R3MK9N last accessed: 2022-11-04

HPRD - Human Protein Reference Database
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

The Human Protein Reference Database (HPRD)
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:57.480032

hprd
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:57.480032

Other names: HPRD, HPRD - Human Protein Reference Database, The Human Protein Reference Database (HPRD), hprd

This source may no longer be available. No known URL could be resolved successfully.

The Human Protein Reference Database represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome.

Webpage:

http://www.hprd.org/

Licence:

Name: Copyrights
URL: https://www.jhu.edu/assets/uploads/2016/11/compliance_policy.pdf

Publications:

Publications
More detailed information about this field from each metasource.

Human Protein Reference Database--2009 update
PMID: 18988627
metasource: Fairsharing.org
version: FAIRsharing.org: HPRD; Human Protein Reference Database; DOI: https://doi.org/10.25504/FAIRsharing.y2qws7; Last edited: Jan. 8, 2019, 1:18 p.m.; Last accessed: Jan 03 2022 7:09 p.m.

Development of human protein reference database as an initial platform for approaching systems biology in humans
PMID: 14525934
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:57.480032

Human protein reference database as a discovery resource for proteomics
PMID: 14681466
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:57.480032

Human Protein Reference Database--2009 update PubMed citations: 1462.

1462 articles citing: Human Protein Reference Database--2009 update

A supervised protein complex prediction method with network representation learning and gene ontology knowledge. PMID:35879648
KSTAR: An algorithm to predict patient-specific kinase activities from phosphoproteomic data. PMID:35879309
An Integrative Heterogeneous Graph Neural Network-Based Method for Multi-Labeled Drug Repurposing. PMID:35873597
NTD-DR: Nonnegative tensor decomposition for drug repositioning. PMID:35862409
DeepND: Deep multitask learning of gene risk for comorbid neurodevelopmental disorders. PMID:35845835
Construction and contextualization approaches for protein-protein interaction networks. PMID:35832626
Deep learning frameworks for protein-protein interaction prediction. PMID:35832624
Network-Based Approaches for Disease-Gene Association Prediction Using Protein-Protein Interaction Networks. PMID:35806415
Identification of the Potential Molecular Mechanisms Linking RUNX1 Activity with Nonalcoholic Fatty Liver Disease, by Means of Systems Biology. PMID:35740337
Identifying Candidate Flavonoids for Non-Alcoholic Fatty Liver Disease by Network-Based Strategy. PMID:35721123
Scalable module detection for attributed networks with applications to breast cancer. PMID:35707802
A novel method for assessing and measuring homophily in networks through second-order statistics. PMID:35697749
A comprehensive SARS-CoV-2-human protein-protein interactome network identifies pathobiology and host-targeting therapies for COVID-19. PMID:35677070
An approach to cellular tropism of SARS-CoV-2 through protein-protein interaction and enrichment analysis. PMID:35672403
Network Pharmacology Approach for Medicinal Plants: Review and Assessment. PMID:35631398
A Novel Ensemble Learning-Based Computational Method to Predict Protein-Protein Interactions from Protein Primary Sequences. PMID:35625503
Human phospho-signaling networks of SARS-CoV-2 infection are rewired by population genetic variants. PMID:35579274
Identification of Potential Muscle Biomarkers in McArdle Disease: Insights from Muscle Proteome Analysis. PMID:35563042
Driver gene detection through Bayesian network integration of mutation and expression profiles. PMID:35561191
Transcriptome analysis of clock disrupted cancer cells reveals differential alternative splicing of cancer hallmarks genes. PMID:35552415
Evaluation of the mechanism of Rujiling capsules in the treatment of hyperplasia of mammary glands based on network pharmacology and molecular docking. PMID:35546462
Novel Protein-Protein Interactions Highlighting the Crosstalk between Hypoplastic Left Heart Syndrome, Ciliopathies and Neurodevelopmental Delays. PMID:35456433
Prioritization of Candidate Biomarkers for Degenerative Aortic Stenosis through a Systems Biology-Based In-Silico Approach. PMID:35455758
An atlas of posttranslational modifications on RNA binding proteins. PMID:35438783
HGDTI: predicting drug-target interaction by using information aggregation based on heterogeneous graph neural network. PMID:35413800
Uncompensated mitochondrial oxidative stress underlies heart failure in an iPSC-derived model of congenital heart disease. PMID:35395180
Mechanisms of action of triptolide against colorectal cancer: insights from proteomic and phosphoproteomic analyses. PMID:35366242
Computational methods, databases and tools for synthetic lethality prediction. PMID:35352098
vWCluster: Vector-valued optimal transport for network based clustering using multi-omics data in breast cancer. PMID:35286348
HAUS5 Is A Potential Prognostic Biomarker With Functional Significance in Breast Cancer. PMID:35280773
HIDTI: integration of heterogeneous information to predict drug-target interactions. PMID:35260608
Identifying individualized risk subpathways reveals pan-cancer molecular classification based on multi-omics data. PMID:35222843
Gene Expression Profile Analyses of the Skin Response of Balb/c-Nu Mice Model Injected by Staphylococcus aureus. PMID:35210800
KeyPathwayMineR: De Novo Pathway Enrichment in the R Ecosystem. PMID:35173764
Pan-Cancer Prediction of Cell-Line Drug Sensitivity Using Network-Based Methods. PMID:35163005
Identification of lapatinib sensitivity-related genes by integrative functional module analysis. PMID:35117483
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
Establishment and characterization of NCC-DMM1-C1, a novel patient-derived cell line of desmoplastic malignant pleural mesothelioma. PMID:35069873
How Far Are We from the Completion of the Human Protein Interactome Reconstruction? PMID:35053288
Multiomic analysis identifies CPT1A as a potential therapeutic target in platinum-refractory, high-grade serous ovarian cancer. PMID:35028612
Hyperphosphorylation of HDAC2 promotes drug resistance in a novel dual drug resistant mouse melanoma cell line model: an in vitro study. PMID:35018231
Potential Molecular Mechanisms and Remdesivir Treatment for Acute Respiratory Syndrome Corona Virus 2 Infection/COVID 19 Through RNA Sequencing and Bioinformatics Analysis. PMID:34992355
A full-proteome, interaction-specific characterization of mutational hotspots across human cancers. PMID:34963661
Exploring complex and heterogeneous correlations on hypergraph for the prediction of drug-target interactions. PMID:34950907
Protein-protein interactions: Methods, databases, and applications in virus-host study. PMID:34909403
MultiCapsNet: A General Framework for Data Integration and Interpretable Classification. PMID:34899854
Metabolic endophenotype associated with right ventricular glucose uptake in pulmonary hypertension. PMID:34888034
A computational approach for the discovery of significant cancer genes by weighted mutation and asymmetric spreading strength in networks. PMID:34876593
Systems biology and machine learning approaches identify drug targets in diabetic nephropathy. PMID:34873190
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
ConsensusPathDB 2022: molecular interactions update as a resource for network biology. PMID:34850110
PharmVIP: A Web-Based Tool for Pharmacogenomic Variant Analysis and Interpretation. PMID:34834582
Geometric network analysis provides prognostic information in patients with high grade serous carcinoma of the ovary treated with immune checkpoint inhibitors. PMID:34819508
Inhibition of bone morphogenetic proteins signaling suppresses metastasis melanoma: a proteomics approach. PMID:34786044
A Deep Learning and XGBoost-Based Method for Predicting Protein-Protein Interaction Sites. PMID:34764983
Locally Adjust Networks Based on Connectivity and Semantic Similarities for Disease Module Detection. PMID:34759955
IID 2021: towards context-specific protein interaction analyses by increased coverage, enhanced annotation and enrichment analysis. PMID:34755877
Tumor relevant protein functional interactions identified using bipartite graph analyses. PMID:34728699
Network-based protein-protein interaction prediction method maps perturbations of cancer interactome. PMID:34727106
RNAInter v4.0: RNA interactome repository with redefined confidence scoring system and improved accessibility. PMID:34718726
Centrality of drug targets in protein networks. PMID:34715787
Improved supervised prediction of aging-related genes via weighted dynamic network analysis. PMID:34696741
Gut-microbiota-microglia-brain interactions in Alzheimer's disease: knowledge-based, multi-dimensional characterization. PMID:34670619
UbiBrowser 2.0: a comprehensive resource for proteome-wide known and predicted ubiquitin ligase/deubiquitinase-substrate interactions in eukaryotic species. PMID:34669962
SYNBIP: synthetic binding proteins for research, diagnosis and therapy. PMID:34664670
Text mining-based word representations for biomedical data analysis and protein-protein interaction networks in machine learning tasks. PMID:34653224
Regulation of ER Composition and Extent, and Putative Action in Protein Networks by ER/NE Protein TMEM147. PMID:34638576
Getting to know each other: PPIMem, a novel approach for predicting transmembrane protein-protein complexes. PMID:34630938
Deep learning in cancer diagnosis, prognosis and treatment selection. PMID:34579788
Identification of driver genes based on gene mutational effects and network centrality. PMID:34560840
A phosphatase-centric mechanism drives stress signaling response. PMID:34558777
Generalized and social anxiety disorder interactomes show distinctive overlaps with striosome and matrix interactomes. PMID:34526518
OGT Protein Interaction Network (OGT-PIN): A Curated Database of Experimentally Identified Interaction Proteins of OGT. PMID:34502531
Identifying Breast Cancer-Related Genes Based on a Novel Computational Framework Involving KEGG Pathways and PPI Network Modularity. PMID:34484285
Machine learning methods, databases and tools for drug combination prediction. PMID:34477201
A machine learning framework for predicting drug-drug interactions. PMID:34475500
Full-length isoform transcriptome of the developing human brain provides further insights into autism. PMID:34469739
A multi-objective genetic algorithm to find active modules in multiplex biological networks. PMID:34460810
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
Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review. PMID:34439912
A global map of associations between types of protein posttranslational modifications and human genetic diseases. PMID:34430807
Molecular Subtypes of Oral Squamous Cell Carcinoma Based on Immunosuppression Genes Using a Deep Learning Approach. PMID:34422810
Fused Lasso Regression for Identifying Differential Correlations in Brain Connectome Graphs. PMID:34386148
LncTx: A network-based method to repurpose drugs acting on the survival-related lncRNAs in lung cancer. PMID:34377365
PPIDomainMiner: Inferring domain-domain interactions from multiple sources of protein-protein interactions. PMID:34370723
Multimodal single-cell omics analysis identifies epithelium-immune cell interactions and immune vulnerability associated with sex differences in COVID-19. PMID:34330889
Cx43 deficiency confers EMT-mediated tamoxifen resistance to breast cancer via c-Src/PI3K/Akt pathway. PMID:34326682
CFTR Lifecycle Map-A Systems Medicine Model of CFTR Maturation to Predict Possible Active Compound Combinations. PMID:34299207
Targeted capture sequencing identifies genetic variations of GRK4 and RDH8 in Han Chinese with essential hypertension in Xinjiang. PMID:34297769
Computational Phosphorylation Network Reconstruction: An Update on Methods and Resources. PMID:34270057
Identification of CXCL13 as an Immune-Related Biomarker Associated with Tumorigenesis and Prognosis in Cutaneous Melanoma Patients. PMID:34247183
Databases for Protein-Protein Interactions. PMID:34236665
A comprehensive review of integrative pharmacology-based investigation: A paradigm shift in traditional Chinese medicine. PMID:34221858
Identification of Diagnostic Markers for Major Depressive Disorder Using Machine Learning Methods. PMID:34220416
Genome-Wide Transcriptomic Analysis of Non-Tumorigenic Tissues Reveals Aging-Related Prognostic Markers and Drug Targets in Renal Cell Carcinoma. PMID:34207247
Identification of Endogenous Kinase Substrates by Proximity Labeling Combined with Kinase Perturbation and Phosphorylation Motifs. PMID:34186244
Recent Progress in FD-LC-MS/MS Proteomics Method. PMID:34178939
FINER: enhancing the prediction of tissue-specific functions of isoforms by refining isoform interaction networks. PMID:34169280
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
Measuring pathway database coverage of the phosphoproteome. PMID:34113485
Phosphorylation of TRIP13 at Y56 induces radiation resistance but sensitizes head and neck cancer to cetuximab. PMID:34111559
Network medicine links SARS-CoV-2/COVID-19 infection to brain microvascular injury and neuroinflammation in dementia-like cognitive impairment. PMID:34108016
LUNAR :Drug Screening for Novel Coronavirus Based on Representation Learning Graph Convolutional Network. PMID:34081583
Predicting phosphorylation sites using machine learning by integrating the sequence, structure, and functional information of proteins. PMID:34030700
KEA3: improved kinase enrichment analysis via data integration. PMID:34019655
Network analysis indicating the pharmacological mechanism of Yunpi-Qufeng-Chushi-prescription in prophylactic treatment of rheumatoid arthritis. PMID:33992108
Application of multiple omics and network projection analyses to drug repositioning for pathogenic mosquito-borne viruses. PMID:33980888
The Links of Ghrelin to Incretins, Insulin, Glucagon, and Leptin After Bariatric Surgery. PMID:33959145
Tumor reversion: a dream or a reality. PMID:33958005
Prioritizing Molecular Biomarkers in Asthma and Respiratory Allergy Using Systems Biology. PMID:33936056
Malignant Pleural Mesothelioma Interactome with 364 Novel Protein-Protein Interactions. PMID:33916178
In silico comparative analysis of LRRK2 interactomes from brain, kidney and lung. PMID:33915162
GADTI: Graph Autoencoder Approach for DTI Prediction From Heterogeneous Network. PMID:33912218
M6ADD: a comprehensive database of m6A modifications in diseases. PMID:33906563
Shared Molecular Mechanisms between Alzheimer's Disease and Periodontitis Revealed by Transcriptomic Analysis. PMID:33869630
Identification of IFN-Induced Transmembrane Protein 1 With Prognostic Value in Pancreatic Cancer Using Network Module-Based Analysis. PMID:33869009
ActiveDriverDB: Interpreting Genetic Variation in Human and Cancer Genomes Using Post-translational Modification Sites and Signaling Networks (2021 Update). PMID:33834021
Predicting Protein-Protein Interactions Using Symmetric Logistic Matrix Factorization. PMID:33831302
Network bioinformatics analysis provides insight into drug repurposing for COVID-19. PMID:33817623
Network medicine links SARS-CoV-2/COVID-19 infection to brain microvascular injury and neuroinflammation in dementia-like cognitive impairment. PMID:33791705
Integrated intra- and intercellular signaling knowledge for multicellular omics analysis. PMID:33749993
Short loop functional commonality identified in leukaemia proteome highlights crucial protein sub-networks. PMID:33709075
Identification of potential and novel target genes in pituitary prolactinoma by bioinformatics analysis. PMID:33709028
Identification of novel prognostic genes of triple-negative breast cancer using meta-analysis and weighted gene co-expressed network analysis. PMID:33708832
Explaining decisions of graph convolutional neural networks: patient-specific molecular subnetworks responsible for metastasis prediction in breast cancer. PMID:33706810
UbiNet 2.0: a verified, classified, annotated and updated database of E3 ubiquitin ligase-substrate interactions. PMID:33693667
DriverSubNet: A Novel Algorithm for Identifying Cancer Driver Genes by Subnetwork Enrichment Analysis. PMID:33679866
HIR V2: a human interactome resource for the biological interpretation of differentially expressed genes via gene set linkage analysis. PMID:33677507
Integrated bioinformatic analysis identifies UBE2Q1 as a potential prognostic marker for high grade serous ovarian cancer. PMID:33663405
An In Silico Method for Predicting Drug Synergy Based on Multitask Learning. PMID:33611781
Proteomics-based approach for differentiation of age-related macular degeneration sub-types. PMID:33595494
KinPred: A unified and sustainable approach for harnessing proteome-level human kinase-substrate predictions. PMID:33556051
Bioinformatics analyses of significant genes, related pathways, and candidate diagnostic biomarkers and molecular targets in SARS-CoV-2/COVID-19. PMID:33553808
Degree Adjusted Large-Scale Network Analysis Reveals Novel Putative Metabolic Disease Genes. PMID:33546175
Construction of a TF-miRNA-gene feed-forward loop network predicts biomarkers and potential drugs for myasthenia gravis. PMID:33510225
Integrative analysis of transcriptomic data for identification of T-cell activation-related mRNA signatures indicative of preterm birth. PMID:33504832
Classification and prediction of protein-protein interaction interface using machine learning algorithm. PMID:33469042
A review of computational drug repositioning: strategies, approaches, opportunities, challenges, and directions. PMID:33431024
Characterization of genome-wide association study data reveals spatiotemporal heterogeneity of mental disorders. PMID:33371872
Neuronal-Glial Interaction in a Triple-Transgenic Mouse Model of Alzheimer's Disease: Gene Ontology and Lithium Pathways. PMID:33335468
ncDRMarker: a computational method for identifying non-coding RNA signatures of drug resistance based on heterogeneous network. PMID:33313140
PDmethDB: A curated Parkinson's disease associated methylation information database. PMID:33304468
Integrated proteome and phosphoproteome analyses of peripheral blood mononuclear cells in primary Sjögren syndrome patients. PMID:33290261
Urinary vitronectin identifies patients with high levels of fibrosis in kidney grafts. PMID:33275196
Identification of Monotonically Differentially Expressed Genes across Pathologic Stages for Cancers. PMID:33273919
Immunoproteomics approach revealed elevated autoantibody levels against ANXA1 in early stage gallbladder carcinoma. PMID:33261560
PINA 3.0: mining cancer interactome. PMID:33231689
Investigation of the Potential Mechanism Governing the Effect of the Shen Zhu San on COVID-19 by Network Pharmacology. PMID:33224256
FunRes: resolving tissue-specific functional cell states based on a cell-cell communication network model. PMID:33179736
H-RACS: a handy tool to rank anti-cancer synergistic drugs. PMID:33173014
Biological network analysis with deep learning. PMID:33169146
A network medicine approach to investigation and population-based validation of disease manifestations and drug repurposing for COVID-19. PMID:33156843
IHP-PING-generating integrated human protein-protein interaction networks on-the-fly. PMID:33129201
Integrated phosphoproteomic and metabolomic profiling reveals perturbed pathways in the hippocampus of gut microbiota dysbiosis mice. PMID:33051451
Tumor Microenvironment-Associated Immune-Related Genes for the Prognosis of Malignant Pleural Mesothelioma. PMID:33042835
Machine learning techniques for sequence-based prediction of viral-host interactions between SARS-CoV-2 and human proteins. PMID:33036956
A review of protein-protein interaction network alignment: From pathway comparison to global alignment. PMID:33033584
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
Role of ACE2 receptor and the landscape of treatment options from convalescent plasma therapy to the drug repurposing in COVID-19. PMID:33029696
Predicting cell-to-cell communication networks using NATMI. PMID:33024107
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
Structure-based validation can drastically underestimate error rate in proteome-wide cross-linking mass spectrometry studies. PMID:32994567
The Cardiac Syndecan-2 Interactome. PMID:32984315
Named Entity Recognition and Relation Detection for Biomedical Information Extraction. PMID:32984300
Cilia interactome with predicted protein-protein interactions reveals connections to Alzheimer's disease, aging and other neuropsychiatric processes. PMID:32973177
Network analysis of KLF5 targets showing the potential oncogenic role of SNHG12 in colorectal cancer. PMID:32943987
A learning-based method for drug-target interaction prediction based on feature representation learning and deep neural network. PMID:32938374
MasterPATH: network analysis of functional genomics screening data. PMID:32928103
A functionally defined high-density NRF2 interactome reveals new conditional regulators of ARE transactivation. PMID:32911434
Network-based modeling of drug effects on disease module in systemic sclerosis. PMID:32770109
KSP: an integrated method for predicting catalyzing kinases of phosphorylation sites in proteins. PMID:32753030
MICA enhances sensitivity to cisplatin in patients with extensive small cell lung cancer via downregulation of ABCG2. PMID:32724354
Risk gene identification and support vector machine learning to construct an early diagnosis model of myocardial infarction. PMID:32705275
Identification of potential markers for type 2 diabetes mellitus via bioinformatics analysis. PMID:32705173
Interactome of SARS-CoV-2 / nCoV19 modulated host proteins with computationally predicted PPIs. PMID:32702714
uKIN Combines New and Prior Information with Guided Network Propagation to Accurately Identify Disease Genes. PMID:32684276
Using phosphoproteomics data to understand cellular signaling: a comprehensive guide to bioinformatics resources. PMID:32676006
Systematic Characterization of Recurrent Genomic Alterations in Cyclin-Dependent Kinases Reveals Potential Therapeutic Strategies for Cancer Treatment. PMID:32668240
Network-principled deep generative models for designing drug combinations as graph sets. PMID:32657357
Harnessing endophenotypes and network medicine for Alzheimer's drug repurposing. PMID:32656864
NAIGO: An Improved Method to Align PPI Networks Based on Gene Ontology and Graphlets. PMID:32637398
Identification of important genes and drug repurposing based on clinical-centered analysis across human cancers. PMID:32555508
Identification of Early Warning Signals at the Critical Transition Point of Colorectal Cancer Based on Dynamic Network Analysis. PMID:32548109
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
Deep belief network-Based Matrix Factorization Model for MicroRNA-Disease Associations Prediction. PMID:32523330
Analysis of extracellular vesicle miRNA profiles in heart failure. PMID:32485073
Repurposed Analog of GLP-1 Ameliorates Hyperglycemia in Type 1 Diabetic Mice Through Pancreatic Cell Reprogramming. PMID:32477262
Genotype-phenotype analysis of LMNA-related diseases predicts phenotype-selective alterations in lamin phosphorylation. PMID:32413188
Mutation severity spectrum of rare alleles in the human genome is predictive of disease type. PMID:32413045
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
Molecular profiling of driver events in metastatic uveal melanoma. PMID:32313009
The Predicted Key Molecules, Functions, and Pathways That Bridge Mild Cognitive Impairment (MCI) and Alzheimer's Disease (AD). PMID:32308643
Nuclear Functions of the Tyrosine Kinase Src. PMID:32290470
Structured reviews for data and knowledge-driven research. PMID:32283553
Identification of Autophagy-Associated Biomarkers and Corresponding Regulatory Factors in the Progression of Colorectal Cancer. PMID:32265986
miRNA target identification and prediction as a function of time in gene expression data. PMID:32249661
Dense module searching for gene networks associated with multiple sclerosis. PMID:32241259
Comparative functional genomic analysis of Alzheimer's affected and naturally aging brains. PMID:32219020
Applications of Network Pharmacology in Traditional Chinese Medicine Research. PMID:32148533
Prioritizing Gene Cascading Paths to Model Colorectal Cancer Through Engineered Organoids. PMID:32117908
CHG: A Systematically Integrated Database of Cancer Hallmark Genes. PMID:32117445
Network Properties of Cancer Prognostic Gene Signatures in the Human Protein Interactome. PMID:32111006
Prediction of Alzheimer's disease using blood gene expression data. PMID:32103140
Exploring Integrative Analysis Using the BioMedical Evidence Graph. PMID:32097025
Exploration of databases and methods supporting drug repurposing: a comprehensive survey. PMID:32055842
In-silico simulated prototype-patients using TPMS technology to study a potential adverse effect of sacubitril and valsartan. PMID:32053711
Predict New Therapeutic Drugs for Hepatocellular Carcinoma Based on Gene Mutation and Expression. PMID:32047745
Identification of a Two-Gene (PML-EPB41) Signature With Independent Prognostic Value in Osteosarcoma. PMID:32039036
PlaPPISite: a comprehensive resource for plant protein-protein interaction sites. PMID:32028878
The cox-filter method identifies respective subtype-specific lncRNA prognostic signatures for two human cancers. PMID:32024523
In silico unravelling pathogen-host signaling cross-talks via pathogen mimicry and human protein-protein interaction networks. PMID:31956393
TP63 isoform expression is linked with distinct clinical outcomes in cancer. PMID:31927310
Identification of Monotonically Differentially Expressed Genes for IFN-β-Treated Multiple Sclerosis Patients. PMID:31915697
Identification of infectious disease-associated host genes using machine learning techniques. PMID:31881961
Refining modules to determine functionally significant clusters in molecular networks. PMID:31874644
Heterogeneous network embedding enabling accurate disease association predictions. PMID:31865913
Identification of breast cancer risk modules via an integrated strategy. PMID:31860871
Weighted gene expression profiles identify diagnostic and prognostic genes for lung adenocarcinoma and squamous cell carcinoma. PMID:31854219
GBDTCDA: Predicting circRNA-disease Associations Based on Gradient Boosting Decision Tree with Multiple Biological Data Fusion. PMID:31853227
MaXLinker: Proteome-wide Cross-link Identifications with High Specificity and Sensitivity. PMID:31839598
Predicting associations among drugs, targets and diseases by tensor decomposition for drug repositioning. PMID:31839008
The human DEPhOsphorylation Database DEPOD: 2019 update. PMID:31836896
Dissecting the Role of NF-κb Protein Family and Its Regulators in Rheumatoid Arthritis Using Weighted Gene Co-Expression Network. PMID:31824568
Identifying Cancer genes by combining two-rounds RWR based on multiple biological data. PMID:31760937
A Computational Framework for Predicting Direct Contacts and Substructures within Protein Complexes. PMID:31717703
Mitochondrial dysfunction in rheumatoid arthritis: A comprehensive analysis by integrating gene expression, protein-protein interactions and gene ontology data. PMID:31703070
BAGSE: a Bayesian hierarchical model approach for gene set enrichment analysis. PMID:31702789
Genomic interrogation of familial short stature contributes to the discovery of the pathophysiological mechanisms and pharmaceutical drug repositioning. PMID:31699087
Computational Methods for Identifying Similar Diseases. PMID:31678735
Dissecting the genetic basis of comorbid epilepsy phenotypes in neurodevelopmental disorders. PMID:31653223
Pathway Commons 2019 Update: integration, analysis and exploration of pathway data. PMID:31647099
HMNPPID-human malignant neoplasm protein-protein interaction database. PMID:31639057
Cerebrospinal Fluid Proteomics For Identification Of α2-Macroglobulin As A Potential Biomarker To Monitor Pharmacological Therapeutic Efficacy In Dopamine Dictated Disease States Of Parkinson's Disease And Schizophrenia. PMID:31632033
Neglog: Homology-Based Negative Data Sampling Method for Genome-Scale Reconstruction of Human Protein-Protein Interaction Networks. PMID:31614890
Biological Network Approaches and Applications in Rare Disease Studies. PMID:31614842
Predicting circRNA-Disease Associations Based on Improved Collaboration Filtering Recommendation System With Multiple Data. PMID:31608124
LOTUS: A single- and multitask machine learning algorithm for the prediction of cancer driver genes. PMID:31568528
A Survey of Gene Prioritization Tools for Mendelian and Complex Human Diseases. PMID:31494632
Targeting amphiregulin (AREG) derived from senescent stromal cells diminishes cancer resistance and averts programmed cell death 1 ligand (PD-L1)-mediated immunosuppression. PMID:31493351
Computer aided analysis of disease linked protein networks. PMID:31485137
The role of microRNA-148a and downstream DLGAP1 on the molecular regulation and tumor progression on human glioblastoma. PMID:31477833
Analyzing the regulation of miRNAs on protein-protein interaction network in Hodgkin lymphoma. PMID:31477006
Enhanced Salt Tolerance of Rhizobia-inoculated Soybean Correlates with Decreased Phosphorylation of the Transcription Factor GmMYB183 and Altered Flavonoid Biosynthesis. PMID:31467032
Quantifying Risk Pathway Crosstalk Mediated by miRNA to Screen Precision drugs for Breast Cancer Patients. PMID:31466383
Transcriptome and Network Dissection of Microsatellite Stable and Highly Instable Colorectal Cancer. PMID:31450919
In silico evidence of de novo interactions between ribosomal and Epstein - Barr virus proteins. PMID:31416416
A network-based pathway-extending approach using DNA methylation and gene expression data to identify altered pathways. PMID:31413306
Evaluation of α-synuclein and apolipoprotein E as potential biomarkers in cerebrospinal fluid to monitor pharmacotherapeutic efficacy in dopamine dictated disease states of Parkinson's disease and schizophrenia. PMID:31410011
A STAT3-based gene signature stratifies glioma patients for targeted therapy. PMID:31399589
A seed-extended algorithm for detecting protein complexes based on density and modularity with topological structure and GO annotations. PMID:31390979
Differential network analysis and protein-protein interaction study reveals active protein modules in glucocorticoid resistance for infant acute lymphoblastic leukemia. PMID:31370801
Detection of dynamic protein complexes through Markov Clustering based on Elephant Herd Optimization Approach. PMID:31366992
Altered transcriptional regulatory proteins in glioblastoma and YBX1 as a potential regulator of tumor invasion. PMID:31358880
Identification of important invasion and proliferation related genes in adrenocortical carcinoma. PMID:31321566
Exploring the Molecular Mechanism of the Drug-Treated Breast Cancer Based on Gene Expression Microarray. PMID:31311202
Patient-specific cancer genes contribute to recurrently perturbed pathways and establish therapeutic vulnerabilities in esophageal adenocarcinoma. PMID:31308377
SCIA: A Novel Gene Set Analysis Applicable to Data With Different Characteristics. PMID:31293623
Quantitative proteomic analysis of sperm in unexplained recurrent pregnancy loss. PMID:31288842
A Novel Genes Signature Associated with the Progression of Polycystic Ovary Syndrome. PMID:31278444
Disease gene prediction for molecularly uncharacterized diseases. PMID:31276496
Identification of key genes involved in myocardial infarction. PMID:31269974
Augmenting subnetwork inference with information extracted from the scientific literature. PMID:31246951
Gradient Boosting Decision Tree-Based Method for Predicting Interactions Between Target Genes and Drugs. PMID:31214240
Protein-protein interaction prediction using a hybrid feature representation and a stacked generalization scheme. PMID:31182027
Conventionally used reference genes are not outstanding for normalization of gene expression in human cancer research. PMID:31138119
Identification of Crucial Candidate Genes and Pathways in Glioblastoma Multiform by Bioinformatics Analysis. PMID:31137733
A rectified factor network based biclustering method for detecting cancer-related coding genes and miRNAs, and their interactions. PMID:31121299
Identification of LIFR, PIK3R1, and MMP12 as Novel Prognostic Signatures in Gallbladder Cancer Using Network-Based Module Analysis. PMID:31119098
Inferring immune-associated signatures based on a co-expression network in Guillain-Barré syndrome. PMID:31094043
Revealing Drug-Target Interactions with Computational Models and Algorithms. PMID:31052598
Genome-wide association study identifies locus at chromosome 2q32.1 associated with syncope and collapse. PMID:31049583
Downregulated UCHL1 Accelerates Gentamicin-Induced Auditory Cell Death via Autophagy. PMID:31041655
Detailed prediction of protein sub-nuclear localization. PMID:31014229
A Comprehensive Drosophila melanogaster Transcription Factor Interactome. PMID:30995488
Comparative Analysis of the Transcriptome and Proteome during Mouse Placental Development. PMID:30986076
Integrated Transcriptomic and Proteomic Analysis of Primary Human Umbilical Vein Endothelial Cells. PMID:30983154
Identification of Important Invasion-Related Genes in Non-functional Pituitary Adenomas. PMID:30982163
Combinatorial Detection of Conserved Alteration Patterns for Identifying Cancer Subnetworks. PMID:30978274
The cardiac syndecan-4 interactome reveals a role for syndecan-4 in nuclear translocation of muscle LIM protein (MLP). PMID:30967474
Structural and Computational Characterization of Disease-Related Mutations Involved in Protein-Protein Interfaces. PMID:30934865
Dark Proteome Database: Studies on Dark Proteins. PMID:30934744
Integrative Genomics Analysis Unravels Tissue-Specific Pathways, Networks, and Key Regulators of Blood Pressure Regulation. PMID:30931314
Individual components of the SWI/SNF chromatin remodelling complex have distinct roles in memory neurons of the Drosophila mushroom body. PMID:30923190
Network Pharmacology Analysis of Damnacanthus indicus C.F.Gaertn in Gene-Phenotype. PMID:30906409
Connectivity problems on heterogeneous graphs. PMID:30899321
A Comprehensive Survey of Tools and Software for Active Subnetwork Identification. PMID:30891064
Prioritization of genes involved in endothelial cell apoptosis by their implication in lymphedema using an analysis of associative gene networks with ANDSystem. PMID:30871556
DeepTACT: predicting 3D chromatin contacts via bootstrapping deep learning. PMID:30869141
Integrated network analysis of transcriptomic and protein-protein interaction data in taurine-treated hepatic stellate cells. PMID:30862995
PIMKL: Pathway-Induced Multiple Kernel Learning. PMID:30854223
Dynamic graphs, community detection, and Riemannian geometry. PMID:30839776
CellSim: a novel software to calculate cell similarity and identify their co-regulation networks. PMID:30832570
Comparative Phosphoproteomic Profiling of Type III Adenylyl Cyclase Knockout and Control, Male, and Female Mice. PMID:30814930
Novel mutation in the ZP1 gene and clinical implications. PMID:30778819
Analysis of Topological Parameters of Complex Disease Genes Reveals the Importance of Location in a Biomolecular Network. PMID:30769902
MDH1 and MPP7 Regulate Autophagy in Pancreatic Ductal Adenocarcinoma. PMID:30765601
deepDriver: Predicting Cancer Driver Genes Based on Somatic Mutations Using Deep Convolutional Neural Networks. PMID:30761181
A data-driven interactome of synergistic genes improves network-based cancer outcome prediction. PMID:30726216
Functional homogeneity and specificity of topological modules in human proteome. PMID:30717667
A High Efficient Biological Language Model for Predicting Protein⁻Protein Interactions. PMID:30717470
Comparative Phosphoproteomic Analysis of Barley Embryos with Different Dormancy during Imbibition. PMID:30669653
Exploiting locational and topological overlap model to identify modules in protein interaction networks. PMID:30642247
Global Phosphoproteomic Analysis Reveals the Defense and Response Mechanisms of Jatropha Curcas Seedling under Chilling Stress. PMID:30626061
GeNeCK: a web server for gene network construction and visualization. PMID:30616521
The Network of Cancer Genes (NCG): a comprehensive catalogue of known and candidate cancer genes from cancer sequencing screens. PMID:30606230
MoMo: discovery of statistically significant post-translational modification motifs. PMID:30596994
Bayesian generalized biclustering analysis via adaptive structured shrinkage. PMID:30596887
Network spectra for drug-target identification in complex diseases: new guns against old foes. PMID:30596144
A Network Pharmacology Analysis to Explore the Effect of Astragali Radix-Radix Angelica Sinensis on Traumatic Brain Injury. PMID:30596090
Molecular subtyping of cancer and nomination of kinase candidates for inhibition with phosphoproteomics: Reanalysis of CPTAC ovarian cancer. PMID:30594550
Integrative network and brain expression analysis reveals mechanistic modules in ataxia. PMID:30591515
The RTK Interactome: Overview and Perspective on RTK Heterointeractions. PMID:30589534
Proteomic Analysis of the Human Anterior Pituitary Gland. PMID:30571610
Interplay Between Amphetamine and Activity Level in Gene Networks of the Mouse Striatum. PMID:30559594
Several genes involved in the JAK-STAT pathway may act as prognostic markers in pancreatic cancer identified by microarray data analysis. PMID:30557977
Predicting protein targets for drug-like compounds using transcriptomics. PMID:30532261
Mapping the Proteome of the Synaptic Cleft through Proximity Labeling Reveals New Cleft Proteins. PMID:30487426
Microarray analysis of the molecular mechanisms associated with age and body mass index in human meniscal injury. PMID:30483788
Adipocyte-secreted BMP8b mediates adrenergic-induced remodeling of the neuro-vascular network in adipose tissue. PMID:30478315
Network Pharmacology to Unveil the Biological Basis of Health-Strengthening Herbal Medicine in Cancer Treatment. PMID:30469422
Structural disorder in the proteome and interactome of Alkhurma virus (ALKV). PMID:30443749
Prior Knowledge Driven Joint NMF Algorithm for ceRNA Co-Module Identification. PMID:30443186
Ma Huang Tang ameliorates bronchial asthma symptoms through the TLR9 pathway. PMID:30415587
A Network Pharmacology Approach to Uncover the Molecular Mechanisms of Herbal Formula Ban-Xia-Xie-Xin-Tang. PMID:30410554
IID 2018 update: context-specific physical protein-protein interactions in human, model organisms and domesticated species. PMID:30407591
Exploring Pharmacological Mechanisms of Xuefu Zhuyu Decoction in the Treatment of Traumatic Brain Injury via a Network Pharmacology Approach. PMID:30402137
Comparative functional analysis of proteins containing low-complexity predicted amyloid regions. PMID:30397544
PWCDA: Path Weighted Method for Predicting circRNA-Disease Associations. PMID:30384427
qPhos: a database of protein phosphorylation dynamics in humans. PMID:30380102
Antiviral activity of the mineralocorticoid receptor NR3C2 against Herpes simplex virus Type 1 (HSV-1) infection. PMID:30367157
Victors: a web-based knowledge base of virulence factors in human and animal pathogens. PMID:30365026
Heterogeneous network embedding for identifying symptom candidate genes. PMID:30357378
Targeting SPINK1 in the damaged tumour microenvironment alleviates therapeutic resistance. PMID:30333494
Genomic data integration systematically biases interactome mapping. PMID:30332399
Evaluation of Serum Apolipoprotein E as a Potential Biomarker for Pharmacological Therapeutic Efficacy Monitoring in Dopamine Dictated Disease Spectrum of Schizophrenia and Parkinson's disease: A Preliminary Study. PMID:30327579
Context-enriched interactome powered by proteomics helps the identification of novel regulators of macrophage activation. PMID:30303482
Systems genetics of nonsyndromic orofacial clefting provides insights into its complex aetiology. PMID:30254216
PTMD: A Database of Human Disease-associated Post-translational Modifications. PMID:30244175
Identifying protein complexes based on node embeddings obtained from protein-protein interaction networks. PMID:30241459
Systematic identification of the key candidate genes in breast cancer stroma. PMID:30237810
Integrating genetic, transcriptional, and biological information provides insights into obesity. PMID:30232418
Data from quantitative proteomic analysis of lung adenocarcinoma and squamous cell carcinoma primary tissues using high resolution mass spectrometry. PMID:30229035
Phosphotyrosine profiling of human cerebrospinal fluid. PMID:30220890
Modeling and Simulating the Aerobic Carbon Metabolism of a Green Microalga Using Petri Nets and New Concepts of VANESA. PMID:30218605
AWESOME: a database of SNPs that affect protein post-translational modifications. PMID:30215764
AnimalTFDB 3.0: a comprehensive resource for annotation and prediction of animal transcription factors. PMID:30204897
Comprehensive network map of interferon gamma signaling. PMID:30191398
Insights into archaeal chaperone machinery: a network-based approach. PMID:30178307
Prediction of Novel Drugs and Diseases for Hepatocellular Carcinoma Based on Multi-Source Simulated Annealing Based Random Walk. PMID:30173379
ESCC ATLAS: A population wide compendium of biomarkers for Esophageal Squamous Cell Carcinoma. PMID:30143675
A New Strategy to Uncover the Anticancer Mechanism of Chinese Compound Formula by Integrating Systems Pharmacology and Bioinformatics. PMID:30108661
Transcriptome analysis of adult Caenorhabditis elegans cells reveals tissue-specific gene and isoform expression. PMID:30096138
Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken. PMID:30086717
A network map of netrin receptor UNC5B-mediated signaling. PMID:30084000
Evolution of In Silico Strategies for Protein-Protein Interaction Drug Discovery. PMID:30082644
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
Explaining cancer type specific mutations with transcriptomic and epigenomic features in normal tissues. PMID:30061703
BioMuta and BioXpress: mutation and expression knowledgebases for cancer biomarker discovery. PMID:30053270
An unsupervised machine learning method for discovering patient clusters based on genetic signatures. PMID:30016722
Integrative analysis of promising molecular biomarkers and pathways for coronary artery disease using WGCNA and MetaDE methods. PMID:30015926
A novel phosphorylation by AMP-activated kinase regulates RUNX2 from ubiquitination in osteogenesis over adipogenesis. PMID:29988028
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
In silico approach in reveal traditional medicine plants pharmacological material basis. PMID:29946351
Proximal Pathway Enrichment Analysis for Targeting Comorbid Diseases via Network Endopharmacology. PMID:29932108
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
Computational Methods for Predicting Protein-Protein Interactions Using Various Protein Features. PMID:29927082
Developments in toxicogenomics: understanding and predicting compound-induced toxicity from gene expression data. PMID:29917034
Subcellular stoichiogenomics reveal cell evolution and electrostatic interaction mechanisms in cytoskeleton. PMID:29914356
An interactome perturbation framework prioritizes damaging missense mutations for developmental disorders. PMID:29892012
A systems immunology approach identifies the collective impact of 5 miRs in Th2 inflammation. PMID:29875322
Network-based machine learning and graph theory algorithms for precision oncology. PMID:29872707
Construction of a specific SVM classifier and identification of molecular markers for lung adenocarcinoma based on lncRNA-miRNA-mRNA network. PMID:29872324
Discovering mutated driver genes through a robust and sparse co-regularized matrix factorization framework with prior information from mRNA expression patterns and interaction network. PMID:29871594
MGOGP: a gene module-based heuristic algorithm for cancer-related gene prioritization. PMID:29871590
Evaluating the Genetics of Common Variable Immunodeficiency: Monogenetic Model and Beyond. PMID:29867916
Role of Toll-Like Receptor 4 on Osteoblast Metabolism and Function. PMID:29867550
Essential genes of the macrophage response to Staphylococcus aureus exposure. PMID:29849669
PhosContext2vec: a distributed representation of residue-level sequence contexts and its application to general and kinase-specific phosphorylation site prediction. PMID:29844483
GIANT 2.0: genome-scale integrated analysis of gene networks in tissues. PMID:29800226
Convergent roles of de novo mutations and common variants in schizophrenia in tissue-specific and spatiotemporal co-expression network. PMID:29799522
Network-Based Disease Module Discovery by a Novel Seed Connector Algorithm with Pathobiological Implications. PMID:29791871
Modeling Transcriptional Rewiring in Neutrophils Through the Course of Treated Juvenile Idiopathic Arthritis. PMID:29773851
Predicting hepatocellular carcinoma through cross-talk genes identified by risk pathways. PMID:29765536
Discovering novel SNPs that are correlated with patient outcome in a Singaporean cancer patient cohort treated with gemcitabine-based chemotherapy. PMID:29751792
A gene interaction network‑based method to measure the common and heterogeneous mechanisms of gynecological cancer. PMID:29749503
PPI network analyses of human WD40 protein family systematically reveal their tendency to assemble complexes and facilitate the complex predictions. PMID:29745845
Multi-target drug repositioning by bipartite block-wise sparse multi-task learning. PMID:29745839
Identification of spleen tyrosine kinase as a potential therapeutic target for esophageal squamous cell carcinoma using reverse phase protein arrays. PMID:29719615
Precision Profiling of the Cardiovascular Post-Translationally Modified Proteome: Where There Is a Will, There Is a Way. PMID:29700069
Signalling maps in cancer research: construction and data analysis. PMID:29688383
Characterizing Cancer Drug Response and Biological Correlates: A Geometric Network Approach. PMID:29686393
In silico epigenetics of metal exposure and subclinical atherosclerosis in middle aged men: pilot results from the Aragon Workers Health Study. PMID:29685964
Measuring phenotype-phenotype similarity through the interactome. PMID:29671400
p52 expression enhances lung cancer progression. PMID:29666445
NIPS, a 3D network-integrated predictor of deleterious protein SAPs, and its application in cancer prognosis. PMID:29662108
Computation and application of tissue-specific gene set weights. PMID:29659714
Combined bioinformatics analysis reveals gene expression and DNA methylation patterns in osteoarthritis. PMID:29658578
Proteomic analysis defines kinase taxonomies specific for subtypes of breast cancer. PMID:29643987
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
Key genes and regulatory networks involved in the initiation, progression and invasion of colorectal cancer. PMID:29568567
Completing sparse and disconnected protein-protein network by deep learning. PMID:29566671
A homologous mapping method for three-dimensional reconstruction of protein networks reveals disease-associated mutations. PMID:29560828
Gastric cancer biomarkers; A systems biology approach. PMID:29556568
Curcumin may serve an anticancer role in human osteosarcoma cell line U-2 OS by targeting ITPR1. PMID:29552196
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
Loss and gain of N-linked glycosylation sequons due to single-nucleotide variation in cancer. PMID:29531238
Combined use of protein biomarkers and network analysis unveils deregulated regulatory circuits in Duchenne muscular dystrophy. PMID:29529088
Extracellular vesicle RNAs reflect placenta dysfunction and are a biomarker source for preterm labour. PMID:29516617
Quantitative Phosphoproteomic and Metabolomic Analyses Reveal GmMYB173 Optimizes Flavonoid Metabolism in Soybean under Salt Stress. PMID:29496908
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
Expression, regulation and targeting of receptor tyrosine kinases in esophageal squamous cell carcinoma. PMID:29455652
Global view of a drug-sensitivity gene network. PMID:29423044
Host-Virus Protein Interaction Network Reveals the Involvement of Multiple Host Processes in the Life Cycle of Hepatitis E Virus. PMID:29404423
Identification of candidate genes that may contribute to the metastasis of prostate cancer by bioinformatics analysis. PMID:29399176
Discovery of Cryoprotective Activity in Human Genome-Derived Intrinsically Disordered Proteins. PMID:29385704
Phosphoproteome profiling reveals critical role of JAK-STAT signaling in maintaining chemoresistance in breast cancer. PMID:29383118
Systematic identification of latent disease-gene associations from PubMed articles. PMID:29373609
Scuba: scalable kernel-based gene prioritization. PMID:29370760
PhenoRank: reducing study bias in gene prioritization through simulation. PMID:29360927
Protein complex finding and ranking: An application to Alzheimer's disease. PMID:29358552
Small-Molecule Activators of Protein Phosphatase 2A for the Treatment of Castration-Resistant Prostate Cancer. PMID:29358171
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
Phosphoproteomics-Based Profiling of Kinase Activities in Cancer Cells. PMID:29344887
Systemic bioinformatics analysis of recurrent aphthous stomatitis gene expression profiles. PMID:29340037
Feature genes in metastatic breast cancer identified by MetaDE and SVM classifier methods. PMID:29328377
Support vector machine classifier for prediction of the metastasis of colorectal cancer. PMID:29328363
Logistic regression analysis for the identification of the metastasis-associated signaling pathways of osteosarcoma. PMID:29328361
Extracting Fitness Relationships and Oncogenic Patterns among Driver Genes in Cancer. PMID:29295608
Construction of a 26‑feature gene support vector machine classifier for smoking and non‑smoking lung adenocarcinoma sample classification. PMID:29257283
A multigene support vector machine predictor for metastasis of cutaneous melanoma. PMID:29257259
Role of exosomes in hepatocellular carcinoma cell mobility alteration. PMID:29250190
FGMD: A novel approach for functional gene module detection in cancer. PMID:29244808
A network-based predictive gene-expression signature for adjuvant chemotherapy benefit in stage II colorectal cancer. PMID:29237416
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
Predicting new indications of compounds with a network pharmacology approach: Liuwei Dihuang Wan as a case study. PMID:29212201
Protein-protein interaction analysis to identify biomarker networks for endometriosis. PMID:29201163
Inference of differentiation time for single cell transcriptomes using cell population reference data. PMID:29187729
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
Phosphoproteomics of cAMP signaling of Bordetella adenylate cyclase toxin in mouse dendritic cells. PMID:29176673
Using molecular functional networks to manifest connections between obesity and obesity-related diseases. PMID:29156709
Molecular Interaction Search Tool (MIST): an integrated resource for mining gene and protein interaction data. PMID:29155944
iPTMnet: an integrated resource for protein post-translational modification network discovery. PMID:29145615
SPRINT: ultrafast protein-protein interaction prediction of the entire human interactome. PMID:29141584
ActiveDriverDB: human disease mutations and genome variation in post-translational modification sites of proteins. PMID:29126202
The UCSC Genome Browser database: 2018 update. PMID:29106570
TumorFusions: an integrative resource for cancer-associated transcript fusions. PMID:29099951
HEDD: Human Enhancer Disease Database. PMID:29077884
The Early Dendritic Cell Signaling Induced by Virulent Francisella tularensis Strain Occurs in Phases and Involves the Activation of Extracellular Signal-Regulated Kinases (ERKs) and p38 In the Later Stage. PMID:29046388
PICKLE 2.0: A human protein-protein interaction meta-database employing data integration via genetic information ontology. PMID:29023571
Bioinformatics analysis of gene expression data for the identification of critical genes in breast invasive carcinoma. PMID:28990063
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
Distinct distributions of genomic features of the 5' and 3' partners of coding somatic cancer gene fusions: arising mechanisms and functional implications. PMID:28977995
Using neural networks for reducing the dimensions of single-cell RNA-Seq data. PMID:28973464
Learning causal networks with latent variables from multivariate information in genomic data. PMID:28968390
Network-Based Coverage of Mutational Profiles Reveals Cancer Genes. PMID:28957656
Pathway Enrichment Analysis with Networks. PMID:28956817
Molecular mechanisms underlying gliomas and glioblastoma pathogenesis revealed by bioinformatics analysis of microarray data. PMID:28952134
NetGen: a novel network-based probabilistic generative model for gene set functional enrichment analysis. PMID:28950861
HTS-Net: An integrated regulome-interactome approach for establishing network regulation models in high-throughput screenings. PMID:28949986
Identification of key genes associated with the effect of osmotic stimuli on intervertebral discs using microarray analysis. PMID:28943935
Network module identification-A widespread theoretical bias and best practices. PMID:28941788
De novo pathway-based biomarker identification. PMID:28934488
A network integration approach for drug-target interaction prediction and computational drug repositioning from heterogeneous information. PMID:28924171
A support vector machine classifier for the prediction of osteosarcoma metastasis with high accuracy. PMID:28901446
Evolutionary analysis and interaction prediction for protein-protein interaction network in geometric space. PMID:28886027
Predicting multicellular function through multi-layer tissue networks. PMID:28881986
Incorporating interaction networks into the determination of functionally related hit genes in genomic experiments with Markov random fields. PMID:28881978
Main active constituent identification in Guanxinjing capsule, a traditional Chinese medicine, for the treatment of coronary heart disease complicated with depression. PMID:28858293
Comprehensive Analyses of Tissue-Specific Networks with Implications to Psychiatric Diseases. PMID:28849569
The effect of Bu Zhong Yi Qi decoction on simulated weightlessness‑induced muscle atrophy and its mechanisms. PMID:28849026
An integrated bioinformatics platform for investigating the human E3 ubiquitin ligase-substrate interaction network. PMID:28839186
A network pharmacology-based strategy deciphers the underlying molecular mechanisms of Qixuehe Capsule in the treatment of menstrual disorders. PMID:28835770
Development of a Multiplexed Assay for Oral Cancer Candidate Biomarkers Using Peptide Immunoaffinity Enrichment and Targeted Mass Spectrometry. PMID:28821604
Chronic Cigarette Smoke Mediated Global Changes in Lung Mucoepidermoid Cells: A Phosphoproteomic Analysis. PMID:28816646
Candidate genes investigation for severe nonalcoholic fatty liver disease based on bioinformatics analysis. PMID:28796060
Unraveling a tumor type-specific regulatory core underlying E2F1-mediated epithelial-mesenchymal transition to predict receptor protein signatures. PMID:28775339
Enriching Traditional Protein-protein Interaction Networks with Alternative Conformations of Proteins. PMID:28775330
Identification of key genes associated with rheumatoid arthritis with bioinformatics approach. PMID:28767591
RNA sequencing identifies gene expression profile changes associated with β-estradiol treatment in U2OS osteosarcoma cells. PMID:28744146
Genetic and functional characterization of disease associations explains comorbidity. PMID:28740175
Significant and unique changes in phosphorylation levels of four phosphoproteins in two apple rootstock genotypes under drought stress. PMID:28710562
HDNetDB: A Molecular Interaction Database for Network-Oriented Investigations into Huntington's Disease. PMID:28701700
Incorporating biological information in sparse principal component analysis with application to genomic data. PMID:28697740
Long-Term Cigarette Smoke Exposure and Changes in MiRNA Expression and Proteome in Non-Small-Cell Lung Cancer. PMID:28692419
Drug Target Protein-Protein Interaction Networks: A Systematic Perspective. PMID:28691014
A Systems Vaccinology Approach Reveals Temporal Transcriptomic Changes of Immune Responses to the Yellow Fever 17D Vaccine. PMID:28687661
Network approaches to systems biology analysis of complex disease: integrative methods for multi-omics data. PMID:28679163
E3 Ubiquitin ligase ZNRF4 negatively regulates NOD2 signalling and induces tolerance to MDP. PMID:28656966
NetNorM: Capturing cancer-relevant information in somatic exome mutation data with gene networks for cancer stratification and prognosis. PMID:28650955
On the performance of de novo pathway enrichment. PMID:28649433
HGPEC: a Cytoscape app for prediction of novel disease-gene and disease-disease associations and evidence collection based on a random walk on heterogeneous network. PMID:28619054
Visualization and Analysis of MicroRNAs within KEGG Pathways using VANESA. PMID:28609293
Neighbours of cancer-related proteins have key influence on pathogenesis and could increase the drug target space for anticancer therapies. PMID:28603644
A novel network regularized matrix decomposition method to detect mutated cancer genes in tumour samples with inter-patient heterogeneity. PMID:28588243
Cross-Kingdom Regulation of Putative miRNAs Derived from Happy Tree in Cancer Pathway: A Systems Biology Approach. PMID:28587194
Investigating critical genes and gene interaction networks that mediate cyclophosphamide sensitivity in chronic myelogenous leukemia. PMID:28560425
Genome-wide network-based pathway analysis of CSF t-tau/Aβ1-42 ratio in the ADNI cohort. PMID:28558704
The complex genetics of hypoplastic left heart syndrome. PMID:28530678
Identification of breast cancer prognostic modules based on weighted protein-protein interaction networks. PMID:28529601
Targeting the CXCR4 pathway using a novel anti-CXCR4 IgG1 antibody (PF-06747143) in chronic lymphocytic leukemia. PMID:28526063
A computational framework for distinguishing direct versus indirect interactions in human functional protein-protein interaction networks. PMID:28524201
An Integrating Approach for Genome-Wide Screening of MicroRNA Polymorphisms Mediated Drug Response Alterations. PMID:28480217
From protein-protein interactions to protein co-expression networks: a new perspective to evaluate large-scale proteomic data. PMID:28477207
Integrative Analysis of Gene Networks and Their Application to Lung Adenocarcinoma Studies. PMID:28469387
Methods, Tools and Current Perspectives in Proteogenomics. PMID:28456751
Network-aided Bi-Clustering for discovering cancer subtypes. PMID:28432308
iTRAQ-based quantitative proteomic analysis of Yamanaka factors reprogrammed breast cancer cells. PMID:28423718
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
Comparison of tissue/disease specific integrated networks using directed graphlet signatures. PMID:28361704
Identifying miRNA sponge modules using biclustering and regulatory scores. PMID:28361682
DIGNiFI: Discovering causative genes for orphan diseases using protein-protein interaction networks. PMID:28361678
Enhanced construction of gene regulatory networks using hub gene information. PMID:28335719
Exploring the FGFR3-related oncogenic mechanism in bladder cancer using bioinformatics strategy. PMID:28320388
Multidimensional Integrative Genomics Approaches to Dissecting Cardiovascular Disease. PMID:28289683
Transcriptional Responses to Ultraviolet and Ionizing Radiation: An Approach Based on Graph Curvature. PMID:28261534
Integrated systems biology analysis of KSHV latent infection reveals viral induction and reliance on peroxisome mediated lipid metabolism. PMID:28257516
Network Biomarkers Constructed from Gene Expression and Protein-Protein Interaction Data for Accurate Prediction of Leukemia. PMID:28243332
Estimation of Directed Acyclic Graphs Through Two-stage Adaptive Lasso for Gene Network Inference. PMID:28239216
Understanding the roles of intrinsic disorder in subunits of hemoglobin and the disease process of sickle cell anemia. PMID:28232898
Identification of miRNA-mRNA Modules in Colorectal Cancer Using Rough Hypercuboid Based Supervised Clustering. PMID:28220871
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
Novel involvement of RhebL1 in sphingosylphosphorylcholine-induced keratin phosphorylation and reorganization: Binding to and activation of AKT1. PMID:28209923
Pathway deviation-based biomarker and multi-effect target identification in asbestos-related squamous cell carcinoma of the lung. PMID:28204826
Targeted sequencing identifies 91 neurodevelopmental-disorder risk genes with autism and developmental-disability biases. PMID:28191889
Integrated analysis of proteome, phosphotyrosine-proteome, tyrosine-kinome, and tyrosine-phosphatome in acute myeloid leukemia. PMID:28176486
Interrogating the hidden phosphoproteome. PMID:28165663
Genome-wide association analysis implicates dysregulation of immunity genes in chronic lymphocytic leukaemia. PMID:28165464
LNDriver: identifying driver genes by integrating mutation and expression data based on gene-gene interaction network. PMID:28155630
Mapping Biological Networks from Quantitative Data-Independent Acquisition Mass Spectrometry: Data to Knowledge Pipelines. PMID:28150249
iPTMnet: Integrative Bioinformatics for Studying PTM Networks. PMID:28150246
Protein Bioinformatics Databases and Resources. PMID:28150231
The use of gene interaction networks to improve the identification of cancer driver genes. PMID:28149674
Meta-analytic support vector machine for integrating multiple omics data. PMID:28149325
SATB1 plays an oncogenic role in esophageal cancer by up-regulation of FN1 and PDGFRB. PMID:28147311
The integration of weighted human gene association networks based on link prediction. PMID:28137253
Identification of protein complexes by integrating multiple alignment of protein interaction networks. PMID:28130237
Identification of Entry Factors Involved in Hepatitis C Virus Infection Based on Host-Mimicking Short Linear Motifs. PMID:28129350
CyNetSVM: A Cytoscape App for Cancer Biomarker Identification Using Network Constrained Support Vector Machines. PMID:28122019
Comparative Phosphoproteomics Reveals an Important Role of MKK2 in Banana (Musa spp.) Cold Signal Network. PMID:28106078
Combining Chemical Profiling and Network Analysis to Investigate the Pharmacology of Complex Prescriptions in Traditional Chinese Medicine. PMID:28084407
Human Lacrimal Gland Gene Expression. PMID:28081151
A Global Analysis of the Receptor Tyrosine Kinase-Protein Phosphatase Interactome. PMID:28065597
Integration of MicroRNA, mRNA, and Protein Expression Data for the Identification of Cancer-Related MicroRNAs. PMID:28056026
Functional constraints on adaptive evolution of protein ubiquitination sites. PMID:28054638
Global Prioritizing Disease Candidate lncRNAs via a Multi-level Composite Network. PMID:28051121
Genomic expression differences between cutaneous cells from red hair color individuals and black hair color individuals based on bioinformatic analysis. PMID:28030792
A Functional Genomic Meta-Analysis of Clinical Trials in Systemic Sclerosis: Toward Precision Medicine and Combination Therapy. PMID:28011145
Transcriptome analyses identify key cellular factors associated with HIV-1-associated neuropathogenesis in infected men. PMID:28005686
Identification of feature genes for smoking-related lung adenocarcinoma based on gene expression profile data. PMID:27994470
Improved method for prioritization of disease associated lncRNAs based on ceRNA theory and functional genomics data. PMID:27992375
CanProVar 2.0: An Updated Database of Human Cancer Proteome Variation. PMID:27977206
Identification of Risk Pathways and Functional Modules for Coronary Artery Disease Based on Genome-wide SNP Data. PMID:27965104
Proteome-Scale Investigation of Protein Allosteric Regulation Perturbed by Somatic Mutations in 7,000 Cancer Genomes. PMID:27939638
Specificity of broad protein interaction surfaces for proteins with multiple binding partners. PMID:27924264
Elucidating the druggable interface of protein-protein interactions using fragment docking and coevolutionary analysis. PMID:27911825
An atlas of human kinase regulation. PMID:27909043
Differential variation patterns between hubs and bottlenecks in human protein-protein interaction networks. PMID:27903259
Microarray analysis of differentially-expressed genes and linker genes associated with the molecular mechanism of colorectal cancer. PMID:27899990
Prediction of Protein-Protein Interactions by Evidence Combining Methods. PMID:27879651
Computational approaches for the identification of cancer genes and pathways. PMID:27863091
Bisdemethoxycurcumin exerts pro-apoptotic effects in human pancreatic adenocarcinoma cells through mitochondrial dysfunction and a GRP78-dependent pathway. PMID:27845899
Feature-based classification of human transcription factors into hypothetical sub-classes related to regulatory function. PMID:27842491
Glucose-regulated and drug-perturbed phosphoproteome reveals molecular mechanisms controlling insulin secretion. PMID:27841257
Intrinsic disorder in proteins involved in amyotrophic lateral sclerosis. PMID:27838743
Systematic Analysis of Protein Interaction Network Associated with Azoospermia. PMID:27834916
CASTIN: a system for comprehensive analysis of cancer-stromal interactome. PMID:27829362
Multi-label ℓ2-regularized logistic regression for predicting activation/inhibition relationships in human protein-protein interaction networks. PMID:27819359
Gene expression profiles and protein-protein interaction networks in amyotrophic lateral sclerosis patients with C9orf72 mutation. PMID:27814735
WORMHOLE: Novel Least Diverged Ortholog Prediction through Machine Learning. PMID:27812085
In Silico Analysis Validates Proteomic Findings of Formalin-fixed Paraffin Embedded Cutaneous Squamous Cell Carcinoma Tissue. PMID:27807068
A network-pathway based module identification for predicting the prognosis of ovarian cancer patients. PMID:27806724
Proteomic profiling of retinoblastoma by high resolution mass spectrometry. PMID:27799869
HIPPIE v2.0: enhancing meaningfulness and reliability of protein-protein interaction networks. PMID:27794551
WERAM: a database of writers, erasers and readers of histone acetylation and methylation in eukaryotes. PMID:27789692
A Systems Biology Comparison of Ovarian Cancers Implicates Putative Somatic Driver Mutations through Protein-Protein Interaction Models. PMID:27788148
Identification of lncRNA functions in lung cancer based on associated protein-protein interaction modules. PMID:27786280
A computational interactome and functional annotation for the human proteome. PMID:27770567
Incorporating topological information for predicting robust cancer subnetwork markers in human protein-protein interaction network. PMID:27766944
Effective comparative analysis of protein-protein interaction networks by measuring the steady-state network flow using a Markov model. PMID:27766938
Global phosphoproteomic profiling reveals perturbed signaling in a mouse model of dilated cardiomyopathy. PMID:27742792
Identifying candidate agents for lung adenocarcinoma by walking the human interactome. PMID:27729798
Exploring the interactions of the RAS family in the human protein network and their potential implications in RAS-directed therapies. PMID:27713118
OAHG: an integrated resource for annotating human genes with multi-level ontologies. PMID:27703231
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
Identification potential biomarkers in pulmonary tuberculosis and latent infection based on bioinformatics analysis. PMID:27655333
Combined Analysis of ChIP Sequencing and Gene Expression Dataset in Breast Cancer. PMID:27654269
Statistical Approaches for the Construction and Interpretation of Human Protein-Protein Interaction Network. PMID:27648447
A Cytokine Signalling Network for the Regulation of Inducible Nitric Oxide Synthase Expression in Rheumatoid Arthritis. PMID:27626941
inFRank: a ranking-based identification of influential genes in biological networks. PMID:27623074
DM-BLD: differential methylation detection using a hierarchical Bayesian model exploiting local dependency. PMID:27616707
Microvesicles from brain-extract-treated mesenchymal stem cells improve neurological functions in a rat model of ischemic stroke. PMID:27609711
Integration of transcriptomic and genomic data suggests candidate mechanisms for APOE4-mediated pathogenic action in Alzheimer's disease. PMID:27585646
Discover the network underlying the connections between aging and age-related diseases. PMID:27582315
Fusing literature and full network data improves disease similarity computation. PMID:27578323
Identification of hub genes and regulatory factors of glioblastoma multiforme subgroups by RNA-seq data analysis. PMID:27572852
Identification of rifampin-regulated functional modules and related microRNAs in human hepatocytes based on the protein interaction network. PMID:27557147
Cancer network activity associated with therapeutic response and synergism. PMID:27553366
A protein network descriptor server and its use in studying protein, disease, metabolic and drug targeted networks. PMID:27542402
Functional characterization of EI24-induced autophagy in the degradation of RING-domain E3 ligases. PMID:27541728
miR-625-3p regulates oxaliplatin resistance by targeting MAP2K6-p38 signalling in human colorectal adenocarcinoma cells. PMID:27526785
Prevalent Accumulation of Non-Optimal Codons through Somatic Mutations in Human Cancers. PMID:27513638
Integrated analysis miRNA and mRNA profiling in patients with severe oligozoospermia reveals miR-34c-3p downregulates PLCXD3 expression. PMID:27486773
Human Prostate Cancer Hallmarks Map. PMID:27476486
NCMine: Core-peripheral based functional module detection using near-clique mining. PMID:27466623
Signaling network map of the aryl hydrocarbon receptor. PMID:27465749
A novel algorithm for network-based prediction of cancer recurrence. PMID:27453286
Unfoldomics of prostate cancer: on the abundance and roles of intrinsically disordered proteins in prostate cancer. PMID:27453073
Small-molecule binding sites to explore protein-protein interactions in the cancer proteome. PMID:27452673
Identification of key target genes and pathways in laryngeal carcinoma. PMID:27446427
Ranking novel cancer driving synthetic lethal gene pairs using TCGA data. PMID:27438146
Multi-omics landscapes of colorectal cancer subtypes discriminated by an individualized prognostic signature for 5-fluorouracil-based chemotherapy. PMID:27429074
A Comprehensive Evaluation of Disease Phenotype Networks for Gene Prioritization. PMID:27415759
Preferentially Expressed Antigen of Melanoma Prevents Lung Cancer Metastasis. PMID:27391090
Clinical significance of mitofusin-2 and its signaling pathways in hepatocellular carcinoma. PMID:27389277
Comparison of large networks with sub-sampling strategies. PMID:27380992
Status of dosage compensation of X chromosome in bovine genome. PMID:27376899
The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. PMID:27374120
Matricellular TSP-1 as a target of interest for impeding melanoma spreading: towards a therapeutic use for TAX2 peptide. PMID:27349907
A new strategy for exploring the hierarchical structure of cancers by adaptively partitioning functional modules from gene expression network. PMID:27349736
Reconstruction and Application of Protein-Protein Interaction Network. PMID:27338356
BioTriangle: a web-accessible platform for generating various molecular representations for chemicals, proteins, DNAs/RNAs and their interactions. PMID:27330567
IntNetLncSim: an integrative network analysis method to infer human lncRNA functional similarity. PMID:27323856
Systems Nutrigenomics Reveals Brain Gene Networks Linking Metabolic and Brain Disorders. PMID:27322469
Rare coding TTN variants are associated with electrocardiographic QT interval in the general population. PMID:27321809
Reconstructing the temporal progression of HIV-1 immune response pathways. PMID:27307624
Multiple-Localization and Hub Proteins. PMID:27285823
Endophenotype Network Models: Common Core of Complex Diseases. PMID:27278246
Guizhi-Shaoyao-Zhimu decoction attenuates rheumatoid arthritis partially by reversing inflammation-immune system imbalance. PMID:27277474
Synovial fluid proteome in rheumatoid arthritis. PMID:27274716
Complexity and Specificity of the Neutrophil Transcriptomes in Juvenile Idiopathic Arthritis. PMID:27271962
Review on Graph Clustering and Subgraph Similarity Based Analysis of Neurological Disorders. PMID:27258269
Systematic analysis of the molecular mechanism underlying atherosclerosis using a text mining approach. PMID:27251057
Microsomal membrane proteome of low grade diffuse astrocytomas: Differentially expressed proteins and candidate surveillance biomarkers. PMID:27246909
Functional/activity network (FAN) analysis of gene-phenotype connectivity liaised by grape polyphenol resveratrol. PMID:27232943
The Prediction of Key Cytoskeleton Components Involved in Glomerular Diseases Based on a Protein-Protein Interaction Network. PMID:27227331
Dysregulated signaling hubs of liver lipid metabolism reveal hepatocellular carcinoma pathogenesis. PMID:27216817
Controllability of protein-protein interaction phosphorylation-based networks: Participation of the hub 14-3-3 protein family. PMID:27195976
Identification of polycystic ovary syndrome potential drug targets based on pathobiological similarity in the protein-protein interaction network. PMID:27191267
Identification of the anti-tumor activity and mechanisms of nuciferine through a network pharmacology approach. PMID:27180984
KeyPathwayMinerWeb: online multi-omics network enrichment. PMID:27150809
Revealing the Effects of the Herbal Pair of Euphorbia kansui and Glycyrrhiza on Hepatocellular Carcinoma Ascites with Integrating Network Target Analysis and Experimental Validation. PMID:27143956
An integrated signal transduction network of macrophage migration inhibitory factor. PMID:27139435
APID interactomes: providing proteome-based interactomes with controlled quality for multiple species and derived networks. PMID:27131791
CoReCG: a comprehensive database of genes associated with colon-rectal cancer. PMID:27114494
UbiNet: an online resource for exploring the functional associations and regulatory networks of protein ubiquitylation. PMID:27114492
A new molecular signature method for prediction of driver cancer pathways from transcriptional data. PMID:27098033
Prioritizing functional phosphorylation sites based on multiple feature integration. PMID:27090940
Computational Reconstruction of NFκB Pathway Interaction Mechanisms during Prostate Cancer. PMID:27078000
Regulation of Platelet Derived Growth Factor Signaling by Leukocyte Common Antigen-related (LAR) Protein Tyrosine Phosphatase: A Quantitative Phosphoproteomics Study. PMID:27074791
Unbiased identification of substrates of protein tyrosine phosphatase ptp-3 in C. elegans. PMID:27067626
The drug-minded protein interaction database (DrumPID) for efficient target analysis and drug development. PMID:27055828
Gene Expression Profiling of Tuberculous Meningitis Co-infected with HIV. PMID:27053842
Prediction and verification of novel peptide targets of protein tyrosine phosphatase 1B. PMID:27025565
Dissecting dysfunctional crosstalk pathways regulated by miRNAs during glioma progression. PMID:27013589
Proteomics-Based Analysis of Protein Complexes in Pluripotent Stem Cells and Cancer Biology. PMID:27011181
Variation at 2q35 (PNKD and TMBIM1) influences colorectal cancer risk and identifies a pleiotropic effect with inflammatory bowel disease. PMID:27005424
Comparative Proteomic Analysis of Advanced Ovarian Cancer Tissue to Identify Potential Biomarkers of Responders and Nonresponders to First-Line Chemotherapy of Carboplatin and Paclitaxel. PMID:26997873
PIPINO: A Software Package to Facilitate the Identification of Protein-Protein Interactions from Affinity Purification Mass Spectrometry Data. PMID:26966684
A NMF based approach for integrating multiple data sources to predict HIV-1-human PPIs. PMID:26956556
A Multi-Method Approach for Proteomic Network Inference in 11 Human Cancers. PMID:26928298
An Atlas of the Human Kinome Reveals the Mutational Landscape Underlying Dysregulated Phosphorylation Cascades in Cancer. PMID:26921330
Genetic Load of Loss-of-Function Polymorphic Variants in Great Apes. PMID:26912403
Complementary Post Transcriptional Regulatory Information is Detected by PUNCH-P and Ribosome Profiling. PMID:26898226
Dysregulation of splicing proteins in head and neck squamous cell carcinoma. PMID:26853621
Estimation of sparse directed acyclic graphs for multivariate counts data. PMID:26849781
Negative regulation of initial steps in skeletal myogenesis by mTOR and other kinases. PMID:26847534
Network-based in silico drug efficacy screening. PMID:26831545
Novel Neuroprotective Multicomponent Therapy for Amyotrophic Lateral Sclerosis Designed by Networked Systems. PMID:26807587
In Silico Insight into Potential Anti-Alzheimer's Disease Mechanisms of Icariin. PMID:26784184
A network analysis of cofactor-protein interactions for analyzing associations between human nutrition and diseases. PMID:26777674
CSGene: a literature-based database for cell senescence genes and its application to identify critical cell aging pathways and associated diseases. PMID:26775705
Systematic Phenomics Analysis Deconvolutes Genes Mutated in Intellectual Disability into Biologically Coherent Modules. PMID:26748517
Largescale Transcriptomics Analysis Suggests Over-Expression of BGH3, MMP9 and PDIA3 in Oral Squamous Cell Carcinoma. PMID:26745629
Identification of novel genes and pathways in carotid atheroma using integrated bioinformatic methods. PMID:26742467
Path2PPI: an R package to predict protein-protein interaction networks for a set of proteins. PMID:26733452
Proteomics and bioinformatics analysis of mouse hypothalamic neurogenesis with or without EPHX2 gene deletion. PMID:26722453
Multi-label multi-instance transfer learning for simultaneous reconstruction and cross-talk modeling of multiple human signaling pathways. PMID:26718335
Compartmentalization and Functionality of Nuclear Disorder: Intrinsic Disorder and Protein-Protein Interactions in Intra-Nuclear Compartments. PMID:26712748
HitPredict version 4: comprehensive reliability scoring of physical protein-protein interactions from more than 100 species. PMID:26708988
Gene-specific DNA methylation profiles and LINE-1 hypomethylation are associated with myocardial infarction risk. PMID:26705428
Network-Based Isoform Quantification with RNA-Seq Data for Cancer Transcriptome Analysis. PMID:26699225
Forward Individualized Medicine from Personal Genomes to Interactomes. PMID:26696898
NERI: network-medicine based integrative approach for disease gene prioritization by relative importance. PMID:26696568
Actions of Huangqi decoction against rat liver fibrosis: a gene expression profiling analysis. PMID:26691002
CancerNet: a database for decoding multilevel molecular interactions across diverse cancer types. PMID:26690544
Fundamentals of protein interaction network mapping. PMID:26681426
LENS: web-based lens for enrichment and network studies of human proteins. PMID:26680011
Common errors in mass spectrometry-based analysis of post-translational modifications. PMID:26667783
Reproducible Analysis of Post-Translational Modifications in Proteomes--Application to Human Mutations. PMID:26659599
Integrated analysis of global proteome, phosphoproteome, and glycoproteome enables complementary interpretation of disease-related protein networks. PMID:26657352
A simple feature construction method for predicting upstream/downstream signal flow in human protein-protein interaction networks. PMID:26648121
Ulocuplumab (BMS-936564 / MDX1338): a fully human anti-CXCR4 antibody induces cell death in chronic lymphocytic leukemia mediated through a reactive oxygen species-dependent pathway. PMID:26646452
Identification of critical genes and gene interaction networks that mediate osteosarcoma metastasis to the lungs. PMID:26640552
An integrative somatic mutation analysis to identify pathways linked with survival outcomes across 19 cancer types. PMID:26635139
CardioGenBase: A Literature Based Multi-Omics Database for Major Cardiovascular Diseases. PMID:26624015
PPIM: A Protein-Protein Interaction Database for Maize. PMID:26620522
Tracking the origins of Yakutian horses and the genetic basis for their fast adaptation to subarctic environments. PMID:26598656
Lynx: a knowledge base and an analytical workbench for integrative medicine. PMID:26590263
dbPTM 2016: 10-year anniversary of a resource for post-translational modification of proteins. PMID:26578568
An Effective Method to Identify Shared Pathways and Common Factors among Neurodegenerative Diseases. PMID:26575483
Uncovering Phosphorylation-Based Specificities through Functional Interaction Networks. PMID:26572964
Temporal protein expression pattern in intracellular signalling cascade during T-cell activation: a computational study. PMID:26564978
A Systems Biology-Based Investigation into the Pharmacological Mechanisms of Sheng-ma-bie-jia-tang Acting on Systemic Lupus Erythematosus by Multi-Level Data Integration. PMID:26560501
Integrative enrichment analysis: a new computational method to detect dysregulated pathways in heterogeneous samples. PMID:26556243
DNA-dependent formation of transcription factor pairs alters their binding specificity. PMID:26550823
Correlation of clinical features and genetic profiles of stromal interaction molecule 1 (STIM1) in colorectal cancers. PMID:26543234
A multi-omic analysis of human naïve CD4+ T cells. PMID:26542228
Protein Kinase Activity Decreases with Higher Braak Stages of Alzheimer's Disease Pathology. PMID:26519433
Integrated interactions database: tissue-specific view of the human and model organism interactomes. PMID:26516188
NCG 5.0: updates of a manually curated repository of cancer genes and associated properties from cancer mutational screenings. PMID:26516186
SENP3 regulates the global protein turnover and the Sp1 level via antagonizing SUMO2/3-targeted ubiquitination and degradation. PMID:26511642
A survey of computational tools for downstream analysis of proteomic and other omic datasets. PMID:26510531
Bioinformatics Knowledge Map for Analysis of Beta-Catenin Function in Cancer. PMID:26509276
Colorectal cancer atlas: An integrative resource for genomic and proteomic annotations from colorectal cancer cell lines and tissues. PMID:26496946
Using Bioinformatics Approach to Explore the Pharmacological Mechanisms of Multiple Ingredients in Shuang-Huang-Lian. PMID:26495421
Discovering distinct functional modules of specific cancer types using protein-protein interaction networks. PMID:26495282
A Pan-Cancer Catalogue of Cancer Driver Protein Interaction Interfaces. PMID:26485003
Predicting Pharmacodynamic Drug-Drug Interactions through Signaling Propagation Interference on Protein-Protein Interaction Networks. PMID:26469276
Temporal transcriptional response to latency reversing agents identifies specific factors regulating HIV-1 viral transcriptional switch. PMID:26438393
ExoCarta: A Web-Based Compendium of Exosomal Cargo. PMID:26434508
ncRDeathDB: A comprehensive bioinformatics resource for deciphering network organization of the ncRNA-mediated cell death system. PMID:26431463
Knockdown of AKR1C3 exposes a potential epigenetic susceptibility in prostate cancer cells. PMID:26429394
New genes drive the evolution of gene interaction networks in the human and mouse genomes. PMID:26424194
Integrative analysis of human protein, function and disease networks. PMID:26399914
A fast and high performance multiple data integration algorithm for identifying human disease genes. PMID:26399620
Targeted sequencing reveals clonal genetic changes in the progression of early lung neoplasms and paired circulating DNA. PMID:26374070
Dissecting Complex and Multifactorial Nature of Alzheimer's Disease Pathogenesis: a Clinical, Genomic, and Systems Biology Perspective. PMID:26351077
End Joining-Mediated Gene Expression in Mammalian Cells Using PCR-Amplified DNA Constructs that Contain Terminator in Front of Promoter. PMID:26350674
Cell type-selective disease-association of genes under high regulatory load. PMID:26338775
Large-scale extraction of gene interactions from full-text literature using DeepDive. PMID:26338771
Integration of 'omics' data in aging research: from biomarkers to systems biology. PMID:26331998
A computational framework for the prioritization of disease-gene candidates. PMID:26330267
Identification of Aberrant Chromosomal Regions in Human Breast Cancer Using Gene Expression Data and Related Gene Information. PMID:26319982
Prediction of Functionally Important Phospho-Regulatory Events in Xenopus laevis Oocytes. PMID:26312481
In vivo hematopoietic Myc activation directs a transcriptional signature in endothelial cells within the bone marrow microenvironment. PMID:26308666
Advances in computational approaches for prioritizing driver mutations and significantly mutated genes in cancer genomes. PMID:26307061
Construction and analysis of lncRNA-lncRNA synergistic networks to reveal clinically relevant lncRNAs in cancer. PMID:26305674
Moyamoya disease susceptibility gene RNF213 links inflammatory and angiogenic signals in endothelial cells. PMID:26278786
Network-Based Association Study of Obesity and Type 2 Diabetes with Gene Expression Profiles. PMID:26273637
Computational analysis of protein interaction networks for infectious diseases. PMID:26261187
Cancer type-dependent genetic interactions between cancer driver alterations indicate plasticity of epistasis across cell types. PMID:26227665
Systematic Analysis of the Molecular Mechanism Underlying Decidualization Using a Text Mining Approach. PMID:26222155
Identification of a multi-cancer gene expression biomarker for cancer clinical outcomes using a network-based algorithm. PMID:26202601
A draft network of ligand-receptor-mediated multicellular signalling in human. PMID:26198319
Atlas of Cancer Signalling Network: a systems biology resource for integrative analysis of cancer data with Google Maps. PMID:26192618
GreedyPlus: An Algorithm for the Alignment of Interface Interaction Networks. PMID:26165520
Systematic Analysis of the Genetic Variability That Impacts SUMO Conjugation and Their Involvement in Human Diseases. PMID:26154679
Chinese Herbal Preparation Xuebijing Potently Inhibits Inflammasome Activation in Hepatocytes and Ameliorates Mouse Liver Ischemia-Reperfusion Injury. PMID:26132490
Non-thermal plasma treatment altered gene expression profiling in non-small-cell lung cancer A549 cells. PMID:26116417
Surfing the Protein-Protein Interaction Surface Using Docking Methods: Application to the Design of PPI Inhibitors. PMID:26111183
Self-Organizing Feature Maps Identify Proteins Critical to Learning in a Mouse Model of Down Syndrome. PMID:26111164
Publisher’s Note:Abstraction for data integration:Fusing mammalian molecular, cellular and phenotype big datasets for better knowledge extraction. PMID:26101093
An integrated approach to reveal miRNAs' impacts on the functional consequence of copy number alterations in cancer. PMID:26099552
dbEMT: an epithelial-mesenchymal transition associated gene resource. PMID:26099468
Proteins interaction network and modeling of IGVH mutational status in chronic lymphocytic leukemia. PMID:26088082
Matrix Factorization-Based Prediction of Novel Drug Indications by Integrating Genomic Space. PMID:26078775
Phenome-driven disease genetics prediction toward drug discovery. PMID:26072493
Natural variability of minimotifs in 1092 people indicates that minimotifs are targets of evolution. PMID:26068475
TRRUST: a reference database of human transcriptional regulatory interactions. PMID:26066708
Identification of Gene and MicroRNA Signatures for Oral Cancer Developed from Oral Leukoplakia. PMID:26064958
Monocyte Proteomics Reveals Involvement of Phosphorylated HSP27 in the Pathogenesis of Osteoporosis. PMID:26063949
Gene set analysis: A step-by-step guide. PMID:26059482
Network-Based Analysis on Orthogonal Separation of Human Plasma Uncovers Distinct High Density Lipoprotein Complexes. PMID:26057100
Study of phosphorylation events for cancer diagnoses and treatment. PMID:26055493
Network-based prediction and knowledge mining of disease genes. PMID:26043920
Mutation burden of rare variants in schizophrenia candidate genes. PMID:26039597
Biased random walk model for the prioritization of drug resistance associated proteins. PMID:26039373
Intrinsic Size Parameters for Palmitoylated and Carboxyamidomethylated Peptides. PMID:26023288
Scoring the correlation of genes by their shared properties using OScal, an improved overlap quantification model. PMID:26015386
DeAnnCNV: a tool for online detection and annotation of copy number variations from whole-exome sequencing data. PMID:26013811
Prioritization of cancer-related genomic variants by SNP association network. PMID:25995611
A systematic investigation based on microRNA-mediated gene regulatory network reveals that dysregulation of microRNA-19a/Cyclin D1 axis confers an oncogenic potential and a worse prognosis in human hepatocellular carcinoma. PMID:25985117
Proteomic analysis of three gonad types of swamp eel reveals genes differentially expressed during sex reversal. PMID:25985063
Herb Network Analysis for a Famous TCM Doctor's Prescriptions on Treatment of Rheumatoid Arthritis. PMID:25983850
Candidate pathways and genes for nasopharyngeal carcinoma based on bioinformatics study. PMID:25973099
A novel method for identifying disease associated protein complexes based on functional similarity protein complex networks. PMID:25969691
Improving the Understanding of Pathogenesis of Human Papillomavirus 16 via Mapping Protein-Protein Interaction Network. PMID:25961044
Identification of differentially expressed serum proteins in gastric adenocarcinoma. PMID:25952687
Large-scale analysis of the evolutionary histories of phosphorylation motifs in the human genome. PMID:25949811
Predicting peptide-mediated interactions on a genome-wide scale. PMID:25938916
MIMP: predicting the impact of mutations on kinase-substrate phosphorylation. PMID:25938373
Deciphering the pharmacological mechanism of the Chinese formula huanglian-jie-du decoction in the treatment of ischemic stroke using a systems biology-based strategy. PMID:25937634
A modularity-based method reveals mixed modules from chemical-gene heterogeneous network. PMID:25927435
NOD-Like Receptor Signaling in Cholesteatoma. PMID:25922834
Understanding multicellular function and disease with human tissue-specific networks. PMID:25915600
Origin of cells and network information. PMID:25914760
A review on computational systems biology of pathogen-host interactions. PMID:25914674
Co-regulation of translation in protein complexes. PMID:25909184
Systems medicine: evolution of systems biology from bench to bedside. PMID:25891169
Prediction of host - pathogen protein interactions between Mycobacterium tuberculosis and Homo sapiens using sequence motifs. PMID:25887594
Integrative network analysis reveals molecular mechanisms of blood pressure regulation. PMID:25882670
Mining disease genes using integrated protein-protein interaction and gene-gene co-regulation information. PMID:25870785
Human cytomegalovirus pUL97 kinase induces global changes in the infected cell phosphoproteome. PMID:25867546
Use of mechanistic models to integrate and analyze multiple proteomic datasets. PMID:25863072
A DIseAse MOdule Detection (DIAMOnD) algorithm derived from a systematic analysis of connectivity patterns of disease proteins in the human interactome. PMID:25853560
Genomic heterogeneity of osteosarcoma - shift from single candidates to functional modules. PMID:25848766
Application of centrality measures in the identification of critical genes in diabetes mellitus. PMID:25848169
Recent positive selection has acted on genes encoding proteins with more interactions within the whole human interactome. PMID:25840415
Primary analysis and screening of microRNAs in gastric cancer side population cells. PMID:25834316
Uncovering pharmacological mechanisms of Wu-tou decoction acting on rheumatoid arthritis through systems approaches: drug-target prediction, network analysis and experimental validation. PMID:25820382
Large-scale determination of absolute phosphorylation stoichiometries in human cells by motif-targeting quantitative proteomics. PMID:25814448
Proper evaluation of alignment-free network comparison methods. PMID:25810431
ICan: an integrated co-alteration network to identify ovarian cancer-related genes. PMID:25803614
Deciphering deterioration mechanisms of complex diseases based on the construction of dynamic networks and systems analysis. PMID:25788156
Systematic analysis to identify a key role of CDK1 in mediating gene interaction networks in cervical cancer development. PMID:25786624
Network-based proteomic approaches reveal the neurodegenerative, neuroprotective and pain-related mechanisms involved after retrograde axonal damage. PMID:25784190
Using network clustering to predict copy number variations associated with health disparities. PMID:25780754
Comprehensive evaluation of composite gene features in cancer outcome prediction. PMID:25780335
LC-MS/MS-based serum proteomics for identification of candidate biomarkers for hepatocellular carcinoma. PMID:25778709
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
BMRF-Net: a software tool for identification of protein interaction subnetworks by a bagging Markov random field-based method. PMID:25755273
Efficient prediction of progesterone receptor interactome using a support vector machine model. PMID:25741764
Biological databases for human research. PMID:25712261
cisPath: an R/Bioconductor package for cloud users for visualization and management of functional protein interaction networks. PMID:25708840
Pinpointing disease genes through phenomic and genomic data fusion. PMID:25708473
Accurate multiple network alignment through context-sensitive random walk. PMID:25707987
Bridging topological and functional information in protein interaction networks by short loops profiling. PMID:25703051
Techniques for transferring host-pathogen protein interactions knowledge to new tasks. PMID:25699028
An integrative approach for a network based meta-analysis of viral RNAi screens. PMID:25691914
Identifying core gene modules in glioblastoma based on multilayer factor-mediated dysfunctional regulatory networks through integrating multi-dimensional genomic data. PMID:25653168
A visual review of the interactome of LRRK2: Using deep-curated molecular interaction data to represent biology. PMID:25648416
Autophagy Regulatory Network - a systems-level bioinformatics resource for studying the mechanism and regulation of autophagy. PMID:25635527
Comparison of human cell signaling pathway databases--evolution, drawbacks and challenges. PMID:25632107
Integrated miRNA and mRNA expression profiling to identify mRNA targets of dysregulated miRNAs in non-obstructive azoospermia. PMID:25628250
Evolutionary constraint and disease associations of post-translational modification sites in human genomes. PMID:25611800
A computational approach to identifying gene-microRNA modules in cancer. PMID:25611546
Amyloid precursor protein interaction network in human testis: sentinel proteins for male reproduction. PMID:25591988
Proteomics-based metabolic modeling reveals that fatty acid oxidation (FAO) controls endothelial cell (EC) permeability. PMID:25573745
A highly efficient approach to protein interactome mapping based on collaborative filtering framework. PMID:25572661
Pathway and network approaches for identification of cancer signature markers from omics data. PMID:25553089
Recent coselection in human populations revealed by protein-protein interaction network. PMID:25532814
Network-based association of hypoxia-responsive genes with cardiovascular diseases. PMID:25530704
INTEGRATING COMPUTATIONAL PROTEIN FUNCTION PREDICTION INTO DRUG DISCOVERY INITIATIVES. PMID:25530654
Empowering biologists with multi-omics data: colorectal cancer as a paradigm. PMID:25527095
Multitask learning of signaling and regulatory networks with application to studying human response to flu. PMID:25522349
Complex-based analysis of dysregulated cellular processes in cancer. PMID:25521701
Assessment of subnetwork detection methods for breast cancer. PMID:25520555
TLR4 signalling in osteoarthritis--finding targets for candidate DMOADs. PMID:25512010
Comprehensive discovery of DNA motifs in 349 human cells and tissues reveals new features of motifs. PMID:25505144
MicroRNA Dysregulation, Gene Networks, and Risk for Schizophrenia in 22q11.2 Deletion Syndrome. PMID:25484875
Graphical algorithm for integration of genetic and biological data: proof of principle using psoriasis as a model. PMID:25480373
Systematic analysis of the in situ crosstalk of tyrosine modifications reveals no additional natural selection on multiply modified residues. PMID:25476580
Database screening of herbal monomers regulating autophagy by constructing a "disease-gene-drug" network. PMID:25475428
The Triple-Negative Breast Cancer Database: an omics platform for reference, integration and analysis of triple-negative breast cancer data. PMID:25472854
Systems Medicine: from molecular features and models to the clinic in COPD. PMID:25471042
Protein-protein interaction networks (PPI) and complex diseases. PMID:25436094
Comprehensive analysis of microRNA-regulated protein interaction network reveals the tumor suppressive role of microRNA-149 in human hepatocellular carcinoma via targeting AKT-mTOR pathway. PMID:25424347
LysargiNase mirrors trypsin for protein C-terminal and methylation-site identification. PMID:25419962
A proteome-scale map of the human interactome network. PMID:25416956
EHFPI: a database and analysis resource of essential host factors for pathogenic infection. PMID:25414353
ProteomeScout: a repository and analysis resource for post-translational modifications and proteins. PMID:25414335
Protein interaction networks reveal novel autism risk genes within GWAS statistical noise. PMID:25409314
Characterization of age signatures of DNA methylation in normal and cancer tissues from multiple studies. PMID:25406591
dbSNO 2.0: a resource for exploring structural environment, functional and disease association and regulatory network of protein S-nitrosylation. PMID:25399423
Cancer3D: understanding cancer mutations through protein structures. PMID:25392415
MatrixDB, the extracellular matrix interaction database: updated content, a new navigator and expanded functionalities. PMID:25378329
The discovery of integrated gene networks for autism and related disorders. PMID:25378250
Human cancer databases (review). PMID:25369839
PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins. PMID:25361965
Identification of novel tumor-associated cell surface sialoglycoproteins in human glioblastoma tumors using quantitative proteomics. PMID:25360666
MiR-101 induces senescence and prevents apoptosis in the background of DNA damage in MCF7 cells. PMID:25353636
NRfamPred: a proteome-scale two level method for prediction of nuclear receptor proteins and their sub-families. PMID:25351274
Prediction of disease-related genes based on weighted tissue-specific networks by using DNA methylation. PMID:25350763
Identifying disease genes by integrating multiple data sources. PMID:25350511
Integrating phosphoproteomics in systems biology. PMID:25349677
ComPPI: a cellular compartment-specific database for protein-protein interaction network analysis. PMID:25348397
MitProNet: A knowledgebase and analysis platform of proteome, interactome and diseases for mammalian mitochondria. PMID:25347823
Network-based analysis of comorbidities risk during an infection: SARS and HIV case studies. PMID:25344230
Identifying roles of "Jun-Chen-Zuo-Shi" component herbs of QiShenYiQi formula in treating acute myocardial ischemia by network pharmacology. PMID:25342960
Integrated analysis of microarray data of atherosclerotic plaques: modulation of the ubiquitin-proteasome system. PMID:25333956
The human DEPhOsphorylation database DEPOD: a 2015 update. PMID:25332398
Network-based Pathway Enrichment Analysis. PMID:25327472
ImmuCo: a database of gene co-expression in immune cells. PMID:25326331
Incorporating computational resources in a cancer research program. PMID:25324189
Inferring protein modulation from gene expression data using conditional mutual information. PMID:25314274
Linear motif-mediated interactions have contributed to the evolution of modularity in complex protein interaction networks. PMID:25299147
Comparative study of computational methods for reconstructing genetic networks of cancer-related pathways. PMID:25288880
Elucidating the genotype-phenotype relationships and network perturbations of human shared and specific disease genes from an evolutionary perspective. PMID:25287147
Hope for GWAS: relevant risk genes uncovered from GWAS statistical noise. PMID:25268625
Prioritisation and network analysis of Crohn's disease susceptibility genes. PMID:25268122
A New Method for Computational Drug Repositioning Using Drug Pairwise Similarity. PMID:25264495
AnimalTFDB 2.0: a resource for expression, prediction and functional study of animal transcription factors. PMID:25262351
Anomalies in network bridges involved in bile Acid metabolism predict outcomes of colorectal cancer patients. PMID:25259881
Characterizing protein interactions employing a genome-wide siRNA cellular phenotyping screen. PMID:25255318
Exploration of potential roles of a new LOXL2 splicing variant using network knowledge in esophageal squamous cell carcinoma. PMID:25254241
GeneMANIA: Fast gene network construction and function prediction for Cytoscape. PMID:25254104
Activation of diverse signalling pathways by oncogenic PIK3CA mutations. PMID:25247763
Transcriptional regulation of adrenomedullin by oncostatin M in human astroglioma cells: implications for tumor invasion and migration. PMID:25246098
System analysis of LWDH related genes based on text mining in biological networks. PMID:25243143
Integration strategy is a key step in network-based analysis and dramatically affects network topological properties and inferring outcomes. PMID:25243127
BRAF activates and physically interacts with PAK to regulate cell motility. PMID:25228413
SANTA: quantifying the functional content of molecular networks. PMID:25210953
Finding trans-regulatory genes and protein complexes modulating meiotic recombination hotspots of human, mouse and yeast. PMID:25208583
Synergistic transcriptional and post-transcriptional regulation of ESC characteristics by core pluripotency transcription factors in protein-protein interaction networks. PMID:25171496
Construction and analysis of the protein-protein interaction networks based on gene expression profiles of Parkinson's disease. PMID:25170921
Alignment-free protein interaction network comparison. PMID:25161230
Making proteomics data accessible and reusable: current state of proteomics databases and repositories. PMID:25158685
Functional and genomic context in pathway analysis of GWAS data. PMID:25154796
A bayesian framework that integrates heterogeneous data for inferring gene regulatory networks. PMID:25152886
WMAXC: a weighted maximum clique method for identifying condition-specific sub-network. PMID:25148538
Network biology in medicine and beyond. PMID:25140061
KeyPathwayMiner 4.0: condition-specific pathway analysis by combining multiple omics studies and networks with Cytoscape. PMID:25134827
Microvascular lesions by estrogen-induced ID3: its implications in cerebral and cardiorenal vascular disease. PMID:25129100
An integrative omics strategy to assess the germ cell secretome and to decipher sertoli-germ cell crosstalk in the Mammalian testis. PMID:25111155
Lean Big Data integration in systems biology and systems pharmacology. PMID:25109570
Proteomic analysis of human vitreous humor. PMID:25097467
Bioinformatic approaches to augment study of epithelial-to-mesenchymal transition in lung cancer. PMID:25096367
PCB153-induced overexpression of ID3 contributes to the development of microvascular lesions. PMID:25090023
PPI layouts: BioJS components for the display of Protein-Protein Interactions. PMID:25075288
Evolutionary analysis of the cystatin family in three Schistosoma species. PMID:25071834
A systems biology-based approach to uncovering the molecular mechanisms underlying the effects of dragon's blood tablet in colitis, involving the integration of chemical analysis, ADME prediction, and network pharmacology. PMID:25068885
Large Scale Chemical Cross-linking Mass Spectrometry Perspectives. PMID:25045217
Bioinformatic analysis of proteomics data. PMID:25033288
Multi-tissue computational modeling analyzes pathophysiology of type 2 diabetes in MKR mice. PMID:25029527
Predicting disease-related proteins based on clique backbone in protein-protein interaction network. PMID:25013377
Quantitative network mapping of the human kinome interactome reveals new clues for rational kinase inhibitor discovery and individualized cancer therapy. PMID:25003367
The domain landscape of virus-host interactomes. PMID:24991570
Simulated annealing based algorithm for identifying mutated driver pathways in cancer. PMID:24982873
Building a hierarchical organization of protein complexes out of protein association data. PMID:24978199
Genome-wide prediction and validation of peptides that bind human prosurvival Bcl-2 proteins. PMID:24967846
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
Increasing the precision of orthology-based complex prediction through network alignment. PMID:24918034
Global phosphoproteomics of activated B cells using complementary metal ion functionalized soluble nanopolymers. PMID:24905233
Protein-protein interactions and genetic diseases: The interactome. PMID:24892209
Network-based identification of key proteins involved in apoptosis and cell cycle regulation. PMID:24889965
The structural and functional signatures of proteins that undergo multiple events of post-translational modification. PMID:24888500
Large-scale phosphoproteome analysis in seedling leaves of Brachypodium distachyon L. PMID:24885693
Studying tumorigenesis through network evolution and somatic mutational perturbations in the cancer interactome. PMID:24881052
Screening of critical genes in lung adenocarcinoma via network analysis of gene expression profile. PMID:24859971
Pancreatic Cancer Database: an integrative resource for pancreatic cancer. PMID:24839966
A Network Map of FGF-1/FGFR Signaling System. PMID:24829797
Complexity of metastasis-associated SDF-1 ligand signaling in breast cancer stem cells. PMID:24828528
Ensemble positive unlabeled learning for disease gene identification. PMID:24816822
Functional module search in protein networks based on semantic similarity improves the analysis of proteomics data. PMID:24807868
A three step network based approach (TSNBA) to finding disease molecular signature and key regulators: a case study of IL-1 and TNF-alpha stimulated inflammation. PMID:24747419
Unraveling human protein interaction networks underlying co-occurrences of diseases and pathological conditions. PMID:24731539
Quantitative phosphoproteomics analysis of nitric oxide-responsive phosphoproteins in cotton leaf. PMID:24714030
Approaches for recognizing disease genes based on network. PMID:24707485
SysPTM 2.0: an updated systematic resource for post-translational modification. PMID:24705204
Building and exploring an integrated human kinase network: global organization and medical entry points. PMID:24704859
Functional annotation of proteome encoded by human chromosome 22. PMID:24669763
GeneSense: a new approach for human gene annotation integrated with protein-protein interaction networks. PMID:24667292
Network and matrix analysis of the respiratory disease interactome. PMID:24655443
Systems-level analysis of innate immunity. PMID:24655298
Cancer-risk module identification and module-based disease risk evaluation: a case study on lung cancer. PMID:24643254
Identification of phenotype deterministic genes using systemic analysis of transcriptional response. PMID:24642983
Feature Selection in the Tensor Product Feature Space. PMID:24632658
A systematic in silico mining of the mechanistic implications and therapeutic potentials of estrogen receptor (ER)-α in breast cancer. PMID:24614816
NCG 4.0: the network of cancer genes in the era of massive mutational screenings of cancer genomes. PMID:24608173
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
Modelling the yeast interactome. PMID:24589662
A network map of the gastrin signaling pathway. PMID:24584707
PARK2 and proinflammatory/anti-inflammatory cytokine gene interactions contribute to the susceptibility to leprosy: a case-control study of North Indian population. PMID:24578538
The Zebrafish GenomeWiki: a crowdsourcing approach to connect the long tail for zebrafish gene annotation. PMID:24578356
Integrating systems biology sources illuminates drug action. PMID:24577151
Computational prediction of the human-microbial oral interactome. PMID:24576332
Incorporating post-translational modifications and unnatural amino acids into high-throughput modeling of protein structures. PMID:24574112
Joint clustering of protein interaction networks through Markov random walk. PMID:24565376
Detection of type 2 diabetes related modules and genes based on epigenetic networks. PMID:24565181
Prioritizing protein complexes implicated in human diseases by network optimization. PMID:24565064
Prediction of protein interaction types based on sequence and network features. PMID:24564924
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
A systems biology-based investigation into the therapeutic effects of Gansui Banxia Tang on reversing the imbalanced network of hepatocellular carcinoma. PMID:24561634
Human transporter database: comprehensive knowledge and discovery tools in the human transporter genes. PMID:24558441
DanQi Pill protects against heart failure through the arachidonic acid metabolism pathway by attenuating different cyclooxygenases and leukotrienes B4. PMID:24555740
Navigating the multilayered organization of eukaryotic signaling: a new trend in data integration. PMID:24550716
Proteomic analysis of human osteoarthritis synovial fluid. PMID:24533825
Modulation of gene expression regulated by the transcription factor NF-κB/RelA. PMID:24523406
VarWalker: personalized mutation network analysis of putative cancer genes from next-generation sequencing data. PMID:24516372
Gene expression signature for biliary atresia and a role for interleukin-8 in pathogenesis of experimental disease. PMID:24493287
Functional Module Connectivity Map (FMCM): a framework for searching repurposed drug compounds for systems treatment of cancer and an application to colorectal adenocarcinoma. PMID:24475102
Identification of human disease genes from interactome network using graphlet interaction. PMID:24465923
Functional divergence and evolutionary turnover in mammalian phosphoproteomes. PMID:24465218
Walking on a tissue-specific disease-protein-complex heterogeneous network for the discovery of disease-related protein complexes. PMID:24455720
Systematic large-scale study of the inheritance mode of Mendelian disorders provides new insight into human diseasome. PMID:24448549
Characterizing and controlling the inflammatory network during influenza A virus infection. PMID:24445954
Network medicine analysis of chondrocyte proteins towards new treatments of osteoarthritis. PMID:24430851
Dynamics of regulatory networks in gastrin-treated adenocarcinoma cells. PMID:24416123
A large scale Huntingtin protein interaction network implicates Rho GTPase signaling pathways in Huntington disease. PMID:24407293
Computational Prediction of Protein-Protein Interaction Networks: Algo-rithms and Resources. PMID:24396273
Differential proteomic analysis of synovial fluid from rheumatoid arthritis and osteoarthritis patients. PMID:24393543
Turning off AKT: PHLPP as a drug target. PMID:24392697
Identification of GRB2 and GAB1 coexpression as an unfavorable prognostic factor for hepatocellular carcinoma by a combination of expression profile and network analysis. PMID:24391994
Current composite-feature classification methods do not outperform simple single-genes classifiers in breast cancer prognosis. PMID:24391662
A pathway and network review on beta-adrenoceptor signaling and beta blockers in cardiac remodeling. PMID:24366330
A systems' biology approach to study microRNA-mediated gene regulatory networks. PMID:24350286
Molecular signatures of antibody responses derived from a systems biology study of five human vaccines. PMID:24336226
Proteome and phosphoproteome characterization reveals new response and defense mechanisms of Brachypodium distachyon leaves under salt stress. PMID:24335353
Gene-gene interaction network analysis of ovarian cancer using TCGA data. PMID:24314048
Candidate gene identification for systemic lupus erythematosus using network centrality measures and gene ontology. PMID:24312583
Transcriptional regulatory network and protein-protein interaction to reveal the mechanism of pancreatic cancer. PMID:24307251
Plasma Proteome Database as a resource for proteomics research: 2014 update. PMID:24304897
A Framework of Knowledge Integration and Discovery for Supporting Pharmacogenomics Target Predication of Adverse Drug Events: A Case Study of Drug-Induced Long QT Syndrome. PMID:24303306
Sharing information to reconstruct patient-specific pathways in heterogeneous diseases. PMID:24297532
Network analysis of GWAS data. PMID:24287332
Integrating structure to protein-protein interaction networks that drive metastasis to brain and lung in breast cancer. PMID:24278371
CentrosomeDB: a new generation of the centrosomal proteins database for Human and Drosophila melanogaster. PMID:24270791
Lynx: a database and knowledge extraction engine for integrative medicine. PMID:24270788
The central role of AMP-kinase and energy homeostasis impairment in Alzheimer's disease: a multifactor network analysis. PMID:24265728
Probability weighted ensemble transfer learning for predicting interactions between HIV-1 and human proteins. PMID:24260261
Gene expression profiling analysis of the putamen for the investigation of compensatory mechanisms in Parkinson's disease. PMID:24256571
Exogenous administration of a recombinant variant of TWEAK impairs healing after myocardial infarction by aggravation of inflammation. PMID:24244389
Drug repositioning by kernel-based integration of molecular structure, molecular activity, and phenotype data. PMID:24244318
P³DB 3.0: From plant phosphorylation sites to protein networks. PMID:24243849
Toward better drug repositioning: prioritizing and integrating existing methods into efficient pipelines. PMID:24239728
Evaluating the pharmacological mechanism of Chinese medicine Si-Wu-Tang through multi-level data integration. PMID:24223693
CPLM: a database of protein lysine modifications. PMID:24214993
UniHI 7: an enhanced database for retrieval and interactive analysis of human molecular interaction networks. PMID:24214987
CEG: a database of essential gene clusters. PMID:24209780
Human intellectual disability genes form conserved functional modules in Drosophila. PMID:24204314
Network cluster analysis of protein-protein interaction network identified biomarker for early onset colorectal cancer. PMID:24197691
Inference of gene-phenotype associations via protein-protein interaction and orthology. PMID:24194887
HypoxiaDB: a database of hypoxia-regulated proteins. PMID:24178989
Experimental validation of 5 in-silico predicted glioma biomarkers. PMID:24158112
VAN: an R package for identifying biologically perturbed networks via differential variability analysis. PMID:24156242
On Crowd-verification of Biological Networks. PMID:24151423
Proteomic profiling of serum samples from chikungunya-infected patients provides insights into host response. PMID:24124767
Protein kinase PKN1 represses Wnt/β-catenin signaling in human melanoma cells. PMID:24114839
Protein microarray characterization of the S-nitrosoproteome. PMID:24105792
Walking the interactome to identify human miRNA-disease associations through the functional link between miRNA targets and disease genes. PMID:24103777
Analysis of nonlinear gene expression progression reveals extensive pathway and age-specific transitions in aging human brains. PMID:24098339
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
Screening of key genes in gastric cancer with DNA microarray analysis. PMID:24093889
The mutational landscape of phosphorylation signaling in cancer. PMID:24089029
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
Mutation of fibulin-1 causes a novel syndrome involving the central nervous system and connective tissues. PMID:24084572
Promoter hypomethylation of EpCAM-regulated bone morphogenetic protein gene family in recurrent endometrial cancer. PMID:24077349
Optimizing a global alignment of protein interaction networks. PMID:24048352
TCPA: a resource for cancer functional proteomics data. PMID:24037243
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
CellMinerHCC: a microarray-based expression database for hepatocellular carcinoma cell lines. PMID:24016071
Genome-wide signatures of convergent evolution in echolocating mammals. PMID:24005325
Research prioritization through prediction of future impact on biomedical science: a position paper on inference-analytics. PMID:24001106
A system biology approach to identify regulatory pathways underlying the neuroendocrine control of female puberty in rats and nonhuman primates. PMID:23998662
Computational analysis of virus-host interactomes. PMID:23996253
Developing microRNA screening as a functional genomics tool for disease research. PMID:23986717
Navigating traditional chinese medicine network pharmacology and computational tools. PMID:23983798
Network clusters analysis based on protein-protein interaction network constructed in phosgene-induced acute lung injury. PMID:23963411
Identification of interconnected markers for T-cell acute lymphoblastic leukemia. PMID:23956970
A systematic analysis of host factors reveals a Med23-interferon-λ regulatory axis against herpes simplex virus type 1 replication. PMID:23950709
Defining cell-type specificity at the transcriptional level in human disease. PMID:23950145
Voting-based cancer module identification by combining topological and data-driven properties. PMID:23940583
Association study of 167 candidate genes for schizophrenia selected by a multi-domain evidence-based prioritization algorithm and neurodevelopmental hypothesis. PMID:23922650
Experimental characterization of the human non-sequence-specific nucleic acid interactome. PMID:23902751
Plot protein: visualization of mutations. PMID:23876180
Genes dysregulated to different extent or oppositely in estrogen receptor-positive and estrogen receptor-negative breast cancers. PMID:23875016
Inferring potential microRNA-microRNA associations based on targeting propensity and connectivity in the context of protein interaction network. PMID:23874989
SMETANA: accurate and scalable algorithm for probabilistic alignment of large-scale biological networks. PMID:23874484
GEMINI: integrative exploration of genetic variation and genome annotations. PMID:23874191
Target essentiality and centrality characterize drug side effects. PMID:23874169
JBioWH: an open-source Java framework for bioinformatics data integration. PMID:23846595
Variants in exons and in transcription factors affect gene expression in trans. PMID:23844908
Complementing the Eukaryotic Protein Interactome. PMID:23825550
Large-scale integrative network-based analysis identifies common pathways disrupted by copy number alterations across cancers. PMID:23822816
CHD@ZJU: a knowledgebase providing network-based research platform on coronary heart disease. PMID:23818526
iBIG: an integrative network tool for supporting human disease mechanism studies. PMID:23809576
Mining breast cancer genes with a network based noise-tolerant approach. PMID:23799982
Cancer missense mutations alter binding properties of proteins and their interaction networks. PMID:23799087
ToP: a trend-of-disease-progression procedure works well for identifying cancer genes from multi-state cohort gene expression data for human colorectal cancer. PMID:23799036
Integrative approaches for predicting protein function and prioritizing genes for complex phenotypes using protein interaction networks. PMID:23788799
The Escherichia coli phosphotyrosine proteome relates to core pathways and virulence. PMID:23785281
Characterizing genes with distinct methylation patterns in the context of protein-protein interaction network: application to human brain tissues. PMID:23776563
Identification of lung-cancer-related genes with the shortest path approach in a protein-protein interaction network. PMID:23762832
Identifying chemicals with potential therapy of HIV based on protein-protein and protein-chemical interaction network. PMID:23762317
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
A network pharmacology approach to evaluating the efficacy of chinese medicine using genome-wide transcriptional expression data. PMID:23737854
Protein co-expression network analysis (ProCoNA). PMID:23724967
MicroRNA-regulated protein-protein interaction networks and their functions in breast cancer. PMID:23722663
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
Cataloging the biomedical world of pain through semi-automated curation of molecular interactions. PMID:23707966
Genome-wide methylated DNA immunoprecipitation analysis of patients with polycystic ovary syndrome. PMID:23705014
Human monogenic disease genes have frequently functionally redundant paralogs. PMID:23696728
Adjusting for background mutation frequency biases improves the identification of cancer driver genes. PMID:23694700
Dissection of protein interactomics highlights microRNA synergy. PMID:23691029
A systems biology-based investigation into the pharmacological mechanisms of wu tou tang acting on rheumatoid arthritis by integrating network analysis. PMID:23690848
Proteome-wide discovery of mislocated proteins in cancer. PMID:23674306
Structure and non-structure of centrosomal proteins. PMID:23671615
An Integrative Platform of TCM Network Pharmacology and Its Application on a Herbal Formula, Qing-Luo-Yin. PMID:23653662
Relaxation response induces temporal transcriptome changes in energy metabolism, insulin secretion and inflammatory pathways. PMID:23650531
Network characteristic analysis of ADR-related proteins and identification of ADR-ADR associations. PMID:23625301
Dynamic modular architecture of protein-protein interaction networks beyond the dichotomy of 'date' and 'party' hubs. PMID:23603706
INstruct: a database of high-quality 3D structurally resolved protein interactome networks. PMID:23599502
Dissecting the roles of tyrosines 490 and 785 of TrkA protein in the induction of downstream protein phosphorylation using chimeric receptors. PMID:23589303
Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. PMID:23586463
Protein-protein interactions: switch from classical methods to proteomics and bioinformatics-based approaches. PMID:23579629
Systematic prediction of pharmacodynamic drug-drug interactions through protein-protein-interaction network. PMID:23555229
Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. PMID:23550210
Glycocapture-assisted global quantitative proteomics (gagQP) reveals multiorgan responses in serum toxicoproteome. PMID:23540550
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
Quantitative proteomics for identifying biomarkers for Rabies. PMID:23521751
Classification of time series gene expression in clinical studies via integration of biological network. PMID:23516469
Identifying dysfunctional miRNA-mRNA regulatory modules by inverse activation, cofunction, and high interconnection of target genes: a case study of glioblastoma. PMID:23516263
Access guide to human proteinpedia. PMID:23504933
An integrated map of corticotropin-releasing hormone signaling pathway. PMID:23504413
Moving H5N1 studies into the era of systems biology. PMID:23499671
Vitexicarpin acts as a novel angiogenesis inhibitor and its target network. PMID:23476684
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
A novel subgradient-based optimization algorithm for blockmodel functional module identification. PMID:23368964
Systematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer drivers. PMID:23340843
SignaLink 2 - a signaling pathway resource with multi-layered regulatory networks. PMID:23331499
mirTarPri: improved prioritization of microRNA targets through incorporation of functional genomics data. PMID:23326485
Mining disease fingerprints from within genetic pathways. PMID:23304411
Adding protein context to the human protein-protein interaction network to reveal meaningful interactions. PMID:23300433
Chapter 4: Protein interactions and disease. PMID:23300410
The human brain online: an open resource for advancing brain research. PMID:23300378
Identification of novel cholesteatoma-related gene expression signatures using full-genome microarrays. PMID:23285167
Mining functional subgraphs from cancer protein-protein interaction networks. PMID:23282132
Cliques for the identification of gene signatures for colorectal cancer across population. PMID:23282040
Discovering pathway cross-talks based on functional relations between pathways. PMID:23282018
Genetic studies of complex human diseases: characterizing SNP-disease associations using Bayesian networks. PMID:23281790
Vesiclepedia: a compendium for extracellular vesicles with continuous community annotation. PMID:23271954
Managing biological complexity across orthologs with a visual knowledgebase of documented biomolecular interactions. PMID:23264875
A novel link prediction algorithm for reconstructing protein-protein interaction networks by topological similarity. PMID:23235927
What you see is not what you get: how sampling affects macroscopic features of biological networks. PMID:23226585
The BioGRID interaction database: 2013 update. PMID:23203989
TCMID: Traditional Chinese Medicine integrative database for herb molecular mechanism analysis. PMID:23203875
COXPRESdb: a database of comparative gene coexpression networks of eleven species for mammals. PMID:23203868
DbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications. PMID:23193290
SpermatogenesisOnline 1.0: a resource for spermatogenesis based on manual literature curation and genome-wide data mining. PMID:23193286
PTMcode: a database of known and predicted functional associations between post-translational modifications in proteins. PMID:23193284
GenomeRNAi: a database for cell-based and in vivo RNAi phenotypes, 2013 update. PMID:23193271
PrePPI: a structure-informed database of protein-protein interactions. PMID:23193263
Systems biology of pathogen-host interaction: networks of protein-protein interaction within pathogens and pathogen-human interactions in the post-genomic era. PMID:23193100
Autworks: a cross-disease network biology application for Autism and related disorders. PMID:23190929
Knowledge-based analysis of proteomics data. PMID:23176192
An efficient heuristic method for active feature acquisition and its application to protein-protein interaction prediction. PMID:23173746
Position-specific analysis and prediction for protein lysine acetylation based on multiple features. PMID:23173045
Dynamic protein-protein interaction subnetworks of lung cancer in cases with smoking history. PMID:23149315
Effects of protein interaction data integration, representation and reliability on the use of network properties for drug target prediction. PMID:23146171
Transcriptional alterations related to neuropathology and clinical manifestation of Alzheimer's disease. PMID:23144955
Insights into the evolutionary features of human neurodegenerative diseases. PMID:23118989
CellLineNavigator: a workbench for cancer cell line analysis. PMID:23118487
SpliceAid-F: a database of human splicing factors and their RNA-binding sites. PMID:23118479
NSort/DB: an intranuclear compartment protein database. PMID:23084778
MK4MDD: a multi-level knowledge base and analysis platform for major depressive disorder. PMID:23071556
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
Identification of significant pathways in gastric cancer based on protein-protein interaction networks and cluster analysis. PMID:23055812
Network analysis of gene lists for finding reproducible prognostic breast cancer gene signatures. PMID:23055628
Systematically characterizing and prioritizing chemosensitivity related gene based on Gene Ontology and protein interaction network. PMID:23031817
Proteins with altered levels in plasma from glioblastoma patients as revealed by iTRAQ-based quantitative proteomic analysis. PMID:23029420
Multi-edge gene set networks reveal novel insights into global relationships between biological themes. PMID:23028852
Therapeutic effects of astragaloside IV on myocardial injuries: multi-target identification and network analysis. PMID:23028693
What evidence is there for the homology of protein-protein interactions? PMID:23028270
Rapid characterization of candidate biomarkers for pancreatic cancer using cell microarrays (CMAs). PMID:22985314
A simple knowledge-based mining method for exploring hidden key molecules in a human biomolecular network. PMID:22979956
Network analysis of the focal adhesion to invadopodia transition identifies a PI3K-PKCα invasive signaling axis. PMID:22969158
RhesusBase: a knowledgebase for the monkey research community. PMID:22965133
Temporal profiling of lapatinib-suppressed phosphorylation signals in EGFR/HER2 pathways. PMID:22964224
Positive-unlabeled learning for disease gene identification. PMID:22923290
A network synthesis model for generating protein interaction network families. PMID:22912671
Dissecting the gene network of dietary restriction to identify evolutionarily conserved pathways and new functional genes. PMID:22912585
Protein abundance is key to distinguish promiscuous from functional phosphorylation based on evolutionary information. PMID:22889910
Screening of candidate genes for primary open angle glaucoma. PMID:22876139
Prediction and analysis of the protein interactome in Pseudomonas aeruginosa to enable network-based drug target selection. PMID:22848443
Embryonic stem cell interactomics: the beginning of a long road to biological function. PMID:22847281
HINT: High-quality protein interactomes and their applications in understanding human disease. PMID:22846459
atBioNet--an integrated network analysis tool for genomics and biomarker discovery. PMID:22817640
Concerted perturbation observed in a hub network in Alzheimer's disease. PMID:22815752
Cancer develops, progresses and responds to therapies through restricted perturbation of the protein-protein interaction network. PMID:22806580
Deciphering a global network of functionally associated post-translational modifications. PMID:22806145
Computational analysis of target hub gene repression regulated by multiple and cooperative miRNAs. PMID:22798498
Systematic analysis of protein phosphorylation networks from phosphoproteomic data. PMID:22798277
Endosomal crosstalk: meeting points for signaling pathways. PMID:22796207
Integration of breast cancer gene signatures based on graph centrality. PMID:22784616
Constructing a gene semantic similarity network for the inference of disease genes. PMID:22784573
SigCS base: an integrated genetic information resource for human cerebral stroke. PMID:22784567
Differentially co-expressed interacting protein pairs discriminate samples under distinct stages of HIV type 1 infection. PMID:22784566
Integration of biological networks and pathways with genetic association studies. PMID:22777728
Computational Analysis of Muscular Dystrophy Sub-types Using A Novel Integrative Scheme. PMID:22773895
Prioritization of candidate genes for attention deficit hyperactivity disorder by computational analysis of multiple data sources. PMID:22773342
Posterior association networks and functional modules inferred from rich phenotypes of gene perturbations. PMID:22761558
Genes2FANs: connecting genes through functional association networks. PMID:22748121
Involvement of microRNA families in cancer. PMID:22743268
Proteome-wide prediction of protein-protein interactions from high-throughput data. PMID:22729399
Network compression as a quality measure for protein interaction networks. PMID:22719828
ChromoHub: a data hub for navigators of chromatin-mediated signalling. PMID:22718786
Beyond hairballs: The use of quantitative mass spectrometry data to understand protein-protein interactions. PMID:22710165
Overexpression of ribosome binding protein 1 (RRBP1) in breast cancer. PMID:22709790
DEFOG: discrete enrichment of functionally organized genes. PMID:22706384
Prioritizing cancer-related key miRNA-target interactions by integrative genomics. PMID:22705797
Dynamic network of transcription and pathway crosstalk to reveal molecular mechanism of MGd-treated human lung cancer cells. PMID:22693540
Cancer core modules identification through genomic and transcriptomic changes correlation detection at network level. PMID:22691569
BIPS: BIANA Interolog Prediction Server. A tool for protein-protein interaction inference. PMID:22689642
Identifying dysregulated pathways in cancers from pathway interaction networks. PMID:22676414
NetAligner--a network alignment server to compare complexes, pathways and whole interactomes. PMID:22618871
SH3 domain tyrosine phosphorylation--sites, role and evolution. PMID:22615764
SurvNet: a web server for identifying network-based biomarkers that most correlate with patient survival data. PMID:22570412
Linking proteins to signaling pathways for experiment design and evaluation. PMID:22558382
A critical evaluation of network and pathway-based classifiers for outcome prediction in breast cancer. PMID:22558100
LDGIdb: a database of gene interactions inferred from long-range strong linkage disequilibrium between pairs of SNPs. PMID:22551073
Improving biomarker list stability by integration of biological knowledge in the learning process. PMID:22536969
FUSE: a profit maximization approach for functional summarization of biological networks. PMID:22536894
MOfinder: a novel algorithm for detecting overlapping modules from protein-protein interaction network. PMID:22500072
Identification of colorectal cancer related genes with mRMR and shortest path in protein-protein interaction network. PMID:22496748
Context-specific protein network miner--an online system for exploring context-specific protein interaction networks from the literature. PMID:22493694
Swimming upstream: identifying proteomic signals that drive transcriptional changes using the interactome and multiple "-omics" datasets. PMID:22482945
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
Protein interaction data curation: the International Molecular Exchange (IMEx) consortium. PMID:22453911
A multilevel layout algorithm for visualizing physical and genetic interaction networks, with emphasis on their modular organization. PMID:22448851
High accordance in prognosis prediction of colorectal cancer across independent datasets by multi-gene module expression profiles. PMID:22438977
Predicting the lethal phenotype of the knockout mouse by integrating comprehensive genomic data. PMID:22419784
Bayesian Joint Modeling of Multiple Gene Networks and Diverse Genomic Data to Identify Target Genes of a Transcription Factor. PMID:22408712
Mammalian X chromosome inactivation evolved as a dosage-compensation mechanism for dosage-sensitive genes on the X chromosome. PMID:22392987
The role of structural disorder in the rewiring of protein interactions through evolution. PMID:22389433
A Resource of Quantitative Functional Annotation for Homo sapiens Genes. PMID:22384401
Construction and analysis of the protein-protein interaction networks for schizophrenia, bipolar disorder, and major depression. PMID:22373040
Prioritizing disease candidate genes by a gene interconnectedness-based approach. PMID:22369140
A novel framework for the comparative analysis of biological networks. PMID:22363585
Rare coding SNP in DZIP1 gene associated with late-onset sporadic Parkinson's disease. PMID:22355768
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
Integrating the Alzheimer's disease proteome and transcriptome: a comprehensive network model of a complex disease. PMID:22321014
Inhibition of pyrimidine synthesis reverses viral virulence factor-mediated block of mRNA nuclear export. PMID:22312003
Oncogene-specific activation of tyrosine kinase networks during prostate cancer progression. PMID:22307624
Mutational robustness of gene regulatory networks. PMID:22295094
TranscriptomeBrowser 3.0: introducing a new compendium of molecular interactions and a new visualization tool for the study of gene regulatory networks. PMID:22292669
SynaptomeDB: an ontology-based knowledgebase for synaptic genes. PMID:22285564
Tools for protein-protein interaction network analysis in cancer research. PMID:22262713
Large-scale mapping of human protein interactome using structural complexes. PMID:22261719
A dynamic view of domain-motif interactions. PMID:22253583
Three-dimensional reconstruction of protein networks provides insight into human genetic disease. PMID:22252508
Differential network biology. PMID:22252388
IMID: integrated molecular interaction database. PMID:22238258
Mass spectrometry-based proteomics: qualitative identification to activity-based protein profiling. PMID:22231900
Prediction and characterization of protein-protein interaction networks in swine. PMID:22230699
A placental sub-proteome: the apical plasma membrane of the syncytiotrophoblast. PMID:22222045
Recovering protein-protein and domain-domain interactions from aggregation of IP-MS proteomics of coregulator complexes. PMID:22219718
LC-MS/MS analysis of differentially expressed glioblastoma membrane proteome reveals altered calcium signaling and other protein groups of regulatory functions. PMID:22219345
MotifMap: integrative genome-wide maps of regulatory motif sites for model species. PMID:22208852
Evolution of biological interaction networks: from models to real data. PMID:22204388
Which clustering algorithm is better for predicting protein complexes? PMID:22185599
Novel search method for the discovery of functional relationships. PMID:22180409
RefNetBuilder: a platform for construction of integrated reference gene regulatory networks from expressed sequence tags. PMID:22166047
Constructing a robust protein-protein interaction network by integrating multiple public databases. PMID:22165958
Minimotif Miner 3.0: database expansion and significantly improved reduction of false-positive predictions from consensus sequences. PMID:22146221
Gene3D: a domain-based resource for comparative genomics, functional annotation and protein network analysis. PMID:22139938
AutismKB: an evidence-based knowledgebase of autism genetics. PMID:22139918
PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. PMID:22135298
iRefR: an R package to manipulate the iRefIndex consolidated protein interaction database. PMID:22115179
Defining the role of essential genes in human disease. PMID:22096564
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
Expression2Kinases: mRNA profiling linked to multiple upstream regulatory layers. PMID:22080467
Research resource: interactome of human embryo implantation: identification of gene expression pathways, regulation, and integrated regulatory networks. PMID:22074951
PINA v2.0: mining interactome modules. PMID:22067443
Network analysis of microRNAs and their regulation in human ovarian cancer. PMID:22050994
Proteomic analysis of Col11a1-associated protein complexes. PMID:22038862
Patient-specific data fusion defines prognostic cancer subtypes. PMID:22028636
Proteomic and functional genomic landscape of receptor tyrosine kinase and ras to extracellular signal-regulated kinase signaling. PMID:22028469
Improving accuracy of protein-protein interaction prediction by considering the converse problem for sequence representation. PMID:22024143
Toward an understanding of the protein interaction network of the human liver. PMID:21988832
Prioritizing cancer-related genes with aberrant methylation based on a weighted protein-protein interaction network. PMID:21985575
MicroRNA regulation and tissue-specific protein interaction network. PMID:21980443
A systems genetics approach provides a bridge from discovered genetic variants to biological pathways in rheumatoid arthritis. PMID:21980439
Structural analysis of hubs in human NR-RTK network. PMID:21974810
A molecular model of phosphorylation-based activation and potentiation of tarantula muscle thick filaments. PMID:21959262
Analysis of VEGF--a regulated gene expression in endothelial cells to identify genes linked to angiogenesis. PMID:21931866
A systematic analysis of eluted fraction of plasma post immunoaffinity depletion: implications in biomarker discovery. PMID:21931718
Superoxide dismutase 1 (SOD1) is a target for a small molecule identified in a screen for inhibitors of the growth of lung adenocarcinoma cell lines. PMID:21930909
Introduction to network analysis in systems biology. PMID:21917719
Disease gene interaction pathways: a potential framework for how disease genes associate by disease-risk modules. PMID:21915342
Mutual exclusivity analysis identifies oncogenic network modules. PMID:21908773
Revisiting the negative example sampling problem for predicting protein-protein interactions. PMID:21908540
Identifying Schistosoma japonicum excretory/secretory proteins and their interactions with host immune system. PMID:21887319
ppiTrim: constructing non-redundant and up-to-date interactomes. PMID:21873645
Intersection of FOXO- and RUNX1-mediated gene expression programs in single breast epithelial cells during morphogenesis and tumor progression. PMID:21873240
HIV protein sequence hotspots for crosstalk with host hub proteins. PMID:21858059
MIRTFnet: analysis of miRNA regulated transcription factors. PMID:21857930
Evaluating experimental bias and completeness in comparative phosphoproteomics analysis. PMID:21853102
Large-scale de novo prediction of physical protein-protein association. PMID:21836163
Prediction of body fluids where proteins are secreted into based on protein interaction network. PMID:21829572
On the quest for selective constraints shaping the expressivity of the genes casting retropseudogenes in human. PMID:21824418
Molecular evolution of cyclin proteins in animals and fungi. PMID:21798004
Network-based prediction for sources of transcriptional dysregulation using latent pathway identification analysis. PMID:21788508
GPS-Prot: a web-based visualization platform for integrating host-pathogen interaction data. PMID:21777475
Differential C3NET reveals disease networks of direct physical interactions. PMID:21777411
A comprehensive manually curated reaction map of RANKL/RANK-signaling pathway. PMID:21742767
Integrated bio-entity network: a system for biological knowledge discovery. PMID:21738677
Sequence- and interactome-based prediction of viral protein hotspots targeting host proteins: a case study for HIV Nef. PMID:21738584
Essential role of endocytosis of the type II transmembrane serine protease TMPRSS6 in regulating its functionality. PMID:21724843
Identification of Novel Phosphorylation Motifs Through an Integrative Computational and Experimental Analysis of the Human Phosphoproteome. PMID:21720494
Integrated genomic analyses of ovarian carcinoma. PMID:21720365
Integrative network analysis reveals active microRNAs and their functions in gastric cancer. PMID:21703006
Structural principles within the human-virus protein-protein interaction network. PMID:21680884
Characterization the regulation of herpesvirus miRNAs from the view of human protein interaction network. PMID:21668952
Protein interactome reveals converging molecular pathways among autism disorders. PMID:21653829
PILGRM: an interactive data-driven discovery platform for expert biologists. PMID:21653547
De novo discovery of mutated driver pathways in cancer. PMID:21653252
Evidence for the additions of clustered interacting nodes during the evolution of protein interaction networks from network motifs. PMID:21595981
Angiogenesis-associated crosstalk between collagens, CXC chemokines, and thrombospondin domain-containing proteins. PMID:21590489
PRIN: a predicted rice interactome network. PMID:21575196
Mining the TRAF6/p62 interactome for a selective ubiquitination motif. PMID:21554762
Inferring the Sign of Kinase-Substrate Interactions by Combining Quantitative Phosphoproteomics with a Literature-Based Mammalian Kinome Network. PMID:21552464
Using graph theory to analyze biological networks. PMID:21527005
A comprehensive map of the human urinary proteome. PMID:21500864
Modification of gene duplicability during the evolution of protein interaction network. PMID:21490719
A systems biology approach for the investigation of the heparin/heparan sulfate interactome. PMID:21454685
Identification of novel ryanodine receptor 1 (RyR1) protein interaction with calcium homeostasis endoplasmic reticulum protein (CHERP). PMID:21454501
Global phosphoproteomics reveals crosstalk between Bcr-Abl and negative feedback mechanisms controlling Src signaling. PMID:21447799
COSINE: COndition-SpecIfic sub-NEtwork identification using a global optimization method. PMID:21414987
The relationships among microRNA regulation, intrinsically disordered regions, and other indicators of protein evolutionary rate. PMID:21398349
A Boolean-based systems biology approach to predict novel genes associated with cancer: Application to colorectal cancer. PMID:21352556
Integrating multiple protein-protein interaction networks to prioritize disease genes: a Bayesian regression approach. PMID:21342540
Overview: the maturing of proteomics in cardiovascular research. PMID:21335431
Virus interactions with human signal transduction pathways. PMID:21330695
Three 4-letter words of hypertension-related cardiac hypertrophy: TRPC, mTOR, and HDAC. PMID:21320507
Dengue-2 structural proteins associate with human proteins to produce a coagulation and innate immune response biased interactome. PMID:21281507
PNAC: a protein nucleolar association classifier. PMID:21272300
Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology. PMID:21249183
The Biomolecular Interaction Network Database in PSI-MI 2.5. PMID:21233089
A data mining approach for classifying DNA repair genes into ageing-related or non-ageing-related. PMID:21226956
RAC3 is a pro-migratory co-activator of ERα. PMID:21217774
The Musite open-source framework for phosphorylation-site prediction. PMID:21210988
A machine learning approach for genome-wide prediction of morbid and druggable human genes based on systems-level data. PMID:21210975
The PluriNetWork: an electronic representation of the network underlying pluripotency in mouse, and its applications. PMID:21179244
IsoBase: a database of functionally related proteins across PPI networks. PMID:21177658
Interactome mapping suggests new mechanistic details underlying Alzheimer's disease. PMID:21163940
Mining recent brain proteomic databases for ion channel phosphosite nuggets. PMID:21149544
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
BISC: binary subcomplexes in proteins database. PMID:21081561
PHOSIDA 2011: the posttranslational modification database. PMID:21081558
The interactome of a PTB domain-containing adapter protein, Odin, revealed by SILAC. PMID:21081186
LocDB: experimental annotations of localization for Homo sapiens and Arabidopsis thaliana. PMID:21071420
Pathway Commons, a web resource for biological pathway data. PMID:21071392
Phospho.ELM: a database of phosphorylation sites--update 2011. PMID:21062810
CPLA 1.0: an integrated database of protein lysine acetylation. PMID:21059677
SAHG, a comprehensive database of predicted structures of all human proteins. PMID:21051360
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. PMID:21045058
Novel mutation of TCIRG1 and clinical pictures of two infantile malignant osteopetrosis patients. PMID:21042819
Resequencing and association analysis of the KALRN and EPHB1 genes and their contribution to schizophrenia susceptibility. PMID:21041834
RegPhos: a system to explore the protein kinase-substrate phosphorylation network in humans. PMID:21037261
Characterising and predicting haploinsufficiency in the human genome. PMID:20976243
hnRNP L regulates the tumorigenic capacity of lung cancer xenografts in mice via caspase-9 pre-mRNA processing. PMID:20972334
Inference of surface membrane factors of HIV-1 infection through functional interaction networks. PMID:20967291
TcoF-DB: dragon database for human transcription co-factors and transcription factor interacting proteins. PMID:20965969
Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions. PMID:20959820
Genetic diversity and striatal gene networks: focus on the heterogeneous stock-collaborative cross (HS-CC) mouse. PMID:20959017
KUPS: constructing datasets of interacting and non-interacting protein pairs with associated attributions. PMID:20952400
Dynamic functional modules in co-expressed protein interaction networks of dilated cardiomyopathy. PMID:20950417
HitPredict: a database of quality assessed protein-protein interactions in nine species. PMID:20947562
HPIDB--a unified resource for host-pathogen interactions. PMID:20946599
Prediction of human protein-protein interaction by a mixed Bayesian model and its application to exploring underlying cancer-related pathway crosstalk. PMID:20943681
A computational tool for identifying minimotifs in protein-protein interactions and improving the accuracy of minimotif predictions. PMID:20938975
MiRNA-miRNA synergistic network: construction via co-regulating functional modules and disease miRNA topological features. PMID:20929877
Human protein reference database and human proteinpedia as discovery resources for molecular biotechnology. PMID:20927658
Toward a complete in silico, multi-layered embryonic stem cell regulatory network. PMID:20890967
Domain altering SNPs in the human proteome and their impact on signaling pathways. PMID:20886114
DAnCER: disease-annotated chromatin epigenetics resource. PMID:20876685
Similarity of molecular phenotype between known epilepsy gene LGI1 and disease candidate gene LGI2. PMID:20863412
FragViz: visualization of fragmented networks. PMID:20860802
MatrixDB, the extracellular matrix interaction database. PMID:20852260
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
Protein connectivity and protein complexity promotes human gene duplicability in a mutually exclusive manner. PMID:20829394
Improving disease gene prioritization using the semantic similarity of Gene Ontology terms. PMID:20823322
A yeast's eye view of mammalian reproduction: cross-species gene co-expression in meiotic prophase. PMID:20819218
Protein networks reveal detection bias and species consistency when analysed by information-theoretic methods. PMID:20805870
Proteomic characterization of human plasma high density lipoprotein fractionated by gel filtration chromatography. PMID:20718489
A systems biology approach identifies inflammatory abnormalities between mouse strains prior to development of metabolic disease. PMID:20713682
Temporal profiling of the secretome during adipogenesis in humans. PMID:20707391
Transcription profiling of Epstein-Barr virus nuclear antigen (EBNA)-1 expressing cells suggests targeting of chromatin remodeling complexes. PMID:20706582
Musite, a tool for global prediction of general and kinase-specific phosphorylation sites. PMID:20702892
A novel tissue-specific meta-analysis approach for gene expression predictions, initiated with a mammalian gene expression testis database. PMID:20699007
Comprehensive transcriptome analysis of mouse embryonic stem cell adipogenesis unravels new processes of adipocyte development. PMID:20678241
Network-based relating pharmacological and genomic spaces for drug target identification. PMID:20668676
Wnt signaling regulates mitochondrial physiology and insulin sensitivity. PMID:20634317
Identifying potential survival strategies of HIV-1 through virus-host protein interaction networks. PMID:20633292
Literature-based discovery of IFN-gamma and vaccine-mediated gene interaction networks. PMID:20625487
Divergence of human and mouse brain transcriptome highlights Alzheimer disease pathways. PMID:20616000
Identifying differentially regulated subnetworks from phosphoproteomic data. PMID:20584295
Modular composition predicts kinase/substrate interactions. PMID:20579376
The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function. PMID:20576703
A Poisson model for random multigraphs. PMID:20554690
Identifying targets of miR-143 using a SILAC-based proteomic approach. PMID:20544124
Phosphorylated and nonphosphorylated serine and threonine residues evolve at different rates in mammals. PMID:20534707
Duplicability of self-interacting human genes. PMID:20509897
Domain distribution and intrinsic disorder in hubs in the human protein-protein interaction network. PMID:20509167
Dynamic cross-talk analysis among TNF-R, TLR-4 and IL-1R signalings in TNFalpha-induced inflammatory responses. PMID:20497537
Phosphoproteome analysis reveals regulatory sites in major pathways of cardiac mitochondria. PMID:20495213
Discovering modulators of gene expression. PMID:20466809
DynaMod: dynamic functional modularity analysis. PMID:20460468
Towards the systematic discovery of signal transduction networks using phosphorylation dynamics data. PMID:20459641
Improved microarray-based decision support with graph encoded interactome data. PMID:20419106
Identification of responsive gene modules by network-based gene clustering and extending: application to inflammation and angiogenesis. PMID:20406493
Restoration of gamma-sarcoglycan localization and mechanical signal transduction are independent in murine skeletal muscle. PMID:20371873
Mutation@A Glance: an integrative web application for analysing mutations from human genetic diseases. PMID:20360267
Analysis of diverse regulatory networks in a hierarchical context shows consistent tendencies for collaboration in the middle levels. PMID:20351254
Construction and analysis of protein-protein interaction networks. PMID:20334628
Differential phosphoproteomics of fibroblast growth factor signaling: identification of Src family kinase-mediated phosphorylation events. PMID:20225815
Increasing alternative promoter repertories is positively associated with differential expression and disease susceptibility. PMID:20208995
AutoSOME: a clustering method for identifying gene expression modules without prior knowledge of cluster number. PMID:20202218
The power of protein interaction networks for associating genes with diseases. PMID:20185403
Network-based elucidation of human disease similarities reveals common functional modules enriched for pluripotent drug targets. PMID:20140234
Extracting consistent knowledge from highly inconsistent cancer gene data sources. PMID:20137077
Prediction of human functional genetic networks from heterogeneous data using RVM-based ensemble learning. PMID:20134029
Detection of characteristic sub pathway network for angiogenesis based on the comprehensive pathway network. PMID:20122205
An ontology-based search engine for protein-protein interactions. PMID:20122195
Biana: a software framework for compiling biological interactions and analyzing networks. PMID:20105306
Comparative proteomics of human embryonic stem cells and embryonal carcinoma cells. PMID:20104618
NetPath: a public resource of curated signal transduction pathways. PMID:20067622
Understanding protein phosphorylation on a systems level. PMID:20056723
In silico functional profiling of human disease-associated and polymorphic amino acid substitutions. PMID:20052762
CanProVar: a human cancer proteome variation database. PMID:20052754
PDbase: a database of Parkinson's disease-related genes and genetic variation using substantia nigra ESTs. PMID:19958497
Human liver rate-limiting enzymes influence metabolic flux via branch points and inhibitors. PMID:19958496
Network properties of complex human disease genes identified through genome-wide association studies. PMID:19956617
Role for protein-protein interaction databases in human genetics. PMID:19929610
ELM: the status of the 2010 eukaryotic linear motif resource. PMID:19920119
Algorithms for effective querying of compound graph-based pathway databases. PMID:19917102
Loss of post-translational modification sites in disease. PMID:19908386
Network of Cancer Genes: a web resource to analyze duplicability, orthology and network properties of cancer genes. PMID:19906700
HLungDB: an integrated database of human lung cancer research. PMID:19900972
An integrative approach to reveal driver gene fusions from paired-end sequencing data in cancer. PMID:19881495
Proteomic and phospho-proteomic profile of human platelets in basal, resting state: insights into integrin signaling. PMID:19859549
Knowledge-based data analysis comes of age. PMID:19854753
Predicting meiotic pathways in human fetal oogenesis. PMID:19846598
Identification of functionally related genes using data mining and data integration: a breast cancer case study. PMID:19828084
Prediction of candidate primary immunodeficiency disease genes using a support vector machine learning approach. PMID:19801557
Functionally guided alignment of protein interaction networks for module detection. PMID:19797409
Tyrosine phosphorylation of nuclear-membrane protein emerin by Src, Abl and other kinases. PMID:19789182
Defining elastic fiber interactions by molecular fishing: an affinity purification and mass spectrometry approach. PMID:19755719
NASCENT: an automatic protein interaction network generation tool for non-model organisms. PMID:19707301
Scaffolds: interaction platforms for cellular signalling circuits. PMID:19651513
Building disease-specific drug-protein connectivity maps from molecular interaction networks and PubMed abstracts. PMID:19649302
Identification of c-Src tyrosine kinase substrates in platelet-derived growth factor receptor signaling. PMID:19632164
PathBuilder--open source software for annotating and developing pathway resources. PMID:19628504
The platelet proteome. PMID:19550320
PIAS proteins: pleiotropic interactors associated with SUMO. PMID:19526197
DASMIweb: online integration, analysis and assessment of distributed protein interaction data. PMID:19502495
MedlineRanker: flexible ranking of biomedical literature. PMID:19429696
DASMI: exchanging, annotating and assessing molecular interaction data. PMID:19420069
POINeT: protein interactome with sub-network analysis and hub prioritization. PMID:19379523
MatrixDB, a database focused on extracellular protein-protein and protein-carbohydrate interactions. PMID:19147664
Development of human protein reference database as an initial platform for approaching systems biology in humans PubMed citations: 427.

427 articles citing: Development of human protein reference database as an initial platform for approaching systems biology in humans

Deep learning frameworks for protein-protein interaction prediction. PMID:35832624
Biomedical Analytics of Four Chinese Medicinals in Treatment of Insomnia Based on Network Pharmacology. PMID:35769674
Identification of the Potential Molecular Mechanisms Linking RUNX1 Activity with Nonalcoholic Fatty Liver Disease, by Means of Systems Biology. PMID:35740337
Transcriptomic analysis reveals pathophysiological relationship between chronic obstructive pulmonary disease (COPD) and periodontitis. PMID:35676670
Proteogenomic characterization of 2002 human cancers reveals pan-cancer molecular subtypes and associated pathways. PMID:35562349
Physical and functional interactome atlas of human receptor tyrosine kinases. PMID:35384245
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
Gene Expression Profile Analyses of the Skin Response of Balb/c-Nu Mice Model Injected by Staphylococcus aureus. PMID:35210800
Clinico-pathological correlation: Teaching aspects, avenues, and advances. PMID:34981007
A computational approach for the discovery of significant cancer genes by weighted mutation and asymmetric spreading strength in networks. PMID:34876593
Calculation of Similarity Between 26 Autoimmune Diseases Based on Three Measurements Including Network, Function, and Semantics. PMID:34858474
PharmVIP: A Web-Based Tool for Pharmacogenomic Variant Analysis and Interpretation. PMID:34834582
In silico Methods for Identification of Potential Therapeutic Targets. PMID:34826045
Geometric network analysis provides prognostic information in patients with high grade serous carcinoma of the ovary treated with immune checkpoint inhibitors. PMID:34819508
Computationally Reconstructed Interactome of Bradyrhizobium diazoefficiens USDA110 Reveals Novel Functional Modules and Protein Hubs for Symbiotic Nitrogen Fixation. PMID:34769335
Regulation of ER Composition and Extent, and Putative Action in Protein Networks by ER/NE Protein TMEM147. PMID:34638576
Getting to know each other: PPIMem, a novel approach for predicting transmembrane protein-protein complexes. PMID:34630938
Molecular Biology Networks and Key Gene Regulators for Inflammatory Biomarkers Shared by Breast Cancer Development: Multi-Omics Systems Analysis. PMID:34572592
STING nuclear partners contribute to innate immune signaling responses. PMID:34541469
Drug Discovery of Spinal Muscular Atrophy (SMA) from the Computational Perspective: A Comprehensive Review. PMID:34445667
Revealing protein-protein interactions at the transcriptome scale by sequencing. PMID:34348091
Inference of kinase-signaling networks in human myeloid cell line models by Phosphoproteomics using kinase activity enrichment analysis (KAEA). PMID:34238254
Databases for Protein-Protein Interactions. PMID:34236665
The expression and clinical prognostic value of protein phosphatase 1 catalytic subunit beta in pancreatic cancer. PMID:34125004
Predicting Protein-Protein Interactions Using Symmetric Logistic Matrix Factorization. PMID:33831302
Multi-Omics Data Analysis Uncovers Molecular Networks and Gene Regulators for Metabolic Biomarkers. PMID:33801830
Sparse linear discriminant analysis for multiview structured data. PMID:33739448
Group I p21-activated kinases in leukemia cell adhesion to fibronectin. PMID:33464167
Quantitative Interactomics of Lck-TurboID in Living Human T Cells Unveils T Cell Receptor Stimulation-Induced Proximal Lck Interactors. PMID:33185455
Biological network analysis with deep learning. PMID:33169146
KSP: an integrated method for predicting catalyzing kinases of phosphorylation sites in proteins. PMID:32753030
Using phosphoproteomics data to understand cellular signaling: a comprehensive guide to bioinformatics resources. PMID:32676006
Quantitative proteomic analysis of the frontal cortex in Alzheimer's disease. PMID:32614981
A flexible network-based imputing-and-fusing approach towards the identification of cell types from single-cell RNA-seq data. PMID:32527285
Genotype-phenotype analysis of LMNA-related diseases predicts phenotype-selective alterations in lamin phosphorylation. PMID:32413188
A massively parallel barcoded sequencing pipeline enables generation of the first ORFeome and interactome map for rice. PMID:32398372
Comprehensive gene and pathway analysis of cervical cancer progression. PMID:32256826
A network analysis to identify pathophysiological pathways distinguishing ischaemic from non-ischaemic heart failure. PMID:32243695
An integrative, genomic, transcriptomic and network-assisted study to identify genes associated with human cleft lip with or without cleft palate. PMID:32241273
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
Unraveling the role of salt-sensitivity genes in obesity with integrated network biology and co-expression analysis. PMID:32027667
Identification of cancer driver genes based on nucleotide context. PMID:32015527
TP63 isoform expression is linked with distinct clinical outcomes in cancer. PMID:31927310
Network Modeling Approaches and Applications to Unravelling Non-Alcoholic Fatty Liver Disease. PMID:31771247
Synchronized replication of genes encoding the same protein complex in fast-proliferating cells. PMID:31662304
Mapping the protein-protein and genetic interactions of cancer to guide precision medicine. PMID:31288129
Analysis and prediction of human acetylation using a cascade classifier based on support vector machine. PMID:31208321
Pathogenicity and functional impact of non-frameshifting insertion/deletion variation in the human genome. PMID:31199787
A Multi-Cohort and Multi-Omics Meta-Analysis Framework to Identify Network-Based Gene Signatures. PMID:30941158
Network Pharmacology Databases for Traditional Chinese Medicine: Review and Assessment. PMID:30846939
Detecting protein complexes based on a combination of topological and biological properties in protein-protein interaction network. PMID:30647725
Mapping the Proteome of the Synaptic Cleft through Proximity Labeling Reveals New Cleft Proteins. PMID:30487426
Protein kinase C iota facilitates insulin-induced glucose transport by phosphorylation of soluble nSF attachment protein receptor regulator (SNARE) double C2 domain protein b. PMID:30369065
Context-specific interactions in literature-curated protein interaction databases. PMID:30340458
Identification of the Transcription Factor Relationships Associated with Androgen Deprivation Therapy Response and Metastatic Progression in Prostate Cancer. PMID:30314329
Systematic Evaluation of Molecular Networks for Discovery of Disease Genes. PMID:29605183
Evaluating the associations between human circadian rhythms and dysregulated genes in liver cancer cells. PMID:29250165
Systems biology: An emerging strategy for discovering novel pathogenetic mechanisms that promote cardiovascular disease. PMID:29043273
PhosphoPredict: A bioinformatics tool for prediction of human kinase-specific phosphorylation substrates and sites by integrating heterogeneous feature selection. PMID:28761071
Screening of the prognostic targets for breast cancer based co-expression modules analysis. PMID:28731166
Network analysis reveals crosstalk between autophagy genes and disease genes. PMID:28295050
The maternal plasma proteome changes as a function of gestational age in normal pregnancy: a longitudinal study. PMID:28263753
An approach to infer putative disease-specific mechanisms using neighboring gene networks. PMID:28200075
Annotating Mutational Effects on Proteins and Protein Interactions: Designing Novel and Revisiting Existing Protocols. PMID:28188534
A network medicine approach to build a comprehensive atlas for the prognosis of human cancer. PMID:27559151
A protein network descriptor server and its use in studying protein, disease, metabolic and drug targeted networks. PMID:27542402
Interpretable per case weighted ensemble method for cancer associations. PMID:27435615
Discovery Proteomics Identifies a Molecular Link between the Coatomer Protein Complex I and Androgen Receptor-dependent Transcription. PMID:27365400
Identification of differentially expressed genes between lung adenocarcinoma and lung squamous cell carcinoma by gene expression profiling. PMID:27356570
Robust Multi-Network Clustering via Joint Cross-Domain Cluster Alignment. PMID:27239167
Key Immune Events of the Pathomechanisms of Early Cardioembolic Stroke: Multi-Database Mining and Systems Biology Approach. PMID:26927091
Using contrast patterns between true complexes and random subgraphs in PPI networks to predict unknown protein complexes. PMID:26868667
Multimodal targeted high relaxivity thermosensitive liposome for in vivo imaging. PMID:26610702
Dealing with the Data Deluge: Handling the Multitude Of Chemical Biology Data Sources. PMID:26609498
Sphingosine kinase 2 is a chikungunya virus host factor co-localized with the viral replication complex. PMID:26576339
Modular organization of the human disease genes: a text-based network inference. PMID:26527852
Systematic evaluation of underlying defects in DNA repair as an approach to case-only assessment of familial prostate cancer. PMID:26485759
Protein interaction network constructing based on text mining and reinforcement learning with application to prostate cancer. PMID:26243825
Research Resource: Androgen Receptor Activity Is Regulated Through the Mobilization of Cell Surface Receptor Networks. PMID:26181434
In Silico Structural and Functional Annotation of Hypothetical Proteins of Vibrio cholerae O139. PMID:26175663
Inference of Low and High-Grade Glioma Gene Regulatory Networks Delineates the Role of Rnd3 in Establishing Multiple Hallmarks of Cancer. PMID:26132659
NET-GE: a novel NETwork-based Gene Enrichment for detecting biological processes associated to Mendelian diseases. PMID:26110971
Publisher’s Note:Abstraction for data integration:Fusing mammalian molecular, cellular and phenotype big datasets for better knowledge extraction. PMID:26101093
Dynamic network-based relevance score reveals essential proteins and functional modules in directed differentiation. PMID:25977693
Urothelial cancer gene regulatory networks inferred from large-scale RNAseq, Bead and Oligo gene expression data. PMID:25971253
Network-based Phenome-Genome Association Prediction by Bi-Random Walk. PMID:25933025
Using network clustering to predict copy number variations associated with health disparities. PMID:25780754
The identification of specific methylation patterns across different cancers. PMID:25774687
Protein complex discovery by interaction filtering from protein interaction networks using mutual rank coexpression and sequence similarity. PMID:25692131
Revealing the potential pathogenesis of glioma by utilizing a glioma associated protein-protein interaction network. PMID:25410026
Protein interaction networks reveal novel autism risk genes within GWAS statistical noise. PMID:25409314
A systems biology strategy to identify molecular mechanisms of action and protein indicators of traumatic brain injury. PMID:25399920
Text mining in cancer gene and pathway prioritization. PMID:25392685
OCT4 mutations in human erythroleukemic cells: implications for multiple drug resistance (MDR) phenotype. PMID:25355160
Hope for GWAS: relevant risk genes uncovered from GWAS statistical noise. PMID:25268625
Grouping annotations on the subcellular layered interactome demonstrates enhanced autophagy activity in a recurrent experimental autoimmune uveitis T cell line. PMID:25116327
Lean Big Data integration in systems biology and systems pharmacology. PMID:25109570
Proteome-wide analysis of human disease mutations in short linear motifs: neglected players in cancer? PMID:25057855
A novel CISD2 intragenic deletion, optic neuropathy and platelet aggregation defect in Wolfram syndrome type 2. PMID:25056293
Multi-tissue computational modeling analyzes pathophysiology of type 2 diabetes in MKR mice. PMID:25029527
Expanding the computational toolbox for mining cancer genomes. PMID:25001846
Pathway reconstruction of airway remodeling in chronic lung diseases: a systems biology approach. PMID:24978043
Phosphokinase antibody arrays on dendron-coated surface. PMID:24802362
Systems biology as an integrated platform for bioinformatics, systems synthetic biology, and systems metabolic engineering. PMID:24709875
In silico prediction of protein-protein interactions in human macrophages. PMID:24636261
ProphNet: a generic prioritization method through propagation of information. PMID:24564336
Screening of hub genes and pathways in colorectal cancer with microarray technology. PMID:24504536
Identifying driver mutations in sequenced cancer genomes: computational approaches to enable precision medicine. PMID:24479672
Computational Prediction of Protein-Protein Interaction Networks: Algo-rithms and Resources. PMID:24396273
Identifying potential cancer driver genes by genomic data integration. PMID:24346768
Integrating human omics data to prioritize candidate genes. PMID:24344781
Using random walks to identify cancer-associated modules in expression data. PMID:24128261
Using protein interaction database and support vector machines to improve gene signatures for prediction of breast cancer recurrence. PMID:24098862
A system biology approach to identify regulatory pathways underlying the neuroendocrine control of female puberty in rats and nonhuman primates. PMID:23998662
Gentrepid V2.0: a web server for candidate disease gene prediction. PMID:23947436
SubNet: a Java application for subnetwork extraction. PMID:23946504
Transcription factor binding profiles reveal cyclic expression of human protein-coding genes and non-coding RNAs. PMID:23874175
Module-based breast cancer classification. PMID:23819260
Integrative analysis of cancer-related signaling pathways. PMID:23760067
Blood RNA profiling in a large cohort of multiple sclerosis patients and healthy controls. PMID:23748426
Prediction and validation of gene-disease associations using methods inspired by social network analyses. PMID:23650495
Network-based survival analysis reveals subnetwork signatures for predicting outcomes of ovarian cancer treatment. PMID:23555212
Imbalanced network biomarkers for traditional Chinese medicine Syndrome in gastritis patients. PMID:23529020
Novel semantic similarity measure improves an integrative approach to predicting gene functional associations. PMID:23497449
A proteomics view of the molecular mechanisms and biomarkers of glaucomatous neurodegeneration. PMID:23396249
Advances for studying clonal evolution in cancer. PMID:23353056
Disentangling function from topology to infer the network properties of disease genes. PMID:23324116
Chapter 2: Data-driven view of disease biology. PMID:23300408
NeuroDNet - an open source platform for constructing and analyzing neurodegenerative disease networks. PMID:23286825
PCDq: human protein complex database with quality index which summarizes different levels of evidences of protein complexes predicted from h-invitational protein-protein interactions integrative dataset. PMID:23282181
Disease gene identification by random walk on multigraphs merging heterogeneous genomic and phenotype data. PMID:23282070
Kaposi's sarcoma: a computational approach through protein-protein interaction and gene regulatory networks analysis. PMID:23266878
An approach for the identification of targets specific to bone metastasis using cancer genes interactome and gene ontology analysis. PMID:23166660
SILAC-based quantitative proteomic analysis of gastric cancer secretome. PMID:23161554
Proteomics-based methods for discovery, quantification, and validation of protein-protein interactions. PMID:23157382
Combing the hairball with BioFabric: a new approach for visualization of large networks. PMID:23102059
Computational structural and functional analysis of hypothetical proteins of Staphylococcus aureus. PMID:23055618
Transcriptional expression patterns triggered by chemically distinct neuroprotective molecules. PMID:22986168
Rapid characterization of candidate biomarkers for pancreatic cancer using cell microarrays (CMAs). PMID:22985314
Comprehensive binary interaction mapping of SH2 domains via fluorescence polarization reveals novel functional diversification of ErbB receptors. PMID:22973453
AbsIDconvert: an absolute approach for converting genetic identifiers at different granularities. PMID:22967011
Multiple biomarker tissue arrays: A computational approach to identifying protein-protein interactions in the EGFR/ERK signalling pathway. PMID:22937740
Phosphoproteome of human glioblastoma initiating cells reveals novel signaling regulators encoded by the transcriptome. PMID:22912867
DTome: a web-based tool for drug-target interactome construction. PMID:22901092
A systems biology approach to the global analysis of transcription factors in colorectal cancer. PMID:22852817
Integrating gene expression and protein-protein interaction network to prioritize cancer-associated genes. PMID:22838965
Subnetwork-based analysis of chronic lymphocytic leukemia identifies pathways that associate with disease progression. PMID:22837534
Positionally biased gene loss after whole genome duplication: evidence from human, yeast, and plant. PMID:22835904
Identification of the dichotomous role of age-related LCK in calorie restriction revealed by integrative analysis of cDNA microarray and interactome. PMID:22828953
Transcriptional interference networks coordinate the expression of functionally related genes clustered in the same genomic loci. PMID:22783276
Genomics and bioinformatics of Parkinson's disease. PMID:22762024
Co-clustering phenome-genome for phenotype classification and disease gene discovery. PMID:22735708
Overexpression of ribosome binding protein 1 (RRBP1) in breast cancer. PMID:22709790
Using the reactome database. PMID:22700314
Transcriptome kinetics of circulating neutrophils during human experimental endotoxemia. PMID:22679495
Proteomic analysis of S-acylated proteins in human B cells reveals palmitoylation of the immune regulators CD20 and CD23. PMID:22615937
Computational and informatics strategies for identification of specific protein interaction partners in affinity purification mass spectrometry experiments. PMID:22611043
Inferring high-confidence human protein-protein interactions. PMID:22558947
Functional organization and its implication in evolution of the human protein-protein interaction network. PMID:22530615
Identification of targets of c-Src tyrosine kinase by chemical complementation and phosphoproteomics. PMID:22499769
Phosphorylation regulates human OCT4. PMID:22474382
An activation force-based affinity measure for analyzing complex networks. PMID:22355630
A systemic network triggered by human cytomegalovirus entry. PMID:22312338
Identification of aberrant pathways and network activities from high-throughput data. PMID:22287794
Systems-based approaches to cardiovascular disease. PMID:22231714
An integer linear programming approach for finding deregulated subgraphs in regulatory networks. PMID:22210863
Transforming growth factor β receptor 1 is a new candidate prognostic biomarker after acute myocardial infarction. PMID:22136666
Identification of dysfunctional modules and disease genes in congenital heart disease by a network-based approach. PMID:22136190
A systems genetics approach provides a bridge from discovered genetic variants to biological pathways in rheumatoid arthritis. PMID:21980439
iRefScape. A Cytoscape plug-in for visualization and data mining of protein interaction data from iRefIndex. PMID:21975162
iCTNet: a Cytoscape plugin to produce and analyze integrative complex traits networks. PMID:21943367
A systematic analysis of eluted fraction of plasma post immunoaffinity depletion: implications in biomarker discovery. PMID:21931718
A network-based approach to prioritize results from genome-wide association studies. PMID:21915301
A physical interaction network of dengue virus and human proteins. PMID:21911577
Protein interaction-based genome-wide analysis of incident coronary heart disease. PMID:21880673
Global organization of protein complexome in the yeast Saccharomyces cerevisiae. PMID:21843333
The collagen chaperone HSP47 is a new interactor of APP that affects the levels of extracellular beta-amyloid peptides. PMID:21829458
Proteomic analysis of palmitoylated platelet proteins. PMID:21813449
Inferring gene-phenotype associations via global protein complex network propagation. PMID:21799737
Systematic approaches towards the development of host-directed antiviral therapeutics. PMID:21747723
Exploring biologically relevant pathways in frailty. PMID:21743092
Network clustering revealed the systemic alterations of mitochondrial protein expression. PMID:21738461
Network target for screening synergistic drug combinations with application to traditional Chinese medicine. PMID:21689469
Uncover disease genes by maximizing information flow in the phenome-interactome network. PMID:21685067
An atlas of tissue-specific conserved coexpression for functional annotation and disease gene prediction. PMID:21654723
Modularity-based credible prediction of disease genes and detection of disease subtypes on the phenotype-gene heterogeneous network. PMID:21599985
Protein annotation from protein interaction networks and Gene Ontology. PMID:21571095
Combinatorial binding of transcription factors in the pluripotency control regions of the genome. PMID:21527551
A comprehensive map of the human urinary proteome. PMID:21500864
COSINE: COndition-SpecIfic sub-NEtwork identification using a global optimization method. PMID:21414987
Assessing the biological significance of gene expression signatures and co-expression modules by studying their network properties. PMID:21408226
Analysis of AML Genes in Dysregulated Molecular Networks. PMID:21347161
Interaction site prediction by structural similarity to neighboring clusters in protein-protein interaction networks. PMID:21342570
Comparative analysis of protein interaction networks reveals that conserved pathways are susceptible to HIV-1 interception. PMID:21342548
Landscape mapping of functional proteins in insulin signal transduction and insulin resistance: a network-based protein-protein interaction analysis. PMID:21305025
Gene expression meta-analysis identifies VDAC1 as a predictor of poor outcome in early stage non-small cell lung cancer. PMID:21297950
Dynamic summarization of bibliographic-based data. PMID:21284871
A knowledge-based weighting framework to boost the power of genome-wide association studies. PMID:21217833
A network-based biomarker approach for molecular investigation and diagnosis of lung cancer. PMID:21211025
SIDEKICK: Genomic data driven analysis and decision-making framework. PMID:21192813
Literature curation of protein interactions: measuring agreement across major public databases. PMID:21183497
Combining modularity, conservation, and interactions of proteins significantly increases precision and coverage of protein function prediction. PMID:21171995
Extending pathways and processes using molecular interaction networks to analyse cancer genome data. PMID:21144022
The interplay between evolution, regulation and tissue specificity in the Human Hereditary Diseasome. PMID:21143807
A comparative study of cancer proteins in the human protein-protein interaction network. PMID:21143787
Regulation patterns in signaling networks of cancer. PMID:21110851
The interactome of a PTB domain-containing adapter protein, Odin, revealed by SILAC. PMID:21081186
CADgene: a comprehensive database for coronary artery disease genes. PMID:21045063
Genetic diversity and striatal gene networks: focus on the heterogeneous stock-collaborative cross (HS-CC) mouse. PMID:20959017
Selection upon genome architecture: conservation of functional neighborhoods with changing genes. PMID:20949098
iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence. PMID:20940177
Biomedical text summarization to support genetic database curation: using Semantic MEDLINE to create a secondary database of genetic information. PMID:20936065
Human protein reference database and human proteinpedia as discovery resources for molecular biotechnology. PMID:20927658
Investigating the validity of current network analysis on static conglomerate networks by protein network stratification. PMID:20846443
Identifying dysfunctional crosstalk of pathways in various regions of Alzheimer's disease brains. PMID:20840725
In silico analysis of kinase expression identifies WEE1 as a gatekeeper against mitotic catastrophe in glioblastoma. PMID:20832752
The BioPAX community standard for pathway data sharing. PMID:20829833
A model-based strategy to investigate the role of microRNA regulation in cancer signalling networks. PMID:20809366
Measuring the physical cohesiveness of proteins using physical interaction enrichment. PMID:20798171
Encoding the states of interacting proteins to facilitate biological pathways reconstruction. PMID:20707925
Inferring modules from human protein interactome classes. PMID:20653930
Duplicability of self-interacting human genes. PMID:20509897
A genome-wide map of human genetic interactions inferred from radiation hybrid genotypes. PMID:20508145
Functional features, biological pathways, and protein interaction networks of addiction-related genes. PMID:20491072
A human functional protein interaction network and its application to cancer data analysis. PMID:20482850
Visual integration of quantitative proteomic data, pathways, and protein interactions. PMID:20467059
Coordinated modular functionality and prognostic potential of a heart failure biomarker-driven interaction network. PMID:20462429
Profiling of protein interaction networks of protein complexes using affinity purification and quantitative mass spectrometry. PMID:20445003
SZGR: a comprehensive schizophrenia gene resource. PMID:20424623
Reconstruction of gene regulatory modules in cancer cell cycle by multi-source data integration. PMID:20422009
Integrated protein network and microarray analysis to identify potential biomarkers after myocardial infarction. PMID:20414696
Identification of responsive gene modules by network-based gene clustering and extending: application to inflammation and angiogenesis. PMID:20406493
Restoration of gamma-sarcoglycan localization and mechanical signal transduction are independent in murine skeletal muscle. PMID:20371873
Predicting protein-protein interactions in unbalanced data using the primary structure of proteins. PMID:20361868
HTAPP: high-throughput autonomous proteomic pipeline. PMID:20336676
Construction and analysis of protein-protein interaction networks. PMID:20334628
Nanodevices in diagnostics. PMID:20229595
A chemical and phosphoproteomic characterization of dasatinib action in lung cancer. PMID:20190765
High-throughput discovery and characterization of fetal protein trafficking in the blood of pregnant women. PMID:20186258
Differential proteome analysis of human gliomas stratified for loss of heterozygosity on chromosomal arms 1p and 19q. PMID:20167812
Immunohistochemistry in diagnostic surgical pathology: contributions of protein life-cycle, use of evidence-based methods and data normalization on interpretation of immunohistochemical stains. PMID:20126585
Integration of multiple data sources to prioritize candidate genes using discounted rating system. PMID:20122192
Predominant occupation of the class I MHC molecule H-2Kwm7 with a single self-peptide suggests a mechanism for its diabetes-protective effect. PMID:20093428
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
Detecting disease associated modules and prioritizing active genes based on high throughput data. PMID:20070902
Cardiovascular networks: systems-based approaches to cardiovascular disease. PMID:20048233
Of mice and men: comparative proteomics of bronchoalveolar fluid. PMID:20032019
Gradients of Eph-A6 expression in primate retina suggest roles in both vascular and axon guidance. PMID:20011078
Critical assessment of sequence-based protein-protein interaction prediction methods that do not require homologous protein sequences. PMID:20003442
Network-based Identification of novel cancer genes. PMID:19959820
Alternative paths in HIV-1 targeted human signal transduction pathways. PMID:19958495
Novel protein-protein interactions inferred from literature context. PMID:19924298
Evaluation of linguistic features useful in extraction of interactions from PubMed; application to annotating known, high-throughput and predicted interactions in I2D. PMID:19850753
Identification of tyrosine-phosphorylated proteins associated with metastasis and functional analysis of FER in human hepatocellular carcinoma cells. PMID:19835603
PeptideDepot: flexible relational database for visual analysis of quantitative proteomic data and integration of existing protein information. PMID:19834895
Protopia: a protein-protein interaction tool. PMID:19828077
An integrated systems analysis implicates EGR1 downregulation in simian immunodeficiency virus encephalitis-induced neural dysfunction. PMID:19812322
Classification of nonenzymatic homologues of protein kinases. PMID:19809514
Disease-aging network reveals significant roles of aging genes in connecting genetic diseases. PMID:19779549
Analysis of AML genes in dysregulated molecular networks. PMID:19761572
Deeply conserved chordate noncoding sequences preserve genome synteny but do not drive gene duplicate retention. PMID:19704032
The human protein coevolution network. PMID:19696150
Knowledge-guided inference of domain-domain interactions from incomplete protein-protein interaction networks. PMID:19667081
A proposed syntax for Minimotif Semantics, version 1. PMID:19656396
Comparison of peptide array substrate phosphorylation of c-Raf and mitogen activated protein kinase kinase kinase 8. PMID:19649278
The organization of the transcriptional network in specific neuronal classes. PMID:19638972
Identification of c-Src tyrosine kinase substrates in platelet-derived growth factor receptor signaling. PMID:19632164
Layered functional network analysis of gene expression in human heart failure. PMID:19629191
Systems-level cancer gene identification from protein interaction network topology applied to melanogenesis-related functional genomics data. PMID:19625303
A systems biology-based gene expression classifier of glioblastoma predicts survival with solid tumors. PMID:19609451
Evolutionary flexibility of protein complexes. PMID:19583842
Pirfenidone is renoprotective in diabetic kidney disease. PMID:19578007
Clustered microRNAs' coordination in regulating protein-protein interaction network. PMID:19558649
Global gene expression analysis of reactive stroma in prostate cancer. PMID:19509179
Proteome-wide prediction of signal flow direction in protein interaction networks based on interacting domains. PMID:19502588
A complex-centric view of protein network evolution. PMID:19465379
Bioinformatics resources for cancer research with an emphasis on gene function and structure prediction tools. PMID:19458756
Germinal center B cell-like (GCB) and activated B cell-like (ABC) type of diffuse large B cell lymphoma (DLBCL): analysis of molecular predictors, signatures, cell cycle state and patient survival. PMID:19455257
SNOW, a web-based tool for the statistical analysis of protein-protein interaction networks. PMID:19454602
In vitro nuclear interactome of the HIV-1 Tat protein. PMID:19454010
Prediction of HIV-1 virus-host protein interactions using virus and host sequence motifs. PMID:19450270
Assessing reliability of protein-protein interactions by integrative analysis of data in model organisms. PMID:19426453
Protein-protein interaction databases: keeping up with growing interactomes. PMID:19403463
Perturbation of interaction networks for application to cancer therapy. PMID:19390668
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
Identifying disease-specific genes based on their topological significance in protein networks. PMID:19309513
Toward accurate reconstruction of functional protein networks. PMID:19293828
Topological and organizational properties of the products of house-keeping and tissue-specific genes in protein-protein interaction networks. PMID:19284572
Noninjurious mechanical ventilation activates a proinflammatory transcriptional program in the lung. PMID:19276240
Tyrosine phosphorylation of the human glutathione S-transferase P1 by epidermal growth factor receptor. PMID:19254954
Gene set-based module discovery in the breast cancer transcriptome. PMID:19243633
Mechanisms of tumor resistance to EGFR-targeted therapies. PMID:19236156
Dissecting the interface between signaling and transcriptional regulation in human B cells. PMID:19209707
Comparison of automated candidate gene prediction systems using genes implicated in type 2 diabetes by genome-wide association studies. PMID:19208173
A complex-based reconstruction of the Saccharomyces cerevisiae interactome. PMID:19176519
Improved homology-driven computational validation of protein-protein interactions motivated by the evolutionary gene duplication and divergence hypothesis. PMID:19152684
Genome-wide analysis to predict protein sequence variations that change phosphorylation sites or their corresponding kinases. PMID:19139070
Effects of tobacco smoke on gene expression and cellular pathways in a cellular model of oral leukoplakia. PMID:19138943
Literature-curated protein interaction datasets. PMID:19116613
Meta-analysis of expression signatures of muscle atrophy: gene interaction networks in early and late stages. PMID:19108710
Integrated network analysis platform for protein-protein interactions. PMID:19079255
Human Gene and Protein Database (HGPD): a novel database presenting a large quantity of experiment-based results in human proteomics. PMID:19073703
PhosphoPep--a database of protein phosphorylation sites in model organisms. PMID:19060867
The human orthologue of murine Mpzl3 with predicted adhesive and immune functions is a potential candidate gene for immune-related hereditary hair loss. PMID:19054061
Network integration and graph analysis in mammalian molecular systems biology. PMID:19045817
A survey of visualization tools for biological network analysis. PMID:19040716
Traumatic brain injury alters expression of hippocampal microRNAs: potential regulators of multiple pathophysiological processes. PMID:19021292
Discovery of phosphorylation motif mixtures in phosphoproteomics data. PMID:18996944
Human Protein Reference Database--2009 update. PMID:18988627
PIPs: human protein-protein interaction prediction database. PMID:18988626
The Human Ageing Genomic Resources: online databases and tools for biogerontologists. PMID:18986374
Finding multiple target optimal intervention in disease-related molecular network. PMID:18985027
Michigan molecular interactions r2: from interacting proteins to pathways. PMID:18978014
Using a 3D virtual muscle model to link gene expression changes during myogenesis to protein spatial location in muscle. PMID:18945372
Bioinformatics analysis of metastasis-related proteins in hepatocellular carcinoma. PMID:18855979
TCMGeneDIT: a database for associated traditional Chinese medicine, gene and disease information using text mining. PMID:18854039
PMAP: databases for analyzing proteolytic events and pathways. PMID:18842634
Detection of the dominant direction of information flow and feedback links in densely interconnected regulatory networks. PMID:18842147
The interactome: predicting the protein-protein interactions in cells. PMID:18839074
The conservation pattern of short linear motifs is highly correlated with the function of interacting protein domains. PMID:18828911
iRefIndex: a consolidated protein interaction database with provenance. PMID:18823568
ProteoLens: a visual analytic tool for multi-scale database-driven biological network data mining. PMID:18793469
MPI-LIT: a literature-curated dataset of microbial binary protein--protein interactions. PMID:18786976
Network-based model weighting to detect multiple loci influencing complex diseases. PMID:18719944
Cell membrane proteomic analysis identifies proteins differentially expressed in osteotropic human breast cancer cells. PMID:18714363
Identification of c-Src tyrosine kinase substrates using mass spectrometry and peptide microarrays. PMID:18698806
Impacts of protein-protein interaction domains on organism and network complexity. PMID:18687879
Integrating protein-protein interactions and text mining for protein function prediction. PMID:18673526
TRANSPATH--a high quality database focused on signal transduction. PMID:18629064
Architectures and functional coverage of protein-protein interfaces. PMID:18620705
Construction of a cancer-perturbed protein-protein interaction network for discovery of apoptosis drug targets. PMID:18590547
Identifying functional modules in protein-protein interaction networks: an integrated exact approach. PMID:18586718
Human Proteinpedia as a resource for clinical proteomics. PMID:18573810
Systems analysis of quantitative shRNA-library screens identifies regulators of cell adhesion. PMID:18549508
ENDEAVOUR update: a web resource for gene prioritization in multiple species. PMID:18508807
A quantitative study of the recruitment potential of all intracellular tyrosine residues on EGFR, FGFR1 and IGF1R. PMID:18493663
Targeting the human cancer pathway protein interaction network by structural genomics. PMID:18487680
Network-based global inference of human disease genes. PMID:18463613
GraphWeb: mining heterogeneous biological networks for gene modules with functional significance. PMID:18460544
Steps towards a repertoire of comprehensive maps of human protein interaction networks: the Human Proteotheque Initiative (HuPI). PMID:18443628
Explorative data analysis of MCL reveals gene expression networks implicated in survival and prognosis supported by explorative CGH analysis. PMID:18416826
Genomic analysis of estrogen cascade reveals histone variant H2A.Z associated with breast cancer progression. PMID:18414489
Genome-wide prediction of SH2 domain targets using structural information and the FoldX algorithm. PMID:18389064
Prediction of human disease genes by human-mouse conserved coexpression analysis. PMID:18369433
Uncovering a macrophage transcriptional program by integrating evidence from motif scanning and expression dynamics. PMID:18369420
The Crohn's disease susceptibility gene DLG5 as a member of the CARD interaction network. PMID:18335190
Exploiting likely-positive and unlabeled data to improve the identification of protein-protein interaction articles. PMID:18315856
An integrated approach to inferring gene-disease associations in humans. PMID:18300252
Prediction of protein-protein interactions using protein signature profiling. PMID:18267299
EST-based identification of genes expressed in perch (Perca fluviatilis, L.). PMID:18257394
Building pathway clusters from Random Forests classification using class votes. PMID:18254968
Protein function assignment through mining cross-species protein-protein interactions. PMID:18253506
Analysis of self-associating proteins by singular value decomposition of solution scattering data. PMID:18212017
MeInfoText: associated gene methylation and cancer information from text mining. PMID:18194557
Linking gene expression and functional network data in human heart failure. PMID:18094754
A modular network model of aging. PMID:18059442
Age-related subproteomic analysis of mouse liver and kidney peroxisomes. PMID:18042274
PRIDE: new developments and new datasets. PMID:18033805
Identification of phosphorylation sites in betaPIX and PAK1. PMID:17989089
Vascular microarray profiling in two models of hypertension identifies caveolin-1, Rgs2 and Rgs5 as antihypertensive targets. PMID:17986358
Network-based classification of breast cancer metastasis. PMID:17940530
Improved human disease candidate gene prioritization using mouse phenotype. PMID:17939863
COXPRESdb: a database of coexpressed gene networks in mammals. PMID:17932064
BNDB - the Biochemical Network Database. PMID:17910766
InSite: a computational method for identifying protein-protein interaction binding sites on a proteome-wide scale. PMID:17868464
A homozygous mutation in a novel zinc-finger protein, ERIS, is responsible for Wolfram syndrome 2. PMID:17846994
An integrative in silico approach for discovering candidates for drug-targetable protein-protein interactions in interactome data. PMID:17705877
Computation of significance scores of unweighted Gene Set Enrichment Analyses. PMID:17683603
Reuse of structural domain-domain interactions in protein networks. PMID:17640363
Network-based analysis of affected biological processes in type 2 diabetes models. PMID:17571924
Transcript-level annotation of Affymetrix probesets improves the interpretation of gene expression data. PMID:17559689
A functional map of NFkappaB signaling identifies novel modulators and multiple system controls. PMID:17553156
Unequal evolutionary conservation of human protein interactions in interologous networks. PMID:17535438
Molecular concepts analysis links tumors, pathways, mechanisms, and drugs. PMID:17534450
GeneTrail--advanced gene set enrichment analysis. PMID:17526521
Analysis of intraviral protein-protein interactions of the SARS coronavirus ORFeome. PMID:17520018
Huntingtin interacting proteins are genetic modifiers of neurodegeneration. PMID:17500595
Epstein-Barr virus and virus human protein interaction maps. PMID:17446270
Protein complexes associated with the Kaposi's sarcoma-associated herpesvirus-encoded LANA. PMID:17434559
Deciphering protein-protein interactions. Part I. Experimental techniques and databases. PMID:17397251
Reactome: a knowledge base of biologic pathways and processes. PMID:17367534
Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles. PMID:17356713
From bytes to bedside: data integration and computational biology for translational cancer research. PMID:17319736
Specificity and evolvability in eukaryotic protein interaction networks. PMID:17305419
Analysis of a set of Australian northern brown bandicoot expressed sequence tags with comparison to the genome sequence of the South American grey short tailed opossum. PMID:17298671
Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry. PMID:17287340
An evaluation of human protein-protein interaction data in the public domain. PMID:17254303
SPIDer: Saccharomyces protein-protein interaction database. PMID:17254300
SNAPPI-DB: a database and API of Structures, iNterfaces and Alignments for Protein-Protein Interactions. PMID:17202171
Identification of the proliferation/differentiation switch in the cellular network of multicellular organisms. PMID:17166053
UniHI: an entry gate to the human protein interactome. PMID:17158159
CutDB: a proteolytic event database. PMID:17142225
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
A correlated motif approach for finding short linear motifs from protein interaction networks. PMID:17107624
cPath: open source software for collecting, storing, and querying biological pathways. PMID:17101041
Analysis of protein sequence and interaction data for candidate disease gene prediction. PMID:17020920
Predicting candidate genes for human deafness disorders: a bioinformatics approach. PMID:16854223
APID: Agile Protein Interaction DataAnalyzer. PMID:16845013
Global topological features of cancer proteins in the human interactome. PMID:16844706
Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae. PMID:16762047
An integrated approach to the prediction of domain-domain interactions. PMID:16725050
Quantitative phosphoproteomics of vasopressin-sensitive renal cells: regulation of aquaporin-2 phosphorylation at two sites. PMID:16641100
Predicting disease genes using protein-protein interactions. PMID:16611749
Further understanding human disease genes by comparing with housekeeping genes and other genes. PMID:16504025
BioGRID: a general repository for interaction datasets. PMID:16381927
Human protein reference database--2006 update. PMID:16381900
Ulysses - an application for the projection of molecular interactions across species. PMID:16356269
HomoMINT: an inferred human network based on orthology mapping of protein interactions discovered in model organisms. PMID:16351748
Molecular diversity of rat brain proteins as revealed by proteomic analysis. PMID:16311815
Systematic discovery of new recognition peptides mediating protein interaction networks. PMID:16279839
Inferring protein domain interactions from databases of interacting proteins. PMID:16207360
Phosphorylation states of cell cycle and DNA repair proteins can be altered by the nsSNPs. PMID:16111488
The impact of the NIH public access policy on literature informatics: What role can the neuroinformaticists play? PMID:15988039
Toward predictive models of mammalian cells. PMID:15869393
Filtering high-throughput protein-protein interaction data using a combination of genomic features. PMID:15833142
Ontological visualization of protein-protein interactions. PMID:15707487
The path to enlightenment: making sense of genomic and proteomic information. PMID:15629052
HAGR: the Human Ageing Genomic Resources. PMID:15608256
Update on genome completion and annotations: Protein Information Resource. PMID:15588483
Large-scale characterization of HeLa cell nuclear phosphoproteins. PMID:15302935
BioBuilder as a database development and functional annotation platform for proteins. PMID:15099404
Human protein reference database as a discovery resource for proteomics. PMID:14681466
Human protein reference database as a discovery resource for proteomics PubMed citations: 265.

265 articles citing: Human protein reference database as a discovery resource for proteomics

Repurposing Drugs via Network Analysis: Opportunities for Psychiatric Disorders. PMID:35890359
Single-cell network biology characterizes cell type gene regulation for drug repurposing and phenotype prediction in Alzheimer's disease. PMID:35849618
Identification of all-against-all protein-protein interactions based on deep hash learning. PMID:35804303
Identifying Candidate Flavonoids for Non-Alcoholic Fatty Liver Disease by Network-Based Strategy. PMID:35721123
Repurposing Histaminergic Drugs in Multiple Sclerosis. PMID:35683024
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
Skeletal muscle transcriptomics identifies common pathways in nerve crush injury and ageing. PMID:35093178
KANPHOS: A Database of Kinase-Associated Neural Protein Phosphorylation in the Brain. PMID:35011609
The protein-protein interaction network alignment using recurrent neural network. PMID:34529185
Measuring pathway database coverage of the phosphoproteome. PMID:34113485
Drug Repurposing: A Network-based Approach to Amyotrophic Lateral Sclerosis. PMID:33987813
Pathogenic missense protein variants affect different functional pathways and proteomic features than healthy population variants. PMID:33909605
Network-based modeling of herb combinations in traditional Chinese medicine. PMID:33834186
The Genetic and Epigenetic Mechanisms Involved in Irreversible Pulp Neural Inflammation. PMID:33777260
Comprehensive characterization of a drug-resistance-related ceRNA network across 15 anti-cancer drug categories. PMID:33738135
Overexpression of miR-1306-5p, miR-3195, and miR-3914 Inhibits Ameloblast Differentiation through Suppression of Genes Associated with Human Amelogenesis Imperfecta. PMID:33672174
Comparative analysis on the anti-inflammatory/immune effect of mesenchymal stem cell therapy for the treatment of pulmonary arterial hypertension. PMID:33479312
Elucidating the network features and evolutionary attributes of intra- and interspecific protein-protein interactions between human and pathogenic bacteria. PMID:33420198
A network-based deep learning methodology for stratification of tumor mutations. PMID:33416857
Development of New Antiproliferative Compound against Human Tumor Cells from the Marine Microalgae Nannochloropsis gaditana by Applied Proteomics. PMID:33374179
Chemocentric Informatics Analysis: Dexamethasone Versus Combination Therapy for COVID-19. PMID:33251412
A Systems Biology Workflow for Drug and Vaccine Repurposing: Identifying Small-Molecule BCG Mimics to Reduce or Prevent COVID-19 Mortality. PMID:33025261
Cilia interactome with predicted protein-protein interactions reveals connections to Alzheimer's disease, aging and other neuropsychiatric processes. PMID:32973177
Analyzing IDPs in Interactomes. PMID:32696395
Using Random Forest Model Combined With Gabor Feature to Predict Protein-Protein Interaction From Protein Sequence. PMID:32655275
Phen2Gene: rapid phenotype-driven gene prioritization for rare diseases. PMID:32500119
Understanding of Zaire ebolavirus-human protein interaction for drug repurposing. PMID:32206696
Association of functional variants and protein-to-protein physical interactions of human MutY homolog linked with familial adenomatous polyposis and colorectal cancer syndrome. PMID:32072083
Discovering the genes mediating the interactions between chronic respiratory diseases in the human interactome. PMID:32041952
NAPAbench 2: A network synthesis algorithm for generating realistic protein-protein interaction (PPI) network families. PMID:31986158
Mechanical forces induce an asthma gene signature in healthy airway epithelial cells. PMID:31969610
Identification of biomarkers and drug repurposing candidates based on an immune-, inflammation- and membranous glomerulonephritis-associated triplets network for membranous glomerulonephritis. PMID:31910852
Computer aided analysis of disease linked protein networks. PMID:31485137
An EV-Associated Gene Signature Correlates with Hypoxic Microenvironment and Predicts Recurrence in Lung Adenocarcinoma. PMID:31473584
Hamiltonian energy as an efficient approach to identify the significant key regulators in biological networks. PMID:31442253
A genome-wide positioning systems network algorithm for in silico drug repurposing. PMID:31375661
A comprehensive study on genome-wide coexpression network of KHDRBS1/Sam68 reveals its cancer and patient-specific association. PMID:31366900
Comprehensive characterization of immune- and inflammation-associated biomarkers based on multi-omics integration in kidney renal clear cell carcinoma. PMID:31133033
A rectified factor network based biclustering method for detecting cancer-related coding genes and miRNAs, and their interactions. PMID:31121299
Disease association of human tumor suppressor genes. PMID:30945018
Mechanism-based disease similarity. PMID:30854526
Compendium of synovial signatures identifies pathologic characteristics for predicting treatment response in rheumatoid arthritis patients. PMID:30831253
Identifying primary site of lung-limited Cancer of unknown primary based on relative gene expression orderings. PMID:30642283
GeNeCK: a web server for gene network construction and visualization. PMID:30616521
DeepPhos: prediction of protein phosphorylation sites with deep learning. PMID:30601936
Computational discovery of dynamic cell line specific Boolean networks from multiplex time-course data. PMID:30372442
Discovering Genetic Factors for psoriasis through exhaustively searching for significant second order SNP-SNP interactions. PMID:30315195
A mitochondrial proteome profile indicative of type 2 diabetes mellitus in skeletal muscles. PMID:30266947
Computational identification and analysis of neurodegenerative disease associated protein kinases in hominid genomes. PMID:30258892
ESCC ATLAS: A population wide compendium of biomarkers for Esophageal Squamous Cell Carcinoma. PMID:30143675
Loss of the E3 ubiquitin ligase MKRN1 represses diet-induced metabolic syndrome through AMPK activation. PMID:30143610
Identification of protein complexes associated with myocardial infarction using a bioinformatics approach. PMID:30132549
Comprehensive identification of immune-associated biomarkers based on network and mRNA expression patterns in membranous glomerulonephritis. PMID:30041664
Network-based approach to prediction and population-based validation of in silico drug repurposing. PMID:30002366
PTM-ssMP: A Web Server for Predicting Different Types of Post-translational Modification Sites Using Novel Site-specific Modification Profile. PMID:29989096
Detection of Protein Complexes Based on Penalized Matrix Decomposition in a Sparse Protein⁻Protein Interaction Network. PMID:29914123
Oxidized phospholipids regulate amino acid metabolism through MTHFD2 to facilitate nucleotide release in endothelial cells. PMID:29895827
Systematic Identification of Druggable Epithelial-Stromal Crosstalk Signaling Networks in Ovarian Cancer. PMID:29860390
Inflammatory genes are novel prognostic biomarkers for colorectal cancer. PMID:29693170
Systematic Evaluation of Molecular Networks for Discovery of Disease Genes. PMID:29605183
Overlapping functional modules detection in PPI network with pair-wise constrained non-negative matrix tri-factorisation. PMID:29533217
The Genomic Landscape and Pharmacogenomic Interactions of Clock Genes in Cancer Chronotherapy. PMID:29525205
A phenotype centric benchmark of variant prioritisation tools. PMID:29423277
A 16-gene expression signature to distinguish stage I from stage II lung squamous carcinoma. PMID:29286069
Cdkn2a deficiency promotes adipose tissue browning. PMID:29237539
A network-based predictive gene-expression signature for adjuvant chemotherapy benefit in stage II colorectal cancer. PMID:29237416
Systems Bioinformatics: increasing precision of computational diagnostics and therapeutics through network-based approaches. PMID:29186305
Proteomic Profiling of a Primary CD4+ T Cell Model of HIV-1 Latency Identifies Proteins Whose Differential Expression Correlates with Reactivation of Latent HIV-1. PMID:29084447
Multi-dimensional histone methylations for coordinated regulation of gene expression under hypoxia. PMID:28977425
Protein complex prediction via dense subgraphs and false positive analysis. PMID:28937982
Pediatric Sarcoma Data Forms a Unique Cluster Measured via the Earth Mover's Distance. PMID:28765612
Strength of functional signature correlates with effect size in autism. PMID:28687074
Colonic Phenotypes Are Associated with Poorer Response to Anti-TNF Therapies in Patients with IBD. PMID:28590340
Identification of potential biomarkers of sepsis using bioinformatics analysis. PMID:28565754
Generating testable hypotheses for schizophrenia and rheumatoid arthritis pathogenesis by integrating epidemiological, genomic, and protein interaction data. PMID:28560257
Network-based characterization and prediction of human DNA repair genes and pathways. PMID:28368026
NFP: An R Package for Characterizing and Comparing of Annotated Biological Networks. PMID:28280740
The maternal plasma proteome changes as a function of gestational age in normal pregnancy: a longitudinal study. PMID:28263753
Benchmarking substrate-based kinase activity inference using phosphoproteomic data. PMID:28200105
An approach to infer putative disease-specific mechanisms using neighboring gene networks. PMID:28200075
The post-genomic era of biological network alignment. PMID:28194172
PROPER: global protein interaction network alignment through percolation matching. PMID:27955623
Immunoglobulin superfamily genes are novel prognostic biomarkers for breast cancer. PMID:27911271
Systematic Analysis of Protein Interaction Network Associated with Azoospermia. PMID:27834916
Mesenchymal state of intimal cells may explain higher propensity to ascending aortic aneurysm in bicuspid aortic valves. PMID:27779199
Celecoxib exhibits an anti-gastric cancer effect by targeting focal adhesion and leukocyte transendothelial migration-associated genes. PMID:27698798
Comprehensive Proteome Profiling of Platelet Identified a Protein Profile Predictive of Responses to An Antiplatelet Agent Sarpogrelate. PMID:27601597
Functional characterization of EI24-induced autophagy in the degradation of RING-domain E3 ligases. PMID:27541728
Multi-OMICs and Genome Editing Perspectives on Liver Cancer Signaling Networks. PMID:27403431
The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. PMID:27374120
Network motif-based method for identifying coronary artery disease. PMID:27347046
Schizophrenia interactome with 504 novel protein-protein interactions. PMID:27336055
Network-Based Protein Biomarker Discovery Platforms. PMID:27103885
Comorbidities of Psoriasis - Exploring the Links by Network Approach. PMID:26966903
Overexpression of Kinesin Associated Protein 3 (KIFAP3) in Breast Cancer. PMID:26843789
Downregulation of S100 Calcium Binding Protein A9 in Esophageal Squamous Cell Carcinoma. PMID:26788548
Prediction of Druggable Proteins Using Machine Learning and Systems Biology: A Mini-Review. PMID:26696900
DeDaL: Cytoscape 3 app for producing and morphing data-driven and structure-driven network layouts. PMID:26271256
A multiobjective approach for identifying protein complexes and studying their association in multiple disorders. PMID:26257820
Phenolyzer: phenotype-based prioritization of candidate genes for human diseases. PMID:26192085
Exploring the structure and function of temporal networks with dynamic graphlets. PMID:26072480
SPECTRA: An Integrated Knowledge Base for Comparing Tissue and Tumor-Specific PPI Networks in Human. PMID:26005672
Regulators associated with clinical outcomes revealed by DNA methylation data in breast cancer. PMID:25996148
Discover the molecular biomarker associated with cell death and extracellular matrix module in ovarian cancer. PMID:25861644
Comprehensive data resources and analytical tools for pathological association of aminoacyl tRNA synthetases with cancer. PMID:25824651
Pathway mapping and development of disease-specific biomarkers: protein-based network biomarkers. PMID:25560835
Locus heterogeneity disease genes encode proteins with high interconnectivity in the human protein interaction network. PMID:25538735
Ensemble-based network aggregation improves the accuracy of gene network reconstruction. PMID:25390635
GroupRank: rank candidate genes in PPI network by differentially expressed gene groups. PMID:25330105
A random set scoring model for prioritization of disease candidate genes using protein complexes and data-mining of GeneRIF, OMIM and PubMed records. PMID:25253562
Human germline and pan-cancer variomes and their distinct functional profiles. PMID:25232094
Fast and accurate discovery of degenerate linear motifs in protein sequences. PMID:25207816
Gene expression profiles on predicting protein interaction network and exploring of new treatments for lung cancer. PMID:25205123
Dynamic modularity of host protein interaction networks in Salmonella Typhi infection. PMID:25144185
A systems biology approach identified different regulatory networks targeted by KSHV miR-K12-11 in B cells and endothelial cells. PMID:25106478
Integration of proteomic and transcriptomic profiles identifies a novel PDGF-MYC network in human smooth muscle cells. PMID:25080971
Two-layer modular analysis of gene and protein networks in breast cancer. PMID:24997799
Proteomics analysis of the non-muscle myosin heavy chain IIa-enriched actin-myosin complex reveals multiple functions within the podocyte. PMID:24949636
Pathway bridge based multiobjective optimization approach for lurking pathway prediction. PMID:24949437
Proteomic analysis of the epidermal growth factor receptor (EGFR) interactome and post-translational modifications associated with receptor endocytosis in response to EGF and stress. PMID:24797263
Approaches for recognizing disease genes based on network. PMID:24707485
Aberrant gene expression in mucosa adjacent to tumor reveals a molecular crosstalk in colon cancer. PMID:24597571
A systems biological approach reveals multiple crosstalk mechanism between gram-positive and negative bacterial infections: an insight into core mechanism and unique molecular signatures. PMID:24587173
Integrated genomic and prospective clinical studies show the importance of modular pleiotropy for disease susceptibility, diagnosis and treatment. PMID:24571673
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
Comprehensive gene expression analysis reveals multiple signal pathways associated with prostate cancer. PMID:24154878
Methods and approaches in the topology-based analysis of biological pathways. PMID:24133454
Network-based penalized regression with application to genomic data. PMID:23822182
Prioritization of candidate disease genes by topological similarity between disease and protein diffusion profiles. PMID:23734762
An integrated approach to uncover driver genes in breast cancer methylation genomes. PMID:23579546
Module cover - a new approach to genotype-phenotype studies. PMID:23424119
Visual data mining of biological networks: one size does not fit all. PMID:23341759
Protein network-based Lasso regression model for the construction of disease-miRNA functional interactions. PMID:23339438
Identification of MFS proteins in sorghum using semantic similarity. PMID:23299296
A systems approach to rheumatoid arthritis. PMID:23240033
Identifying grade/stage-related active modules in human co-regulatory networks: a case study for breast cancer. PMID:23215806
Investigation of stable and transient protein-protein interactions: Past, present, and future. PMID:23193082
Modeling dynamic regulatory processes in stroke. PMID:23071432
Enhancing the prioritization of disease-causing genes through tissue specific protein interaction networks. PMID:23028288
SRC Homology 2 Domain Binding Sites in Insulin, IGF-1 and FGF receptor mediated signaling networks reveal an extensive potential interactome. PMID:22974441
An integrated approach to identify causal network modules of complex diseases with application to colorectal cancer. PMID:22967703
Graphlet-based edge clustering reveals pathogen-interacting proteins. PMID:22962470
Biological function through network topology: a survey of the human diseasome. PMID:22962330
Detecting microRNAs of high influence on protein functional interaction networks: a prostate cancer case study. PMID:22929553
Finding minimum gene subsets with heuristic breadth-first search algorithm for robust tumor classification. PMID:22830977
Sets2Networks: network inference from repeated observations of sets. PMID:22824380
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
From genome-wide association studies to disease mechanisms: celiac disease as a model for autoimmune diseases. PMID:22580835
Network- and attribute-based classifiers can prioritize genes and pathways for autism spectrum disorders and intellectual disability. PMID:22499558
Investigation and identification of protein γ-glutamyl carboxylation sites. PMID:22372765
A network-based, integrative study to identify core biological pathways that drive breast cancer clinical subtypes. PMID:22343619
Comparing statistical methods for constructing large scale gene networks. PMID:22272232
Computational prediction of host-parasite protein interactions between P. falciparum and H. sapiens. PMID:22114664
The SARS-coronavirus-host interactome: identification of cyclophilins as target for pan-coronavirus inhibitors. PMID:22046132
Carboxylator: incorporating solvent-accessible surface area for identifying protein carboxylation sites. PMID:22038416
Proteome-wide post-translational modification statistics: frequency analysis and curation of the swiss-prot database. PMID:22034591
A comprehensive curated resource for follicle stimulating hormone signaling. PMID:21996254
A systematic analysis of eluted fraction of plasma post immunoaffinity depletion: implications in biomarker discovery. PMID:21931718
A computational method based on the integration of heterogeneous networks for predicting disease-gene associations. PMID:21912671
Identification of candidate genes related to bovine marbling using protein-protein interaction networks. PMID:21912507
Insight into bacterial virulence mechanisms against host immune response via the Yersinia pestis-human protein-protein interaction network. PMID:21911467
Dominating biological networks. PMID:21887225
Computational simulations to predict creatine kinase-associated factors: protein-protein interaction studies of brain and muscle types of creatine kinases. PMID:21826261
Disease embryo development network reveals the relationship between disease genes and embryo development genes. PMID:21824480
Computational approach to identify enzymes that are potential therapeutic candidates for psoriasis. PMID:21822480
Quantitative tissue proteomics of esophageal squamous cell carcinoma for novel biomarker discovery. PMID:21743296
Proteomic patterns of cervical cancer cell lines, a network perspective. PMID:21696634
Integrative computational biology for cancer research. PMID:21691773
Shared molecular strategies of the malaria parasite P. falciparum and the human virus HIV-1. PMID:21586753
Immunological network signatures of cancer progression and survival. PMID:21453479
Identifying causal genes and dysregulated pathways in complex diseases. PMID:21390271
The expanded human disease network combining protein-protein interaction information. PMID:21386875
Single-nucleotide polymorphisms in LPA explain most of the ancestry-specific variation in Lp(a) levels in African Americans. PMID:21283670
Context-dependent transcriptional regulations between signal transduction pathways. PMID:21232126
The interactome of a PTB domain-containing adapter protein, Odin, revealed by SILAC. PMID:21081186
Multi-level reproducibility of signature hubs in human interactome for breast cancer metastasis. PMID:21059271
Incorporating significant amino acid pairs to identify O-linked glycosylation sites on transmembrane proteins and non-transmembrane proteins. PMID:21034461
Human protein reference database and human proteinpedia as discovery resources for molecular biotechnology. PMID:20927658
Finding the "dark matter" in human and yeast protein network prediction and modelling. PMID:20885791
Protein network prediction and topological analysis in Leishmania major as a tool for drug target selection. PMID:20875130
Gene pathways and subnetworks distinguish between major glioma subtypes and elucidate potential underlying biology. PMID:20828632
Patterns of HIV-1 protein interaction identify perturbed host-cellular subsystems. PMID:20686668
SILAC-based quantitative proteomic approach to identify potential biomarkers from the esophageal squamous cell carcinoma secretome. PMID:20686364
Uncovering packaging features of co-regulated modules based on human protein interaction and transcriptional regulatory networks. PMID:20649980
Development of a novel bioinformatics tool for in silico validation of protein interactions. PMID:20625507
Neighborhood rough set reduction-based gene selection and prioritization for gene expression profile analysis and molecular cancer classification. PMID:20625410
Protein interaction network topology uncovers melanogenesis regulatory network components within functional genomics datasets. PMID:20550706
PRED_PPI: a server for predicting protein-protein interactions based on sequence data with probability assignment. PMID:20500905
Support Vector Machines with Disease-gene-centric Network Penalty for High Dimensional Microarray Data. PMID:20401316
TopoGSA: network topological gene set analysis. PMID:20335277
Bioinformatic tools for identifying disease gene and SNP candidates. PMID:20238089
Topological network alignment uncovers biological function and phylogeny. PMID:20236959
Peripheral endothelin B receptor agonist-induced antinociception involves endogenous opioids in mice. PMID:20206445
Biana: a software framework for compiling biological interactions and analyzing networks. PMID:20105306
Transcriptomic analysis identifies phosphatases as novel targets for adenotonsillar hypertrophy of pediatric obstructive sleep apnea. PMID:20093640
Associating genes and protein complexes with disease via network propagation. PMID:20090828
Expression-based network biology identifies alteration in key regulatory pathways of type 2 diabetes and associated risk/complications. PMID:19997558
MitoInteractome: mitochondrial protein interactome database, and its application in 'aging network' analysis. PMID:19958484
PutidaNET: interactome database service and network analysis of Pseudomonas putida KT2440. PMID:19958481
Functional features of gene expression profiles differentiating gastrointestinal stromal tumours according to KIT mutations and expression. PMID:19943934
Automated quantitative assessment of proteins' biological function in protein knowledge bases. PMID:19920991
Looking at cerebellar malformations through text-mined interactomes of mice and humans. PMID:19893633
NAViGaTOR: Network Analysis, Visualization and Graphing Toronto. PMID:19837718
Identification of tyrosine-phosphorylated proteins associated with metastasis and functional analysis of FER in human hepatocellular carcinoma cells. PMID:19835603
Discovering cancer genes by integrating network and functional properties. PMID:19765316
The ordering of expression among a few genes can provide simple cancer biomarkers and signal BRCA1 mutations. PMID:19695104
CAPIH: a Web interface for comparative analyses and visualization of host-HIV protein-protein interactions. PMID:19674441
ToppGene Suite for gene list enrichment analysis and candidate gene prioritization. PMID:19465376
Inferring novel disease indications for known drugs by semantically linking drug action and disease mechanism relationships. PMID:19426461
FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions. PMID:19374773
Uncovering biological network function via graphlet degree signatures. PMID:19259413
Disease candidate gene identification and prioritization using protein interaction networks. PMID:19245720
A survey of available tools and web servers for analysis of protein-protein interactions and interfaces. PMID:19240123
Enumeration of condition-dependent dense modules in protein interaction networks. PMID:19213739
An empirical framework for binary interactome mapping. PMID:19060904
Network integration and graph analysis in mammalian molecular systems biology. PMID:19045817
Human Protein Reference Database--2009 update. PMID:18988627
Hepatitis C virus infection protein network. PMID:18985028
Human Proteinpedia: a unified discovery resource for proteomics research. PMID:18948298
Physical and in silico approaches identify DNA-PK in a Tax DNA-damage response interactome. PMID:18922151
Short Linear Motifs recognized by SH2, SH3 and Ser/Thr Kinase domains are conserved in disordered protein regions. PMID:18831792
The conservation pattern of short linear motifs is highly correlated with the function of interacting protein domains. PMID:18828911
Parasite burden and CD36-mediated sequestration are determinants of acute lung injury in an experimental malaria model. PMID:18483551
Resolving the network of cell signaling pathways using the evolving yeast two-hybrid system. PMID:18474041
Inferring the role of transcription factors in regulatory networks. PMID:18460200
MassNet: a functional annotation service for protein mass spectrometry data. PMID:18448467
A map of human protein interactions derived from co-expression of human mRNAs and their orthologs. PMID:18414481
Walking the interactome for prioritization of candidate disease genes. PMID:18371930
Predicting cancer involvement of genes from heterogeneous data. PMID:18371197
Predicting the interactome of Xanthomonas oryzae pathovar oryzae for target selection and DB service. PMID:18215330
Protein interactions in human genetic diseases. PMID:18199329
Linking the ovarian cancer transcriptome and immunome. PMID:18173842
PARPs database: a LIMS systems for protein-protein interaction data mining or laboratory information management system. PMID:18093328
Quantitative systems-level determinants of human genes targeted by successful drugs. PMID:18083776
A new computational approach to analyze human protein complexes and predict novel protein interactions. PMID:18053208
Functional pathways shared by liver and lung metastases: a mitochondrial chaperone machine is up-regulated in soft-tissue breast cancer metastasis. PMID:18008173
Integration of biological networks and gene expression data using Cytoscape. PMID:17947979
Characterization of protein hubs by inferring interacting motifs from protein interactions. PMID:17941705
Systems analysis of chaperone networks in the malarial parasite Plasmodium falciparum. PMID:17941702
A protein interaction atlas for the nuclear receptors: properties and quality of a hub-based dimerisation network. PMID:17672894
Characterization of protein-interaction networks in tumors. PMID:17597514
Evidence for systems-level molecular mechanisms of tumorigenesis. PMID:17584915
RCPdb: An evolutionary classification and codon usage database for repeat-containing proteins. PMID:17567984
bZIPDB: a database of regulatory information for human bZIP transcription factors. PMID:17535445
Large-scale phosphorylation analysis of mouse liver. PMID:17242355
Discovering regulated networks during HIV-1 latency and reactivation. PMID:17094252
Modelling protein-protein interaction networks via a stickiness index. PMID:16971339
Reconstruction of a functional human gene network, with an application for prioritizing positional candidate genes. PMID:16685651
SNPs3D: candidate gene and SNP selection for association studies. PMID:16551372
pSTIING: a 'systems' approach towards integrating signalling pathways, interaction and transcriptional regulatory networks in inflammation and cancer. PMID:16381926
MPact: the MIPS protein interaction resource on yeast. PMID:16381906
Human protein reference database--2006 update. PMID:16381900
SMART 5: domains in the context of genomes and networks. PMID:16381859
Tools enabling the elucidation of molecular pathways active in human disease: application to Hepatitis C virus infection. PMID:15967031
Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome. PMID:15892868
Atlas - a data warehouse for integrative bioinformatics. PMID:15723693
The path to enlightenment: making sense of genomic and proteomic information. PMID:15629052
T1DBase, a community web-based resource for type 1 diabetes research. PMID:15608258
Reactome: a knowledgebase of biological pathways. PMID:15608231
Predicting subcellular localization via protein motif co-occurrence. PMID:15466294
System-based proteomic analysis of the interferon response in human liver cells. PMID:15287976

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More detailed information about this field from each metasource.

protein
metasource: Fairsharing.org
version: FAIRsharing.org: HPRD; Human Protein Reference Database; DOI: https://doi.org/10.25504/FAIRsharing.y2qws7; Last edited: Jan. 8, 2019, 1:18 p.m.; Last accessed: Jan 03 2022 7:09 p.m.

structure
metasource: Fairsharing.org
version: FAIRsharing.org: HPRD; Human Protein Reference Database; DOI: https://doi.org/10.25504/FAIRsharing.y2qws7; Last edited: Jan. 8, 2019, 1:18 p.m.; Last accessed: Jan 03 2022 7:09 p.m.

human and other vertebrate genomes
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

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

bioinformatics
metasource: re3data.org
version: re3data.org: Human Protein Reference Database; editing status 2021-11-09; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3MK9N last accessed: 2022-11-04

mass spectrometry
metasource: re3data.org
version: re3data.org: Human Protein Reference Database; editing status 2021-11-09; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3MK9N last accessed: 2022-11-04

protein c
metasource: re3data.org
version: re3data.org: Human Protein Reference Database; editing status 2021-11-09; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3MK9N last accessed: 2022-11-04

protein s
metasource: re3data.org
version: re3data.org: Human Protein Reference Database; editing status 2021-11-09; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3MK9N last accessed: 2022-11-04

protein binding
metasource: re3data.org
version: re3data.org: Human Protein Reference Database; editing status 2021-11-09; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3MK9N last accessed: 2022-11-04

molecular interactions, pathways and networks
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:57.480032

human biology
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:57.480032

proteins
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:57.480032

protein interactions
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:57.480032

proteomics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:57.480032

protein structure human and other vertebrate genomes human orfs bioinformatics mass spectrometry protein c protein s protein binding molecular interactions, pathways and networks human proteins protein interaction proteomics

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Human Proteinpedia

Human Protein-Protein Interaction rEference

Human Protein Atlas

HPID - Human Protein Interaction database

Human protein-protein interaction network database search

AtPID

Human Reference Protein Interactome Mapping Project

Extracellular Matrix Interaction Database

Molecular INTeraction database

neXtProt

Human Gene and Protein Database

Human Histone Database

PIPs

The human DEPhOsphorylation Database

trome, trEST and trGEN

dbPTM

RSSsite

Interaction Reference Index Web Interface

SAHG

GeneCards: human genes, protein and diseases