of self-interacting proteins based on multiple properties. PMID:23422585
Genome-wide analysis of LXRα activation reveals new transcriptional networks in human atherosclerotic foam cells. PMID:23393188
SNPranker 2.0: a gene-centric data mining tool for diseases associated SNP prioritization in GWAS. PMID:23369106
FitSearch: a robust way to interpret a yeast fitness profile in terms of drug's mode-of-action. PMID:23368702
Visual data mining of biological networks: one size does not fit all. PMID:23341759
A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis. PMID:23334424
Synthetic lethality and cancer: cohesin and PARP at the replication fork. PMID:23333522
mirTarPri: improved prioritization of microRNA targets through incorporation of functional genomics data. PMID:23326485
An RS motif within the Epstein-Barr virus BLRF2 tegument protein is phosphorylated by SRPK2 and is important for viral replication. PMID:23326445
Using graph models to find transcription factor modules: the hitting set problem and an exact algorithm. PMID:23324335
Disentangling function from topology to infer the network properties of disease genes. PMID:23324116
A ceRNA analysis on LMNA gene focusing on the Hutchinson-Gilford progeria syndrome. PMID:23317481
Transcriptome-wide expansion of non-coding regulatory switches: evidence from co-occurrence of Alu exonization, antisense and editing. PMID:23303787
Transcriptional program of ciliated epithelial cells reveals new cilium and centrosome components and links to human disease. PMID:23300604
Inferring the Brassica rapa Interactome Using Protein-Protein Interaction Data from Arabidopsis thaliana. PMID:23293649
Labeling nodes using three degrees of propagation. PMID:23284828
Genes contributing to pain sensitivity in the normal population: an exome sequencing study. PMID:23284290
A systems approach to rheumatoid arthritis. PMID:23240033
FoxO6 regulates memory consolidation and synaptic function. PMID:23222102
Mitotic exit and separation of mother and daughter cells. PMID:23212898
Identifying complexes from protein interaction networks according to different types of neighborhood density. PMID:23210476
Wiki-pi: a web-server of annotated human protein-protein interactions to aid in discovery of protein function. PMID:23209562
Biological databases for behavioral neurobiology. PMID:23195119
PrePPI: a structure-informed database of protein-protein interactions. PMID:23193263
Visual analysis of transcriptome data in the context of anatomical structures and biological networks. PMID:23162564
High-resolution genome-wide scan of genes, gene-networks and cellular systems impacting the yeast ionome. PMID:23151179
DLocalMotif: a discriminative approach for discovering local motifs in protein sequences. PMID:23142965
Bioinformatic identification of genes suppressing genome instability. PMID:23129647
Insights into the evolutionary features of human neurodegenerative diseases. PMID:23118989
Knowledge building insights on biomarkers of arsenic toxicity to keratinocytes and melanocytes. PMID:23115478
Systems analysis of plant functional, transcriptional, physical interaction, and metabolic networks. PMID:23110892
Linkers of cell polarity and cell cycle regulation in the fission yeast protein interaction network. PMID:23093924
Linking the signaling cascades and dynamic regulatory networks controlling stress responses. PMID:23064748
Bayesian correlated clustering to integrate multiple datasets. PMID:23047558
Ranking relations between diseases, drugs and genes for a curation task. PMID:23046495
Taxonomies of networks from community structure. PMID:23030977
Multi-edge gene set networks reveal novel insights into global relationships between biological themes. PMID:23028852
What evidence is there for the homology of protein-protein interactions? PMID:23028270
Protein stickiness, rather than number of functional protein-protein interactions, predicts expression noise and plasticity in yeast. PMID:23017156
A simple knowledge-based mining method for exploring hidden key molecules in a human biomolecular network. PMID:22979956
Fungal Hsp90: a biological transistor that tunes cellular outputs to thermal inputs. PMID:22976491
An integrated approach to identify causal network modules of complex diseases with application to colorectal cancer. PMID:22967703
ReLiance: a machine learning and literature-based prioritization of receptor--ligand pairings. PMID:22962483
A network-based maximum link approach towards MS identifies potentially important roles for undetected ARRB1/2 and ACTB in liver cancer progression. PMID:22961449
Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors. PMID:22955990
A computational framework for boosting confidence in high-throughput protein-protein interaction datasets. PMID:22937800
Exploring overlapping functional units with various structure in protein interaction networks. PMID:22916212
Identification of a complex genetic network underlying Saccharomyces cerevisiae colony morphology. PMID:22882838
NEXCADE: perturbation analysis for complex networks. PMID:22870252
Robust co-regulation of tyrosine phosphorylation sites on proteins reveals novel protein interactions. PMID:22851037
Identifying responsive modules by mathematical programming: an application to budding yeast cell cycle. PMID:22848637
One Hand Clapping: detection of condition-specific transcription factor interactions from genome-wide gene activity data. PMID:22844089
Subnetwork-based analysis of chronic lymphocytic leukemia identifies pathways that associate with disease progression. PMID:22837534
Sets2Networks: network inference from repeated observations of sets. PMID:22824380
A strategy based on protein-protein interface motifs may help in identifying drug off-targets. PMID:22817115
Integration of biological networks and pathways with genetic association studies. PMID:22777728
In-silico identification of phenotype-biased functional modules. PMID:22759578
Predicting multiplex subcellular localization of proteins using protein-protein interaction network: a comparative study. PMID:22759426
Minimalist ensemble algorithms for genome-wide protein localization prediction. PMID:22759391
Conserved rules govern genetic interaction degree across species. PMID:22747640
MC EMiNEM maps the interaction landscape of the Mediator. PMID:22737066
Proteome-wide prediction of protein-protein interactions from high-throughput data. PMID:22729399
Network analysis identifies a putative role for the PPAR and type 1 interferon pathways in glucocorticoid actions in asthmatics. PMID:22713245
Algorithm to identify frequent coupled modules from two-layered network series: application to study transcription and splicing coupling. PMID:22697243
Tackling drought stress: receptor-like kinases present new approaches. PMID:22693282
Cancer core modules identification through genomic and transcriptomic changes correlation detection at network level. PMID:22691569
A single source k-shortest paths algorithm to infer regulatory pathways in a gene network. PMID:22689778
How networks change with time. PMID:22689777
Genome-wide functional profiling identifies genes and processes important for zinc-limited growth of Saccharomyces cerevisiae. PMID:22685415
Identification of novel ATP13A2 interactors and their role in α-synuclein misfolding and toxicity. PMID:22645275
DroPNet: a web portal for integrated analysis of Drosophila protein-protein interaction networks. PMID:22641854
High-throughput analysis of peptide-binding modules. PMID:22610655
Mycobacterium tuberculosis and Clostridium difficille interactomes: demonstration of rapid development of computational system for bacterial interactome prediction. PMID:22587966
Inferring high-confidence human protein-protein interactions. PMID:22558947
LDGIdb: a database of gene interactions inferred from long-range strong linkage disequilibrium between pairs of SNPs. PMID:22551073
Revisiting the variation of clustering coefficient of biological networks suggests new modular structure. PMID:22548803
A comparative analysis of protein targets of withdrawn cardiovascular drugs in human and mouse. PMID:22548699
A framework for mapping, visualisation and automatic model creation of signal-transduction networks. PMID:22531118
Functional organization and its implication in evolution of the human protein-protein interaction network. PMID:22530615
Prediction of phenotype-associated genes via a cellular network approach: a Candida albicans infection case study. PMID:22509408
Network- and attribute-based classifiers can prioritize genes and pathways for autism spectrum disorders and intellectual disability. PMID:22499558
The functions of Mediator in Candida albicans support a role in shaping species-specific gene expression. PMID:22496666
Context-specific protein network miner--an online system for exploring context-specific protein interaction networks from the literature. PMID:22493694
Drug target prediction based on the herbs components: the study on the multitargets pharmacological mechanism of qishenkeli acting on the coronary heart disease. PMID:22474514
Interactomic and pharmacological insights on human sirt-1. PMID:22470339
A stochastic model for the development of Bateson-Dobzhansky-Muller incompatibilities that incorporates protein interaction networks. PMID:22465838
High accordance in prognosis prediction of colorectal cancer across independent datasets by multi-gene module expression profiles. PMID:22438977
Coordination of the transcriptome and metabolome by the circadian clock. PMID:22431615
Detecting overlapping protein complexes in protein-protein interaction networks. PMID:22426491
Chaperones divide yeast proteins into classes of expression level and evolutionary rate. PMID:22417914
Crosstalk between transcription factors and microRNAs in human protein interaction network. PMID:22413876
Sirtuins as regulators of the yeast metabolic network. PMID:22408620
A study on promoter characteristics of head-to-head genes in Saccharomyces cerevisiae. PMID:22369481
Prioritizing disease candidate genes by a gene interconnectedness-based approach. PMID:22369140
SAINT-MS1: protein-protein interaction scoring using label-free intensity data in affinity purification-mass spectrometry experiments. PMID:22352807
ANAP: an integrated knowledge base for Arabidopsis protein interaction network analysis. PMID:22345505
Integrating the Alzheimer's disease proteome and transcriptome: a comprehensive network model of a complex disease. PMID:22321014
Identifying gene interaction networks. PMID:22307715
Functional wiring of the yeast kinome revealed by global analysis of genetic network motifs. PMID:22282571
IMID: integrated molecular interaction database. PMID:22238258
A searchable cross-platform gene expression database reveals connections between drug treatments and disease. PMID:22233519
Mass spectrometry-based proteomics: qualitative identification to activity-based protein profiling. PMID:22231900
A network-based approach on elucidating the multi-faceted nature of chronological aging in S. cerevisiae. PMID:22216232
Modeling community-wide molecular networks of multicellular systems. PMID:22210865
MotifMap: integrative genome-wide maps of regulatory motif sites for model species. PMID:22208852
Global landscape of HIV-human protein complexes. PMID:22190034
Which clustering algorithm is better for predicting protein complexes? PMID:22185599
Antibody colocalization microarray: a scalable technology for multiplex protein analysis in complex samples. PMID:22171321
Constructing a robust protein-protein interaction network by integrating multiple public databases. PMID:22165958
Protein complex detection with semi-supervised learning in protein interaction networks. PMID:22165896
Decomposing PPI networks for complex discovery. PMID:22165860
Advances in omics and bioinformatics tools for systems analyses of plant functions. PMID:22156726
Detection of interaction articles and experimental methods in biomedical literature. PMID:22151872
Simple and efficient machine learning frameworks for identifying protein-protein interaction relevant articles and experimental methods used to study the interactions. PMID:22151701
Heterozygous yeast deletion collection screens reveal essential targets of Hsp90. PMID:22140548
Identification of dysfunctional modules and disease genes in congenital heart disease by a network-based approach. PMID:22136190
Multiple means to the same end: the genetic basis of acquired stress resistance in yeast. PMID:22102822
Biochemical and computational analysis of LNX1 interacting proteins. PMID:22087225
Construction of regulatory networks using expression time-series data of a genotyped population. PMID:22084118
Genome-wide analysis of chromatin features identifies histone modification sensitive and insensitive yeast transcription factors. PMID:22060676
Computationally efficient measure of topological redundancy of biological and social networks. PMID:22060466
Identification of common and cell type specific LXXLL motif EcR cofactors using a bioinformatics refined candidate RNAi screen in Drosophila melanogaster cell lines. PMID:22050674
PomBase: a comprehensive online resource for fission yeast. PMID:22039153
Proteomic and functional genomic landscape of receptor tyrosine kinase and ras to extracellular signal-regulated kinase signaling. PMID:22028469
An in silico approach combined with in vivo experiments enables the identification of a new protein whose overexpression can compensate for specific respiratory defects in Saccharomyces cerevisiae. PMID:22027258
Learning cellular sorting pathways using protein interactions and sequence motifs. PMID:21999284
Copy-number variation: the balance between gene dosage and expression in Drosophila melanogaster. PMID:21979154
iRefScape. A Cytoscape plug-in for visualization and data mining of protein interaction data from iRefIndex. PMID:21975162
Aconitase regulation of erythropoiesis correlates with a novel licensing function in erythropoietin-induced ERK signaling. PMID:21887333
Inferring mechanisms of compensation from E-MAP and SGA data using local search algorithms for max cut. PMID:21882903
Biological interaction networks are conserved at the module level. PMID:21861884
Application of computational systems biology to explore environmental toxicity hazards. PMID:21846611
Conserved and differential gene interactions in dynamical biological systems. PMID:21840874
Computational simulations to predict creatine kinase-associated factors: protein-protein interaction studies of brain and muscle types of creatine kinases. PMID:21826261
NETGEM: Network Embedded Temporal GEnerative Model for gene expression data. PMID:21824426
Computational approach to identify enzymes that are potential therapeutic candidates for psoriasis. PMID:21822480
Differential C3NET reveals disease networks of direct physical interactions. PMID:21777411
Fine-tuning of the Msn2/4-mediated yeast stress responses as revealed by systematic deletion of Msn2/4 partners. PMID:21757539
Reactome pathway analysis to enrich biological discovery in proteomics data sets. PMID:21751369
A novel method to identify cooperative functional modules: study of module coordination in the Saccharomyces cerevisiae cell cycle. PMID:21749690
Integrated bio-entity network: a system for biological knowledge discovery. PMID:21738677
InterMitoBase: an annotated database and analysis platform of protein-protein interactions for human mitochondria. PMID:21718467
Proteomic patterns of cervical cancer cell lines, a network perspective. PMID:21696634
BioGraph: unsupervised biomedical knowledge discovery via automated hypothesis generation. PMID:21696594
Integrative computational biology for cancer research. PMID:21691773
Generative probabilistic models for protein-protein interaction networks--the biclique perspective. PMID:21685063
Noise reduction in protein-protein interaction graphs by the implementation of a novel weighting scheme. PMID:21679454
Repression of mitochondrial translation, respiration and a metabolic cycle-regulated gene, SLF1, by the yeast Pumilio-family protein Puf3p. PMID:21655263
A network of SCOP hidden Markov models and its analysis. PMID:21635719
A gene-phenotype network for the laboratory mouse and its implications for systematic phenotyping. PMID:21625554
MINE: Module Identification in Networks. PMID:21605434
Plasmodium falciparum enolase complements yeast enolase functions and associates with the parasite food vacuole. PMID:21600245
Evidence for the additions of clustered interacting nodes during the evolution of protein interaction networks from network motifs. PMID:21595981
Meta analysis of Chronic Fatigue Syndrome through integration of clinical, gene expression, SNP and proteomic data. PMID:21584188
PRIN: a predicted rice interactome network. PMID:21575196
Protein annotation from protein interaction networks and Gene Ontology. PMID:21571095
Computational integration of homolog and pathway gene module expression reveals general stemness signatures. PMID:21559491
Using graph theory to analyze biological networks. PMID:21527005
A quantitative literature-curated gold standard for kinase-substrate pairs. PMID:21492431
The synthetic genetic interaction network reveals small molecules that target specific pathways in Sacchromyces cerevisiae. PMID:21487606
The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods. PMID:21472436
Diverse protein kinase interactions identified by protein microarrays reveal novel connections between cellular processes. PMID:21460040
Computational study of associations between histone modification and protein-DNA binding in yeast genome by integrating diverse information. PMID:21457549
The CRIT framework for identifying cross patterns in systems biology and application to chemogenomics. PMID:21453526
The predicted Arabidopsis interactome resource and network topology-based systems biology analyses. PMID:21441435
Quantitative maps of genetic interactions in yeast - comparative evaluation and integrative analysis. PMID:21435228
Customizable views on semantically integrated networks for systems biology. PMID:21414991
Network-based pipeline for analyzing MS data: an application toward liver cancer. PMID:21410269
TargetMine, an integrated data warehouse for candidate gene prioritisation and target discovery. PMID:21408081
A probabilistic model of nuclear import of proteins. PMID:21372083
Topology of protein interaction network shapes protein abundances and strengths of their functional and nonspecific interactions. PMID:21368118
Connectedness of PPI network neighborhoods identifies regulatory hub proteins. PMID:21367871
Histoplasma capsulatum heat-shock 60 orchestrates the adaptation of the fungus to temperature stress. PMID:21347364
Resolving the structure of interactomes with hierarchical agglomerative clustering. PMID:21342576
Integrating multiple protein-protein interaction networks to prioritize disease genes: a Bayesian regression approach. PMID:21342540
Dengue-2 structural proteins associate with human proteins to produce a coagulation and innate immune response biased interactome. PMID:21281507
HTSanalyzeR: an R/Bioconductor package for integrated network analysis of high-throughput screens. PMID:21258062
Measuring the evolutionary rewiring of biological networks. PMID:21253555
Proteomic snapshot of the EGF-induced ubiquitin network. PMID:21245847
Context-dependent transcriptional regulations between signal transduction pathways. PMID:21232126
A network-based biomarker approach for molecular investigation and diagnosis of lung cancer. PMID:21211025
Large-scale discovery and characterization of protein regulatory motifs in eukaryotes. PMID:21206902
Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast. PMID:21206491
Reconstruction of protein-protein interaction network of insulin signaling in Homo sapiens. PMID:21197403
Integrated functional networks of process, tissue, and developmental stage specific interactions in Arabidopsis thaliana. PMID:21194434
SIDEKICK: Genomic data driven analysis and decision-making framework. PMID:21192813
Literature curation of protein interactions: measuring agreement across major public databases. PMID:21183497
The Protein Information and Property Explorer 2: gaggle-like exploration of biological proteomic data within one webpage. PMID:21182202
Defining the budding yeast chromatin-associated interactome. PMID:21179020
New insights into protein-protein interaction data lead to increased estimates of the S. cerevisiae interactome size. PMID:21176124
Combining modularity, conservation, and interactions of proteins significantly increases precision and coverage of protein function prediction. PMID:21171995
PETALS: Proteomic Evaluation and Topological Analysis of a mutated Locus' Signaling. PMID:21144021
iWRAP: An interface threading approach with application to prediction of cancer-related protein-protein interactions. PMID:21130772
Global analysis of phase locking in gene expression during cell cycle: the potential in network modeling. PMID:21129191
A computational approach to analyze the mechanism of action of the kinase inhibitor bafetinib. PMID:21124949
Modeling contaminants in AP-MS/MS experiments. PMID:21117706
Discovering pathways by orienting edges in protein interaction networks. PMID:21109539
Integrating diverse biological and computational sources for reliable protein-protein interactions. PMID:21106130
An improved method for scoring protein-protein interactions using semantic similarity within the gene ontology. PMID:21078182
Concept and application of a computational vaccinology workflow. PMID:21067549
CPLA 1.0: an integrated database of protein lysine acetylation. PMID:21059677
Module discovery by exhaustive search for densely connected, co-expressed regions in biomolecular interaction networks. PMID:21049092
Predicting gene function using few positive examples and unlabeled ones. PMID:21047378
Pif1- and Exo1-dependent nucleases coordinate checkpoint activation following telomere uncapping. PMID:21045806
CADgene: a comprehensive database for coronary artery disease genes. PMID:21045063
Discover protein complexes in protein-protein interaction networks using parametric local modularity. PMID:20958996
PAIR: the predicted Arabidopsis interactome resource. PMID:20952401
Dynamic functional modules in co-expressed protein interaction networks of dilated cardiomyopathy. PMID:20950417
iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence. PMID:20940177
Examination of the relationship between essential genes in PPI network and hub proteins in reverse nearest neighbor topology. PMID:20939873
ChemProt: a disease chemical biology database. PMID:20935044
Toward a complete in silico, multi-layered embryonic stem cell regulatory network. PMID:20890967
A QUICK screen for Lrrk2 interaction partners--leucine-rich repeat kinase 2 is involved in actin cytoskeleton dynamics. PMID:20876399
Protein network prediction and topological analysis in Leishmania major as a tool for drug target selection. PMID:20875130
Identifying the genetic determinants of transcription factor activity. PMID:20865005
Gene expression variations are predictive for stochastic noise. PMID:20860999
Eukaryotic genes of archaebacterial origin are more important than the more numerous eubacterial genes, irrespective of function. PMID:20852068
Protein complex prediction based on k-connected subgraphs in protein interaction network. PMID:20846398
Tailored graph ensembles as proxies or null models for real networks I: tools for quantifying structure. PMID:20844594
Candidate gene prioritization by network analysis of differential expression using machine learning approaches. PMID:20840752
Identifying dysfunctional crosstalk of pathways in various regions of Alzheimer's disease brains. PMID:20840725
A global census of fission yeast deubiquitinating enzyme localization and interaction networks reveals distinct compartmentalization profiles and overlapping functions in endocytosis and polarity. PMID:20838651
Identification of response-modulated genetic interactions by sensitivity-based epistatic analysis. PMID:20831804
The BioPAX community standard for pathway data sharing. PMID:20829833
A yeast's eye view of mammalian reproduction: cross-species gene co-expression in meiotic prophase. PMID:20819218
Molecular mechanistic associations of human diseases. PMID:20815942
Protein networks reveal detection bias and species consistency when analysed by information-theoretic methods. PMID:20805870
Identification of epistatic effects using a protein-protein interaction database. PMID:20736252
A strategy for interaction site prediction between phospho-binding modules and their partners identified from proteomic data. PMID:20733106
A genome-wide gene function prediction resource for Drosophila melanogaster. PMID:20711346
Encoding the states of interacting proteins to facilitate biological pathways reconstruction. PMID:20707925
Patterns of HIV-1 protein interaction identify perturbed host-cellular subsystems. PMID:20686668
Open source tool for prediction of genome wide protein-protein interaction network based on ortholog information. PMID:20684769
A systems approach to mapping transcriptional networks controlling surfactant homeostasis. PMID:20659319
Genome-wide scoring of positive and negative epistasis through decomposition of quantitative genetic interaction fitness matrices. PMID:20657656
The function of communities in protein interaction networks at multiple scales. PMID:20649971
Predicting functional associations from metabolism using bi-partite network algorithms. PMID:20630077
Annotation of SBML models through rule-based semantic integration. PMID:20626923
Development of a novel bioinformatics tool for in silico validation of protein interactions. PMID:20625507
Protein complex prediction via verifying and reconstructing the topology of domain-domain interactions. PMID:20584269
A semi-supervised learning approach to predict synthetic genetic interactions by combining functional and topological properties of functional gene network. PMID:20573270
Protein interaction network topology uncovers melanogenesis regulatory network components within functional genomics datasets. PMID:20550706
Systematic analysis of essential genes reveals important regulators of G protein signaling. PMID:20542006
Protein interface conservation across structure space. PMID:20534496
A quick guide to large-scale genomic data mining. PMID:20523745
Integrative structure modeling of macromolecular assemblies from proteomics data. PMID:20507923
Fast integration of heterogeneous data sources for predicting gene function with limited annotation. PMID:20507895
Reconstruction of the yeast protein-protein interaction network involved in nutrient sensing and global metabolic regulation. PMID:20500839
Dynamic cross-talk analysis among TNF-R, TLR-4 and IL-1R signalings in TNFalpha-induced inflammatory responses. PMID:20497537
Structural interpretation of protein-protein interaction network. PMID:20487511
Protein evolution in yeast transcription factor subnetworks. PMID:20466810
Coordinated modular functionality and prognostic potential of a heart failure biomarker-driven interaction network. PMID:20462429
Natural selection on cis and trans regulation in yeasts. PMID:20445163
Molecular signaling in zebrafish development and the vertebrate phylotypic period. PMID:20433455
Reconstruction of gene regulatory modules in cancer cell cycle by multi-source data integration. PMID:20422009
Simultaneous clustering of multiple gene expression and physical interaction datasets. PMID:20419151
Response network analysis of differential gene expression in human epithelial lung cells during avian influenza infections. PMID:20370926
TopoGSA: network topological gene set analysis. PMID:20335277
Construction and analysis of protein-protein interaction networks. PMID:20334628
Gene regulatory networks modelling using a dynamic evolutionary hybrid. PMID:20298548
Topological network alignment uncovers biological function and phylogeny. PMID:20236959
A simple technique for the prediction of interacting proteins reveals a direct Brn-3a-androgen receptor interaction. PMID:20228055
Toward design-based engineering of industrial microbes. PMID:20226723
Integrated cellular network of transcription regulations and protein-protein interactions. PMID:20211003
Pathway Palette: a rich internet application for peptide-, protein- and network-oriented analysis of MS data. PMID:20198642
SING: subgraph search in non-homogeneous graphs. PMID:20170516
BisoGenet: a new tool for gene network building, visualization and analysis. PMID:20163717
Feedback between p21 and reactive oxygen production is necessary for cell senescence. PMID:20160708
The trypanosome Pumilio-domain protein PUF7 associates with a nuclear cyclophilin and is involved in ribosomal RNA maturation. PMID:20153321
Lists2Networks: integrated analysis of gene/protein lists. PMID:20152038
Madm (Mlf1 adapter molecule) cooperates with Bunched A to promote growth in Drosophila. PMID:20149264
Inference of RhoGAP/GTPase regulation using single-cell morphological data from a combinatorial RNAi screen. PMID:20144944
Global approaches to study protein-protein interactions among viruses and hosts. PMID:20143950
Protein interactions and ligand binding: from protein subfamilies to functional specificity. PMID:20133844
A general co-expression network-based approach to gene expression analysis: comparison and applications. PMID:20122284
Integration of multiple data sources to prioritize candidate genes using discounted rating system. PMID:20122192
Comparative evolutionary analysis of protein complexes in E. coli and yeast. PMID:20122144
Biana: a software framework for compiling biological interactions and analyzing networks. PMID:20105306
Automatic inference of multicellular regulatory networks using informative priors. PMID:20090166
A manually curated network of the PML nuclear body interactome reveals an important role for PML-NBs in SUMOylation dynamics. PMID:20087442
CORNET: a user-friendly tool for data mining and integration. PMID:20053712
AtPIN: Arabidopsis thaliana protein interaction network. PMID:20043823
Pandora, a pathway and network discovery approach based on common biological evidence. PMID:20031970
Expanding the definition of the classical bipartite nuclear localization signal. PMID:20028483
On the classification of epistatic interactions. PMID:20026678
Human synthetic lethal inference as potential anti-cancer target gene detection. PMID:20015360
A cassette of N-terminal amino acids of histone H2B are required for efficient cell survival, DNA repair and Swi/Snf binding in UV irradiated yeast. PMID:20007597
Towards accurate imputation of quantitative genetic interactions. PMID:20003301
PutidaNET: interactome database service and network analysis of Pseudomonas putida KT2440. PMID:19958481
Chromatin regulation and gene centrality are essential for controlling fitness pleiotropy in yeast. PMID:19956643
Spectral affinity in protein networks. PMID:19943959
Functional features of gene expression profiles differentiating gastrointestinal stromal tumours according to KIT mutations and expression. PMID:19943934
Exploiting amino acid composition for predicting protein-protein interactions. PMID:19936254
Novel protein-protein interactions inferred from literature context. PMID:19924298
Reconstruction of the yeast Snf1 kinase regulatory network reveals its role as a global energy regulator. PMID:19888214
DRYGIN: a database of quantitative genetic interaction networks in yeast. PMID:19880385
Predicting meiotic pathways in human fetal oogenesis. PMID:19846598
XML-based approaches for the integration of heterogeneous bio-molecular data. PMID:19828083
VANLO--interactive visual exploration of aligned biological networks. PMID:19821976
How to visually interpret biological data using networks. PMID:19816451
Proteomics data repositories. PMID:19795424
The MAPK signaling cascade is a central hub in the regulation of cell cycle, apoptosis and cytoskeleton remodeling by tripeptidyl-peptidase II. PMID:19787088
A protein-protein interaction guided method for competitive transcription factor binding improves target predictions. PMID:19786498
How and when should interactome-derived clusters be used to predict functional modules and protein function? PMID:19770263
Finding local communities in protein networks. PMID:19765306
Gene networks in Drosophila melanogaster: integrating experimental data to predict gene function. PMID:19758432
Defining elastic fiber interactions by molecular fishing: an affinity purification and mass spectrometry approach. PMID:19755719
Usefulness and limitations of dK random graph models to predict interactions and functional homogeneity in biological networks under a pseudo-likelihood parameter estimation approach. PMID:19728875
A reliable measure of similarity based on dependency for short time series: an application to gene expression networks. PMID:19712487
The ordering of expression among a few genes can provide simple cancer biomarkers and signal BRCA1 mutations. PMID:19695104
Knowledge-guided inference of domain-domain interactions from incomplete protein-protein interaction networks. PMID:19667081
Geometric de-noising of protein-protein interaction networks. PMID:19662157
Predicting eukaryotic transcriptional cooperativity by Bayesian network integration of genome-wide data. PMID:19661283
Local network topology in human protein interaction data predicts functional association. PMID:19641626
Integrating proteomic, transcriptional, and interactome data reveals hidden components of signaling and regulatory networks. PMID:19638617
Detection of mammalian virulence determinants in highly pathogenic avian influenza H5N1 viruses: multivariate analysis of published data. PMID:19625397
Systems-level cancer gene identification from protein interaction network topology applied to melanogenesis-related functional genomics data. PMID:19625303
Ontogeny and phylogeny: molecular signatures of selection, constraint, and temporal pleiotropy in the development of Drosophila. PMID:19622136
Defining the human deubiquitinating enzyme interaction landscape. PMID:19615732
A network model of a cooperative genetic landscape in brain tumors. PMID:19602686
Computational identification of potential molecular interactions in Arabidopsis. PMID:19592425
Translational disease interpretation with molecular networks. PMID:19591646
BowTieBuilder: modeling signal transduction pathways. PMID:19566957
RNAiCut: automated detection of significant genes from functional genomic screens. PMID:19564846
Predicting protein-protein interactions in Arabidopsis thaliana through integration of orthology, gene ontology and co-expression. PMID:19563678
Systems approach to explore components and interactions in the presynapse. PMID:19562802
ITM Probe: analyzing information flow in protein networks. PMID:19561335
Evolution of phosphoregulation: comparison of phosphorylation patterns across yeast species. PMID:19547744
Interactome for auxiliary splicing factor U2AF(65) suggests diverse roles. PMID:19540372
Backup in gene regulatory networks explains differences between binding and knockout results. PMID:19536199
An atlas of chaperone-protein interactions in Saccharomyces cerevisiae: implications to protein folding pathways in the cell. PMID:19536198
PIAS proteins: pleiotropic interactors associated with SUMO. PMID:19526197
Directed mammalian gene regulatory networks using expression and comparative genomic hybridization microarray data from radiation hybrids. PMID:19521529
Integrated assessment of genomic correlates of protein evolutionary rate. PMID:19521505
Approaches to neuroscience data integration. PMID:19505888
Information flow analysis of interactome networks. PMID:19503817
myGRN: a database and visualisation system for the storage and analysis of developmental genetic regulatory networks. PMID:19500400
IsoRankN: spectral methods for global alignment of multiple protein networks. PMID:19477996
A complex-centric view of protein network evolution. PMID:19465379
Public databases and software for the pathway analysis of cancer genomes. PMID:19455256
The role of intrinsically unstructured proteins in neurodegenerative diseases. PMID:19440375
Incorporating functional inter-relationships into protein function prediction algorithms. PMID:19435516
Inferring novel disease indications for known drugs by semantically linking drug action and disease mechanism relationships. PMID:19426461
Assessing reliability of protein-protein interactions by integrative analysis of data in model organisms. PMID:19426453
PPISearch: a web server for searching homologous protein-protein interactions across multiple species. PMID:19417070
Protein-protein interaction databases: keeping up with growing interactomes. PMID:19403463
Fault tolerance in protein interaction networks: stable bipartite subgraphs and redundant pathways. PMID:19399174
Identifying hubs in protein interaction networks. PMID:19399170
Biological process linkage networks. PMID:19390589
POINeT: protein interactome with sub-network analysis and hub prioritization. PMID:19379523
Dynamic reprogramming of transcription factors to and from the subtelomere. PMID:19372386
Bayesian inference of protein-protein interactions from biological literature. PMID:19369495
Tissue specificity and the human protein interaction network. PMID:19357639
Spinal muscular atrophy and a model for survival of motor neuron protein function in axonal ribonucleoprotein complexes. PMID:19343312
Reconstructing the ubiquitin network: cross-talk with other systems and identification of novel functions. PMID:19331687
Markov clustering versus affinity propagation for the partitioning of protein interaction graphs. PMID:19331680
A general pipeline for quality and statistical assessment of protein interaction data using R and Bioconductor. PMID:19325550
On the growth of scientific knowledge: yeast biology as a case study. PMID:19300476
Modeling and analyzing gene co-expression in hepatocellular carcinoma using actor-semiotic networks and centrality signatures. PMID:19259423
Uncovering biological network function via graphlet degree signatures. PMID:19259413
Characterization of mouse IFT complex B. PMID:19253336
A survey of available tools and web servers for analysis of protein-protein interactions and interfaces. PMID:19240123
Specific synthetic lethal killing of RAD54B-deficient human colorectal cancer cells by FEN1 silencing. PMID:19218431
High throughput interaction data reveals degree conservation of hub proteins. PMID:19209717
Metabolic flux correlations, genetic interactions, and disease. PMID:19193147
Integrating computational biology and forward genetics in Drosophila. PMID:19165344
An integrated workflow for charting the human interaction proteome: insights into the PP2A system. PMID:19156129
A Drosophila systems model of pentylenetetrazole induced locomotor plasticity responsive to antiepileptic drugs. PMID:19154620
ben Functions with scamp during synaptic transmission and long-term memory formation in Drosophila. PMID:19144841
Predicting genetic interactions with random walks on biological networks. PMID:19138426
Questioning the ubiquity of neofunctionalization. PMID:19119408
A novel proteomics approach for the discovery of chromatin-associated protein networks. PMID:19106085
Up-to-date catalogues of yeast protein complexes. PMID:19095691
POLAR MAPPER: a computational tool for integrated visualization of protein interaction networks and mRNA expression data. PMID:19091689
Predicted mouse peroxisome-targeted proteins and their actual subcellular locations. PMID:19091015
Ortholog-based protein-protein interaction prediction and its application to inter-species interactions. PMID:19091010
Buffering by gene duplicates: an analysis of molecular correlates and evolutionary conservation. PMID:19087332
Improvements to cardiovascular gene ontology. PMID:19046747
Network integration and graph analysis in mammalian molecular systems biology. PMID:19045817
Age-dependent evolution of the yeast protein interaction network suggests a limited role of gene duplication and divergence. PMID:19043579
The integrated analysis of metabolic and protein interaction networks reveals novel molecular organizing principles. PMID:19032748
Training set expansion: an approach to improving the reconstruction of biological networks from limited and uneven reliable interactions. PMID:19015141
Combining multiple positive training sets to generate confidence scores for protein-protein interactions. PMID:19010802
MoKCa database--mutations of kinases in cancer. PMID:18986996
Network hubs buffer environmental variation in Saccharomyces cerevisiae. PMID:18986213
Hepatitis C virus infection protein network. PMID:18985028
Michigan molecular interactions r2: from interacting proteins to pathways. PMID:18978014
Organization of physical interactomes as uncovered by network schemas. PMID:18949022
Combination chemical genetics. PMID:18936752
A genomewide suppressor and enhancer analysis of cdc13-1 reveals varied cellular processes influencing telomere capping in Saccharomyces cerevisiae. PMID:18845848
Prediction of evolutionarily conserved interologs in Mus musculus. PMID:18842131
DroID: the Drosophila Interactions Database, a comprehensive resource for annotated gene and protein interactions. PMID:18840285
Protein networks markedly improve prediction of subcellular localization in multiple eukaryotic species. PMID:18836191
Finding friends and enemies in an enemies-only network: a graph diffusion kernel for predicting novel genetic interactions and co-complex membership from yeast genetic interactions. PMID:18832443
A genome wide analysis of the response to uncapped telomeres in budding yeast reveals a novel role for the NAD+ biosynthetic gene BNA2 in chromosome end protection. PMID:18828915
iRefIndex: a consolidated protein interaction database with provenance. PMID:18823568
Conservation and rewiring of functional modules revealed by an epistasis map in fission yeast. PMID:18818364
Modeling synthetic lethality. PMID:18789146
Inference of protein complex activities from chemical-genetic profile and its applications: predicting drug-target pathways. PMID:18769708
Probing the extent of randomness in protein interaction networks. PMID:18769589
Comparative analysis of function and interaction of transcription factors in nematodes: extensive conservation of orthology coupled to rapid sequence evolution. PMID:18752680
The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: a scaffold to query lipid metabolism. PMID:18687109
Structural similarity of genetically interacting proteins. PMID:18671848
Predicting and validating protein interactions using network structure. PMID:18654616
Transcription factor control of growth rate dependent genes in Saccharomyces cerevisiae: a three factor design. PMID:18638364
From E-MAPs to module maps: dissecting quantitative genetic interactions using physical interactions. PMID:18628749
Genetic interaction network of the Saccharomyces cerevisiae type 1 phosphatase Glc7. PMID:18627629
Susceptibility to glaucoma: differential comparison of the astrocyte transcriptome from glaucomatous African American and Caucasian American donors. PMID:18613964
Combining guilt-by-association and guilt-by-profiling to predict Saccharomyces cerevisiae gene function. PMID:18613951
Genetic interactions of MAF1 identify a role for Med20 in transcriptional repression of ribosomal protein genes. PMID:18604275
Global investigation of protein-protein interactions in yeast Saccharomyces cerevisiae using re-occurring short polypeptide sequences. PMID:18586826
Assessing the functional structure of genomic data. PMID:18586732
The effects of protein interactions, gene essentiality and regulatory regions on expression variation. PMID:18582382
Early vertebrate chromosome duplications and the evolution of the neuropeptide Y receptor gene regions. PMID:18578868
Human Proteinpedia as a resource for clinical proteomics. PMID:18573810
The emerging CK2 interactome: insights into the regulation and functions of CK2. PMID:18553055
Exploiting the proteome to improve the genome-wide genetic analysis of epistasis in common human diseases. PMID:18551320
Phosphoprotein profiling by PA-GeLC-MS/MS. PMID:18510356
ENDEAVOUR update: a web resource for gene prioritization in multiple species. PMID:18508807
Design logic of a cannabinoid receptor signaling network that triggers neurite outgrowth. PMID:18487186
GPS 2.0, a tool to predict kinase-specific phosphorylation sites in hierarchy. PMID:18463090
MassNet: a functional annotation service for protein mass spectrometry data. PMID:18448467
A microtubule interactome: complexes with roles in cell cycle and mitosis. PMID:18433294
Predicting co-complexed protein pairs from heterogeneous data. PMID:18421371
Genomic analysis of estrogen cascade reveals histone variant H2A.Z associated with breast cancer progression. PMID:18414489
Linking functionally related genes by sensitive and quantitative characterization of genetic interaction profiles. PMID:18408161
Extracting expression modules from perturbational gene expression compendia. PMID:18402676
Mapping genetically compensatory pathways from synthetic lethal interactions in yeast. PMID:18398455
Membrane transporters and protein traffic networks differentially affecting metal tolerance: a genomic phenotyping study in yeast. PMID:18394190
The MoVIN server for the analysis of protein interaction networks. PMID:18387199
Walking the interactome for prioritization of candidate disease genes. PMID:18371930
Predicting cancer involvement of genes from heterogeneous data. PMID:18371197
The role of disorder in interaction networks: a structural analysis. PMID:18364713
Functional diversification of duplicate genes through subcellular adaptation of encoded proteins. PMID:18336717
Mining phenotypes for gene function prediction. PMID:18315868
Defining genetic interaction. PMID:18305163
Genome-wide expression profiling, in vivo DNA binding analysis, and probabilistic motif prediction reveal novel Abf1 target genes during fermentation, respiration, and sporulation in yeast. PMID:18305101
Dissecting microregulation of a master regulatory network. PMID:18294391
The Annotation, Mapping, Expression and Network (AMEN) suite of tools for molecular systems biology. PMID:18254954
Protein function assignment through mining cross-species protein-protein interactions. PMID:18253506
CASCADE: a novel quasi all paths-based network analysis algorithm for clustering biological interactions. PMID:18230159
Gene function prediction using labeled and unlabeled data. PMID:18221567
Predicting the interactome of Xanthomonas oryzae pathovar oryzae for target selection and DB service. PMID:18215330
Analysis of self-associating proteins by singular value decomposition of solution scattering data. PMID:18212017
Protein interactions in human genetic diseases. PMID:18199329
Annotating novel genes by integrating synthetic lethals and genomic information. PMID:18194531
Quantitative analysis on the characteristics of targets with FDA approved drugs. PMID:18167532
Nonequilibrium thermodynamics of thiol/disulfide redox systems: a perspective on redox systems biology. PMID:18155672
Consistent dissection of the protein interaction network by combining global and local metrics. PMID:18154653
Multiple kinases and system robustness: a link between Cdc37 and genome integrity. PMID:18075309
A portrait of copy-number polymorphism in Drosophila melanogaster. PMID:18056801
Spreading out of perturbations in reversible reaction networks. PMID:18046464
Where have all the interactions gone? Estimating the coverage of two-hybrid protein interaction maps. PMID:18039026
Quantification of ortholog losses in insects and vertebrates. PMID:18021399
The BioGRID Interaction Database: 2008 update. PMID:18000002
DIMA 2.0--predicted and known domain interactions. PMID:17999995
The Molecule Pages database. PMID:17965093
TransfactomeDB: a resource for exploring the nucleotide sequence specificity and condition-specific regulatory activity of trans-acting factors. PMID:17947326
Bacteriome.org--an integrated protein interaction database for E. coli. PMID:17942431
CMGSDB: integrating heterogeneous Caenorhabditis elegans data sources using compositional data mining. PMID:17942411
Improved human disease candidate gene prioritization using mouse phenotype. PMID:17939863
Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions. PMID:17925023
All duplicates are not equal: the difference between small-scale and genome duplication. PMID:17916239
A global analysis of genetic interactions in Caenorhabditis elegans. PMID:17897480
PathFinder: mining signal transduction pathway segments from protein-protein interaction networks. PMID:17854489
The RAGNYA fold: a novel fold with multiple topological variants found in functionally diverse nucleic acid, nucleotide and peptide-binding proteins. PMID:17715145
Propagation of large concentration changes in reversible protein-binding networks. PMID:17699619
Disparate effects of p24alpha and p24delta on secretory protein transport and processing. PMID:17684551
A data integration approach for cell cycle analysis oriented to model simulation in systems biology. PMID:17678529
Reuse of structural domain-domain interactions in protein networks. PMID:17640363
Bayesian Orthogonal Least Squares (BOLS) algorithm for reverse engineering of gene regulatory networks. PMID:17626641
Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution. PMID:17535793
Unequal evolutionary conservation of human protein interactions in interologous networks. PMID:17535438
Huntingtin interacting proteins are genetic modifiers of neurodegeneration. PMID:17500595
Reconstruction of human protein interolog network using evolutionary conserved network. PMID:17493278
The role of Trs65 in the Ypt/Rab guanine nucleotide exchange factor function of the TRAPP II complex. PMID:17475775
Specificity in protein interactions and its relationship with sequence diversity and coevolution. PMID:17468399
The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics. PMID:17447836
Pathway redundancy and protein essentiality revealed in the Saccharomyces cerevisiae interaction networks. PMID:17437029
Inferring condition-specific transcription factor function from DNA binding and gene expression data. PMID:17437025
Why are there still over 1000 uncharacterized yeast genes? PMID:17435240
In silico pathway reconstruction: Iron-sulfur cluster biogenesis in Saccharomyces cerevisiae. PMID:17408500
Deciphering protein-protein interactions. Part I. Experimental techniques and databases. PMID:17397251
Systematic genome instability screens in yeast and their potential relevance to cancer. PMID:17360454
Network-based prediction of protein function. PMID:17353930
Chemical combination effects predict connectivity in biological systems. PMID:17332758
From bytes to bedside: data integration and computational biology for translational cancer research. PMID:17319736
Gene network interconnectedness and the generalized topological overlap measure. PMID:17250769
Evolutionary conservation of domain-domain interactions. PMID:17184549
Classical nuclear localization signals: definition, function, and interaction with importin alpha. PMID:17170104
Expanded protein information at SGD: new pages and proteome browser. PMID:17142221
CellCircuits: a database of protein network models. PMID:17135207
DOMINO: a database of domain-peptide interactions. PMID:17135199
Michigan Molecular Interactions (MiMI): putting the jigsaw puzzle together. PMID:17130145
IntNetDB v1.0: an integrated protein-protein interaction network database generated by a probabilistic model. PMID:17112386
STRING 7--recent developments in the integration and prediction of protein interactions. PMID:17098935
Stratus not altocumulus: a new view of the yeast protein interaction network. PMID:16984220
Intrinsic disorder is a common feature of hub proteins from four eukaryotic interactomes. PMID:16884331
The interaction map of yeast: terra incognita? PMID:16762048
Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae. PMID:16762047
The F-box protein Dia2 overcomes replication impedance to promote genome stability in Saccharomyces cerevisiae. PMID:16751663
The BioGRID interaction database: 2015 update PubMed citations: 465.

465 articles citing: The BioGRID interaction database: 2015 update

SIPGCN: A Novel Deep Learning Model for Predicting Self-Interacting Proteins from Sequence Information Using Graph Convolutional Networks. PMID:35884848
Single-cell network biology characterizes cell type gene regulation for drug repurposing and phenotype prediction in Alzheimer's disease. PMID:35849618
Systems Drug Discovery for Diffuse Large B Cell Lymphoma Based on Pathogenic Molecular Mechanism via Big Data Mining and Deep Learning Method. PMID:35743172
Repurposing Histaminergic Drugs in Multiple Sclerosis. PMID:35683024
Machine Learning in Causal Inference: Application in Pharmacovigilance. PMID:35579811
Comprehensive molecular characterization of hypertension-related genes in cancer. PMID:35513851
Comprehensive network medicine-based drug repositioning via integration of therapeutic efficacy and side effects. PMID:35443763
Function of SYDE C2-RhoGAP family as signaling hubs for neuronal development deduced by computational analysis. PMID:35279680
Investigating the Role of Obesity in Prostate Cancer and Identifying Biomarkers for Drug Discovery: Systems Biology and Deep Learning Approaches. PMID:35164166
A full-proteome, interaction-specific characterization of mutational hotspots across human cancers. PMID:34963661
Targeting uPA-uPAR interaction to improve intestinal epithelial barrier integrity in inflammatory bowel disease. PMID:34933179
Protein-protein interactions: Methods, databases, and applications in virus-host study. PMID:34909403
Interpretation of network-based integration from multi-omics longitudinal data. PMID:34883510
Network Biology Approaches to Achieve Precision Medicine in Inflammatory Bowel Disease. PMID:34745229
Tumor relevant protein functional interactions identified using bipartite graph analyses. PMID:34728699
Computational repurposing of therapeutic small molecules from cancer to pulmonary hypertension. PMID:34669463
A machine learning framework for predicting drug-drug interactions. PMID:34475500
A neural network-based method for polypharmacy side effects prediction. PMID:34303360
Identification of anticancer drug target genes using an outside competitive dynamics model on cancer signaling networks. PMID:34238960
Identification of Diagnostic Markers for Major Depressive Disorder Using Machine Learning Methods. PMID:34220416
EvoProDom: evolutionary modeling of protein families by assessing translocations of protein domains. PMID:34196123
Molecular signatures of silencing suppression degeneracy from a complex RNA virus. PMID:34181647
Gene expression signatures predict response to therapy with growth hormone. PMID:34045667
PolyQ length co-evolution in neural proteins. PMID:34017944
Drug Repurposing: A Network-based Approach to Amyotrophic Lateral Sclerosis. PMID:33987813
Differential expression of miRNAs in the presence of B chromosome in the cichlid fish Astatotilapia latifasciata. PMID:33980143
A Bayesian Approach for Learning Gene Networks Underlying Disease Severity in COPD. PMID:33912251
Immune Subtyping in Latent Tuberculosis. PMID:33897680
Identification of IFN-Induced Transmembrane Protein 1 With Prognostic Value in Pancreatic Cancer Using Network Module-Based Analysis. PMID:33869009
Network-based modeling of herb combinations in traditional Chinese medicine. PMID:33834186
Identification of human glucocorticoid response markers using integrated multi-omic analysis from a randomized crossover trial. PMID:33821793
Systems Medicine Design for Triple-Negative Breast Cancer and Non-Triple-Negative Breast Cancer Based on Systems Identification and Carcinogenic Mechanisms. PMID:33802957
Comprehensive characterization of a drug-resistance-related ceRNA network across 15 anti-cancer drug categories. PMID:33738135
Short loop functional commonality identified in leukaemia proteome highlights crucial protein sub-networks. PMID:33709075
Drug-Target Interaction Prediction Based on Adversarial Bayesian Personalized Ranking. PMID:33628808
A systems-based method to repurpose marketed therapeutics for antiviral use: a SARS-CoV-2 case study. PMID:33593923
A Deep Learning-Based Approach for Identifying the Medicinal Uses of Plant-Derived Natural Compounds. PMID:33519445
A network-based deep learning methodology for stratification of tumor mutations. PMID:33416857
Tumor Microenvironment-Associated Immune-Related Genes for the Prognosis of Malignant Pleural Mesothelioma. PMID:33042835
De novo missense variants disrupting protein-protein interactions affect risk for autism through gene co-expression and protein networks in neuronal cell types. PMID:33032641
Structure-based validation can drastically underestimate error rate in proteome-wide cross-linking mass spectrometry studies. PMID:32994567
Role of SARS-CoV-2 in Altering the RNA-Binding Protein and miRNA-Directed Post-Transcriptional Regulatory Networks in Humans. PMID:32993015
Integrated regulatory models for inference of subtype-specific susceptibilities in glioblastoma. PMID:32974985
An optimized quantitative proteomics method establishes the cell type-resolved mouse brain secretome. PMID:32954517
Identification of potential markers for type 2 diabetes mellitus via bioinformatics analysis. PMID:32705173
Role of SARS-CoV-2 in altering the RNA binding protein and miRNA directed post-transcriptional regulatory networks in humans. PMID:32676599
NAIGO: An Improved Method to Align PPI Networks Based on Gene Ontology and Graphlets. PMID:32637398
Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses. PMID:32597660
Prediction of the Secretome and the Surfaceome: A Strategy to Decipher the Crosstalk between Adipose Tissue and Muscle during Fetal Growth. PMID:32575512
Multilevel regulation of muscle-specific transcription factor hlh-1 during Caenorhabditis elegans embryogenesis. PMID:32556563
PINOT: an intuitive resource for integrating protein-protein interactions. PMID:32527260
Omics Integration Analyses Reveal the Early Evolution of Malignancy in Breast Cancer. PMID:32512721
Predicting Polypharmacy Side-effects Using Knowledge Graph Embeddings. PMID:32477666
Integrative analysis of large-scale loss-of-function screens identifies robust cancer-associated genetic interactions. PMID:32463358
HIPPIE2: a method for fine-scale identification of physically interacting chromatin regions. PMID:32270138
Deep graph embedding for prioritizing synergistic anticancer drug combinations. PMID:32153729
Edgetic perturbation signatures represent known and novel cancer biomarkers. PMID:32152446
Gold nanoclusters elicit homeostatic perturbations in glioblastoma cells and adaptive changes of lysosomes. PMID:32042327
Discovering the genes mediating the interactions between chronic respiratory diseases in the human interactome. PMID:32041952
Patient similarity by joint matrix trifactorization to identify subgroups in acute myeloid leukemia. PMID:31984320
Mechanical forces induce an asthma gene signature in healthy airway epithelial cells. PMID:31969610
In silico unravelling pathogen-host signaling cross-talks via pathogen mimicry and human protein-protein interaction networks. PMID:31956393
A phenomics-based approach for the detection and interpretation of shared genetic influences on 29 biochemical indices in southern Chinese men. PMID:31842750
MaXLinker: Proteome-wide Cross-link Identifications with High Specificity and Sensitivity. PMID:31839598
A Computational Framework for Predicting Direct Contacts and Substructures within Protein Complexes. PMID:31717703
Genome-wide analysis of Homo sapiens, Arabidopsis thaliana, and Saccharomyces cerevisiae reveals novel attributes of tail-anchored membrane proteins. PMID:31711414
Mitochondrial dysfunction in rheumatoid arthritis: A comprehensive analysis by integrating gene expression, protein-protein interactions and gene ontology data. PMID:31703070
Dissecting the Shared and Context-Dependent Pathways Mediated by the p140Cap Adaptor Protein in Cancer and in Neurons. PMID:31681758
HMNPPID-human malignant neoplasm protein-protein interaction database. PMID:31639057
Universal concept signature analysis: genome-wide quantification of new biological and pathological functions of genes and pathways. PMID:31631213
Interactome of the Autoimmune Risk Protein ANKRD55. PMID:31620119
Neglog: Homology-Based Negative Data Sampling Method for Genome-Scale Reconstruction of Human Protein-Protein Interaction Networks. PMID:31614890
Compound Dynamics and Combinatorial Patterns of Amino Acid Repeats Encode a System of Evolutionary and Developmental Markers. PMID:31589292
Paralog dependency indirectly affects the robustness of human cells. PMID:31556487
Discovery of Inhibitors for Proliferating Cell Nuclear Antigen Using a Computational-Based Linked-Multiple-Fragment Screen. PMID:31552364
FunDMDeep-m6A: identification and prioritization of functional differential m6A methylation genes. PMID:31510685
Synaptic and Gene Regulatory Mechanisms in Schizophrenia, Autism, and 22q11.2 Copy Number Variant-Mediated Risk for Neuropsychiatric Disorders. PMID:31500805
A Novel Computational Model for Predicting microRNA-Disease Associations Based on Heterogeneous Graph Convolutional Networks. PMID:31455028
Precise Prediction of Calpain Cleavage Sites and Their Aberrance Caused by Mutations in Cancer. PMID:31440276
A genome-wide positioning systems network algorithm for in silico drug repurposing. PMID:31375661
The Methods Employed in Mass Spectrometric Analysis of Posttranslational Modifications (PTMs) and Protein-Protein Interactions (PPIs). PMID:31347048
In Silico Toxicology Data Resources to Support Read-Across and (Q)SAR. PMID:31244651
Comparing progression molecular mechanisms between lung adenocarcinoma and lung squamous cell carcinoma based on genetic and epigenetic networks: big data mining and genome-wide systems identification. PMID:31217907
A linear delay algorithm for enumerating all connected induced subgraphs. PMID:31216984
Natural Product Target Network Reveals Potential for Cancer Combination Therapies. PMID:31214023
Combining learning and constraints for genome-wide protein annotation. PMID:31208327
CODA-ML: context-specific biological knowledge representation for systemic physiology analysis. PMID:31138123
Multi-Omic Data Interpretation to Repurpose Subtype Specific Drug Candidates for Breast Cancer. PMID:31134131
Identification of LIFR, PIK3R1, and MMP12 as Novel Prognostic Signatures in Gallbladder Cancer Using Network-Based Module Analysis. PMID:31119098
Investigating function roles of hypothetical proteins encoded by the Mycobacterium tuberculosis H37Rv genome. PMID:31113361
Computational identification of tissue-specific transcription factor cooperation in ten cattle tissues. PMID:31095599
The Promoter Regions of Intellectual Disability-Associated Genes Are Uniquely Enriched in LTR Sequences of the MER41 Primate-Specific Endogenous Retrovirus: An Evolutionary Connection Between Immunity and Cognition. PMID:31031802
Conformational Dynamics and Allosteric Regulation Landscapes of Germline PTEN Mutations Associated with Autism Compared to Those Associated with Cancer. PMID:31006514
Structural and Computational Characterization of Disease-Related Mutations Involved in Protein-Protein Interfaces. PMID:30934865
Connectivity problems on heterogeneous graphs. PMID:30899321
Parkinson's Disease is Associated with Dysregulations of a Dopamine-Modulated Gene Network Relevant to Sleep and Affective Neurobehaviors in the Striatum. PMID:30886221
DeepTACT: predicting 3D chromatin contacts via bootstrapping deep learning. PMID:30869141
Topological scoring of protein interaction networks. PMID:30850613
Systems based analysis of human embryos and gene networks involved in cell lineage allocation. PMID:30836937
BGFE: A Deep Learning Model for ncRNA-Protein Interaction Predictions Based on Improved Sequence Information. PMID:30813451
A network-centric approach to drugging TNF-induced NF-κB signaling. PMID:30808860
DYRK1A regulates the recruitment of 53BP1 to the sites of DNA damage in part through interaction with RNF169. PMID:30773093
Investigating Common Pathogenic Mechanisms between Homo sapiens and Different Strains of Candida albicans for Drug Design: Systems Biology Approach via Two-Sided NGS Data Identification. PMID:30769958
Inferring Gene Regulatory Networks from a Population of Yeast Segregants. PMID:30718595
Exploiting locational and topological overlap model to identify modules in protein interaction networks. PMID:30642247
Exploring the underlying biology of intrinsic cardiorespiratory fitness through integrative analysis of genomic variants and muscle gene expression profiling. PMID:30605401
Global analysis of N6-methyladenosine functions and its disease association using deep learning and network-based methods. PMID:30601803
Prediction of protein self-interactions using stacked long short-term memory from protein sequences information. PMID:30577794
Classifying mild traumatic brain injuries with functional network analysis. PMID:30577783
Personalized Medicine and Molecular Interaction Networks in Amyotrophic Lateral Sclerosis (ALS): Current Knowledge. PMID:30551677
Gene expression models based on transcription factor binding events confer insight into functional cis-regulatory variants. PMID:30541050
Predicting protein targets for drug-like compounds using transcriptomics. PMID:30532261
Genomic identification and functional analysis of essential genes in Caenorhabditis elegans. PMID:30514206
Structural disorder in the proteome and interactome of Alkhurma virus (ALKV). PMID:30443749
Heterogeneous network embedding for identifying symptom candidate genes. PMID:30357378
An integrative tissue-network approach to identify and test human disease genes. PMID:30346941
Investigating Pathogenic and Hepatocarcinogenic Mechanisms from Normal Liver to HCC by Constructing Genetic and Epigenetic Networks via Big Genetic and Epigenetic Data Mining and Genome-Wide NGS Data Identification. PMID:30344796
Context-specific interactions in literature-curated protein interaction databases. PMID:30340458
Integration of Molecular Interactome and Targeted Interaction Analysis to Identify a COPD Disease Network Module. PMID:30262855
Deep learning-based transcriptome data classification for drug-target interaction prediction. PMID:30255785
Systems genetics of nonsyndromic orofacial clefting provides insights into its complex aetiology. PMID:30254216
Viruses.STRING: A Virus-Host Protein-Protein Interaction Database. PMID:30249048
PTMD: A Database of Human Disease-associated Post-translational Modifications. PMID:30244175
Targeting Focal Adhesion Kinase Using Inhibitors of Protein-Protein Interactions. PMID:30134553
Proteome-wide analysis of phospho-regulated PDZ domain interactions. PMID:30126976
Multifunctional Proteins: Involvement in Human Diseases and Targets of Current Drugs. PMID:30123928
Identification of novel immune-relevant drug target genes for Alzheimer's Disease by combining ontology inference with network analysis. PMID:30106219
Discovering Health Benefits of Phytochemicals with Integrated Analysis of the Molecular Network, Chemical Properties and Ethnopharmacological Evidence. PMID:30096807
Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken. PMID:30086717
Factors Associated with Heritable Pulmonary Arterial Hypertension Exert Convergent Actions on the miR-130/301-Vascular Matrix Feedback Loop. PMID:30081553
Phenotype-oriented network analysis for discovering pharmacological effects of natural compounds. PMID:30076354
Integrative analysis of promising molecular biomarkers and pathways for coronary artery disease using WGCNA and MetaDE methods. PMID:30015926
Integrating Rio1 activities discloses its nutrient-activated network in Saccharomyces cerevisiae. PMID:30011030
Network-based approach to prediction and population-based validation of in silico drug repurposing. PMID:30002366
Improving Prediction of Self-interacting Proteins Using Stacked Sparse Auto-Encoder with PSSM profiles. PMID:29989064
The role of PCNA as a scaffold protein in cellular signaling is functionally conserved between yeast and humans. PMID:29988559
Identification of two distinct peptide-binding pockets in the SH3 domain of human mixed-lineage kinase 3. PMID:29980598
Transferring knowledge of bacterial protein interaction networks to predict pathogen targeted human genes and immune signaling pathways: a case study on M. tuberculosis. PMID:29954330
Two critical positions in zinc finger domains are heavily mutated in three human cancer types. PMID:29953437
Post-translational buffering leads to convergent protein expression levels between primates. PMID:29950183
Modeling polypharmacy side effects with graph convolutional networks. PMID:29949996
Gold Nanoparticles Impinge on Nucleoli and the Stress Response in MCF7 Breast Cancer Cells. PMID:29942378
IL-1ɑ C376A Transversion Variant and Risk of Idiopathic Male Infertility in Iranian Men: A Genetic Association Study. PMID:29935069
Exploring the functional impact of alternative splicing on human protein isoforms using available annotation sources. PMID:29931155
A cytokine protein-protein interaction network for identifying key molecules in rheumatoid arthritis. PMID:29928007
Developments in toxicogenomics: understanding and predicting compound-induced toxicity from gene expression data. PMID:29917034
Aberrantly expressed genes and miRNAs in human hypopharyngeal squamous cell carcinoma based on RNA‑sequencing analysis. PMID:29916534
Removing Background Co-occurrences of Transcription Factor Binding Sites Greatly Improves the Prediction of Specific Transcription Factor Cooperations. PMID:29896218
An interactome perturbation framework prioritizes damaging missense mutations for developmental disorders. PMID:29892012
Function, dynamics and evolution of network motif modules in integrated gene regulatory networks of worm and plant. PMID:29873777
Construction of a specific SVM classifier and identification of molecular markers for lung adenocarcinoma based on lncRNA-miRNA-mRNA network. PMID:29872324
Network-Based Disease Module Discovery by a Novel Seed Connector Algorithm with Pathobiological Implications. PMID:29791871
Archetypal transcriptional blocks underpin yeast gene regulation in response to changes in growth conditions. PMID:29785040
PAF1 complex interactions with SETDB1 mediate promoter H3K9 methylation and transcriptional repression of Hoxa9 and Meis1 in acute myeloid leukemia. PMID:29774127
PregOMICS-Leveraging systems biology and bioinformatics for drug repurposing in maternal-child health. PMID:29726581
NF-Y-dependent regulation of glutamate receptor 4 expression and cell survival in cells of the oligodendrocyte lineage. PMID:29704264
Signalling maps in cancer research: construction and data analysis. PMID:29688383
YAAM: Yeast Amino Acid Modifications Database. PMID:29688347
Upregulated VEGFA and DLL4 act as potential prognostic genes for clear cell renal cell carcinoma. PMID:29618931
Systematic Evaluation of Molecular Networks for Discovery of Disease Genes. PMID:29605183
Loss of TDP43 inhibits progression of triple-negative breast cancer in coordination with SRSF3. PMID:29581274
Systematic characterization of pan-cancer mutation clusters. PMID:29572294
Uncovering the regeneration strategies of zebrafish organs: a comprehensive systems biology study on heart, cerebellum, fin, and retina regeneration. PMID:29560825
The Genomic Landscape and Pharmacogenomic Interactions of Clock Genes in Cancer Chronotherapy. PMID:29525205
A Vitis vinifera basic helix-loop-helix transcription factor enhances plant cell size, vegetative biomass and reproductive yield. PMID:29520945
Comparative Protein Interaction Network Analysis Identifies Shared and Distinct Functions for the Human ROCO Proteins. PMID:29513927
A recombinant Fasciola gigantica 14-3-3 epsilon protein (rFg14-3-3e) modulates various functions of goat peripheral blood mononuclear cells. PMID:29510740
Brain-specific functional relationship networks inform autism spectrum disorder gene prediction. PMID:29507298
FunGeneNet: a web tool to estimate enrichment of functional interactions in experimental gene sets. PMID:29504895
Identification of Shared Molecular Signatures Indicate the Susceptibility of Endometriosis to Multiple Sclerosis. PMID:29503661
Network analysis of coronary artery disease risk genes elucidates disease mechanisms and druggable targets. PMID:29467471
Identification of potential target genes for ankylosing spondylitis treatment. PMID:29465556
Recognition of sites of functional specialisation in all known eukaryotic protein kinase families. PMID:29438395
Cholangiocarcinoma‑associated genes identified by integrative analysis of gene expression data. PMID:29436659
Prioritizing disease genes with an improved dual label propagation framework. PMID:29422030
In silico profiling of systemic effects of drugs to predict unexpected interactions. PMID:29371651
PhenoRank: reducing study bias in gene prioritization through simulation. PMID:29360927
Interactome INSIDER: a structural interactome browser for genomic studies. PMID:29355848
Investigating the Mechanisms of Action of Depside Salt from Salvia miltiorrhiza Using Bioinformatic Analysis. PMID:29348768
Logistic regression analysis for the identification of the metastasis-associated signaling pathways of osteosarcoma. PMID:29328361
Mitogen-activated protein kinases, Fus3 and Kss1, regulate chronological lifespan in yeast. PMID:29273704
A multigene support vector machine predictor for metastasis of cutaneous melanoma. PMID:29257259
Bioinformatics analysis of gene expression profiles to identify causal genes in luminal B2 breast cancer. PMID:29250180
Unravelling Protein-Protein Interaction Networks Linked to Aliphatic and Indole Glucosinolate Biosynthetic Pathways in Arabidopsis. PMID:29238354
Text mining and expert curation to develop a database on psychiatric diseases and their genes. PMID:29220439
Large-scale analysis of disease pathways in the human interactome. PMID:29218874
Predicting new indications of compounds with a network pharmacology approach: Liuwei Dihuang Wan as a case study. PMID:29212201
Properties of human genes guided by their enrichment in rare and common variants. PMID:29197136
The OncoPPi Portal: an integrative resource to explore and prioritize protein-protein interactions for cancer target discovery. PMID:29186335
Computational systems biology approaches for Parkinson's disease. PMID:29185073
Uncovering the relationship and mechanisms of Tartary buckwheat (Fagopyrum tataricum) and Type II diabetes, hypertension, and hyperlipidemia using a network pharmacology approach. PMID:29177114
Investigation of candidate genes and mechanisms underlying postmenopausal osteoporosis using bioinformatics analysis. PMID:29138843
TCMID 2.0: a comprehensive resource for TCM. PMID:29106634
SalmoNet, an integrated network of ten Salmonella enterica strains reveals common and distinct pathways to host adaptation. PMID:29057095
A High-Resolution Genome-Wide CRISPR/Cas9 Viability Screen Reveals Structural Features and Contextual Diversity of the Human Cell-Essential Proteome. PMID:29038160
Rapamycin-induced miR-21 promotes mitochondrial homeostasis and adaptation in mTORC1 activated cells. PMID:29029388
Review of computational methods for virus-host protein interaction prediction: a case study on novel Ebola-human interactions. PMID:29028879
TSPYL Family Regulates CYP17A1 and CYP3A4 Expression: Potential Mechanism Contributing to Abiraterone Response in Metastatic Castration-Resistant Prostate Cancer. PMID:29027195
Identification of a novel synaptic protein, TMTC3, involved in periventricular nodular heterotopia with intellectual disability and epilepsy. PMID:28973161
HSF1-dependent and -independent regulation of the mammalian in vivo heat shock response and its impairment in Huntington's disease mouse models. PMID:28970536
A composite network of conserved and tissue specific gene interactions reveals possible genetic interactions in glioma. PMID:28957313
A non-transcriptional role for the glucocorticoid receptor in mediating the cell stress response. PMID:28935859
A support vector machine classifier for the prediction of osteosarcoma metastasis with high accuracy. PMID:28901446
Predicting multicellular function through multi-layer tissue networks. PMID:28881986
Protein-Protein Interactions in Virus-Host Systems. PMID:28861068
Position Matters: Network Centrality Considerably Impacts Rates of Protein Evolution in the Human Protein-Protein Interaction Network. PMID:28854629
Mapping architectural and transcriptional alterations in non-lesional and lesional epidermis in vitiligo. PMID:28852211
Comprehensive Analyses of Tissue-Specific Networks with Implications to Psychiatric Diseases. PMID:28849569
Wide-scale comparative analysis of longevity genes and interventions. PMID:28836369
EGF hijacks miR-198/FSTL1 wound-healing switch and steers a two-pronged pathway toward metastasis. PMID:28827448
Genome-wide association study and gene set analysis for understanding candidate genes involved in salt tolerance at the rice seedling stage. PMID:28821952
eDGAR: a database of Disease-Gene Associations with annotated Relationships among genes. PMID:28812536
ePlant: Visualizing and Exploring Multiple Levels of Data for Hypothesis Generation in Plant Biology. PMID:28808136
Network analyses elucidate the role of SMYD3 in esophageal squamous cell carcinoma. PMID:28781952
RNA Polymerase Tags To Monitor Multidimensional Protein-Protein Interactions Reveal Pharmacological Engagement of Bcl-2 Proteins. PMID:28767232
Identification of key genes and pathways in Parkinson's disease through integrated analysis. PMID:28765971
Dynamic scaffolds for neuronal signaling: in silico analysis of the TANC protein family. PMID:28754924
Expression of NAD(P)H quinone dehydrogenase 1 (NQO1) is increased in the endometrium of women with endometrial cancer and women with polycystic ovary syndrome. PMID:28748640
Genetic and functional characterization of disease associations explains comorbidity. PMID:28740175
Network reconstruction and validation of the Snf1/AMPK pathway in baker's yeast based on a comprehensive literature review. PMID:28725459
Recruitment of histone modifications to assist mRNA dosage maintenance after degeneration of cytosine DNA methylation during animal evolution. PMID:28720579
Synaptic Interactome Mining Reveals p140Cap as a New Hub for PSD Proteins Involved in Psychiatric and Neurological Disorders. PMID:28713243
Network approaches to systems biology analysis of complex disease: integrative methods for multi-omics data. PMID:28679163
Isoelectric point-based fractionation by HiRIEF coupled to LC-MS allows for in-depth quantitative analysis of the phosphoproteome. PMID:28674419
Systematic discovery of novel eukaryotic transcriptional regulators using sequence homology independent prediction. PMID:28651538
Meta-analysis of host response networks identifies a common core in tuberculosis. PMID:28649431
Analysis of K-Ras Interactions by Biotin Ligase Tagging. PMID:28647697
Integrated genome and transcriptome sequencing identifies a noncoding mutation in the genome replication factor DONSON as the cause of microcephaly-micromelia syndrome. PMID:28630177
Network Analysis Reveals a Common Host-Pathogen Interaction Pattern in Arabidopsis Immune Responses. PMID:28611808
Knowledge Discovery in Biological Databases for Revealing Candidate Genes Linked to Complex Phenotypes. PMID:28609292
Identification of novel dysregulated key genes in Breast cancer through high throughput ChIP-Seq data analysis. PMID:28607444
ChiPPI: a novel method for mapping chimeric protein-protein interactions uncovers selection principles of protein fusion events in cancer. PMID:28549153
Large scale meta-analysis characterizes genetic architecture for common psoriasis associated variants. PMID:28537254
The complex genetics of hypoplastic left heart syndrome. PMID:28530678
A computational framework for distinguishing direct versus indirect interactions in human functional protein-protein interaction networks. PMID:28524201
GeMSTONE: orchestrated prioritization of human germline mutations in the cloud. PMID:28521008
Bioinformatics in translational drug discovery. PMID:28487472
Soft Sweeps Are the Dominant Mode of Adaptation in the Human Genome. PMID:28482049
Screening of Tumor Suppressor Genes in Metastatic Colorectal Cancer. PMID:28473981
HER2-positive breast cancer cells expressing elevated FAM83A are sensitive to FAM83A loss. PMID:28463969
Linearity of network proximity measures: implications for set-based queries and significance testing. PMID:28453667
Intrinsic protein disorder reduces small-scale gene duplicability. PMID:28430886
Increased taxon sampling reveals thousands of hidden orthologs in flatworms. PMID:28400424
Spinal motor neuron protein supersaturation patterns are associated with inclusion body formation in ALS. PMID:28396410
Protease-Inhibitor Interaction Predictions: Lessons on the Complexity of Protein-Protein Interactions. PMID:28385878
Using structural knowledge in the protein data bank to inform the search for potential host-microbe protein interactions in sequence space: application to Mycobacterium tuberculosis. PMID:28376709
Active module identification in intracellular networks using a memetic algorithm with a new binary decoding scheme. PMID:28361692
Combinatorial Ranking of Gene Sets to Predict Disease Relapse: The Retinoic Acid Pathway in Early Prostate Cancer. PMID:28361034
HIVed, a knowledgebase for differentially expressed human genes and proteins during HIV infection, replication and latency. PMID:28358052
Identification of dysregulated genes in rheumatoid arthritis based on bioinformatics analysis. PMID:28316886
Proteome and Protein Network Analyses of Memory T Cells Find Altered Translation and Cell Stress Signaling in Treated Human Immunodeficiency Virus Patients Exhibiting Poor CD4 Recovery. PMID:28293663
Identification of Topological Network Modules in Perturbed Protein Interaction Networks. PMID:28272416
Bioinformatics analysis of the proteins interacting with LASP-1 and their association with HBV-related hepatocellular carcinoma. PMID:28266596
Evolution of protein-protein interaction networks in yeast. PMID:28248977
A c-Myc-regulated stem cell-like signature in high-risk neuroblastoma: A systematic discovery (Target neuroblastoma ESC-like signature). PMID:28246384
Drug voyager: a computational platform for exploring unintended drug action. PMID:28241745
Understanding the roles of intrinsic disorder in subunits of hemoglobin and the disease process of sickle cell anemia. PMID:28232898
Human enterovirus 71 protein interaction network prompts antiviral drug repositioning. PMID:28220872
The OncoPPi network of cancer-focused protein-protein interactions to inform biological insights and therapeutic strategies. PMID:28205554
Weighted gene co-expression network analysis in identification of metastasis-related genes of lung squamous cell carcinoma based on the Cancer Genome Atlas database. PMID:28203405
Haploinsufficiency networks identify targetable patterns of allelic deficiency in low mutation ovarian cancer. PMID:28198375
Time-resolved Phosphoproteome Analysis of Paradoxical RAF Activation Reveals Novel Targets of ERK. PMID:28188228
GPR155 Serves as a Predictive Biomarker for Hematogenous Metastasis in Patients with Gastric Cancer. PMID:28165032
Transcriptome-wide co-expression analysis identifies LRRC2 as a novel mediator of mitochondrial and cardiac function. PMID:28158196
TrypsNetDB: An integrated framework for the functional characterization of trypanosomatid proteins. PMID:28158179
Protein Bioinformatics Databases and Resources. PMID:28150231
SATB1 plays an oncogenic role in esophageal cancer by up-regulation of FN1 and PDGFRB. PMID:28147311
Skewing in Arabidopsis roots involves disparate environmental signaling pathways. PMID:28143395
Therapeutic properties of Scutellaria baicalensis in db/db mice evaluated using Connectivity Map and network pharmacology. PMID:28139721
The integration of weighted human gene association networks based on link prediction. PMID:28137253
Functional Analysis of Kinases and Transcription Factors in Saccharomyces cerevisiae Using an Integrated Overexpression Library. PMID:28122947
GSNFS: Gene subnetwork biomarker identification of lung cancer expression data. PMID:28117655
Functional analysis of keratinocyte and fibroblast gene expression in skin and keloid scar tissue based on deviation analysis of dynamic capabilities. PMID:28101157
Evidence of neofunctionalization after the duplication of the highly conserved Polycomb group gene Caf1-55 in the obscura group of Drosophila. PMID:28094282
AKT1, LKB1, and YAP1 Revealed as MYC Interactors with NanoLuc-Based Protein-Fragment Complementation Assay. PMID:28087810
Non-interacting proteins may resemble interacting proteins: prevalence and implications. PMID:28084410
Automatic query generation using word embeddings for retrieving passages describing experimental methods. PMID:28077568
A Chemogenomic Screen Reveals Novel Snf1p/AMPK Independent Regulators of Acetyl-CoA Carboxylase. PMID:28076367
Systematic Analysis of Transcriptional and Post-transcriptional Regulation of Metabolism in Yeast. PMID:28072816
Unbiased Identification of Blood-based Biomarkers for Pulmonary Tuberculosis by Modeling and Mining Molecular Interaction Networks. PMID:28065665
A Global Analysis of the Receptor Tyrosine Kinase-Protein Phosphatase Interactome. PMID:28065597
ccNET: Database of co-expression networks with functional modules for diploid and polyploid Gossypium. PMID:28053168
The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes. PMID:28053160
Network Centrality Analysis in Fungi Reveals Complex Regulation of Lost and Gained Genes. PMID:28046110
Emerging Roles for Ciz1 in Cell Cycle Regulation and as a Driver of Tumorigenesis. PMID:28036012
Neuroblastoma, a Paradigm for Big Data Science in Pediatric Oncology. PMID:28035989
m6A-Driver: Identifying Context-Specific mRNA m6A Methylation-Driven Gene Interaction Networks. PMID:28027310
Selecting optimal combinations of transcription factors to promote axon regeneration: Why mechanisms matter. PMID:28025113
VaProS: a database-integration approach for protein/genome information retrieval. PMID:28012137
Flexible model-based clustering of mixed binary and continuous data: application to genetic regulation and cancer. PMID:27994031
Identification of disease comorbidity through hidden molecular mechanisms. PMID:27991583
A Data Fusion Approach to Enhance Association Study in Epilepsy. PMID:27984588
Pan- and core- network analysis of co-expression genes in a model plant. PMID:27982071
The BioGRID interaction database: 2017 update. PMID:27980099
Interactomic analysis of REST/NRSF and implications of its functional links with the transcription suppressor TRIM28 during neuronal differentiation. PMID:27976729
Investigating the human Calcineurin Interaction Network using the πɸLxVP SLiM. PMID:27974827
Conservation of coevolving protein interfaces bridges prokaryote-eukaryote homologies in the twilight zone. PMID:27965389
Landscape of Pleiotropic Proteins Causing Human Disease: Structural and System Biology Insights. PMID:27957775
Specificity of broad protein interaction surfaces for proteins with multiple binding partners. PMID:27924264
The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible. PMID:27924014
Differential variation patterns between hubs and bottlenecks in human protein-protein interaction networks. PMID:27903259
AtPID: a genome-scale resource for genotype-phenotype associations in Arabidopsis. PMID:27899679
The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species. PMID:27899636
The TissueNet v.2 database: A quantitative view of protein-protein interactions across human tissues. PMID:27899616
XTalkDB: a database of signaling pathway crosstalk. PMID:27899583
Identification of differentially expressed genes in the development of osteosarcoma using RNA-seq. PMID:27888627
Prediction of Protein-Protein Interactions by Evidence Combining Methods. PMID:27879651
Systematic chemical-genetic and chemical-chemical interaction datasets for prediction of compound synergism. PMID:27874849
Intrinsic disorder in proteins involved in amyotrophic lateral sclerosis. PMID:27838743
Local Action with Global Impact: Highly Similar Infection Patterns of Human Viruses and Bacteriophages. PMID:27822522
Investigating the mechanism of hepatocellular carcinoma progression by constructing genetic and epigenetic networks using NGS data identification and big database mining method. PMID:27821810
Identification of the Key Genes and Pathways in Esophageal Carcinoma. PMID:27818681
EphA2 proteomics in human keratinocytes reveals a novel association with afadin and epidermal tight junctions. PMID:27815408
AMP-activated protein kinase fortifies epithelial tight junctions during energetic stress via its effector GIV/Girdin. PMID:27813479
Characterization and Genetic Analyses of New Genes Coding for NOD2 Interacting Proteins. PMID:27812135
Coupling an EML4-ALK-centric interactome with RNA interference identifies sensitizers to ALK inhibitors. PMID:27811184
mirDNMR: a gene-centered database of background de novo mutation rates in human. PMID:27799474
HIPPIE v2.0: enhancing meaningfulness and reliability of protein-protein interaction networks. PMID:27794551
Elastic-Net Copula Granger Causality for Inference of Biological Networks. PMID:27792750
TcoF-DB v2: update of the database of human and mouse transcription co-factors and transcription factor interactions. PMID:27789689
Incorporating topological information for predicting robust cancer subnetwork markers in human protein-protein interaction network. PMID:27766944
Identification of self-interacting proteins by exploring evolutionary information embedded in PSI-BLAST-constructed position specific scoring matrix. PMID:27732957
Using FlyBase, a Database of Drosophila Genes and Genomes. PMID:27730573
Functional Metabolomics Describes the Yeast Biosynthetic Regulome. PMID:27693354
Prediction and validation of protein-protein interactors from genome-wide DNA-binding data using a knowledge-based machine-learning approach. PMID:27683156
To Unveil the Molecular Mechanisms of Qi and Blood through Systems Biology-Based Investigation into Si-Jun-Zi-Tang and Si-Wu-Tang formulae. PMID:27677604
Exposure to the widely used herbicide atrazine results in deregulation of global tissue-specific RNA transcription in the third generation and is associated with a global decrease of histone trimethylation in mice. PMID:27655631
The Comparative Toxicogenomics Database: update 2017. PMID:27651457
Detecting Cooperativity between Transcription Factors Based on Functional Coherence and Similarity of Their Target Gene Sets. PMID:27623007
DenHunt - A Comprehensive Database of the Intricate Network of Dengue-Human Interactions. PMID:27618709
EPRS is a critical regulator of cell proliferation and estrogen signaling in ER+ breast cancer. PMID:27612429
Implication of Terminal Residues at Protein-Protein and Protein-DNA Interfaces. PMID:27611671
Dynamics of Human Mitochondrial Complex I Assembly: Implications for Neurodegenerative Diseases. PMID:27597947
BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID. PMID:27589962
A Synthetic Dosage Lethal Genetic Interaction Between CKS1B and PLK1 Is Conserved in Yeast and Human Cancer Cells. PMID:27558135
G9a and ZNF644 Physically Associate to Suppress Progenitor Gene Expression during Neurogenesis. PMID:27546533
The G1/S Specific Cyclin D2 Is a Regulator of HIV-1 Restriction in Non-proliferating Cells. PMID:27541004
Robust de novo pathway enrichment with KeyPathwayMiner 5. PMID:27540470
SFRP1 is a possible candidate for epigenetic therapy in non-small cell lung cancer. PMID:27534621
BioC viewer: a web-based tool for displaying and merging annotations in BioC. PMID:27515823
VHLdb: A database of von Hippel-Lindau protein interactors and mutations. PMID:27511743
Membranome: a database for proteome-wide analysis of single-pass membrane proteins. PMID:27510400
A Genome-Scale Investigation of How Sequence, Function, and Tree-Based Gene Properties Influence Phylogenetic Inference. PMID:27492233
Prediction and Validation of Transcription Factors Modulating the Expression of Sestrin3 Gene Using an Integrated Computational and Experimental Approach. PMID:27466818
Systematic identification of protein combinations mediating chromatin looping. PMID:27461729
Unfoldomics of prostate cancer: on the abundance and roles of intrinsically disordered proteins in prostate cancer. PMID:27453073
Investigating the Combinatory Effects of Biological Networks on Gene Co-expression. PMID:27445830
The HSA21 gene EURL/C21ORF91 controls neurogenesis within the cerebral cortex and is implicated in the pathogenesis of Down Syndrome. PMID:27404227
Integrating Transcriptomic and Proteomic Data Using Predictive Regulatory Network Models of Host Response to Pathogens. PMID:27403523
Multi-OMICs and Genome Editing Perspectives on Liver Cancer Signaling Networks. PMID:27403431
A Split-Ubiquitin Based Strategy Selecting for Protein Complex-Interfering Mutations. PMID:27402358
YCRD: Yeast Combinatorial Regulation Database. PMID:27392072
Clinical significance of mitofusin-2 and its signaling pathways in hepatocellular carcinoma. PMID:27389277
HVint: A Strategy for Identifying Novel Protein-Protein Interactions in Herpes Simplex Virus Type 1. PMID:27384951
HPIDB 2.0: a curated database for host-pathogen interactions. PMID:27374121
The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. PMID:27374120
Discovery Proteomics Identifies a Molecular Link between the Coatomer Protein Complex I and Androgen Receptor-dependent Transcription. PMID:27365400
Missense splice variant (g.20746A>G, p.Ile183Val) of interferon gamma receptor 1 (IFNGR1) coincidental with mycobacterial osteomyelitis - a screen of osteoarticular lesions. PMID:27356097
Reconstruction and Application of Protein-Protein Interaction Network. PMID:27338356
Yeast two-hybrid screening identified WDR77 as a novel interacting partner of TSC22D2. PMID:27337956
Comprehensive analysis of high-throughput screens with HiTSeekR. PMID:27330136
Negative autoregulation of BMP dependent transcription by SIN3B splicing reveals a role for RBM39. PMID:27324164
Jumping across biomedical contexts using compressive data fusion. PMID:27307649
Identification of S-phase DNA damage-response targets in fission yeast reveals conservation of damage-response networks. PMID:27298342
Non-random distribution of homo-repeats: links with biological functions and human diseases. PMID:27256590
Future paradigms for precision oncology. PMID:27223079
Research Resources for Nuclear Receptor Signaling Pathways. PMID:27216565
Genome-Wide Inference of Protein-Protein Interaction Networks Identifies Crosstalk in Abscisic Acid Signaling. PMID:27208273
Controllability of protein-protein interaction phosphorylation-based networks: Participation of the hub 14-3-3 protein family. PMID:27195976
Practical aspects of NGS-based pathways analysis for personalized cancer science and medicine. PMID:27191992
Advances in Autophagy Regulatory Mechanisms. PMID:27187479
Inference of biological networks using Bi-directional Random Forest Granger causality. PMID:27186478
Biological function derived from predicted structures in CASP11. PMID:27181425
Frequent mutations in acetylation and ubiquitination sites suggest novel driver mechanisms of cancer. PMID:27175787
Recent advances in large-scale protein interactome mapping. PMID:27158474
Characterizing gene sets using discriminative random walks with restart on heterogeneous biological networks. PMID:27153592
KeyPathwayMinerWeb: online multi-omics network enrichment. PMID:27150809
De novo truncating variants in the AHDC1 gene encoding the AT-hook DNA-binding motif-containing protein 1 are associated with intellectual disability and developmental delay. PMID:27148574
Data-based Reconstruction of Gene Regulatory Networks of Fungal Pathogens. PMID:27148247
Prediction of Synergism from Chemical-Genetic Interactions by Machine Learning. PMID:27136353
APID interactomes: providing proteome-based interactomes with controlled quality for multiple species and derived networks. PMID:27131791
Candidate gene prioritization with Endeavour. PMID:27131783
Positive Selection and Centrality in the Yeast and Fly Protein-Protein Interaction Networks. PMID:27119079
Network-driven plasma proteomics expose molecular changes in the Alzheimer's brain. PMID:27112350
g:Profiler-a web server for functional interpretation of gene lists (2016 update). PMID:27098042
GIANT API: an application programming interface for functional genomics. PMID:27098035
Genome-wide profiles of methylation, microRNAs, and gene expression in chemoresistant breast cancer. PMID:27094684
Tissue repair genes: the TiRe database and its implication for skin wound healing. PMID:27049721
FlyOde - a platform for community curation and interactive visualization of dynamic gene regulatory networks in Drosophila eye development. PMID:26998229
PolyQ 2.0: an improved version of PolyQ, a database of human polyglutamine proteins. PMID:26980520
Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases. PMID:26950747
Large-Scale Profiling of Kinase Dependencies in Cancer Cell Lines. PMID:26947069
Approaches to Investigating Complex Genetic Traits in a Large-Scale Inbred Mouse Aging Study. PMID:26936752
Structure-Based Identification of HDAC8 Non-histone Substrates. PMID:26933971
An Atlas of the Human Kinome Reveals the Mutational Landscape Underlying Dysregulated Phosphorylation Cascades in Cancer. PMID:26921330
PP2A as a master regulator of the cell cycle. PMID:26906453
A Systems Biology Approach to the Coordination of Defensive and Offensive Molecular Mechanisms in the Innate and Adaptive Host-Pathogen Interaction Networks. PMID:26881892
Structural and Functional Characterization of a Caenorhabditis elegans Genetic Interaction Network within Pathways. PMID:26871911
The Sigma-1 Receptor as a Pluripotent Modulator in Living Systems. PMID:26869505
Determining the Composition and Stability of Protein Complexes Using an Integrated Label-Free and Stable Isotope Labeling Strategy. PMID:26867737
Temporal Genetic Modifications after Controlled Cortical Impact--Understanding Traumatic Brain Injury through a Systematic Network Approach. PMID:26861311
Inositol 1,4,5-trisphosphate receptors and their protein partners as signalling hubs. PMID:26830355
Interaction network of tobacco etch potyvirus NIa protein with the host proteome during infection. PMID:26830344
Zfrp8/PDCD2 Interacts with RpS2 Connecting Ribosome Maturation and Gene-Specific Translation. PMID:26807849
Proteomic peptide phage display uncovers novel interactions of the PDZ1-2 supramodule of syntenin. PMID:26787460
Genomic Signatures of Selective Pressures and Introgression from Archaic Hominins at Human Innate Immunity Genes. PMID:26748513
Chromosome-wide histone deacetylation by sirtuins prevents hyperactivation of DNA damage-induced signaling upon replicative stress. PMID:26748095
TRAPLINE: a standardized and automated pipeline for RNA sequencing data analysis, evaluation and annotation. PMID:26738481
Path2PPI: an R package to predict protein-protein interaction networks for a set of proteins. PMID:26733452
Quantitative analysis of the interplay between hsc70 and its co-chaperone HspBP1. PMID:26713263
HitPredict version 4: comprehensive reliability scoring of physical protein-protein interactions from more than 100 species. PMID:26708988
Biocuration with insufficient resources and fixed timelines. PMID:26708987
Search for the Function of NWC, Third Gene Within RAG Locus: Generation and Characterization of NWC-Deficient Mice. PMID:26703212
Bioinformatics Mining and Modeling Methods for the Identification of Disease Mechanisms in Neurodegenerative Disorders. PMID:26690135
Fundamentals of protein interaction network mapping. PMID:26681426
Identification of network-based biomarkers of cardioembolic stroke using a systems biology approach with time series data. PMID:26679092
A deep proteomics perspective on CRM1-mediated nuclear export and nucleocytoplasmic partitioning. PMID:26673895
HRGRN: A Graph Search-Empowered Integrative Database of Arabidopsis Signaling Transduction, Metabolism and Gene Regulation Networks. PMID:26657893
The Proteomic Profile of Deleted in Breast Cancer 1 (DBC1) Interactions Points to a Multifaceted Regulation of Gene Expression. PMID:26657080
PC-TraFF: identification of potentially collaborating transcription factors using pointwise mutual information. PMID:26627005
MacroH2A1 associates with nuclear lamina and maintains chromatin architecture in mouse liver cells. PMID:26603343
Systematic identification and correction of annotation errors in the genetic interaction map of Saccharomyces cerevisiae. PMID:26602688
Transcriptomics of diapause in an isogenic self-fertilizing vertebrate. PMID:26597228
Lynx: a knowledge base and an analytical workbench for integrative medicine. PMID:26590263
Genetic determinants of fibro-osseous lesions in aged inbred mice. PMID:26589134
Experimental detection of short regulatory motifs in eukaryotic proteins: tips for good practice as well as for bad. PMID:26581338
Prediction of Genetic Interactions Using Machine Learning and Network Properties. PMID:26579514
Integrating transcriptional and protein interaction networks to prioritize condition-specific master regulators. PMID:26576632
DESM: portal for microbial knowledge exploration systems. PMID:26546514
Getting the most out of RNA-seq data analysis. PMID:26539333
Survey of Natural Language Processing Techniques in Bioinformatics. PMID:26525745
Integrated interactions database: tissue-specific view of the human and model organism interactomes. PMID:26516188
SynLethDB: synthetic lethality database toward discovery of selective and sensitive anticancer drug targets. PMID:26516187
NCG 5.0: updates of a manually curated repository of cancer genes and associated properties from cancer mutational screenings. PMID:26516186
Building a KATalogue of acetyllysine targeting and function. PMID:26512033
Colorectal cancer atlas: An integrative resource for genomic and proteomic annotations from colorectal cancer cell lines and tissues. PMID:26496946
Integrated multi-omics analyses reveal the pleiotropic nature of the control of gene expression by Puf3p. PMID:26493364
F-actin clustering and cell dysmotility induced by the pathological W148R missense mutation of filamin B at the actin-binding domain. PMID:26491051
Integrative Genomics-Based Discovery of Novel Regulators of the Innate Antiviral Response. PMID:26485378
A Pan-Cancer Catalogue of Cancer Driver Protein Interaction Interfaces. PMID:26485003
Identification of shared and unique susceptibility pathways among cancers of the lung, breast, and prostate from genome-wide association studies and tissue-specific protein interactions. PMID:26483192
Bovine Genome Database: new tools for gleaning function from the Bos taurus genome. PMID:26481361
PlantPAN 2.0: an update of plant promoter analysis navigator for reconstructing transcriptional regulatory networks in plants. PMID:26476450
An overview of bioinformatics methods for modeling biological pathways in yeast. PMID:26476430
Evolutionary rescue by compensatory mutations is constrained by genomic and environmental backgrounds. PMID:26459777
A survey about methods dedicated to epistasis detection. PMID:26442103
ExoCarta: A Web-Based Compendium of Exosomal Cargo. PMID:26434508
High-Throughput Identification of Cis-Regulatory Rewiring Events in Yeast. PMID:26399482
Human protein interaction networks across tissues and diseases. PMID:26347769
Large-scale extraction of gene interactions from full-text literature using DeepDive. PMID:26338771
Targeting SOD1 induces synthetic lethal killing in BLM- and CHEK2-deficient colorectal cancer cells. PMID:26318585
In vivo hematopoietic Myc activation directs a transcriptional signature in endothelial cells within the bone marrow microenvironment. PMID:26308666
ExAtlas: An interactive online tool for meta-analysis of gene expression data. PMID:26223199
Comprehensive Protein Interactome Analysis of a Key RNA Helicase: Detection of Novel Stress Granule Proteins. PMID:26184334
Implications of Big Data for cell biology. PMID:26174066
Surfing the Protein-Protein Interaction Surface Using Docking Methods: Application to the Design of PPI Inhibitors. PMID:26111183
TRRUST: a reference database of human transcriptional regulatory interactions. PMID:26066708
DeAnnCNV: a tool for online detection and annotation of copy number variations from whole-exome sequencing data. PMID:26013811
Databases for Microbiologists. PMID:26013493
Biocuration at the Saccharomyces genome database. PMID:25997651
IMP 2.0: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks. PMID:25969450
Exploiting the yeast stress-activated signaling network to inform on stress biology and disease signaling. PMID:25957506
Systems medicine: evolution of systems biology from bench to bedside. PMID:25891169
Intrinsically disordered proteins and their (disordered) proteomes in neurodegenerative disorders. PMID:25784874
The last enzyme of the de novo purine synthesis pathway 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase (ATIC) plays a central role in insulin signaling and the Golgi/endosomes protein network. PMID:25687571
The BioGRID interaction database: 2019 update PubMed citations: 454.

454 articles citing: The BioGRID interaction database: 2019 update

Gene networks under circadian control exhibit diurnal organization in primate organs. PMID:35906476
Network Embedding Across Multiple Tissues and Data Modalities Elucidates the Context of Host Factors Important for COVID-19 Infection. PMID:35903362
Mitochondrial Oxidative Stress Induces Cardiac Fibrosis in Obese Rats through Modulation of Transthyretin. PMID:35897655
An accurate prediction model of digenic interaction for estimating pathogenic gene pairs of human diseases. PMID:35891796
Integration of probabilistic functional networks without an external Gold Standard. PMID:35879662
Systematic prediction of degrons and E3 ubiquitin ligase binding via deep learning. PMID:35836176
Construction and contextualization approaches for protein-protein interaction networks. PMID:35832626
Deep learning frameworks for protein-protein interaction prediction. PMID:35832624
HumanMine: advanced data searching, analysis and cross-species comparison. PMID:35820040
Bioinformatics-Driven Identification of p62 as A Crucial Oncogene in Liver Cancer. PMID:35814476
RPpocket: An RNA-Protein Intuitive Database with RNA Pocket Topology Resources. PMID:35805909
Aberrant SPOP-CHAF1A ubiquitination axis triggers tumor autophagy that endows a therapeutical vulnerability in diffuse large B cell lymphoma. PMID:35773729
Inferring functional communities from partially observed biological networks exploiting geometric topology and side information. PMID:35760826
Deep learning uncovers distinct behavior of rice network to pathogens response. PMID:35754717
Systematic inference of indirect transcriptional regulation by protein kinases and phosphatases. PMID:35731801
Network approaches for modeling the effect of drugs and diseases. PMID:35704883
Assessing sequence-based protein-protein interaction predictors for use in therapeutic peptide engineering. PMID:35688894
A comprehensive SARS-CoV-2-human protein-protein interactome network identifies pathobiology and host-targeting therapies for COVID-19. PMID:35677070
Estrogen hormone is an essential sex factor inhibiting inflammation and immune response in COVID-19. PMID:35676404
An approach to cellular tropism of SARS-CoV-2 through protein-protein interaction and enrichment analysis. PMID:35672403
Network assisted analysis of de novo variants using protein-protein interaction information identified 46 candidate genes for congenital heart disease. PMID:35671298
Predicting which genes will respond to transcription factor perturbations. PMID:35666184
SSRTool: A web tool for evaluating RNA secondary structure predictions based on species-specific functional interpretability. PMID:35664227
A tensor-based bi-random walks model for protein function prediction. PMID:35637427
Immunopathogenic overlap between COVID-19 and tuberculosis identified from transcriptomic meta-analysis and human macrophage infection. PMID:35634577
Comprehensive Interactome Mapping of Nuclear Receptors Using Proximity Biotinylation. PMID:35612745
Targeting TROY-mediated P85a/AKT/TBX3 signaling attenuates tumor stemness and elevates treatment response in hepatocellular carcinoma. PMID:35610614
GenePlexus: a web-server for gene discovery using network-based machine learning. PMID:35580053
Identification of Potential Muscle Biomarkers in McArdle Disease: Insights from Muscle Proteome Analysis. PMID:35563042
SynLethDB 2.0: a web-based knowledge graph database on synthetic lethality for novel anticancer drug discovery. PMID:35562840
Bioinformatics-Based Approaches to Study Virus-Host Interactions During SARS-CoV-2 Infection. PMID:35554909
SARS-CoV-2 Employ BSG/CD147 and ACE2 Receptors to Directly Infect Human Induced Pluripotent Stem Cell-Derived Kidney Podocytes. PMID:35517495
A hybrid approach unveils drug repurposing candidates targeting an Alzheimer pathophysiology mechanism. PMID:35510183
GURFAP: A Platform for Gene Function Analysis in Glycyrrhiza Uralensis. PMID:35495163
Membranome 3.0: Database of single-pass membrane proteins with AlphaFold models. PMID:35481632
PregTox: A Resource of Knowledge about Drug Fetal Toxicity. PMID:35469349
On the influence of several factors on pathway enrichment analysis. PMID:35453140
Phosphate dysregulation via the XPR1-KIDINS220 protein complex is a therapeutic vulnerability in ovarian cancer. PMID:35437317
Integrative Analysis for Identification of Therapeutic Targets and Prognostic Signatures in Non-Small Cell Lung Cancer. PMID:35422618
Phylogenetic profiling in eukaryotes: The effect of species, orthologous group, and interactome selection on protein interaction prediction. PMID:35421089
Predicted mouse interactome and network-based interpretation of differentially expressed genes. PMID:35390003
DWPPI: A Deep Learning Approach for Predicting Protein-Protein Interactions in Plants Based on Multi-Source Information With a Large-Scale Biological Network. PMID:35387292
Multiomic profiling of the acute stress response in the mouse hippocampus. PMID:35383160
CPIELA: Computational Prediction of Plant Protein-Protein Interactions by Ensemble Learning Approach From Protein Sequences and Evolutionary Information. PMID:35360876
Computational methods, databases and tools for synthetic lethality prediction. PMID:35352098
Protein Biomarkers in Monocytes and CD4+ Lymphocytes for Predicting Lithium Treatment Response of Bipolar Disorder: a Feasibility Study with Tyramine-Based Signal-Amplified Flow Cytometry. PMID:35342205
Serine hydroxymethyltransferase 2 (SHMT2) potentiates the aggressive process of oral squamous cell carcinoma by binding to interleukin enhancer-binding factor 2 (ILF2). PMID:35333683
Dynamical Analysis of a Boolean Network Model of the Oncogene Role of lncRNA ANRIL and lncRNA UFC1 in Non-Small Cell Lung Cancer. PMID:35327612
BRCA1 mutations in high-grade serous ovarian cancer are associated with proteomic changes in DNA repair, splicing, transcription regulation and signaling. PMID:35292711
A comprehensive WGS-based pipeline for the identification of new candidate genes in inherited retinal dystrophies. PMID:35246562
Host-microbiome protein-protein interactions capture disease-relevant pathways. PMID:35246229
The microprotein Nrs1 rewires the G1/S transcriptional machinery during nitrogen limitation in budding yeast. PMID:35239649
PSINDB: the postsynaptic protein-protein interaction database. PMID:35234850
Comprehensive Analysis of the Glycolysis-Related Gene Prognostic Signature and Immune Infiltration in Endometrial Cancer. PMID:35223866
Functional network motifs defined through integration of protein-protein and genetic interactions. PMID:35223214
Antifungal activity of an artificial peptide aptamer SNP-D4 against Fusarium oxysporum. PMID:35223198
Single-Cell Technologies to Decipher the Immune Microenvironment in Myeloid Neoplasms: Perspectives and Opportunities. PMID:35186713
The S100A7 nuclear interactors in autoimmune diseases: a coevolutionary study in mammals. PMID:35174412
KeyPathwayMineR: De Novo Pathway Enrichment in the R Ecosystem. PMID:35173764
Using Surface Hydrophobicity Together with Empirical Potentials to Identify Protein-Protein Binding Sites: Application to the Interactions of E-cadherins. PMID:35167069
The Landscape of Aminoacyl-tRNA Synthetases Involved in Severe Acute Respiratory Syndrome Coronavirus 2 Infection. PMID:35153822
An Integrative Network Approach to Identify Common Genes for the Therapeutics in Tuberculosis and Its Overlapping Non-Communicable Diseases. PMID:35153741
Chemoproteomic-enabled characterization of small GTPase Rab1a as a target of an N-arylbenzimidazole ligand's rescue of Parkinson's-associated cell toxicity. PMID:35128413
Transcriptomic Landscape of Herbivore Oviposition in Arabidopsis: A Systematic Review. PMID:35126411
Structure-based prediction of HDAC6 substrates validated by enzymatic assay reveals determinants of promiscuity and detects new potential substrates. PMID:35110592
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
Towards an Ideal In Cell Hybridization-Based Strategy to Discover Protein Interactomes of Selected RNA Molecules. PMID:35055128
Correcting Differential Gene Expression Analysis for Cyto-Architectural Alterations in Substantia Nigra of Parkinson's Disease Patients Reveals Known and Potential Novel Disease-Associated Genes and Pathways. PMID:35053314
Multi-time scale transcriptomic analysis on the dynamic process of tamoxifen resistance development in breast cancer cell lines. PMID:35041152
Plant Reactome and PubChem: The Plant Pathway and (Bio)Chemical Entity Knowledgebases. PMID:35037224
RNA-binding protein p54nrb/NONO potentiates nuclear EGFR-mediated tumorigenesis of triple-negative breast cancer. PMID:35013116
RAD50 deficiency is a predictor of platinum sensitivity in sporadic epithelial ovarian cancers. PMID:35006434
Meta-analysis of whole-genome gene expression datasets assessing the effects of IDH1 and IDH2 mutations in isogenic disease models. PMID:34997121
Potential Molecular Mechanisms and Remdesivir Treatment for Acute Respiratory Syndrome Corona Virus 2 Infection/COVID 19 Through RNA Sequencing and Bioinformatics Analysis. PMID:34992355
Single-cell transcriptome atlas of human mesenchymal stem cells exploring cellular heterogeneity. PMID:34965030
Data analysis methods for defining biomarkers from omics data. PMID:34951658
Spatial and Temporal Expression of High-Mobility-Group Nucleosome-Binding (HMGN) Genes in Brain Areas Associated with Cognition in Individuals with Down Syndrome. PMID:34946949
GRWD1-WDR5-MLL2 Epigenetic Complex Mediates H3K4me3 Mark and Is Essential for Kaposi's Sarcoma-Associated Herpesvirus-Induced Cellular Transformation. PMID:34933446
Small molecules for cell reprogramming: a systems biology analysis. PMID:34919532
Where all the Roads Meet? A Crossover Perspective on Host Factors Regulating SARS-CoV-2 infection. PMID:34914966
Protein-protein interactions: Methods, databases, and applications in virus-host study. PMID:34909403
Improving Analysis and Annotation of Microarray Data with Protein Interactions. PMID:34902122
Shared Molecular Mechanisms between Atherosclerosis and Periodontitis by Analyzing the Transcriptomic Alterations of Peripheral Blood Monocytes. PMID:34899963
Interrogating cell type-specific cooperation of transcriptional regulators in 3D chromatin. PMID:34888502
Metabolic endophenotype associated with right ventricular glucose uptake in pulmonary hypertension. PMID:34888034
Computational Network Pharmacology-Based Strategy to Capture Key Functional Components and Decode the Mechanism of Chai-Hu-Shu-Gan-San in Treating Depression. PMID:34867413
GFI1 tethers the NuRD complex to open and transcriptionally active chromatin in myeloid progenitors. PMID:34857890
Multiscale interactome analysis coupled with off-target drug predictions reveals drug repurposing candidates for human coronavirus disease. PMID:34857794
Functional enrichment of alternative splicing events with NEASE reveals insights into tissue identity and diseases. PMID:34857024
Inhibitor tolerance and bioethanol fermentability of levoglucosan-utilizing Escherichia coli were enhanced by overexpression of stress-responsive gene ycfR: The proteomics-guided metabolic engineering. PMID:34853817
BP180/Collagen XVII: A Molecular View. PMID:34830116
Transcription Factor Action Orchestrates the Complex Expression Pattern of CRABS CLAW in Arabidopsis. PMID:34828269
CyFi-MAP: an interactive pathway-based resource for cystic fibrosis. PMID:34782688
Pairwise Biological Network Alignment Based on Discrete Bat Algorithm. PMID:34777564
Individualized Proteogenomics Reveals the Mutational Landscape of Melanoma Patients in Response to Immunotherapy. PMID:34771574
Systematic Analysis of FASTK Gene Family Alterations in Cancer. PMID:34768773
Computational methods for protein localization prediction. PMID:34765098
Recognition of DNA Methylation Molecular Features for Diagnosis and Prognosis in Gastric Cancer. PMID:34745226
TcoFBase: a comprehensive database for decoding the regulatory transcription co-factors in human and mouse. PMID:34718747
Proximity-dependent biotin identification (BioID) reveals a dynamic LSD1-CoREST interactome during embryonic stem cell differentiation. PMID:34709266
A Graph Feature Auto-Encoder for the prediction of unobserved node features on biological networks. PMID:34706640
ANAT 3.0: a framework for elucidating functional protein subnetworks using graph-theoretic and machine learning approaches. PMID:34706638
A Markov random field model for network-based differential expression analysis of single-cell RNA-seq data. PMID:34702190
Biallelic FRA10AC1 variants cause a neurodevelopmental disorder with growth retardation. PMID:34694367
DeepTrio: a ternary prediction system for protein-protein interaction using mask multiple parallel convolutional neural networks. PMID:34694333
Precise Characterization of Genetic Interactions in Cancer via Molecular Network Refining Processes. PMID:34681774
Proteogenomics Reveals Perturbed Signaling Networks in Malignant Melanoma Cells Resistant to BRAF Inhibition. PMID:34673281
Sequence-Based Prediction of Plant Protein-Protein Interactions by Combining Discrete Sine Transformation With Rotation Forest. PMID:34671178
Two classes of functional connectivity in dynamical processes in networks. PMID:34665977
SYNBIP: synthetic binding proteins for research, diagnosis and therapy. PMID:34664670
Network potential identifies therapeutic miRNA cocktails in Ewing sarcoma. PMID:34662337
A Systematic Analysis Identifies Key Regulators Involved in Cell Proliferation and Potential Drugs for the Treatment of Human Lung Adenocarcinoma. PMID:34650921
Differential Transcriptional Regulation of Polymorphic p53 Codon 72 in Metabolic Pathways. PMID:34639134
Predicting PY motif-mediated protein-protein interactions in the Nedd4 family of ubiquitin ligases. PMID:34637467
SignaLink3: a multi-layered resource to uncover tissue-specific signaling networks. PMID:34634810
A survey on computational methods in discovering protein inhibitors of SARS-CoV-2. PMID:34623382
An overview of machine learning methods for monotherapy drug response prediction. PMID:34619752
iRegNet: an integrative Regulatory Network analysis tool for Arabidopsis thaliana. PMID:34618085
Estrogen Hormone Is an Essential Sex Factor Inhibiting Inflammation and Immune Response in COVID-19. PMID:34611658
Systems biology analysis of lung fibrosis-related genes in the bleomycin mouse model. PMID:34588506
CPLM 4.0: an updated database with rich annotations for protein lysine modifications. PMID:34581824
Defining Functions of Mannoproteins in Saccharomyces cerevisiae by High-Dimensional Morphological Phenotyping. PMID:34575807
Network neighbors of viral targets and differentially expressed genes in COVID-19 are drug target candidates. PMID:34556735
Vtc5 Is Localized to the Vacuole Membrane by the Conserved AP-3 Complex to Regulate Polyphosphate Synthesis in Budding Yeast. PMID:34544285
Proteomic Tools for the Analysis of Cytoskeleton Proteins. PMID:34542864
GRASP55 restricts early-stage autophagy and regulates spatial organization of the early secretory network. PMID:34533192
The protein-protein interaction network alignment using recurrent neural network. PMID:34529185
Time-resolved in vivo ubiquitinome profiling by DIA-MS reveals USP7 targets on a proteome-wide scale. PMID:34518535
MOV10 Helicase Interacts with Coronavirus Nucleocapsid Protein and Has Antiviral Activity. PMID:34517762
Protein Arginine Methyltransferase 5 Functions via Interacting Proteins. PMID:34513846
ACE2 Netlas: In silico Functional Characterization and Drug-Gene Interactions of ACE2 Gene Network to Understand Its Potential Involvement in COVID-19 Susceptibility. PMID:34512723
Identifying Protein Complexes With Clear Module Structure Using Pairwise Constraints in Protein Interaction Networks. PMID:34512712
A functionally divergent intrinsically disordered region underlying the conservation of stochastic signaling. PMID:34506483
Mitochondria-localized AMPK responds to local energetics and contributes to exercise and energetic stress-induced mitophagy. PMID:34493662
Arabidopsis-Based Dual-Layered Biological Network Analysis Elucidates Fully Modulated Pathways Related to Sugarcane Resistance on Biotrophic Pathogen Infection. PMID:34490009
Machine learning methods, databases and tools for drug combination prediction. PMID:34477201
ACAA2 is a ligand-dependent coactivator for thyroid hormone receptor β1. PMID:34474245
Secreted retrovirus-like GAG-domain-containing protein PEG10 is regulated by UBE3A and is involved in Angelman syndrome pathophysiology. PMID:34467244
CANVS: an easy-to-use application for the analysis and visualization of mass spectrometry-based protein-protein interaction/association data. PMID:34432510
MetaCancer: A deep learning-based pan-cancer metastasis prediction model developed using multi-omics data. PMID:34429856
MeCP2 prevents age-associated cognitive decline via restoring synaptic plasticity in a senescence-accelerated mouse model. PMID:34363729
Global effects of RAB3GAP1 dysexpression on the proteome of mouse cortical neurons. PMID:34363538
Investigation of RNA metabolism through large-scale genetic interaction profiling in yeast. PMID:34358317
Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture. PMID:34357701
Thiol-disulphide independent in-cell trapping for the identification of peroxiredoxin 2 interactors. PMID:34340028
Comprehensive Analysis of the Value of SMYD Family Members in the Prognosis and Immune Infiltration of Malignant Digestive System Tumors. PMID:34335697
Multimodal single-cell omics analysis identifies epithelium-immune cell interactions and immune vulnerability associated with sex differences in COVID-19. PMID:34330889
Targeted capture sequencing identifies genetic variations of GRK4 and RDH8 in Han Chinese with essential hypertension in Xinjiang. PMID:34297769
Identification and Validation of Potential Biomarkers and Pathways for Idiopathic Pulmonary Fibrosis by Comprehensive Bioinformatics Analysis. PMID:34285914
YPIBP: A repository for phosphoinositide-binding proteins in yeast. PMID:34285772
An integrative study of genetic variants with brain tissue expression identifies viral etiology and potential drug targets of multiple sclerosis. PMID:34284104
NTNG1 Modulates Cisplatin Resistance in Epithelial Ovarian Cancer Cells via the GAS6/AXL/Akt Pathway. PMID:34277602
A computational and structural analysis of germline and somatic variants affecting the DDR mechanism, and their impact on human diseases. PMID:34253785
Loss of UCHL1 rescues the defects related to Parkinson's disease by suppressing glycolysis. PMID:34244144
A quantitative yeast aging proteomics analysis reveals novel aging regulators. PMID:34241809
The Silence of PSMC6 Inhibits Cell Growth and Metastasis in Lung Adenocarcinoma. PMID:34239933
Databases for Protein-Protein Interactions. PMID:34236665
Integrated analysis of Shank1 PDZ interactions with C-terminal and internal binding motifs. PMID:34235485
Integration of transcriptomic data identifies key hallmark genes in hypertrophic cardiomyopathy. PMID:34225646
Linear functional organization of the omic embedding space. PMID:34213534
Pathogen Moonlighting Proteins: From Ancestral Key Metabolic Enzymes to Virulence Factors. PMID:34203698
Towards a global investigation of transcriptomic signatures through co-expression networks and pathway knowledge for the identification of disease mechanisms. PMID:34197603
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
Network-based analysis of virulence factors for uncovering Aeromonas veronii pathogenesis. PMID:34162325
Precision omics data integration and analysis with interoperable ontologies and their application for COVID-19 research. PMID:34159360
Insights into how environment shapes post-mortem RNA transcription in mouse brain. PMID:34155272
Interferon-Gamma-Producing CD8+ Tissue Resident Memory T Cells Are a Targetable Hallmark of Immune Checkpoint Inhibitor-Colitis. PMID:34147519
Dynamic Host Immune and Transcriptomic Responses to Respiratory Syncytial Virus Infection in a Vaccination-Challenge Mouse Model. PMID:34138405
Making fundamental scientific discoveries by combining information from literature, databases, and computational tools - An example. PMID:34136100
Matrix-screening reveals a vast potential for direct protein-protein interactions among RNA binding proteins. PMID:34133714
The expression and clinical prognostic value of protein phosphatase 1 catalytic subunit beta in pancreatic cancer. PMID:34125004
Target identification among known drugs by deep learning from heterogeneous networks. PMID:34123272
DeepR2cov: deep representation learning on heterogeneous drug networks to discover anti-inflammatory agents for COVID-19. PMID:34117734
Integrating protein networks and machine learning for disease stratification in the Hereditary Spastic Paraplegias. PMID:34113825
Network medicine links SARS-CoV-2/COVID-19 infection to brain microvascular injury and neuroinflammation in dementia-like cognitive impairment. PMID:34108016
PIGNON: a protein-protein interaction-guided functional enrichment analysis for quantitative proteomics. PMID:34088263
Functional characterization of RebL1 highlights the evolutionary conservation of oncogenic activities of the RBBP4/7 orthologue in Tetrahymena thermophila. PMID:34086947
A Genetic Study of Cerebral Atherosclerosis Reveals Novel Associations with NTNG1 and CNOT3. PMID:34073619
Model-based analysis uncovers mutations altering autophagy selectivity in human cancer. PMID:34059679
Natural variants suppress mutations in hundreds of essential genes. PMID:34042294
Genetic interaction network has a very limited impact on the evolutionary trajectories in continuous culture-grown populations of yeast. PMID:34039270
driveR: a novel method for prioritizing cancer driver genes using somatic genomics data. PMID:34030627
Circulating hsa-miR-323b-3p in Huntington's Disease: A Pilot Study. PMID:34025560
KEA3: improved kinase enrichment analysis via data integration. PMID:34019655
A computational approach for detecting physiological homogeneity in the midst of genetic heterogeneity. PMID:34015270
An overview of graph databases and their applications in the biomedical domain. PMID:34003247
Targeting SUMOylation dependency in human cancer stem cells through a unique SAE2 motif revealed by chemical genomics. PMID:33979648
A unified resource and configurable model of the synapse proteome and its role in disease. PMID:33976238
Timer-based proteomic profiling of the ubiquitin-proteasome system reveals a substrate receptor of the GID ubiquitin ligase. PMID:33974913
CLEP: A Hybrid Data- and Knowledge- Driven Framework for Generating Patient Representations. PMID:33964127
Proteo3Dnet: a web server for the integration of structural information with interactomics data. PMID:33963857
Dual proteome-scale networks reveal cell-specific remodeling of the human interactome. PMID:33961781
A New Sequential Forward Feature Selection (SFFS) Algorithm for Mining Best Topological and Biological Features to Predict Protein Complexes from Protein-Protein Interaction Networks (PPINs). PMID:33959851
Employing core regulatory circuits to define cell identity. PMID:33934382
The EAR Motif in the Arabidopsis MADS Transcription Factor AGAMOUS-Like 15 Is Not Necessary to Promote Somatic Embryogenesis. PMID:33924312
An integrative drug repositioning framework discovered a potential therapeutic agent targeting COVID-19. PMID:33895786
The VRNetzer platform enables interactive network analysis in Virtual Reality. PMID:33893283
Genetic Architecture Underlying Nascent Speciation-The Evolution of Eurasian Pigs under Domestication. PMID:33892509
Correlation AnalyzeR: functional predictions from gene co-expression correlations. PMID:33879054
Modeling transcriptional regulation using gene regulatory networks based on multi-omics data sources. PMID:33874910
Algorithm-Based Meta-Analysis Reveals the Mechanistic Interaction of the Tumor Suppressor LIMD1 With Non-Small-Cell Lung Carcinoma. PMID:33869018
RRM2B Is Frequently Amplified Across Multiple Tumor Types: Implications for DNA Repair, Cellular Survival, and Cancer Therapy. PMID:33868369
Non-Genomic AhR-Signaling Modulates the Immune Response in Endotoxin-Activated Macrophages After Activation by the Environmental Stressor BaP. PMID:33868237
PCprophet: a framework for protein complex prediction and differential analysis using proteomic data. PMID:33859439
A novel predicted ADP-ribosyltransferase-like family conserved in eukaryotic evolution. PMID:33854844
A combined RAD-Seq and WGS approach reveals the genomic basis of yellow color variation in bumble bee Bombus terrestris. PMID:33846496
Exploring the Imbalance of Periodontitis Immune System From the Cellular to Molecular Level. PMID:33841510
High ELF4 expression in human cancers is associated with worse disease outcomes and increased resistance to anticancer drugs. PMID:33836003
Reprogramming enriches for somatic cell clones with small-scale mutations in cancer-associated genes. PMID:33831558
Posttranslational modifications in proteins: resources, tools and prediction methods. PMID:33826699
In silico investigation of the viroporin E as a vaccine target against SARS-CoV-2. PMID:33822639
A bioinformatic analysis of the inhibin-betaglycan-endoglin/CD105 network reveals prognostic value in multiple solid tumors. PMID:33819300
Network bioinformatics analysis provides insight into drug repurposing for COVID-19. PMID:33817623
Improved sequence-based prediction of interaction sites in α-helical transmembrane proteins by deep learning. PMID:33815689
Huntingtin: A Protein with a Peculiar Solvent Accessible Surface. PMID:33809039
Quantitative Proteomic Approach Reveals Altered Metabolic Pathways in Response to the Inhibition of Lysine Deacetylases in A549 Cells under Normoxia and Hypoxia. PMID:33806075
Detection of H3K4me3 Identifies NeuroHIV Signatures, Genomic Effects of Methamphetamine and Addiction Pathways in Postmortem HIV+ Brain Specimens that Are Not Amenable to Transcriptome Analysis. PMID:33805201
Assessing the Function of the ZFP90 Variant rs1170426 in SLE and the Association Between SLE Drug Target and Susceptibility Genes. PMID:33796098
Network medicine links SARS-CoV-2/COVID-19 infection to brain microvascular injury and neuroinflammation in dementia-like cognitive impairment. PMID:33791705
A Critical Role of Peptidylprolyl Isomerase A Pseudogene 22/microRNA-197-3p/Peptidylprolyl Isomerase A Axis in Hepatocellular Carcinoma. PMID:33790943
Loss of the abasic site sensor HMCES is synthetic lethal with the activity of the APOBEC3A cytosine deaminase in cancer cells. PMID:33788831
Protein interaction potential landscapes for yeast replicative aging. PMID:33785798
Genome-wide RNAi screen for regulators of UPRmt in Caenorhabditis elegans mutants with defects in mitochondrial fusion. PMID:33784383
Adenosine Receptor and Its Downstream Targets, Mod(mdg4) and Hsp70, Work as a Signaling Pathway Modulating Cytotoxic Damage in Drosophila. PMID:33777958
The Genetic and Epigenetic Mechanisms Involved in Irreversible Pulp Neural Inflammation. PMID:33777260
Versatile knowledge guided network inference method for prioritizing key regulatory factors in multi-omics data. PMID:33762588
SH3BP4 promotes neuropilin-1 and α5-integrin endocytosis and is inhibited by Akt. PMID:33761321
Integrated intra- and intercellular signaling knowledge for multicellular omics analysis. PMID:33749993
Integrating 3D structural information into systems biology. PMID:33744294
Identification of disease treatment mechanisms through the multiscale interactome. PMID:33741907
Genetic Interaction Network Interpretation: A Tidy Data Science Perspective. PMID:33733367
Molecular clues in the regulation of mini-puberty involve neuronal DNA binding transcription factor NHLH2. PMID:33731013
Gene variants of coagulation related proteins that interact with SARS-CoV-2. PMID:33730015
Mapping specificity, cleavage entropy, allosteric changes and substrates of blood proteases in a high-throughput screen. PMID:33727531
Alternatively Splicing Interactomes Identify Novel Isoform-Specific Partners for NSD2. PMID:33718354
Do Molecular Profiles of Primary Versus Metastatic Radioiodine Refractory Differentiated Thyroid Cancer Differ? PMID:33716974
Soluble ACE2-mediated cell entry of SARS-CoV-2 via interaction with proteins related to the renin-angiotensin system. PMID:33713620
Integrative analysis regarding the correlation between GAS2 family genes and human glioma prognosis. PMID:33713047
B7-H6 is a new potential biomarker and therapeutic target of T-lymphoblastic lymphoma. PMID:33708955
Systemic Multi-Omics Analysis Reveals Amplified P4HA1 Gene Associated With Prognostic and Hypoxic Regulation in Breast Cancer. PMID:33692831
Mutational Pattern in Multiple Pulmonary Nodules Are Associated With Early Stage Lung Adenocarcinoma. PMID:33680914
HIR V2: a human interactome resource for the biological interpretation of differentially expressed genes via gene set linkage analysis. PMID:33677507
Structural basis for the DNA-binding activity of human ARID4B Tudor domain. PMID:33675746
Molecular disruption of DNA polymerase β for platinum sensitisation and synthetic lethality in epithelial ovarian cancers. PMID:33674744
The overexpression of DNA repair genes in invasive ductal and lobular breast carcinomas: Insights on individual variations and precision medicine. PMID:33662042
Dual DNA and protein tagging of open chromatin unveils dynamics of epigenomic landscapes in leukemia. PMID:33649590
Cysteinyl-specialized proresolving mediators link resolution of infectious inflammation and tissue regeneration via TRAF3 activation. PMID:33649212
Hippocampal transcriptome-wide association study and neurobiological pathway analysis for Alzheimer's disease. PMID:33630843
Identification of host proteins differentially associated with HIV-1 RNA splice variants. PMID:33629952
Evolution, structure and emerging roles of C1ORF112 in DNA replication, DNA damage responses, and cancer. PMID:33625522
Ageing transcriptome meta-analysis reveals similarities and differences between key mammalian tissues. PMID:33611312
Genome-wide association analysis of cognitive function in Danish long-lived individuals. PMID:33607172
The Srs2 helicase dampens DNA damage checkpoint by recycling RPA from chromatin. PMID:33602817
WDR5 facilitates EMT and metastasis of CCA by increasing HIF-1α accumulation in Myc-dependent and independent pathways. PMID:33601056
Differentiation of two human neuroblastoma cell lines alters SV2 expression patterns. PMID:33588752
The CLAIRE COVID-19 initiative: approach, experiences and recommendations. PMID:33584129
Systematic characterization of mutations altering protein degradation in human cancers. PMID:33567269
RNA Sequencing Reveals Distinct Immune Responses in the Chorioamniotic Membranes of Women with Preterm Labor and Microbial or Sterile Intra-amniotic Inflammation. PMID:33558326
Bioinformatics analyses of significant genes, related pathways, and candidate diagnostic biomarkers and molecular targets in SARS-CoV-2/COVID-19. PMID:33553808
BioMaster: An Integrated Database and Analytic Platform to Provide Comprehensive Information About BioBrick Parts. PMID:33552037
Protein-protein interaction analysis reveals a novel cancer stem cell related target TMEM17 in colorectal cancer. PMID:33549114
Degree Adjusted Large-Scale Network Analysis Reveals Novel Putative Metabolic Disease Genes. PMID:33546175
Convergent organization of aberrant MYB complex controls oncogenic gene expression in acute myeloid leukemia. PMID:33527899
Human pathways in animal models: possibilities and limitations. PMID:33524155
The translocon-associated protein (TRAP) complex regulates quality control of N-linked glycosylation during ER stress. PMID:33523898
Structural similarity-based prediction of host factors associated with SARS-CoV-2 infection and pathogenesis. PMID:33506741
Intestinal mRNA expression profile and bioinformatics analysis in a methamphetamine-induced mouse model of inflammatory bowel disease. PMID:33490181
NLPEI: A Novel Self-Interacting Protein Prediction Model Based on Natural Language Processing and Evolutionary Information. PMID:33488064
Ontological modeling and analysis of experimentally or clinically verified drugs against coronavirus infection. PMID:33441564
Application of graphical lasso in estimating network structure in gene set. PMID:33437755
Combined RNA/tissue profiling identifies novel Cancer/testis genes. PMID:33426787
An Integrative Computational Approach for the Prediction of Human-Plasmodium Protein-Protein Interactions. PMID:33426052
Model systems for studying polyphosphate biology: a focus on microorganisms. PMID:33420907
Identification and Characterization of Plant-Interacting Targets of Tomato Spotted Wilt Virus Silencing Suppressor. PMID:33401462
Distinct p63 and p73 Protein Interactions Predict Specific Functions in mRNA Splicing and Polyploidy Control in Epithelia. PMID:33375680
Metric Labeling and Semimetric Embedding for Protein Annotation Prediction. PMID:33370163
PICKLE 3.0: Enriching the human Meta-database with the mouse protein interactome extended via mouse-human orthology. PMID:33367505
Dosage-sensitive molecular mechanisms are associated with the tissue-specificity of traits and diseases. PMID:33363699
Multi-resolution visualization and analysis of biomolecular networks through hierarchical community detection and web-based graphical tools. PMID:33351828
Mouse Embryonic Fibroblast Adipogenic Potential: A Comprehensive Transcriptome Analysis. PMID:33345692
SECAT: Quantifying Protein Complex Dynamics across Cell States by Network-Centric Analysis of SEC-SWATH-MS Profiles. PMID:33333029
TMEM132A, a Novel Wnt Signaling Pathway Regulator Through Wntless (WLS) Interaction. PMID:33324648
Differential Co-Expression Analyses Allow the Identification of Critical Signalling Pathways Altered during Tumour Transformation and Progression. PMID:33322692
Protein Interaction Network Biology in Neuroscience. PMID:33314619
Suboptimal Global Transcriptional Response Increases the Harmful Effects of Loss-of-Function Mutations. PMID:33306797
Applications and advancements of FT-ICR-MS for interactome studies. PMID:33289940
Active Learning for Node Classification: An Evaluation. PMID:33286933
A Novel Proximity Biotinylation Assay Based on the Self-Associating Split GFP1-10/11. PMID:33276494
CovMulNet19, Integrating Proteins, Diseases, Drugs, and Symptoms: A Network Medicine Approach to COVID-19. PMID:33274348
Filamin A Orchestrates Cytoskeletal Structure, Cell Migration and Stem Cell Characteristics in Human Seminoma TCam-2 Cells. PMID:33266100
Drug2ways: Reasoning over causal paths in biological networks for drug discovery. PMID:33264280
Towards a unified open access dataset of molecular interactions. PMID:33262342
A ligand-based computational drug repurposing pipeline using KNIME and Programmatic Data Access: case studies for rare diseases and COVID-19. PMID:33250934
TRP Channels Regulation of Rho GTPases in Brain Context and Diseases. PMID:33240883
A thorough analysis of the contribution of experimental, derived and sequence-based predicted protein-protein interactions for functional annotation of proteins. PMID:33237964
The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets. PMID:33237311
PINA 3.0: mining cancer interactome. PMID:33231689
Inferring the molecular and phenotypic impact of amino acid variants with MutPred2. PMID:33219223
Predicted rat interactome database and gene set linkage analysis. PMID:33216897
Emerging Evidences for an Implication of the Neurodegeneration-Associated Protein TAU in Cancer. PMID:33207722
The IMEx coronavirus interactome: an evolving map of Coronaviridae-host molecular interactions. PMID:33206959
In silico and in vitro studies reveal complement system drives coagulation cascade in SARS-CoV-2 pathogenesis. PMID:33200027
DPPN-SVM: Computational Identification of Mis-Localized Proteins in Cancers by Integrating Differential Gene Expressions With Dynamic Protein-Protein Interaction Networks. PMID:33193746
Virtual screening and network pharmacology-based synergistic mechanism identification of multiple components contained in Guanxin V against coronary artery disease. PMID:33187508
YQFC: a web tool to compare quantitative biological features between two yeast gene lists. PMID:33186464
A ubiquitin ligase mediates target-directed microRNA decay independently of tailing and trimming. PMID:33184234
LL-37-Induced Autophagy Contributed to the Elimination of Live Porphyromonas gingivalis Internalized in Keratinocytes. PMID:33178622
Amyotrophic Lateral Sclerosis Is Accompanied by Protein Derangements in the Olfactory Bulb-Tract Axis. PMID:33167591
A network medicine approach to investigation and population-based validation of disease manifestations and drug repurposing for COVID-19. PMID:33156843
Human Gene Functional Network-Informed Prediction of HIV-1 Host Dependency Factors. PMID:33144314
ACE2 Netlas: In-silico functional characterization and drug-gene interactions of ACE2 gene network to understand its potential involvement in COVID-19 susceptibility. PMID:33140059
BIKE regulates dengue virus infection and is a cellular target for broad-spectrum antivirals. PMID:33137362
iCSDB: an integrated database of CRISPR screens. PMID:33137185
Synthetic Lethality through the Lens of Medicinal Chemistry. PMID:33135887
TCONS_00012883 promotes proliferation and metastasis via DDX3/YY1/MMP1/PI3K-AKT axis in colorectal cancer. PMID:33135346
IHP-PING-generating integrated human protein-protein interaction networks on-the-fly. PMID:33129201
Plasma Proteomics Identify Biomarkers and Pathogenesis of COVID-19. PMID:33128875
FFAT motif phosphorylation controls formation and lipid transfer function of inter-organelle contacts. PMID:33124732
Designing a Network Proximity-Based Drug Repurposing Strategy for COVID-19. PMID:33123533
In silico Method in CRISPR/Cas System: An Expedite and Powerful Booster. PMID:33123486
Virus-Host Protein-Protein Interactions between Human Papillomavirus 16 E6 A1 and D2/D3 Sub-Lineages: Variances and Similarities. PMID:33121134
Comprehensive Evaluation of Endocytosis-Associated Protein SCAMP3 in Hepatocellular Carcinoma. PMID:33116758
Roles of Farnesyl-Diphosphate Farnesyltransferase 1 in Tumour and Tumour Microenvironments. PMID:33113804
FlyRNAi.org-the database of the Drosophila RNAi screening center and transgenic RNAi project: 2021 update. PMID:33104800
Evolution of Sequence-based Bioinformatics Tools for Protein-protein Interaction Prediction. PMID:33093807
Assessing the Direct Binding of Ark-Like E3 RING Ligases to Ubiquitin and Its Implication on Their Protein Interaction Network. PMID:33086510
Predicted functional interactome of Caenorhabditis elegans and a web tool for the functional interpretation of differentially expressed genes. PMID:33076954
The BioGRID database: A comprehensive biomedical resource of curated protein, genetic, and chemical interactions. PMID:33070389
Comparative Toxicogenomics Database (CTD): update 2021. PMID:33068428
A review of protein-protein interaction network alignment: From pathway comparison to global alignment. PMID:33033584
Serpin peptidase inhibitor clade A member 1-overexpression in gastric cancer promotes tumor progression in vitro and is associated with poor prognosis. PMID:33014156
Pseudo2GO: A Graph-Based Deep Learning Method for Pseudogene Function Prediction by Borrowing Information From Coding Genes. PMID:33014009
CRISP-view: a database of functional genetic screens spanning multiple phenotypes. PMID:33010154
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
Robust edge-based biomarker discovery improves prediction of breast cancer metastasis. PMID:32998692
PML Regulates the Epidermal Differentiation Complex and Skin Morphogenesis during Mouse Embryogenesis. PMID:32992884
DIGGER: exploring the functional role of alternative splicing in protein interactions. PMID:32976589
The effect of hybridization on transposable element accumulation in an undomesticated fungal species. PMID:32955438
Benchmarking orthology methods using phylogenetic patterns defined at the base of Eukaryotes. PMID:32935832
Potential impact on coagulopathy of gene variants of coagulation related proteins that interact with SARS-CoV-2. PMID:32935103
Comparative host-pathogen protein-protein interaction analysis of recent coronavirus outbreaks and important host targets identification. PMID:32914167
Comprehensive host-pathogen protein-protein interaction network analysis. PMID:32912135
A functionally defined high-density NRF2 interactome reveals new conditional regulators of ARE transactivation. PMID:32911434
Transcription Factors That Regulate the Pathogenesis of Ulcerative Colitis. PMID:32908909
Targeting TRIM37-driven centrosome dysfunction in 17q23-amplified breast cancer. PMID:32908313
GAB2 and GAB3 are expressed in a tumor stage-, grade- and histotype-dependent manner and are associated with shorter progression-free survival in ovarian cancer. PMID:32888136
RNA-binding and prion domains: the Yin and Yang of phase separation. PMID:32857852
Analysis of APPL1 Gene Polymorphisms in Patients with a Phenotype of Maturity Onset Diabetes of the Young. PMID:32854233
Determining the interaction status and evolutionary fate of duplicated homomeric proteins. PMID:32853212
Systems Biology Approaches to Understanding the Human Immune System. PMID:32849587
RNA-protein interaction mapping via MS2- or Cas13-based APEX targeting. PMID:32839320
SARS-CoV-2-human protein-protein interaction network. PMID:32838020
A Human IgSF Cell-Surface Interactome Reveals a Complex Network of Protein-Protein Interactions. PMID:32822567
Analytical Guidelines for co-fractionation Mass Spectrometry Obtained through Global Profiling of Gold Standard Saccharomyces cerevisiae Protein Complexes. PMID:32817346
NPF:network propagation for protein function prediction. PMID:32787776
Transcriptomic analysis delineates potential signature genes and miRNAs associated with the pathogenesis of asthma. PMID:32770056
FLUTE: Fast and reliable knowledge retrieval from biomedical literature. PMID:32761077
NuRD subunit CHD4 regulates super-enhancer accessibility in rhabdomyosarcoma and represents a general tumor dependency. PMID:32744500
FEN1 endonuclease as a therapeutic target for human cancers with defects in homologous recombination. PMID:32719125
Piggybacking on Classical Import and Other Non-Classical Mechanisms of Nuclear Import Appear Highly Prevalent within the Human Proteome. PMID:32718019
Genetic and environmental determinants of variation in the plasma lipidome of older Australian twins. PMID:32697195
Analyzing IDPs in Interactomes. PMID:32696395
Robustness of plant quantitative disease resistance is provided by a decentralized immune network. PMID:32669441
Seedling Chloroplast Responses Induced by N-Linolenoylethanolamine Require Intact G-Protein Complexes. PMID:32665332
Structural biology of DNA abasic site protection by SRAP proteins. PMID:32663791
Leveraging the Comparative Toxicogenomics Database to Fill in Knowledge Gaps for Environmental Health: A Test Case for Air Pollution-induced Cardiovascular Disease. PMID:32663284
Interaction mapping of endoplasmic reticulum ubiquitin ligases identifies modulators of innate immune signalling. PMID:32614325
Seq-ing answers: Current data integration approaches to uncover mechanisms of transcriptional regulation. PMID:32612756
Association study based on topological constraints of protein-protein interaction networks. PMID:32612246
Extensive signal integration by the phytohormone protein network. PMID:32612234
Genome-wide investigation of gene-cancer associations for the prediction of novel therapeutic targets in oncology. PMID:32612205
Selective Neuronal Vulnerability in Alzheimer's Disease: A Network-Based Analysis. PMID:32603655
Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses. PMID:32597660
Exploring whole-genome duplicate gene retention with complex genetic interaction analysis. PMID:32586993
Role of Anillin in Tumour: From a Prognostic Biomarker to a Novel Target. PMID:32560530
Genome-wide CRISPR synthetic lethality screen identifies a role for the ADP-ribosyltransferase PARP14 in DNA replication dynamics controlled by ATR. PMID:32542389
A novel landscape of nuclear human CDK2 substrates revealed by in situ phosphorylation. PMID:32494624
Identification and characterization of male reproduction-related genes in pig (Sus scrofa) using transcriptome analysis. PMID:32487021
Protein Network Studies on PCOS Biomarkers With S100A8, Druggability Assessment, and RNA Aptamer Designing to Control Its Cyst Migration Effect. PMID:32478041
dbPSP 2.0, an updated database of protein phosphorylation sites in prokaryotes. PMID:32472030
A Bayesian data fusion based approach for learning genome-wide transcriptional regulatory networks. PMID:32471360
piNET: a versatile web platform for downstream analysis and visualization of proteomics data. PMID:32469073
Pleiotropic Roles of Calmodulin in the Regulation of KRas and Rac1 GTPases: Functional Diversity in Health and Disease. PMID:32456244
Genome-Wide Analysis of the GRAS Gene Family in Barley (Hordeum vulgare L.). PMID:32423019
Mutation severity spectrum of rare alleles in the human genome is predictive of disease type. PMID:32413045
The multifaceted nature of αB-crystallin. PMID:32383140
Targeting ERK-Hippo Interplay in Cancer Therapy. PMID:32375238
Community curation in PomBase: enabling fission yeast experts to provide detailed, standardized, sharable annotation from research publications. PMID:32353878
Hepatitis B Virus Core Particles Containing a Conserved Region of the G Protein Combined with Interleukin-35 Protected Mice against Respiratory Syncytial Virus Infection without Vaccine-Enhanced Immunopathology. PMID:32321805
Fold-Change-Specific Enrichment Analysis (FSEA): Quantification of Transcriptional Response Magnitude for Functional Gene Groups. PMID:32316383
Structured reviews for data and knowledge-driven research. PMID:32283553
Bioinformatics Analysis for Multiple Gene Expression Profiles in Sepsis. PMID:32280132
Essential gene prediction in Drosophila melanogaster using machine learning approaches based on sequence and functional features. PMID:32257045
Sex-specific and shared expression profiles of vulnerability and resilience to trauma in brain and blood. PMID:32228684
Absence of Nuclear p16 Is a Diagnostic and Independent Prognostic Biomarker in Squamous Cell Carcinoma of the Cervix. PMID:32204550
Multi-level and lineage-specific interactomes of the Hox transcription factor Ubx contribute to its functional specificity. PMID:32170121
A widespread family of heat-resistant obscure (Hero) proteins protect against protein instability and aggregation. PMID:32163402
Genetic and Chemical-Genetic Interactions Map Biogenesis and Permeability Determinants of the Outer Membrane of Escherichia coli. PMID:32156814
Transcript profiling reveals potential regulators for oxidative stress response of a necrotrophic chickpea pathogen Ascochyta rabiei. PMID:32117678
RhoBTB Proteins Regulate the Hippo Pathway by Antagonizing Ubiquitination of LKB1. PMID:32111652
Genetic Modifiers and Rare Mendelian Disease. PMID:32106447
Predicted Drosophila Interactome Resource and web tool for functional interpretation of differentially expressed genes. PMID:32103267
Data libraries - the missing element for modeling biological systems. PMID:32100391
Diverse and dynamic roles of F-box proteins in plant biology. PMID:32072251
Overcoming cisplatin resistance by targeting the MTDH-PTEN interaction in ovarian cancer with sera derived from rats exposed to Guizhi Fuling wan extract. PMID:32066429
Exploration of databases and methods supporting drug repurposing: a comprehensive survey. PMID:32055842
Alpha-Synuclein Physiology and Pathology: A Perspective on Cellular Structures and Organelles. PMID:32038126
In Silico Strategies in Tuberculosis Drug Discovery. PMID:32033144
Genome-wide identification of cold responsive transcription factors in Brassica napus L. PMID:32028890
Unraveling the role of salt-sensitivity genes in obesity with integrated network biology and co-expression analysis. PMID:32027667
PIPE4: Fast PPI Predictor for Comprehensive Inter- and Cross-Species Interactomes. PMID:31996697
Open Data for Differential Network Analysis in Glioma. PMID:31952211
Domain-mediated interactions for protein subfamily identification. PMID:31937869
Structure of the BRK domain of the SWI/SNF chromatin remodeling complex subunit BRG1 reveals a potential role in protein-protein interactions. PMID:31909846
Familial globular glial tauopathy linked to MAPT mutations: molecular neuropathology and seeding capacity of a prototypical mixed neuronal and glial tauopathy. PMID:31907603
Peroxiredoxin-1 regulates lipid peroxidation in corneal endothelial cells. PMID:31901729
AMPK Interactome Reveals New Function in Non-homologous End Joining DNA Repair. PMID:31900314
Transcription factor regulatory modules provide the molecular mechanisms for functional redundancy observed among transcription factors in yeast. PMID:31881824
Analysis of Differentially Expressed Genes in Coronary Artery Disease by Integrated Microarray Analysis. PMID:31881747
MASS SPECTROMETRY IN VIROLOGICAL SCIENCES. PMID:31876329
The Emerging Role of Cytidine Deaminase in Human Diseases: A New Opportunity for Therapy? PMID:31870623
Robust cullin-RING ligase function is established by a multiplicity of poly-ubiquitylation pathways. PMID:31868589
Common Neurodegeneration-Associated Proteins Are Physiologically Expressed by Human B Lymphocytes and Are Interconnected via the Inflammation/Autophagy-Related Proteins TRAF6 and SQSTM1. PMID:31824497
Transcriptome Meta-Analysis Deciphers a Dysregulation in Immune Response-Associated Gene Signatures during Sepsis. PMID:31817302
Human SNORA31 variations impair cortical neuron-intrinsic immunity to HSV-1 and underlie herpes simplex encephalitis. PMID:31806906
Sequence-Derived Markers of Drug Targets and Potentially Druggable Human Proteins. PMID:31803227
The Alliance of Genome Resources: Building a Modern Data Ecosystem for Model Organism Databases. PMID:31796553
TGFB1-Mediated Gliosis in Multiple Sclerosis Spinal Cords Is Favored by the Regionalized Expression of HOXA5 and the Age-Dependent Decline in Androgen Receptor Ligands. PMID:31779094
A single ChIP-seq dataset is sufficient for comprehensive analysis of motifs co-occurrence with MCOT package. PMID:31750523
Sudden unexpected death in asymptomatic infants due to PPA2 variants. PMID:31705601
The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species. PMID:31701156
AppleMDO: A Multi-Dimensional Omics Database for Apple Co-Expression Networks and Chromatin States. PMID:31695717
Therapeutic target database 2020: enriched resource for facilitating research and early development of targeted therapeutics. PMID:31691823
SIGNOR 2.0, the SIGnaling Network Open Resource 2.0: 2019 update. PMID:31665520
DNA Replication Inhibitor Geminin and Retinoic Acid Signaling Participate in Complex Interactions Associated With Pluripotency. PMID:31659113
Bovine Genome Database: new annotation tools for a new reference genome. PMID:31647100
Integrated bioinformatics analysis reveals role of the LINC01093/miR-96-5p/ZFAND5/NF-κB signaling axis in hepatocellular carcinoma. PMID:31641376
Biological Network Approaches and Applications in Rare Disease Studies. PMID:31614842
VarSite: Disease variants and protein structure. PMID:31606900
Alliance of Genome Resources Portal: unified model organism research platform. PMID:31552413
Computer aided analysis of disease linked protein networks. PMID:31485137
Protein-Protein Interactions in Candida albicans. PMID:31440220
Network dynamics of the yeast methyltransferome. PMID:31403050
Hallmarks of ribosomopathies. PMID:31350888
Identification of important invasion and proliferation related genes in adrenocortical carcinoma. PMID:31321566
Ultra-soft X-ray system for imaging the early cellular responses to X-ray induced DNA damage. PMID:31318974
Comprehensive in vivo identification of the c-Myc mRNA protein interactome using HyPR-MS. PMID:31296583
Proteomics Approaches for Biomarker and Drug Target Discovery in ALS and FTD. PMID:31244593
Gene Information eXtension (GIX): effortless retrieval of gene product information on any website. PMID:31217594
A Robust Approach for Identification of Cancer Biomarkers and Candidate Drugs. PMID:31212673
To Embed or Not: Network Embedding as a Paradigm in Computational Biology. PMID:31118945
ResponseNet v.3: revealing signaling and regulatory pathways connecting your proteins and genes across human tissues. PMID:31114913
Cell contact and Nf2/Merlin-dependent regulation of TEAD palmitoylation and activity. PMID:31043565
Mining Featured Biomarkers Linked with Epithelial Ovarian CancerBased on Bioinformatics. PMID:30970615
The BioGRID interaction database: 2017 update PubMed citations: 428.

428 articles citing: The BioGRID interaction database: 2017 update

Integration of probabilistic functional networks without an external Gold Standard. PMID:35879662
Protocol for establishing a protein-protein interaction network using tandem affinity purification followed by mass spectrometry in mammalian cells. PMID:35874475
NTD-DR: Nonnegative tensor decomposition for drug repositioning. PMID:35862409
TritiKBdb: A Functional Annotation Resource for Deciphering the Complete Interaction Networks in Wheat-Karnal Bunt Pathosystem. PMID:35806459
Deciphering the Crosstalk Mechanisms of Wheat-Stem Rust Pathosystem: Genome-Scale Prediction Unravels Novel Host Targets. PMID:35800602
Identifying Candidate Flavonoids for Non-Alcoholic Fatty Liver Disease by Network-Based Strategy. PMID:35721123
WeCoNET: a host-pathogen interactome database for deciphering crucial molecular networks of wheat-common bunt cross-talk mechanisms. PMID:35658913
Analysis of the lncRNA-Associated Competing Endogenous RNA (ceRNA) Network for Tendinopathy. PMID:35645614
Driver gene detection through Bayesian network integration of mutation and expression profiles. PMID:35561191
Bioinformatics-Based Approaches to Study Virus-Host Interactions During SARS-CoV-2 Infection. PMID:35554909
Degron masking outlines degronons, co-degrading functional modules in the proteome. PMID:35545699
Prioritization of Candidate Biomarkers for Degenerative Aortic Stenosis through a Systems Biology-Based In-Silico Approach. PMID:35455758
A Boolean Model of the Proliferative Role of the lncRNA XIST in Non-Small Cell Lung Cancer Cells. PMID:35453680
Second-Generation JK-206 Targets the Oncogenic Signal Mediator RHOA in Gastric Cancer. PMID:35406376
Dynamical modeling of miR-34a, miR-449a, and miR-16 reveals numerous DDR signaling pathways regulating senescence, autophagy, and apoptosis in HeLa cells. PMID:35318393
Eucalyptus grandis AUX/INDOLE-3-ACETIC ACID 13 (EgrIAA13) is a novel transcriptional regulator of xylogenesis. PMID:35292886
Intrinsically disordered signaling proteins: Essential hub players in the control of stress responses in Saccharomyces cerevisiae. PMID:35290420
Deciphering the Host-Pathogen Interactome of the Wheat-Common Bunt System: A Step towards Enhanced Resilience in Next Generation Wheat. PMID:35269732
Computational Systems Biology of Alfalfa - Bacterial Blight Host-Pathogen Interactions: Uncovering the Complex Molecular Networks for Developing Durable Disease Resistant Crop. PMID:35251063
Characterization of the pVHL Interactome in Human Testis Using High-Throughput Library Screening. PMID:35205757
Exploration of the Potential Transcriptional Regulatory Mechanisms of DNA Methyltransferases and MBD Genes in Petunia Anther Development and Multi-Stress Responses. PMID:35205359
Network Pharmacology Integrated Molecular Docking Revealed the Mechanism of Jianpi Yiqi Taohua Decoction Against Ulcerative Colitis. PMID:35173140
UbE3-APA: A Bioinformatic Strategy to Elucidate Ubiquitin E3 Ligase Activities in Quantitative Proteomics Study. PMID:35139152
XSSJS inhibits hepatic fibrosis by promoting the miR-29b-3p/VEGFA axis in vitro and in vivo. PMID:35118493
Thalidomide Exerts Anti-Inflammatory Effects in Cutaneous Lupus by Inhibiting the IRF4/NF-ҡB and AMPK1/mTOR Pathways. PMID:34944673
Subnetwork representation learning for discovering network biomarkers in predicting lymph node metastasis in early oral cancer. PMID:34907266
Relation Extraction of Protein Complexes from Dynamic Protein-Protein Interaction Network. PMID:34904064
Altered H3 histone acetylation impairs high-fidelity DNA repair to promote cerebellar degeneration in spinocerebellar ataxia type 7. PMID:34852229
Interactome analysis illustrates diverse gene regulatory processes associated with LIN28A in human iPS cell-derived neural progenitor cells. PMID:34816099
A Network-Based Methodology to Identify Subnetwork Markers for Diagnosis and Prognosis of Colorectal Cancer. PMID:34790220
FusionGDB 2.0: fusion gene annotation updates aided by deep learning. PMID:34755868
Co-evolution based machine-learning for predicting functional interactions between human genes. PMID:34753957
Therapeutic inhibition of GAS6-AS1/YBX1/MYC axis suppresses cell propagation and disease progression of acute myeloid leukemia. PMID:34753494
Network-driven analysis of human-Plasmodium falciparum interactome: processes for malaria drug discovery and extracting in silico targets. PMID:34702263
GreeningDB: A Database of Host-Pathogen Protein-Protein Interactions and Annotation Features of the Bacteria Causing Huanglongbing HLB Disease. PMID:34639237
Getting to know each other: PPIMem, a novel approach for predicting transmembrane protein-protein complexes. PMID:34630938
Differentiable biology: using deep learning for biophysics-based and data-driven modeling of molecular mechanisms. PMID:34608321
Interpretation of cancer mutations using a multiscale map of protein systems. PMID:34591613
Prioritizing de novo autism risk variants with calibrated gene- and variant-scoring models. PMID:34549350
Using informative features in machine learning based method for COVID-19 drug repurposing. PMID:34544500
A Novel Network-Based Algorithm for Predicting Protein-Protein Interactions Using Gene Ontology. PMID:34512614
Identification of Immune-Related Genes in Sepsis due to Community-Acquired Pneumonia. PMID:34484417
Full-length isoform transcriptome of the developing human brain provides further insights into autism. PMID:34469739
PPIDomainMiner: Inferring domain-domain interactions from multiple sources of protein-protein interactions. PMID:34370723
alfaNET: A Database of Alfalfa-Bacterial Stem Blight Protein-Protein Interactions Revealing the Molecular Features of the Disease-causing Bacteria. PMID:34361108
Transcriptional landscape of cellular networks reveal interactions driving the dormancy mechanisms in cancer. PMID:34349126
Topological network based drug repurposing for coronavirus 2019. PMID:34324563
Identification of covalent modifications regulating immune signaling complex composition and phenotype. PMID:34318608
Computational Phosphorylation Network Reconstruction: An Update on Methods and Resources. PMID:34270057
Utilizing image and caption information for biomedical document classification. PMID:34252939
A global overview of genetically interpretable multimorbidities among common diseases in the UK Biobank. PMID:34225788
Global identification of phospho-dependent SCF substrates reveals a FBXO22 phosphodegron and an ERK-FBXO22-BAG3 axis in tumorigenesis. PMID:34215846
EvoProDom: evolutionary modeling of protein families by assessing translocations of protein domains. PMID:34196123
PRISMA and BioID disclose a motifs-based interactome of the intrinsically disordered transcription factor C/EBPα. PMID:34189442
FINER: enhancing the prediction of tissue-specific functions of isoforms by refining isoform interaction networks. PMID:34169280
The dual role of SrbA from Paracoccidioides lutzii: a hypoxic regulator. PMID:34148216
DGLinker: flexible knowledge-graph prediction of disease-gene associations. PMID:34125897
A proximity-dependent biotinylation map of a human cell. PMID:34079125
Human Immunodeficiency Virus Type 1 Vpr Mediates Degradation of APC1, a Scaffolding Component of the Anaphase-Promoting Complex/Cyclosome. PMID:34011540
Analysis of Zika virus capsid-Aedes aegypti mosquito interactome reveals pro-viral host factors critical for establishing infection. PMID:33986255
Deep learning integration of molecular and interactome data for protein-compound interaction prediction. PMID:33933121
A SARS-CoV-2 (COVID-19) biological network to find targets for drug repurposing. PMID:33931664
In silico comparative analysis of LRRK2 interactomes from brain, kidney and lung. PMID:33915162
Pathogenic missense protein variants affect different functional pathways and proteomic features than healthy population variants. PMID:33909605
Knockdown of PNO1 inhibits esophageal cancer progression. PMID:33864661
Imputation of spatially-resolved transcriptomes by graph-regularized tensor completion. PMID:33826608
Quantifying evolutionary importance of protein sites: A Tale of two measures. PMID:33826605
Atg9-centered multi-omics integration reveals new autophagy regulators in Saccharomyces cerevisiae. PMID:33722159
Identification of potential and novel target genes in pituitary prolactinoma by bioinformatics analysis. PMID:33709028
Differential Interactome Proposes Subtype-Specific Biomarkers and Potential Therapeutics in Renal Cell Carcinomas. PMID:33672271
Overexpression of miR-1306-5p, miR-3195, and miR-3914 Inhibits Ameloblast Differentiation through Suppression of Genes Associated with Human Amelogenesis Imperfecta. PMID:33672174
Identifying critical protein-coding genes and long non-coding RNAs in non-functioning pituitary adenoma recurrence. PMID:33664827
Proximity-dependent Mapping of the Androgen Receptor Identifies Kruppel-like Factor 4 as a Functional Partner. PMID:33640491
Genome-wide meta-analysis, fine-mapping and integrative prioritization implicate new Alzheimer's disease risk genes. PMID:33589840
Single-Cell Analysis Reveals Characterization of Infiltrating T Cells in Moderately Differentiated Colorectal Cancer. PMID:33584715
UniProt-Related Documents (UniReD): assisting wet lab biologists in their quest on finding novel counterparts in a protein network. PMID:33575553
Pan-Cancer analysis of the expression and regulation of matrisome genes across 32 tumor types. PMID:33543003
Xia-Gibbs Syndrome: A Review of Literature. PMID:33520547
Data-driven biological network alignment that uses topological, sequence, and functional information. PMID:33514304
Causal network inference from gene transcriptional time-series response to glucocorticoids. PMID:33513136
NLPEI: A Novel Self-Interacting Protein Prediction Model Based on Natural Language Processing and Evolutionary Information. PMID:33488064
DeORFanizing Candida albicans Genes using Coexpression. PMID:33472984
Transcutaneous Electrical Acupoint Stimulation in Early Life Changes Synaptic Plasticity and Improves Symptoms in a Valproic Acid-Induced Rat Model of Autism. PMID:33456456
Internetwork connectivity of molecular networks across species of life. PMID:33441907
Large-scale survey and database of high affinity ligands for peptide recognition modules. PMID:33438817
A computational framework for identifying the transcription factors involved in enhancer-promoter loop formation. PMID:33425492
Alteration in Gene Pair Correlations in Tryptophan Metabolism as a Hallmark in Cancer Diagnosis. PMID:33354111
Scanning Protein Surfaces with DNA-Encoded Libraries. PMID:33295694
Network analysis reveals essential proteins that regulate sodium-iodide symporter expression in anaplastic thyroid carcinoma. PMID:33293661
SARS-CoV-2 receptor ACE2 is co-expressed with genes related to transmembrane serine proteases, viral entry, immunity and cellular stress. PMID:33293627
Frequent Assembly of Chimeric Complexes in the Protein Interaction Network of an Interspecies Yeast Hybrid. PMID:33252673
COVID-19 research risks ignoring important host genes due to pre-established research patterns. PMID:33231169
ATP13A2-mediated endo-lysosomal polyamine export counters mitochondrial oxidative stress. PMID:33229544
TREM2 Alzheimer's variant R47H causes similar transcriptional dysregulation to knockout, yet only subtle functional phenotypes in human iPSC-derived macrophages. PMID:33198789
A compound downregulation of SRRM2 and miR-27a-3p with upregulation of miR-27b-3p in PBMCs of Parkinson's patients is associated with the early stage onset of disease. PMID:33171483
Triage of documents containing protein interactions affected by mutations using an NLP based machine learning approach. PMID:33167858
Evolution of Sequence-based Bioinformatics Tools for Protein-protein Interaction Prediction. PMID:33093807
PyGNA: a unified framework for geneset network analysis. PMID:33092528
A method for estimating coherence of molecular mechanisms in major human disease and traits. PMID:33087046
The effect of statistical normalization on network propagation scores. PMID:33070187
A practical guide to mechanistic systems modeling in biology using a logic-based approach. PMID:33064138
Protein interactome mapping in Caenorhabditis elegans. PMID:32984658
Design principles of gene evolution for niche adaptation through changes in protein-protein interaction networks. PMID:32973219
Regulation of neuronal commitment in mouse embryonic stem cells by the Reno1/Bahcc1 locus. PMID:32969152
NAUTICA: classifying transcription factor interactions by positional and protein-protein interaction information. PMID:32938476
IER5, a DNA damage response gene, is required for Notch-mediated induction of squamous cell differentiation. PMID:32936072
Oncoprotein-specific molecular interaction maps (SigMaps) for cancer network analyses. PMID:32929263
Dynamic remodelling of the human host cell proteome and phosphoproteome upon enterovirus infection. PMID:32859902
Sex differences in circulating proteins in heart failure with preserved ejection fraction. PMID:32831121
Mycoplasma hyopneumoniae J elicits an antioxidant response and decreases the expression of ciliary genes in infected swine epithelial cells. PMID:32792522
Network-based modeling of drug effects on disease module in systemic sclerosis. PMID:32770109
Pharmacoproteomics Identifies Kinase Pathways that Drive the Epithelial-Mesenchymal Transition and Drug Resistance in Hepatocellular Carcinoma. PMID:32755597
Co-phosphorylation networks reveal subtype-specific signaling modules in breast cancer. PMID:32730576
Combined Proteomic and Genetic Interaction Mapping Reveals New RAS Effector Pathways and Susceptibilities. PMID:32727735
Stress response in periodontal ligament stem cells may contribute to bisphosphonate‑associated osteonecrosis of the jaw: A gene expression array analysis. PMID:32705175
Araport Lives: An Updated Framework for Arabidopsis Bioinformatics. PMID:32699173
Similarities in biological processes can be used to bridge ecology and molecular biology. PMID:32684962
Advancing computer-aided drug discovery (CADD) by big data and data-driven machine learning modeling. PMID:32663517
Comprehensive nucleosome interactome screen establishes fundamental principles of nucleosome binding. PMID:32658293
Harnessing endophenotypes and network medicine for Alzheimer's drug repurposing. PMID:32656864
Quality Matters: Biocuration Experts on the Impact of Duplication and Other Data Quality Issues in Biological Databases. PMID:32652120
MAP4K Interactome Reveals STRN4 as a Key STRIPAK Complex Component in Hippo Pathway Regulation. PMID:32640226
IPSC-Derived Neuronal Cultures Carrying the Alzheimer's Disease Associated TREM2 R47H Variant Enables the Construction of an Aβ-Induced Gene Regulatory Network. PMID:32630447
Data-driven network alignment. PMID:32614833
Extensive signal integration by the phytohormone protein network. PMID:32612234
2018 Update on Protein-Protein Interaction Data in WormBase. PMID:32550373
Network Medicine Framework for Identifying Drug Repurposing Opportunities for COVID-19. PMID:32550253
Kir2.1 Interactome Mapping Uncovers PKP4 as a Modulator of the Kir2.1-Regulated Inward Rectifier Potassium Currents. PMID:32541000
Dynamic rewiring of the human interactome by interferon signaling. PMID:32539747
A flexible network-based imputing-and-fusing approach towards the identification of cell types from single-cell RNA-seq data. PMID:32527285
Integrated omics in Drosophila uncover a circadian kinome. PMID:32483184
A network of RNA-binding proteins controls translation efficiency to activate anaerobic metabolism. PMID:32472050
Post-translational Modification Crosstalk and Hotspots in Sirtuin Interactors Implicated in Cardiovascular Diseases. PMID:32425973
Neural networks for open and closed Literature-based Discovery. PMID:32413059
Ellagic acid and human cancers: a systems pharmacology and docking study to identify principal hub genes and main mechanisms of action. PMID:32410114
Single-cell transcriptional networks in differentiating preadipocytes suggest drivers associated with tissue heterogeneity. PMID:32355218
Genotype-phenotype correlations of Berardinelli-Seip congenital lipodystrophy and novel candidate genes prediction. PMID:32349771
ppiGReMLIN: a graph mining based detection of conserved structural arrangements in protein-protein interfaces. PMID:32293241
A multidimensional systems biology analysis of cellular senescence in aging and disease. PMID:32264951
EpiMOLAS: an intuitive web-based framework for genome-wide DNA methylation analysis. PMID:32241255
Transcriptomic analysis of marine endophytic fungi extract identifies highly enriched anti-fungal fractions targeting cancer pathways in HepG2 cell lines. PMID:32228434
Understanding of Zaire ebolavirus-human protein interaction for drug repurposing. PMID:32206696
Human-Specific Transcriptome of Ventral and Dorsal Midbrain Dopamine Neurons. PMID:32167609
A Genome-wide ER-phagy Screen Highlights Key Roles of Mitochondrial Metabolism and ER-Resident UFMylation. PMID:32160526
Meta-analysis of human prefrontal cortex reveals activation of GFAP and decline of synaptic transmission in the aging brain. PMID:32138778
Pan-cancer mapping of differential protein-protein interactions. PMID:32094374
Similarity of therapeutic networks induced by a multi-component herbal remedy, Ukgansan, in neurovascular unit cells. PMID:32060346
Integrative data modeling from lung and lymphatic cancer predicts functional roles for miR-34a and miR-16 in cell fate regulation. PMID:32054948
In-silico simulated prototype-patients using TPMS technology to study a potential adverse effect of sacubitril and valsartan. PMID:32053711
Using the Gibbs Function as a Measure of Human Brain Development Trends from Fetal Stage to Advanced Age. PMID:32046179
Hierarchical cooperation of transcription factors from integration analysis of DNA sequences, ChIP-Seq and ChIA-PET data. PMID:32039697
Quantifying Gene Essentiality Based on the Context of Cellular Components. PMID:32038710
Kinobead/LC-MS Phosphokinome Profiling Enables Rapid Analyses of Kinase-Dependent Cell Signaling Networks. PMID:32037842
PlaPPISite: a comprehensive resource for plant protein-protein interaction sites. PMID:32028878
Pathway and network analysis of more than 2500 whole cancer genomes. PMID:32024854
ATP13A2 deficiency disrupts lysosomal polyamine export. PMID:31996848
Environmental arginine controls multinuclear giant cell metabolism and formation. PMID:31969567
TMEM98 is a negative regulator of FRAT mediated Wnt/ß-catenin signalling. PMID:31961879
The FGF, TGFβ and WNT axis Modulate Self-renewal of Human SIX2+ Urine Derived Renal Progenitor Cells. PMID:31959818
BCOR-coupled H2A monoubiquitination represses a subset of androgen receptor target genes regulating prostate cancer proliferation. PMID:31925334
Defining the TLT-1 interactome from resting and activated human platelets. PMID:31923473
MELK promotes Endometrial carcinoma progression via activating mTOR signaling pathway. PMID:31915116
Presence and structure-activity relationship of intrinsically disordered regions across mucins. PMID:31908009
Biophysical prediction of protein-peptide interactions and signaling networks using machine learning. PMID:31907444
Genetic variation drives seasonal onset of hibernation in the 13-lined ground squirrel. PMID:31886416
The impact of the genetic background on gene deletion phenotypes in Saccharomyces cerevisiae. PMID:31885205
Identification of self-interacting proteins by integrating random projection classifier and finite impulse response filter. PMID:31881833
LePrimAlign: local entropy-based alignment of PPI networks to predict conserved modules. PMID:31874635
Joint learning improves protein abundance prediction in cancers. PMID:31870366
Predicting synthetic lethal interactions in human cancers using graph regularized self-representative matrix factorization. PMID:31870274
Dissecting the Role of NF-κb Protein Family and Its Regulators in Rheumatoid Arthritis Using Weighted Gene Co-Expression Network. PMID:31824568
PsyMuKB: An Integrative De Novo Variant Knowledge Base for Developmental Disorders. PMID:31809863
Leveraging User-Friendly Network Approaches to Extract Knowledge From High-Throughput Omics Datasets. PMID:31798629
Integrating protein localization with automated signaling pathway reconstruction. PMID:31787091
Systematic prediction of FFAT motifs across eukaryote proteomes identifies nucleolar and eisosome proteins with the predicted capacity to form bridges to the endoplasmic reticulum. PMID:31777772
Validation of a priori candidate Alzheimer's disease SNPs with brain amyloid-beta deposition. PMID:31745181
Global Vectors Representation of Protein Sequences and Its Application for Predicting Self-Interacting Proteins with Multi-Grained Cascade Forest Model. PMID:31726752
In Silico Study of Rett Syndrome Treatment-Related Genes, MECP2, CDKL5, and FOXG1, by Evolutionary Classification and Disordered Region Assessment. PMID:31717404
RPGeNet v2.0: expanding the universe of retinal disease gene interactions network. PMID:31712826
Sustained transgene expression from sleeping beauty DNA transposons containing a core fragment of the HNRPA2B1-CBX3 ubiquitous chromatin opening element (UCOE). PMID:31706316
Therapeutic target database 2020: enriched resource for facilitating research and early development of targeted therapeutics. PMID:31691823
Proteomic Analysis Reveals a Role for RSK in p120-catenin Phosphorylation and Melanoma Cell-Cell Adhesion. PMID:31678930
Co-expression of synaptic genes in the sponge Amphimedon queenslandica uncovers ancient neural submodules. PMID:31673079
FKBP4 connects mTORC2 and PI3K to activate the PDK1/Akt-dependent cell proliferation signaling in breast cancer. PMID:31660083
Uncovering and characterizing splice variants associated with survival in lung cancer patients. PMID:31652257
The RNA-binding ubiquitin ligase MKRN1 functions in ribosome-associated quality control of poly(A) translation. PMID:31640799
Head and Neck Cancers Promote an Inflammatory Transcriptome through Coactivation of Classic and Alternative NF-κB Pathways. PMID:31624067
Extraction of chemical-protein interactions from the literature using neural networks and narrow instance representation. PMID:31622463
MUDENG Expression Profiling in Cohorts and Brain Tumor Biospecimens to Evaluate Its Role in Cancer. PMID:31616474
An Integrated System Biology Approach Yields Drug Repositioning Candidates for the Treatment of Heart Failure. PMID:31608126
pathfindR: An R Package for Comprehensive Identification of Enriched Pathways in Omics Data Through Active Subnetworks. PMID:31608109
Therapeutic Targeting of MZF1-AS1/PARP1/E2F1 Axis Inhibits Proline Synthesis and Neuroblastoma Progression. PMID:31592410
Tissue-specific mouse mRNA isoform networks. PMID:31562339
Paralog dependency indirectly affects the robustness of human cells. PMID:31556487
A perturbed gene network containing PI3K-AKT, RAS-ERK and WNT-β-catenin pathways in leukocytes is linked to ASD genetics and symptom severity. PMID:31551593
Biclustering-based association rule mining approach for predicting cancer-associated protein interactions. PMID:31538957
Machine-learning techniques for the prediction of protein-protein interactions. PMID:31502581
A Survey of Gene Prioritization Tools for Mendelian and Complex Human Diseases. PMID:31494632
Computer aided analysis of disease linked protein networks. PMID:31485137
Benchmarking network propagation methods for disease gene identification. PMID:31479437
Analyzing the regulation of miRNAs on protein-protein interaction network in Hodgkin lymphoma. PMID:31477006
Delineating the role of FANCA in glucose-stimulated insulin secretion in β cells through its protein interactome. PMID:31461451
The role of structural pleiotropy and regulatory evolution in the retention of heteromers of paralogs. PMID:31454312
Protein-Protein Interactions in Candida albicans. PMID:31440220
Large-effect flowering time mutations reveal conditionally adaptive paths through fitness landscapes in Arabidopsis thaliana. PMID:31420516
UNIPred-Web: a web tool for the integration and visualization of biomolecular networks for protein function prediction. PMID:31412768
Novel deep learning model for more accurate prediction of drug-drug interaction effects. PMID:31387547
Prediction of regulatory motifs from human Chip-sequencing data using a deep learning framework. PMID:31372637
Key inflammatory pathway activations in the MCI stage of Alzheimer's disease. PMID:31353852
Network analysis of hyphae forming proteins in Candida albicans identifies important proteins responsible for pathovirulence in the organism. PMID:31338453
Identification of differentially expressed genes in small and non-small cell lung cancer based on meta-analysis of mRNA. PMID:31338439
AraPPINet: An Updated Interactome for the Analysis of Hormone Signaling Crosstalk in Arabidopsis thaliana. PMID:31333706
Identifying potential drug targets in hepatocellular carcinoma based on network analysis and one-class support vector machine. PMID:31320657
Exploring the Molecular Mechanism of the Drug-Treated Breast Cancer Based on Gene Expression Microarray. PMID:31311202
EPIC: software toolkit for elution profile-based inference of protein complexes. PMID:31308550
Patient-specific cancer genes contribute to recurrently perturbed pathways and establish therapeutic vulnerabilities in esophageal adenocarcinoma. PMID:31308377
Ligand Binding Site Structure Shapes Folding, Assembly and Degradation of Homomeric Protein Complexes. PMID:31306664
Global proteomic analyses define an environmentally contingent Hsp90 interactome and reveal chaperone-dependent regulation of stress granule proteins and the R2TP complex in a fungal pathogen. PMID:31283755
Genome-wide functional association networks: background, data & state-of-the-art resources. PMID:31281921
Disease gene prediction for molecularly uncharacterized diseases. PMID:31276496
Cancer driver genes: a guilty by resemblance doctrine. PMID:31275738
Meta-Analysis of Microarray Expression Studies on Metformin in Cancer Cell Lines. PMID:31261735
The chromatin remodeler Chd1 regulates cohesin in budding yeast and humans. PMID:31222142
Characterization of a sandwich ELISA for quantification of total human soluble neuropilin-1. PMID:31219204
Computational identification of protein-protein interactions in model plant proteomes. PMID:31217453
Mediator complex interaction partners organize the transcriptional network that defines neural stem cells. PMID:31209209
DeepPhagy: a deep learning framework for quantitatively measuring autophagy activity in Saccharomyces cerevisiae. PMID:31204567
Knockdown of STIL suppresses the progression of gastric cancer by down-regulating the IGF-1/PI3K/AKT pathway. PMID:31187582
Syndromic Intellectual Disability Caused by a Novel Truncating Variant in AHDC1: A Case Report. PMID:31182893
A Multidimensional Characterization of E3 Ubiquitin Ligase and Substrate Interaction Network. PMID:31181401
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
The Impact of Protein Architecture on Adaptive Evolution. PMID:31147689
CNet: a multi-omics approach to detecting clinically associated, combinatory genomic signatures. PMID:31141125
Identification of Crucial Candidate Genes and Pathways in Glioblastoma Multiform by Bioinformatics Analysis. PMID:31137733
BAG6 deficiency induces mis-distribution of mitochondrial clusters under depolarization. PMID:31125507
Genome-wide DNA methylation profile in the peripheral blood of cocaine and crack dependents. PMID:31116258
Protein Melting Temperature Cannot Fully Assess Whether Protein Folding Free Energy Underlies the Universal Abundance-Evolutionary Rate Correlation Seen in Proteins. PMID:31093676
c-Met as a new marker of cellular senescence. PMID:31085799
Optimized Cross-Linking Mass Spectrometry for in Situ Interaction Proteomics. PMID:31083951
Associating expression and genomic data using co-occurrence measures. PMID:31072345
Plasma protein biomarkers and their association with mutually exclusive cardiovascular phenotypes: the FIBRO-TARGETS case-control analyses. PMID:31062082
Genes with High Network Connectivity Are Enriched for Disease Heritability. PMID:31051114
Human COQ10A and COQ10B are distinct lipid-binding START domain proteins required for coenzyme Q function. PMID:31048406
Identification of DNA methylation patterns predisposing for an efficient response to BCG vaccination in healthy BCG-naïve subjects. PMID:31010371
Understanding Human-Virus Protein-Protein Interactions Using a Human Protein Complex-Based Analysis Framework. PMID:30984872
Identification of Important Invasion-Related Genes in Non-functional Pituitary Adenomas. PMID:30982163
A network of human functional gene interactions from knockout fitness screens in cancer cells. PMID:30979825
ULK1 and ULK2 Regulate Stress Granule Disassembly Through Phosphorylation and Activation of VCP/p97. PMID:30979586
Crystal structure of the SH3 domain of human Lyn non-receptor tyrosine kinase. PMID:30969999
croFGD: Catharanthus roseus Functional Genomics Database. PMID:30967897
Large-scale proteomic analysis of human brain identifies proteins associated with cognitive trajectory in advanced age. PMID:30962425
Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. PMID:30944313
A Network Module for the Perseus Software for Computational Proteomics Facilitates Proteome Interaction Graph Analysis. PMID:30931570
Individual components of the SWI/SNF chromatin remodelling complex have distinct roles in memory neurons of the Drosophila mushroom body. PMID:30923190
Human iPSC-derived MSCs (iMSCs) from aged individuals acquire a rejuvenation signature. PMID:30885246
An Improved Deep Forest Model for Predicting Self-Interacting Proteins From Protein Sequence Using Wavelet Transformation. PMID:30881376
Identification of Important Effector Proteins in the FOXJ1 Transcriptional Network Associated With Ciliogenesis and Ciliary Function. PMID:30881373
The Balancing Act of Intrinsically Disordered Proteins: Enabling Functional Diversity while Minimizing Promiscuity. PMID:30878482
Assessing diversity in multiplex networks. PMID:30872604
Rewired cellular signaling coordinates sugar and hypoxic responses for anaerobic xylose fermentation in yeast. PMID:30856163
Cross-disease analysis of Alzheimer's disease and type-2 Diabetes highlights the role of autophagy in the pathophysiology of two highly comorbid diseases. PMID:30850634
Functional protein representations from biological networks enable diverse cross-species inference. PMID:30847485
Functional Segments on Intrinsically Disordered Regions in Disease-Related Proteins. PMID:30841624
Brain Imaging-Guided Analysis Reveals DNA Methylation Profiles Correlated with Insular Surface Area and Alcohol Use Disorder. PMID:30830696
Systematic analysis reveals the prevalence and principles of bypassable gene essentiality. PMID:30824696
Genome-scale network model of metabolism and histone acetylation reveals metabolic dependencies of histone deacetylase inhibitors. PMID:30823893
YESdb: integrative analysis of environmental stress in yeast. PMID:30821814
Functional geometry of protein interactomes. PMID:30821317
Synergy from gene expression and network mining (SynGeNet) method predicts synergistic drug combinations for diverse melanoma genomic subtypes. PMID:30820351
An integrative systems genetic analysis of mammalian lipid metabolism. PMID:30814737
Distinct isoforms of Nrf1 diversely regulate different subsets of its cognate target genes. PMID:30814566
Protocol Update for large-scale genome and gene function analysis with the PANTHER classification system (v.14.0). PMID:30804569
Cytoplasmic control of Rab family small GTPases through BAG6. PMID:30804014
Somatic mutations in early metazoan genes disrupt regulatory links between unicellular and multicellular genes in cancer. PMID:30803482
Membrane metallo-endopeptidase (Neprilysin) regulates inflammatory response and insulin signaling in white preadipocytes. PMID:30795914
Prediction of Self-Interacting Proteins from Protein Sequence Information Based on Random Projection Model and Fast Fourier Transform. PMID:30795499
Towards a data-integrated cell. PMID:30778056
Analysis of Topological Parameters of Complex Disease Genes Reveals the Importance of Location in a Biomolecular Network. PMID:30769902
deepDriver: Predicting Cancer Driver Genes Based on Somatic Mutations Using Deep Convolutional Neural Networks. PMID:30761181
A systematic genetic screen identifies essential factors involved in nuclear size control. PMID:30759079
APID database: redefining protein-protein interaction experimental evidences and binary interactomes. PMID:30715274
Matching tRNA modifications in humans to their known and predicted enzymes. PMID:30698754
Overview of the BioCreative VI Precision Medicine Track: mining protein interactions and mutations for precision medicine. PMID:30689846
Proteome-wide, Structure-Based Prediction of Protein-Protein Interactions/New Molecular Interactions Viewer. PMID:30679268
Deciphering the Potential Pharmaceutical Mechanism of GUI-ZHI-FU-LING-WAN on Systemic Sclerosis based on Systems Biology Approaches. PMID:30674993
Surface expression of TTYH2 is attenuated by direct interaction with β-COP. PMID:30670146
Building Bridges Between Structural and Network-Based Systems Biology. PMID:30656572
An interaction-based model for neuropsychiatric features of copy-number variants. PMID:30653500
Translational control mechanisms in cutaneous malignant melanoma: the role of eIF2α. PMID:30634982
Maternal choline supplementation ameliorates Alzheimer's disease pathology by reducing brain homocysteine levels across multiple generations. PMID:30622336
Admixture Effects on Coevolved Metabolic Systems. PMID:30619461
The Network of Cancer Genes (NCG): a comprehensive catalogue of known and candidate cancer genes from cancer sequencing screens. PMID:30606230
Network spectra for drug-target identification in complex diseases: new guns against old foes. PMID:30596144
Integrative network and brain expression analysis reveals mechanistic modules in ataxia. PMID:30591515
Bayesian inference of networks across multiple sample groups and data types. PMID:30590505
The RTK Interactome: Overview and Perspective on RTK Heterointeractions. PMID:30589534
Genome-wide analysis of consistently RNA edited sites in human blood reveals interactions with mRNA processing genes and suggests correlations with cell types and biological variables. PMID:30587120
TICA: Transcriptional Interaction and Coregulation Analyzer. PMID:30578913
BioCreative VI Precision Medicine Track system performance is constrained by entity recognition and variations in corpus characteristics. PMID:30576491
iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data. PMID:30567491
A protein-protein interaction map of the TNF-induced NF-κB signal transduction pathway. PMID:30561431
Nrf1-mediated transcriptional regulation of the proteasome requires a functional TIP60 complex. PMID:30559296
Several genes involved in the JAK-STAT pathway may act as prognostic markers in pancreatic cancer identified by microarray data analysis. PMID:30557977
PlantEAR: Functional Analysis Platform for Plant EAR Motif-Containing Proteins. PMID:30555515
Time-resolved interaction proteomics of the GIGANTEA protein under diurnal cycles in Arabidopsis. PMID:30536871
A Primer on Data Analytics in Functional Genomics: How to Move from Data to Insight? PMID:30522862
Both Intrinsically Disordered Regions and Structural Domains Evolve Rapidly in Immune-Related Mammalian Proteins. PMID:30518031
Genomic identification and functional analysis of essential genes in Caenorhabditis elegans. PMID:30514206
Vimentin on the move: new developments in cell migration. PMID:30505430
ARP3 Controls the Podocyte Architecture at the Kidney Filtration Barrier. PMID:30503751
STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. PMID:30476243
The BioGRID interaction database: 2019 update. PMID:30476227
A PxL motif promotes timely cell cycle substrate dephosphorylation by the Cdc14 phosphatase. PMID:30455435
Physiological and pathophysiological characteristics of ataxin-3 isoforms. PMID:30455355
How do we know that plants listen: Advancements and limitations of transcriptomic profiling for the identification of sound-specific biomarkers in tomato. PMID:30445891
Higher-order molecular organization as a source of biological function. PMID:30423061
ALMS1 and Alström syndrome: a recessive form of metabolic, neurosensory and cardiac deficits. PMID:30421101
IID 2018 update: context-specific physical protein-protein interactions in human, model organisms and domesticated species. PMID:30407591
FusionGDB: fusion gene annotation DataBase. PMID:30407583
The pervasive effects of recombinant Fasciola gigantica Ras-related protein Rab10 on the functions of goat peripheral blood mononuclear cells. PMID:30400957
Whole Proteome Profiling of N-Myristoyltransferase Activity and Inhibition Using Sortase A. PMID:30341083
Identification of Kinases and Interactors of p53 Using Kinase-Catalyzed Cross-Linking and Immunoprecipitation. PMID:30339384
Genomic data integration systematically biases interactome mapping. PMID:30332399
Structural basis for receptor-regulated SMAD recognition by MAN1. PMID:30321401
PomBase 2018: user-driven reimplementation of the fission yeast database provides rapid and intuitive access to diverse, interconnected information. PMID:30321395
Document triage for identifying protein-protein interactions affected by mutations: a neural network ensemble approach. PMID:30295718
Chromosome 17 Missing Proteins: Recent Progress and Future Directions as Part of the neXt-MP50 Challenge. PMID:30280577
The Systems Biology of Single-Cell Aging. PMID:30267677
PlaD: A Transcriptomics Database for Plant Defense Responses to Pathogens, Providing New Insights into Plant Immune System. PMID:30266409
Potential use of compounds from sea cucumbers as MDM2 and CXCR4 inhibitors to control cancer cell growth. PMID:30250516
The Comparative Toxicogenomics Database: update 2019. PMID:30247620
A Quantitative Chemical Proteomic Strategy for Profiling Phosphoprotein Phosphatases from Yeast to Humans. PMID:30228194
Large-scale investigation of the reasons why potentially important genes are ignored. PMID:30226837
The PIN-FORMED Auxin Efflux Carriers in Plants. PMID:30223430
Reduced intrinsic DNA curvature leads to increased mutation rate. PMID:30217230
G2Vec: Distributed gene representations for identification of cancer prognostic genes. PMID:30213980
AnimalTFDB 3.0: a comprehensive resource for annotation and prediction of animal transcription factors. PMID:30204897
Exploring the Mechanism of Flavonoids Through Systematic Bioinformatics Analysis. PMID:30158870
An analysis of aging-related genes derived from the Genotype-Tissue Expression project (GTEx). PMID:30155276
ESCC ATLAS: A population wide compendium of biomarkers for Esophageal Squamous Cell Carcinoma. PMID:30143675
A High-Throughput Candida albicans Two-Hybrid System. PMID:30135223
Molecular signatures and functional analysis of beige adipocytes induced from in vivo intra-abdominal adipocytes. PMID:30116775
FBXW7: a critical tumor suppressor of human cancers. PMID:30086763
Evolution of In Silico Strategies for Protein-Protein Interaction Drug Discovery. PMID:30082644
Regional Diversity in the Postsynaptic Proteome of the Mouse Brain. PMID:30071621
FusionPathway: Prediction of pathways and therapeutic targets associated with gene fusions in cancer. PMID:30040819
An unsupervised machine learning method for discovering patient clusters based on genetic signatures. PMID:30016722
Exploring the sound-modulated delay in tomato ripening through expression analysis of coding and non-coding RNAs. PMID:30010774
Proteomic Analysis of NCK1/2 Adaptors Uncovers Paralog-specific Interactions That Reveal a New Role for NCK2 in Cell Abscission During Cytokinesis. PMID:30002203
Positional specificity of different transcription factor classes within enhancers. PMID:29987030
Identification of Antifungal Targets Based on Computer Modeling. PMID:29973534
PrimAlign: PageRank-inspired Markovian alignment for large biological networks. PMID:29949962
In silico approach in reveal traditional medicine plants pharmacological material basis. PMID:29946351
Computational Methods for Predicting Protein-Protein Interactions Using Various Protein Features. PMID:29927082
Hub Protein Controversy: Taking a Closer Look at Plant Stress Response Hubs. PMID:29922309
A quantitative mass spectrometry-based approach to monitor the dynamics of endogenous chromatin-associated protein complexes. PMID:29899353
Stratification of candidate genes for Parkinson's disease using weighted protein-protein interaction network analysis. PMID:29898659
Identification of Central Regulators of Calcium Signaling and ECM-Receptor Interaction Genetically Associated With the Progression and Recurrence of Atrial Fibrillation. PMID:29868113
Chemical-Induced Phenotypes at CTD Help Inform the Predisease State and Construct Adverse Outcome Pathways. PMID:29846728
Time-Resolved Analysis Reveals Rapid Dynamics and Broad Scope of the CBP/p300 Acetylome. PMID:29804834
GIANT 2.0: genome-scale integrated analysis of gene networks in tissues. PMID:29800226
Neural networks for link prediction in realistic biomedical graphs: a multi-dimensional evaluation of graph embedding-based approaches. PMID:29783926
A Primer for the Rat Genome Database (RGD). PMID:29761460
Assessing the functional association of intronic miRNAs with their host genes. PMID:29752351
MEGADOCK-Web: an integrated database of high-throughput structure-based protein-protein interaction predictions. PMID:29745830
In vitro study on role of σB protein in avian reovirus pathogenesis. PMID:29731966
Comparative Analysis of Human Genes Frequently and Occasionally Regulated by m6A Modification. PMID:29730206
New perspectives: systems medicine in cardiovascular disease. PMID:29699591
Mut2Vec: distributed representation of cancerous mutations. PMID:29697361
Annotating activation/inhibition relationships to protein-protein interactions using gene ontology relations. PMID:29671402
DNA Repair Network Analysis Reveals Shieldin as a Key Regulator of NHEJ and PARP Inhibitor Sensitivity. PMID:29656893
Evaluation of Animal Models by Comparison with Human Late-Onset Alzheimer's Disease. PMID:29656362
JAMI: a Java library for molecular interactions and data interoperability. PMID:29642846
DDX49 is an RNA helicase that affects translation by regulating mRNA export and the levels of pre-ribosomal RNA. PMID:29618122
Multi-omics analysis reveals neoantigen-independent immune cell infiltration in copy-number driven cancers. PMID:29615613
Textpresso Central: a customizable platform for searching, text mining, viewing, and curating biomedical literature. PMID:29523070
Extracellular vesicle RNAs reflect placenta dysfunction and are a biomarker source for preterm labour. PMID:29516617
SUMO E3 ligase Mms21 prevents spontaneous DNA damage induced genome rearrangements. PMID:29505562
How Surrogate and Chemical Genetics in Model Organisms Can Suggest Therapies for Human Genetic Diseases. PMID:29487144
The dynamic life of the glycogen granule. PMID:29483195
Structural principles that enable oligomeric small heat-shock protein paralogs to evolve distinct functions. PMID:29472485
ZFP36L2 is a cell cycle-regulated CCCH protein necessary for DNA lesion-induced S-phase arrest. PMID:29449217
scEpath: energy landscape-based inference of transition probabilities and cellular trajectories from single-cell transcriptomic data. PMID:29415263
Systematic Analysis of mRNA and miRNA Expression of 3D-Cultured Neural Stem Cells (NSCs) in Spaceflight. PMID:29375320
Protein Tyrosine Phosphatase Receptor Type G (PTPRG) Controls Fibroblast Growth Factor Receptor (FGFR) 1 Activity and Influences Sensitivity to FGFR Kinase Inhibitors. PMID:29371290
Using genetic buffering relationships identified in fission yeast to reveal susceptibilities in cells lacking hamartin or tuberin function. PMID:29343513
Systemic bioinformatics analysis of recurrent aphthous stomatitis gene expression profiles. PMID:29340037
Aux/IAA Gene Family in Plants: Molecular Structure, Regulation, and Function. PMID:29337875
Feature genes in metastatic breast cancer identified by MetaDE and SVM classifier methods. PMID:29328377
Circulating microRNA (miRNA) Expression Profiling in Plasma of Patients with Gestational Diabetes Mellitus Reveals Upregulation of miRNA miR-330-3p. PMID:29312141
Biosystems Study of the Molecular Networks Underlying Hippocampal Aging Progression and Anti-aging Treatment in Mice. PMID:29311893
TRANSPARENT TESTA GLABRA 1-Dependent Regulation of Flavonoid Biosynthesis. PMID:29261137
Functional Analysis of Human Hub Proteins and Their Interactors Involved in the Intrinsic Disorder-Enriched Interactions. PMID:29257115
Weighted Gene Co-expression Network Analysis Identifies FKBP11 as a Key Regulator in Acute Aortic Dissection through a NF-kB Dependent Pathway. PMID:29255427
Constructing a comprehensive gene co-expression based interactome in Bos taurus. PMID:29226034
MiRIAD update: using alternative polyadenylation, protein interaction network analysis and additional species to enhance exploration of the role of intragenic miRNAs and their host genes. PMID:29220447
Extended Linkers Improve the Detection of Protein-protein Interactions (PPIs) by Dihydrofolate Reductase Protein-fragment Complementation Assay (DHFR PCA) in Living Cells. PMID:29203496
Systems Bioinformatics: increasing precision of computational diagnostics and therapeutics through network-based approaches. PMID:29186305
FunCoup 4: new species, data, and visualization. PMID:29165593
Molecular Interaction Search Tool (MIST): an integrated resource for mining gene and protein interaction data. PMID:29155944
Constructing Genetic Networks using Biomedical Literature and Rare Event Classification. PMID:29150626
ANAT 2.0: reconstructing functional protein subnetworks. PMID:29145805
Saccharomyces genome database informs human biology. PMID:29140510
Protein Moonlighting Revealed by Noncatalytic Phenotypes of Yeast Enzymes. PMID:29127264
The UCSC Genome Browser database: 2018 update. PMID:29106570
The DifferentialNet database of differential protein-protein interactions in human tissues. PMID:29069447
The online Tabloid Proteome: an annotated database of protein associations. PMID:29040688
A Compendium of Co-regulated Protein Complexes in Breast Cancer Reveals Collateral Loss Events. PMID:29032073
PICKLE 2.0: A human protein-protein interaction meta-database employing data integration via genetic information ontology. PMID:29023571
A Unique TGFB1-Driven Genomic Program Links Astrocytosis, Low-Grade Inflammation and Partial Demyelination in Spinal Cord Periplaques from Progressive Multiple Sclerosis Patients. PMID:28981455
Molecular mechanisms underlying gliomas and glioblastoma pathogenesis revealed by bioinformatics analysis of microarray data. PMID:28952134
Detecting gene subnetworks under selection in biological pathways. PMID:28934485
Digoxin-induced anemia among patients with atrial fibrillation and heart failure: clinical data analysis and drug-gene interaction network. PMID:28915649
Knowledge-guided gene prioritization reveals new insights into the mechanisms of chemoresistance. PMID:28800781
CytoMCS: A Multiple Maximum Common Subgraph Detection Tool for Cytoscape. PMID:28731857
HDNetDB: A Molecular Interaction Database for Network-Oriented Investigations into Huntington's Disease. PMID:28701700
NetNorM: Capturing cancer-relevant information in somatic exome mutation data with gene networks for cancer stratification and prognosis. PMID:28650955
Agonist-specific Protein Interactomes of Glucocorticoid and Androgen Receptor as Revealed by Proximity Mapping. PMID:28611094
Comparative analysis of genes frequently regulated by drugs based on connectivity map transcriptome data. PMID:28575118
GLADIATOR: a global approach for elucidating disease modules. PMID:28549478
CLMSVault: A Software Suite for Protein Cross-Linking Mass-Spectrometry Data Analysis and Visualization. PMID:28537071
Unbiased Protein Association Study on the Public Human Proteome Reveals Biological Connections between Co-Occurring Protein Pairs. PMID:28480704
WebGestalt 2017: a more comprehensive, powerful, flexible and interactive gene set enrichment analysis toolkit. PMID:28472511
Mapping the Synthetic Dosage Lethality Network of CDK1/CDC28. PMID:28428242
Diagnostic and prognostic relevance of CP2c and YY1 expression in hepatocellular carcinoma. PMID:28412749
Cancer/Testis Antigens: "Smart" Biomarkers for Diagnosis and Prognosis of Prostate and Other Cancers. PMID:28362316
Protein Kinase CK2: Intricate Relationships within Regulatory Cellular Networks. PMID:28273877
Emerging Roles for Ciz1 in Cell Cycle Regulation and as a Driver of Tumorigenesis. PMID:28036012
The BioGRID Interaction Database: 2011 update PubMed citations: 422.

422 articles citing: The BioGRID Interaction Database: 2011 update

DEMA: a distance-bounded energy-field minimization algorithm to model and layout biomolecular networks with quantitative features. PMID:35758816
Contribution of Model Organisms to Investigating the Far-Reaching Consequences of PRPP Metabolism on Human Health and Well-Being. PMID:35741038
Protein-Protein Interaction (PPI) Network of Zebrafish Oestrogen Receptors: A Bioinformatics Workflow. PMID:35629318
Uncompensated mitochondrial oxidative stress underlies heart failure in an iPSC-derived model of congenital heart disease. PMID:35395180
Integrating protein copy numbers with interaction networks to quantify stoichiometry in clathrin-mediated endocytosis. PMID:35354856
Protein interaction networks provide insight into fetal origins of chronic obstructive pulmonary disease. PMID:35331221
Correlation Imputation for Single-Cell RNA-seq. PMID:35325552
Identifying large-scale interaction atlases using probabilistic graphs and external knowledge. PMID:35321220
Protein Function Prediction Based on PPI Networks: Network Reconstruction vs Edge Enrichment. PMID:34970299
The Hippo Signaling Pathway in Cancer: A Cell Cycle Perspective. PMID:34944834
Convolutional neural network for human cancer types prediction by integrating protein interaction networks and omics data. PMID:34667236
LncTx: A network-based method to repurpose drugs acting on the survival-related lncRNAs in lung cancer. PMID:34377365
Correlation Imputation in Single cell RNA-seq using Auxiliary Information and Ensemble Learning. PMID:34278382
Environmental robustness of the global yeast genetic interaction network. PMID:33958448
The contributions from the progenitor genomes of the mesopolyploid Brassiceae are evolutionarily distinct but functionally compatible. PMID:33863805
Genome analyses of 174 strains of Mycobacterium tuberculosis provide insight into the evolution of drug resistance and reveal potential drug targets. PMID:33750515
Chemical-Genetic Interactions of Bacopa monnieri Constituents in Cells Deficient for the DNA Repair Endonuclease RAD1 Appear Linked to Vacuolar Disruption. PMID:33668176
A large accessory protein interactome is rewired across environments. PMID:32924934
Network-principled deep generative models for designing drug combinations as graph sets. PMID:32657357
Predicting Self-Interacting Proteins Using a Recurrent Neural Network and Protein Evolutionary Information. PMID:32550764
Systematic analysis of ovarian cancer platinum-resistance mechanisms via text mining. PMID:32160916
The Need for SMN-Independent Treatments of Spinal Muscular Atrophy (SMA) to Complement SMN-Enhancing Drugs. PMID:32117013
Systematic genetics and single-cell imaging reveal widespread morphological pleiotropy and cell-to-cell variability. PMID:32064787
Genome-wide inference of the Camponotus floridanus protein-protein interaction network using homologous mapping and interacting domain profile pairs. PMID:32047225
A comparative study of topology-based pathway enrichment analysis methods. PMID:31684881
Speeding up the drug discovery process: structural similarity searches using molecular surfaces. PMID:31440460
Membrane protein-regulated networks across human cancers. PMID:31311925
Gnal haploinsufficiency causes genomic instability and increased sensitivity to haloperidol. PMID:31034808
A Comprehensive Drosophila melanogaster Transcription Factor Interactome. PMID:30995488
Analysis of Predicted Host-Parasite Interactomes Reveals Commonalities and Specificities Related to Parasitic Lifestyle and Tissues Tropism. PMID:30815000
Molecular subtyping of cancer and nomination of kinase candidates for inhibition with phosphoproteomics: Reanalysis of CPTAC ovarian cancer. PMID:30594550
A Network Pharmacology Approach to Uncover the Molecular Mechanisms of Herbal Formula Ban-Xia-Xie-Xin-Tang. PMID:30410554
Context-enriched interactome powered by proteomics helps the identification of novel regulators of macrophage activation. PMID:30303482
Evidence that RNA Viruses Drove Adaptive Introgression between Neanderthals and Modern Humans. PMID:30290142
MiRNA-BD: an evidence-based bioinformatics model and software tool for microRNA biomarker discovery. PMID:30081733
Automatic extraction of protein-protein interactions using grammatical relationship graph. PMID:30066644
Proximal Pathway Enrichment Analysis for Targeting Comorbid Diseases via Network Endopharmacology. PMID:29932108
A systems immunology approach identifies the collective impact of 5 miRs in Th2 inflammation. PMID:29875322
Systematic Evaluation of Molecular Networks for Discovery of Disease Genes. PMID:29605183
Preferential retention of genes from one parental genome after polyploidy illustrates the nature and scope of the genomic conflicts induced by hybridization. PMID:29590103
Key genes and regulatory networks involved in the initiation, progression and invasion of colorectal cancer. PMID:29568567
A homologous mapping method for three-dimensional reconstruction of protein networks reveals disease-associated mutations. PMID:29560828
Prediction of Disordered Regions and Their Roles in the Anti-Pathogenic and Immunomodulatory Functions of Butyrophilins. PMID:29401697
Co-complex protein membership evaluation using Maximum Entropy on GO ontology and InterPro annotation. PMID:29390084
Support vector machine classifier for prediction of the metastasis of colorectal cancer. PMID:29328363
Protein-protein interaction analysis to identify biomarker networks for endometriosis. PMID:29201163
SPRINT: ultrafast protein-protein interaction prediction of the entire human interactome. PMID:29141584
CRISPR/Cas9-Based Engineering of the Epigenome. PMID:28985525
High rate of adaptation of mammalian proteins that interact with Plasmodium and related parasites. PMID:28957326
Genome wide host gene expression analysis in mice experimentally infected with Pasteurella multocida. PMID:28704394
Application of a systems approach to study developmental gene regulation. PMID:28510076
iTRAQ-based quantitative proteomic analysis of Yamanaka factors reprogrammed breast cancer cells. PMID:28423718
RNA Seq analysis for transcriptome profiling in response to classical swine fever vaccination in indigenous and crossbred pigs. PMID:28361233
Gene Expression, Protein Function and Pathways of Arabidopsis thaliana Responding to Silver Nanoparticles in Comparison to Silver Ions, Cold, Salt, Drought, and Heat. PMID:28347022
Downstream targets of GWAS-detected genes for breast, lung, and prostate and colon cancer converge to G1/S transition pathway. PMID:28334950
IODNE: An integrated optimization method for identifying the deregulated subnetwork for precision medicine in cancer. PMID:28266149
Systematic analysis of molecular mechanisms for HCC metastasis via text mining approach. PMID:28108733
Properties of human disease genes and the role of genes linked to Mendelian disorders in complex disease aetiology. PMID:28053046
CanProVar 2.0: An Updated Database of Human Cancer Proteome Variation. PMID:27977206
Personalized anticancer therapy selection using molecular landscape topology and thermodynamics. PMID:27793055
Protein folding, binding, and droplet formation in cell-like conditions. PMID:27771543
A computational interactome and functional annotation for the human proteome. PMID:27770567
A global genetic interaction network maps a wiring diagram of cellular function. PMID:27708008
Systems Medicine as an Emerging Tool for Cardiovascular Genetics. PMID:27626034
Entropy-based divergent and convergent modular pattern reveals additive and synergistic anticerebral ischemia mechanisms. PMID:27480252
Identification of key target genes and pathways in laryngeal carcinoma. PMID:27446427
Mining Functional Modules in Heterogeneous Biological Networks Using Multiplex PageRank Approach. PMID:27446133
Relational Network for Knowledge Discovery through Heterogeneous Biomedical and Clinical Features. PMID:27427091
Network analysis and juvenile idiopathic arthritis (JIA): a new horizon for the understanding of disease pathogenesis and therapeutic target identification. PMID:27411317
Quantitative Determination of Flexible Pharmacological Mechanisms Based On Topological Variation in Mice Anti-Ischemic Modular Networks. PMID:27383195
BcCluster: A Bladder Cancer Database at the Molecular Level. PMID:27376128
Endophenotype Network Models: Common Core of Complex Diseases. PMID:27278246
Systematic analysis of the molecular mechanism underlying atherosclerosis using a text mining approach. PMID:27251057
Viruses are a dominant driver of protein adaptation in mammals. PMID:27187613
A Network of Splice Isoforms for the Mouse. PMID:27079421
Dissecting dysfunctional crosstalk pathways regulated by miRNAs during glioma progression. PMID:27013589
Regulatory consequences of neuronal ELAV-like protein binding to coding and non-coding RNAs in human brain. PMID:26894958
Network-based in silico drug efficacy screening. PMID:26831545
Identification of miRNA-mRNA regulatory modules by exploring collective group relationships. PMID:26817421
CSGene: a literature-based database for cell senescence genes and its application to identify critical cell aging pathways and associated diseases. PMID:26775705
BioGRID: A Resource for Studying Biological Interactions in Yeast. PMID:26729913
Scope and limitations of yeast as a model organism for studying human tissue-specific pathways. PMID:26714768
Transcriptome analysis in calorie-restricted rats implicates epigenetic and post-translational mechanisms in neuroprotection and aging. PMID:26694192
CancerNet: a database for decoding multilevel molecular interactions across diverse cancer types. PMID:26690544
Properly defining the targets of a transcription factor significantly improves the computational identification of cooperative transcription factor pairs in yeast. PMID:26679776
YAGM: a web tool for mining associated genes in yeast based on diverse biological associations. PMID:26678566
PCTFPeval: a web tool for benchmarking newly developed algorithms for predicting cooperative transcription factor pairs in yeast. PMID:26677932
A network pharmacology approach reveals new candidate caloric restriction mimetics in C. elegans. PMID:26676933
Application of Gene Expression Trajectories Initiated from ErbB Receptor Activation Highlights the Dynamics of Divergent Promoter Usage. PMID:26658111
NDEx, the Network Data Exchange. PMID:26594663
Interpreting functional effects of coding variants: challenges in proteome-scale prediction, annotation and assessment. PMID:26494363
Integrative analysis of human protein, function and disease networks. PMID:26399914
Systematic Analysis of the Molecular Mechanism Underlying Decidualization Using a Text Mining Approach. PMID:26222155
Genes Caught In Flagranti: Integrating Renal Transcriptional Profiles With Genotypes and Phenotypes. PMID:26215861
The BioPlex Network: A Systematic Exploration of the Human Interactome. PMID:26186194
Transcriptomic-Wide Discovery of Direct and Indirect HuR RNA Targets in Activated CD4+ T Cells. PMID:26162078
A reproducible approach to high-throughput biological data acquisition and integration. PMID:26157642
Biology-Driven Gene-Gene Interaction Analysis of Age-Related Cataract in the eMERGE Network. PMID:25982363
FNTM: a server for predicting functional networks of tissues in mouse. PMID:25940632
Follicle Online: an integrated database of follicle assembly, development and ovulation. PMID:25931457
Lineage-specific sequence evolution and exon edge conservation partially explain the relationship between evolutionary rate and expression level in A. thaliana. PMID:25930165
Predicted protein-protein interactions in the moss Physcomitrella patens: a new bioinformatic resource. PMID:25885037
Inhibition of cathepsin proteases attenuates migration and sensitizes aggressive N-Myc amplified human neuroblastoma cells to doxorubicin. PMID:25883214
A DIseAse MOdule Detection (DIAMOnD) algorithm derived from a systematic analysis of connectivity patterns of disease proteins in the human interactome. PMID:25853560
Recent positive selection has acted on genes encoding proteins with more interactions within the whole human interactome. PMID:25840415
Genomic analysis of host - Peste des petits ruminants vaccine viral transcriptome uncovers transcription factors modulating immune regulatory pathways. PMID:25827022
The pentameric nucleoplasmin fold is present in Drosophila FKBP39 and a large number of chromatin-related proteins. PMID:25813344
MDM2 turnover and expression of ATRX determine the choice between quiescence and senescence in response to CDK4 inhibition. PMID:25803170
Module organization and variance in protein-protein interaction networks. PMID:25797237
Network-based proteomic approaches reveal the neurodegenerative, neuroprotective and pain-related mechanisms involved after retrograde axonal damage. PMID:25784190
LC-MS/MS-based serum proteomics for identification of candidate biomarkers for hepatocellular carcinoma. PMID:25778709
The identification of specific methylation patterns across different cancers. PMID:25774687
Expression profile of mitrogen-activated protein kinase (MAPK) signaling genes in the skeletal muscle & liver of rat with type 2 diabetes: role in disease pathology. PMID:25758573
Efficient prediction of progesterone receptor interactome using a support vector machine model. PMID:25741764
Network tuned multiple rank aggregation and applications to gene ranking. PMID:25708095
An integrative approach for a network based meta-analysis of viral RNAi screens. PMID:25691914
Reconstructing genome-wide protein-protein interaction networks using multiple strategies with homologous mapping. PMID:25602759
The molecular genetic architecture of attention deficit hyperactivity disorder. PMID:25600112
Protein interactome of muscle invasive bladder cancer. PMID:25569276
Integrated systems analysis reveals a molecular network underlying autism spectrum disorders. PMID:25549968
Network-based association of hypoxia-responsive genes with cardiovascular diseases. PMID:25530704
Complex-based analysis of dysregulated cellular processes in cancer. PMID:25521701
A comprehensive performance evaluation on the prediction results of existing cooperative transcription factors identification algorithms. PMID:25521604
A proteomic analysis reveals that Snail regulates the expression of the nuclear orphan receptor Nuclear Receptor Subfamily 2 Group F Member 6 (Nr2f6) and interleukin 17 (IL-17) to inhibit adipocyte differentiation. PMID:25505127
Pathway crosstalk analysis of microarray gene expression profile in human hepatocellular carcinoma. PMID:25480734
Systems Medicine: from molecular features and models to the clinic in COPD. PMID:25471042
In silico prediction of synthetic lethality by meta-analysis of genetic interactions, functions, and pathways in yeast and human cancer. PMID:25452682
Tissue-aware data integration approach for the inference of pathway interactions in metazoan organisms. PMID:25431329
Systematic identification of cell size regulators in budding yeast. PMID:25411401
Spotlite: web application and augmented algorithms for predicting co-complexed proteins from affinity purification--mass spectrometry data. PMID:25300367
Identification of essential proteins based on ranking edge-weights in protein-protein interaction networks. PMID:25268881
Characterizing protein interactions employing a genome-wide siRNA cellular phenotyping screen. PMID:25255318
Drug-Like Protein-Protein Interaction Modulators: Challenges and Opportunities for Drug Discovery and Chemical Biology. PMID:25254076
Integration strategy is a key step in network-based analysis and dramatically affects network topological properties and inferring outcomes. PMID:25243127
Finding trans-regulatory genes and protein complexes modulating meiotic recombination hotspots of human, mouse and yeast. PMID:25208583
Unbiased functional clustering of gene variants with a phenotypic-linkage network. PMID:25166029
Bioinformatics analysis of biomarkers and transcriptional factor motifs in Down syndrome. PMID:25118625
Modeling dynamic functional relationship networks and application to ex vivo human erythroid differentiation. PMID:25115705
An integrative omics strategy to assess the germ cell secretome and to decipher sertoli-germ cell crosstalk in the Mammalian testis. PMID:25111155
Prediction and functional analysis of the sweet orange protein-protein interaction network. PMID:25091279
A dedicated database system for handling multi-level data in systems biology. PMID:25053973
Large Scale Chemical Cross-linking Mass Spectrometry Perspectives. PMID:25045217
Construction and analysis of microRNA-transcription factor regulation network in Arabidopsis. PMID:25014374
The domain landscape of virus-host interactomes. PMID:24991570
Building a hierarchical organization of protein complexes out of protein association data. PMID:24978199
Correlating information contents of gene ontology terms to infer semantic similarity of gene products. PMID:24963342
Scale-space measures for graph topology link protein network architecture to function. PMID:24931989
Improving functional annotation for industrial microbes: a case study with Pichia pastoris. PMID:24929579
Comparative analysis of human tissue interactomes reveals factors leading to tissue-specific manifestation of hereditary diseases. PMID:24921629
Essential functional modules for pathogenic and defensive mechanisms in Candida albicans infections. PMID:24757665
Stringent homology-based prediction of H. sapiens-M. tuberculosis H37Rv protein-protein interactions. PMID:24708540
Tissue-specific expression and regulatory networks of pig microRNAome. PMID:24699212
A second-generation protein-protein interaction network of Helicobacter pylori. PMID:24627523
Modelling the yeast interactome. PMID:24589662
Protein-protein interactions prediction based on iterative clique extension with gene ontology filtering. PMID:24578640
M-Finder: Uncovering functionally associated proteins from interactome data integrated with GO annotations. PMID:24565382
Stringent DDI-based prediction of H. sapiens-M. tuberculosis H37Rv protein-protein interactions. PMID:24564941
Identifying conserved protein complexes between species by constructing interolog networks. PMID:24564762
RRHGE: a novel approach to classify the estrogen receptor based breast cancer subtypes. PMID:24563630
Navigating the multilayered organization of eukaryotic signaling: a new trend in data integration. PMID:24550716
A Network Approach to Wound Healing. PMID:24527361
Discovery and characterization of two Nimrod superfamily members in Anopheles gambiae. PMID:24428830
Dynamics of regulatory networks in gastrin-treated adenocarcinoma cells. PMID:24416123
Computational Prediction of Protein-Protein Interaction Networks: Algo-rithms and Resources. PMID:24396273
Identifying functional transcription factor binding sites in yeast by considering their positional preference in the promoters. PMID:24386279
Low frequency variants, collapsed based on biological knowledge, uncover complexity of population stratification in 1000 genomes project data. PMID:24385916
Reverse engineering molecular hypergraphs. PMID:24384702
An association-adjusted consensus deleterious scheme to classify homozygous Mis-sense mutations for personal genome interpretation. PMID:24365473
Identification of unstable network modules reveals disease modules associated with the progression of Alzheimer's disease. PMID:24348898
Causal inference of gene regulation with subnetwork assembly from genetical genomics data. PMID:24322297
SysBioCube: A Data Warehouse and Integrative Data Analysis Platform Facilitating Systems Biology Studies of Disorders of Military Relevance. PMID:24303294
Expression of integrin alpha 10 is transcriptionally activated by pRb in mouse osteoblasts and is downregulated in multiple solid tumors. PMID:24287699
Integrating structure to protein-protein interaction networks that drive metastasis to brain and lung in breast cancer. PMID:24278371
Protein function prediction by collective classification with explicit and implicit edges in protein-protein interaction networks. PMID:24267980
P³DB 3.0: From plant phosphorylation sites to protein networks. PMID:24243849
Integrating protein-protein interaction networks with phenotypes reveals signs of interactions. PMID:24240319
Genotype to phenotype via network analysis. PMID:24238873
Integrating in silico resources to map a signaling network. PMID:24233784
Discovering disease-disease associations by fusing systems-level molecular data. PMID:24232732
Bayesian network prior: network analysis of biological data using external knowledge. PMID:24215027
Synthetic genetic targeting of genome instability in cancer. PMID:24202319
High-resolution network biology: connecting sequence with function. PMID:24197012
Conserved versatile master regulators in signalling pathways in response to stress in plants. PMID:24147216
Systematic identification of transcriptional regulatory modules from protein-protein interaction networks. PMID:24137002
NP-MuScL: unsupervised global prediction of interaction networks from multiple data sources. PMID:24134391
Simple topological features reflect dynamics and modularity in protein interaction networks. PMID:24130468
Protein kinase PKN1 represses Wnt/β-catenin signaling in human melanoma cells. PMID:24114839
Exploring mechanisms of human disease through structurally resolved protein interactome networks. PMID:24096645
Identification of small exonic CNV from whole-exome sequence data and application to autism spectrum disorder. PMID:24094742
Integration of new genes into cellular networks, and their structural maturation. PMID:24056411
Detecting non-uniform clusters in large-scale interaction graphs. PMID:24050498
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
Predicting whole genome protein interaction networks from primary sequence data in model and non-model organisms using ENTS. PMID:24015873
ExoCarta as a resource for exosomal research. PMID:24009883
Inferring the effective TOR-dependent network: a computational study in yeast. PMID:24005029
Research prioritization through prediction of future impact on biomedical science: a position paper on inference-analytics. PMID:24001106
Computational analysis of virus-host interactomes. PMID:23996253
Network clusters analysis based on protein-protein interaction network constructed in phosgene-induced acute lung injury. PMID:23963411
Ultrasensitivity in phosphorylation-dephosphorylation cycles with little substrate. PMID:23950701
Human growth is associated with distinct patterns of gene expression in evolutionarily conserved networks. PMID:23941278
Association study of 167 candidate genes for schizophrenia selected by a multi-domain evidence-based prioritization algorithm and neurodevelopmental hypothesis. PMID:23922650
Cloud-based uniform ChIP-Seq processing tools for modENCODE and ENCODE. PMID:23875683
SMETANA: accurate and scalable algorithm for probabilistic alignment of large-scale biological networks. PMID:23874484
Genome evolution predicts genetic interactions in protein complexes and reveals cancer drug targets. PMID:23851603
Widespread evidence of cooperative DNA binding by transcription factors in Drosophila development. PMID:23847101
DBATE: database of alternative transcripts expression. PMID:23842462
PhosphoChain: a novel algorithm to predict kinase and phosphatase networks from high-throughput expression data. PMID:23832245
Mapping the functional yeast ABC transporter interactome. PMID:23831759
Link clustering reveals structural characteristics and biological contexts in signed molecular networks. PMID:23826198
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
Integrating sequence, expression and interaction data to determine condition-specific miRNA regulation. PMID:23813013
A context-sensitive framework for the analysis of human signalling pathways in molecular interaction networks. PMID:23812986
Arbor: comparative analysis workflows for the tree of life. PMID:23811960
Mining breast cancer genes with a network based noise-tolerant approach. PMID:23799982
Integrative approaches for predicting protein function and prioritizing genes for complex phenotypes using protein interaction networks. PMID:23788799
ResponseNet2.0: Revealing signaling and regulatory pathways connecting your proteins and genes--now with human data. PMID:23761447
Optimization criteria and biological process enrichment in homologous multiprotein modules. PMID:23757502
Construction of protein phosphorylation networks by data mining, text mining and ontology integration: analysis of the spindle checkpoint. PMID:23749465
The development of a universal in silico predictor of protein-protein interactions. PMID:23741499
Comparison of modules of wild type and mutant Huntingtin and TP53 protein interaction networks: implications in biological processes and functions. PMID:23741403
Passing messages between biological networks to refine predicted interactions. PMID:23741402
Integrated analysis of recurrent properties of cancer genes to identify novel drivers. PMID:23718799
NRF2-ome: an integrated web resource to discover protein interaction and regulatory networks of NRF2. PMID:23710289
Genome-wide methylated DNA immunoprecipitation analysis of patients with polycystic ovary syndrome. PMID:23705014
Evolutionary pressure on the topology of protein interface interaction networks. PMID:23701316
A genome-wide resource of cell cycle and cell shape genes of fission yeast. PMID:23697806
A "candidate-interactome" aggregate analysis of genome-wide association data in multiple sclerosis. PMID:23696811
Human monogenic disease genes have frequently functionally redundant paralogs. PMID:23696728
Interface-resolved network of protein-protein interactions. PMID:23696724
Cross-species protein interactome mapping reveals species-specific wiring of stress response pathways. PMID:23695164
Adjusting for High-dimensional Covariates in Sparse Precision Matrix Estimation by ℓ1-Penalization. PMID:23687392
The PhosphoGRID Saccharomyces cerevisiae protein phosphorylation site database: version 2.0 update. PMID:23674503
All or nothing: protein complexes flip essentiality between distantly related eukaryotes. PMID:23661563
Protein complex detection via weighted ensemble clustering based on Bayesian nonnegative matrix factorization. PMID:23658709
Genotype to phenotype mapping and the fitness landscape of the E. coli lac promoter. PMID:23650500
Top-down network analysis to drive bottom-up modeling of physiological processes. PMID:23641868
PCorral--interactive mining of protein interactions from MEDLINE. PMID:23640984
Use of the protein ontology for multi-faceted analysis of biological processes: a case study of the spindle checkpoint. PMID:23637705
Chapter 15: disease gene prioritization. PMID:23633938
Genome-wide association study of sleep in Drosophila melanogaster. PMID:23617951
Large-scale event extraction from literature with multi-level gene normalization. PMID:23613707
INstruct: a database of high-quality 3D structurally resolved protein interactome networks. PMID:23599502
Interplay between chromatin state, regulator binding, and regulatory motifs in six human cell types. PMID:23595227
Evolutionary capacitance and control of protein stability in protein-protein interaction networks. PMID:23592969
Physical and genetic-interaction density reveals functional organization and informs significance cutoffs in genome-wide screens. PMID:23589890
Endometrial receptivity: a revisit to functional genomics studies on human endometrium and creation of HGEx-ERdb. PMID:23555582
Comparison of hepatocellular carcinoma (HCC), cholangiocarcinoma (CC), and combined HCC-CC (CHC) with each other based on microarray dataset. PMID:23532688
Network pharmacology strategies toward multi-target anticancer therapies: from computational models to experimental design principles. PMID:23530504
Functional knowledge transfer for high-accuracy prediction of under-studied biological processes. PMID:23516347
Functional site plasticity in domain superfamilies. PMID:23499848
Preferential duplication of intermodular hub genes: an evolutionary signature in eukaryotes genome networks. PMID:23468868
Predicting the binding patterns of hub proteins: a study using yeast protein interaction networks. PMID:23431393
Using BioBin to explore rare variant population stratification. PMID:23424138
Next-generation analysis of cataracts: determining knowledge driven gene-gene interactions using Biofilter, and gene-environment interactions using the PhenX Toolkit. PMID:23424120
Epigenetic epistatic interactions constrain the evolution of gene expression. PMID:23423319
Quantitative analysis of chaperone network throughput in budding yeast. PMID:23420633
A genomic toolkit to investigate kinesin and myosin motor function in cells. PMID:23417121
Linking proteomic and transcriptional data through the interactome and epigenome reveals a map of oncogene-induced signaling. PMID:23408876
Benchmarking human protein complexes to investigate drug-related systems and evaluate predicted protein complexes. PMID:23405067
Interactome3D: adding structural details to protein networks. PMID:23399932
A survey of protein interaction data and multigenic inherited disorders. PMID:23398688
The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies. PMID:23398680
The YeastGenome app: the Saccharomyces Genome Database at your fingertips. PMID:23396302
Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review. PMID:23384594
Identification of ovarian cancer associated genes using an integrated approach in a Boolean framework. PMID:23383610
Turning gold into 'junk': transposable elements utilize central proteins of cellular networks. PMID:23341038
Predicting PDZ domain mediated protein interactions from structure. PMID:23336252
SignaLink 2 - a signaling pathway resource with multi-layered regulatory networks. PMID:23331499
Identification of new protein interactions between dengue fever virus and its hosts, human and mosquito. PMID:23326450
Systems biology approach reveals genome to phenome correlation in type 2 diabetes. PMID:23308243
Evidence for the robustness of protein complexes to inter-species hybridization. PMID:23300466
Adding protein context to the human protein-protein interaction network to reveal meaningful interactions. PMID:23300433
Distinct transcriptional regulatory modules underlie STAT3's cell type-independent and cell type-specific functions. PMID:23295670
Supervised maximum-likelihood weighting of composite protein networks for complex prediction. PMID:23281936
Helminth secretome database (HSD): a collection of helminth excretory/secretory proteins predicted from expressed sequence tags (ESTs). PMID:23281827
GWIDD: a comprehensive resource for genome-wide structural modeling of protein-protein interactions. PMID:23245398
A gene ontology inferred from molecular networks. PMID:23242164
A novel link prediction algorithm for reconstructing protein-protein interaction networks by topological similarity. PMID:23235927
Building an efficient curation workflow for the Arabidopsis literature corpus. PMID:23221298
Mitotic exit and separation of mother and daughter cells. PMID:23212898
An evolutionarily conserved innate immunity protein interaction network. PMID:23209288
Identification of pharmacological targets in amyotrophic lateral sclerosis through genomic analysis of deregulated genes and pathways. PMID:23204922
The BioGRID interaction database: 2013 update. PMID:23203989
STRING v9.1: protein-protein interaction networks, with increased coverage and integration. PMID:23203871
The Disease and Gene Annotations (DGA): an annotation resource for human disease. PMID:23197658
SpermatogenesisOnline 1.0: a resource for spermatogenesis based on manual literature curation and genome-wide data mining. PMID:23193286
The TissueNet database of human tissue protein-protein interactions. PMID:23193266
Systems biology of pathogen-host interaction: networks of protein-protein interaction within pathogens and pathogen-human interactions in the post-genomic era. PMID:23193100
Evolutionary rate and duplicability in the Arabidopsis thaliana protein-protein interaction network. PMID:23160177
Proteomics-based methods for discovery, quantification, and validation of protein-protein interactions. PMID:23157382
Discovery of cell compartment specific protein-protein interactions using affinity purification combined with tandem mass spectrometry. PMID:23157168
Effects of protein interaction data integration, representation and reliability on the use of network properties for drug target prediction. PMID:23146171
The ConsensusPathDB interaction database: 2013 update. PMID:23143270
A travel guide to Cytoscape plugins. PMID:23132118
Spliceosome database: a tool for tracking components of the spliceosome. PMID:23118483
SpliceAid-F: a database of human splicing factors and their RNA-binding sites. PMID:23118479
Identifying novel protein complexes in cancer cells using epitope-tagging of endogenous human genes and affinity-purification mass spectrometry. PMID:23106643
Popular computational methods to assess multiprotein complexes derived from label-free affinity purification and mass spectrometry (AP-MS) experiments. PMID:23071097
Dr. PIAS 2.0: an update of a database of predicted druggable protein-protein interactions. PMID:23060433
Aminopropyltransferases involved in polyamine biosynthesis localize preferentially in the nucleus of plant cells. PMID:23056524
Identification of significant pathways in gastric cancer based on protein-protein interaction networks and cluster analysis. PMID:23055812
PRD: A protein-RNA interaction database. PMID:23055619
Cluster-based assessment of protein-protein interaction confidence. PMID:23050565
Evaluating caveolin interactions: do proteins interact with the caveolin scaffolding domain through a widespread aromatic residue-rich motif? PMID:23028656
Tissue-specific functional networks for prioritizing phenotype and disease genes. PMID:23028291
Protein stickiness, rather than number of functional protein-protein interactions, predicts expression noise and plasticity in yeast. PMID:23017156
Fungal Hsp90: a biological transistor that tunes cellular outputs to thermal inputs. PMID:22976491
RhesusBase: a knowledgebase for the monkey research community. PMID:22965133
Identifying functional modules in interaction networks through overlapping Markov clustering. PMID:22962469
Architecture of the human regulatory network derived from ENCODE data. PMID:22955619
Feature Identification of Compensatory Gene Pairs without Sequence Homology in Yeast. PMID:22952430
Using ProHits to store, annotate, and analyze affinity purification-mass spectrometry (AP-MS) data. PMID:22948730
Analyzing protein-protein interactions from affinity purification-mass spectrometry data with SAINT. PMID:22948729
A network-based approach for predicting missing pathway interactions. PMID:22916002
A network synthesis model for generating protein interaction network families. PMID:22912671
A SPARSE CONDITIONAL GAUSSIAN GRAPHICAL MODEL FOR ANALYSIS OF GENETICAL GENOMICS DATA. PMID:22905077
Minireview: progress and challenges in proteomics data management, sharing, and integration. PMID:22902541
Identifying biologically interpretable transcription factor knockout targets by jointly analyzing the transcription factor knockout microarray and the ChIP-chip data. PMID:22898448
Screening of candidate genes for primary open angle glaucoma. PMID:22876139
HINT: High-quality protein interactomes and their applications in understanding human disease. PMID:22846459
Computational framework for analysis of prey-prey associations in interaction proteomics identifies novel human protein-protein interactions and networks. PMID:22845868
Discovering the hidden sub-network component in a ranked list of genes or proteins derived from genomic experiments. PMID:22844098
atBioNet--an integrated network analysis tool for genomics and biomarker discovery. PMID:22817640
INDI: a computational framework for inferring drug interactions and their associated recommendations. PMID:22806140
Endosomal crosstalk: meeting points for signaling pathways. PMID:22796207
The core regulation module of stress-responsive regulatory networks in yeast. PMID:22784859
Combinatorial drug therapy for cancer in the post-genomic era. PMID:22781697
Integrating genome and functional genomics data to reveal perturbed signaling pathways in ovarian cancers. PMID:22779056
Posterior association networks and functional modules inferred from rich phenotypes of gene perturbations. PMID:22761558
Accuracy improvement in protein complex prediction from protein interaction networks by refining cluster overlaps. PMID:22759580
Genes2FANs: connecting genes through functional association networks. PMID:22748121
MC EMiNEM maps the interaction landscape of the Mediator. PMID:22737066
Detecting mutually exclusive interactions in protein-protein interaction maps. PMID:22715412
Beyond hairballs: The use of quantitative mass spectrometry data to understand protein-protein interactions. PMID:22710165
DEFOG: discrete enrichment of functionally organized genes. PMID:22706384
Dynamic network of transcription and pathway crosstalk to reveal molecular mechanism of MGd-treated human lung cancer cells. PMID:22693540
MoNetFamily: a web server to infer homologous modules and module-module interaction networks in vertebrates. PMID:22689643
BIPS: BIANA Interolog Prediction Server. A tool for protein-protein interaction inference. PMID:22689642
IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks. PMID:22684505
Hierarchical modularity and the evolution of genetic interactomes across species. PMID:22681890
MAGNET: MicroArray Gene expression and Network Evaluation Toolkit. PMID:22669910
A topology-based metric for measuring term similarity in the gene ontology. PMID:22666244
An interaction map of endoplasmic reticulum chaperones and foldases. PMID:22665516
Integrated analysis of transcriptome and lipid profiling reveals the co-influences of inositol-choline and Snf1 in controlling lipid biosynthesis in yeast. PMID:22622761
MGEx-Udb: a mammalian uterus database for expression-based cataloguing of genes across conditions, including endometriosis and cervical cancer. PMID:22606288
Prediction and comparison of Salmonella-human and Salmonella-Arabidopsis interactomes. PMID:22589098
Mycobacterium tuberculosis and Clostridium difficille interactomes: demonstration of rapid development of computational system for bacterial interactome prediction. PMID:22587966
The human proteome - a scientific opportunity for transforming diagnostics, therapeutics, and healthcare. PMID:22583803
M-Track: detecting short-lived protein-protein interactions in vivo. PMID:22581371
Exploring the yeast acetylome using functional genomics. PMID:22579291
Functional and topological characterization of transcriptional cooperativity in yeast. PMID:22574744
Linking proteins to signaling pathways for experiment design and evaluation. PMID:22558382
System approaches reveal the molecular networks involved in neural stem cell differentiation. PMID:22492180
Swimming upstream: identifying proteomic signals that drive transcriptional changes using the interactome and multiple "-omics" datasets. PMID:22482945
Integrated inference and analysis of regulatory networks from multi-level measurements. PMID:22482944
Network-based functional enrichment. PMID:22479706
The protein expression landscape of the Arabidopsis root. PMID:22447775
A systematic analysis of cell cycle regulators in yeast reveals that most factors act independently of cell size to control initiation of division. PMID:22438835
How to link ontologies and protein-protein interactions to literature: text-mining approaches and the BioCreative experience. PMID:22438567
An Interspecies Regulatory Network Inferred from Simultaneous RNA-seq of Candida albicans Invading Innate Immune Cells. PMID:22416242
Protein misinteraction avoidance causes highly expressed proteins to evolve slowly. PMID:22416125
Purification of the COP9 signalosome complex and binding partners from human T cells. PMID:22414063
Reducing false-positive prediction of minimotifs with a genetic interaction filter. PMID:22403687
AtPAN: an integrated system for reconstructing transcriptional regulatory networks in Arabidopsis thaliana. PMID:22397531
The role of structural disorder in the rewiring of protein interactions through evolution. PMID:22389433
Transparent mediation-based access to multiple yeast data sources using an ontology driven interface. PMID:22372975
Detection of interacting transcription factors in human tissues using predicted DNA binding affinity. PMID:22369666
Transcriptional activity and nuclear localization of Cabut, the Drosophila ortholog of vertebrate TGF-β-inducible early-response gene (TIEG) proteins. PMID:22359651
Short Co-occurring Polypeptide Regions Can Predict Global Protein Interaction Maps. PMID:22355752
HIPPIE: Integrating protein interaction networks with experiment based quality scores. PMID:22348130
Infection Strategies of Bacterial and Viral Pathogens through Pathogen-Human Protein-Protein Interactions. PMID:22347880
Rewiring of PDZ domain-ligand interaction network contributed to eukaryotic evolution. PMID:22346764
ANAP: an integrated knowledge base for Arabidopsis protein interaction network analysis. PMID:22345505
The identification of short linear motif-mediated interfaces within the human interactome. PMID:22328783
Functional dissection of lysine deacetylases reveals that HDAC1 and p300 regulate AMPK. PMID:22318606
Evolution and function of CAG/polyglutamine repeats in protein-protein interaction networks. PMID:22287626
Putting the pieces together: integrative modeling platform software for structure determination of macromolecular assemblies. PMID:22272186
Differential network biology. PMID:22252388
The genetic control of growth rate: a systems biology study in yeast. PMID:22244311
IMID: integrated molecular interaction database. PMID:22238258
Systems pharmacology: network analysis to identify multiscale mechanisms of drug action. PMID:22235860
Prediction and characterization of protein-protein interaction networks in swine. PMID:22230699
Tramtrack is genetically upstream of genes controlling tracheal tube size in Drosophila. PMID:22216153
Evolution of biological interaction networks: from models to real data. PMID:22204388
Molecular links between cellular senescence, longevity and age-related diseases - a systems biology perspective. PMID:22184282
RefNetBuilder: a platform for construction of integrated reference gene regulatory networks from expressed sequence tags. PMID:22166047
The dichotomy in degree correlation of biological networks. PMID:22164269
The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text. PMID:22151929
Benchmarking of the 2010 BioCreative Challenge III text-mining competition by the BioGRID and MINT interaction databases. PMID:22151178
The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. PMID:22140109
AutismKB: an evidence-based knowledgebase of autism genetics. PMID:22139918
iRefR: an R package to manipulate the iRefIndex consolidated protein interaction database. PMID:22115179
modMine: flexible access to modENCODE data. PMID:22080565
AnimalTFDB: a comprehensive animal transcription factor database. PMID:22080564
Network of Cancer Genes (NCG 3.0): integration and analysis of genetic and network properties of cancer genes. PMID:22080562
Systematic exploration of synergistic drug pairs. PMID:22068327
WormBase 2012: more genomes, more data, new website. PMID:22067452
PINA v2.0: mining interactome modules. PMID:22067443
InterEvol database: exploring the structure and evolution of protein complex interfaces. PMID:22053089
PomBase: a comprehensive online resource for fission yeast. PMID:22039153
Heat shock partially dissociates the overlapping modules of the yeast protein-protein interaction network: a systems level model of adaptation. PMID:22022244
PhenoM: a database of morphological phenotypes caused by mutation of essential genes in Saccharomyces cerevisiae. PMID:22009677
Systems-biology approaches to discover anti-viral effectors of the human innate immune response. PMID:21994773
Gadd45 proteins: relevance to aging, longevity and age-related pathologies. PMID:21986581
Structural analysis of hubs in human NR-RTK network. PMID:21974810
Global identification of modular cullin-RING ligase substrates. PMID:21963094
Using the Saccharomyces Genome Database (SGD) for analysis of genomic information. PMID:21901739
ppiTrim: constructing non-redundant and up-to-date interactomes. PMID:21873645
Conserved and differential gene interactions in dynamical biological systems. PMID:21840874
Prediction of body fluids where proteins are secreted into based on protein interaction network. PMID:21829572
Dynamics of the putative RNA helicase Spb4 during ribosome assembly in Saccharomyces cerevisiae. PMID:21825077
Reactome pathway analysis to enrich biological discovery in proteomics data sets. PMID:21751369
g:Profiler--a web server for functional interpretation of gene lists (2011 update). PMID:21646343
A network of SCOP hidden Markov models and its analysis. PMID:21635719
SLiMSearch 2.0: biological context for short linear motifs in proteins. PMID:21622654
CASCADE_SCAN: mining signal transduction network from high-throughput data based on steepest descent method. PMID:21575263
Actin-binding protein ABP140 is a methyltransferase for 3-methylcytidine at position 32 of tRNAs in Saccharomyces cerevisiae. PMID:21518805
Sig2BioPAX: Java tool for converting flat files to BioPAX Level 3 format. PMID:21418653
Worm Phenotype Ontology: integrating phenotype data within and beyond the C. elegans community. PMID:21261995
Protein databases on the internet. PMID:18265344