Biological General Repository for Interaction Datasets
Names
More detailed information about this field from each metasource.
Biological General Repository for Interaction Datasets
metasource: Fairsharing.org
version: FAIRsharing.org: BioGRID; Biological General Repository for Interaction Datasets; DOI: https://doi.org/10.25504/FAIRsharing.9d5f5r; Last edited: March 9, 2021, 4:07 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
BioGRID
metasource: Fairsharing.org
version: FAIRsharing.org: BioGRID; Biological General Repository for Interaction Datasets; DOI: https://doi.org/10.25504/FAIRsharing.9d5f5r; Last edited: March 9, 2021, 4:07 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
The BioGRID Interaction Database
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:34.038241
biogrid
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:34.038241
Names
More detailed information about this field from each metasource.
Biological General Repository for Interaction Datasets
metasource: Fairsharing.orgversion: FAIRsharing.org: BioGRID; Biological General Repository for Interaction Datasets; DOI: https://doi.org/10.25504/FAIRsharing.9d5f5r; Last edited: March 9, 2021, 4:07 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
BioGRID
metasource: Fairsharing.orgversion: FAIRsharing.org: BioGRID; Biological General Repository for Interaction Datasets; DOI: https://doi.org/10.25504/FAIRsharing.9d5f5r; Last edited: March 9, 2021, 4:07 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
The BioGRID Interaction Database
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:34:34.038241
biogrid
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:34:34.038241
Other names: BioGRID, The BioGRID Interaction Database, biogrid
Names
More detailed information about this field from each metasource.
Biological General Repository for Interaction Datasets
metasource: Fairsharing.orgversion: FAIRsharing.org: BioGRID; Biological General Repository for Interaction Datasets; DOI: https://doi.org/10.25504/FAIRsharing.9d5f5r; Last edited: March 9, 2021, 4:07 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
BioGRID
metasource: Fairsharing.orgversion: FAIRsharing.org: BioGRID; Biological General Repository for Interaction Datasets; DOI: https://doi.org/10.25504/FAIRsharing.9d5f5r; Last edited: March 9, 2021, 4:07 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
The BioGRID Interaction Database
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:34:34.038241
biogrid
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:34:34.038241
The Biological General Repository for Interaction Datasets (BioGRID) is a curated biological database of protein-protein interactions, genetic interactions, chemical interactions, and post-translational modifications.
Description
More detailed information about this field from each metasource.
The Biological General Repository for Interaction Datasets (BioGRID) is a curated biological database of protein-protein interactions, genetic interactions, chemical interactions, and post-translational modifications.
metasource: BiŌkeanós-Medsourcingversion: 0.0.1:2022-11-04T13:34:25.975929
The Biological General Repository for Interaction Datasets (BioGRID) is a public database that archives and disseminates genetic and protein interaction data from model organisms and humans. BioGRID currently holds over 1,740,000 interactions curated from both high-throughput datasets and individual focused studies, as derived from over 70,000+ publications in the primary literature. Complete coverage of the entire literature is maintained for budding yeast (S. cerevisiae), fission yeast (S. pombe) and thale cress (A. thaliana), and efforts to expand curation across multiple metazoan species are underway. All data are freely provided via our search index and available for download in many standardized formats.
metasource: Fairsharing.orgversion: FAIRsharing.org: BioGRID; Biological General Repository for Interaction Datasets; DOI: https://doi.org/10.25504/FAIRsharing.9d5f5r; Last edited: March 9, 2021, 4:07 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Access to unified datasets of protein and genetic interactions is critical for interrogation of gene/protein function and analysis of global network properties. BioGRID is a freely accessible database of physical and genetic interactions available at http://www.thebiogrid.org. BioGRID release version 2.0 includes more than 116,000 interactions from Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster and Homo sapiens. An internally hyper-linked web interface allows for rapid search and retrieval of interaction data. Full or user-defined datasets are freely downloadable as tab-delimited text files and PSI-MI XML. Pre-computed graphical layouts of interactions are available in a variety of file formats. User-customized graphs with embedded protein, gene and interaction attributes can be constructed with a visualization system called Osprey that is dynamically linked to the BioGRID. Over 30,000 protein and genetic interactions have been added from 5,778 sources through exhaustive curation of the S. cerevisiae primary literature (Reguly et al, submitted). An analogous systematically curated set of interactions compiled from the Schizosaccharomyces pombe (fission yeast) literature will also be deposited shortly. Selected physical interaction datasets for TGF-b, TOR and cancer networks in mammalian cells will also be deposited in the near future. A new quantitative genetic interaction experimental descriptor has been added to accommodate recent Epistatic Mini-Array Profiles (E-MAP) and other forms of quantitative genetic interaction data generated in S. cerevisiae.
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Public database that archives and disseminates genetic and protein interaction data from model organisms and humans. Complete coverage of the entire literature is maintained for budding yeast (Saccharomyces cerevisiae), fission yeast (Schizosaccharomyces pombe) and thale cress (Arabidopsis thaliana).
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:34:34.038241
Webpage:
https://thebiogrid.orgWebpage
More detailed information about this field from each metasource.
https://thebiogrid.org
metasource: BiŌkeanós-Medsourcingversion: 0.0.1:2022-11-04T13:34:25.975929
http://www.thebiogrid.org
metasource: Fairsharing.orgversion: FAIRsharing.org: BioGRID; Biological General Repository for Interaction Datasets; DOI: https://doi.org/10.25504/FAIRsharing.9d5f5r; Last edited: March 9, 2021, 4:07 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:34.038241
Licence:
Name: MITLicence name
More detailed information about this field from each metasource.
MIT
metasource: BiŌkeanós-Medsourcingversion: 0.0.1:2022-11-04T13:34:25.975929
BioGRID Terms and Conditions
metasource: Fairsharing.orgversion: FAIRsharing.org: BioGRID; Biological General Repository for Interaction Datasets; DOI: https://doi.org/10.25504/FAIRsharing.9d5f5r; Last edited: March 9, 2021, 4:07 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Licence URL
More detailed information about this field from each metasource.
https://downloads.thebiogrid.org/BioGRID
metasource: BiŌkeanós-Medsourcingversion: 0.0.1:2022-11-04T13:34:25.975929
https://wiki.thebiogrid.org/doku.php/terms_and_conditions
metasource: Fairsharing.orgversion: FAIRsharing.org: BioGRID; Biological General Repository for Interaction Datasets; DOI: https://doi.org/10.25504/FAIRsharing.9d5f5r; Last edited: March 9, 2021, 4:07 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Publications:
(10)
Publications
More detailed information about this field from each metasource.
BioGRID: a general repository for interaction datasets
PMID: 16381927
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
metasource: Fairsharing.org
version: FAIRsharing.org: BioGRID; Biological General Repository for Interaction Datasets; DOI: https://doi.org/10.25504/FAIRsharing.9d5f5r; Last edited: March 9, 2021, 4:07 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
The BioGRID interaction database: 2015 update
PMID: 25428363
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
The BioGRID interaction database: 2019 update
PMID: 30476227
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
metasource: Fairsharing.org
version: FAIRsharing.org: BioGRID; Biological General Repository for Interaction Datasets; DOI: https://doi.org/10.25504/FAIRsharing.9d5f5r; Last edited: March 9, 2021, 4:07 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
The BioGRID interaction database: 2017 update
PMID: 27980099
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
The BioGRID Interaction Database: 2011 update
PMID: 21071413
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:34.038241
The BioGRID interaction database: 2013 update
PMID: 23203989
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
The BioGRID Interaction Database: 2008 update
PMID: 18000002
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
The BioGRID database: A comprehensive biomedical resource of curated protein, genetic, and chemical interactions
PMID: 33070389
metasource: Fairsharing.org
version: FAIRsharing.org: BioGRID; Biological General Repository for Interaction Datasets; DOI: https://doi.org/10.25504/FAIRsharing.9d5f5r; Last edited: March 9, 2021, 4:07 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
The GRID: the General Repository for Interaction Datasets
PMID: 12620108
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
metasource: Fairsharing.org
version: FAIRsharing.org: BioGRID; Biological General Repository for Interaction Datasets; DOI: https://doi.org/10.25504/FAIRsharing.9d5f5r; Last edited: March 9, 2021, 4:07 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
http://dx.doi.org/10.1093/nar/
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Publications
More detailed information about this field from each metasource.
BioGRID: a general repository for interaction datasets
PMID: 16381927
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
metasource: Fairsharing.org
version: FAIRsharing.org: BioGRID; Biological General Repository for Interaction Datasets; DOI: https://doi.org/10.25504/FAIRsharing.9d5f5r; Last edited: March 9, 2021, 4:07 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
The BioGRID interaction database: 2015 update
PMID: 25428363
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
The BioGRID interaction database: 2019 update
PMID: 30476227
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
metasource: Fairsharing.org
version: FAIRsharing.org: BioGRID; Biological General Repository for Interaction Datasets; DOI: https://doi.org/10.25504/FAIRsharing.9d5f5r; Last edited: March 9, 2021, 4:07 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
The BioGRID interaction database: 2017 update
PMID: 27980099
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
The BioGRID Interaction Database: 2011 update
PMID: 21071413
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:34.038241
The BioGRID interaction database: 2013 update
PMID: 23203989
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
The BioGRID Interaction Database: 2008 update
PMID: 18000002
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
The BioGRID database: A comprehensive biomedical resource of curated protein, genetic, and chemical interactions
PMID: 33070389
metasource: Fairsharing.org
version: FAIRsharing.org: BioGRID; Biological General Repository for Interaction Datasets; DOI: https://doi.org/10.25504/FAIRsharing.9d5f5r; Last edited: March 9, 2021, 4:07 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
The GRID: the General Repository for Interaction Datasets
PMID: 12620108
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
metasource: Fairsharing.org
version: FAIRsharing.org: BioGRID; Biological General Repository for Interaction Datasets; DOI: https://doi.org/10.25504/FAIRsharing.9d5f5r; Last edited: March 9, 2021, 4:07 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
http://dx.doi.org/10.1093/nar/
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
-
BioGRID: a general repository for interaction datasets
PubMed citations: 1602.
1602 articles citing: BioGRID: a general repository for interaction datasets
BioAlign: An Accurate Global PPI Network Alignment Algorithm. PMID:35898232
Challenges and Limitations of Biological Network Analysis. PMID:35892929
Analyzing the Systems Biology Effects of COVID-19 mRNA Vaccines to Assess Their Safety and Putative Side Effects. PMID:35889989
Drug-Target Network Study Reveals the Core Target-Protein Interactions of Various COVID-19 Treatments. PMID:35885993
Network Proximity-Based Drug Repurposing Strategy for Early and Late Stages of Primary Biliary Cholangitis. PMID:35884999
Integration of probabilistic functional networks without an external Gold Standard. PMID:35879662
Consensus clustering for Bayesian mixture models. PMID:35864476
DeepND: Deep multitask learning of gene risk for comorbid neurodevelopmental disorders. PMID:35845835
Deep learning frameworks for protein-protein interaction prediction. PMID:35832624
A functional reference map of the RNF8 interactome in cancer. PMID:35831895
Bioinformatics-Driven Identification of p62 as A Crucial Oncogene in Liver Cancer. PMID:35814476
Conserved recombination patterns across coronavirus subgenera. PMID:35814334
In-silico screening and in-vitro assay show the antiviral effect of Indomethacin against SARS-CoV-2. PMID:35809412
PHILM2Web: A high-throughput database of macromolecular host-pathogen interactions on the Web. PMID:35776535
N(6)-methyladenosine methylation-regulated polo-like kinase 1 cell cycle homeostasis as a potential target of radiotherapy in pancreatic adenocarcinoma. PMID:35773310
Molecular characterization of low-grade serous ovarian carcinoma identifies genomic aberrations according to hormone receptor expression. PMID:35768582
Unique SMYD5 Structure Revealed by AlphaFold Correlates with Its Functional Divergence. PMID:35740908
Identification of the Potential Molecular Mechanisms Linking RUNX1 Activity with Nonalcoholic Fatty Liver Disease, by Means of Systems Biology. PMID:35740337
Integrating multi-omics data reveals function and therapeutic potential of deubiquitinating enzymes. PMID:35737447
A Conserved Long Intergenic Non-coding RNA Containing snoRNA Sequences, lncCOBRA1, Affects Arabidopsis Germination and Development. PMID:35693169
Computational identification of protein complexes from network interactions: Present state, challenges, and the way forward. PMID:35685359
Transcriptomic analysis reveals pathophysiological relationship between chronic obstructive pulmonary disease (COPD) and periodontitis. PMID:35676670
Complementary omics strategies to dissect p53 signaling networks under nutrient stress. PMID:35635656
Network Pharmacology Approach for Medicinal Plants: Review and Assessment. PMID:35631398
The R Language: An Engine for Bioinformatics and Data Science. PMID:35629316
Targeting HIF-1α Function in Cancer through the Chaperone Action of NQO1: Implications of Genetic Diversity of NQO1. PMID:35629169
Proteome-wide prediction and analysis of the Cryptosporidium parvum protein-protein interaction network through integrative methods. PMID:35615014
FAM198B promotes colorectal cancer progression by regulating the polarization of tumor-associated macrophages via the SMAD2 signaling pathway. PMID:35587159
GenePlexus: a web-server for gene discovery using network-based machine learning. PMID:35580053
Bioinformatics-Based Approaches to Study Virus-Host Interactions During SARS-CoV-2 Infection. PMID:35554909
Transcriptome analysis of clock disrupted cancer cells reveals differential alternative splicing of cancer hallmarks genes. PMID:35552415
Long-read sequencing unveils high-resolution HPV integration and its oncogenic progression in cervical cancer. PMID:35538075
Small RNA sequencing and bioinformatics analysis of RAW264.7-derived exosomes after Mycobacterium Bovis Bacillus Calmette-Guérin infection. PMID:35525953
Dynamic and widespread control of poly(A) tail length during macrophage activation. PMID:35512831
ImitateDB: A database for domain and motif mimicry incorporating host and pathogen protein interactions. PMID:35487995
Cyclin-Dependent Kinase 6 Identified as the Target Protein in the Antitumor Activity of Tetrastigma hemsleyanum. PMID:35480115
Identification of dynamic driver sets controlling phenotypical landscapes. PMID:35465155
Novel Protein-Protein Interactions Highlighting the Crosstalk between Hypoplastic Left Heart Syndrome, Ciliopathies and Neurodevelopmental Delays. PMID:35456433
The cargo adapter protein CLINT1 is phosphorylated by the Numb-associated kinase BIKE and mediates dengue virus infection. PMID:35452674
An interolog-based barley interactome as an integration framework for immune signaling. PMID:35435213
Transcriptome Analysis in Hippocampus of Rats Prenatally Exposed to Valproic Acid and Effects of Intranasal Treatment of Oxytocin. PMID:35432011
Phylogenetic profiling in eukaryotes: The effect of species, orthologous group, and interactome selection on protein interaction prediction. PMID:35421089
Repurposing Multiple-Molecule Drugs for COVID-19-Associated Acute Respiratory Distress Syndrome and Non-Viral Acute Respiratory Distress Syndrome via a Systems Biology Approach and a DNN-DTI Model Based on Five Drug Design Specifications. PMID:35409008
Expansion of Schizophrenia Gene Network Knowledge Using Machine Learning Selected Signals From Dorsolateral Prefrontal Cortex and Amygdala RNA-seq Data. PMID:35386517
The Prognostic Significance and Gene Expression Characteristics of Gastric Signet-Ring Cell Carcinoma: A Study Based on the SEER and TCGA Databases. PMID:35372476
The D2R-DISC1 protein complex and associated proteins are altered in schizophrenia and normalized with antipsychotic treatment. PMID:35361701
Computational methods, databases and tools for synthetic lethality prediction. PMID:35352098
Predicting protein-protein interactions between banana and Fusarium oxysporum f. sp. cubense race 4 integrating sequence and domain homologous alignment and neural network verification. PMID:35351140
Discrete Logic Modeling of Cell Signaling Pathways. PMID:35347689
Transposon insertional mutagenesis of diverse yeast strains suggests coordinated gene essentiality polymorphisms. PMID:35314699
Finding New Ways How to Control BACE1. PMID:35305135
Reconstructing codependent cellular cross-talk in lung adenocarcinoma using REMI. PMID:35302849
Eucalyptus grandis AUX/INDOLE-3-ACETIC ACID 13 (EgrIAA13) is a novel transcriptional regulator of xylogenesis. PMID:35292886
HAUS5 Is A Potential Prognostic Biomarker With Functional Significance in Breast Cancer. PMID:35280773
A pan-cancer analysis of the oncogenic role of Holliday junction recognition protein in human tumors. PMID:35274047
MESH1 knockdown triggers proliferation arrest through TAZ repression. PMID:35273140
Proximity Profiling of the CFTR Interaction Landscape in Response to Orkambi. PMID:35269585
The long-term effects of genomic selection: 1. Response to selection, additive genetic variance, and genetic architecture. PMID:35255802
Modeling multi-scale data via a network of networks. PMID:35238343
Methods to Improve Molecular Diagnosis in Genomic Cold Cases in Pediatric Neurology. PMID:35205378
Gene Ontology Groups and Signaling Pathways Regulating the Process of Avian Satellite Cell Differentiation. PMID:35205287
p53-mediated neurodegeneration in the absence of the nuclear protein Akirin2. PMID:35198879
PARK2 regulates eIF4B-driven lymphomagenesis. PMID:35191952
Tcf12 and NeuroD1 cooperatively drive neuronal migration during cortical development. PMID:35147187
Barcode fusion genetics-protein-fragment complementation assay (BFG-PCA): tools and resources that expand the potential for binary protein interaction discovery. PMID:35137167
A systematic study of motif pairs that may facilitate enhancer-promoter interactions. PMID:35130376
Polygenic networks in peripheral leukocytes indicate patterns associated with HIV infection and context-dependent effects of cannabis use. PMID:35128491
Chemoproteomic-enabled characterization of small GTPase Rab1a as a target of an N-arylbenzimidazole ligand's rescue of Parkinson's-associated cell toxicity. PMID:35128413
Profiling of RNA-binding Proteins Interacting With Glucagon and Adipokinetic Hormone mRNAs. PMID:35118022
Probabilistic Graphical Models Applied to Biological Networks. PMID:35113399
Visualization of a curated Oryza sativa L. CDPKs Protein-Protein Interaction Network (CDPK-OsPPIN). PMID:35098050
Phosphopeptide enrichment using Phos-tag technology reveals functional phosphorylation of the nucleocapsid protein of SARS-CoV-2. PMID:35093569
MED12 is overexpressed in glioblastoma patients and serves as an oncogene by targeting the VDR/BCL6/p53 axis. PMID:35091793
From communities to protein complexes: A local community detection algorithm on PPI networks. PMID:35085263
Graphlet eigencentralities capture novel central roles of genes in pathways. PMID:35077468
β-Synuclein: An Enigmatic Protein with Diverse Functionality. PMID:35053291
Gene Network of Susceptibility to Atypical Femoral Fractures Related to Bisphosphonate Treatment. PMID:35052486
Single-cell transcriptomics of human iPSC differentiation dynamics reveal a core molecular network of Parkinson's disease. PMID:35027645
Benchmark Evaluation of Protein-Protein Interaction Prediction Algorithms. PMID:35011283
Prognostic Significance of CCNB2 Expression in Triple-Negative Breast Cancer. PMID:35002325
Cytochrome b561 Serves as a Potential Prognostic Biomarker and Target for Breast Cancer. PMID:35002301
Network analysis of host-pathogen protein interactions in microbe induced cardiovascular diseases. PMID:35001887
Machine learning-based predictions of dietary restriction associations across ageing-related genes. PMID:34983372
Understanding Gene Expression and Transcriptome Profiling of COVID-19: An Initiative Towards the Mapping of Protective Immunity Genes Against SARS-CoV-2 Infection. PMID:34975833
Integrative analysis of the molecular mechanisms, immunological features and immunotherapy response of ferroptosis regulators across 33 cancer types. PMID:34975326
A novel circRNA-miRNA-mRNA network reveals hsa-circ-0040039 as a biomarker for intervertebral disc degeneration. PMID:34939437
Targeting CK2 mediated signaling to impair/tackle SARS-CoV-2 infection: a computational biology approach. PMID:34930105
Characterization of the AGR2 Interactome Uncovers New Players of Protein Disulfide Isomerase Network in Cancer Cells. PMID:34929376
Protein network analysis to prioritize key genes in amyotrophic lateral sclerosis. PMID:34918006
DNA methylation of ARHGAP30 is negatively associated with ARHGAP30 expression in lung adenocarcinoma, which reduces tumor immunity and is detrimental to patient survival. PMID:34910688
XDeathDB: a visualization platform for cell death molecular interactions. PMID:34907160
MultiCapsNet: A General Framework for Data Integration and Interpretable Classification. PMID:34899854
Histone Chaperone Nucleophosmin Regulates Transcription of Key Genes Involved in Oral Tumorigenesis. PMID:34898280
MYC assembles and stimulates topoisomerases 1 and 2 in a "topoisome". PMID:34890565
Prolyl endopeptidase-like is a (thio)esterase involved in mitochondrial respiratory chain function. PMID:34888501
Study of Neuronal Apoptosis ceRNA Network in Hippocampal Sclerosis of Human Temporal Lobe Epilepsy by RNA-Seq. PMID:34867172
Predicting Bone Metastasis Using Gene Expression-Based Machine Learning Models. PMID:34858485
Loss of full-length hnRNP R isoform impairs DNA damage response in motoneurons by inhibiting Yb1 recruitment to chromatin. PMID:34850154
ConsensusPathDB 2022: molecular interactions update as a resource for network biology. PMID:34850110
Knowledge-guided artificial intelligence technologies for decoding complex multiomics interactions in cells. PMID:34844399
Therapeutic targeting of SPIB/SPI1-facilitated interplay of cancer cells and neutrophils inhibits aerobic glycolysis and cancer progression. PMID:34841706
Chromatin Accessibility and Transcriptomic Alterations in Murine Ovarian Granulosa Cells upon Deoxynivalenol Exposure. PMID:34831041
Immune Infiltration-Related Signature Predicts Risk Stratification and Immunotherapy Efficacy in Grade II and III Gliomas. PMID:34805164
Transcriptomic taxonomy and neurogenic trajectories of adult human, macaque, and pig hippocampal and entorhinal cells. PMID:34798047
Trends in biological data integration for the selection of enzymes and transcription factors related to cellulose and hemicellulose degradation in fungi. PMID:34777932
Bioinformatics approach to identify common gene signatures of patients with coronavirus 2019 and lung adenocarcinoma. PMID:34775559
Computationally Reconstructed Interactome of Bradyrhizobium diazoefficiens USDA110 Reveals Novel Functional Modules and Protein Hubs for Symbiotic Nitrogen Fixation. PMID:34769335
Computed structures of core eukaryotic protein complexes. PMID:34762488
The titin N2B and N2A regions: biomechanical and metabolic signaling hubs in cross-striated muscles. PMID:34745373
Network Biology Approaches to Achieve Precision Medicine in Inflammatory Bowel Disease. PMID:34745229
Network-based protein-protein interaction prediction method maps perturbations of cancer interactome. PMID:34727106
Hsp90 interaction networks in fungi-tools and techniques. PMID:34718512
Importance-Penalized Joint Graphical Lasso (IPJGL): differential network inference via GGMs. PMID:34718410
Centrality of drug targets in protein networks. PMID:34715787
AKIRIN2 controls the nuclear import of proteasomes in vertebrates. PMID:34711951
Improved supervised prediction of aging-related genes via weighted dynamic network analysis. PMID:34696741
DeepTrio: a ternary prediction system for protein-protein interaction using mask multiple parallel convolutional neural networks. PMID:34694333
Convergent genomic signatures of high-altitude adaptation among domestic mammals. PMID:34692117
Alternative Splicing Mechanisms Underlying Opioid-Induced Hyperalgesia. PMID:34680965
GAK and PRKCD are positive regulators of PRKN-independent mitophagy. PMID:34671015
Transcriptome profiling of pepper leaves by RNA-Seq during an incompatible and a compatible pepper-tobamovirus interaction. PMID:34667194
Identifying disease-gene associations using a convolutional neural network-based model by embedding a biological knowledge graph with entity descriptions. PMID:34653225
Predicting PY motif-mediated protein-protein interactions in the Nedd4 family of ubiquitin ligases. PMID:34637467
Efficient and accurate identification of protein complexes from protein-protein interaction networks based on the clustering coefficient. PMID:34630943
A survey on computational methods in discovering protein inhibitors of SARS-CoV-2. PMID:34623382
Pan-Cancer Analysis Reveals That E1A Binding Protein p300 Mutations Increase Genome Instability and Antitumor Immunity. PMID:34616736
Prediction of Protein-Protein Interactions in Arabidopsis, Maize, and Rice by Combining Deep Neural Network With Discrete Hilbert Transform. PMID:34616437
Proteomic analysis identifies novel binding partners of BAP1. PMID:34591877
Molecular Characterization of NDL1-AGB1 Mediated Salt Stress Signaling: Further Exploration of the Role of NDL1 Interacting Partners. PMID:34571915
Selectivity of Lewy body protein interactions along the aggregation pathway of α-synuclein. PMID:34556785
Identification of Novel Choroidal Neovascularization-Related Genes Using Laplacian Heat Diffusion Algorithm. PMID:34532497
Generalized and social anxiety disorder interactomes show distinctive overlaps with striosome and matrix interactomes. PMID:34526518
Towards Building a Quantitative Proteomics Toolbox in Precision Medicine: A Mini-Review. PMID:34512391
Exosomes Secreted by Adipose-Derived Stem Cells Following FK506 Stimulation Reduce Autophagy of Macrophages in Spine after Nerve Crush Injury. PMID:34502537
Inflammatory gene expression profiling in peripheral blood from patients with Alzheimer's disease reveals key pathways and hub genes with potential diagnostic utility: a preliminary study. PMID:34484988
Prospects and challenges of cancer systems medicine: from genes to disease networks. PMID:34471925
The chemical biology of coronavirus host-cell interactions. PMID:34458775
Drug Discovery of Spinal Muscular Atrophy (SMA) from the Computational Perspective: A Comprehensive Review. PMID:34445667
Proteomics of Mouse Heart Ventricles Reveals Mitochondria and Metabolism as Major Targets of a Post-Infarction Short-Acting GLP1Ra-Therapy. PMID:34445425
Bioinformatics analysis of the transcriptional expression of minichromosome maintenance proteins as potential indicators of survival in patients with cervical cancer. PMID:34404366
Machine learning approaches for drug combination therapies. PMID:34368832
Application and Perspectives of MALDI-TOF Mass Spectrometry in Clinical Microbiology Laboratories. PMID:34361974
TMEM135 is a Novel Regulator of Mitochondrial Dynamics and Physiology with Implications for Human Health Conditions. PMID:34359920
Revealing protein-protein interactions at the transcriptome scale by sequencing. PMID:34348091
Functional Roles of Bromodomain Proteins in Cancer. PMID:34298819
Integrating ensemble systems biology feature selection and bimodal deep neural network for breast cancer prognosis prediction. PMID:34290286
New approaches to predict the effect of co-occurring variants on protein characteristics. PMID:34256028
In silico-driven analysis of the Glossina morsitans morsitans antennae transcriptome in response to repellent or attractant compounds. PMID:34249514
Single-nucleus chromatin accessibility and transcriptomic characterization of Alzheimer's disease. PMID:34239132
E-type prostanoid receptor 4 drives resolution of intestinal inflammation by blocking epithelial necroptosis. PMID:34239062
GABA-receptive microglia selectively sculpt developing inhibitory circuits. PMID:34233165
Molecular Mechanisms Regulating the DNA Repair Protein APE1: A Focus on Its Flexible N-Terminal Tail Domain. PMID:34208390
Aurora Kinase A proximity map reveals centriolar satellites as regulators of its ciliary function. PMID:34169630
An information theoretic approach to link prediction in multiplex networks. PMID:34168194
LSTM-PHV: prediction of human-virus protein-protein interactions by LSTM with word2vec. PMID:34160596
Novel loci and potential mechanisms of major depressive disorder, bipolar disorder, and schizophrenia. PMID:34159505
Evolving scenario of big data and Artificial Intelligence (AI) in drug discovery. PMID:34159484
Genomes reveal selective sweeps in kiang and donkey for high-altitude adaptation. PMID:34156172
Side effect prediction based on drug-induced gene expression profiles and random forest with iterative feature selection. PMID:34155353
Mapping the multiscale structure of biological systems. PMID:34139169
Overexpression of human BAG3P209L in mice causes restrictive cardiomyopathy. PMID:34117258
Measuring pathway database coverage of the phosphoproteome. PMID:34113485
Proteomimetic surface fragments distinguish targets by function. PMID:34094300
Construction of Condition-Specific Gene Regulatory Network Using Kernel Canonical Correlation Analysis. PMID:34093651
PIGNON: a protein-protein interaction-guided functional enrichment analysis for quantitative proteomics. PMID:34088263
Mapping Proximity Associations of Core Spindle Assembly Checkpoint Proteins. PMID:34087075
A proximity-dependent biotinylation map of a human cell. PMID:34079125
Proteomic Analyses of Vitreous in Proliferative Diabetic Retinopathy: Prior Studies and Future Outlook. PMID:34070658
driveR: a novel method for prioritizing cancer driver genes using somatic genomics data. PMID:34030627
Up-regulated RFC2 predicts unfavorable progression in hepatocellular carcinoma. PMID:34022962
Utilizing graph machine learning within drug discovery and development. PMID:34013350
ERG transcription factors have a splicing regulatory function involving RBFOX2 that is altered in the EWS-FLI1 oncogenic fusion. PMID:34009296
Analyzing host-viral interactome of SARS-CoV-2 for identifying vulnerable host proteins during COVID-19 pathogenesis. PMID:34004362
SynLeGG: analysis and visualization of multiomics data for discovery of cancer 'Achilles Heels' and gene function relationships. PMID:33997893
The SARS-CoV-2 RNA interactome. PMID:33989516
Crinet: A computational tool to infer genome-wide competing endogenous RNA (ceRNA) interactions. PMID:33983999
Capturing dynamic relevance in Boolean networks using graph theoretical measures. PMID:33983406
Simultaneous learning of individual microRNA-gene interactions and regulatory comodules. PMID:33971820
A scheme for inferring viral-host associations based on codon usage patterns identifies the most affected signaling pathways during COVID-19. PMID:33965637
Integration of peripheral transcriptomics, genomics, and interactomics following trauma identifies causal genes for symptoms of post-traumatic stress and major depression. PMID:33963278
Muscle Glycogen Phosphorylase and Its Functional Partners in Health and Disease. PMID:33924466
Intrinsically Disordered Proteins as Regulators of Transient Biological Processes and as Untapped Drug Targets. PMID:33917117
Malignant Pleural Mesothelioma Interactome with 364 Novel Protein-Protein Interactions. PMID:33916178
Identification of the Key Role of NF-κB Signaling Pathway in the Treatment of Osteoarthritis With Bushen Zhuangjin Decoction, a Verification Based on Network Pharmacology Approach. PMID:33912052
Spatially resolved cell polarity proteomics of a human epiblast model. PMID:33893097
MultiVERSE: a multiplex and multiplex-heterogeneous network embedding approach. PMID:33888761
Algorithm-Based Meta-Analysis Reveals the Mechanistic Interaction of the Tumor Suppressor LIMD1 With Non-Small-Cell Lung Carcinoma. PMID:33869018
DUSP7 regulates the activity of ERK2 to promote proper chromosome alignment during cell division. PMID:33865857
Bioinformatic Analysis of Key Genes and Pathways Related to Keloids. PMID:33860039
Elucidating transcriptomic profiles from single-cell RNA sequencing data using nature-inspired compressed sensing. PMID:33855366
Persona2vec: a flexible multi-role representations learning framework for graphs. PMID:33834106
Predicting Protein-Protein Interactions Using Symmetric Logistic Matrix Factorization. PMID:33831302
Quantifying evolutionary importance of protein sites: A Tale of two measures. PMID:33826605
Detection of H3K4me3 Identifies NeuroHIV Signatures, Genomic Effects of Methamphetamine and Addiction Pathways in Postmortem HIV+ Brain Specimens that Are Not Amenable to Transcriptome Analysis. PMID:33805201
Next-generation yeast-two-hybrid analysis with Y2H-SCORES identifies novel interactors of the MLA immune receptor. PMID:33798202
A lysosomal enigma CLN5 and its significance in understanding neuronal ceroid lipofuscinosis. PMID:33792748
Gene Tracer: A smart, interactive, voice-controlled Alexa skill for gene information retrieval and browsing, mutation annotation, and network visualization. PMID:33792640
Structural and Drug Screening Analysis of the Non-structural Proteins of Severe Acute Respiratory Syndrome Coronavirus 2 Virus Extracted From Indian Coronavirus Disease 2019 Patients. PMID:33767730
PecanPy: a fast, efficient, and parallelized Python implementation of node2vec. PMID:33760066
Removing auto-activators from yeast-two-hybrid assays by conditional negative selection. PMID:33750818
Logical modeling of thymus and natural killer lymphocyte differentiation. PMID:33735399
Prioritization of schizophrenia risk genes from GWAS results by integrating multi-omics data. PMID:33731678
Gene variants of coagulation related proteins that interact with SARS-CoV-2. PMID:33730015
Protein context shapes the specificity of SH3 domain-mediated interactions in vivo. PMID:33712617
Repurposing novel therapeutic candidate drugs for coronavirus disease-19 based on protein-protein interaction network analysis. PMID:33711981
B7-H6 is a new potential biomarker and therapeutic target of T-lymphoblastic lymphoma. PMID:33708955
Identification of novel prognostic genes of triple-negative breast cancer using meta-analysis and weighted gene co-expressed network analysis. PMID:33708832
A Molecular Interaction Map of Klebsiella pneumoniae and Its Human Host Reveals Potential Mechanisms of Host Cell Subversion. PMID:33679637
Integrative Analysis Identified Key Schizophrenia Risk Factors from an Abnormal Behavior Mouse Gene Set. PMID:33672431
A weakened interface in the P182L variant of HSP27 associated with severe Charcot-Marie-Tooth neuropathy causes aberrant binding to interacting proteins. PMID:33644875
Gene Size Matters: An Analysis of Gene Length in the Human Genome. PMID:33643374
Enhanced Understanding of Molecular Interactions and Function Underlying Pain Processes Through Networks of Transcript Isoforms, Genes, and Gene Families. PMID:33633454
The Fate of Speckled Protein 100 (Sp100) During Herpesviruses Infection. PMID:33598438
Drug repurposing for COVID-19 via knowledge graph completion. PMID:33571675
Genetic control of the human brain proteome. PMID:33571421
RNA Sequencing Reveals Distinct Immune Responses in the Chorioamniotic Membranes of Women with Preterm Labor and Microbial or Sterile Intra-amniotic Inflammation. PMID:33558326
Protein-protein interaction analysis reveals a novel cancer stem cell related target TMEM17 in colorectal cancer. PMID:33549114
Role of Antizyme Inhibitor Proteins in Cancers and Beyond. PMID:33531815
Integrative analysis of transcriptomic data for identification of T-cell activation-related mRNA signatures indicative of preterm birth. PMID:33504832
Comparative analysis on the anti-inflammatory/immune effect of mesenchymal stem cell therapy for the treatment of pulmonary arterial hypertension. PMID:33479312
An empirical meta-analysis of the life sciences linked open data on the web. PMID:33479214
System-Wide Pollution of Biomedical Data: Consequence of the Search for Hub Genes of Hepatocellular Carcinoma Without Spatiotemporal Consideration. PMID:33475988
DeORFanizing Candida albicans Genes using Coexpression. PMID:33472984
Insights into the Mechanism of Bovine Spermiogenesis Based on Comparative Transcriptomic Studies. PMID:33466297
Devil in the details: Mechanistic variations impact information transfer across models of transcriptional cascades. PMID:33439904
Complementary and divergent functions of zebrafish Tango1 and Ctage5 in tissue development and homeostasis. PMID:33439675
Transcriptome analysis of cepharanthine against a SARS-CoV-2-related coronavirus. PMID:33423067
Biotin Proximity Labeling for Protein-Protein Interaction Discovery: The BioID Method. PMID:33421001
Elucidating the network features and evolutionary attributes of intra- and interspecific protein-protein interactions between human and pathogenic bacteria. PMID:33420198
PC2P: Parameter-free network-based prediction of protein complexes. PMID:33416831
Chemical Decorations of "MARs" Residents in Orchestrating Eukaryotic Gene Regulation. PMID:33409278
Bioinformatics analysis of common key genes and pathways of intracranial, abdominal, and thoracic aneurysms. PMID:33407182
Novel RB1 and MET Gene Mutations in a Case with Bilateral Retinoblastoma Followed by Multiple Metastatic Osteosarcoma. PMID:33375764
Systems Approach to Pathogenic Mechanism of Type 2 Diabetes and Drug Discovery Design Based on Deep Learning and Drug Design Specifications. PMID:33375269
Multi-task learning for the simultaneous reconstruction of the human and mouse gene regulatory networks. PMID:33339842
Identification of Interleukin-9 Producing Immune Cells in Endometrial Carcinoma and Establishment of a Prognostic Nomogram. PMID:33329510
Identifying Influencers in Social Networks. PMID:33286224
Growth of pancreatic cancers with hemizygous chromosomal 17p loss of MYBBP1A can be preferentially targeted by PARP inhibitors. PMID:33277249
A Novel Proximity Biotinylation Assay Based on the Self-Associating Split GFP1-10/11. PMID:33276494
CovMulNet19, Integrating Proteins, Diseases, Drugs, and Symptoms: A Network Medicine Approach to COVID-19. PMID:33274348
Tgfb3 and Mmp13 regulated the initiation of liver fibrosis progression as dynamic network biomarkers. PMID:33269546
BPI and KIR6.1 as significant hub genes for vein graft restenosis. PMID:33259239
The Path towards Predicting Evolution as Illustrated in Yeast Cell Polarity. PMID:33255231
EffectorK, a comprehensive resource to mine for Ralstonia, Xanthomonas, and other published effector interactors in the Arabidopsis proteome. PMID:33245626
Perversely expressed long noncoding RNAs can alter host response and viral proliferation in SARS-CoV-2 infection. PMID:33224264
ClusterM: a scalable algorithm for computational prediction of conserved protein complexes across multiple protein interaction networks. PMID:33208103
Tau Pathology Drives Dementia Risk-Associated Gene Networks toward Chronic Inflammatory States and Immunosuppression. PMID:33207193
The Landscape of Coronavirus Disease 2019 (COVID-19) and Integrated Analysis SARS-CoV-2 Receptors and Potential Inhibitors in Lung Adenocarcinoma Patients. PMID:33195212
H-RACS: a handy tool to rank anti-cancer synergistic drugs. PMID:33173014
Deciphering cell-cell interactions and communication from gene expression. PMID:33168968
SAlign-a structure aware method for global PPI network alignment. PMID:33148180
Functional module detection through integration of single-cell RNA sequencing data with protein-protein interaction networks. PMID:33138772
Extraction and Integration of Genetic Networks from Short-Profile Omic Data Sets. PMID:33137869
BIKE regulates dengue virus infection and is a cellular target for broad-spectrum antivirals. PMID:33137362
Genome-Wide Search for SNP Interactions in GWAS Data: Algorithm, Feasibility, Replication Using Schizophrenia Datasets. PMID:33133133
LAMP: disease classification derived from layered assessment on modules and pathways in the human gene network. PMID:33126852
Preclinical validation of therapeutic targets predicted by tensor factorization on heterogeneous graphs. PMID:33106501
Determinants of correlated expression of transcription factors and their target genes. PMID:33104784
Plasmatic Membrane Expression of Adhesion Molecules in Human Cardiac Progenitor/Stem Cells Might Explain Their Superior Cell Engraftment after Cell Transplantation. PMID:33101423
Discover novel disease-associated genes based on regulatory networks of long-range chromatin interactions. PMID:33096239
PyGNA: a unified framework for geneset network analysis. PMID:33092528
Implementation of homology based and non-homology based computational methods for the identification and annotation of orphan enzymes: using Mycobacterium tuberculosis H37Rv as a case study. PMID:33076816
The BioGRID database: A comprehensive biomedical resource of curated protein, genetic, and chemical interactions. PMID:33070389
LRRK2 mediates microglial neurotoxicity via NFATc2 in rodent models of synucleinopathies. PMID:33055242
Identification of Latent Oncogenes with a Network Embedding Method and Random Forest. PMID:33029511
Nano-ellagic acid: inhibitory actions on aldose reductase and α-glucosidase in secondary complications of diabetes, strengthened by in silico docking studies. PMID:32999815
Identification of potential gene drivers of cutaneous squamous cell carcinoma: Analysis of microarray data. PMID:32991423
Yeast Ppz1 protein phosphatase toxicity involves the alteration of multiple cellular targets. PMID:32973189
Cilia interactome with predicted protein-protein interactions reveals connections to Alzheimer's disease, aging and other neuropsychiatric processes. PMID:32973177
Graph embedding-based novel protein interaction prediction via higher-order graph convolutional network. PMID:32970681
Mining genetic and transcriptomic data using machine learning approaches in Parkinson's disease. PMID:32964109
DeepHE: Accurately predicting human essential genes based on deep learning. PMID:32936825
Potential impact on coagulopathy of gene variants of coagulation related proteins that interact with SARS-CoV-2. PMID:32935103
MasterPATH: network analysis of functional genomics screening data. PMID:32928103
Genome-Wide Identification of RNA Editing Sites Affecting Intramuscular Fat in Pigs. PMID:32927662
A large accessory protein interactome is rewired across environments. PMID:32924934
A functionally defined high-density NRF2 interactome reveals new conditional regulators of ARE transactivation. PMID:32911434
Investigating the Role of Telomere and Telomerase Associated Genes and Proteins in Endometrial Cancer. PMID:32899298
Investigating Core Signaling Pathways of Hepatitis B Virus Pathogenesis for Biomarkers Identification and Drug Discovery via Systems Biology and Deep Learning Method. PMID:32878239
Link prediction in real-world multiplex networks via layer reconstruction method. PMID:32874603
Systems Analysis of Biliary Atresia Through Integration of High-Throughput Biological Data. PMID:32848883
Lasting and Sex-Dependent Impact of Maternal Immune Activation on Molecular Pathways of the Amygdala. PMID:32848554
Hypoxia Predicts Poor Prognosis in Neuroblastoma Patients and Associates with Biological Mechanisms Involved in Telomerase Activation and Tumor Microenvironment Reprogramming. PMID:32825087
Analytical Guidelines for co-fractionation Mass Spectrometry Obtained through Global Profiling of Gold Standard Saccharomyces cerevisiae Protein Complexes. PMID:32817346
Integrative genomics approach identifies conserved transcriptomic networks in Alzheimer's disease. PMID:32803238
Mycoplasma hyopneumoniae J elicits an antioxidant response and decreases the expression of ciliary genes in infected swine epithelial cells. PMID:32792522
Computational Methods for Predicting Functions at the mRNA Isoform Level. PMID:32784445
The REGγ inhibitor NIP30 increases sensitivity to chemotherapy in p53-deficient tumor cells. PMID:32764536
Global Analysis of Cereal microProteins Suggests Diverse Roles in Crop Development and Environmental Adaptation. PMID:32763954
Regulation of Trpm activation and calcium wave initiation during Drosophila egg activation. PMID:32735035
Network Approaches for Dissecting the Immune System. PMID:32717640
Kinase Interaction Network Expands Functional and Disease Roles of Human Kinases. PMID:32707033
Interactome of SARS-CoV-2 / nCoV19 modulated host proteins with computationally predicted PPIs. PMID:32702714
Proteinarium: Multi-sample protein-protein interaction analysis and visualization tool. PMID:32702417
Identification of COVID-19 Infection-Related Human Genes Based on a Random Walk Model in a Virus-Human Protein Interaction Network. PMID:32685484
uKIN Combines New and Prior Information with Guided Network Propagation to Accurately Identify Disease Genes. PMID:32684276
Phylogenetic analysis of the Tc1/mariner superfamily reveals the unexplored diversity of pogo-like elements. PMID:32612713
Extensive signal integration by the phytohormone protein network. PMID:32612234
Selective Neuronal Vulnerability in Alzheimer's Disease: A Network-Based Analysis. PMID:32603655
Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses. PMID:32597660
Expansions of chemosensory gene orthologs among selected tsetse fly species and their expressions in Glossina morsitans morsitans tsetse fly. PMID:32589659
Symmetries and cluster synchronization in multilayer networks. PMID:32576813
Genome-wide Enrichment of De Novo Coding Mutations in Orofacial Cleft Trios. PMID:32574564
Comprehensive Analysis of Prognostic Alternative Splicing Signatures in Endometrial Cancer. PMID:32547595
A flexible network-based imputing-and-fusing approach towards the identification of cell types from single-cell RNA-seq data. PMID:32527285
Proteomic profiling of the monothiol glutaredoxin Grx3 reveals its global role in the regulation of iron dependent processes. PMID:32525871
MIPPIE: the mouse integrated protein-protein interaction reference. PMID:32496562
MeCP2 facilitates breast cancer growth via promoting ubiquitination-mediated P53 degradation by inhibiting RPL5/RPL11 transcription. PMID:32483207
Updating dual-specificity tyrosine-phosphorylation-regulated kinase 2 (DYRK2): molecular basis, functions and role in diseases. PMID:32462403
Structural and Functional Analyses of the FAM46C/Plk4 Complex. PMID:32433990
Humanization of yeast genes with multiple human orthologs reveals functional divergence between paralogs. PMID:32421706
G2G: A web-server for the prediction of human synthetic lethal interactions. PMID:32419903
Neural networks for open and closed Literature-based Discovery. PMID:32413059
Mutation severity spectrum of rare alleles in the human genome is predictive of disease type. PMID:32413045
Molecular determinants underlying functional innovations of TBP and their impact on transcription initiation. PMID:32404905
A massively parallel barcoded sequencing pipeline enables generation of the first ORFeome and interactome map for rice. PMID:32398372
RESTful API for iPTMnet: a resource for protein post-translational modification network discovery. PMID:32395768
The tapeworm interactome: inferring confidence scored protein-protein interactions from the proteome of Hymenolepis microstoma. PMID:32380953
PDZ Domains as Drug Targets. PMID:32313833
Predicting Protein Functions Based on Differential Co-expression and Neighborhood Analysis. PMID:32302512
Modulation of stress and immune response by Amblyomin-X results in tumor cell death in a horse melanoma model. PMID:32286411
Systems Biology Analysis of the Antagonizing Effects of HIV-1 Tat Expression in the Brain over Transcriptional Changes Caused by Methamphetamine Sensitization. PMID:32283831
HIPPIE2: a method for fine-scale identification of physically interacting chromatin regions. PMID:32270138
Whole-Genome and RNA Sequencing Reveal Variation and Transcriptomic Coordination in the Developing Human Prefrontal Cortex. PMID:32268104
Proximity mapping of the microtubule plus-end tracking protein SLAIN2 using the BioID approach. PMID:32256142
A network analysis to identify pathophysiological pathways distinguishing ischaemic from non-ischaemic heart failure. PMID:32243695
Loss-of-function tolerance of enhancers in the human genome. PMID:32243438
Sex-specific and shared expression profiles of vulnerability and resilience to trauma in brain and blood. PMID:32228684
HNF4A-AS1/hnRNPU/CTCF axis as a therapeutic target for aerobic glycolysis and neuroblastoma progression. PMID:32216806
Coupled matrix-matrix and coupled tensor-matrix completion methods for predicting drug-target interactions. PMID:32186716
A homozygous missense variant in CACNB4 encoding the auxiliary calcium channel beta4 subunit causes a severe neurodevelopmental disorder and impairs channel and non-channel functions. PMID:32176688
Overexpression of the Selective Autophagy Cargo Receptor NBR1 Modifies Plant Response to Sulfur Deficit. PMID:32164165
Supervised learning is an accurate method for network-based gene classification. PMID:32129827
Stitching the synapse: Cross-linking mass spectrometry into resolving synaptic protein interactions. PMID:32128395
Exploring Integrative Analysis Using the BioMedical Evidence Graph. PMID:32097025
Hierarchy and levels: analysing networks to study mechanisms in molecular biology. PMID:32089112
A Guide to Conquer the Biological Network Era Using Graph Theory. PMID:32083072
FibroAtlas: A Database for the Exploration of Fibrotic Diseases and Their Genes. PMID:32082621
Long-term survivors of early breast cancer treated with chemotherapy are characterized by a pro-inflammatory biomarker profile compared to matched controls. PMID:32078215
Collective intelligence defines biological functions in Wikipedia as communities in the hidden protein connection network. PMID:32069277
Integrated analysis and knockdown of RAB23 indicate the role of RAB23 in gastric adenocarcinoma. PMID:32042761
Genetic screens in isogenic mammalian cell lines without single cell cloning. PMID:32029722
Pathway and network analysis of more than 2500 whole cancer genomes. PMID:32024854
Identification of cancer driver genes based on nucleotide context. PMID:32015527
Genomic Features and Clinical Characteristics of Adolescents and Young Adults With Cholangiocarcinoma. PMID:32010606
Developing a virus-microRNA interactome using cytoscape. PMID:31993337
Comparative Genomic Mapping Implicates LRRK2 for Intellectual Disability and Autism at 12q12, and HDHD1, as Well as PNPLA4, for X-Linked Intellectual Disability at Xp22.31. PMID:31963867
TMEM98 is a negative regulator of FRAT mediated Wnt/ß-catenin signalling. PMID:31961879
Mmi1, the Yeast Ortholog of Mammalian Translationally Controlled Tumor Protein (TCTP), Negatively Affects Rapamycin-Induced Autophagy in Post-Diauxic Growth Phase. PMID:31936125
BCOR-coupled H2A monoubiquitination represses a subset of androgen receptor target genes regulating prostate cancer proliferation. PMID:31925334
Puupehenone, a Marine-Sponge-Derived Sesquiterpene Quinone, Potentiates the Antifungal Drug Caspofungin by Disrupting Hsp90 Activity and the Cell Wall Integrity Pathway. PMID:31915228
Casein Kinase 1δ Stabilizes Mature Axons by Inhibiting Transcription Termination of Ankyrin. PMID:31910362
Interpreting pathways to discover cancer driver genes with Moonlight. PMID:31900418
Substrate specificity of thioredoxins and glutaredoxins - towards a functional classification. PMID:31890941
Human protein-RNA interaction network is highly stable across mammals. PMID:31888461
Matrisome-Associated Gene Expression Patterns Correlating with TIMP2 in Cancer. PMID:31882975
Transcription factor regulatory modules provide the molecular mechanisms for functional redundancy observed among transcription factors in yeast. PMID:31881824
Refining modules to determine functionally significant clusters in molecular networks. PMID:31874644
HPOAnnotator: improving large-scale prediction of HPO annotations by low-rank approximation with HPO semantic similarities and multiple PPI networks. PMID:31865916
LRRK2 Biology from structure to dysfunction: research progresses, but the themes remain the same. PMID:31864390
Nuclear factor erythroid 2 - related factor 2 and its relationship with cellular response in nickel exposure: a systems biology analysis. PMID:31852525
Improving drug response prediction by integrating multiple data sources: matrix factorization, kernel and network-based approaches. PMID:31838491
The human DEPhOsphorylation Database DEPOD: 2019 update. PMID:31836896
An Integrated Pan-Cancer Analysis and Structure-Based Virtual Screening of GPR15. PMID:31835584
Defined factors to reactivate cell cycle activity in adult mouse cardiomyocytes. PMID:31827131
Transcriptome Meta-Analysis Deciphers a Dysregulation in Immune Response-Associated Gene Signatures during Sepsis. PMID:31817302
The oncogenic potential of small nuclear ribonucleoprotein polypeptide G: a comprehensive and perspective view. PMID:31814883
Impact of negative lymph nodes on colon cancer survival and exploring relevant transcriptomics differences through real-world data analyses. PMID:31807507
Leveraging User-Friendly Network Approaches to Extract Knowledge From High-Throughput Omics Datasets. PMID:31798629
CERENKOV3: Clustering and molecular network-derived features improve computational prediction of functional noncoding SNPs. PMID:31797625
DeepEP: a deep learning framework for identifying essential proteins. PMID:31787076
Glycogen branching enzyme controls cellular iron homeostasis via Iron Regulatory Protein 1 and mitoNEET. PMID:31784520
Network Modeling Approaches and Applications to Unravelling Non-Alcoholic Fatty Liver Disease. PMID:31771247
Identifying gene function and module connections by the integration of multispecies expression compendia. PMID:31754022
Estimating network changes from lifespan measurements using a parsimonious gene network model of cellular aging. PMID:31747877
Is MYND Domain-Mediated Assembly of SMYD3 Complexes Involved in Calcium Dependent Signaling? PMID:31737645
Investigation of Proteomic and Phosphoproteomic Responses to Signaling Network Perturbations Reveals Functional Pathway Organizations in Yeast. PMID:31722220
Genetic Loci Associated with Early Salt Stress Responses of Roots. PMID:31707259
Sudden unexpected death in asymptomatic infants due to PPA2 variants. PMID:31705601
Co-regulation map of the human proteome enables identification of protein functions. PMID:31690884
Oxoglutarate dehydrogenase and acetyl-CoA acyltransferase 2 selectively associate with H2A.Z-occupied promoters and are required for histone modifications. PMID:31682939
UBASH3A Regulates the Synthesis and Dynamics of TCR-CD3 Complexes. PMID:31659016
Pathway Commons 2019 Update: integration, analysis and exploration of pathway data. PMID:31647099
Common Nodes of Virus-Host Interaction Revealed Through an Integrated Network Analysis. PMID:31636628
Gene Repositioning Is Under Constraints After Evolutionary Conserved Gene Neighborhood Separate. PMID:31632448
Experimental evolution reveals a general role for the methyltransferase Hmt1 in noise buffering. PMID:31613873
pathfindR: An R Package for Comprehensive Identification of Enriched Pathways in Omics Data Through Active Subnetworks. PMID:31608109
Filaments and phenotypes: cellular roles and orphan effects associated with mutations in cytoplasmic intermediate filament proteins. PMID:31602295
Patterns and Constraints in the Evolution of Sperm Individualization Genes in Insects, with an Emphasis on Beetles. PMID:31590243
Conserved Central Intraviral Protein Interactome of the Herpesviridae Family. PMID:31575665
Pyk2-dependent phosphorylation of LSR enhances localization of LSR and tricellulin at tricellular tight junctions. PMID:31574128
Broad Phenotypes of Disorders/Differences of Sex Development in MAMLD1 Patients Through Oligogenic Disease. PMID:31555317
Single-cell transcriptomic profiling of the aging mouse brain. PMID:31551601
Enabling Web-scale data integration in biomedicine through Linked Open Data. PMID:31531395
Identifying Protein Complexes from Dynamic Temporal Interval Protein-Protein Interaction Networks. PMID:31531351
Identifying protein complexes based on an edge weight algorithm and core-attachment structure. PMID:31521132
miR-486 is modulated by stretch and increases ventricular growth. PMID:31513548
In vivo epigenetic editing of Sema6a promoter reverses transcallosal dysconnectivity caused by C11orf46/Arl14ep risk gene. PMID:31511512
CSF1R inhibitor JNJ-40346527 attenuates microglial proliferation and neurodegeneration in P301S mice. PMID:31504240
Gene Cascade Finder: A tool for identification of gene cascades and its application in Caenorhabditis elegans. PMID:31504044
Chromobox homolog 8 (CBX8) Interacts with Y-Box binding protein 1 (YBX1) to promote cellular proliferation in hepatocellular carcinoma cells. PMID:31495785
The MyMOMA domain of MYO19 encodes for distinct Miro-dependent and Miro-independent mechanisms of interaction with mitochondrial membranes. PMID:31479585
Application of hyperbolic geometry in link prediction of multiplex networks. PMID:31471541
The role of structural pleiotropy and regulatory evolution in the retention of heteromers of paralogs. PMID:31454312
Transcriptome and Network Dissection of Microsatellite Stable and Highly Instable Colorectal Cancer. PMID:31450919
Hamiltonian energy as an efficient approach to identify the significant key regulators in biological networks. PMID:31442253
Machine learning empowers phosphoproteome prediction in cancers. PMID:31410451
The interactome of KRAB zinc finger proteins reveals the evolutionary history of their functional diversification. PMID:31403225
A seed-extended algorithm for detecting protein complexes based on density and modularity with topological structure and GO annotations. PMID:31390979
Nuclear envelope deformation controls cell cycle progression in response to mechanical force. PMID:31368207
Detection of dynamic protein complexes through Markov Clustering based on Elephant Herd Optimization Approach. PMID:31366992
A comprehensive study on genome-wide coexpression network of KHDRBS1/Sam68 reveals its cancer and patient-specific association. PMID:31366900
Endogenous IQGAP1 and IQGAP3 do not functionally interact with Ras. PMID:31363101
Identification of Upregulated HNRNPs Associated with Poor Prognosis in Pancreatic Cancer. PMID:31355266
Rad5 dysregulation drives hyperactive recombination at replication forks resulting in cisplatin sensitivity and genome instability. PMID:31350889
Identification of differentially expressed genes in small and non-small cell lung cancer based on meta-analysis of mRNA. PMID:31338439
Tunicamycin Sensitivity-Suppression by High Gene Dosage Reveals New Functions of the Yeast Hog1 MAP Kinase. PMID:31336877
Contrasting Gene Expression Profiles of Monocytes and Lymphocytes From Peste-Des-Petits-Ruminants Virus Infected Goats. PMID:31333643
CAGI5: Objective performance assessments of predictions based on the Evolutionary Action equation. PMID:31317604
A systematic approach to orient the human protein-protein interaction network. PMID:31289271
Uncovering biomarker genes with enriched classification potential from Hallmark gene sets. PMID:31278367
Cancer driver genes: a guilty by resemblance doctrine. PMID:31275738
Fibril-induced glutamine-/asparagine-rich prions recruit stress granule proteins in mammalian cells. PMID:31266883
Inferring Interaction Networks From Multi-Omics Data. PMID:31249591
Augmenting subnetwork inference with information extracted from the scientific literature. PMID:31246951
Multi-omics Characterization of Interaction-mediated Control of Human Protein Abundance levels. PMID:31239291
Computational analysis of single-cell transcriptomics data elucidates the stabilization of Oct4 expression in the E3.25 mouse preimplantation embryo. PMID:31222057
Protein interactions and consensus clustering analysis uncover insights into herpesvirus virion structure and function relationships. PMID:31199794
Using genetics to understand biology. PMID:31189902
Rapid Evolution of Gained Essential Developmental Functions of a Young Gene via Interactions with Other Essential Genes. PMID:31187122
Differential gene expression analysis of human cumulus cells. PMID:31181875
Boolean gene regulatory network model of centromere function in Saccharomyces cerevisiae. PMID:31175490
Identification of Endogenous Adenomatous Polyposis Coli Interaction Partners and β-Catenin-Independent Targets by Proteomics. PMID:31160382
Opioid-Induced Hyperalgesia Is Associated with Dysregulation of Circadian Rhythm and Adaptive Immune Pathways in the Mouse Trigeminal Ganglia and Nucleus Accumbens. PMID:31129808
Identification of genes underlying phenotypic plasticity of wing size via insulin signaling pathway by network-based analysis in Sogatella furcifera. PMID:31113376
Murine obscurin and Obsl1 have functionally redundant roles in sarcolemmal integrity, sarcoplasmic reticulum organization, and muscle metabolism. PMID:31098411
Optimized Cross-Linking Mass Spectrometry for in Situ Interaction Proteomics. PMID:31083951
A White-Box Machine Learning Approach for Revealing Antibiotic Mechanisms of Action. PMID:31080069
Associating expression and genomic data using co-occurrence measures. PMID:31072345
modEnrichr: a suite of gene set enrichment analysis tools for model organisms. PMID:31069376
Automated assessment of biological database assertions using the scientific literature. PMID:31035936
Topological and functional comparison of community detection algorithms in biological networks. PMID:31029085
Deciphering the three-domain architecture in schlafens and the structures and roles of human schlafen12 and serpinB12 in transcriptional regulation. PMID:31026779
A context-based ABC model for literature-based discovery. PMID:31017923
Predicting synthetic lethal interactions using conserved patterns in protein interaction networks. PMID:30995217
Cullin-3 dependent deregulation of ACTN1 represents a new pathogenic mechanism in nemaline myopathy. PMID:30990797
Pathway centrality in protein interaction networks identifies putative functional mediating pathways in pulmonary disease. PMID:30971743
Downregulation of CENPF Remodels Prostate Cancer Cells and Alters Cellular Metabolism. PMID:30957416
GNE: a deep learning framework for gene network inference by aggregating biological information. PMID:30953525
Disease association of human tumor suppressor genes. PMID:30945018
Cx43-Associated Secretome and Interactome Reveal Synergistic Mechanisms for Glioma Migration and MMP3 Activation. PMID:30941001
Meta-path Based Prioritization of Functional Drug Actions with Multi-Level Biological Networks. PMID:30940832
A Genome-Wide Analysis of the Penumbral Volume in Inbred Mice following Middle Cerebral Artery Occlusion. PMID:30911049
Expression, purification and crystallization of the novel Xenopus tropicalis ALDH16B1, a homologue of human ALDH16A1. PMID:30894314
Identification of Important Effector Proteins in the FOXJ1 Transcriptional Network Associated With Ciliogenesis and Ciliary Function. PMID:30881373
DDOT: A Swiss Army Knife for Investigating Data-Driven Biological Ontologies. PMID:30878356
Prioritization of genes involved in endothelial cell apoptosis by their implication in lymphedema using an analysis of associative gene networks with ANDSystem. PMID:30871556
AIControl: replacing matched control experiments with machine learning improves ChIP-seq peak identification. PMID:30869146
MorCVD: A Unified Database for Host-Pathogen Protein-Protein Interactions of Cardiovascular Diseases Related to Microbes. PMID:30858555
Expression and Characterization of Human Fragile X Mental Retardation Protein Isoforms and Interacting Proteins in Human Cells. PMID:30853789
Deciphering the complex role of thrombospondin-1 in glioblastoma development. PMID:30850588
Environment-dependent fitness gains can be driven by horizontal gene transfer of transporter-encoding genes. PMID:30842288
Compendium of synovial signatures identifies pathologic characteristics for predicting treatment response in rheumatoid arthritis patients. PMID:30831253
Magic roundabout is an endothelial-specific ohnolog of ROBO1 which neo-functionalized to an essential new role in angiogenesis. PMID:30802244
Reduced mitochondrial fusion and Huntingtin levels contribute to impaired dendritic maturation and behavioral deficits in Fmr1-mutant mice. PMID:30742117
Data mining for mutation-specific targets in acute myeloid leukemia. PMID:30728456
Ubiquinol-cytochrome C reductase core protein II promotes tumorigenesis by facilitating p53 degradation. PMID:30674441
A De Novo Shape Motif Discovery Algorithm Reveals Preferences of Transcription Factors for DNA Shape Beyond Sequence Motifs. PMID:30660610
Translational control mechanisms in cutaneous malignant melanoma: the role of eIF2α. PMID:30634982
UbiHub: a data hub for the explorers of ubiquitination pathways. PMID:30601939
Time-lagged Ordered Lasso for network inference. PMID:30594121
Identification of genes required for eye development by high-throughput screening of mouse knockouts. PMID:30588515
Protein complexes identification based on go attributed network embedding. PMID:30572820
Systems biology analysis reveals new insights into invasive lung cancer. PMID:30547817
Aberrantly expressed long noncoding RNAs and genes in Parkinson's disease. PMID:30538480
Genomic identification and functional analysis of essential genes in Caenorhabditis elegans. PMID:30514206
Subgrouping breast cancer patients based on immune evasion mechanisms unravels a high involvement of transforming growth factor-beta and decoy receptor 3. PMID:30513096
Identification of evolutionarily conserved gene networks mediating neurodegenerative dementia. PMID:30510257
Genome-wide identification of RETINOBLASTOMA RELATED 1 binding sites in Arabidopsis reveals novel DNA damage regulators. PMID:30500810
ERRα promotes breast cancer cell dissemination to bone by increasing RANK expression in primary breast tumors. PMID:30478447
Heterologous Hsp90 promotes phenotypic diversity through network evolution. PMID:30439936
An E2-ubiquitin thioester-driven approach to identify substrates modified with ubiquitin and ubiquitin-like molecules. PMID:30429481
Integration of Tumor Genomic Data with Cell Lines Using Multi-dimensional Network Modules Improves Cancer Pharmacogenomics. PMID:30414925
The protein interaction networks of mucolipins and two-pore channels. PMID:30395881
Characterization of Squamous Cell Lung Cancers from Appalachian Kentucky. PMID:30377206
Computational discovery of dynamic cell line specific Boolean networks from multiplex time-course data. PMID:30372442
Antiviral activity of the mineralocorticoid receptor NR3C2 against Herpes simplex virus Type 1 (HSV-1) infection. PMID:30367157
Transcriptomic and functional network features of lung squamous cell carcinoma through integrative analysis of GEO and TCGA data. PMID:30367091
Establishment of stably expandable induced myogenic stem cells by four transcription factors. PMID:30361642
Modelling Self-Organization in Complex Networks Via a Brain-Inspired Network Automata Theory Improves Link Reliability in Protein Interactomes. PMID:30361555
Defining Essentiality Score of Protein-Coding Genes and Long Noncoding RNAs. PMID:30356729
Use of Laplacian Heat Diffusion Algorithm to Infer Novel Genes With Functions Related to Uveitis. PMID:30349554
Affinity capture of polyribosomes followed by RNAseq (ACAPseq), a discovery platform for protein-protein interactions. PMID:30345971
The 7q11.23 Protein DNAJC30 Interacts with ATP Synthase and Links Mitochondria to Brain Development. PMID:30318146
Discovering Genetic Factors for psoriasis through exhaustively searching for significant second order SNP-SNP interactions. PMID:30315195
Domain architecture of BAF250a reveals the ARID and ARM-repeat domains with implication in function and assembly of the BAF remodeling complex. PMID:30307988
Fyn Regulates Binding Partners of Cyclic-AMP Dependent Protein Kinase A. PMID:30274258
Launching the C-HPP neXt-CP50 Pilot Project for Functional Characterization of Identified Proteins with No Known Function. PMID:30269496
The Systems Biology of Single-Cell Aging. PMID:30267677
A mitochondrial proteome profile indicative of type 2 diabetes mellitus in skeletal muscles. PMID:30266947
Deubiquitinase Usp12 functions noncatalytically to induce autophagy and confer neuroprotection in models of Huntington's disease. PMID:30266909
WEADE: A workflow for enrichment analysis and data exploration. PMID:30265728
Identifying Drivers of Parallel Evolution: A Regression Model Approach. PMID:30252076
Bioinformatics Analysis Identifies p53 as a Candidate Prognostic Biomarker for Neuropathic Pain. PMID:30233637
Exploring transcription factors reveals crucial members and regulatory networks involved in different abiotic stresses in Brassica napus L. PMID:30231862
Quantifying layer similarity in multiplex networks: a systematic study. PMID:30224981
Insights into archaeal chaperone machinery: a network-based approach. PMID:30178307
Loss of the E3 ubiquitin ligase MKRN1 represses diet-induced metabolic syndrome through AMPK activation. PMID:30143610
Multi-omic Directed Networks Describe Features of Gene Regulation in Aged Brains and Expand the Set of Genes Driving Cognitive Decline. PMID:30140277
Targeting Focal Adhesion Kinase Using Inhibitors of Protein-Protein Interactions. PMID:30134553
Bioinformatics analysis to screen for critical genes between survived and non‑survived patients with sepsis. PMID:30132542
Genome-wide Identification and Characterization of Enhancers Across 10 Human Tissues. PMID:30123079
Dynamical Analysis of the Regulatory Network Controlling Natural Killer Cells Differentiation. PMID:30116200
Synstable Fusion: A Network-Based Algorithm for Estimating Driver Genes in Fusion Structures. PMID:30115851
Convex skeletons of complex networks. PMID:30111666
A Methodological Assessment and Characterization of Genetically-Driven Variation in Three Human Phosphoproteomes. PMID:30108239
Reconstruction of the Protein-Protein Interaction Network for Protein Complexes Identification by Walking on the Protein Pair Fingerprints Similarity Network. PMID:30087694
Evolution of In Silico Strategies for Protein-Protein Interaction Drug Discovery. PMID:30082644
Brain region-dependent gene networks associated with selective breeding for increased voluntary wheel-running behavior. PMID:30071007
Automatic extraction of protein-protein interactions using grammatical relationship graph. PMID:30066644
Cross-species systems analysis identifies gene networks differentially altered by sleep loss and depression. PMID:30050989
From systems to biology: A computational analysis of the research articles on systems biology from 1992 to 2013. PMID:30044828
ProfPPIdb: Pairs of physical protein-protein interactions predicted for entire proteomes. PMID:30020956
Cancerin: A computational pipeline to infer cancer-associated ceRNA interaction networks. PMID:30011266
Leveraging prior knowledge for protein-protein interaction extraction with memory network. PMID:30010731
Loss of tumor suppressor IGFBP4 drives epigenetic reprogramming in hepatic carcinogenesis. PMID:29992318
Genome-wide SWAp-Tag yeast libraries for proteome exploration. PMID:29988094
Time-resolved transcriptomics in neural stem cells identifies a v-ATPase/Notch regulatory loop. PMID:29959232
Systems-Based Interactome Analysis for Hematopoiesis Effect of Angelicae sinensis Radix: Regulated Network of Cell Proliferation towards Hemopoiesis. PMID:29943236
Chromatin That Guides Dosage Compensation Is Modulated by the siRNA Pathway in Drosophila melanogaster. PMID:29921620
A new method for predicting essential proteins based on participation degree in protein complex and subgraph density. PMID:29894517
Exploring Landscape of Drug-Target-Pathway-Side Effect Associations. PMID:29888057
Network-based machine learning and graph theory algorithms for precision oncology. PMID:29872707
Identification of MOSPD2, a novel scaffold for endoplasmic reticulum membrane contact sites. PMID:29858488
PhosContext2vec: a distributed representation of residue-level sequence contexts and its application to general and kinase-specific phosphorylation site prediction. PMID:29844483
Evidence for interaction between Hsp90 and the ER membrane complex. PMID:29808299
eXpression2Kinases (X2K) Web: linking expression signatures to upstream cell signaling networks. PMID:29800326
A website to identify shared genes in Saccharomyces cerevisiae homozygous deletion library screens. PMID:29792161
Neural networks for link prediction in realistic biomedical graphs: a multi-dimensional evaluation of graph embedding-based approaches. PMID:29783926
Discovering novel SNPs that are correlated with patient outcome in a Singaporean cancer patient cohort treated with gemcitabine-based chemotherapy. PMID:29751792
INTERSPIA: a web application for exploring the dynamics of protein-protein interactions among multiple species. PMID:29746660
PPI network analyses of human WD40 protein family systematically reveal their tendency to assemble complexes and facilitate the complex predictions. PMID:29745845
Network inference reveals novel connections in pathways regulating growth and defense in the yeast salt response. PMID:29738528
LncRNA OIP5-AS1 is overexpressed in undifferentiated oral tumors and integrated analysis identifies as a downstream effector of stemness-associated transcription factors. PMID:29728583
Core signaling pathways in ovarian cancer stem cell revealed by integrative analysis of multi-marker genomics data. PMID:29723215
Role of duplicate genes in determining the tissue-selectivity of hereditary diseases. PMID:29723191
Delineating the HMGB1 and HMGB2 interactome in prostate and ovary epithelial cells and its relationship with cancer. PMID:29721183
An RNAi-mediated screen identifies novel targets for next-generation antiepileptic drugs based on increased expression of the homeostatic regulator pumilio. PMID:29718742
New perspectives: systems medicine in cardiovascular disease. PMID:29699591
Determining the minimum number of protein-protein interactions required to support known protein complexes. PMID:29698482
An epistatic effect of KRT25 on SP6 is involved in curly coat in horses. PMID:29686323
Integrative bioinformatics analysis characterizing the role of EDC3 in mRNA decay and its association to intellectual disability. PMID:29685133
The Interactomic Analysis Reveals Pathogenic Protein Networks in Phomopsis longicolla Underlying Seed Decay of Soybean. PMID:29666630
Functional Analysis of Hif1 Histone Chaperone in Saccharomyces cerevisiae. PMID:29661843
Massive mining of publicly available RNA-seq data from human and mouse. PMID:29636450
Predicting essential proteins by integrating orthology, gene expressions, and PPI networks. PMID:29634727
MTGO: PPI Network Analysis Via Topological and Functional Module Identification. PMID:29615773
Systematic Evaluation of Molecular Networks for Discovery of Disease Genes. PMID:29605183
Promoter architecture determines cotranslational regulation of mRNA. PMID:29567675
Predicting protein complexes using a supervised learning method combined with local structural information. PMID:29554120
Integrated analysis of microarray data to identify the genes critical for the rupture of intracranial aneurysm. PMID:29552131
BIOPYDB: A Dynamic Human Cell Specific Biochemical Pathway Database with Advanced Computational Analyses Platform. PMID:29547394
Expression of reactive species related genes is associated with patient survival in luminal B breast cancer. PMID:29545070
Formation of chimeric genes with essential functions at the origin of eukaryotes. PMID:29534719
Predicted Arabidopsis Interactome Resource and Gene Set Linkage Analysis: A Transcriptomic Analysis Resource. PMID:29530937
Combined use of protein biomarkers and network analysis unveils deregulated regulatory circuits in Duchenne muscular dystrophy. PMID:29529088
Analysis of Gene Regulatory Networks of Maize in Response to Nitrogen. PMID:29518046
A peripheral blood transcriptomic signature predicts autoantibody development in infants at risk of type 1 diabetes. PMID:29515040
Multi-chaperone function modulation and association with cytoskeletal proteins are key features of the function of AIP in the pituitary gland. PMID:29507682
Improving prediction of heterodimeric protein complexes using combination with pairwise kernel. PMID:29504897
Yersinia pestis Targets the Host Endosome Recycling Pathway during the Biogenesis of the Yersinia-Containing Vacuole To Avoid Killing by Macrophages. PMID:29463656
Combinatorial CRISPR-Cas9 Metabolic Screens Reveal Critical Redox Control Points Dependent on the KEAP1-NRF2 Regulatory Axis. PMID:29452643
Distinct methylation profile of mucinous ovarian carcinoma reveals susceptibility to proteasome inhibitors. PMID:29451304
Dynamic network biomarker indicates pulmonary metastasis at the tipping point of hepatocellular carcinoma. PMID:29445139
The rolB plant oncogene affects multiple signaling protein modules related to hormone signaling and plant defense. PMID:29396465
Binding and entry of peste des petits ruminants virus into caprine endometrial epithelial cells profoundly affect early cellular gene expression. PMID:29368634
Three-dimensional spatial analysis of missense variants in RTEL1 identifies pathogenic variants in patients with Familial Interstitial Pneumonia. PMID:29361909
Using Yeast Synthetic Lethality To Inform Drug Combination for Malaria. PMID:29358287
Morphological inversion of complex diffusion. PMID:29346889
Discovering Altered Regulation and Signaling Through Network-based Integration of Transcriptomic, Epigenomic, and Proteomic Tumor Data. PMID:29344883
Using genetic buffering relationships identified in fission yeast to reveal susceptibilities in cells lacking hamartin or tuberin function. PMID:29343513
Genomic Identification and Functional Characterization of Essential Genes in Caenorhabditis elegans. PMID:29339407
MicroRNA-200a confers chemoresistance by antagonizing TP53INP1 and YAP1 in human breast cancer. PMID:29329575
Integrating transcriptional activity in genome-scale models of metabolism. PMID:29322933
Inferring ontology graph structures using OWL reasoning. PMID:29304741
The phosphatidylinositide 3-kinase (PI3K) signaling pathway is a determinant of zileuton response in adults with asthma. PMID:29298996
The node-weighted Steiner tree approach to identify elements of cancer-related signaling pathways. PMID:29297291
A Seed Expansion Graph Clustering Method for Protein Complexes Detection in Protein Interaction Networks. PMID:29292776
Identification of genes highly downregulated in pancreatic cancer through a meta-analysis of microarray datasets: implications for discovery of novel tumor-suppressor genes and therapeutic targets. PMID:29288362
The integration of weighted gene association networks based on information entropy. PMID:29272314
Germline TTN variants are enriched in PTEN-wildtype Bannayan-Riley-Ruvalcaba syndrome. PMID:29263846
Deciphering the Relationship between Obesity and Various Diseases from a Network Perspective. PMID:29258237
Evaluating the associations between human circadian rhythms and dysregulated genes in liver cancer cells. PMID:29250165
Multi-Objective Optimization Algorithm to Discover Condition-Specific Modules in Multiple Networks. PMID:29240706
LeishDB: a database of coding gene annotation and non-coding RNAs in Leishmania braziliensis. PMID:29220437
Prediction of essential proteins based on subcellular localization and gene expression correlation. PMID:29219067
Annotating gene sets by mining large literature collections with protein networks. PMID:29218918
HIDEEP: a systems approach to predict hormone impacts on drug efficacy based on effect paths. PMID:29192270
PlanNET: homology-based predicted interactome for multiple planarian transcriptomes. PMID:29186384
Systems Bioinformatics: increasing precision of computational diagnostics and therapeutics through network-based approaches. PMID:29186305
Optimal percolation on multiplex networks. PMID:29147014
CommWalker: correctly evaluating modules in molecular networks in light of annotation bias. PMID:29112702
Inferring gene and protein interactions using PubMed citations and consensus Bayesian networks. PMID:29049295
A nonparametric significance test for sampled networks. PMID:29036452
Native KCC2 interactome reveals PACSIN1 as a critical regulator of synaptic inhibition. PMID:29028184
PICKLE 2.0: A human protein-protein interaction meta-database employing data integration via genetic information ontology. PMID:29023571
Mutational landscape of RNA-binding proteins in human cancers. PMID:29023197
A novel network analysis approach reveals DNA damage, oxidative stress and calcium/cAMP homeostasis-associated biomarkers in frontotemporal dementia. PMID:29020091
MD-Miner: a network-based approach for personalized drug repositioning. PMID:28984195
A Comprehensive Analysis of Transcript-Supported De Novo Genes in Saccharomyces sensu stricto Yeasts. PMID:28981695
Functional 5' UTR motif discovery with LESMoN: Local Enrichment of Sequence Motifs in biological Networks. PMID:28977652
MAPPIN: a method for annotating, predicting pathogenicity and mode of inheritance for nonsynonymous variants. PMID:28977528
Multi-dimensional histone methylations for coordinated regulation of gene expression under hypoxia. PMID:28977425
Network-Based Method for Identifying Co- Regeneration Genes in Bone, Dentin, Nerve and Vessel Tissues. PMID:28974058
Using neural networks for reducing the dimensions of single-cell RNA-Seq data. PMID:28973464
Network-Based Coverage of Mutational Profiles Reveals Cancer Genes. PMID:28957656
Conjecture Regarding Posttranslational Modifications to the Arabidopsis Type I Proton-Pumping Pyrophosphatase (AVP1). PMID:28955362
Stable Gene Regulatory Network Modeling From Steady-State Data. PMID:28952574
Computational Approaches to Identify Genetic Interactions for Cancer Therapeutics. PMID:28941356
A computational method using the random walk with restart algorithm for identifying novel epigenetic factors. PMID:28932904
P-body proteins regulate transcriptional rewiring to promote DNA replication stress resistance. PMID:28916784
MPZL1 forms a signalling complex with GRB2 adaptor and PTPN11 phosphatase in HER2-positive breast cancer cells. PMID:28912526
MCbiclust: a novel algorithm to discover large-scale functionally related gene sets from massive transcriptomics data collections. PMID:28911113
Identification of high-confidence RNA regulatory elements by combinatorial classification of RNA-protein binding sites. PMID:28886744
Evolutionary analysis and interaction prediction for protein-protein interaction network in geometric space. PMID:28886027
Chronic obstructive pulmonary disease candidate gene prioritization based on metabolic networks and functional information. PMID:28873096
Vertebrate GAF/ThPOK: emerging functions in chromatin architecture and transcriptional regulation. PMID:28856379
Using ALoFT to determine the impact of putative loss-of-function variants in protein-coding genes. PMID:28851873
The effect of Bu Zhong Yi Qi decoction on simulated weightlessness‑induced muscle atrophy and its mechanisms. PMID:28849026
Domain-based prediction of the human isoform interactome provides insights into the functional impact of alternative splicing. PMID:28846689
Taxonomically Restricted Genes with Essential Functions Frequently Play Roles in Chromosome Segregation in Caenorhabditis elegans and Saccharomyces cerevisiae. PMID:28839119
Construction of an integrated gene regulatory network link to stress-related immune system in cattle. PMID:28825201
Integrative network and transcriptomics-based approach predicts genotype- specific drug combinations for melanoma. PMID:28815138
ODG: Omics database generator - a tool for generating, querying, and analyzing multi-omics comparative databases to facilitate biological understanding. PMID:28797229
CODA: Integrating multi-level context-oriented directed associations for analysis of drug effects. PMID:28790372
Interchromosomal Transfer of Immune Regulation During Infection of Barley with the Powdery Mildew Pathogen. PMID:28790145
Identification of essential genes for cancer immunotherapy. PMID:28783722
Global Gene Expression Analysis Reveals Crosstalk between Response Mechanisms to Cold and Drought Stresses in Cassava Seedlings. PMID:28769962
CrossCheck: an open-source web tool for high-throughput screen data analysis. PMID:28724888
Development of an in silico method for the identification of subcomplexes involved in the biogenesis of multiprotein complexes in Saccharomyces cerevisiae. PMID:28693620
Metabolic modeling to identify engineering targets for Komagataella phaffii: The effect of biomass composition on gene target identification. PMID:28691262
Drug Target Protein-Protein Interaction Networks: A Systematic Perspective. PMID:28691014
Strength of functional signature correlates with effect size in autism. PMID:28687074
Prognostic cancer gene signatures share common regulatory motifs. PMID:28684851
Global gene expression profiling and senescence biomarker analysis of hESC exposed to H2O2 induced non-cytotoxic oxidative stress. PMID:28676096
Spatiotemporal profile of postsynaptic interactomes integrates components of complex brain disorders. PMID:28671696
Systematic bacterialization of yeast genes identifies a near-universally swappable pathway. PMID:28661399
CrY2H-seq: a massively multiplexed assay for deep-coverage interactome mapping. PMID:28650476
APPL1 is a multifunctional endosomal signaling adaptor protein. PMID:28620038
Contextualization of drug-mediator relations using evidence networks. PMID:28617226
Agonist-specific Protein Interactomes of Glucocorticoid and Androgen Receptor as Revealed by Proximity Mapping. PMID:28611094
Neighbours of cancer-related proteins have key influence on pathogenesis and could increase the drug target space for anticancer therapies. PMID:28603644
A methodology for elucidating regulatory mechanisms leading to changes in lipid profiles. PMID:28596719
Integration of over 9,000 mass spectrometry experiments builds a global map of human protein complexes. PMID:28596423
Characterization of developmental defects in the forebrain resulting from hyperactivated mTOR signaling by integrative analysis of transcriptomic and proteomic data. PMID:28588230
Network-assisted target identification for haploinsufficiency and homozygous profiling screens. PMID:28574983
Genetic wiring maps of single-cell protein states reveal an off-switch for GPCR signalling. PMID:28562590
Generating testable hypotheses for schizophrenia and rheumatoid arthritis pathogenesis by integrating epidemiological, genomic, and protein interaction data. PMID:28560257
A scalable double-barcode sequencing platform for characterization of dynamic protein-protein interactions. PMID:28541284
Methylation of human eukaryotic elongation factor alpha (eEF1A) by a member of a novel protein lysine methyltransferase family modulates mRNA translation. PMID:28520920
Combining inferred regulatory and reconstructed metabolic networks enhances phenotype prediction in yeast. PMID:28520713
Network-aided Bi-Clustering for discovering cancer subtypes. PMID:28432308
Use of Graph Database for the Integration of Heterogeneous Biological Data. PMID:28416946
Drebrin restricts rotavirus entry by inhibiting dynamin-mediated endocytosis. PMID:28416666
Transcriptional regulatory networks underlying the reprogramming of spermatogonial stem cells to multipotent stem cells. PMID:28408750
Inferring modulators of genetic interactions with epistatic nested effects models. PMID:28406896
Knockdown of Broad-Complex Gene Expression of Bombyx mori by Oligopyrrole Carboxamides Enhances Silk Production. PMID:28400559
Finding low-conductance sets with dense interactions (FLCD) for better protein complex prediction. PMID:28361714
Comparison of tissue/disease specific integrated networks using directed graphlet signatures. PMID:28361704
Net2Align: An Algorithm For Pairwise Global Alignment of Biological Networks. PMID:28356678
Computational identifying and characterizing circular RNAs and their associated genes in hepatocellular carcinoma. PMID:28346469
Bacterial Carriers for Glioblastoma Therapy. PMID:28345020
A Comprehensive View of the β-Arrestinome. PMID:28321204
NaviGO: interactive tool for visualization and functional similarity and coherence analysis with gene ontology. PMID:28320317
Predicting drug-drug interactions through drug structural similarities and interaction networks incorporating pharmacokinetics and pharmacodynamics knowledge. PMID:28316654
Systematic morphological profiling of human gene and allele function via Cell Painting. PMID:28315521
Delineating functional principles of the bow tie structure of a kinase-phosphatase network in the budding yeast. PMID:28298210
Modeling anorexia nervosa: transcriptional insights from human iPSC-derived neurons. PMID:28291261
Ornithine Aminotransferase, an Important Glutamate-Metabolizing Enzyme at the Crossroads of Multiple Metabolic Pathways. PMID:28272331
Pathway Cross-Talk Analysis in Detecting Significant Pathways in Barrett's Esophagus Patients. PMID:28263955
Integrated systems biology analysis of KSHV latent infection reveals viral induction and reliance on peroxisome mediated lipid metabolism. PMID:28257516
The amyloid interactome: Exploring protein aggregation. PMID:28249044
CLK-dependent exon recognition and conjoined gene formation revealed with a novel small molecule inhibitor. PMID:28232751
HAPPI-2: a Comprehensive and High-quality Map of Human Annotated and Predicted Protein Interactions. PMID:28212602
A Comprehensive Gene Expression Meta-analysis Identifies Novel Immune Signatures in Rheumatoid Arthritis Patients. PMID:28210261
An approach to infer putative disease-specific mechanisms using neighboring gene networks. PMID:28200075
Evaluating the effect of annotation size on measures of semantic similarity. PMID:28193260
Incorporating prior biological knowledge for network-based differential gene expression analysis using differentially weighted graphical LASSO. PMID:28187708
Protein complex prediction for large protein protein interaction networks with the Core&Peel method. PMID:28185552
How can functional annotations be derived from profiles of phenotypic annotations? PMID:28183267
Nestedness across biological scales. PMID:28166284
Accurate prediction of human essential genes using only nucleotide composition and association information. PMID:28158612
Skewing in Arabidopsis roots involves disparate environmental signaling pathways. PMID:28143395
Epigenetic profiling of human brain differential DNA methylation networks in schizophrenia. PMID:28117656
GSNFS: Gene subnetwork biomarker identification of lung cancer expression data. PMID:28117655
Methyl-CpG-Binding Protein MBD1 Regulates Neuronal Lineage Commitment through Maintaining Adult Neural Stem Cell Identity. PMID:28100736
Is the average shortest path length of gene set a reflection of their biological relatedness? PMID:28073302
Drug Response Prediction as a Link Prediction Problem. PMID:28067293
Non-Coding RNAs in Lung Cancer: Contribution of Bioinformatics Analysis to the Development of Non-Invasive Diagnostic Tools. PMID:28035947
The role of prostate tumor overexpressed 1 in cancer progression. PMID:28029646
Predictability of Genetic Interactions from Functional Gene Modules. PMID:28007839
Transcriptome analyses identify key cellular factors associated with HIV-1-associated neuropathogenesis in infected men. PMID:28005686
Improved method for prioritization of disease associated lncRNAs based on ceRNA theory and functional genomics data. PMID:27992375
Brassinosteroid signaling converges with SUPPRESSOR OF PHYTOCHROME B4-#3 to influence the expression of SMALL AUXIN UP RNA genes and hypocotyl growth. PMID:27984677
HOXA repression is mediated by nucleoporin Nup93 assisted by its interactors Nup188 and Nup205. PMID:27980680
Integrating Information in Biological Ontologies and Molecular Networks to Infer Novel Terms. PMID:27976738
Investigating the human Calcineurin Interaction Network using the πɸLxVP SLiM. PMID:27974827
PlaMoM: a comprehensive database compiles plant mobile macromolecules. PMID:27924044
Rheumatoid arthritis: Modelling cytokine signalling networks. PMID:27904145
Role of Hepatic-Specific Transcription Factors and Polycomb Repressive Complex 2 during Induction of Fibroblasts to Hepatic Fate. PMID:27902735
A genome wide dosage suppressor network reveals genomic robustness. PMID:27899637
A scored human protein-protein interaction network to catalyze genomic interpretation. PMID:27892958
Biomolecular Network-Based Synergistic Drug Combination Discovery. PMID:27891522
PLK1, A Potential Target for Cancer Therapy. PMID:27888710
Mitochondrial Sirtuin Network Reveals Dynamic SIRT3-Dependent Deacetylation in Response to Membrane Depolarization. PMID:27881304
Computational approaches for the identification of cancer genes and pathways. PMID:27863091
Increasing Role of Titin Mutations in Neuromuscular Disorders. PMID:27854229
DGCA: A comprehensive R package for Differential Gene Correlation Analysis. PMID:27846853
iSeq: A New Double-Barcode Method for Detecting Dynamic Genetic Interactions in Yeast. PMID:27821633
Asc1p/RACK1 Connects Ribosomes to Eukaryotic Phosphosignaling. PMID:27821475
Exploring genetic suppression interactions on a global scale. PMID:27811238
Genetic-and-Epigenetic Interspecies Networks for Cross-Talk Mechanisms in Human Macrophages and Dendritic Cells during MTB Infection. PMID:27803888
An Integrative Analysis of Preeclampsia Based on the Construction of an Extended Composite Network Featuring Protein-Protein Physical Interactions and Transcriptional Relationships. PMID:27802351
yMap: an automated method to map yeast variants to protein modifications and functional regions. PMID:27797766
A prior-based integrative framework for functional transcriptional regulatory network inference. PMID:27794550
A Systems Biology Comparison of Ovarian Cancers Implicates Putative Somatic Driver Mutations through Protein-Protein Interaction Models. PMID:27788148
Systems biology analysis reveals role of MDM2 in diabetic nephropathy. PMID:27777973
Genome-Wide Gene/Genome Dosage Imbalance Regulates Gene Expressions in Synthetic Brassica napus and Derivatives (AC, AAC, CCA, CCAA). PMID:27721820
SONAR Discovers RNA-Binding Proteins from Analysis of Large-Scale Protein-Protein Interactomes. PMID:27720645
Intrinsic noise and deviations from criticality in Boolean gene-regulatory networks. PMID:27713479
DBSecSys 2.0: a database of Burkholderia mallei and Burkholderia pseudomallei secretion systems. PMID:27650316
Reduction strategies for hierarchical multi-label classification in protein function prediction. PMID:27627880
inFRank: a ranking-based identification of influential genes in biological networks. PMID:27623074
Structural and mechanistic insights into human splicing factor SF3b complex derived using an integrated approach guided by the cryo-EM density maps. PMID:27618338
Exploring Quantitative Yeast Phenomics with Single-Cell Analysis of DNA Damage Foci. PMID:27617677
Positive Selection Linked with Generation of Novel Mammalian Dentition Patterns. PMID:27613398
Comprehensive Proteome Profiling of Platelet Identified a Protein Profile Predictive of Responses to An Antiplatelet Agent Sarpogrelate. PMID:27601597
Fast Inference for the Latent Space Network Model Using a Case-Control Approximate Likelihood. PMID:27570438
An ensemble framework for identifying essential proteins. PMID:27557880
Functional characterization of EI24-induced autophagy in the degradation of RING-domain E3 ligases. PMID:27541728
Nuclear autophagy: An evolutionarily conserved mechanism of nuclear degradation in the cytoplasm. PMID:27541589
Predicting diabetes mellitus genes via protein-protein interaction and protein subcellular localization information. PMID:27535125
Interaction Between Peroxisome Proliferator Activated Receptor δ and Epithelial Membrane Protein 2 Polymorphisms Influences HDL-C Levels in the Chinese Population. PMID:27530449
The Role of Node Heterogeneity in the Coupled Spreading of Epidemics and Awareness. PMID:27517715
VHLdb: A database of von Hippel-Lindau protein interactors and mutations. PMID:27511743
Systems Analysis of the Complement-Induced Priming Phase of Liver Regeneration. PMID:27511733
ARN: analysis and prediction by adipogenic professional database. PMID:27503118
Whole Exome Sequencing Identifies TSC1/TSC2 Biallelic Loss as the Primary and Sufficient Driver Event for Renal Angiomyolipoma Development. PMID:27494029
Evaluating the impact of single nucleotide variants on transcription factor binding. PMID:27492288
Context-specific functional module based drug efficacy prediction. PMID:27490093
Ligand Similarity Complements Sequence, Physical Interaction, and Co-Expression for Gene Function Prediction. PMID:27467773
Small-molecule binding sites to explore protein-protein interactions in the cancer proteome. PMID:27452673
Investigating the Combinatory Effects of Biological Networks on Gene Co-expression. PMID:27445830
TSSC1 is novel component of the endosomal retrieval machinery. PMID:27440922
The nonessentiality of essential genes in yeast provides therapeutic insights into a human disease. PMID:27440870
Defining the Protein-Protein Interaction Network of the Human Protein Tyrosine Phosphatase Family. PMID:27432908
Valosin-containing protein (VCP)-Adaptor Interactions are Exceptionally Dynamic and Subject to Differential Modulation by a VCP Inhibitor. PMID:27406709
Transcriptomic response of yeast cells to ATX1 deletion under different copper levels. PMID:27401861
Systems view of adipogenesis via novel omics-driven and tissue-specific activity scoring of network functional modules. PMID:27385551
The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. PMID:27374120
Intrinsic protein disorder in histone lysine methylation. PMID:27356874
SorghumFDB: sorghum functional genomics database with multidimensional network analysis. PMID:27352859
FOXR2 Interacts with MYC to Promote Its Transcriptional Activities and Tumorigenesis. PMID:27346356
A noncatalytic function of the topoisomerase II CTD in Aurora B recruitment to inner centromeres during mitosis. PMID:27325791
Reconstructing the temporal progression of HIV-1 immune response pathways. PMID:27307624
Computational approaches in target identification and drug discovery. PMID:27293534
The Drosophila ETV5 Homologue Ets96B: Molecular Link between Obesity and Bipolar Disorder. PMID:27280443
ELAVL2-regulated transcriptional and splicing networks in human neurons link neurodevelopment and autism. PMID:27260404
Review on Graph Clustering and Subgraph Similarity Based Analysis of Neurological Disorders. PMID:27258269
Data set of interactomes and metabolic pathways of proteins differentially expressed in brains with Alzheimer׳s disease. PMID:27257613
Ribosome recycling defects modify the balance between the synthesis and assembly of specific subunits of the oxidative phosphorylation complexes in yeast mitochondria. PMID:27257059
The Use of Protein-Protein Interactions for the Analysis of the Associations between PM2.5 and Some Diseases. PMID:27243032
Future paradigms for precision oncology. PMID:27223079
The probability of speciation on an interaction network with unequal substitution rates. PMID:27177943
Dissecting the expression relationships between RNA-binding proteins and their cognate targets in eukaryotic post-transcriptional regulatory networks. PMID:27161996
Genome-scale prediction of moonlighting proteins using diverse protein association information. PMID:27153604
Building a glaucoma interaction network using a text mining approach. PMID:27152122
ChromNet: Learning the human chromatin network from all ENCODE ChIP-seq data. PMID:27139377
Network-Based Protein Biomarker Discovery Platforms. PMID:27103885
Quantitative Tagless Copurification: A Method to Validate and Identify Protein-Protein Interactions. PMID:27099342
Synthetic protein interactions reveal a functional map of the cell. PMID:27098839
APP Is a Context-Sensitive Regulator of the Hippocampal Presynaptic Active Zone. PMID:27092780
AuPairWise: A Method to Estimate RNA-Seq Replicability through Co-expression. PMID:27082953
Visualization of Metabolic Interaction Networks in Microbial Communities Using VisANT 5.0. PMID:27081850
Uncovering disease mechanisms through network biology in the era of Next Generation Sequencing. PMID:27080396
Pharmacometabolomics-aided Pharmacogenomics in Autoimmune Disease. PMID:27077110
Biomolecular Relationships Discovered from Biological Labyrinth and Lost in Ocean of Literature: Community Efforts Can Rescue Until Automated Artificial Intelligence Takes Over. PMID:27066067
FAM46 proteins are novel eukaryotic non-canonical poly(A) polymerases. PMID:27060136
Protein Interaction Networks Link Schizophrenia Risk Loci to Synaptic Function. PMID:27056717
A Consensus Network of Gene Regulatory Factors in the Human Frontal Lobe. PMID:27014338
Thermodynamic measures of cancer: Gibbs free energy and entropy of protein-protein interactions. PMID:27012959
A graph theoretical approach to data fusion. PMID:26992203
An integrative data analysis platform for gene set analysis and knowledge discovery in a data warehouse framework. PMID:26989145
Constitutive Negative Regulation of R Proteins in Arabidopsis also via Autophagy Related Pathway? PMID:26973696
PIPINO: A Software Package to Facilitate the Identification of Protein-Protein Interactions from Affinity Purification Mass Spectrometry Data. PMID:26966684
Trifunctional cross-linker for mapping protein-protein interaction networks and comparing protein conformational states. PMID:26952210
Involvement of Polycomb Repressive Complex 2 in Maturation of Induced Pluripotent Stem Cells during Reprogramming of Mouse and Human Fibroblasts. PMID:26938987
Key Immune Events of the Pathomechanisms of Early Cardioembolic Stroke: Multi-Database Mining and Systems Biology Approach. PMID:26927091
The human DNA ends proteome uncovers an unexpected entanglement of functional pathways. PMID:26921407
Functional Evaluations of Genes Disrupted in Patients with Tourette's Disorder. PMID:26903887
An interactive web-based application for Comprehensive Analysis of RNAi-screen Data. PMID:26902267
Comparative analysis of housekeeping and tissue-selective genes in human based on network topologies and biological properties. PMID:26897376
Constructing an integrated genetic and epigenetic cellular network for whole cellular mechanism using high-throughput next-generation sequencing data. PMID:26897165
A high definition look at the NF-Y regulome reveals genome-wide associations with selected transcription factors. PMID:26896797
Investigating the specific core genetic-and-epigenetic networks of cellular mechanisms involved in human aging in peripheral blood mononuclear cells. PMID:26895224
Binding interface change and cryptic variation in the evolution of protein-protein interactions. PMID:26892785
Protection or resection: BOD1L as a novel replication fork protection factor. PMID:26889944
Comprehensive Expression Profiling and Functional Network Analysis of p53-Regulated MicroRNAs in HepG2 Cells Treated with Doxorubicin. PMID:26886852
Using contrast patterns between true complexes and random subgraphs in PPI networks to predict unknown protein complexes. PMID:26868667
Topological characteristics of target genes regulated by abiotic-stress-responsible miRNAs in a rice interactome network. PMID:26830287
Accelerating Adverse Outcome Pathway Development Using Publicly Available Data Sources. PMID:26809562
A multiple kernel learning algorithm for drug-target interaction prediction. PMID:26801218
Lamina Associated Polypeptide 1 (LAP1) Interactome and Its Functional Features. PMID:26784240
Prediction and characterization of protein-protein interaction network in Bacillus licheniformis WX-02. PMID:26782814
Multi-omic measurement of mutually exclusive loss-of-function enriches for candidate synthetic lethal gene pairs. PMID:26781748
A Factor Graph Approach to Automated GO Annotation. PMID:26771463
Focused Analysis of Exome Sequencing Data for Rare Germline Mutations in Familial and Sporadic Lung Cancer. PMID:26762739
Systematic Phenomics Analysis Deconvolutes Genes Mutated in Intellectual Disability into Biologically Coherent Modules. PMID:26748517
Differential Occurrence of Interactions and Interaction Domains in Proteins Containing Homopolymeric Amino Acid Repeats. PMID:26734058
BioGRID: A Resource for Studying Biological Interactions in Yeast. PMID:26729913
Use of the BioGRID Database for Analysis of Yeast Protein and Genetic Interactions. PMID:26729909
Identifying novel protein phenotype annotations by hybridizing protein-protein interactions and protein sequence similarities. PMID:26728152
Scope and limitations of yeast as a model organism for studying human tissue-specific pathways. PMID:26714768
JMJD5 (Jumonji Domain-containing 5) Associates with Spindle Microtubules and Is Required for Proper Mitosis. PMID:26710852
Forward Individualized Medicine from Personal Genomes to Interactomes. PMID:26696898
Transcriptome analysis in calorie-restricted rats implicates epigenetic and post-translational mechanisms in neuroprotection and aging. PMID:26694192
Genome-Wide Analysis of the TORC1 and Osmotic Stress Signaling Network in Saccharomyces cerevisiae. PMID:26681516
A computational method for drug repositioning using publicly available gene expression data. PMID:26679199
Disentangling the multigenic and pleiotropic nature of molecular function. PMID:26678917
A deep proteomics perspective on CRM1-mediated nuclear export and nucleocytoplasmic partitioning. PMID:26673895
Integrated analysis of global proteome, phosphoproteome, and glycoproteome enables complementary interpretation of disease-related protein networks. PMID:26657352
Analysis of COPII Vesicles Indicates a Role for the Emp47-Ssp120 Complex in Transport of Cell Surface Glycoproteins. PMID:26650540
AnGeLi: A Tool for the Analysis of Gene Lists from Fission Yeast. PMID:26635866
PPIM: A Protein-Protein Interaction Database for Maize. PMID:26620522
Dominance from the perspective of gene-gene and gene-chemical interactions. PMID:26613610
The cytoplasmic peptide:N-glycanase (NGLY1) - Structure, expression and cellular functions. PMID:26611529
Evolution of disorder in Mediator complex and its functional relevance. PMID:26590257
Re-analysis of protein data reveals the germination pathway and up accumulation mechanism of cell wall hydrolases during the radicle protrusion step of seed germination in Podophyllum hexandrum- a high altitude plant. PMID:26579141
Investigation of Pathogenic Genes in Chinese sporadic Hypertrophic Cardiomyopathy Patients by Whole Exome Sequencing. PMID:26573135
Transposable elements at the center of the crossroads between embryogenesis, embryonic stem cells, reprogramming, and long non-coding RNAs. PMID:26543668
Getting the most out of RNA-seq data analysis. PMID:26539333
Inferring plant microRNA functional similarity using a weighted protein-protein interaction network. PMID:26538106
Multiple SNP Set Analysis for Genome-Wide Association Studies Through Bayesian Latent Variable Selection. PMID:26515609
A Glimpse to Background and Characteristics of Major Molecular Biological Networks. PMID:26491677
Characterization of the Cardiac Overexpression of HSPB2 Reveals Mitochondrial and Myogenic Roles Supported by a Cardiac HspB2 Interactome. PMID:26465331
Connectivity Homology Enables Inter-Species Network Models of Synthetic Lethality. PMID:26451775
PPCheck: A Webserver for the Quantitative Analysis of Protein-Protein Interfaces and Prediction of Residue Hotspots. PMID:26448684
Condition-specific genetic interaction maps reveal crosstalk between the cAMP/PKA and the HOG MAPK pathways in the activation of the general stress response. PMID:26446933
Integrated analysis of gene expression and genomic aberration data in osteosarcoma (OS). PMID:26427513
Global multiple protein-protein interaction network alignment by combining pairwise network alignments. PMID:26423128
A fast and high performance multiple data integration algorithm for identifying human disease genes. PMID:26399620
Genome-wide prediction of prokaryotic two-component system networks using a sequence-based meta-predictor. PMID:26384938
The Role of ARF6 in Biliary Atresia. PMID:26379158
Interactive Big Data Resource to Elucidate Human Immune Pathways and Diseases. PMID:26362267
Panorama of ancient metazoan macromolecular complexes. PMID:26344197
Targeting SOD1 induces synthetic lethal killing in BLM- and CHEK2-deficient colorectal cancer cells. PMID:26318585
Novel Application of Junction Trees to the Interpretation of Epigenetic Differences among Lung Cancer Subtypes. PMID:26306226
Network Modules of the Cross-Species Genotype-Phenotype Map Reflect the Clinical Severity of Human Diseases. PMID:26301634
Gene Function Prediction from Functional Association Networks Using Kernel Partial Least Squares Regression. PMID:26288239
Functional Analysis and Characterization of Differential Coexpression Networks. PMID:26282208
Distilling a Visual Network of Retinitis Pigmentosa Gene-Protein Interactions to Uncover New Disease Candidates. PMID:26267445
Computational analysis of protein interaction networks for infectious diseases. PMID:26261187
Algorithms for modeling global and context-specific functional relationship networks. PMID:26254431
Environmental Interactions and Epistasis Are Revealed in the Proteomic Responses to Complex Stimuli. PMID:26247773
Revisiting topological properties and models of protein-protein interaction networks from the perspective of dataset evolution. PMID:26243826
An Integrative Approach for Mapping Differentially Expressed Genes and Network Components Using Novel Parameters to Elucidate Key Regulatory Genes in Colorectal Cancer. PMID:26222778
Isoform-specific interactions of the von Hippel-Lindau tumor suppressor protein. PMID:26211615
Network-Based Logistic Classification with an Enhanced L 1/2 Solver Reveals Biomarker and Subnetwork Signatures for Diagnosing Lung Cancer. PMID:26185761
Acquisition of estrogen independence induces TOB1-related mechanisms supporting breast cancer cell proliferation. PMID:26165839
Transcriptomic-Wide Discovery of Direct and Indirect HuR RNA Targets in Activated CD4+ T Cells. PMID:26162078
Computational Inferences of the Functions of Alternative/Noncanonical Splice Isoforms Specific to HER2+/ER-/PR- Breast Cancers, a Chromosome 17 C-HPP Study. PMID:26147891
Arabidopsis MAS2, an Essential Gene That Encodes a Homolog of Animal NF-κ B Activating Protein, Is Involved in 45S Ribosomal DNA Silencing. PMID:26139346
α2-Macroglobulin Can Crosslink Multiple Plasmodium falciparum Erythrocyte Membrane Protein 1 (PfEMP1) Molecules and May Facilitate Adhesion of Parasitized Erythrocytes. PMID:26134405
Inference of Low and High-Grade Glioma Gene Regulatory Networks Delineates the Role of Rnd3 in Establishing Multiple Hallmarks of Cancer. PMID:26132659
Rechecking the Centrality-Lethality Rule in the Scope of Protein Subcellular Localization Interaction Networks. PMID:26115027
Self-Organizing Feature Maps Identify Proteins Critical to Learning in a Mouse Model of Down Syndrome. PMID:26111164
A computational method for clinically relevant cancer stratification and driver mutation module discovery using personal genomics profiles. PMID:26099165
Gene Expression Associated with Early and Late Chronotypes in Drosophila melanogaster. PMID:26097463
A predicted protein interactome identifies conserved global networks and disease resistance subnetworks in maize. PMID:26089837
By the company they keep: interaction networks define the binding ability of transcription factors. PMID:26089389
Biallelic Mutations in NBAS Cause Recurrent Acute Liver Failure with Onset in Infancy. PMID:26073778
Inferring orthologous gene regulatory networks using interspecies data fusion. PMID:26072515
Dietary MicroRNA Database (DMD): An Archive Database and Analytic Tool for Food-Borne microRNAs. PMID:26030752
A functional biological network centered on XRCC3: a new possible marker of chemoradiotherapy resistance in rectal cancer patients. PMID:26023803
Causal Modeling of Cancer-Stromal Communication Identifies PAPPA as a Novel Stroma-Secreted Factor Activating NFκB Signaling in Hepatocellular Carcinoma. PMID:26020769
A density-based clustering approach for identifying overlapping protein complexes with functional preferences. PMID:26013799
SPECTRA: An Integrated Knowledge Base for Comparing Tissue and Tumor-Specific PPI Networks in Human. PMID:26005672
From raw data to biological discoveries: a computational analysis pipeline for mass spectrometry-based proteomics. PMID:26002791
Evolution. Systematic humanization of yeast genes reveals conserved functions and genetic modularity. PMID:25999509
Proteomic analysis of three gonad types of swamp eel reveals genes differentially expressed during sex reversal. PMID:25985063
Reverse enGENEering of Regulatory Networks from Big Data: A Roadmap for Biologists. PMID:25983554
Dynamic network-based relevance score reveals essential proteins and functional modules in directed differentiation. PMID:25977693
NetworkAnalyst for statistical, visual and network-based meta-analysis of gene expression data. PMID:25950236
Predicting peptide-mediated interactions on a genome-wide scale. PMID:25938916
Hierarchical ensemble methods for protein function prediction. PMID:25937954
Lineage-specific sequence evolution and exon edge conservation partially explain the relationship between evolutionary rate and expression level in A. thaliana. PMID:25930165
Genetic similarity between cancers and comorbid Mendelian diseases identifies candidate driver genes. PMID:25926297
Predicting involvement of polycomb repressive complex 2 in direct conversion of mouse fibroblasts into induced neural stem cells. PMID:25890371
Identifying module biomarker in type 2 diabetes mellitus by discriminative area of functional activity. PMID:25888350
Probabilistic inference of biological networks via data integration. PMID:25874225
Genome-wide protein-protein interaction screening by protein-fragment complementation assay (PCA) in living cells. PMID:25867901
cDREM: inferring dynamic combinatorial gene regulation. PMID:25844671
Combinatorial proteomic analysis of intercellular signaling applied to the CD28 T-cell costimulatory receptor. PMID:25829543
Uncovering RNA binding proteins associated with age and gender during liver maturation. PMID:25824884
Comprehensive data resources and analytical tools for pathological association of aminoacyl tRNA synthetases with cancer. PMID:25824651
Control of cell-cell forces and collective cell dynamics by the intercellular adhesome. PMID:25812522
Proper evaluation of alignment-free network comparison methods. PMID:25810431
A hybrid computational method for the discovery of novel reproduction-related genes. PMID:25768094
Scoring Large-Scale Affinity Purification Mass Spectrometry Datasets with MiST. PMID:25754993
Characterization of the interaction between Rfa1 and Rad24 in Saccharomyces cerevisiae. PMID:25719602
Spatiotemporal 16p11.2 protein network implicates cortical late mid-fetal brain development and KCTD13-Cul3-RhoA pathway in psychiatric diseases. PMID:25695269
Data Imputation in Epistatic MAPs by Network-Guided Matrix Completion. PMID:25658751
A Comprehensive Membrane Interactome Mapping of Sho1p Reveals Fps1p as a Novel Key Player in the Regulation of the HOG Pathway in S. cerevisiae. PMID:25644660
Comparison of human cell signaling pathway databases--evolution, drawbacks and challenges. PMID:25632107
Database of Gene Co-Regulation (dGCR): A Web Tool for Analysing Patterns of Gene Co-regulation across Publicly Available Expression Data. PMID:25628763
Protein folding and binding can emerge as evolutionary spandrels through structural coupling. PMID:25624494
Computational deconvolution of genome wide expression data from Parkinson's and Huntington's disease brain tissues using population-specific expression analysis. PMID:25620908
Ror2 as a therapeutic target in cancer. PMID:25614331
Topology-function conservation in protein-protein interaction networks. PMID:25609797
Proteomic analyses reveal distinct chromatin-associated and soluble transcription factor complexes. PMID:25609649
Robustness analysis on interspecies interaction network for iron and glucose competition between Candida albicans and zebrafish during infection. PMID:25603810
Properties of sparse penalties on inferring gene regulatory networks from time-course gene expression data. PMID:25569860
Application of quantitative trait locus mapping and transcriptomics to studies of the senescence-accelerated phenotype in rats. PMID:25563673
Pathway mapping and development of disease-specific biomarkers: protein-based network biomarkers. PMID:25560835
Identifying cooperative transcription factors in yeast using multiple data sources. PMID:25559499
Altered Transcriptional Control Networks with Trans-Differentiation of Isogenic Mutant-KRas NSCLC Models. PMID:25538889
Locus heterogeneity disease genes encode proteins with high interconnectivity in the human protein interaction network. PMID:25538735
Multitask learning of signaling and regulatory networks with application to studying human response to flu. PMID:25522349
MicroRNA Dysregulation, Gene Networks, and Risk for Schizophrenia in 22q11.2 Deletion Syndrome. PMID:25484875
Dynamics of re-constitution of the human nuclear proteome after cell division is regulated by NLS-adjacent phosphorylation. PMID:25483092
OntoGene web services for biomedical text mining. PMID:25472638
ModuleBlast: identifying activated sub-networks within and across species. PMID:25428368
Community structure detection for overlapping modules through mathematical programming in protein interaction networks. PMID:25412367
Pathway connectivity and signaling coordination in the yeast stress-activated signaling network. PMID:25411400
Protein interaction networks reveal novel autism risk genes within GWAS statistical noise. PMID:25409314
A least square method based model for identifying protein complexes in protein-protein interaction network. PMID:25405206
A systems biology strategy to identify molecular mechanisms of action and protein indicators of traumatic brain injury. PMID:25399920
β-CateninC429S mice exhibit sterility consequent to spatiotemporally sustained Wnt signalling in the internal genitalia. PMID:25376241
Identification of SUMO-2/3-modified proteins associated with mitotic chromosomes. PMID:25367092
From molecular signatures to predictive biomarkers: modeling disease pathophysiology and drug mechanism of action. PMID:25364744
Prediction of disease-related genes based on weighted tissue-specific networks by using DNA methylation. PMID:25350763
A group LASSO-based method for robustly inferring gene regulatory networks from multiple time-course datasets. PMID:25350697
Integrating PPI datasets with the PPI data from biomedical literature for protein complex detection. PMID:25350598
Identifying disease genes by integrating multiple data sources. PMID:25350511
MitProNet: A knowledgebase and analysis platform of proteome, interactome and diseases for mammalian mitochondria. PMID:25347823
Identifying roles of "Jun-Chen-Zuo-Shi" component herbs of QiShenYiQi formula in treating acute myocardial ischemia by network pharmacology. PMID:25342960
The role of TGF-β signaling and apoptosis in innate and adaptive immunity in zebrafish: a systems biology approach. PMID:25341656
GroupRank: rank candidate genes in PPI network by differentially expressed gene groups. PMID:25330105
Yeast systems biology: our best shot at modeling a cell. PMID:25316779
The Hsp90-dependent proteome is conserved and enriched for hub proteins with high levels of protein-protein connectivity. PMID:25316598
Enhancing the functional content of eukaryotic protein interaction networks. PMID:25275489
Hope for GWAS: relevant risk genes uncovered from GWAS statistical noise. PMID:25268625
Collaborative mining and interpretation of large-scale data for biomedical research insights. PMID:25268270
Interactions Among Plant Transcription Factors Regulating Expression of Stress-responsive Genes. PMID:25249757
Predicting disease associations via biological network analysis. PMID:25228247
Systems cell biology. PMID:25225336
Pulsatile dynamics in the yeast proteome. PMID:25220054
Global analysis of protein aggregation in yeast during physiological conditions and arsenite stress. PMID:25217615
Human Tra2 proteins jointly control a CHEK1 splicing switch among alternative and constitutive target exons. PMID:25208576
Pvr expression regulators in equilibrium signal control and maintenance of Drosophila blood progenitors. PMID:25201876
Transcriptome sequencing of a large human family identifies the impact of rare noncoding variants. PMID:25192044
Controlled sumoylation of the mevalonate pathway enzyme HMGS-1 regulates metabolism during aging. PMID:25187565
Construction and analysis of the protein-protein interaction networks based on gene expression profiles of Parkinson's disease. PMID:25170921
TEMPI: probabilistic modeling time-evolving differential PPI networks with multiPle information. PMID:25161233
The genomic landscape of compensatory evolution. PMID:25157590
The exocyst and regulatory GTPases in urinary exosomes. PMID:25138791
From pathways to networks: connecting dots by establishing protein-protein interaction networks in signaling pathways using affinity purification and mass spectrometry. PMID:25137225
A novel mutation in VCP causes Charcot-Marie-Tooth Type 2 disease. PMID:25125609
A systems biology approach identified different regulatory networks targeted by KSHV miR-K12-11 in B cells and endothelial cells. PMID:25106478
A system based network approach to ethanol tolerance in Saccharomyces cerevisiae. PMID:25103914
Phen-Gen: combining phenotype and genotype to analyze rare disorders. PMID:25086502
Integration of proteomic and transcriptomic profiles identifies a novel PDGF-MYC network in human smooth muscle cells. PMID:25080971
Integrative analysis reveals disease-associated genes and biomarkers for prostate cancer progression. PMID:25080090
Finding pathway-modulating genes from a novel Ontology Fingerprint-derived gene network. PMID:25063300
Proteome-wide analysis of human disease mutations in short linear motifs: neglected players in cancer? PMID:25057855
Bioinformatic analysis of proteomics data. PMID:25033288
DBSecSys: a database of Burkholderia mallei secretion systems. PMID:25030112
Gene network-based analysis identifies two potential subtypes of small intestinal neuroendocrine tumors. PMID:25023465
Network-based analysis identifies epigenetic biomarkers of esophageal squamous cell carcinoma progression. PMID:25015989
Brefeldin A-inhibited guanine nucleotide-exchange protein 3 (BIG3) is predicted to interact with its partner through an ARM-type α-helical structure. PMID:24997568
Proteogenomic convergence for understanding cancer pathways and networks. PMID:24994965
Minimal metabolic pathway structure is consistent with associated biomolecular interactions. PMID:24987116
Systems biology in the context of big data and networks. PMID:24982882
Correlating information contents of gene ontology terms to infer semantic similarity of gene products. PMID:24963342
Homology-based prediction of interactions between proteins using Averaged One-Dependence Estimators. PMID:24953126
Proteomics analysis of the non-muscle myosin heavy chain IIa-enriched actin-myosin complex reveals multiple functions within the podocyte. PMID:24949636
IIS--Integrated Interactome System: a web-based platform for the annotation, analysis and visualization of protein-metabolite-gene-drug interactions by integrating a variety of data sources and tools. PMID:24949626
Detecting protein complexes in protein interaction networks using a ranking algorithm with a refined merging procedure. PMID:24944073
Scale-space measures for graph topology link protein network architecture to function. PMID:24931989
DrugComboRanker: drug combination discovery based on target network analysis. PMID:24931988
New directions for diffusion-based network prediction of protein function: incorporating pathways with confidence. PMID:24931987
Network-dosage compensation topologies as recurrent network motifs in natural gene networks. PMID:24929807
On the crucial cerebellar wound healing-related pathways and their cross-talks after traumatic brain injury in Danio rerio. PMID:24926785
Alterations in the cerebellar (Phospho)proteome of a cyclic guanosine monophosphate (cGMP)-dependent protein kinase knockout mouse. PMID:24925903
GASOLINE: a Greedy And Stochastic algorithm for optimal Local multiple alignment of Interaction NEtworks. PMID:24911103
Genome-wide survey of tissue-specific microRNA and transcription factor regulatory networks in 12 tissues. PMID:24889152
TGF-β stimulation in human and murine cells reveals commonly affected biological processes and pathways at transcription level. PMID:24886091
The Index-based Subgraph Matching Algorithm with General Symmetries (ISMAGS): exploiting symmetry for faster subgraph enumeration. PMID:24879305
Poly (ADP-ribose) in the pathogenesis of Parkinson's disease. PMID:24874851
Inferring host gene subnetworks involved in viral replication. PMID:24874113
Insights from cerebellar transcriptomic analysis into the pathogenesis of ataxia. PMID:24862029
Analysis pipeline for the epistasis search - statistical versus biological filtering. PMID:24817878
Controllability in protein interaction networks. PMID:24778220
Prediction and experimental characterization of nsSNPs altering human PDZ-binding motifs. PMID:24722214
Systems biology as an integrated platform for bioinformatics, systems synthetic biology, and systems metabolic engineering. PMID:24709875
Protein-protein interaction detection: methods and analysis. PMID:24693427
Global quantitative modeling of chromatin factor interactions. PMID:24675896
Plant systems biology: insights, advances and challenges. PMID:24671625
Improving protein function prediction using domain and protein complexes in PPI networks. PMID:24655481
Synthetic cytotoxicity: digenic interactions with TEL1/ATM mutations reveal sensitivity to low doses of camptothecin. PMID:24653001
Detecting overlapping protein complexes by rough-fuzzy clustering in protein-protein interaction networks. PMID:24642838
REIL proteins of Arabidopsis thaliana interact in yeast-2-hybrid assays with homologs of the yeast Rlp24, Rpl24A, Rlp24B, Arx1, and Jjj1 proteins. PMID:24603461
DAWN: a framework to identify autism genes and subnetworks using gene expression and genetics. PMID:24602502
Family-based analysis identified CD2 as a susceptibility gene for primary open angle glaucoma in Chinese Han population. PMID:24597656
Inferring regulatory networks by combining perturbation screens and steady state gene expression profiles. PMID:24586224
Integrative analysis of many RNA-seq datasets to study alternative splicing. PMID:24583115
Computational prediction of the human-microbial oral interactome. PMID:24576332
Inferring functional transcription factor-gene binding pairs by integrating transcription factor binding data with transcription factor knockout data. PMID:24565265
Corbi: a new R package for biological network alignment and querying. PMID:24565104
Conceptualization of molecular findings by mining gene annotations. PMID:24564884
Prediction of heterotrimeric protein complexes by two-phase learning using neighboring kernels. PMID:24564744
Molecular pathway identification using biological network-regularized logistic models. PMID:24564637
PLW: Probabilistic Local Walks for detecting protein complexes from protein interaction networks. PMID:24564427
Modulation of gene expression regulated by the transcription factor NF-κB/RelA. PMID:24523406
Computational developments in microRNA-regulated protein-protein interactions. PMID:24507415
Increased expression of c-Jun in nonalcoholic fatty liver disease. PMID:24492282
Identifying driver mutations in sequenced cancer genomes: computational approaches to enable precision medicine. PMID:24479672
A comparative study of Whi5 and retinoblastoma proteins: from sequence and structure analysis to intracellular networks. PMID:24478706
Identification of human disease genes from interactome network using graphlet interaction. PMID:24465923
Review of biological network data and its applications. PMID:24465231
Characterizing and controlling the inflammatory network during influenza A virus infection. PMID:24445954
A protein profile of visceral adipose tissues linked to early pathogenesis of type 2 diabetes mellitus. PMID:24403596
Computational Prediction of Protein-Protein Interaction Networks: Algo-rithms and Resources. PMID:24396273
Protein interaction network for Alzheimer's disease using computational approach. PMID:24391359
Protein complex identification by integrating protein-protein interaction evidence from multiple sources. PMID:24386289
Systems biology approach to stage-wise characterization of epigenetic genes in lung adenocarcinoma. PMID:24369052
Chemical genetics of rapamycin-insensitive TORC2 in S. cerevisiae. PMID:24360963
Discovering implicit entity relation with the gene-citation-gene network. PMID:24358368
Predicting protein-protein interaction by the mirrortree method: possibilities and limitations. PMID:24349035
Identification of unstable network modules reveals disease modules associated with the progression of Alzheimer's disease. PMID:24348898
Establishing an osteosarcoma associated protein-protein interaction network to explore the pathogenesis of osteosarcoma. PMID:24330838
Network analysis of GWAS data. PMID:24287332
Integrative functional genomic analyses implicate specific molecular pathways and circuits in autism. PMID:24267887
Dynamic trans-acting factor colocalization in human cells. PMID:24243024
Evolutionary rate patterns of genes involved in the Drosophila Toll and Imd signaling pathway. PMID:24209511
Synthetic genetic targeting of genome instability in cancer. PMID:24202319
Network cluster analysis of protein-protein interaction network identified biomarker for early onset colorectal cancer. PMID:24197691
Going the distance for protein function prediction: a new distance metric for protein interaction networks. PMID:24194834
Mutations in the gene encoding IFT dynein complex component WDR34 cause Jeune asphyxiating thoracic dystrophy. PMID:24183451
Cumulative haploinsufficiency and triplosensitivity drive aneuploidy patterns and shape the cancer genome. PMID:24183448
Methods and approaches in the topology-based analysis of biological pathways. PMID:24133454
Mass spectrometry coupled experiments and protein structure modeling methods. PMID:24132151
Intrinsically disordered regions in autophagy proteins. PMID:24115198
A sampling framework for incorporating quantitative mass spectrometry data in protein interaction analysis. PMID:24093595
Reconstruction of the experimentally supported human protein interactome: what can we learn? PMID:24088582
Functional module identification in protein interaction networks by interaction patterns. PMID:24085567
Using PPI network autocorrelation in hierarchical multi-label classification trees for gene function prediction. PMID:24070402
Clustering based on multiple biological information: approach for predicting protein complexes. PMID:24067423
JunD/AP1 regulatory network analysis during macrophage activation in a rat model of crescentic glomerulonephritis. PMID:24053712
Evolution after whole-genome duplication: a network perspective. PMID:24048644
Characterization and prediction of haploinsufficiency using systems-level gene properties in yeast. PMID:24048642
Integrative approaches for finding modular structure in biological networks. PMID:24045689
Horizontal gene transfer in osmotrophs: playing with public goods. PMID:24018383
Inferring the effective TOR-dependent network: a computational study in yeast. PMID:24005029
Interspecies protein-protein interaction network construction for characterization of host-pathogen interactions: a Candida albicans-zebrafish interaction study. PMID:23947337
Discovery of cell-type specific regulatory elements in the human genome using differential chromatin modification analysis. PMID:23945931
A miniaturized chemical proteomic approach for target profiling of clinical kinase inhibitors in tumor biopsies. PMID:23901793
Identification of yeast cell cycle regulated genes based on genomic features. PMID:23895232
Inferring potential microRNA-microRNA associations based on targeting propensity and connectivity in the context of protein interaction network. PMID:23874989
Mining differential top-k co-expression patterns from time course comparative gene expression datasets. PMID:23870110
Identification of Novel Stress Granule Components That Are Involved in Nuclear Transport. PMID:23826389
Genome-Wide Responses of Female Fruit Flies Subjected to Divergent Mating Regimes. PMID:23826372
Towards systematic discovery of signaling networks in budding yeast filamentous growth stress response using interventional phosphorylation data. PMID:23825934
CHD@ZJU: a knowledgebase providing network-based research platform on coronary heart disease. PMID:23818526
Identifying proteins controlling key disease signaling pathways. PMID:23812988
PIMiner: a web tool for extraction of protein interactions from biomedical literature. PMID:23798227
Prediction of heterodimeric protein complexes from weighted protein-protein interaction networks using novel features and kernel functions. PMID:23776458
The functional interactome landscape of the human histone deacetylase family. PMID:23752268
Passing messages between biological networks to refine predicted interactions. PMID:23741402
A network pharmacology approach to evaluating the efficacy of chinese medicine using genome-wide transcriptional expression data. PMID:23737854
Protein complex detection using interaction reliability assessment and weighted clustering coefficient. PMID:23688127
Structure and non-structure of centrosomal proteins. PMID:23671615
Interfacing cellular networks of S. cerevisiae and E. coli: connecting dynamic and genetic information. PMID:23663484
Modular biological function is most effectively captured by combining molecular interaction data types. PMID:23658761
Protein complex detection via weighted ensemble clustering based on Bayesian nonnegative matrix factorization. PMID:23658709
The role of protein interactions in mediating essentiality and synthetic lethality. PMID:23638160
Bioinformatics analysis identify novel OB fold protein coding genes in C. elegans. PMID:23638006
Systematic analysis of experimental phenotype data reveals gene functions. PMID:23626672
The index-based subgraph matching algorithm (ISMA): fast subgraph enumeration in large networks using optimized search trees. PMID:23620730
Evolutionary capacitance and control of protein stability in protein-protein interaction networks. PMID:23592969
Function relaxation followed by diversifying selection after whole-genome duplication in flowering plants. PMID:23580595
Improved method for protein complex detection using bottleneck proteins. PMID:23566214
t-LSE: a novel robust geometric approach for modeling protein-protein interaction networks. PMID:23560036
The potential of text mining in data integration and network biology for plant research: a case study on Arabidopsis. PMID:23532071
Copy-number variation of cancer-gene orthologs is sufficient to induce cancer-like symptoms in Saccharomyces cerevisiae. PMID:23531409
Parametric Bayesian priors and better choice of negative examples improve protein function prediction. PMID:23511543
Interpretation of genomic variants using a unified biological network approach. PMID:23505346
Novel semantic similarity measure improves an integrative approach to predicting gene functional associations. PMID:23497449
A role for the nucleoporin Nup170p in chromatin structure and gene silencing. PMID:23452847
Neurodevelopmental and neuropsychiatric disorders represent an interconnected molecular system. PMID:23439483
From hub proteins to hub modules: the relationship between essentiality and centrality in the yeast interactome at different scales of organization. PMID:23436988
Proteome-wide prediction of self-interacting proteins based on multiple properties. PMID:23422585
Genome-wide analysis of LXRα activation reveals new transcriptional networks in human atherosclerotic foam cells. PMID:23393188
SNPranker 2.0: a gene-centric data mining tool for diseases associated SNP prioritization in GWAS. PMID:23369106
FitSearch: a robust way to interpret a yeast fitness profile in terms of drug's mode-of-action. PMID:23368702
Visual data mining of biological networks: one size does not fit all. PMID:23341759
A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis. PMID:23334424
Synthetic lethality and cancer: cohesin and PARP at the replication fork. PMID:23333522
mirTarPri: improved prioritization of microRNA targets through incorporation of functional genomics data. PMID:23326485
An RS motif within the Epstein-Barr virus BLRF2 tegument protein is phosphorylated by SRPK2 and is important for viral replication. PMID:23326445
Using graph models to find transcription factor modules: the hitting set problem and an exact algorithm. PMID:23324335
Disentangling function from topology to infer the network properties of disease genes. PMID:23324116
A ceRNA analysis on LMNA gene focusing on the Hutchinson-Gilford progeria syndrome. PMID:23317481
Transcriptome-wide expansion of non-coding regulatory switches: evidence from co-occurrence of Alu exonization, antisense and editing. PMID:23303787
Transcriptional program of ciliated epithelial cells reveals new cilium and centrosome components and links to human disease. PMID:23300604
Inferring the Brassica rapa Interactome Using Protein-Protein Interaction Data from Arabidopsis thaliana. PMID:23293649
Labeling nodes using three degrees of propagation. PMID:23284828
Genes contributing to pain sensitivity in the normal population: an exome sequencing study. PMID:23284290
A systems approach to rheumatoid arthritis. PMID:23240033
FoxO6 regulates memory consolidation and synaptic function. PMID:23222102
Mitotic exit and separation of mother and daughter cells. PMID:23212898
Identifying complexes from protein interaction networks according to different types of neighborhood density. PMID:23210476
Wiki-pi: a web-server of annotated human protein-protein interactions to aid in discovery of protein function. PMID:23209562
Biological databases for behavioral neurobiology. PMID:23195119
PrePPI: a structure-informed database of protein-protein interactions. PMID:23193263
Visual analysis of transcriptome data in the context of anatomical structures and biological networks. PMID:23162564
High-resolution genome-wide scan of genes, gene-networks and cellular systems impacting the yeast ionome. PMID:23151179
DLocalMotif: a discriminative approach for discovering local motifs in protein sequences. PMID:23142965
Bioinformatic identification of genes suppressing genome instability. PMID:23129647
Insights into the evolutionary features of human neurodegenerative diseases. PMID:23118989
Knowledge building insights on biomarkers of arsenic toxicity to keratinocytes and melanocytes. PMID:23115478
Systems analysis of plant functional, transcriptional, physical interaction, and metabolic networks. PMID:23110892
Linkers of cell polarity and cell cycle regulation in the fission yeast protein interaction network. PMID:23093924
Linking the signaling cascades and dynamic regulatory networks controlling stress responses. PMID:23064748
Bayesian correlated clustering to integrate multiple datasets. PMID:23047558
Ranking relations between diseases, drugs and genes for a curation task. PMID:23046495
Taxonomies of networks from community structure. PMID:23030977
Multi-edge gene set networks reveal novel insights into global relationships between biological themes. PMID:23028852
What evidence is there for the homology of protein-protein interactions? PMID:23028270
Protein stickiness, rather than number of functional protein-protein interactions, predicts expression noise and plasticity in yeast. PMID:23017156
A simple knowledge-based mining method for exploring hidden key molecules in a human biomolecular network. PMID:22979956
Fungal Hsp90: a biological transistor that tunes cellular outputs to thermal inputs. PMID:22976491
An integrated approach to identify causal network modules of complex diseases with application to colorectal cancer. PMID:22967703
ReLiance: a machine learning and literature-based prioritization of receptor--ligand pairings. PMID:22962483
A network-based maximum link approach towards MS identifies potentially important roles for undetected ARRB1/2 and ACTB in liver cancer progression. PMID:22961449
Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors. PMID:22955990
A computational framework for boosting confidence in high-throughput protein-protein interaction datasets. PMID:22937800
Exploring overlapping functional units with various structure in protein interaction networks. PMID:22916212
Identification of a complex genetic network underlying Saccharomyces cerevisiae colony morphology. PMID:22882838
NEXCADE: perturbation analysis for complex networks. PMID:22870252
Robust co-regulation of tyrosine phosphorylation sites on proteins reveals novel protein interactions. PMID:22851037
Identifying responsive modules by mathematical programming: an application to budding yeast cell cycle. PMID:22848637
One Hand Clapping: detection of condition-specific transcription factor interactions from genome-wide gene activity data. PMID:22844089
Subnetwork-based analysis of chronic lymphocytic leukemia identifies pathways that associate with disease progression. PMID:22837534
Sets2Networks: network inference from repeated observations of sets. PMID:22824380
A strategy based on protein-protein interface motifs may help in identifying drug off-targets. PMID:22817115
Integration of biological networks and pathways with genetic association studies. PMID:22777728
In-silico identification of phenotype-biased functional modules. PMID:22759578
Predicting multiplex subcellular localization of proteins using protein-protein interaction network: a comparative study. PMID:22759426
Minimalist ensemble algorithms for genome-wide protein localization prediction. PMID:22759391
Conserved rules govern genetic interaction degree across species. PMID:22747640
MC EMiNEM maps the interaction landscape of the Mediator. PMID:22737066
Proteome-wide prediction of protein-protein interactions from high-throughput data. PMID:22729399
Network analysis identifies a putative role for the PPAR and type 1 interferon pathways in glucocorticoid actions in asthmatics. PMID:22713245
Algorithm to identify frequent coupled modules from two-layered network series: application to study transcription and splicing coupling. PMID:22697243
Tackling drought stress: receptor-like kinases present new approaches. PMID:22693282
Cancer core modules identification through genomic and transcriptomic changes correlation detection at network level. PMID:22691569
A single source k-shortest paths algorithm to infer regulatory pathways in a gene network. PMID:22689778
How networks change with time. PMID:22689777
Genome-wide functional profiling identifies genes and processes important for zinc-limited growth of Saccharomyces cerevisiae. PMID:22685415
Identification of novel ATP13A2 interactors and their role in α-synuclein misfolding and toxicity. PMID:22645275
DroPNet: a web portal for integrated analysis of Drosophila protein-protein interaction networks. PMID:22641854
High-throughput analysis of peptide-binding modules. PMID:22610655
Mycobacterium tuberculosis and Clostridium difficille interactomes: demonstration of rapid development of computational system for bacterial interactome prediction. PMID:22587966
Inferring high-confidence human protein-protein interactions. PMID:22558947
LDGIdb: a database of gene interactions inferred from long-range strong linkage disequilibrium between pairs of SNPs. PMID:22551073
Revisiting the variation of clustering coefficient of biological networks suggests new modular structure. PMID:22548803
A comparative analysis of protein targets of withdrawn cardiovascular drugs in human and mouse. PMID:22548699
A framework for mapping, visualisation and automatic model creation of signal-transduction networks. PMID:22531118
Functional organization and its implication in evolution of the human protein-protein interaction network. PMID:22530615
Prediction of phenotype-associated genes via a cellular network approach: a Candida albicans infection case study. PMID:22509408
Network- and attribute-based classifiers can prioritize genes and pathways for autism spectrum disorders and intellectual disability. PMID:22499558
The functions of Mediator in Candida albicans support a role in shaping species-specific gene expression. PMID:22496666
Context-specific protein network miner--an online system for exploring context-specific protein interaction networks from the literature. PMID:22493694
Drug target prediction based on the herbs components: the study on the multitargets pharmacological mechanism of qishenkeli acting on the coronary heart disease. PMID:22474514
Interactomic and pharmacological insights on human sirt-1. PMID:22470339
A stochastic model for the development of Bateson-Dobzhansky-Muller incompatibilities that incorporates protein interaction networks. PMID:22465838
High accordance in prognosis prediction of colorectal cancer across independent datasets by multi-gene module expression profiles. PMID:22438977
Coordination of the transcriptome and metabolome by the circadian clock. PMID:22431615
Detecting overlapping protein complexes in protein-protein interaction networks. PMID:22426491
Chaperones divide yeast proteins into classes of expression level and evolutionary rate. PMID:22417914
Crosstalk between transcription factors and microRNAs in human protein interaction network. PMID:22413876
Sirtuins as regulators of the yeast metabolic network. PMID:22408620
A study on promoter characteristics of head-to-head genes in Saccharomyces cerevisiae. PMID:22369481
Prioritizing disease candidate genes by a gene interconnectedness-based approach. PMID:22369140
SAINT-MS1: protein-protein interaction scoring using label-free intensity data in affinity purification-mass spectrometry experiments. PMID:22352807
ANAP: an integrated knowledge base for Arabidopsis protein interaction network analysis. PMID:22345505
Integrating the Alzheimer's disease proteome and transcriptome: a comprehensive network model of a complex disease. PMID:22321014
Identifying gene interaction networks. PMID:22307715
Functional wiring of the yeast kinome revealed by global analysis of genetic network motifs. PMID:22282571
IMID: integrated molecular interaction database. PMID:22238258
A searchable cross-platform gene expression database reveals connections between drug treatments and disease. PMID:22233519
Mass spectrometry-based proteomics: qualitative identification to activity-based protein profiling. PMID:22231900
A network-based approach on elucidating the multi-faceted nature of chronological aging in S. cerevisiae. PMID:22216232
Modeling community-wide molecular networks of multicellular systems. PMID:22210865
MotifMap: integrative genome-wide maps of regulatory motif sites for model species. PMID:22208852
Global landscape of HIV-human protein complexes. PMID:22190034
Which clustering algorithm is better for predicting protein complexes? PMID:22185599
Antibody colocalization microarray: a scalable technology for multiplex protein analysis in complex samples. PMID:22171321
Constructing a robust protein-protein interaction network by integrating multiple public databases. PMID:22165958
Protein complex detection with semi-supervised learning in protein interaction networks. PMID:22165896
Decomposing PPI networks for complex discovery. PMID:22165860
Advances in omics and bioinformatics tools for systems analyses of plant functions. PMID:22156726
Detection of interaction articles and experimental methods in biomedical literature. PMID:22151872
Simple and efficient machine learning frameworks for identifying protein-protein interaction relevant articles and experimental methods used to study the interactions. PMID:22151701
Heterozygous yeast deletion collection screens reveal essential targets of Hsp90. PMID:22140548
Identification of dysfunctional modules and disease genes in congenital heart disease by a network-based approach. PMID:22136190
Multiple means to the same end: the genetic basis of acquired stress resistance in yeast. PMID:22102822
Biochemical and computational analysis of LNX1 interacting proteins. PMID:22087225
Construction of regulatory networks using expression time-series data of a genotyped population. PMID:22084118
Genome-wide analysis of chromatin features identifies histone modification sensitive and insensitive yeast transcription factors. PMID:22060676
Computationally efficient measure of topological redundancy of biological and social networks. PMID:22060466
Identification of common and cell type specific LXXLL motif EcR cofactors using a bioinformatics refined candidate RNAi screen in Drosophila melanogaster cell lines. PMID:22050674
PomBase: a comprehensive online resource for fission yeast. PMID:22039153
Proteomic and functional genomic landscape of receptor tyrosine kinase and ras to extracellular signal-regulated kinase signaling. PMID:22028469
An in silico approach combined with in vivo experiments enables the identification of a new protein whose overexpression can compensate for specific respiratory defects in Saccharomyces cerevisiae. PMID:22027258
Learning cellular sorting pathways using protein interactions and sequence motifs. PMID:21999284
Copy-number variation: the balance between gene dosage and expression in Drosophila melanogaster. PMID:21979154
iRefScape. A Cytoscape plug-in for visualization and data mining of protein interaction data from iRefIndex. PMID:21975162
Aconitase regulation of erythropoiesis correlates with a novel licensing function in erythropoietin-induced ERK signaling. PMID:21887333
Inferring mechanisms of compensation from E-MAP and SGA data using local search algorithms for max cut. PMID:21882903
Biological interaction networks are conserved at the module level. PMID:21861884
Application of computational systems biology to explore environmental toxicity hazards. PMID:21846611
Conserved and differential gene interactions in dynamical biological systems. PMID:21840874
Computational simulations to predict creatine kinase-associated factors: protein-protein interaction studies of brain and muscle types of creatine kinases. PMID:21826261
NETGEM: Network Embedded Temporal GEnerative Model for gene expression data. PMID:21824426
Computational approach to identify enzymes that are potential therapeutic candidates for psoriasis. PMID:21822480
Differential C3NET reveals disease networks of direct physical interactions. PMID:21777411
Fine-tuning of the Msn2/4-mediated yeast stress responses as revealed by systematic deletion of Msn2/4 partners. PMID:21757539
Reactome pathway analysis to enrich biological discovery in proteomics data sets. PMID:21751369
A novel method to identify cooperative functional modules: study of module coordination in the Saccharomyces cerevisiae cell cycle. PMID:21749690
Integrated bio-entity network: a system for biological knowledge discovery. PMID:21738677
InterMitoBase: an annotated database and analysis platform of protein-protein interactions for human mitochondria. PMID:21718467
Proteomic patterns of cervical cancer cell lines, a network perspective. PMID:21696634
BioGraph: unsupervised biomedical knowledge discovery via automated hypothesis generation. PMID:21696594
Integrative computational biology for cancer research. PMID:21691773
Generative probabilistic models for protein-protein interaction networks--the biclique perspective. PMID:21685063
Noise reduction in protein-protein interaction graphs by the implementation of a novel weighting scheme. PMID:21679454
Repression of mitochondrial translation, respiration and a metabolic cycle-regulated gene, SLF1, by the yeast Pumilio-family protein Puf3p. PMID:21655263
A network of SCOP hidden Markov models and its analysis. PMID:21635719
A gene-phenotype network for the laboratory mouse and its implications for systematic phenotyping. PMID:21625554
MINE: Module Identification in Networks. PMID:21605434
Plasmodium falciparum enolase complements yeast enolase functions and associates with the parasite food vacuole. PMID:21600245
Evidence for the additions of clustered interacting nodes during the evolution of protein interaction networks from network motifs. PMID:21595981
Meta analysis of Chronic Fatigue Syndrome through integration of clinical, gene expression, SNP and proteomic data. PMID:21584188
PRIN: a predicted rice interactome network. PMID:21575196
Protein annotation from protein interaction networks and Gene Ontology. PMID:21571095
Computational integration of homolog and pathway gene module expression reveals general stemness signatures. PMID:21559491
Using graph theory to analyze biological networks. PMID:21527005
A quantitative literature-curated gold standard for kinase-substrate pairs. PMID:21492431
The synthetic genetic interaction network reveals small molecules that target specific pathways in Sacchromyces cerevisiae. PMID:21487606
The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods. PMID:21472436
Diverse protein kinase interactions identified by protein microarrays reveal novel connections between cellular processes. PMID:21460040
Computational study of associations between histone modification and protein-DNA binding in yeast genome by integrating diverse information. PMID:21457549
The CRIT framework for identifying cross patterns in systems biology and application to chemogenomics. PMID:21453526
The predicted Arabidopsis interactome resource and network topology-based systems biology analyses. PMID:21441435
Quantitative maps of genetic interactions in yeast - comparative evaluation and integrative analysis. PMID:21435228
Customizable views on semantically integrated networks for systems biology. PMID:21414991
Network-based pipeline for analyzing MS data: an application toward liver cancer. PMID:21410269
TargetMine, an integrated data warehouse for candidate gene prioritisation and target discovery. PMID:21408081
A probabilistic model of nuclear import of proteins. PMID:21372083
Topology of protein interaction network shapes protein abundances and strengths of their functional and nonspecific interactions. PMID:21368118
Connectedness of PPI network neighborhoods identifies regulatory hub proteins. PMID:21367871
Histoplasma capsulatum heat-shock 60 orchestrates the adaptation of the fungus to temperature stress. PMID:21347364
Resolving the structure of interactomes with hierarchical agglomerative clustering. PMID:21342576
Integrating multiple protein-protein interaction networks to prioritize disease genes: a Bayesian regression approach. PMID:21342540
Dengue-2 structural proteins associate with human proteins to produce a coagulation and innate immune response biased interactome. PMID:21281507
HTSanalyzeR: an R/Bioconductor package for integrated network analysis of high-throughput screens. PMID:21258062
Measuring the evolutionary rewiring of biological networks. PMID:21253555
Proteomic snapshot of the EGF-induced ubiquitin network. PMID:21245847
Context-dependent transcriptional regulations between signal transduction pathways. PMID:21232126
A network-based biomarker approach for molecular investigation and diagnosis of lung cancer. PMID:21211025
Large-scale discovery and characterization of protein regulatory motifs in eukaryotes. PMID:21206902
Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast. PMID:21206491
Reconstruction of protein-protein interaction network of insulin signaling in Homo sapiens. PMID:21197403
Integrated functional networks of process, tissue, and developmental stage specific interactions in Arabidopsis thaliana. PMID:21194434
SIDEKICK: Genomic data driven analysis and decision-making framework. PMID:21192813
Literature curation of protein interactions: measuring agreement across major public databases. PMID:21183497
The Protein Information and Property Explorer 2: gaggle-like exploration of biological proteomic data within one webpage. PMID:21182202
Defining the budding yeast chromatin-associated interactome. PMID:21179020
New insights into protein-protein interaction data lead to increased estimates of the S. cerevisiae interactome size. PMID:21176124
Combining modularity, conservation, and interactions of proteins significantly increases precision and coverage of protein function prediction. PMID:21171995
PETALS: Proteomic Evaluation and Topological Analysis of a mutated Locus' Signaling. PMID:21144021
iWRAP: An interface threading approach with application to prediction of cancer-related protein-protein interactions. PMID:21130772
Global analysis of phase locking in gene expression during cell cycle: the potential in network modeling. PMID:21129191
A computational approach to analyze the mechanism of action of the kinase inhibitor bafetinib. PMID:21124949
Modeling contaminants in AP-MS/MS experiments. PMID:21117706
Discovering pathways by orienting edges in protein interaction networks. PMID:21109539
Integrating diverse biological and computational sources for reliable protein-protein interactions. PMID:21106130
An improved method for scoring protein-protein interactions using semantic similarity within the gene ontology. PMID:21078182
Concept and application of a computational vaccinology workflow. PMID:21067549
CPLA 1.0: an integrated database of protein lysine acetylation. PMID:21059677
Module discovery by exhaustive search for densely connected, co-expressed regions in biomolecular interaction networks. PMID:21049092
Predicting gene function using few positive examples and unlabeled ones. PMID:21047378
Pif1- and Exo1-dependent nucleases coordinate checkpoint activation following telomere uncapping. PMID:21045806
CADgene: a comprehensive database for coronary artery disease genes. PMID:21045063
Discover protein complexes in protein-protein interaction networks using parametric local modularity. PMID:20958996
PAIR: the predicted Arabidopsis interactome resource. PMID:20952401
Dynamic functional modules in co-expressed protein interaction networks of dilated cardiomyopathy. PMID:20950417
iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence. PMID:20940177
Examination of the relationship between essential genes in PPI network and hub proteins in reverse nearest neighbor topology. PMID:20939873
ChemProt: a disease chemical biology database. PMID:20935044
Toward a complete in silico, multi-layered embryonic stem cell regulatory network. PMID:20890967
A QUICK screen for Lrrk2 interaction partners--leucine-rich repeat kinase 2 is involved in actin cytoskeleton dynamics. PMID:20876399
Protein network prediction and topological analysis in Leishmania major as a tool for drug target selection. PMID:20875130
Identifying the genetic determinants of transcription factor activity. PMID:20865005
Gene expression variations are predictive for stochastic noise. PMID:20860999
Eukaryotic genes of archaebacterial origin are more important than the more numerous eubacterial genes, irrespective of function. PMID:20852068
Protein complex prediction based on k-connected subgraphs in protein interaction network. PMID:20846398
Tailored graph ensembles as proxies or null models for real networks I: tools for quantifying structure. PMID:20844594
Candidate gene prioritization by network analysis of differential expression using machine learning approaches. PMID:20840752
Identifying dysfunctional crosstalk of pathways in various regions of Alzheimer's disease brains. PMID:20840725
A global census of fission yeast deubiquitinating enzyme localization and interaction networks reveals distinct compartmentalization profiles and overlapping functions in endocytosis and polarity. PMID:20838651
Identification of response-modulated genetic interactions by sensitivity-based epistatic analysis. PMID:20831804
The BioPAX community standard for pathway data sharing. PMID:20829833
A yeast's eye view of mammalian reproduction: cross-species gene co-expression in meiotic prophase. PMID:20819218
Molecular mechanistic associations of human diseases. PMID:20815942
Protein networks reveal detection bias and species consistency when analysed by information-theoretic methods. PMID:20805870
Identification of epistatic effects using a protein-protein interaction database. PMID:20736252
A strategy for interaction site prediction between phospho-binding modules and their partners identified from proteomic data. PMID:20733106
A genome-wide gene function prediction resource for Drosophila melanogaster. PMID:20711346
Encoding the states of interacting proteins to facilitate biological pathways reconstruction. PMID:20707925
Patterns of HIV-1 protein interaction identify perturbed host-cellular subsystems. PMID:20686668
Open source tool for prediction of genome wide protein-protein interaction network based on ortholog information. PMID:20684769
A systems approach to mapping transcriptional networks controlling surfactant homeostasis. PMID:20659319
Genome-wide scoring of positive and negative epistasis through decomposition of quantitative genetic interaction fitness matrices. PMID:20657656
The function of communities in protein interaction networks at multiple scales. PMID:20649971
Predicting functional associations from metabolism using bi-partite network algorithms. PMID:20630077
Annotation of SBML models through rule-based semantic integration. PMID:20626923
Development of a novel bioinformatics tool for in silico validation of protein interactions. PMID:20625507
Protein complex prediction via verifying and reconstructing the topology of domain-domain interactions. PMID:20584269
A semi-supervised learning approach to predict synthetic genetic interactions by combining functional and topological properties of functional gene network. PMID:20573270
Protein interaction network topology uncovers melanogenesis regulatory network components within functional genomics datasets. PMID:20550706
Systematic analysis of essential genes reveals important regulators of G protein signaling. PMID:20542006
Protein interface conservation across structure space. PMID:20534496
A quick guide to large-scale genomic data mining. PMID:20523745
Integrative structure modeling of macromolecular assemblies from proteomics data. PMID:20507923
Fast integration of heterogeneous data sources for predicting gene function with limited annotation. PMID:20507895
Reconstruction of the yeast protein-protein interaction network involved in nutrient sensing and global metabolic regulation. PMID:20500839
Dynamic cross-talk analysis among TNF-R, TLR-4 and IL-1R signalings in TNFalpha-induced inflammatory responses. PMID:20497537
Structural interpretation of protein-protein interaction network. PMID:20487511
Protein evolution in yeast transcription factor subnetworks. PMID:20466810
Coordinated modular functionality and prognostic potential of a heart failure biomarker-driven interaction network. PMID:20462429
Natural selection on cis and trans regulation in yeasts. PMID:20445163
Molecular signaling in zebrafish development and the vertebrate phylotypic period. PMID:20433455
Reconstruction of gene regulatory modules in cancer cell cycle by multi-source data integration. PMID:20422009
Simultaneous clustering of multiple gene expression and physical interaction datasets. PMID:20419151
Response network analysis of differential gene expression in human epithelial lung cells during avian influenza infections. PMID:20370926
TopoGSA: network topological gene set analysis. PMID:20335277
Construction and analysis of protein-protein interaction networks. PMID:20334628
Gene regulatory networks modelling using a dynamic evolutionary hybrid. PMID:20298548
Topological network alignment uncovers biological function and phylogeny. PMID:20236959
A simple technique for the prediction of interacting proteins reveals a direct Brn-3a-androgen receptor interaction. PMID:20228055
Toward design-based engineering of industrial microbes. PMID:20226723
Integrated cellular network of transcription regulations and protein-protein interactions. PMID:20211003
Pathway Palette: a rich internet application for peptide-, protein- and network-oriented analysis of MS data. PMID:20198642
SING: subgraph search in non-homogeneous graphs. PMID:20170516
BisoGenet: a new tool for gene network building, visualization and analysis. PMID:20163717
Feedback between p21 and reactive oxygen production is necessary for cell senescence. PMID:20160708
The trypanosome Pumilio-domain protein PUF7 associates with a nuclear cyclophilin and is involved in ribosomal RNA maturation. PMID:20153321
Lists2Networks: integrated analysis of gene/protein lists. PMID:20152038
Madm (Mlf1 adapter molecule) cooperates with Bunched A to promote growth in Drosophila. PMID:20149264
Inference of RhoGAP/GTPase regulation using single-cell morphological data from a combinatorial RNAi screen. PMID:20144944
Global approaches to study protein-protein interactions among viruses and hosts. PMID:20143950
Protein interactions and ligand binding: from protein subfamilies to functional specificity. PMID:20133844
A general co-expression network-based approach to gene expression analysis: comparison and applications. PMID:20122284
Integration of multiple data sources to prioritize candidate genes using discounted rating system. PMID:20122192
Comparative evolutionary analysis of protein complexes in E. coli and yeast. PMID:20122144
Biana: a software framework for compiling biological interactions and analyzing networks. PMID:20105306
Automatic inference of multicellular regulatory networks using informative priors. PMID:20090166
A manually curated network of the PML nuclear body interactome reveals an important role for PML-NBs in SUMOylation dynamics. PMID:20087442
CORNET: a user-friendly tool for data mining and integration. PMID:20053712
AtPIN: Arabidopsis thaliana protein interaction network. PMID:20043823
Pandora, a pathway and network discovery approach based on common biological evidence. PMID:20031970
Expanding the definition of the classical bipartite nuclear localization signal. PMID:20028483
On the classification of epistatic interactions. PMID:20026678
Human synthetic lethal inference as potential anti-cancer target gene detection. PMID:20015360
A cassette of N-terminal amino acids of histone H2B are required for efficient cell survival, DNA repair and Swi/Snf binding in UV irradiated yeast. PMID:20007597
Towards accurate imputation of quantitative genetic interactions. PMID:20003301
PutidaNET: interactome database service and network analysis of Pseudomonas putida KT2440. PMID:19958481
Chromatin regulation and gene centrality are essential for controlling fitness pleiotropy in yeast. PMID:19956643
Spectral affinity in protein networks. PMID:19943959
Functional features of gene expression profiles differentiating gastrointestinal stromal tumours according to KIT mutations and expression. PMID:19943934
Exploiting amino acid composition for predicting protein-protein interactions. PMID:19936254
Novel protein-protein interactions inferred from literature context. PMID:19924298
Reconstruction of the yeast Snf1 kinase regulatory network reveals its role as a global energy regulator. PMID:19888214
DRYGIN: a database of quantitative genetic interaction networks in yeast. PMID:19880385
Predicting meiotic pathways in human fetal oogenesis. PMID:19846598
XML-based approaches for the integration of heterogeneous bio-molecular data. PMID:19828083
VANLO--interactive visual exploration of aligned biological networks. PMID:19821976
How to visually interpret biological data using networks. PMID:19816451
Proteomics data repositories. PMID:19795424
The MAPK signaling cascade is a central hub in the regulation of cell cycle, apoptosis and cytoskeleton remodeling by tripeptidyl-peptidase II. PMID:19787088
A protein-protein interaction guided method for competitive transcription factor binding improves target predictions. PMID:19786498
How and when should interactome-derived clusters be used to predict functional modules and protein function? PMID:19770263
Finding local communities in protein networks. PMID:19765306
Gene networks in Drosophila melanogaster: integrating experimental data to predict gene function. PMID:19758432
Defining elastic fiber interactions by molecular fishing: an affinity purification and mass spectrometry approach. PMID:19755719
Usefulness and limitations of dK random graph models to predict interactions and functional homogeneity in biological networks under a pseudo-likelihood parameter estimation approach. PMID:19728875
A reliable measure of similarity based on dependency for short time series: an application to gene expression networks. PMID:19712487
The ordering of expression among a few genes can provide simple cancer biomarkers and signal BRCA1 mutations. PMID:19695104
Knowledge-guided inference of domain-domain interactions from incomplete protein-protein interaction networks. PMID:19667081
Geometric de-noising of protein-protein interaction networks. PMID:19662157
Predicting eukaryotic transcriptional cooperativity by Bayesian network integration of genome-wide data. PMID:19661283
Local network topology in human protein interaction data predicts functional association. PMID:19641626
Integrating proteomic, transcriptional, and interactome data reveals hidden components of signaling and regulatory networks. PMID:19638617
Detection of mammalian virulence determinants in highly pathogenic avian influenza H5N1 viruses: multivariate analysis of published data. PMID:19625397
Systems-level cancer gene identification from protein interaction network topology applied to melanogenesis-related functional genomics data. PMID:19625303
Ontogeny and phylogeny: molecular signatures of selection, constraint, and temporal pleiotropy in the development of Drosophila. PMID:19622136
Defining the human deubiquitinating enzyme interaction landscape. PMID:19615732
A network model of a cooperative genetic landscape in brain tumors. PMID:19602686
Computational identification of potential molecular interactions in Arabidopsis. PMID:19592425
Translational disease interpretation with molecular networks. PMID:19591646
BowTieBuilder: modeling signal transduction pathways. PMID:19566957
RNAiCut: automated detection of significant genes from functional genomic screens. PMID:19564846
Predicting protein-protein interactions in Arabidopsis thaliana through integration of orthology, gene ontology and co-expression. PMID:19563678
Systems approach to explore components and interactions in the presynapse. PMID:19562802
ITM Probe: analyzing information flow in protein networks. PMID:19561335
Evolution of phosphoregulation: comparison of phosphorylation patterns across yeast species. PMID:19547744
Interactome for auxiliary splicing factor U2AF(65) suggests diverse roles. PMID:19540372
Backup in gene regulatory networks explains differences between binding and knockout results. PMID:19536199
An atlas of chaperone-protein interactions in Saccharomyces cerevisiae: implications to protein folding pathways in the cell. PMID:19536198
PIAS proteins: pleiotropic interactors associated with SUMO. PMID:19526197
Directed mammalian gene regulatory networks using expression and comparative genomic hybridization microarray data from radiation hybrids. PMID:19521529
Integrated assessment of genomic correlates of protein evolutionary rate. PMID:19521505
Approaches to neuroscience data integration. PMID:19505888
Information flow analysis of interactome networks. PMID:19503817
myGRN: a database and visualisation system for the storage and analysis of developmental genetic regulatory networks. PMID:19500400
IsoRankN: spectral methods for global alignment of multiple protein networks. PMID:19477996
A complex-centric view of protein network evolution. PMID:19465379
Public databases and software for the pathway analysis of cancer genomes. PMID:19455256
The role of intrinsically unstructured proteins in neurodegenerative diseases. PMID:19440375
Incorporating functional inter-relationships into protein function prediction algorithms. PMID:19435516
Inferring novel disease indications for known drugs by semantically linking drug action and disease mechanism relationships. PMID:19426461
Assessing reliability of protein-protein interactions by integrative analysis of data in model organisms. PMID:19426453
PPISearch: a web server for searching homologous protein-protein interactions across multiple species. PMID:19417070
Protein-protein interaction databases: keeping up with growing interactomes. PMID:19403463
Fault tolerance in protein interaction networks: stable bipartite subgraphs and redundant pathways. PMID:19399174
Identifying hubs in protein interaction networks. PMID:19399170
Biological process linkage networks. PMID:19390589
POINeT: protein interactome with sub-network analysis and hub prioritization. PMID:19379523
Dynamic reprogramming of transcription factors to and from the subtelomere. PMID:19372386
Bayesian inference of protein-protein interactions from biological literature. PMID:19369495
Tissue specificity and the human protein interaction network. PMID:19357639
Spinal muscular atrophy and a model for survival of motor neuron protein function in axonal ribonucleoprotein complexes. PMID:19343312
Reconstructing the ubiquitin network: cross-talk with other systems and identification of novel functions. PMID:19331687
Markov clustering versus affinity propagation for the partitioning of protein interaction graphs. PMID:19331680
A general pipeline for quality and statistical assessment of protein interaction data using R and Bioconductor. PMID:19325550
On the growth of scientific knowledge: yeast biology as a case study. PMID:19300476
Modeling and analyzing gene co-expression in hepatocellular carcinoma using actor-semiotic networks and centrality signatures. PMID:19259423
Uncovering biological network function via graphlet degree signatures. PMID:19259413
Characterization of mouse IFT complex B. PMID:19253336
A survey of available tools and web servers for analysis of protein-protein interactions and interfaces. PMID:19240123
Specific synthetic lethal killing of RAD54B-deficient human colorectal cancer cells by FEN1 silencing. PMID:19218431
High throughput interaction data reveals degree conservation of hub proteins. PMID:19209717
Metabolic flux correlations, genetic interactions, and disease. PMID:19193147
Integrating computational biology and forward genetics in Drosophila. PMID:19165344
An integrated workflow for charting the human interaction proteome: insights into the PP2A system. PMID:19156129
A Drosophila systems model of pentylenetetrazole induced locomotor plasticity responsive to antiepileptic drugs. PMID:19154620
ben Functions with scamp during synaptic transmission and long-term memory formation in Drosophila. PMID:19144841
Predicting genetic interactions with random walks on biological networks. PMID:19138426
Questioning the ubiquity of neofunctionalization. PMID:19119408
A novel proteomics approach for the discovery of chromatin-associated protein networks. PMID:19106085
Up-to-date catalogues of yeast protein complexes. PMID:19095691
POLAR MAPPER: a computational tool for integrated visualization of protein interaction networks and mRNA expression data. PMID:19091689
Predicted mouse peroxisome-targeted proteins and their actual subcellular locations. PMID:19091015
Ortholog-based protein-protein interaction prediction and its application to inter-species interactions. PMID:19091010
Buffering by gene duplicates: an analysis of molecular correlates and evolutionary conservation. PMID:19087332
Improvements to cardiovascular gene ontology. PMID:19046747
Network integration and graph analysis in mammalian molecular systems biology. PMID:19045817
Age-dependent evolution of the yeast protein interaction network suggests a limited role of gene duplication and divergence. PMID:19043579
The integrated analysis of metabolic and protein interaction networks reveals novel molecular organizing principles. PMID:19032748
Training set expansion: an approach to improving the reconstruction of biological networks from limited and uneven reliable interactions. PMID:19015141
Combining multiple positive training sets to generate confidence scores for protein-protein interactions. PMID:19010802
MoKCa database--mutations of kinases in cancer. PMID:18986996
Network hubs buffer environmental variation in Saccharomyces cerevisiae. PMID:18986213
Hepatitis C virus infection protein network. PMID:18985028
Michigan molecular interactions r2: from interacting proteins to pathways. PMID:18978014
Organization of physical interactomes as uncovered by network schemas. PMID:18949022
Combination chemical genetics. PMID:18936752
A genomewide suppressor and enhancer analysis of cdc13-1 reveals varied cellular processes influencing telomere capping in Saccharomyces cerevisiae. PMID:18845848
Prediction of evolutionarily conserved interologs in Mus musculus. PMID:18842131
DroID: the Drosophila Interactions Database, a comprehensive resource for annotated gene and protein interactions. PMID:18840285
Protein networks markedly improve prediction of subcellular localization in multiple eukaryotic species. PMID:18836191
Finding friends and enemies in an enemies-only network: a graph diffusion kernel for predicting novel genetic interactions and co-complex membership from yeast genetic interactions. PMID:18832443
A genome wide analysis of the response to uncapped telomeres in budding yeast reveals a novel role for the NAD+ biosynthetic gene BNA2 in chromosome end protection. PMID:18828915
iRefIndex: a consolidated protein interaction database with provenance. PMID:18823568
Conservation and rewiring of functional modules revealed by an epistasis map in fission yeast. PMID:18818364
Modeling synthetic lethality. PMID:18789146
Inference of protein complex activities from chemical-genetic profile and its applications: predicting drug-target pathways. PMID:18769708
Probing the extent of randomness in protein interaction networks. PMID:18769589
Comparative analysis of function and interaction of transcription factors in nematodes: extensive conservation of orthology coupled to rapid sequence evolution. PMID:18752680
The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: a scaffold to query lipid metabolism. PMID:18687109
Structural similarity of genetically interacting proteins. PMID:18671848
Predicting and validating protein interactions using network structure. PMID:18654616
Transcription factor control of growth rate dependent genes in Saccharomyces cerevisiae: a three factor design. PMID:18638364
From E-MAPs to module maps: dissecting quantitative genetic interactions using physical interactions. PMID:18628749
Genetic interaction network of the Saccharomyces cerevisiae type 1 phosphatase Glc7. PMID:18627629
Susceptibility to glaucoma: differential comparison of the astrocyte transcriptome from glaucomatous African American and Caucasian American donors. PMID:18613964
Combining guilt-by-association and guilt-by-profiling to predict Saccharomyces cerevisiae gene function. PMID:18613951
Genetic interactions of MAF1 identify a role for Med20 in transcriptional repression of ribosomal protein genes. PMID:18604275
Global investigation of protein-protein interactions in yeast Saccharomyces cerevisiae using re-occurring short polypeptide sequences. PMID:18586826
Assessing the functional structure of genomic data. PMID:18586732
The effects of protein interactions, gene essentiality and regulatory regions on expression variation. PMID:18582382
Early vertebrate chromosome duplications and the evolution of the neuropeptide Y receptor gene regions. PMID:18578868
Human Proteinpedia as a resource for clinical proteomics. PMID:18573810
The emerging CK2 interactome: insights into the regulation and functions of CK2. PMID:18553055
Exploiting the proteome to improve the genome-wide genetic analysis of epistasis in common human diseases. PMID:18551320
Phosphoprotein profiling by PA-GeLC-MS/MS. PMID:18510356
ENDEAVOUR update: a web resource for gene prioritization in multiple species. PMID:18508807
Design logic of a cannabinoid receptor signaling network that triggers neurite outgrowth. PMID:18487186
GPS 2.0, a tool to predict kinase-specific phosphorylation sites in hierarchy. PMID:18463090
MassNet: a functional annotation service for protein mass spectrometry data. PMID:18448467
A microtubule interactome: complexes with roles in cell cycle and mitosis. PMID:18433294
Predicting co-complexed protein pairs from heterogeneous data. PMID:18421371
Genomic analysis of estrogen cascade reveals histone variant H2A.Z associated with breast cancer progression. PMID:18414489
Linking functionally related genes by sensitive and quantitative characterization of genetic interaction profiles. PMID:18408161
Extracting expression modules from perturbational gene expression compendia. PMID:18402676
Mapping genetically compensatory pathways from synthetic lethal interactions in yeast. PMID:18398455
Membrane transporters and protein traffic networks differentially affecting metal tolerance: a genomic phenotyping study in yeast. PMID:18394190
The MoVIN server for the analysis of protein interaction networks. PMID:18387199
Walking the interactome for prioritization of candidate disease genes. PMID:18371930
Predicting cancer involvement of genes from heterogeneous data. PMID:18371197
The role of disorder in interaction networks: a structural analysis. PMID:18364713
Functional diversification of duplicate genes through subcellular adaptation of encoded proteins. PMID:18336717
Mining phenotypes for gene function prediction. PMID:18315868
Defining genetic interaction. PMID:18305163
Genome-wide expression profiling, in vivo DNA binding analysis, and probabilistic motif prediction reveal novel Abf1 target genes during fermentation, respiration, and sporulation in yeast. PMID:18305101
Dissecting microregulation of a master regulatory network. PMID:18294391
The Annotation, Mapping, Expression and Network (AMEN) suite of tools for molecular systems biology. PMID:18254954
Protein function assignment through mining cross-species protein-protein interactions. PMID:18253506
CASCADE: a novel quasi all paths-based network analysis algorithm for clustering biological interactions. PMID:18230159
Gene function prediction using labeled and unlabeled data. PMID:18221567
Predicting the interactome of Xanthomonas oryzae pathovar oryzae for target selection and DB service. PMID:18215330
Analysis of self-associating proteins by singular value decomposition of solution scattering data. PMID:18212017
Protein interactions in human genetic diseases. PMID:18199329
Annotating novel genes by integrating synthetic lethals and genomic information. PMID:18194531
Quantitative analysis on the characteristics of targets with FDA approved drugs. PMID:18167532
Nonequilibrium thermodynamics of thiol/disulfide redox systems: a perspective on redox systems biology. PMID:18155672
Consistent dissection of the protein interaction network by combining global and local metrics. PMID:18154653
Multiple kinases and system robustness: a link between Cdc37 and genome integrity. PMID:18075309
A portrait of copy-number polymorphism in Drosophila melanogaster. PMID:18056801
Spreading out of perturbations in reversible reaction networks. PMID:18046464
Where have all the interactions gone? Estimating the coverage of two-hybrid protein interaction maps. PMID:18039026
Quantification of ortholog losses in insects and vertebrates. PMID:18021399
The BioGRID Interaction Database: 2008 update. PMID:18000002
DIMA 2.0--predicted and known domain interactions. PMID:17999995
The Molecule Pages database. PMID:17965093
TransfactomeDB: a resource for exploring the nucleotide sequence specificity and condition-specific regulatory activity of trans-acting factors. PMID:17947326
Bacteriome.org--an integrated protein interaction database for E. coli. PMID:17942431
CMGSDB: integrating heterogeneous Caenorhabditis elegans data sources using compositional data mining. PMID:17942411
Improved human disease candidate gene prioritization using mouse phenotype. PMID:17939863
Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions. PMID:17925023
All duplicates are not equal: the difference between small-scale and genome duplication. PMID:17916239
A global analysis of genetic interactions in Caenorhabditis elegans. PMID:17897480
PathFinder: mining signal transduction pathway segments from protein-protein interaction networks. PMID:17854489
The RAGNYA fold: a novel fold with multiple topological variants found in functionally diverse nucleic acid, nucleotide and peptide-binding proteins. PMID:17715145
Propagation of large concentration changes in reversible protein-binding networks. PMID:17699619
Disparate effects of p24alpha and p24delta on secretory protein transport and processing. PMID:17684551
A data integration approach for cell cycle analysis oriented to model simulation in systems biology. PMID:17678529
Reuse of structural domain-domain interactions in protein networks. PMID:17640363
Bayesian Orthogonal Least Squares (BOLS) algorithm for reverse engineering of gene regulatory networks. PMID:17626641
Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution. PMID:17535793
Unequal evolutionary conservation of human protein interactions in interologous networks. PMID:17535438
Huntingtin interacting proteins are genetic modifiers of neurodegeneration. PMID:17500595
Reconstruction of human protein interolog network using evolutionary conserved network. PMID:17493278
The role of Trs65 in the Ypt/Rab guanine nucleotide exchange factor function of the TRAPP II complex. PMID:17475775
Specificity in protein interactions and its relationship with sequence diversity and coevolution. PMID:17468399
The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics. PMID:17447836
Pathway redundancy and protein essentiality revealed in the Saccharomyces cerevisiae interaction networks. PMID:17437029
Inferring condition-specific transcription factor function from DNA binding and gene expression data. PMID:17437025
Why are there still over 1000 uncharacterized yeast genes? PMID:17435240
In silico pathway reconstruction: Iron-sulfur cluster biogenesis in Saccharomyces cerevisiae. PMID:17408500
Deciphering protein-protein interactions. Part I. Experimental techniques and databases. PMID:17397251
Systematic genome instability screens in yeast and their potential relevance to cancer. PMID:17360454
Network-based prediction of protein function. PMID:17353930
Chemical combination effects predict connectivity in biological systems. PMID:17332758
From bytes to bedside: data integration and computational biology for translational cancer research. PMID:17319736
Gene network interconnectedness and the generalized topological overlap measure. PMID:17250769
Evolutionary conservation of domain-domain interactions. PMID:17184549
Classical nuclear localization signals: definition, function, and interaction with importin alpha. PMID:17170104
Expanded protein information at SGD: new pages and proteome browser. PMID:17142221
CellCircuits: a database of protein network models. PMID:17135207
DOMINO: a database of domain-peptide interactions. PMID:17135199
Michigan Molecular Interactions (MiMI): putting the jigsaw puzzle together. PMID:17130145
IntNetDB v1.0: an integrated protein-protein interaction network database generated by a probabilistic model. PMID:17112386
STRING 7--recent developments in the integration and prediction of protein interactions. PMID:17098935
Stratus not altocumulus: a new view of the yeast protein interaction network. PMID:16984220
Intrinsic disorder is a common feature of hub proteins from four eukaryotic interactomes. PMID:16884331
The interaction map of yeast: terra incognita? PMID:16762048
Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae. PMID:16762047
The F-box protein Dia2 overcomes replication impedance to promote genome stability in Saccharomyces cerevisiae. PMID:16751663 -
The BioGRID interaction database: 2015 update
PubMed citations: 465.
465 articles citing: The BioGRID interaction database: 2015 update
SIPGCN: A Novel Deep Learning Model for Predicting Self-Interacting Proteins from Sequence Information Using Graph Convolutional Networks. PMID:35884848
Single-cell network biology characterizes cell type gene regulation for drug repurposing and phenotype prediction in Alzheimer's disease. PMID:35849618
Systems Drug Discovery for Diffuse Large B Cell Lymphoma Based on Pathogenic Molecular Mechanism via Big Data Mining and Deep Learning Method. PMID:35743172
Repurposing Histaminergic Drugs in Multiple Sclerosis. PMID:35683024
Machine Learning in Causal Inference: Application in Pharmacovigilance. PMID:35579811
Comprehensive molecular characterization of hypertension-related genes in cancer. PMID:35513851
Comprehensive network medicine-based drug repositioning via integration of therapeutic efficacy and side effects. PMID:35443763
Function of SYDE C2-RhoGAP family as signaling hubs for neuronal development deduced by computational analysis. PMID:35279680
Investigating the Role of Obesity in Prostate Cancer and Identifying Biomarkers for Drug Discovery: Systems Biology and Deep Learning Approaches. PMID:35164166
A full-proteome, interaction-specific characterization of mutational hotspots across human cancers. PMID:34963661
Targeting uPA-uPAR interaction to improve intestinal epithelial barrier integrity in inflammatory bowel disease. PMID:34933179
Protein-protein interactions: Methods, databases, and applications in virus-host study. PMID:34909403
Interpretation of network-based integration from multi-omics longitudinal data. PMID:34883510
Network Biology Approaches to Achieve Precision Medicine in Inflammatory Bowel Disease. PMID:34745229
Tumor relevant protein functional interactions identified using bipartite graph analyses. PMID:34728699
Computational repurposing of therapeutic small molecules from cancer to pulmonary hypertension. PMID:34669463
A machine learning framework for predicting drug-drug interactions. PMID:34475500
A neural network-based method for polypharmacy side effects prediction. PMID:34303360
Identification of anticancer drug target genes using an outside competitive dynamics model on cancer signaling networks. PMID:34238960
Identification of Diagnostic Markers for Major Depressive Disorder Using Machine Learning Methods. PMID:34220416
EvoProDom: evolutionary modeling of protein families by assessing translocations of protein domains. PMID:34196123
Molecular signatures of silencing suppression degeneracy from a complex RNA virus. PMID:34181647
Gene expression signatures predict response to therapy with growth hormone. PMID:34045667
PolyQ length co-evolution in neural proteins. PMID:34017944
Drug Repurposing: A Network-based Approach to Amyotrophic Lateral Sclerosis. PMID:33987813
Differential expression of miRNAs in the presence of B chromosome in the cichlid fish Astatotilapia latifasciata. PMID:33980143
A Bayesian Approach for Learning Gene Networks Underlying Disease Severity in COPD. PMID:33912251
Immune Subtyping in Latent Tuberculosis. PMID:33897680
Identification of IFN-Induced Transmembrane Protein 1 With Prognostic Value in Pancreatic Cancer Using Network Module-Based Analysis. PMID:33869009
Network-based modeling of herb combinations in traditional Chinese medicine. PMID:33834186
Identification of human glucocorticoid response markers using integrated multi-omic analysis from a randomized crossover trial. PMID:33821793
Systems Medicine Design for Triple-Negative Breast Cancer and Non-Triple-Negative Breast Cancer Based on Systems Identification and Carcinogenic Mechanisms. PMID:33802957
Comprehensive characterization of a drug-resistance-related ceRNA network across 15 anti-cancer drug categories. PMID:33738135
Short loop functional commonality identified in leukaemia proteome highlights crucial protein sub-networks. PMID:33709075
Drug-Target Interaction Prediction Based on Adversarial Bayesian Personalized Ranking. PMID:33628808
A systems-based method to repurpose marketed therapeutics for antiviral use: a SARS-CoV-2 case study. PMID:33593923
A Deep Learning-Based Approach for Identifying the Medicinal Uses of Plant-Derived Natural Compounds. PMID:33519445
A network-based deep learning methodology for stratification of tumor mutations. PMID:33416857
Tumor Microenvironment-Associated Immune-Related Genes for the Prognosis of Malignant Pleural Mesothelioma. PMID:33042835
De novo missense variants disrupting protein-protein interactions affect risk for autism through gene co-expression and protein networks in neuronal cell types. PMID:33032641
Structure-based validation can drastically underestimate error rate in proteome-wide cross-linking mass spectrometry studies. PMID:32994567
Role of SARS-CoV-2 in Altering the RNA-Binding Protein and miRNA-Directed Post-Transcriptional Regulatory Networks in Humans. PMID:32993015
Integrated regulatory models for inference of subtype-specific susceptibilities in glioblastoma. PMID:32974985
An optimized quantitative proteomics method establishes the cell type-resolved mouse brain secretome. PMID:32954517
Identification of potential markers for type 2 diabetes mellitus via bioinformatics analysis. PMID:32705173
Role of SARS-CoV-2 in altering the RNA binding protein and miRNA directed post-transcriptional regulatory networks in humans. PMID:32676599
NAIGO: An Improved Method to Align PPI Networks Based on Gene Ontology and Graphlets. PMID:32637398
Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses. PMID:32597660
Prediction of the Secretome and the Surfaceome: A Strategy to Decipher the Crosstalk between Adipose Tissue and Muscle during Fetal Growth. PMID:32575512
Multilevel regulation of muscle-specific transcription factor hlh-1 during Caenorhabditis elegans embryogenesis. PMID:32556563
PINOT: an intuitive resource for integrating protein-protein interactions. PMID:32527260
Omics Integration Analyses Reveal the Early Evolution of Malignancy in Breast Cancer. PMID:32512721
Predicting Polypharmacy Side-effects Using Knowledge Graph Embeddings. PMID:32477666
Integrative analysis of large-scale loss-of-function screens identifies robust cancer-associated genetic interactions. PMID:32463358
HIPPIE2: a method for fine-scale identification of physically interacting chromatin regions. PMID:32270138
Deep graph embedding for prioritizing synergistic anticancer drug combinations. PMID:32153729
Edgetic perturbation signatures represent known and novel cancer biomarkers. PMID:32152446
Gold nanoclusters elicit homeostatic perturbations in glioblastoma cells and adaptive changes of lysosomes. PMID:32042327
Discovering the genes mediating the interactions between chronic respiratory diseases in the human interactome. PMID:32041952
Patient similarity by joint matrix trifactorization to identify subgroups in acute myeloid leukemia. PMID:31984320
Mechanical forces induce an asthma gene signature in healthy airway epithelial cells. PMID:31969610
In silico unravelling pathogen-host signaling cross-talks via pathogen mimicry and human protein-protein interaction networks. PMID:31956393
A phenomics-based approach for the detection and interpretation of shared genetic influences on 29 biochemical indices in southern Chinese men. PMID:31842750
MaXLinker: Proteome-wide Cross-link Identifications with High Specificity and Sensitivity. PMID:31839598
A Computational Framework for Predicting Direct Contacts and Substructures within Protein Complexes. PMID:31717703
Genome-wide analysis of Homo sapiens, Arabidopsis thaliana, and Saccharomyces cerevisiae reveals novel attributes of tail-anchored membrane proteins. PMID:31711414
Mitochondrial dysfunction in rheumatoid arthritis: A comprehensive analysis by integrating gene expression, protein-protein interactions and gene ontology data. PMID:31703070
Dissecting the Shared and Context-Dependent Pathways Mediated by the p140Cap Adaptor Protein in Cancer and in Neurons. PMID:31681758
HMNPPID-human malignant neoplasm protein-protein interaction database. PMID:31639057
Universal concept signature analysis: genome-wide quantification of new biological and pathological functions of genes and pathways. PMID:31631213
Interactome of the Autoimmune Risk Protein ANKRD55. PMID:31620119
Neglog: Homology-Based Negative Data Sampling Method for Genome-Scale Reconstruction of Human Protein-Protein Interaction Networks. PMID:31614890
Compound Dynamics and Combinatorial Patterns of Amino Acid Repeats Encode a System of Evolutionary and Developmental Markers. PMID:31589292
Paralog dependency indirectly affects the robustness of human cells. PMID:31556487
Discovery of Inhibitors for Proliferating Cell Nuclear Antigen Using a Computational-Based Linked-Multiple-Fragment Screen. PMID:31552364
FunDMDeep-m6A: identification and prioritization of functional differential m6A methylation genes. PMID:31510685
Synaptic and Gene Regulatory Mechanisms in Schizophrenia, Autism, and 22q11.2 Copy Number Variant-Mediated Risk for Neuropsychiatric Disorders. PMID:31500805
A Novel Computational Model for Predicting microRNA-Disease Associations Based on Heterogeneous Graph Convolutional Networks. PMID:31455028
Precise Prediction of Calpain Cleavage Sites and Their Aberrance Caused by Mutations in Cancer. PMID:31440276
A genome-wide positioning systems network algorithm for in silico drug repurposing. PMID:31375661
The Methods Employed in Mass Spectrometric Analysis of Posttranslational Modifications (PTMs) and Protein-Protein Interactions (PPIs). PMID:31347048
In Silico Toxicology Data Resources to Support Read-Across and (Q)SAR. PMID:31244651
Comparing progression molecular mechanisms between lung adenocarcinoma and lung squamous cell carcinoma based on genetic and epigenetic networks: big data mining and genome-wide systems identification. PMID:31217907
A linear delay algorithm for enumerating all connected induced subgraphs. PMID:31216984
Natural Product Target Network Reveals Potential for Cancer Combination Therapies. PMID:31214023
Combining learning and constraints for genome-wide protein annotation. PMID:31208327
CODA-ML: context-specific biological knowledge representation for systemic physiology analysis. PMID:31138123
Multi-Omic Data Interpretation to Repurpose Subtype Specific Drug Candidates for Breast Cancer. PMID:31134131
Identification of LIFR, PIK3R1, and MMP12 as Novel Prognostic Signatures in Gallbladder Cancer Using Network-Based Module Analysis. PMID:31119098
Investigating function roles of hypothetical proteins encoded by the Mycobacterium tuberculosis H37Rv genome. PMID:31113361
Computational identification of tissue-specific transcription factor cooperation in ten cattle tissues. PMID:31095599
The Promoter Regions of Intellectual Disability-Associated Genes Are Uniquely Enriched in LTR Sequences of the MER41 Primate-Specific Endogenous Retrovirus: An Evolutionary Connection Between Immunity and Cognition. PMID:31031802
Conformational Dynamics and Allosteric Regulation Landscapes of Germline PTEN Mutations Associated with Autism Compared to Those Associated with Cancer. PMID:31006514
Structural and Computational Characterization of Disease-Related Mutations Involved in Protein-Protein Interfaces. PMID:30934865
Connectivity problems on heterogeneous graphs. PMID:30899321
Parkinson's Disease is Associated with Dysregulations of a Dopamine-Modulated Gene Network Relevant to Sleep and Affective Neurobehaviors in the Striatum. PMID:30886221
DeepTACT: predicting 3D chromatin contacts via bootstrapping deep learning. PMID:30869141
Topological scoring of protein interaction networks. PMID:30850613
Systems based analysis of human embryos and gene networks involved in cell lineage allocation. PMID:30836937
BGFE: A Deep Learning Model for ncRNA-Protein Interaction Predictions Based on Improved Sequence Information. PMID:30813451
A network-centric approach to drugging TNF-induced NF-κB signaling. PMID:30808860
DYRK1A regulates the recruitment of 53BP1 to the sites of DNA damage in part through interaction with RNF169. PMID:30773093
Investigating Common Pathogenic Mechanisms between Homo sapiens and Different Strains of Candida albicans for Drug Design: Systems Biology Approach via Two-Sided NGS Data Identification. PMID:30769958
Inferring Gene Regulatory Networks from a Population of Yeast Segregants. PMID:30718595
Exploiting locational and topological overlap model to identify modules in protein interaction networks. PMID:30642247
Exploring the underlying biology of intrinsic cardiorespiratory fitness through integrative analysis of genomic variants and muscle gene expression profiling. PMID:30605401
Global analysis of N6-methyladenosine functions and its disease association using deep learning and network-based methods. PMID:30601803
Prediction of protein self-interactions using stacked long short-term memory from protein sequences information. PMID:30577794
Classifying mild traumatic brain injuries with functional network analysis. PMID:30577783
Personalized Medicine and Molecular Interaction Networks in Amyotrophic Lateral Sclerosis (ALS): Current Knowledge. PMID:30551677
Gene expression models based on transcription factor binding events confer insight into functional cis-regulatory variants. PMID:30541050
Predicting protein targets for drug-like compounds using transcriptomics. PMID:30532261
Genomic identification and functional analysis of essential genes in Caenorhabditis elegans. PMID:30514206
Structural disorder in the proteome and interactome of Alkhurma virus (ALKV). PMID:30443749
Heterogeneous network embedding for identifying symptom candidate genes. PMID:30357378
An integrative tissue-network approach to identify and test human disease genes. PMID:30346941
Investigating Pathogenic and Hepatocarcinogenic Mechanisms from Normal Liver to HCC by Constructing Genetic and Epigenetic Networks via Big Genetic and Epigenetic Data Mining and Genome-Wide NGS Data Identification. PMID:30344796
Context-specific interactions in literature-curated protein interaction databases. PMID:30340458
Integration of Molecular Interactome and Targeted Interaction Analysis to Identify a COPD Disease Network Module. PMID:30262855
Deep learning-based transcriptome data classification for drug-target interaction prediction. PMID:30255785
Systems genetics of nonsyndromic orofacial clefting provides insights into its complex aetiology. PMID:30254216
Viruses.STRING: A Virus-Host Protein-Protein Interaction Database. PMID:30249048
PTMD: A Database of Human Disease-associated Post-translational Modifications. PMID:30244175
Targeting Focal Adhesion Kinase Using Inhibitors of Protein-Protein Interactions. PMID:30134553
Proteome-wide analysis of phospho-regulated PDZ domain interactions. PMID:30126976
Multifunctional Proteins: Involvement in Human Diseases and Targets of Current Drugs. PMID:30123928
Identification of novel immune-relevant drug target genes for Alzheimer's Disease by combining ontology inference with network analysis. PMID:30106219
Discovering Health Benefits of Phytochemicals with Integrated Analysis of the Molecular Network, Chemical Properties and Ethnopharmacological Evidence. PMID:30096807
Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken. PMID:30086717
Factors Associated with Heritable Pulmonary Arterial Hypertension Exert Convergent Actions on the miR-130/301-Vascular Matrix Feedback Loop. PMID:30081553
Phenotype-oriented network analysis for discovering pharmacological effects of natural compounds. PMID:30076354
Integrative analysis of promising molecular biomarkers and pathways for coronary artery disease using WGCNA and MetaDE methods. PMID:30015926
Integrating Rio1 activities discloses its nutrient-activated network in Saccharomyces cerevisiae. PMID:30011030
Network-based approach to prediction and population-based validation of in silico drug repurposing. PMID:30002366
Improving Prediction of Self-interacting Proteins Using Stacked Sparse Auto-Encoder with PSSM profiles. PMID:29989064
The role of PCNA as a scaffold protein in cellular signaling is functionally conserved between yeast and humans. PMID:29988559
Identification of two distinct peptide-binding pockets in the SH3 domain of human mixed-lineage kinase 3. PMID:29980598
Transferring knowledge of bacterial protein interaction networks to predict pathogen targeted human genes and immune signaling pathways: a case study on M. tuberculosis. PMID:29954330
Two critical positions in zinc finger domains are heavily mutated in three human cancer types. PMID:29953437
Post-translational buffering leads to convergent protein expression levels between primates. PMID:29950183
Modeling polypharmacy side effects with graph convolutional networks. PMID:29949996
Gold Nanoparticles Impinge on Nucleoli and the Stress Response in MCF7 Breast Cancer Cells. PMID:29942378
IL-1ɑ C376A Transversion Variant and Risk of Idiopathic Male Infertility in Iranian Men: A Genetic Association Study. PMID:29935069
Exploring the functional impact of alternative splicing on human protein isoforms using available annotation sources. PMID:29931155
A cytokine protein-protein interaction network for identifying key molecules in rheumatoid arthritis. PMID:29928007
Developments in toxicogenomics: understanding and predicting compound-induced toxicity from gene expression data. PMID:29917034
Aberrantly expressed genes and miRNAs in human hypopharyngeal squamous cell carcinoma based on RNA‑sequencing analysis. PMID:29916534
Removing Background Co-occurrences of Transcription Factor Binding Sites Greatly Improves the Prediction of Specific Transcription Factor Cooperations. PMID:29896218
An interactome perturbation framework prioritizes damaging missense mutations for developmental disorders. PMID:29892012
Function, dynamics and evolution of network motif modules in integrated gene regulatory networks of worm and plant. PMID:29873777
Construction of a specific SVM classifier and identification of molecular markers for lung adenocarcinoma based on lncRNA-miRNA-mRNA network. PMID:29872324
Network-Based Disease Module Discovery by a Novel Seed Connector Algorithm with Pathobiological Implications. PMID:29791871
Archetypal transcriptional blocks underpin yeast gene regulation in response to changes in growth conditions. PMID:29785040
PAF1 complex interactions with SETDB1 mediate promoter H3K9 methylation and transcriptional repression of Hoxa9 and Meis1 in acute myeloid leukemia. PMID:29774127
PregOMICS-Leveraging systems biology and bioinformatics for drug repurposing in maternal-child health. PMID:29726581
NF-Y-dependent regulation of glutamate receptor 4 expression and cell survival in cells of the oligodendrocyte lineage. PMID:29704264
Signalling maps in cancer research: construction and data analysis. PMID:29688383
YAAM: Yeast Amino Acid Modifications Database. PMID:29688347
Upregulated VEGFA and DLL4 act as potential prognostic genes for clear cell renal cell carcinoma. PMID:29618931
Systematic Evaluation of Molecular Networks for Discovery of Disease Genes. PMID:29605183
Loss of TDP43 inhibits progression of triple-negative breast cancer in coordination with SRSF3. PMID:29581274
Systematic characterization of pan-cancer mutation clusters. PMID:29572294
Uncovering the regeneration strategies of zebrafish organs: a comprehensive systems biology study on heart, cerebellum, fin, and retina regeneration. PMID:29560825
The Genomic Landscape and Pharmacogenomic Interactions of Clock Genes in Cancer Chronotherapy. PMID:29525205
A Vitis vinifera basic helix-loop-helix transcription factor enhances plant cell size, vegetative biomass and reproductive yield. PMID:29520945
Comparative Protein Interaction Network Analysis Identifies Shared and Distinct Functions for the Human ROCO Proteins. PMID:29513927
A recombinant Fasciola gigantica 14-3-3 epsilon protein (rFg14-3-3e) modulates various functions of goat peripheral blood mononuclear cells. PMID:29510740
Brain-specific functional relationship networks inform autism spectrum disorder gene prediction. PMID:29507298
FunGeneNet: a web tool to estimate enrichment of functional interactions in experimental gene sets. PMID:29504895
Identification of Shared Molecular Signatures Indicate the Susceptibility of Endometriosis to Multiple Sclerosis. PMID:29503661
Network analysis of coronary artery disease risk genes elucidates disease mechanisms and druggable targets. PMID:29467471
Identification of potential target genes for ankylosing spondylitis treatment. PMID:29465556
Recognition of sites of functional specialisation in all known eukaryotic protein kinase families. PMID:29438395
Cholangiocarcinoma‑associated genes identified by integrative analysis of gene expression data. PMID:29436659
Prioritizing disease genes with an improved dual label propagation framework. PMID:29422030
In silico profiling of systemic effects of drugs to predict unexpected interactions. PMID:29371651
PhenoRank: reducing study bias in gene prioritization through simulation. PMID:29360927
Interactome INSIDER: a structural interactome browser for genomic studies. PMID:29355848
Investigating the Mechanisms of Action of Depside Salt from Salvia miltiorrhiza Using Bioinformatic Analysis. PMID:29348768
Logistic regression analysis for the identification of the metastasis-associated signaling pathways of osteosarcoma. PMID:29328361
Mitogen-activated protein kinases, Fus3 and Kss1, regulate chronological lifespan in yeast. PMID:29273704
A multigene support vector machine predictor for metastasis of cutaneous melanoma. PMID:29257259
Bioinformatics analysis of gene expression profiles to identify causal genes in luminal B2 breast cancer. PMID:29250180
Unravelling Protein-Protein Interaction Networks Linked to Aliphatic and Indole Glucosinolate Biosynthetic Pathways in Arabidopsis. PMID:29238354
Text mining and expert curation to develop a database on psychiatric diseases and their genes. PMID:29220439
Large-scale analysis of disease pathways in the human interactome. PMID:29218874
Predicting new indications of compounds with a network pharmacology approach: Liuwei Dihuang Wan as a case study. PMID:29212201
Properties of human genes guided by their enrichment in rare and common variants. PMID:29197136
The OncoPPi Portal: an integrative resource to explore and prioritize protein-protein interactions for cancer target discovery. PMID:29186335
Computational systems biology approaches for Parkinson's disease. PMID:29185073
Uncovering the relationship and mechanisms of Tartary buckwheat (Fagopyrum tataricum) and Type II diabetes, hypertension, and hyperlipidemia using a network pharmacology approach. PMID:29177114
Investigation of candidate genes and mechanisms underlying postmenopausal osteoporosis using bioinformatics analysis. PMID:29138843
TCMID 2.0: a comprehensive resource for TCM. PMID:29106634
SalmoNet, an integrated network of ten Salmonella enterica strains reveals common and distinct pathways to host adaptation. PMID:29057095
A High-Resolution Genome-Wide CRISPR/Cas9 Viability Screen Reveals Structural Features and Contextual Diversity of the Human Cell-Essential Proteome. PMID:29038160
Rapamycin-induced miR-21 promotes mitochondrial homeostasis and adaptation in mTORC1 activated cells. PMID:29029388
Review of computational methods for virus-host protein interaction prediction: a case study on novel Ebola-human interactions. PMID:29028879
TSPYL Family Regulates CYP17A1 and CYP3A4 Expression: Potential Mechanism Contributing to Abiraterone Response in Metastatic Castration-Resistant Prostate Cancer. PMID:29027195
Identification of a novel synaptic protein, TMTC3, involved in periventricular nodular heterotopia with intellectual disability and epilepsy. PMID:28973161
HSF1-dependent and -independent regulation of the mammalian in vivo heat shock response and its impairment in Huntington's disease mouse models. PMID:28970536
A composite network of conserved and tissue specific gene interactions reveals possible genetic interactions in glioma. PMID:28957313
A non-transcriptional role for the glucocorticoid receptor in mediating the cell stress response. PMID:28935859
A support vector machine classifier for the prediction of osteosarcoma metastasis with high accuracy. PMID:28901446
Predicting multicellular function through multi-layer tissue networks. PMID:28881986
Protein-Protein Interactions in Virus-Host Systems. PMID:28861068
Position Matters: Network Centrality Considerably Impacts Rates of Protein Evolution in the Human Protein-Protein Interaction Network. PMID:28854629
Mapping architectural and transcriptional alterations in non-lesional and lesional epidermis in vitiligo. PMID:28852211
Comprehensive Analyses of Tissue-Specific Networks with Implications to Psychiatric Diseases. PMID:28849569
Wide-scale comparative analysis of longevity genes and interventions. PMID:28836369
EGF hijacks miR-198/FSTL1 wound-healing switch and steers a two-pronged pathway toward metastasis. PMID:28827448
Genome-wide association study and gene set analysis for understanding candidate genes involved in salt tolerance at the rice seedling stage. PMID:28821952
eDGAR: a database of Disease-Gene Associations with annotated Relationships among genes. PMID:28812536
ePlant: Visualizing and Exploring Multiple Levels of Data for Hypothesis Generation in Plant Biology. PMID:28808136
Network analyses elucidate the role of SMYD3 in esophageal squamous cell carcinoma. PMID:28781952
RNA Polymerase Tags To Monitor Multidimensional Protein-Protein Interactions Reveal Pharmacological Engagement of Bcl-2 Proteins. PMID:28767232
Identification of key genes and pathways in Parkinson's disease through integrated analysis. PMID:28765971
Dynamic scaffolds for neuronal signaling: in silico analysis of the TANC protein family. PMID:28754924
Expression of NAD(P)H quinone dehydrogenase 1 (NQO1) is increased in the endometrium of women with endometrial cancer and women with polycystic ovary syndrome. PMID:28748640
Genetic and functional characterization of disease associations explains comorbidity. PMID:28740175
Network reconstruction and validation of the Snf1/AMPK pathway in baker's yeast based on a comprehensive literature review. PMID:28725459
Recruitment of histone modifications to assist mRNA dosage maintenance after degeneration of cytosine DNA methylation during animal evolution. PMID:28720579
Synaptic Interactome Mining Reveals p140Cap as a New Hub for PSD Proteins Involved in Psychiatric and Neurological Disorders. PMID:28713243
Network approaches to systems biology analysis of complex disease: integrative methods for multi-omics data. PMID:28679163
Isoelectric point-based fractionation by HiRIEF coupled to LC-MS allows for in-depth quantitative analysis of the phosphoproteome. PMID:28674419
Systematic discovery of novel eukaryotic transcriptional regulators using sequence homology independent prediction. PMID:28651538
Meta-analysis of host response networks identifies a common core in tuberculosis. PMID:28649431
Analysis of K-Ras Interactions by Biotin Ligase Tagging. PMID:28647697
Integrated genome and transcriptome sequencing identifies a noncoding mutation in the genome replication factor DONSON as the cause of microcephaly-micromelia syndrome. PMID:28630177
Network Analysis Reveals a Common Host-Pathogen Interaction Pattern in Arabidopsis Immune Responses. PMID:28611808
Knowledge Discovery in Biological Databases for Revealing Candidate Genes Linked to Complex Phenotypes. PMID:28609292
Identification of novel dysregulated key genes in Breast cancer through high throughput ChIP-Seq data analysis. PMID:28607444
ChiPPI: a novel method for mapping chimeric protein-protein interactions uncovers selection principles of protein fusion events in cancer. PMID:28549153
Large scale meta-analysis characterizes genetic architecture for common psoriasis associated variants. PMID:28537254
The complex genetics of hypoplastic left heart syndrome. PMID:28530678
A computational framework for distinguishing direct versus indirect interactions in human functional protein-protein interaction networks. PMID:28524201
GeMSTONE: orchestrated prioritization of human germline mutations in the cloud. PMID:28521008
Bioinformatics in translational drug discovery. PMID:28487472
Soft Sweeps Are the Dominant Mode of Adaptation in the Human Genome. PMID:28482049
Screening of Tumor Suppressor Genes in Metastatic Colorectal Cancer. PMID:28473981
HER2-positive breast cancer cells expressing elevated FAM83A are sensitive to FAM83A loss. PMID:28463969
Linearity of network proximity measures: implications for set-based queries and significance testing. PMID:28453667
Intrinsic protein disorder reduces small-scale gene duplicability. PMID:28430886
Increased taxon sampling reveals thousands of hidden orthologs in flatworms. PMID:28400424
Spinal motor neuron protein supersaturation patterns are associated with inclusion body formation in ALS. PMID:28396410
Protease-Inhibitor Interaction Predictions: Lessons on the Complexity of Protein-Protein Interactions. PMID:28385878
Using structural knowledge in the protein data bank to inform the search for potential host-microbe protein interactions in sequence space: application to Mycobacterium tuberculosis. PMID:28376709
Active module identification in intracellular networks using a memetic algorithm with a new binary decoding scheme. PMID:28361692
Combinatorial Ranking of Gene Sets to Predict Disease Relapse: The Retinoic Acid Pathway in Early Prostate Cancer. PMID:28361034
HIVed, a knowledgebase for differentially expressed human genes and proteins during HIV infection, replication and latency. PMID:28358052
Identification of dysregulated genes in rheumatoid arthritis based on bioinformatics analysis. PMID:28316886
Proteome and Protein Network Analyses of Memory T Cells Find Altered Translation and Cell Stress Signaling in Treated Human Immunodeficiency Virus Patients Exhibiting Poor CD4 Recovery. PMID:28293663
Identification of Topological Network Modules in Perturbed Protein Interaction Networks. PMID:28272416
Bioinformatics analysis of the proteins interacting with LASP-1 and their association with HBV-related hepatocellular carcinoma. PMID:28266596
Evolution of protein-protein interaction networks in yeast. PMID:28248977
A c-Myc-regulated stem cell-like signature in high-risk neuroblastoma: A systematic discovery (Target neuroblastoma ESC-like signature). PMID:28246384
Drug voyager: a computational platform for exploring unintended drug action. PMID:28241745
Understanding the roles of intrinsic disorder in subunits of hemoglobin and the disease process of sickle cell anemia. PMID:28232898
Human enterovirus 71 protein interaction network prompts antiviral drug repositioning. PMID:28220872
The OncoPPi network of cancer-focused protein-protein interactions to inform biological insights and therapeutic strategies. PMID:28205554
Weighted gene co-expression network analysis in identification of metastasis-related genes of lung squamous cell carcinoma based on the Cancer Genome Atlas database. PMID:28203405
Haploinsufficiency networks identify targetable patterns of allelic deficiency in low mutation ovarian cancer. PMID:28198375
Time-resolved Phosphoproteome Analysis of Paradoxical RAF Activation Reveals Novel Targets of ERK. PMID:28188228
GPR155 Serves as a Predictive Biomarker for Hematogenous Metastasis in Patients with Gastric Cancer. PMID:28165032
Transcriptome-wide co-expression analysis identifies LRRC2 as a novel mediator of mitochondrial and cardiac function. PMID:28158196
TrypsNetDB: An integrated framework for the functional characterization of trypanosomatid proteins. PMID:28158179
Protein Bioinformatics Databases and Resources. PMID:28150231
SATB1 plays an oncogenic role in esophageal cancer by up-regulation of FN1 and PDGFRB. PMID:28147311
Skewing in Arabidopsis roots involves disparate environmental signaling pathways. PMID:28143395
Therapeutic properties of Scutellaria baicalensis in db/db mice evaluated using Connectivity Map and network pharmacology. PMID:28139721
The integration of weighted human gene association networks based on link prediction. PMID:28137253
Functional Analysis of Kinases and Transcription Factors in Saccharomyces cerevisiae Using an Integrated Overexpression Library. PMID:28122947
GSNFS: Gene subnetwork biomarker identification of lung cancer expression data. PMID:28117655
Functional analysis of keratinocyte and fibroblast gene expression in skin and keloid scar tissue based on deviation analysis of dynamic capabilities. PMID:28101157
Evidence of neofunctionalization after the duplication of the highly conserved Polycomb group gene Caf1-55 in the obscura group of Drosophila. PMID:28094282
AKT1, LKB1, and YAP1 Revealed as MYC Interactors with NanoLuc-Based Protein-Fragment Complementation Assay. PMID:28087810
Non-interacting proteins may resemble interacting proteins: prevalence and implications. PMID:28084410
Automatic query generation using word embeddings for retrieving passages describing experimental methods. PMID:28077568
A Chemogenomic Screen Reveals Novel Snf1p/AMPK Independent Regulators of Acetyl-CoA Carboxylase. PMID:28076367
Systematic Analysis of Transcriptional and Post-transcriptional Regulation of Metabolism in Yeast. PMID:28072816
Unbiased Identification of Blood-based Biomarkers for Pulmonary Tuberculosis by Modeling and Mining Molecular Interaction Networks. PMID:28065665
A Global Analysis of the Receptor Tyrosine Kinase-Protein Phosphatase Interactome. PMID:28065597
ccNET: Database of co-expression networks with functional modules for diploid and polyploid Gossypium. PMID:28053168
The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes. PMID:28053160
Network Centrality Analysis in Fungi Reveals Complex Regulation of Lost and Gained Genes. PMID:28046110
Emerging Roles for Ciz1 in Cell Cycle Regulation and as a Driver of Tumorigenesis. PMID:28036012
Neuroblastoma, a Paradigm for Big Data Science in Pediatric Oncology. PMID:28035989
m6A-Driver: Identifying Context-Specific mRNA m6A Methylation-Driven Gene Interaction Networks. PMID:28027310
Selecting optimal combinations of transcription factors to promote axon regeneration: Why mechanisms matter. PMID:28025113
VaProS: a database-integration approach for protein/genome information retrieval. PMID:28012137
Flexible model-based clustering of mixed binary and continuous data: application to genetic regulation and cancer. PMID:27994031
Identification of disease comorbidity through hidden molecular mechanisms. PMID:27991583
A Data Fusion Approach to Enhance Association Study in Epilepsy. PMID:27984588
Pan- and core- network analysis of co-expression genes in a model plant. PMID:27982071
The BioGRID interaction database: 2017 update. PMID:27980099
Interactomic analysis of REST/NRSF and implications of its functional links with the transcription suppressor TRIM28 during neuronal differentiation. PMID:27976729
Investigating the human Calcineurin Interaction Network using the πɸLxVP SLiM. PMID:27974827
Conservation of coevolving protein interfaces bridges prokaryote-eukaryote homologies in the twilight zone. PMID:27965389
Landscape of Pleiotropic Proteins Causing Human Disease: Structural and System Biology Insights. PMID:27957775
Specificity of broad protein interaction surfaces for proteins with multiple binding partners. PMID:27924264
The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible. PMID:27924014
Differential variation patterns between hubs and bottlenecks in human protein-protein interaction networks. PMID:27903259
AtPID: a genome-scale resource for genotype-phenotype associations in Arabidopsis. PMID:27899679
The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species. PMID:27899636
The TissueNet v.2 database: A quantitative view of protein-protein interactions across human tissues. PMID:27899616
XTalkDB: a database of signaling pathway crosstalk. PMID:27899583
Identification of differentially expressed genes in the development of osteosarcoma using RNA-seq. PMID:27888627
Prediction of Protein-Protein Interactions by Evidence Combining Methods. PMID:27879651
Systematic chemical-genetic and chemical-chemical interaction datasets for prediction of compound synergism. PMID:27874849
Intrinsic disorder in proteins involved in amyotrophic lateral sclerosis. PMID:27838743
Local Action with Global Impact: Highly Similar Infection Patterns of Human Viruses and Bacteriophages. PMID:27822522
Investigating the mechanism of hepatocellular carcinoma progression by constructing genetic and epigenetic networks using NGS data identification and big database mining method. PMID:27821810
Identification of the Key Genes and Pathways in Esophageal Carcinoma. PMID:27818681
EphA2 proteomics in human keratinocytes reveals a novel association with afadin and epidermal tight junctions. PMID:27815408
AMP-activated protein kinase fortifies epithelial tight junctions during energetic stress via its effector GIV/Girdin. PMID:27813479
Characterization and Genetic Analyses of New Genes Coding for NOD2 Interacting Proteins. PMID:27812135
Coupling an EML4-ALK-centric interactome with RNA interference identifies sensitizers to ALK inhibitors. PMID:27811184
mirDNMR: a gene-centered database of background de novo mutation rates in human. PMID:27799474
HIPPIE v2.0: enhancing meaningfulness and reliability of protein-protein interaction networks. PMID:27794551
Elastic-Net Copula Granger Causality for Inference of Biological Networks. PMID:27792750
TcoF-DB v2: update of the database of human and mouse transcription co-factors and transcription factor interactions. PMID:27789689
Incorporating topological information for predicting robust cancer subnetwork markers in human protein-protein interaction network. PMID:27766944
Identification of self-interacting proteins by exploring evolutionary information embedded in PSI-BLAST-constructed position specific scoring matrix. PMID:27732957
Using FlyBase, a Database of Drosophila Genes and Genomes. PMID:27730573
Functional Metabolomics Describes the Yeast Biosynthetic Regulome. PMID:27693354
Prediction and validation of protein-protein interactors from genome-wide DNA-binding data using a knowledge-based machine-learning approach. PMID:27683156
To Unveil the Molecular Mechanisms of Qi and Blood through Systems Biology-Based Investigation into Si-Jun-Zi-Tang and Si-Wu-Tang formulae. PMID:27677604
Exposure to the widely used herbicide atrazine results in deregulation of global tissue-specific RNA transcription in the third generation and is associated with a global decrease of histone trimethylation in mice. PMID:27655631
The Comparative Toxicogenomics Database: update 2017. PMID:27651457
Detecting Cooperativity between Transcription Factors Based on Functional Coherence and Similarity of Their Target Gene Sets. PMID:27623007
DenHunt - A Comprehensive Database of the Intricate Network of Dengue-Human Interactions. PMID:27618709
EPRS is a critical regulator of cell proliferation and estrogen signaling in ER+ breast cancer. PMID:27612429
Implication of Terminal Residues at Protein-Protein and Protein-DNA Interfaces. PMID:27611671
Dynamics of Human Mitochondrial Complex I Assembly: Implications for Neurodegenerative Diseases. PMID:27597947
BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID. PMID:27589962
A Synthetic Dosage Lethal Genetic Interaction Between CKS1B and PLK1 Is Conserved in Yeast and Human Cancer Cells. PMID:27558135
G9a and ZNF644 Physically Associate to Suppress Progenitor Gene Expression during Neurogenesis. PMID:27546533
The G1/S Specific Cyclin D2 Is a Regulator of HIV-1 Restriction in Non-proliferating Cells. PMID:27541004
Robust de novo pathway enrichment with KeyPathwayMiner 5. PMID:27540470
SFRP1 is a possible candidate for epigenetic therapy in non-small cell lung cancer. PMID:27534621
BioC viewer: a web-based tool for displaying and merging annotations in BioC. PMID:27515823
VHLdb: A database of von Hippel-Lindau protein interactors and mutations. PMID:27511743
Membranome: a database for proteome-wide analysis of single-pass membrane proteins. PMID:27510400
A Genome-Scale Investigation of How Sequence, Function, and Tree-Based Gene Properties Influence Phylogenetic Inference. PMID:27492233
Prediction and Validation of Transcription Factors Modulating the Expression of Sestrin3 Gene Using an Integrated Computational and Experimental Approach. PMID:27466818
Systematic identification of protein combinations mediating chromatin looping. PMID:27461729
Unfoldomics of prostate cancer: on the abundance and roles of intrinsically disordered proteins in prostate cancer. PMID:27453073
Investigating the Combinatory Effects of Biological Networks on Gene Co-expression. PMID:27445830
The HSA21 gene EURL/C21ORF91 controls neurogenesis within the cerebral cortex and is implicated in the pathogenesis of Down Syndrome. PMID:27404227
Integrating Transcriptomic and Proteomic Data Using Predictive Regulatory Network Models of Host Response to Pathogens. PMID:27403523
Multi-OMICs and Genome Editing Perspectives on Liver Cancer Signaling Networks. PMID:27403431
A Split-Ubiquitin Based Strategy Selecting for Protein Complex-Interfering Mutations. PMID:27402358
YCRD: Yeast Combinatorial Regulation Database. PMID:27392072
Clinical significance of mitofusin-2 and its signaling pathways in hepatocellular carcinoma. PMID:27389277
HVint: A Strategy for Identifying Novel Protein-Protein Interactions in Herpes Simplex Virus Type 1. PMID:27384951
HPIDB 2.0: a curated database for host-pathogen interactions. PMID:27374121
The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. PMID:27374120
Discovery Proteomics Identifies a Molecular Link between the Coatomer Protein Complex I and Androgen Receptor-dependent Transcription. PMID:27365400
Missense splice variant (g.20746A>G, p.Ile183Val) of interferon gamma receptor 1 (IFNGR1) coincidental with mycobacterial osteomyelitis - a screen of osteoarticular lesions. PMID:27356097
Reconstruction and Application of Protein-Protein Interaction Network. PMID:27338356
Yeast two-hybrid screening identified WDR77 as a novel interacting partner of TSC22D2. PMID:27337956
Comprehensive analysis of high-throughput screens with HiTSeekR. PMID:27330136
Negative autoregulation of BMP dependent transcription by SIN3B splicing reveals a role for RBM39. PMID:27324164
Jumping across biomedical contexts using compressive data fusion. PMID:27307649
Identification of S-phase DNA damage-response targets in fission yeast reveals conservation of damage-response networks. PMID:27298342
Non-random distribution of homo-repeats: links with biological functions and human diseases. PMID:27256590
Future paradigms for precision oncology. PMID:27223079
Research Resources for Nuclear Receptor Signaling Pathways. PMID:27216565
Genome-Wide Inference of Protein-Protein Interaction Networks Identifies Crosstalk in Abscisic Acid Signaling. PMID:27208273
Controllability of protein-protein interaction phosphorylation-based networks: Participation of the hub 14-3-3 protein family. PMID:27195976
Practical aspects of NGS-based pathways analysis for personalized cancer science and medicine. PMID:27191992
Advances in Autophagy Regulatory Mechanisms. PMID:27187479
Inference of biological networks using Bi-directional Random Forest Granger causality. PMID:27186478
Biological function derived from predicted structures in CASP11. PMID:27181425
Frequent mutations in acetylation and ubiquitination sites suggest novel driver mechanisms of cancer. PMID:27175787
Recent advances in large-scale protein interactome mapping. PMID:27158474
Characterizing gene sets using discriminative random walks with restart on heterogeneous biological networks. PMID:27153592
KeyPathwayMinerWeb: online multi-omics network enrichment. PMID:27150809
De novo truncating variants in the AHDC1 gene encoding the AT-hook DNA-binding motif-containing protein 1 are associated with intellectual disability and developmental delay. PMID:27148574
Data-based Reconstruction of Gene Regulatory Networks of Fungal Pathogens. PMID:27148247
Prediction of Synergism from Chemical-Genetic Interactions by Machine Learning. PMID:27136353
APID interactomes: providing proteome-based interactomes with controlled quality for multiple species and derived networks. PMID:27131791
Candidate gene prioritization with Endeavour. PMID:27131783
Positive Selection and Centrality in the Yeast and Fly Protein-Protein Interaction Networks. PMID:27119079
Network-driven plasma proteomics expose molecular changes in the Alzheimer's brain. PMID:27112350
g:Profiler-a web server for functional interpretation of gene lists (2016 update). PMID:27098042
GIANT API: an application programming interface for functional genomics. PMID:27098035
Genome-wide profiles of methylation, microRNAs, and gene expression in chemoresistant breast cancer. PMID:27094684
Tissue repair genes: the TiRe database and its implication for skin wound healing. PMID:27049721
FlyOde - a platform for community curation and interactive visualization of dynamic gene regulatory networks in Drosophila eye development. PMID:26998229
PolyQ 2.0: an improved version of PolyQ, a database of human polyglutamine proteins. PMID:26980520
Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases. PMID:26950747
Large-Scale Profiling of Kinase Dependencies in Cancer Cell Lines. PMID:26947069
Approaches to Investigating Complex Genetic Traits in a Large-Scale Inbred Mouse Aging Study. PMID:26936752
Structure-Based Identification of HDAC8 Non-histone Substrates. PMID:26933971
An Atlas of the Human Kinome Reveals the Mutational Landscape Underlying Dysregulated Phosphorylation Cascades in Cancer. PMID:26921330
PP2A as a master regulator of the cell cycle. PMID:26906453
A Systems Biology Approach to the Coordination of Defensive and Offensive Molecular Mechanisms in the Innate and Adaptive Host-Pathogen Interaction Networks. PMID:26881892
Structural and Functional Characterization of a Caenorhabditis elegans Genetic Interaction Network within Pathways. PMID:26871911
The Sigma-1 Receptor as a Pluripotent Modulator in Living Systems. PMID:26869505
Determining the Composition and Stability of Protein Complexes Using an Integrated Label-Free and Stable Isotope Labeling Strategy. PMID:26867737
Temporal Genetic Modifications after Controlled Cortical Impact--Understanding Traumatic Brain Injury through a Systematic Network Approach. PMID:26861311
Inositol 1,4,5-trisphosphate receptors and their protein partners as signalling hubs. PMID:26830355
Interaction network of tobacco etch potyvirus NIa protein with the host proteome during infection. PMID:26830344
Zfrp8/PDCD2 Interacts with RpS2 Connecting Ribosome Maturation and Gene-Specific Translation. PMID:26807849
Proteomic peptide phage display uncovers novel interactions of the PDZ1-2 supramodule of syntenin. PMID:26787460
Genomic Signatures of Selective Pressures and Introgression from Archaic Hominins at Human Innate Immunity Genes. PMID:26748513
Chromosome-wide histone deacetylation by sirtuins prevents hyperactivation of DNA damage-induced signaling upon replicative stress. PMID:26748095
TRAPLINE: a standardized and automated pipeline for RNA sequencing data analysis, evaluation and annotation. PMID:26738481
Path2PPI: an R package to predict protein-protein interaction networks for a set of proteins. PMID:26733452
Quantitative analysis of the interplay between hsc70 and its co-chaperone HspBP1. PMID:26713263
HitPredict version 4: comprehensive reliability scoring of physical protein-protein interactions from more than 100 species. PMID:26708988
Biocuration with insufficient resources and fixed timelines. PMID:26708987
Search for the Function of NWC, Third Gene Within RAG Locus: Generation and Characterization of NWC-Deficient Mice. PMID:26703212
Bioinformatics Mining and Modeling Methods for the Identification of Disease Mechanisms in Neurodegenerative Disorders. PMID:26690135
Fundamentals of protein interaction network mapping. PMID:26681426
Identification of network-based biomarkers of cardioembolic stroke using a systems biology approach with time series data. PMID:26679092
A deep proteomics perspective on CRM1-mediated nuclear export and nucleocytoplasmic partitioning. PMID:26673895
HRGRN: A Graph Search-Empowered Integrative Database of Arabidopsis Signaling Transduction, Metabolism and Gene Regulation Networks. PMID:26657893
The Proteomic Profile of Deleted in Breast Cancer 1 (DBC1) Interactions Points to a Multifaceted Regulation of Gene Expression. PMID:26657080
PC-TraFF: identification of potentially collaborating transcription factors using pointwise mutual information. PMID:26627005
MacroH2A1 associates with nuclear lamina and maintains chromatin architecture in mouse liver cells. PMID:26603343
Systematic identification and correction of annotation errors in the genetic interaction map of Saccharomyces cerevisiae. PMID:26602688
Transcriptomics of diapause in an isogenic self-fertilizing vertebrate. PMID:26597228
Lynx: a knowledge base and an analytical workbench for integrative medicine. PMID:26590263
Genetic determinants of fibro-osseous lesions in aged inbred mice. PMID:26589134
Experimental detection of short regulatory motifs in eukaryotic proteins: tips for good practice as well as for bad. PMID:26581338
Prediction of Genetic Interactions Using Machine Learning and Network Properties. PMID:26579514
Integrating transcriptional and protein interaction networks to prioritize condition-specific master regulators. PMID:26576632
DESM: portal for microbial knowledge exploration systems. PMID:26546514
Getting the most out of RNA-seq data analysis. PMID:26539333
Survey of Natural Language Processing Techniques in Bioinformatics. PMID:26525745
Integrated interactions database: tissue-specific view of the human and model organism interactomes. PMID:26516188
SynLethDB: synthetic lethality database toward discovery of selective and sensitive anticancer drug targets. PMID:26516187
NCG 5.0: updates of a manually curated repository of cancer genes and associated properties from cancer mutational screenings. PMID:26516186
Building a KATalogue of acetyllysine targeting and function. PMID:26512033
Colorectal cancer atlas: An integrative resource for genomic and proteomic annotations from colorectal cancer cell lines and tissues. PMID:26496946
Integrated multi-omics analyses reveal the pleiotropic nature of the control of gene expression by Puf3p. PMID:26493364
F-actin clustering and cell dysmotility induced by the pathological W148R missense mutation of filamin B at the actin-binding domain. PMID:26491051
Integrative Genomics-Based Discovery of Novel Regulators of the Innate Antiviral Response. PMID:26485378
A Pan-Cancer Catalogue of Cancer Driver Protein Interaction Interfaces. PMID:26485003
Identification of shared and unique susceptibility pathways among cancers of the lung, breast, and prostate from genome-wide association studies and tissue-specific protein interactions. PMID:26483192
Bovine Genome Database: new tools for gleaning function from the Bos taurus genome. PMID:26481361
PlantPAN 2.0: an update of plant promoter analysis navigator for reconstructing transcriptional regulatory networks in plants. PMID:26476450
An overview of bioinformatics methods for modeling biological pathways in yeast. PMID:26476430
Evolutionary rescue by compensatory mutations is constrained by genomic and environmental backgrounds. PMID:26459777
A survey about methods dedicated to epistasis detection. PMID:26442103
ExoCarta: A Web-Based Compendium of Exosomal Cargo. PMID:26434508
High-Throughput Identification of Cis-Regulatory Rewiring Events in Yeast. PMID:26399482
Human protein interaction networks across tissues and diseases. PMID:26347769
Large-scale extraction of gene interactions from full-text literature using DeepDive. PMID:26338771
Targeting SOD1 induces synthetic lethal killing in BLM- and CHEK2-deficient colorectal cancer cells. PMID:26318585
In vivo hematopoietic Myc activation directs a transcriptional signature in endothelial cells within the bone marrow microenvironment. PMID:26308666
ExAtlas: An interactive online tool for meta-analysis of gene expression data. PMID:26223199
Comprehensive Protein Interactome Analysis of a Key RNA Helicase: Detection of Novel Stress Granule Proteins. PMID:26184334
Implications of Big Data for cell biology. PMID:26174066
Surfing the Protein-Protein Interaction Surface Using Docking Methods: Application to the Design of PPI Inhibitors. PMID:26111183
TRRUST: a reference database of human transcriptional regulatory interactions. PMID:26066708
DeAnnCNV: a tool for online detection and annotation of copy number variations from whole-exome sequencing data. PMID:26013811
Databases for Microbiologists. PMID:26013493
Biocuration at the Saccharomyces genome database. PMID:25997651
IMP 2.0: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks. PMID:25969450
Exploiting the yeast stress-activated signaling network to inform on stress biology and disease signaling. PMID:25957506
Systems medicine: evolution of systems biology from bench to bedside. PMID:25891169
Intrinsically disordered proteins and their (disordered) proteomes in neurodegenerative disorders. PMID:25784874
The last enzyme of the de novo purine synthesis pathway 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase (ATIC) plays a central role in insulin signaling and the Golgi/endosomes protein network. PMID:25687571 -
The BioGRID interaction database: 2019 update
PubMed citations: 454.
454 articles citing: The BioGRID interaction database: 2019 update
Gene networks under circadian control exhibit diurnal organization in primate organs. PMID:35906476
Network Embedding Across Multiple Tissues and Data Modalities Elucidates the Context of Host Factors Important for COVID-19 Infection. PMID:35903362
Mitochondrial Oxidative Stress Induces Cardiac Fibrosis in Obese Rats through Modulation of Transthyretin. PMID:35897655
An accurate prediction model of digenic interaction for estimating pathogenic gene pairs of human diseases. PMID:35891796
Integration of probabilistic functional networks without an external Gold Standard. PMID:35879662
Systematic prediction of degrons and E3 ubiquitin ligase binding via deep learning. PMID:35836176
Construction and contextualization approaches for protein-protein interaction networks. PMID:35832626
Deep learning frameworks for protein-protein interaction prediction. PMID:35832624
HumanMine: advanced data searching, analysis and cross-species comparison. PMID:35820040
Bioinformatics-Driven Identification of p62 as A Crucial Oncogene in Liver Cancer. PMID:35814476
RPpocket: An RNA-Protein Intuitive Database with RNA Pocket Topology Resources. PMID:35805909
Aberrant SPOP-CHAF1A ubiquitination axis triggers tumor autophagy that endows a therapeutical vulnerability in diffuse large B cell lymphoma. PMID:35773729
Inferring functional communities from partially observed biological networks exploiting geometric topology and side information. PMID:35760826
Deep learning uncovers distinct behavior of rice network to pathogens response. PMID:35754717
Systematic inference of indirect transcriptional regulation by protein kinases and phosphatases. PMID:35731801
Network approaches for modeling the effect of drugs and diseases. PMID:35704883
Assessing sequence-based protein-protein interaction predictors for use in therapeutic peptide engineering. PMID:35688894
A comprehensive SARS-CoV-2-human protein-protein interactome network identifies pathobiology and host-targeting therapies for COVID-19. PMID:35677070
Estrogen hormone is an essential sex factor inhibiting inflammation and immune response in COVID-19. PMID:35676404
An approach to cellular tropism of SARS-CoV-2 through protein-protein interaction and enrichment analysis. PMID:35672403
Network assisted analysis of de novo variants using protein-protein interaction information identified 46 candidate genes for congenital heart disease. PMID:35671298
Predicting which genes will respond to transcription factor perturbations. PMID:35666184
SSRTool: A web tool for evaluating RNA secondary structure predictions based on species-specific functional interpretability. PMID:35664227
A tensor-based bi-random walks model for protein function prediction. PMID:35637427
Immunopathogenic overlap between COVID-19 and tuberculosis identified from transcriptomic meta-analysis and human macrophage infection. PMID:35634577
Comprehensive Interactome Mapping of Nuclear Receptors Using Proximity Biotinylation. PMID:35612745
Targeting TROY-mediated P85a/AKT/TBX3 signaling attenuates tumor stemness and elevates treatment response in hepatocellular carcinoma. PMID:35610614
GenePlexus: a web-server for gene discovery using network-based machine learning. PMID:35580053
Identification of Potential Muscle Biomarkers in McArdle Disease: Insights from Muscle Proteome Analysis. PMID:35563042
SynLethDB 2.0: a web-based knowledge graph database on synthetic lethality for novel anticancer drug discovery. PMID:35562840
Bioinformatics-Based Approaches to Study Virus-Host Interactions During SARS-CoV-2 Infection. PMID:35554909
SARS-CoV-2 Employ BSG/CD147 and ACE2 Receptors to Directly Infect Human Induced Pluripotent Stem Cell-Derived Kidney Podocytes. PMID:35517495
A hybrid approach unveils drug repurposing candidates targeting an Alzheimer pathophysiology mechanism. PMID:35510183
GURFAP: A Platform for Gene Function Analysis in Glycyrrhiza Uralensis. PMID:35495163
Membranome 3.0: Database of single-pass membrane proteins with AlphaFold models. PMID:35481632
PregTox: A Resource of Knowledge about Drug Fetal Toxicity. PMID:35469349
On the influence of several factors on pathway enrichment analysis. PMID:35453140
Phosphate dysregulation via the XPR1-KIDINS220 protein complex is a therapeutic vulnerability in ovarian cancer. PMID:35437317
Integrative Analysis for Identification of Therapeutic Targets and Prognostic Signatures in Non-Small Cell Lung Cancer. PMID:35422618
Phylogenetic profiling in eukaryotes: The effect of species, orthologous group, and interactome selection on protein interaction prediction. PMID:35421089
Predicted mouse interactome and network-based interpretation of differentially expressed genes. PMID:35390003
DWPPI: A Deep Learning Approach for Predicting Protein-Protein Interactions in Plants Based on Multi-Source Information With a Large-Scale Biological Network. PMID:35387292
Multiomic profiling of the acute stress response in the mouse hippocampus. PMID:35383160
CPIELA: Computational Prediction of Plant Protein-Protein Interactions by Ensemble Learning Approach From Protein Sequences and Evolutionary Information. PMID:35360876
Computational methods, databases and tools for synthetic lethality prediction. PMID:35352098
Protein Biomarkers in Monocytes and CD4+ Lymphocytes for Predicting Lithium Treatment Response of Bipolar Disorder: a Feasibility Study with Tyramine-Based Signal-Amplified Flow Cytometry. PMID:35342205
Serine hydroxymethyltransferase 2 (SHMT2) potentiates the aggressive process of oral squamous cell carcinoma by binding to interleukin enhancer-binding factor 2 (ILF2). PMID:35333683
Dynamical Analysis of a Boolean Network Model of the Oncogene Role of lncRNA ANRIL and lncRNA UFC1 in Non-Small Cell Lung Cancer. PMID:35327612
BRCA1 mutations in high-grade serous ovarian cancer are associated with proteomic changes in DNA repair, splicing, transcription regulation and signaling. PMID:35292711
A comprehensive WGS-based pipeline for the identification of new candidate genes in inherited retinal dystrophies. PMID:35246562
Host-microbiome protein-protein interactions capture disease-relevant pathways. PMID:35246229
The microprotein Nrs1 rewires the G1/S transcriptional machinery during nitrogen limitation in budding yeast. PMID:35239649
PSINDB: the postsynaptic protein-protein interaction database. PMID:35234850
Comprehensive Analysis of the Glycolysis-Related Gene Prognostic Signature and Immune Infiltration in Endometrial Cancer. PMID:35223866
Functional network motifs defined through integration of protein-protein and genetic interactions. PMID:35223214
Antifungal activity of an artificial peptide aptamer SNP-D4 against Fusarium oxysporum. PMID:35223198
Single-Cell Technologies to Decipher the Immune Microenvironment in Myeloid Neoplasms: Perspectives and Opportunities. PMID:35186713
The S100A7 nuclear interactors in autoimmune diseases: a coevolutionary study in mammals. PMID:35174412
KeyPathwayMineR: De Novo Pathway Enrichment in the R Ecosystem. PMID:35173764
Using Surface Hydrophobicity Together with Empirical Potentials to Identify Protein-Protein Binding Sites: Application to the Interactions of E-cadherins. PMID:35167069
The Landscape of Aminoacyl-tRNA Synthetases Involved in Severe Acute Respiratory Syndrome Coronavirus 2 Infection. PMID:35153822
An Integrative Network Approach to Identify Common Genes for the Therapeutics in Tuberculosis and Its Overlapping Non-Communicable Diseases. PMID:35153741
Chemoproteomic-enabled characterization of small GTPase Rab1a as a target of an N-arylbenzimidazole ligand's rescue of Parkinson's-associated cell toxicity. PMID:35128413
Transcriptomic Landscape of Herbivore Oviposition in Arabidopsis: A Systematic Review. PMID:35126411
Structure-based prediction of HDAC6 substrates validated by enzymatic assay reveals determinants of promiscuity and detects new potential substrates. PMID:35110592
Comparative assessment of genes driving cancer and somatic evolution in non-cancer tissues: an update of the Network of Cancer Genes (NCG) resource. PMID:35078504
Towards an Ideal In Cell Hybridization-Based Strategy to Discover Protein Interactomes of Selected RNA Molecules. PMID:35055128
Correcting Differential Gene Expression Analysis for Cyto-Architectural Alterations in Substantia Nigra of Parkinson's Disease Patients Reveals Known and Potential Novel Disease-Associated Genes and Pathways. PMID:35053314
Multi-time scale transcriptomic analysis on the dynamic process of tamoxifen resistance development in breast cancer cell lines. PMID:35041152
Plant Reactome and PubChem: The Plant Pathway and (Bio)Chemical Entity Knowledgebases. PMID:35037224
RNA-binding protein p54nrb/NONO potentiates nuclear EGFR-mediated tumorigenesis of triple-negative breast cancer. PMID:35013116
RAD50 deficiency is a predictor of platinum sensitivity in sporadic epithelial ovarian cancers. PMID:35006434
Meta-analysis of whole-genome gene expression datasets assessing the effects of IDH1 and IDH2 mutations in isogenic disease models. PMID:34997121
Potential Molecular Mechanisms and Remdesivir Treatment for Acute Respiratory Syndrome Corona Virus 2 Infection/COVID 19 Through RNA Sequencing and Bioinformatics Analysis. PMID:34992355
Single-cell transcriptome atlas of human mesenchymal stem cells exploring cellular heterogeneity. PMID:34965030
Data analysis methods for defining biomarkers from omics data. PMID:34951658
Spatial and Temporal Expression of High-Mobility-Group Nucleosome-Binding (HMGN) Genes in Brain Areas Associated with Cognition in Individuals with Down Syndrome. PMID:34946949
GRWD1-WDR5-MLL2 Epigenetic Complex Mediates H3K4me3 Mark and Is Essential for Kaposi's Sarcoma-Associated Herpesvirus-Induced Cellular Transformation. PMID:34933446
Small molecules for cell reprogramming: a systems biology analysis. PMID:34919532
Where all the Roads Meet? A Crossover Perspective on Host Factors Regulating SARS-CoV-2 infection. PMID:34914966
Protein-protein interactions: Methods, databases, and applications in virus-host study. PMID:34909403
Improving Analysis and Annotation of Microarray Data with Protein Interactions. PMID:34902122
Shared Molecular Mechanisms between Atherosclerosis and Periodontitis by Analyzing the Transcriptomic Alterations of Peripheral Blood Monocytes. PMID:34899963
Interrogating cell type-specific cooperation of transcriptional regulators in 3D chromatin. PMID:34888502
Metabolic endophenotype associated with right ventricular glucose uptake in pulmonary hypertension. PMID:34888034
Computational Network Pharmacology-Based Strategy to Capture Key Functional Components and Decode the Mechanism of Chai-Hu-Shu-Gan-San in Treating Depression. PMID:34867413
GFI1 tethers the NuRD complex to open and transcriptionally active chromatin in myeloid progenitors. PMID:34857890
Multiscale interactome analysis coupled with off-target drug predictions reveals drug repurposing candidates for human coronavirus disease. PMID:34857794
Functional enrichment of alternative splicing events with NEASE reveals insights into tissue identity and diseases. PMID:34857024
Inhibitor tolerance and bioethanol fermentability of levoglucosan-utilizing Escherichia coli were enhanced by overexpression of stress-responsive gene ycfR: The proteomics-guided metabolic engineering. PMID:34853817
BP180/Collagen XVII: A Molecular View. PMID:34830116
Transcription Factor Action Orchestrates the Complex Expression Pattern of CRABS CLAW in Arabidopsis. PMID:34828269
CyFi-MAP: an interactive pathway-based resource for cystic fibrosis. PMID:34782688
Pairwise Biological Network Alignment Based on Discrete Bat Algorithm. PMID:34777564
Individualized Proteogenomics Reveals the Mutational Landscape of Melanoma Patients in Response to Immunotherapy. PMID:34771574
Systematic Analysis of FASTK Gene Family Alterations in Cancer. PMID:34768773
Computational methods for protein localization prediction. PMID:34765098
Recognition of DNA Methylation Molecular Features for Diagnosis and Prognosis in Gastric Cancer. PMID:34745226
TcoFBase: a comprehensive database for decoding the regulatory transcription co-factors in human and mouse. PMID:34718747
Proximity-dependent biotin identification (BioID) reveals a dynamic LSD1-CoREST interactome during embryonic stem cell differentiation. PMID:34709266
A Graph Feature Auto-Encoder for the prediction of unobserved node features on biological networks. PMID:34706640
ANAT 3.0: a framework for elucidating functional protein subnetworks using graph-theoretic and machine learning approaches. PMID:34706638
A Markov random field model for network-based differential expression analysis of single-cell RNA-seq data. PMID:34702190
Biallelic FRA10AC1 variants cause a neurodevelopmental disorder with growth retardation. PMID:34694367
DeepTrio: a ternary prediction system for protein-protein interaction using mask multiple parallel convolutional neural networks. PMID:34694333
Precise Characterization of Genetic Interactions in Cancer via Molecular Network Refining Processes. PMID:34681774
Proteogenomics Reveals Perturbed Signaling Networks in Malignant Melanoma Cells Resistant to BRAF Inhibition. PMID:34673281
Sequence-Based Prediction of Plant Protein-Protein Interactions by Combining Discrete Sine Transformation With Rotation Forest. PMID:34671178
Two classes of functional connectivity in dynamical processes in networks. PMID:34665977
SYNBIP: synthetic binding proteins for research, diagnosis and therapy. PMID:34664670
Network potential identifies therapeutic miRNA cocktails in Ewing sarcoma. PMID:34662337
A Systematic Analysis Identifies Key Regulators Involved in Cell Proliferation and Potential Drugs for the Treatment of Human Lung Adenocarcinoma. PMID:34650921
Differential Transcriptional Regulation of Polymorphic p53 Codon 72 in Metabolic Pathways. PMID:34639134
Predicting PY motif-mediated protein-protein interactions in the Nedd4 family of ubiquitin ligases. PMID:34637467
SignaLink3: a multi-layered resource to uncover tissue-specific signaling networks. PMID:34634810
A survey on computational methods in discovering protein inhibitors of SARS-CoV-2. PMID:34623382
An overview of machine learning methods for monotherapy drug response prediction. PMID:34619752
iRegNet: an integrative Regulatory Network analysis tool for Arabidopsis thaliana. PMID:34618085
Estrogen Hormone Is an Essential Sex Factor Inhibiting Inflammation and Immune Response in COVID-19. PMID:34611658
Systems biology analysis of lung fibrosis-related genes in the bleomycin mouse model. PMID:34588506
CPLM 4.0: an updated database with rich annotations for protein lysine modifications. PMID:34581824
Defining Functions of Mannoproteins in Saccharomyces cerevisiae by High-Dimensional Morphological Phenotyping. PMID:34575807
Network neighbors of viral targets and differentially expressed genes in COVID-19 are drug target candidates. PMID:34556735
Vtc5 Is Localized to the Vacuole Membrane by the Conserved AP-3 Complex to Regulate Polyphosphate Synthesis in Budding Yeast. PMID:34544285
Proteomic Tools for the Analysis of Cytoskeleton Proteins. PMID:34542864
GRASP55 restricts early-stage autophagy and regulates spatial organization of the early secretory network. PMID:34533192
The protein-protein interaction network alignment using recurrent neural network. PMID:34529185
Time-resolved in vivo ubiquitinome profiling by DIA-MS reveals USP7 targets on a proteome-wide scale. PMID:34518535
MOV10 Helicase Interacts with Coronavirus Nucleocapsid Protein and Has Antiviral Activity. PMID:34517762
Protein Arginine Methyltransferase 5 Functions via Interacting Proteins. PMID:34513846
ACE2 Netlas: In silico Functional Characterization and Drug-Gene Interactions of ACE2 Gene Network to Understand Its Potential Involvement in COVID-19 Susceptibility. PMID:34512723
Identifying Protein Complexes With Clear Module Structure Using Pairwise Constraints in Protein Interaction Networks. PMID:34512712
A functionally divergent intrinsically disordered region underlying the conservation of stochastic signaling. PMID:34506483
Mitochondria-localized AMPK responds to local energetics and contributes to exercise and energetic stress-induced mitophagy. PMID:34493662
Arabidopsis-Based Dual-Layered Biological Network Analysis Elucidates Fully Modulated Pathways Related to Sugarcane Resistance on Biotrophic Pathogen Infection. PMID:34490009
Machine learning methods, databases and tools for drug combination prediction. PMID:34477201
ACAA2 is a ligand-dependent coactivator for thyroid hormone receptor β1. PMID:34474245
Secreted retrovirus-like GAG-domain-containing protein PEG10 is regulated by UBE3A and is involved in Angelman syndrome pathophysiology. PMID:34467244
CANVS: an easy-to-use application for the analysis and visualization of mass spectrometry-based protein-protein interaction/association data. PMID:34432510
MetaCancer: A deep learning-based pan-cancer metastasis prediction model developed using multi-omics data. PMID:34429856
MeCP2 prevents age-associated cognitive decline via restoring synaptic plasticity in a senescence-accelerated mouse model. PMID:34363729
Global effects of RAB3GAP1 dysexpression on the proteome of mouse cortical neurons. PMID:34363538
Investigation of RNA metabolism through large-scale genetic interaction profiling in yeast. PMID:34358317
Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture. PMID:34357701
Thiol-disulphide independent in-cell trapping for the identification of peroxiredoxin 2 interactors. PMID:34340028
Comprehensive Analysis of the Value of SMYD Family Members in the Prognosis and Immune Infiltration of Malignant Digestive System Tumors. PMID:34335697
Multimodal single-cell omics analysis identifies epithelium-immune cell interactions and immune vulnerability associated with sex differences in COVID-19. PMID:34330889
Targeted capture sequencing identifies genetic variations of GRK4 and RDH8 in Han Chinese with essential hypertension in Xinjiang. PMID:34297769
Identification and Validation of Potential Biomarkers and Pathways for Idiopathic Pulmonary Fibrosis by Comprehensive Bioinformatics Analysis. PMID:34285914
YPIBP: A repository for phosphoinositide-binding proteins in yeast. PMID:34285772
An integrative study of genetic variants with brain tissue expression identifies viral etiology and potential drug targets of multiple sclerosis. PMID:34284104
NTNG1 Modulates Cisplatin Resistance in Epithelial Ovarian Cancer Cells via the GAS6/AXL/Akt Pathway. PMID:34277602
A computational and structural analysis of germline and somatic variants affecting the DDR mechanism, and their impact on human diseases. PMID:34253785
Loss of UCHL1 rescues the defects related to Parkinson's disease by suppressing glycolysis. PMID:34244144
A quantitative yeast aging proteomics analysis reveals novel aging regulators. PMID:34241809
The Silence of PSMC6 Inhibits Cell Growth and Metastasis in Lung Adenocarcinoma. PMID:34239933
Databases for Protein-Protein Interactions. PMID:34236665
Integrated analysis of Shank1 PDZ interactions with C-terminal and internal binding motifs. PMID:34235485
Integration of transcriptomic data identifies key hallmark genes in hypertrophic cardiomyopathy. PMID:34225646
Linear functional organization of the omic embedding space. PMID:34213534
Pathogen Moonlighting Proteins: From Ancestral Key Metabolic Enzymes to Virulence Factors. PMID:34203698
Towards a global investigation of transcriptomic signatures through co-expression networks and pathway knowledge for the identification of disease mechanisms. PMID:34197603
A systems pharmacology approach based on oncogenic signalling pathways to determine the mechanisms of action of natural products in breast cancer from transcriptome data. PMID:34193143
Network-based analysis of virulence factors for uncovering Aeromonas veronii pathogenesis. PMID:34162325
Precision omics data integration and analysis with interoperable ontologies and their application for COVID-19 research. PMID:34159360
Insights into how environment shapes post-mortem RNA transcription in mouse brain. PMID:34155272
Interferon-Gamma-Producing CD8+ Tissue Resident Memory T Cells Are a Targetable Hallmark of Immune Checkpoint Inhibitor-Colitis. PMID:34147519
Dynamic Host Immune and Transcriptomic Responses to Respiratory Syncytial Virus Infection in a Vaccination-Challenge Mouse Model. PMID:34138405
Making fundamental scientific discoveries by combining information from literature, databases, and computational tools - An example. PMID:34136100
Matrix-screening reveals a vast potential for direct protein-protein interactions among RNA binding proteins. PMID:34133714
The expression and clinical prognostic value of protein phosphatase 1 catalytic subunit beta in pancreatic cancer. PMID:34125004
Target identification among known drugs by deep learning from heterogeneous networks. PMID:34123272
DeepR2cov: deep representation learning on heterogeneous drug networks to discover anti-inflammatory agents for COVID-19. PMID:34117734
Integrating protein networks and machine learning for disease stratification in the Hereditary Spastic Paraplegias. PMID:34113825
Network medicine links SARS-CoV-2/COVID-19 infection to brain microvascular injury and neuroinflammation in dementia-like cognitive impairment. PMID:34108016
PIGNON: a protein-protein interaction-guided functional enrichment analysis for quantitative proteomics. PMID:34088263
Functional characterization of RebL1 highlights the evolutionary conservation of oncogenic activities of the RBBP4/7 orthologue in Tetrahymena thermophila. PMID:34086947
A Genetic Study of Cerebral Atherosclerosis Reveals Novel Associations with NTNG1 and CNOT3. PMID:34073619
Model-based analysis uncovers mutations altering autophagy selectivity in human cancer. PMID:34059679
Natural variants suppress mutations in hundreds of essential genes. PMID:34042294
Genetic interaction network has a very limited impact on the evolutionary trajectories in continuous culture-grown populations of yeast. PMID:34039270
driveR: a novel method for prioritizing cancer driver genes using somatic genomics data. PMID:34030627
Circulating hsa-miR-323b-3p in Huntington's Disease: A Pilot Study. PMID:34025560
KEA3: improved kinase enrichment analysis via data integration. PMID:34019655
A computational approach for detecting physiological homogeneity in the midst of genetic heterogeneity. PMID:34015270
An overview of graph databases and their applications in the biomedical domain. PMID:34003247
Targeting SUMOylation dependency in human cancer stem cells through a unique SAE2 motif revealed by chemical genomics. PMID:33979648
A unified resource and configurable model of the synapse proteome and its role in disease. PMID:33976238
Timer-based proteomic profiling of the ubiquitin-proteasome system reveals a substrate receptor of the GID ubiquitin ligase. PMID:33974913
CLEP: A Hybrid Data- and Knowledge- Driven Framework for Generating Patient Representations. PMID:33964127
Proteo3Dnet: a web server for the integration of structural information with interactomics data. PMID:33963857
Dual proteome-scale networks reveal cell-specific remodeling of the human interactome. PMID:33961781
A New Sequential Forward Feature Selection (SFFS) Algorithm for Mining Best Topological and Biological Features to Predict Protein Complexes from Protein-Protein Interaction Networks (PPINs). PMID:33959851
Employing core regulatory circuits to define cell identity. PMID:33934382
The EAR Motif in the Arabidopsis MADS Transcription Factor AGAMOUS-Like 15 Is Not Necessary to Promote Somatic Embryogenesis. PMID:33924312
An integrative drug repositioning framework discovered a potential therapeutic agent targeting COVID-19. PMID:33895786
The VRNetzer platform enables interactive network analysis in Virtual Reality. PMID:33893283
Genetic Architecture Underlying Nascent Speciation-The Evolution of Eurasian Pigs under Domestication. PMID:33892509
Correlation AnalyzeR: functional predictions from gene co-expression correlations. PMID:33879054
Modeling transcriptional regulation using gene regulatory networks based on multi-omics data sources. PMID:33874910
Algorithm-Based Meta-Analysis Reveals the Mechanistic Interaction of the Tumor Suppressor LIMD1 With Non-Small-Cell Lung Carcinoma. PMID:33869018
RRM2B Is Frequently Amplified Across Multiple Tumor Types: Implications for DNA Repair, Cellular Survival, and Cancer Therapy. PMID:33868369
Non-Genomic AhR-Signaling Modulates the Immune Response in Endotoxin-Activated Macrophages After Activation by the Environmental Stressor BaP. PMID:33868237
PCprophet: a framework for protein complex prediction and differential analysis using proteomic data. PMID:33859439
A novel predicted ADP-ribosyltransferase-like family conserved in eukaryotic evolution. PMID:33854844
A combined RAD-Seq and WGS approach reveals the genomic basis of yellow color variation in bumble bee Bombus terrestris. PMID:33846496
Exploring the Imbalance of Periodontitis Immune System From the Cellular to Molecular Level. PMID:33841510
High ELF4 expression in human cancers is associated with worse disease outcomes and increased resistance to anticancer drugs. PMID:33836003
Reprogramming enriches for somatic cell clones with small-scale mutations in cancer-associated genes. PMID:33831558
Posttranslational modifications in proteins: resources, tools and prediction methods. PMID:33826699
In silico investigation of the viroporin E as a vaccine target against SARS-CoV-2. PMID:33822639
A bioinformatic analysis of the inhibin-betaglycan-endoglin/CD105 network reveals prognostic value in multiple solid tumors. PMID:33819300
Network bioinformatics analysis provides insight into drug repurposing for COVID-19. PMID:33817623
Improved sequence-based prediction of interaction sites in α-helical transmembrane proteins by deep learning. PMID:33815689
Huntingtin: A Protein with a Peculiar Solvent Accessible Surface. PMID:33809039
Quantitative Proteomic Approach Reveals Altered Metabolic Pathways in Response to the Inhibition of Lysine Deacetylases in A549 Cells under Normoxia and Hypoxia. PMID:33806075
Detection of H3K4me3 Identifies NeuroHIV Signatures, Genomic Effects of Methamphetamine and Addiction Pathways in Postmortem HIV+ Brain Specimens that Are Not Amenable to Transcriptome Analysis. PMID:33805201
Assessing the Function of the ZFP90 Variant rs1170426 in SLE and the Association Between SLE Drug Target and Susceptibility Genes. PMID:33796098
Network medicine links SARS-CoV-2/COVID-19 infection to brain microvascular injury and neuroinflammation in dementia-like cognitive impairment. PMID:33791705
A Critical Role of Peptidylprolyl Isomerase A Pseudogene 22/microRNA-197-3p/Peptidylprolyl Isomerase A Axis in Hepatocellular Carcinoma. PMID:33790943
Loss of the abasic site sensor HMCES is synthetic lethal with the activity of the APOBEC3A cytosine deaminase in cancer cells. PMID:33788831
Protein interaction potential landscapes for yeast replicative aging. PMID:33785798
Genome-wide RNAi screen for regulators of UPRmt in Caenorhabditis elegans mutants with defects in mitochondrial fusion. PMID:33784383
Adenosine Receptor and Its Downstream Targets, Mod(mdg4) and Hsp70, Work as a Signaling Pathway Modulating Cytotoxic Damage in Drosophila. PMID:33777958
The Genetic and Epigenetic Mechanisms Involved in Irreversible Pulp Neural Inflammation. PMID:33777260
Versatile knowledge guided network inference method for prioritizing key regulatory factors in multi-omics data. PMID:33762588
SH3BP4 promotes neuropilin-1 and α5-integrin endocytosis and is inhibited by Akt. PMID:33761321
Integrated intra- and intercellular signaling knowledge for multicellular omics analysis. PMID:33749993
Integrating 3D structural information into systems biology. PMID:33744294
Identification of disease treatment mechanisms through the multiscale interactome. PMID:33741907
Genetic Interaction Network Interpretation: A Tidy Data Science Perspective. PMID:33733367
Molecular clues in the regulation of mini-puberty involve neuronal DNA binding transcription factor NHLH2. PMID:33731013
Gene variants of coagulation related proteins that interact with SARS-CoV-2. PMID:33730015
Mapping specificity, cleavage entropy, allosteric changes and substrates of blood proteases in a high-throughput screen. PMID:33727531
Alternatively Splicing Interactomes Identify Novel Isoform-Specific Partners for NSD2. PMID:33718354
Do Molecular Profiles of Primary Versus Metastatic Radioiodine Refractory Differentiated Thyroid Cancer Differ? PMID:33716974
Soluble ACE2-mediated cell entry of SARS-CoV-2 via interaction with proteins related to the renin-angiotensin system. PMID:33713620
Integrative analysis regarding the correlation between GAS2 family genes and human glioma prognosis. PMID:33713047
B7-H6 is a new potential biomarker and therapeutic target of T-lymphoblastic lymphoma. PMID:33708955
Systemic Multi-Omics Analysis Reveals Amplified P4HA1 Gene Associated With Prognostic and Hypoxic Regulation in Breast Cancer. PMID:33692831
Mutational Pattern in Multiple Pulmonary Nodules Are Associated With Early Stage Lung Adenocarcinoma. PMID:33680914
HIR V2: a human interactome resource for the biological interpretation of differentially expressed genes via gene set linkage analysis. PMID:33677507
Structural basis for the DNA-binding activity of human ARID4B Tudor domain. PMID:33675746
Molecular disruption of DNA polymerase β for platinum sensitisation and synthetic lethality in epithelial ovarian cancers. PMID:33674744
The overexpression of DNA repair genes in invasive ductal and lobular breast carcinomas: Insights on individual variations and precision medicine. PMID:33662042
Dual DNA and protein tagging of open chromatin unveils dynamics of epigenomic landscapes in leukemia. PMID:33649590
Cysteinyl-specialized proresolving mediators link resolution of infectious inflammation and tissue regeneration via TRAF3 activation. PMID:33649212
Hippocampal transcriptome-wide association study and neurobiological pathway analysis for Alzheimer's disease. PMID:33630843
Identification of host proteins differentially associated with HIV-1 RNA splice variants. PMID:33629952
Evolution, structure and emerging roles of C1ORF112 in DNA replication, DNA damage responses, and cancer. PMID:33625522
Ageing transcriptome meta-analysis reveals similarities and differences between key mammalian tissues. PMID:33611312
Genome-wide association analysis of cognitive function in Danish long-lived individuals. PMID:33607172
The Srs2 helicase dampens DNA damage checkpoint by recycling RPA from chromatin. PMID:33602817
WDR5 facilitates EMT and metastasis of CCA by increasing HIF-1α accumulation in Myc-dependent and independent pathways. PMID:33601056
Differentiation of two human neuroblastoma cell lines alters SV2 expression patterns. PMID:33588752
The CLAIRE COVID-19 initiative: approach, experiences and recommendations. PMID:33584129
Systematic characterization of mutations altering protein degradation in human cancers. PMID:33567269
RNA Sequencing Reveals Distinct Immune Responses in the Chorioamniotic Membranes of Women with Preterm Labor and Microbial or Sterile Intra-amniotic Inflammation. PMID:33558326
Bioinformatics analyses of significant genes, related pathways, and candidate diagnostic biomarkers and molecular targets in SARS-CoV-2/COVID-19. PMID:33553808
BioMaster: An Integrated Database and Analytic Platform to Provide Comprehensive Information About BioBrick Parts. PMID:33552037
Protein-protein interaction analysis reveals a novel cancer stem cell related target TMEM17 in colorectal cancer. PMID:33549114
Degree Adjusted Large-Scale Network Analysis Reveals Novel Putative Metabolic Disease Genes. PMID:33546175
Convergent organization of aberrant MYB complex controls oncogenic gene expression in acute myeloid leukemia. PMID:33527899
Human pathways in animal models: possibilities and limitations. PMID:33524155
The translocon-associated protein (TRAP) complex regulates quality control of N-linked glycosylation during ER stress. PMID:33523898
Structural similarity-based prediction of host factors associated with SARS-CoV-2 infection and pathogenesis. PMID:33506741
Intestinal mRNA expression profile and bioinformatics analysis in a methamphetamine-induced mouse model of inflammatory bowel disease. PMID:33490181
NLPEI: A Novel Self-Interacting Protein Prediction Model Based on Natural Language Processing and Evolutionary Information. PMID:33488064
Ontological modeling and analysis of experimentally or clinically verified drugs against coronavirus infection. PMID:33441564
Application of graphical lasso in estimating network structure in gene set. PMID:33437755
Combined RNA/tissue profiling identifies novel Cancer/testis genes. PMID:33426787
An Integrative Computational Approach for the Prediction of Human-Plasmodium Protein-Protein Interactions. PMID:33426052
Model systems for studying polyphosphate biology: a focus on microorganisms. PMID:33420907
Identification and Characterization of Plant-Interacting Targets of Tomato Spotted Wilt Virus Silencing Suppressor. PMID:33401462
Distinct p63 and p73 Protein Interactions Predict Specific Functions in mRNA Splicing and Polyploidy Control in Epithelia. PMID:33375680
Metric Labeling and Semimetric Embedding for Protein Annotation Prediction. PMID:33370163
PICKLE 3.0: Enriching the human Meta-database with the mouse protein interactome extended via mouse-human orthology. PMID:33367505
Dosage-sensitive molecular mechanisms are associated with the tissue-specificity of traits and diseases. PMID:33363699
Multi-resolution visualization and analysis of biomolecular networks through hierarchical community detection and web-based graphical tools. PMID:33351828
Mouse Embryonic Fibroblast Adipogenic Potential: A Comprehensive Transcriptome Analysis. PMID:33345692
SECAT: Quantifying Protein Complex Dynamics across Cell States by Network-Centric Analysis of SEC-SWATH-MS Profiles. PMID:33333029
TMEM132A, a Novel Wnt Signaling Pathway Regulator Through Wntless (WLS) Interaction. PMID:33324648
Differential Co-Expression Analyses Allow the Identification of Critical Signalling Pathways Altered during Tumour Transformation and Progression. PMID:33322692
Protein Interaction Network Biology in Neuroscience. PMID:33314619
Suboptimal Global Transcriptional Response Increases the Harmful Effects of Loss-of-Function Mutations. PMID:33306797
Applications and advancements of FT-ICR-MS for interactome studies. PMID:33289940
Active Learning for Node Classification: An Evaluation. PMID:33286933
A Novel Proximity Biotinylation Assay Based on the Self-Associating Split GFP1-10/11. PMID:33276494
CovMulNet19, Integrating Proteins, Diseases, Drugs, and Symptoms: A Network Medicine Approach to COVID-19. PMID:33274348
Filamin A Orchestrates Cytoskeletal Structure, Cell Migration and Stem Cell Characteristics in Human Seminoma TCam-2 Cells. PMID:33266100
Drug2ways: Reasoning over causal paths in biological networks for drug discovery. PMID:33264280
Towards a unified open access dataset of molecular interactions. PMID:33262342
A ligand-based computational drug repurposing pipeline using KNIME and Programmatic Data Access: case studies for rare diseases and COVID-19. PMID:33250934
TRP Channels Regulation of Rho GTPases in Brain Context and Diseases. PMID:33240883
A thorough analysis of the contribution of experimental, derived and sequence-based predicted protein-protein interactions for functional annotation of proteins. PMID:33237964
The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets. PMID:33237311
PINA 3.0: mining cancer interactome. PMID:33231689
Inferring the molecular and phenotypic impact of amino acid variants with MutPred2. PMID:33219223
Predicted rat interactome database and gene set linkage analysis. PMID:33216897
Emerging Evidences for an Implication of the Neurodegeneration-Associated Protein TAU in Cancer. PMID:33207722
The IMEx coronavirus interactome: an evolving map of Coronaviridae-host molecular interactions. PMID:33206959
In silico and in vitro studies reveal complement system drives coagulation cascade in SARS-CoV-2 pathogenesis. PMID:33200027
DPPN-SVM: Computational Identification of Mis-Localized Proteins in Cancers by Integrating Differential Gene Expressions With Dynamic Protein-Protein Interaction Networks. PMID:33193746
Virtual screening and network pharmacology-based synergistic mechanism identification of multiple components contained in Guanxin V against coronary artery disease. PMID:33187508
YQFC: a web tool to compare quantitative biological features between two yeast gene lists. PMID:33186464
A ubiquitin ligase mediates target-directed microRNA decay independently of tailing and trimming. PMID:33184234
LL-37-Induced Autophagy Contributed to the Elimination of Live Porphyromonas gingivalis Internalized in Keratinocytes. PMID:33178622
Amyotrophic Lateral Sclerosis Is Accompanied by Protein Derangements in the Olfactory Bulb-Tract Axis. PMID:33167591
A network medicine approach to investigation and population-based validation of disease manifestations and drug repurposing for COVID-19. PMID:33156843
Human Gene Functional Network-Informed Prediction of HIV-1 Host Dependency Factors. PMID:33144314
ACE2 Netlas: In-silico functional characterization and drug-gene interactions of ACE2 gene network to understand its potential involvement in COVID-19 susceptibility. PMID:33140059
BIKE regulates dengue virus infection and is a cellular target for broad-spectrum antivirals. PMID:33137362
iCSDB: an integrated database of CRISPR screens. PMID:33137185
Synthetic Lethality through the Lens of Medicinal Chemistry. PMID:33135887
TCONS_00012883 promotes proliferation and metastasis via DDX3/YY1/MMP1/PI3K-AKT axis in colorectal cancer. PMID:33135346
IHP-PING-generating integrated human protein-protein interaction networks on-the-fly. PMID:33129201
Plasma Proteomics Identify Biomarkers and Pathogenesis of COVID-19. PMID:33128875
FFAT motif phosphorylation controls formation and lipid transfer function of inter-organelle contacts. PMID:33124732
Designing a Network Proximity-Based Drug Repurposing Strategy for COVID-19. PMID:33123533
In silico Method in CRISPR/Cas System: An Expedite and Powerful Booster. PMID:33123486
Virus-Host Protein-Protein Interactions between Human Papillomavirus 16 E6 A1 and D2/D3 Sub-Lineages: Variances and Similarities. PMID:33121134
Comprehensive Evaluation of Endocytosis-Associated Protein SCAMP3 in Hepatocellular Carcinoma. PMID:33116758
Roles of Farnesyl-Diphosphate Farnesyltransferase 1 in Tumour and Tumour Microenvironments. PMID:33113804
FlyRNAi.org-the database of the Drosophila RNAi screening center and transgenic RNAi project: 2021 update. PMID:33104800
Evolution of Sequence-based Bioinformatics Tools for Protein-protein Interaction Prediction. PMID:33093807
Assessing the Direct Binding of Ark-Like E3 RING Ligases to Ubiquitin and Its Implication on Their Protein Interaction Network. PMID:33086510
Predicted functional interactome of Caenorhabditis elegans and a web tool for the functional interpretation of differentially expressed genes. PMID:33076954
The BioGRID database: A comprehensive biomedical resource of curated protein, genetic, and chemical interactions. PMID:33070389
Comparative Toxicogenomics Database (CTD): update 2021. PMID:33068428
A review of protein-protein interaction network alignment: From pathway comparison to global alignment. PMID:33033584
Serpin peptidase inhibitor clade A member 1-overexpression in gastric cancer promotes tumor progression in vitro and is associated with poor prognosis. PMID:33014156
Pseudo2GO: A Graph-Based Deep Learning Method for Pseudogene Function Prediction by Borrowing Information From Coding Genes. PMID:33014009
CRISP-view: a database of functional genetic screens spanning multiple phenotypes. PMID:33010154
In-silico drug repurposing study predicts the combination of pirfenidone and melatonin as a promising candidate therapy to reduce SARS-CoV-2 infection progression and respiratory distress caused by cytokine storm. PMID:33006999
Robust edge-based biomarker discovery improves prediction of breast cancer metastasis. PMID:32998692
PML Regulates the Epidermal Differentiation Complex and Skin Morphogenesis during Mouse Embryogenesis. PMID:32992884
DIGGER: exploring the functional role of alternative splicing in protein interactions. PMID:32976589
The effect of hybridization on transposable element accumulation in an undomesticated fungal species. PMID:32955438
Benchmarking orthology methods using phylogenetic patterns defined at the base of Eukaryotes. PMID:32935832
Potential impact on coagulopathy of gene variants of coagulation related proteins that interact with SARS-CoV-2. PMID:32935103
Comparative host-pathogen protein-protein interaction analysis of recent coronavirus outbreaks and important host targets identification. PMID:32914167
Comprehensive host-pathogen protein-protein interaction network analysis. PMID:32912135
A functionally defined high-density NRF2 interactome reveals new conditional regulators of ARE transactivation. PMID:32911434
Transcription Factors That Regulate the Pathogenesis of Ulcerative Colitis. PMID:32908909
Targeting TRIM37-driven centrosome dysfunction in 17q23-amplified breast cancer. PMID:32908313
GAB2 and GAB3 are expressed in a tumor stage-, grade- and histotype-dependent manner and are associated with shorter progression-free survival in ovarian cancer. PMID:32888136
RNA-binding and prion domains: the Yin and Yang of phase separation. PMID:32857852
Analysis of APPL1 Gene Polymorphisms in Patients with a Phenotype of Maturity Onset Diabetes of the Young. PMID:32854233
Determining the interaction status and evolutionary fate of duplicated homomeric proteins. PMID:32853212
Systems Biology Approaches to Understanding the Human Immune System. PMID:32849587
RNA-protein interaction mapping via MS2- or Cas13-based APEX targeting. PMID:32839320
SARS-CoV-2-human protein-protein interaction network. PMID:32838020
A Human IgSF Cell-Surface Interactome Reveals a Complex Network of Protein-Protein Interactions. PMID:32822567
Analytical Guidelines for co-fractionation Mass Spectrometry Obtained through Global Profiling of Gold Standard Saccharomyces cerevisiae Protein Complexes. PMID:32817346
NPF:network propagation for protein function prediction. PMID:32787776
Transcriptomic analysis delineates potential signature genes and miRNAs associated with the pathogenesis of asthma. PMID:32770056
FLUTE: Fast and reliable knowledge retrieval from biomedical literature. PMID:32761077
NuRD subunit CHD4 regulates super-enhancer accessibility in rhabdomyosarcoma and represents a general tumor dependency. PMID:32744500
FEN1 endonuclease as a therapeutic target for human cancers with defects in homologous recombination. PMID:32719125
Piggybacking on Classical Import and Other Non-Classical Mechanisms of Nuclear Import Appear Highly Prevalent within the Human Proteome. PMID:32718019
Genetic and environmental determinants of variation in the plasma lipidome of older Australian twins. PMID:32697195
Analyzing IDPs in Interactomes. PMID:32696395
Robustness of plant quantitative disease resistance is provided by a decentralized immune network. PMID:32669441
Seedling Chloroplast Responses Induced by N-Linolenoylethanolamine Require Intact G-Protein Complexes. PMID:32665332
Structural biology of DNA abasic site protection by SRAP proteins. PMID:32663791
Leveraging the Comparative Toxicogenomics Database to Fill in Knowledge Gaps for Environmental Health: A Test Case for Air Pollution-induced Cardiovascular Disease. PMID:32663284
Interaction mapping of endoplasmic reticulum ubiquitin ligases identifies modulators of innate immune signalling. PMID:32614325
Seq-ing answers: Current data integration approaches to uncover mechanisms of transcriptional regulation. PMID:32612756
Association study based on topological constraints of protein-protein interaction networks. PMID:32612246
Extensive signal integration by the phytohormone protein network. PMID:32612234
Genome-wide investigation of gene-cancer associations for the prediction of novel therapeutic targets in oncology. PMID:32612205
Selective Neuronal Vulnerability in Alzheimer's Disease: A Network-Based Analysis. PMID:32603655
Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses. PMID:32597660
Exploring whole-genome duplicate gene retention with complex genetic interaction analysis. PMID:32586993
Role of Anillin in Tumour: From a Prognostic Biomarker to a Novel Target. PMID:32560530
Genome-wide CRISPR synthetic lethality screen identifies a role for the ADP-ribosyltransferase PARP14 in DNA replication dynamics controlled by ATR. PMID:32542389
A novel landscape of nuclear human CDK2 substrates revealed by in situ phosphorylation. PMID:32494624
Identification and characterization of male reproduction-related genes in pig (Sus scrofa) using transcriptome analysis. PMID:32487021
Protein Network Studies on PCOS Biomarkers With S100A8, Druggability Assessment, and RNA Aptamer Designing to Control Its Cyst Migration Effect. PMID:32478041
dbPSP 2.0, an updated database of protein phosphorylation sites in prokaryotes. PMID:32472030
A Bayesian data fusion based approach for learning genome-wide transcriptional regulatory networks. PMID:32471360
piNET: a versatile web platform for downstream analysis and visualization of proteomics data. PMID:32469073
Pleiotropic Roles of Calmodulin in the Regulation of KRas and Rac1 GTPases: Functional Diversity in Health and Disease. PMID:32456244
Genome-Wide Analysis of the GRAS Gene Family in Barley (Hordeum vulgare L.). PMID:32423019
Mutation severity spectrum of rare alleles in the human genome is predictive of disease type. PMID:32413045
The multifaceted nature of αB-crystallin. PMID:32383140
Targeting ERK-Hippo Interplay in Cancer Therapy. PMID:32375238
Community curation in PomBase: enabling fission yeast experts to provide detailed, standardized, sharable annotation from research publications. PMID:32353878
Hepatitis B Virus Core Particles Containing a Conserved Region of the G Protein Combined with Interleukin-35 Protected Mice against Respiratory Syncytial Virus Infection without Vaccine-Enhanced Immunopathology. PMID:32321805
Fold-Change-Specific Enrichment Analysis (FSEA): Quantification of Transcriptional Response Magnitude for Functional Gene Groups. PMID:32316383
Structured reviews for data and knowledge-driven research. PMID:32283553
Bioinformatics Analysis for Multiple Gene Expression Profiles in Sepsis. PMID:32280132
Essential gene prediction in Drosophila melanogaster using machine learning approaches based on sequence and functional features. PMID:32257045
Sex-specific and shared expression profiles of vulnerability and resilience to trauma in brain and blood. PMID:32228684
Absence of Nuclear p16 Is a Diagnostic and Independent Prognostic Biomarker in Squamous Cell Carcinoma of the Cervix. PMID:32204550
Multi-level and lineage-specific interactomes of the Hox transcription factor Ubx contribute to its functional specificity. PMID:32170121
A widespread family of heat-resistant obscure (Hero) proteins protect against protein instability and aggregation. PMID:32163402
Genetic and Chemical-Genetic Interactions Map Biogenesis and Permeability Determinants of the Outer Membrane of Escherichia coli. PMID:32156814
Transcript profiling reveals potential regulators for oxidative stress response of a necrotrophic chickpea pathogen Ascochyta rabiei. PMID:32117678
RhoBTB Proteins Regulate the Hippo Pathway by Antagonizing Ubiquitination of LKB1. PMID:32111652
Genetic Modifiers and Rare Mendelian Disease. PMID:32106447
Predicted Drosophila Interactome Resource and web tool for functional interpretation of differentially expressed genes. PMID:32103267
Data libraries - the missing element for modeling biological systems. PMID:32100391
Diverse and dynamic roles of F-box proteins in plant biology. PMID:32072251
Overcoming cisplatin resistance by targeting the MTDH-PTEN interaction in ovarian cancer with sera derived from rats exposed to Guizhi Fuling wan extract. PMID:32066429
Exploration of databases and methods supporting drug repurposing: a comprehensive survey. PMID:32055842
Alpha-Synuclein Physiology and Pathology: A Perspective on Cellular Structures and Organelles. PMID:32038126
In Silico Strategies in Tuberculosis Drug Discovery. PMID:32033144
Genome-wide identification of cold responsive transcription factors in Brassica napus L. PMID:32028890
Unraveling the role of salt-sensitivity genes in obesity with integrated network biology and co-expression analysis. PMID:32027667
PIPE4: Fast PPI Predictor for Comprehensive Inter- and Cross-Species Interactomes. PMID:31996697
Open Data for Differential Network Analysis in Glioma. PMID:31952211
Domain-mediated interactions for protein subfamily identification. PMID:31937869
Structure of the BRK domain of the SWI/SNF chromatin remodeling complex subunit BRG1 reveals a potential role in protein-protein interactions. PMID:31909846
Familial globular glial tauopathy linked to MAPT mutations: molecular neuropathology and seeding capacity of a prototypical mixed neuronal and glial tauopathy. PMID:31907603
Peroxiredoxin-1 regulates lipid peroxidation in corneal endothelial cells. PMID:31901729
AMPK Interactome Reveals New Function in Non-homologous End Joining DNA Repair. PMID:31900314
Transcription factor regulatory modules provide the molecular mechanisms for functional redundancy observed among transcription factors in yeast. PMID:31881824
Analysis of Differentially Expressed Genes in Coronary Artery Disease by Integrated Microarray Analysis. PMID:31881747
MASS SPECTROMETRY IN VIROLOGICAL SCIENCES. PMID:31876329
The Emerging Role of Cytidine Deaminase in Human Diseases: A New Opportunity for Therapy? PMID:31870623
Robust cullin-RING ligase function is established by a multiplicity of poly-ubiquitylation pathways. PMID:31868589
Common Neurodegeneration-Associated Proteins Are Physiologically Expressed by Human B Lymphocytes and Are Interconnected via the Inflammation/Autophagy-Related Proteins TRAF6 and SQSTM1. PMID:31824497
Transcriptome Meta-Analysis Deciphers a Dysregulation in Immune Response-Associated Gene Signatures during Sepsis. PMID:31817302
Human SNORA31 variations impair cortical neuron-intrinsic immunity to HSV-1 and underlie herpes simplex encephalitis. PMID:31806906
Sequence-Derived Markers of Drug Targets and Potentially Druggable Human Proteins. PMID:31803227
The Alliance of Genome Resources: Building a Modern Data Ecosystem for Model Organism Databases. PMID:31796553
TGFB1-Mediated Gliosis in Multiple Sclerosis Spinal Cords Is Favored by the Regionalized Expression of HOXA5 and the Age-Dependent Decline in Androgen Receptor Ligands. PMID:31779094
A single ChIP-seq dataset is sufficient for comprehensive analysis of motifs co-occurrence with MCOT package. PMID:31750523
Sudden unexpected death in asymptomatic infants due to PPA2 variants. PMID:31705601
The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species. PMID:31701156
AppleMDO: A Multi-Dimensional Omics Database for Apple Co-Expression Networks and Chromatin States. PMID:31695717
Therapeutic target database 2020: enriched resource for facilitating research and early development of targeted therapeutics. PMID:31691823
SIGNOR 2.0, the SIGnaling Network Open Resource 2.0: 2019 update. PMID:31665520
DNA Replication Inhibitor Geminin and Retinoic Acid Signaling Participate in Complex Interactions Associated With Pluripotency. PMID:31659113
Bovine Genome Database: new annotation tools for a new reference genome. PMID:31647100
Integrated bioinformatics analysis reveals role of the LINC01093/miR-96-5p/ZFAND5/NF-κB signaling axis in hepatocellular carcinoma. PMID:31641376
Biological Network Approaches and Applications in Rare Disease Studies. PMID:31614842
VarSite: Disease variants and protein structure. PMID:31606900
Alliance of Genome Resources Portal: unified model organism research platform. PMID:31552413
Computer aided analysis of disease linked protein networks. PMID:31485137
Protein-Protein Interactions in Candida albicans. PMID:31440220
Network dynamics of the yeast methyltransferome. PMID:31403050
Hallmarks of ribosomopathies. PMID:31350888
Identification of important invasion and proliferation related genes in adrenocortical carcinoma. PMID:31321566
Ultra-soft X-ray system for imaging the early cellular responses to X-ray induced DNA damage. PMID:31318974
Comprehensive in vivo identification of the c-Myc mRNA protein interactome using HyPR-MS. PMID:31296583
Proteomics Approaches for Biomarker and Drug Target Discovery in ALS and FTD. PMID:31244593
Gene Information eXtension (GIX): effortless retrieval of gene product information on any website. PMID:31217594
A Robust Approach for Identification of Cancer Biomarkers and Candidate Drugs. PMID:31212673
To Embed or Not: Network Embedding as a Paradigm in Computational Biology. PMID:31118945
ResponseNet v.3: revealing signaling and regulatory pathways connecting your proteins and genes across human tissues. PMID:31114913
Cell contact and Nf2/Merlin-dependent regulation of TEAD palmitoylation and activity. PMID:31043565
Mining Featured Biomarkers Linked with Epithelial Ovarian CancerBased on Bioinformatics. PMID:30970615 -
The BioGRID interaction database: 2017 update
PubMed citations: 428.
428 articles citing: The BioGRID interaction database: 2017 update
Integration of probabilistic functional networks without an external Gold Standard. PMID:35879662
Protocol for establishing a protein-protein interaction network using tandem affinity purification followed by mass spectrometry in mammalian cells. PMID:35874475
NTD-DR: Nonnegative tensor decomposition for drug repositioning. PMID:35862409
TritiKBdb: A Functional Annotation Resource for Deciphering the Complete Interaction Networks in Wheat-Karnal Bunt Pathosystem. PMID:35806459
Deciphering the Crosstalk Mechanisms of Wheat-Stem Rust Pathosystem: Genome-Scale Prediction Unravels Novel Host Targets. PMID:35800602
Identifying Candidate Flavonoids for Non-Alcoholic Fatty Liver Disease by Network-Based Strategy. PMID:35721123
WeCoNET: a host-pathogen interactome database for deciphering crucial molecular networks of wheat-common bunt cross-talk mechanisms. PMID:35658913
Analysis of the lncRNA-Associated Competing Endogenous RNA (ceRNA) Network for Tendinopathy. PMID:35645614
Driver gene detection through Bayesian network integration of mutation and expression profiles. PMID:35561191
Bioinformatics-Based Approaches to Study Virus-Host Interactions During SARS-CoV-2 Infection. PMID:35554909
Degron masking outlines degronons, co-degrading functional modules in the proteome. PMID:35545699
Prioritization of Candidate Biomarkers for Degenerative Aortic Stenosis through a Systems Biology-Based In-Silico Approach. PMID:35455758
A Boolean Model of the Proliferative Role of the lncRNA XIST in Non-Small Cell Lung Cancer Cells. PMID:35453680
Second-Generation JK-206 Targets the Oncogenic Signal Mediator RHOA in Gastric Cancer. PMID:35406376
Dynamical modeling of miR-34a, miR-449a, and miR-16 reveals numerous DDR signaling pathways regulating senescence, autophagy, and apoptosis in HeLa cells. PMID:35318393
Eucalyptus grandis AUX/INDOLE-3-ACETIC ACID 13 (EgrIAA13) is a novel transcriptional regulator of xylogenesis. PMID:35292886
Intrinsically disordered signaling proteins: Essential hub players in the control of stress responses in Saccharomyces cerevisiae. PMID:35290420
Deciphering the Host-Pathogen Interactome of the Wheat-Common Bunt System: A Step towards Enhanced Resilience in Next Generation Wheat. PMID:35269732
Computational Systems Biology of Alfalfa - Bacterial Blight Host-Pathogen Interactions: Uncovering the Complex Molecular Networks for Developing Durable Disease Resistant Crop. PMID:35251063
Characterization of the pVHL Interactome in Human Testis Using High-Throughput Library Screening. PMID:35205757
Exploration of the Potential Transcriptional Regulatory Mechanisms of DNA Methyltransferases and MBD Genes in Petunia Anther Development and Multi-Stress Responses. PMID:35205359
Network Pharmacology Integrated Molecular Docking Revealed the Mechanism of Jianpi Yiqi Taohua Decoction Against Ulcerative Colitis. PMID:35173140
UbE3-APA: A Bioinformatic Strategy to Elucidate Ubiquitin E3 Ligase Activities in Quantitative Proteomics Study. PMID:35139152
XSSJS inhibits hepatic fibrosis by promoting the miR-29b-3p/VEGFA axis in vitro and in vivo. PMID:35118493
Thalidomide Exerts Anti-Inflammatory Effects in Cutaneous Lupus by Inhibiting the IRF4/NF-ҡB and AMPK1/mTOR Pathways. PMID:34944673
Subnetwork representation learning for discovering network biomarkers in predicting lymph node metastasis in early oral cancer. PMID:34907266
Relation Extraction of Protein Complexes from Dynamic Protein-Protein Interaction Network. PMID:34904064
Altered H3 histone acetylation impairs high-fidelity DNA repair to promote cerebellar degeneration in spinocerebellar ataxia type 7. PMID:34852229
Interactome analysis illustrates diverse gene regulatory processes associated with LIN28A in human iPS cell-derived neural progenitor cells. PMID:34816099
A Network-Based Methodology to Identify Subnetwork Markers for Diagnosis and Prognosis of Colorectal Cancer. PMID:34790220
FusionGDB 2.0: fusion gene annotation updates aided by deep learning. PMID:34755868
Co-evolution based machine-learning for predicting functional interactions between human genes. PMID:34753957
Therapeutic inhibition of GAS6-AS1/YBX1/MYC axis suppresses cell propagation and disease progression of acute myeloid leukemia. PMID:34753494
Network-driven analysis of human-Plasmodium falciparum interactome: processes for malaria drug discovery and extracting in silico targets. PMID:34702263
GreeningDB: A Database of Host-Pathogen Protein-Protein Interactions and Annotation Features of the Bacteria Causing Huanglongbing HLB Disease. PMID:34639237
Getting to know each other: PPIMem, a novel approach for predicting transmembrane protein-protein complexes. PMID:34630938
Differentiable biology: using deep learning for biophysics-based and data-driven modeling of molecular mechanisms. PMID:34608321
Interpretation of cancer mutations using a multiscale map of protein systems. PMID:34591613
Prioritizing de novo autism risk variants with calibrated gene- and variant-scoring models. PMID:34549350
Using informative features in machine learning based method for COVID-19 drug repurposing. PMID:34544500
A Novel Network-Based Algorithm for Predicting Protein-Protein Interactions Using Gene Ontology. PMID:34512614
Identification of Immune-Related Genes in Sepsis due to Community-Acquired Pneumonia. PMID:34484417
Full-length isoform transcriptome of the developing human brain provides further insights into autism. PMID:34469739
PPIDomainMiner: Inferring domain-domain interactions from multiple sources of protein-protein interactions. PMID:34370723
alfaNET: A Database of Alfalfa-Bacterial Stem Blight Protein-Protein Interactions Revealing the Molecular Features of the Disease-causing Bacteria. PMID:34361108
Transcriptional landscape of cellular networks reveal interactions driving the dormancy mechanisms in cancer. PMID:34349126
Topological network based drug repurposing for coronavirus 2019. PMID:34324563
Identification of covalent modifications regulating immune signaling complex composition and phenotype. PMID:34318608
Computational Phosphorylation Network Reconstruction: An Update on Methods and Resources. PMID:34270057
Utilizing image and caption information for biomedical document classification. PMID:34252939
A global overview of genetically interpretable multimorbidities among common diseases in the UK Biobank. PMID:34225788
Global identification of phospho-dependent SCF substrates reveals a FBXO22 phosphodegron and an ERK-FBXO22-BAG3 axis in tumorigenesis. PMID:34215846
EvoProDom: evolutionary modeling of protein families by assessing translocations of protein domains. PMID:34196123
PRISMA and BioID disclose a motifs-based interactome of the intrinsically disordered transcription factor C/EBPα. PMID:34189442
FINER: enhancing the prediction of tissue-specific functions of isoforms by refining isoform interaction networks. PMID:34169280
The dual role of SrbA from Paracoccidioides lutzii: a hypoxic regulator. PMID:34148216
DGLinker: flexible knowledge-graph prediction of disease-gene associations. PMID:34125897
A proximity-dependent biotinylation map of a human cell. PMID:34079125
Human Immunodeficiency Virus Type 1 Vpr Mediates Degradation of APC1, a Scaffolding Component of the Anaphase-Promoting Complex/Cyclosome. PMID:34011540
Analysis of Zika virus capsid-Aedes aegypti mosquito interactome reveals pro-viral host factors critical for establishing infection. PMID:33986255
Deep learning integration of molecular and interactome data for protein-compound interaction prediction. PMID:33933121
A SARS-CoV-2 (COVID-19) biological network to find targets for drug repurposing. PMID:33931664
In silico comparative analysis of LRRK2 interactomes from brain, kidney and lung. PMID:33915162
Pathogenic missense protein variants affect different functional pathways and proteomic features than healthy population variants. PMID:33909605
Knockdown of PNO1 inhibits esophageal cancer progression. PMID:33864661
Imputation of spatially-resolved transcriptomes by graph-regularized tensor completion. PMID:33826608
Quantifying evolutionary importance of protein sites: A Tale of two measures. PMID:33826605
Atg9-centered multi-omics integration reveals new autophagy regulators in Saccharomyces cerevisiae. PMID:33722159
Identification of potential and novel target genes in pituitary prolactinoma by bioinformatics analysis. PMID:33709028
Differential Interactome Proposes Subtype-Specific Biomarkers and Potential Therapeutics in Renal Cell Carcinomas. PMID:33672271
Overexpression of miR-1306-5p, miR-3195, and miR-3914 Inhibits Ameloblast Differentiation through Suppression of Genes Associated with Human Amelogenesis Imperfecta. PMID:33672174
Identifying critical protein-coding genes and long non-coding RNAs in non-functioning pituitary adenoma recurrence. PMID:33664827
Proximity-dependent Mapping of the Androgen Receptor Identifies Kruppel-like Factor 4 as a Functional Partner. PMID:33640491
Genome-wide meta-analysis, fine-mapping and integrative prioritization implicate new Alzheimer's disease risk genes. PMID:33589840
Single-Cell Analysis Reveals Characterization of Infiltrating T Cells in Moderately Differentiated Colorectal Cancer. PMID:33584715
UniProt-Related Documents (UniReD): assisting wet lab biologists in their quest on finding novel counterparts in a protein network. PMID:33575553
Pan-Cancer analysis of the expression and regulation of matrisome genes across 32 tumor types. PMID:33543003
Xia-Gibbs Syndrome: A Review of Literature. PMID:33520547
Data-driven biological network alignment that uses topological, sequence, and functional information. PMID:33514304
Causal network inference from gene transcriptional time-series response to glucocorticoids. PMID:33513136
NLPEI: A Novel Self-Interacting Protein Prediction Model Based on Natural Language Processing and Evolutionary Information. PMID:33488064
DeORFanizing Candida albicans Genes using Coexpression. PMID:33472984
Transcutaneous Electrical Acupoint Stimulation in Early Life Changes Synaptic Plasticity and Improves Symptoms in a Valproic Acid-Induced Rat Model of Autism. PMID:33456456
Internetwork connectivity of molecular networks across species of life. PMID:33441907
Large-scale survey and database of high affinity ligands for peptide recognition modules. PMID:33438817
A computational framework for identifying the transcription factors involved in enhancer-promoter loop formation. PMID:33425492
Alteration in Gene Pair Correlations in Tryptophan Metabolism as a Hallmark in Cancer Diagnosis. PMID:33354111
Scanning Protein Surfaces with DNA-Encoded Libraries. PMID:33295694
Network analysis reveals essential proteins that regulate sodium-iodide symporter expression in anaplastic thyroid carcinoma. PMID:33293661
SARS-CoV-2 receptor ACE2 is co-expressed with genes related to transmembrane serine proteases, viral entry, immunity and cellular stress. PMID:33293627
Frequent Assembly of Chimeric Complexes in the Protein Interaction Network of an Interspecies Yeast Hybrid. PMID:33252673
COVID-19 research risks ignoring important host genes due to pre-established research patterns. PMID:33231169
ATP13A2-mediated endo-lysosomal polyamine export counters mitochondrial oxidative stress. PMID:33229544
TREM2 Alzheimer's variant R47H causes similar transcriptional dysregulation to knockout, yet only subtle functional phenotypes in human iPSC-derived macrophages. PMID:33198789
A compound downregulation of SRRM2 and miR-27a-3p with upregulation of miR-27b-3p in PBMCs of Parkinson's patients is associated with the early stage onset of disease. PMID:33171483
Triage of documents containing protein interactions affected by mutations using an NLP based machine learning approach. PMID:33167858
Evolution of Sequence-based Bioinformatics Tools for Protein-protein Interaction Prediction. PMID:33093807
PyGNA: a unified framework for geneset network analysis. PMID:33092528
A method for estimating coherence of molecular mechanisms in major human disease and traits. PMID:33087046
The effect of statistical normalization on network propagation scores. PMID:33070187
A practical guide to mechanistic systems modeling in biology using a logic-based approach. PMID:33064138
Protein interactome mapping in Caenorhabditis elegans. PMID:32984658
Design principles of gene evolution for niche adaptation through changes in protein-protein interaction networks. PMID:32973219
Regulation of neuronal commitment in mouse embryonic stem cells by the Reno1/Bahcc1 locus. PMID:32969152
NAUTICA: classifying transcription factor interactions by positional and protein-protein interaction information. PMID:32938476
IER5, a DNA damage response gene, is required for Notch-mediated induction of squamous cell differentiation. PMID:32936072
Oncoprotein-specific molecular interaction maps (SigMaps) for cancer network analyses. PMID:32929263
Dynamic remodelling of the human host cell proteome and phosphoproteome upon enterovirus infection. PMID:32859902
Sex differences in circulating proteins in heart failure with preserved ejection fraction. PMID:32831121
Mycoplasma hyopneumoniae J elicits an antioxidant response and decreases the expression of ciliary genes in infected swine epithelial cells. PMID:32792522
Network-based modeling of drug effects on disease module in systemic sclerosis. PMID:32770109
Pharmacoproteomics Identifies Kinase Pathways that Drive the Epithelial-Mesenchymal Transition and Drug Resistance in Hepatocellular Carcinoma. PMID:32755597
Co-phosphorylation networks reveal subtype-specific signaling modules in breast cancer. PMID:32730576
Combined Proteomic and Genetic Interaction Mapping Reveals New RAS Effector Pathways and Susceptibilities. PMID:32727735
Stress response in periodontal ligament stem cells may contribute to bisphosphonate‑associated osteonecrosis of the jaw: A gene expression array analysis. PMID:32705175
Araport Lives: An Updated Framework for Arabidopsis Bioinformatics. PMID:32699173
Similarities in biological processes can be used to bridge ecology and molecular biology. PMID:32684962
Advancing computer-aided drug discovery (CADD) by big data and data-driven machine learning modeling. PMID:32663517
Comprehensive nucleosome interactome screen establishes fundamental principles of nucleosome binding. PMID:32658293
Harnessing endophenotypes and network medicine for Alzheimer's drug repurposing. PMID:32656864
Quality Matters: Biocuration Experts on the Impact of Duplication and Other Data Quality Issues in Biological Databases. PMID:32652120
MAP4K Interactome Reveals STRN4 as a Key STRIPAK Complex Component in Hippo Pathway Regulation. PMID:32640226
IPSC-Derived Neuronal Cultures Carrying the Alzheimer's Disease Associated TREM2 R47H Variant Enables the Construction of an Aβ-Induced Gene Regulatory Network. PMID:32630447
Data-driven network alignment. PMID:32614833
Extensive signal integration by the phytohormone protein network. PMID:32612234
2018 Update on Protein-Protein Interaction Data in WormBase. PMID:32550373
Network Medicine Framework for Identifying Drug Repurposing Opportunities for COVID-19. PMID:32550253
Kir2.1 Interactome Mapping Uncovers PKP4 as a Modulator of the Kir2.1-Regulated Inward Rectifier Potassium Currents. PMID:32541000
Dynamic rewiring of the human interactome by interferon signaling. PMID:32539747
A flexible network-based imputing-and-fusing approach towards the identification of cell types from single-cell RNA-seq data. PMID:32527285
Integrated omics in Drosophila uncover a circadian kinome. PMID:32483184
A network of RNA-binding proteins controls translation efficiency to activate anaerobic metabolism. PMID:32472050
Post-translational Modification Crosstalk and Hotspots in Sirtuin Interactors Implicated in Cardiovascular Diseases. PMID:32425973
Neural networks for open and closed Literature-based Discovery. PMID:32413059
Ellagic acid and human cancers: a systems pharmacology and docking study to identify principal hub genes and main mechanisms of action. PMID:32410114
Single-cell transcriptional networks in differentiating preadipocytes suggest drivers associated with tissue heterogeneity. PMID:32355218
Genotype-phenotype correlations of Berardinelli-Seip congenital lipodystrophy and novel candidate genes prediction. PMID:32349771
ppiGReMLIN: a graph mining based detection of conserved structural arrangements in protein-protein interfaces. PMID:32293241
A multidimensional systems biology analysis of cellular senescence in aging and disease. PMID:32264951
EpiMOLAS: an intuitive web-based framework for genome-wide DNA methylation analysis. PMID:32241255
Transcriptomic analysis of marine endophytic fungi extract identifies highly enriched anti-fungal fractions targeting cancer pathways in HepG2 cell lines. PMID:32228434
Understanding of Zaire ebolavirus-human protein interaction for drug repurposing. PMID:32206696
Human-Specific Transcriptome of Ventral and Dorsal Midbrain Dopamine Neurons. PMID:32167609
A Genome-wide ER-phagy Screen Highlights Key Roles of Mitochondrial Metabolism and ER-Resident UFMylation. PMID:32160526
Meta-analysis of human prefrontal cortex reveals activation of GFAP and decline of synaptic transmission in the aging brain. PMID:32138778
Pan-cancer mapping of differential protein-protein interactions. PMID:32094374
Similarity of therapeutic networks induced by a multi-component herbal remedy, Ukgansan, in neurovascular unit cells. PMID:32060346
Integrative data modeling from lung and lymphatic cancer predicts functional roles for miR-34a and miR-16 in cell fate regulation. PMID:32054948
In-silico simulated prototype-patients using TPMS technology to study a potential adverse effect of sacubitril and valsartan. PMID:32053711
Using the Gibbs Function as a Measure of Human Brain Development Trends from Fetal Stage to Advanced Age. PMID:32046179
Hierarchical cooperation of transcription factors from integration analysis of DNA sequences, ChIP-Seq and ChIA-PET data. PMID:32039697
Quantifying Gene Essentiality Based on the Context of Cellular Components. PMID:32038710
Kinobead/LC-MS Phosphokinome Profiling Enables Rapid Analyses of Kinase-Dependent Cell Signaling Networks. PMID:32037842
PlaPPISite: a comprehensive resource for plant protein-protein interaction sites. PMID:32028878
Pathway and network analysis of more than 2500 whole cancer genomes. PMID:32024854
ATP13A2 deficiency disrupts lysosomal polyamine export. PMID:31996848
Environmental arginine controls multinuclear giant cell metabolism and formation. PMID:31969567
TMEM98 is a negative regulator of FRAT mediated Wnt/ß-catenin signalling. PMID:31961879
The FGF, TGFβ and WNT axis Modulate Self-renewal of Human SIX2+ Urine Derived Renal Progenitor Cells. PMID:31959818
BCOR-coupled H2A monoubiquitination represses a subset of androgen receptor target genes regulating prostate cancer proliferation. PMID:31925334
Defining the TLT-1 interactome from resting and activated human platelets. PMID:31923473
MELK promotes Endometrial carcinoma progression via activating mTOR signaling pathway. PMID:31915116
Presence and structure-activity relationship of intrinsically disordered regions across mucins. PMID:31908009
Biophysical prediction of protein-peptide interactions and signaling networks using machine learning. PMID:31907444
Genetic variation drives seasonal onset of hibernation in the 13-lined ground squirrel. PMID:31886416
The impact of the genetic background on gene deletion phenotypes in Saccharomyces cerevisiae. PMID:31885205
Identification of self-interacting proteins by integrating random projection classifier and finite impulse response filter. PMID:31881833
LePrimAlign: local entropy-based alignment of PPI networks to predict conserved modules. PMID:31874635
Joint learning improves protein abundance prediction in cancers. PMID:31870366
Predicting synthetic lethal interactions in human cancers using graph regularized self-representative matrix factorization. PMID:31870274
Dissecting the Role of NF-κb Protein Family and Its Regulators in Rheumatoid Arthritis Using Weighted Gene Co-Expression Network. PMID:31824568
PsyMuKB: An Integrative De Novo Variant Knowledge Base for Developmental Disorders. PMID:31809863
Leveraging User-Friendly Network Approaches to Extract Knowledge From High-Throughput Omics Datasets. PMID:31798629
Integrating protein localization with automated signaling pathway reconstruction. PMID:31787091
Systematic prediction of FFAT motifs across eukaryote proteomes identifies nucleolar and eisosome proteins with the predicted capacity to form bridges to the endoplasmic reticulum. PMID:31777772
Validation of a priori candidate Alzheimer's disease SNPs with brain amyloid-beta deposition. PMID:31745181
Global Vectors Representation of Protein Sequences and Its Application for Predicting Self-Interacting Proteins with Multi-Grained Cascade Forest Model. PMID:31726752
In Silico Study of Rett Syndrome Treatment-Related Genes, MECP2, CDKL5, and FOXG1, by Evolutionary Classification and Disordered Region Assessment. PMID:31717404
RPGeNet v2.0: expanding the universe of retinal disease gene interactions network. PMID:31712826
Sustained transgene expression from sleeping beauty DNA transposons containing a core fragment of the HNRPA2B1-CBX3 ubiquitous chromatin opening element (UCOE). PMID:31706316
Therapeutic target database 2020: enriched resource for facilitating research and early development of targeted therapeutics. PMID:31691823
Proteomic Analysis Reveals a Role for RSK in p120-catenin Phosphorylation and Melanoma Cell-Cell Adhesion. PMID:31678930
Co-expression of synaptic genes in the sponge Amphimedon queenslandica uncovers ancient neural submodules. PMID:31673079
FKBP4 connects mTORC2 and PI3K to activate the PDK1/Akt-dependent cell proliferation signaling in breast cancer. PMID:31660083
Uncovering and characterizing splice variants associated with survival in lung cancer patients. PMID:31652257
The RNA-binding ubiquitin ligase MKRN1 functions in ribosome-associated quality control of poly(A) translation. PMID:31640799
Head and Neck Cancers Promote an Inflammatory Transcriptome through Coactivation of Classic and Alternative NF-κB Pathways. PMID:31624067
Extraction of chemical-protein interactions from the literature using neural networks and narrow instance representation. PMID:31622463
MUDENG Expression Profiling in Cohorts and Brain Tumor Biospecimens to Evaluate Its Role in Cancer. PMID:31616474
An Integrated System Biology Approach Yields Drug Repositioning Candidates for the Treatment of Heart Failure. PMID:31608126
pathfindR: An R Package for Comprehensive Identification of Enriched Pathways in Omics Data Through Active Subnetworks. PMID:31608109
Therapeutic Targeting of MZF1-AS1/PARP1/E2F1 Axis Inhibits Proline Synthesis and Neuroblastoma Progression. PMID:31592410
Tissue-specific mouse mRNA isoform networks. PMID:31562339
Paralog dependency indirectly affects the robustness of human cells. PMID:31556487
A perturbed gene network containing PI3K-AKT, RAS-ERK and WNT-β-catenin pathways in leukocytes is linked to ASD genetics and symptom severity. PMID:31551593
Biclustering-based association rule mining approach for predicting cancer-associated protein interactions. PMID:31538957
Machine-learning techniques for the prediction of protein-protein interactions. PMID:31502581
A Survey of Gene Prioritization Tools for Mendelian and Complex Human Diseases. PMID:31494632
Computer aided analysis of disease linked protein networks. PMID:31485137
Benchmarking network propagation methods for disease gene identification. PMID:31479437
Analyzing the regulation of miRNAs on protein-protein interaction network in Hodgkin lymphoma. PMID:31477006
Delineating the role of FANCA in glucose-stimulated insulin secretion in β cells through its protein interactome. PMID:31461451
The role of structural pleiotropy and regulatory evolution in the retention of heteromers of paralogs. PMID:31454312
Protein-Protein Interactions in Candida albicans. PMID:31440220
Large-effect flowering time mutations reveal conditionally adaptive paths through fitness landscapes in Arabidopsis thaliana. PMID:31420516
UNIPred-Web: a web tool for the integration and visualization of biomolecular networks for protein function prediction. PMID:31412768
Novel deep learning model for more accurate prediction of drug-drug interaction effects. PMID:31387547
Prediction of regulatory motifs from human Chip-sequencing data using a deep learning framework. PMID:31372637
Key inflammatory pathway activations in the MCI stage of Alzheimer's disease. PMID:31353852
Network analysis of hyphae forming proteins in Candida albicans identifies important proteins responsible for pathovirulence in the organism. PMID:31338453
Identification of differentially expressed genes in small and non-small cell lung cancer based on meta-analysis of mRNA. PMID:31338439
AraPPINet: An Updated Interactome for the Analysis of Hormone Signaling Crosstalk in Arabidopsis thaliana. PMID:31333706
Identifying potential drug targets in hepatocellular carcinoma based on network analysis and one-class support vector machine. PMID:31320657
Exploring the Molecular Mechanism of the Drug-Treated Breast Cancer Based on Gene Expression Microarray. PMID:31311202
EPIC: software toolkit for elution profile-based inference of protein complexes. PMID:31308550
Patient-specific cancer genes contribute to recurrently perturbed pathways and establish therapeutic vulnerabilities in esophageal adenocarcinoma. PMID:31308377
Ligand Binding Site Structure Shapes Folding, Assembly and Degradation of Homomeric Protein Complexes. PMID:31306664
Global proteomic analyses define an environmentally contingent Hsp90 interactome and reveal chaperone-dependent regulation of stress granule proteins and the R2TP complex in a fungal pathogen. PMID:31283755
Genome-wide functional association networks: background, data & state-of-the-art resources. PMID:31281921
Disease gene prediction for molecularly uncharacterized diseases. PMID:31276496
Cancer driver genes: a guilty by resemblance doctrine. PMID:31275738
Meta-Analysis of Microarray Expression Studies on Metformin in Cancer Cell Lines. PMID:31261735
The chromatin remodeler Chd1 regulates cohesin in budding yeast and humans. PMID:31222142
Characterization of a sandwich ELISA for quantification of total human soluble neuropilin-1. PMID:31219204
Computational identification of protein-protein interactions in model plant proteomes. PMID:31217453
Mediator complex interaction partners organize the transcriptional network that defines neural stem cells. PMID:31209209
DeepPhagy: a deep learning framework for quantitatively measuring autophagy activity in Saccharomyces cerevisiae. PMID:31204567
Knockdown of STIL suppresses the progression of gastric cancer by down-regulating the IGF-1/PI3K/AKT pathway. PMID:31187582
Syndromic Intellectual Disability Caused by a Novel Truncating Variant in AHDC1: A Case Report. PMID:31182893
A Multidimensional Characterization of E3 Ubiquitin Ligase and Substrate Interaction Network. PMID:31181401
Identification of key modules and hub genes for small-cell lung carcinoma and large-cell neuroendocrine lung carcinoma by weighted gene co-expression network analysis of clinical tissue-proteomes. PMID:31166966
The Impact of Protein Architecture on Adaptive Evolution. PMID:31147689
CNet: a multi-omics approach to detecting clinically associated, combinatory genomic signatures. PMID:31141125
Identification of Crucial Candidate Genes and Pathways in Glioblastoma Multiform by Bioinformatics Analysis. PMID:31137733
BAG6 deficiency induces mis-distribution of mitochondrial clusters under depolarization. PMID:31125507
Genome-wide DNA methylation profile in the peripheral blood of cocaine and crack dependents. PMID:31116258
Protein Melting Temperature Cannot Fully Assess Whether Protein Folding Free Energy Underlies the Universal Abundance-Evolutionary Rate Correlation Seen in Proteins. PMID:31093676
c-Met as a new marker of cellular senescence. PMID:31085799
Optimized Cross-Linking Mass Spectrometry for in Situ Interaction Proteomics. PMID:31083951
Associating expression and genomic data using co-occurrence measures. PMID:31072345
Plasma protein biomarkers and their association with mutually exclusive cardiovascular phenotypes: the FIBRO-TARGETS case-control analyses. PMID:31062082
Genes with High Network Connectivity Are Enriched for Disease Heritability. PMID:31051114
Human COQ10A and COQ10B are distinct lipid-binding START domain proteins required for coenzyme Q function. PMID:31048406
Identification of DNA methylation patterns predisposing for an efficient response to BCG vaccination in healthy BCG-naïve subjects. PMID:31010371
Understanding Human-Virus Protein-Protein Interactions Using a Human Protein Complex-Based Analysis Framework. PMID:30984872
Identification of Important Invasion-Related Genes in Non-functional Pituitary Adenomas. PMID:30982163
A network of human functional gene interactions from knockout fitness screens in cancer cells. PMID:30979825
ULK1 and ULK2 Regulate Stress Granule Disassembly Through Phosphorylation and Activation of VCP/p97. PMID:30979586
Crystal structure of the SH3 domain of human Lyn non-receptor tyrosine kinase. PMID:30969999
croFGD: Catharanthus roseus Functional Genomics Database. PMID:30967897
Large-scale proteomic analysis of human brain identifies proteins associated with cognitive trajectory in advanced age. PMID:30962425
Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. PMID:30944313
A Network Module for the Perseus Software for Computational Proteomics Facilitates Proteome Interaction Graph Analysis. PMID:30931570
Individual components of the SWI/SNF chromatin remodelling complex have distinct roles in memory neurons of the Drosophila mushroom body. PMID:30923190
Human iPSC-derived MSCs (iMSCs) from aged individuals acquire a rejuvenation signature. PMID:30885246
An Improved Deep Forest Model for Predicting Self-Interacting Proteins From Protein Sequence Using Wavelet Transformation. PMID:30881376
Identification of Important Effector Proteins in the FOXJ1 Transcriptional Network Associated With Ciliogenesis and Ciliary Function. PMID:30881373
The Balancing Act of Intrinsically Disordered Proteins: Enabling Functional Diversity while Minimizing Promiscuity. PMID:30878482
Assessing diversity in multiplex networks. PMID:30872604
Rewired cellular signaling coordinates sugar and hypoxic responses for anaerobic xylose fermentation in yeast. PMID:30856163
Cross-disease analysis of Alzheimer's disease and type-2 Diabetes highlights the role of autophagy in the pathophysiology of two highly comorbid diseases. PMID:30850634
Functional protein representations from biological networks enable diverse cross-species inference. PMID:30847485
Functional Segments on Intrinsically Disordered Regions in Disease-Related Proteins. PMID:30841624
Brain Imaging-Guided Analysis Reveals DNA Methylation Profiles Correlated with Insular Surface Area and Alcohol Use Disorder. PMID:30830696
Systematic analysis reveals the prevalence and principles of bypassable gene essentiality. PMID:30824696
Genome-scale network model of metabolism and histone acetylation reveals metabolic dependencies of histone deacetylase inhibitors. PMID:30823893
YESdb: integrative analysis of environmental stress in yeast. PMID:30821814
Functional geometry of protein interactomes. PMID:30821317
Synergy from gene expression and network mining (SynGeNet) method predicts synergistic drug combinations for diverse melanoma genomic subtypes. PMID:30820351
An integrative systems genetic analysis of mammalian lipid metabolism. PMID:30814737
Distinct isoforms of Nrf1 diversely regulate different subsets of its cognate target genes. PMID:30814566
Protocol Update for large-scale genome and gene function analysis with the PANTHER classification system (v.14.0). PMID:30804569
Cytoplasmic control of Rab family small GTPases through BAG6. PMID:30804014
Somatic mutations in early metazoan genes disrupt regulatory links between unicellular and multicellular genes in cancer. PMID:30803482
Membrane metallo-endopeptidase (Neprilysin) regulates inflammatory response and insulin signaling in white preadipocytes. PMID:30795914
Prediction of Self-Interacting Proteins from Protein Sequence Information Based on Random Projection Model and Fast Fourier Transform. PMID:30795499
Towards a data-integrated cell. PMID:30778056
Analysis of Topological Parameters of Complex Disease Genes Reveals the Importance of Location in a Biomolecular Network. PMID:30769902
deepDriver: Predicting Cancer Driver Genes Based on Somatic Mutations Using Deep Convolutional Neural Networks. PMID:30761181
A systematic genetic screen identifies essential factors involved in nuclear size control. PMID:30759079
APID database: redefining protein-protein interaction experimental evidences and binary interactomes. PMID:30715274
Matching tRNA modifications in humans to their known and predicted enzymes. PMID:30698754
Overview of the BioCreative VI Precision Medicine Track: mining protein interactions and mutations for precision medicine. PMID:30689846
Proteome-wide, Structure-Based Prediction of Protein-Protein Interactions/New Molecular Interactions Viewer. PMID:30679268
Deciphering the Potential Pharmaceutical Mechanism of GUI-ZHI-FU-LING-WAN on Systemic Sclerosis based on Systems Biology Approaches. PMID:30674993
Surface expression of TTYH2 is attenuated by direct interaction with β-COP. PMID:30670146
Building Bridges Between Structural and Network-Based Systems Biology. PMID:30656572
An interaction-based model for neuropsychiatric features of copy-number variants. PMID:30653500
Translational control mechanisms in cutaneous malignant melanoma: the role of eIF2α. PMID:30634982
Maternal choline supplementation ameliorates Alzheimer's disease pathology by reducing brain homocysteine levels across multiple generations. PMID:30622336
Admixture Effects on Coevolved Metabolic Systems. PMID:30619461
The Network of Cancer Genes (NCG): a comprehensive catalogue of known and candidate cancer genes from cancer sequencing screens. PMID:30606230
Network spectra for drug-target identification in complex diseases: new guns against old foes. PMID:30596144
Integrative network and brain expression analysis reveals mechanistic modules in ataxia. PMID:30591515
Bayesian inference of networks across multiple sample groups and data types. PMID:30590505
The RTK Interactome: Overview and Perspective on RTK Heterointeractions. PMID:30589534
Genome-wide analysis of consistently RNA edited sites in human blood reveals interactions with mRNA processing genes and suggests correlations with cell types and biological variables. PMID:30587120
TICA: Transcriptional Interaction and Coregulation Analyzer. PMID:30578913
BioCreative VI Precision Medicine Track system performance is constrained by entity recognition and variations in corpus characteristics. PMID:30576491
iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data. PMID:30567491
A protein-protein interaction map of the TNF-induced NF-κB signal transduction pathway. PMID:30561431
Nrf1-mediated transcriptional regulation of the proteasome requires a functional TIP60 complex. PMID:30559296
Several genes involved in the JAK-STAT pathway may act as prognostic markers in pancreatic cancer identified by microarray data analysis. PMID:30557977
PlantEAR: Functional Analysis Platform for Plant EAR Motif-Containing Proteins. PMID:30555515
Time-resolved interaction proteomics of the GIGANTEA protein under diurnal cycles in Arabidopsis. PMID:30536871
A Primer on Data Analytics in Functional Genomics: How to Move from Data to Insight? PMID:30522862
Both Intrinsically Disordered Regions and Structural Domains Evolve Rapidly in Immune-Related Mammalian Proteins. PMID:30518031
Genomic identification and functional analysis of essential genes in Caenorhabditis elegans. PMID:30514206
Vimentin on the move: new developments in cell migration. PMID:30505430
ARP3 Controls the Podocyte Architecture at the Kidney Filtration Barrier. PMID:30503751
STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. PMID:30476243
The BioGRID interaction database: 2019 update. PMID:30476227
A PxL motif promotes timely cell cycle substrate dephosphorylation by the Cdc14 phosphatase. PMID:30455435
Physiological and pathophysiological characteristics of ataxin-3 isoforms. PMID:30455355
How do we know that plants listen: Advancements and limitations of transcriptomic profiling for the identification of sound-specific biomarkers in tomato. PMID:30445891
Higher-order molecular organization as a source of biological function. PMID:30423061
ALMS1 and Alström syndrome: a recessive form of metabolic, neurosensory and cardiac deficits. PMID:30421101
IID 2018 update: context-specific physical protein-protein interactions in human, model organisms and domesticated species. PMID:30407591
FusionGDB: fusion gene annotation DataBase. PMID:30407583
The pervasive effects of recombinant Fasciola gigantica Ras-related protein Rab10 on the functions of goat peripheral blood mononuclear cells. PMID:30400957
Whole Proteome Profiling of N-Myristoyltransferase Activity and Inhibition Using Sortase A. PMID:30341083
Identification of Kinases and Interactors of p53 Using Kinase-Catalyzed Cross-Linking and Immunoprecipitation. PMID:30339384
Genomic data integration systematically biases interactome mapping. PMID:30332399
Structural basis for receptor-regulated SMAD recognition by MAN1. PMID:30321401
PomBase 2018: user-driven reimplementation of the fission yeast database provides rapid and intuitive access to diverse, interconnected information. PMID:30321395
Document triage for identifying protein-protein interactions affected by mutations: a neural network ensemble approach. PMID:30295718
Chromosome 17 Missing Proteins: Recent Progress and Future Directions as Part of the neXt-MP50 Challenge. PMID:30280577
The Systems Biology of Single-Cell Aging. PMID:30267677
PlaD: A Transcriptomics Database for Plant Defense Responses to Pathogens, Providing New Insights into Plant Immune System. PMID:30266409
Potential use of compounds from sea cucumbers as MDM2 and CXCR4 inhibitors to control cancer cell growth. PMID:30250516
The Comparative Toxicogenomics Database: update 2019. PMID:30247620
A Quantitative Chemical Proteomic Strategy for Profiling Phosphoprotein Phosphatases from Yeast to Humans. PMID:30228194
Large-scale investigation of the reasons why potentially important genes are ignored. PMID:30226837
The PIN-FORMED Auxin Efflux Carriers in Plants. PMID:30223430
Reduced intrinsic DNA curvature leads to increased mutation rate. PMID:30217230
G2Vec: Distributed gene representations for identification of cancer prognostic genes. PMID:30213980
AnimalTFDB 3.0: a comprehensive resource for annotation and prediction of animal transcription factors. PMID:30204897
Exploring the Mechanism of Flavonoids Through Systematic Bioinformatics Analysis. PMID:30158870
An analysis of aging-related genes derived from the Genotype-Tissue Expression project (GTEx). PMID:30155276
ESCC ATLAS: A population wide compendium of biomarkers for Esophageal Squamous Cell Carcinoma. PMID:30143675
A High-Throughput Candida albicans Two-Hybrid System. PMID:30135223
Molecular signatures and functional analysis of beige adipocytes induced from in vivo intra-abdominal adipocytes. PMID:30116775
FBXW7: a critical tumor suppressor of human cancers. PMID:30086763
Evolution of In Silico Strategies for Protein-Protein Interaction Drug Discovery. PMID:30082644
Regional Diversity in the Postsynaptic Proteome of the Mouse Brain. PMID:30071621
FusionPathway: Prediction of pathways and therapeutic targets associated with gene fusions in cancer. PMID:30040819
An unsupervised machine learning method for discovering patient clusters based on genetic signatures. PMID:30016722
Exploring the sound-modulated delay in tomato ripening through expression analysis of coding and non-coding RNAs. PMID:30010774
Proteomic Analysis of NCK1/2 Adaptors Uncovers Paralog-specific Interactions That Reveal a New Role for NCK2 in Cell Abscission During Cytokinesis. PMID:30002203
Positional specificity of different transcription factor classes within enhancers. PMID:29987030
Identification of Antifungal Targets Based on Computer Modeling. PMID:29973534
PrimAlign: PageRank-inspired Markovian alignment for large biological networks. PMID:29949962
In silico approach in reveal traditional medicine plants pharmacological material basis. PMID:29946351
Computational Methods for Predicting Protein-Protein Interactions Using Various Protein Features. PMID:29927082
Hub Protein Controversy: Taking a Closer Look at Plant Stress Response Hubs. PMID:29922309
A quantitative mass spectrometry-based approach to monitor the dynamics of endogenous chromatin-associated protein complexes. PMID:29899353
Stratification of candidate genes for Parkinson's disease using weighted protein-protein interaction network analysis. PMID:29898659
Identification of Central Regulators of Calcium Signaling and ECM-Receptor Interaction Genetically Associated With the Progression and Recurrence of Atrial Fibrillation. PMID:29868113
Chemical-Induced Phenotypes at CTD Help Inform the Predisease State and Construct Adverse Outcome Pathways. PMID:29846728
Time-Resolved Analysis Reveals Rapid Dynamics and Broad Scope of the CBP/p300 Acetylome. PMID:29804834
GIANT 2.0: genome-scale integrated analysis of gene networks in tissues. PMID:29800226
Neural networks for link prediction in realistic biomedical graphs: a multi-dimensional evaluation of graph embedding-based approaches. PMID:29783926
A Primer for the Rat Genome Database (RGD). PMID:29761460
Assessing the functional association of intronic miRNAs with their host genes. PMID:29752351
MEGADOCK-Web: an integrated database of high-throughput structure-based protein-protein interaction predictions. PMID:29745830
In vitro study on role of σB protein in avian reovirus pathogenesis. PMID:29731966
Comparative Analysis of Human Genes Frequently and Occasionally Regulated by m6A Modification. PMID:29730206
New perspectives: systems medicine in cardiovascular disease. PMID:29699591
Mut2Vec: distributed representation of cancerous mutations. PMID:29697361
Annotating activation/inhibition relationships to protein-protein interactions using gene ontology relations. PMID:29671402
DNA Repair Network Analysis Reveals Shieldin as a Key Regulator of NHEJ and PARP Inhibitor Sensitivity. PMID:29656893
Evaluation of Animal Models by Comparison with Human Late-Onset Alzheimer's Disease. PMID:29656362
JAMI: a Java library for molecular interactions and data interoperability. PMID:29642846
DDX49 is an RNA helicase that affects translation by regulating mRNA export and the levels of pre-ribosomal RNA. PMID:29618122
Multi-omics analysis reveals neoantigen-independent immune cell infiltration in copy-number driven cancers. PMID:29615613
Textpresso Central: a customizable platform for searching, text mining, viewing, and curating biomedical literature. PMID:29523070
Extracellular vesicle RNAs reflect placenta dysfunction and are a biomarker source for preterm labour. PMID:29516617
SUMO E3 ligase Mms21 prevents spontaneous DNA damage induced genome rearrangements. PMID:29505562
How Surrogate and Chemical Genetics in Model Organisms Can Suggest Therapies for Human Genetic Diseases. PMID:29487144
The dynamic life of the glycogen granule. PMID:29483195
Structural principles that enable oligomeric small heat-shock protein paralogs to evolve distinct functions. PMID:29472485
ZFP36L2 is a cell cycle-regulated CCCH protein necessary for DNA lesion-induced S-phase arrest. PMID:29449217
scEpath: energy landscape-based inference of transition probabilities and cellular trajectories from single-cell transcriptomic data. PMID:29415263
Systematic Analysis of mRNA and miRNA Expression of 3D-Cultured Neural Stem Cells (NSCs) in Spaceflight. PMID:29375320
Protein Tyrosine Phosphatase Receptor Type G (PTPRG) Controls Fibroblast Growth Factor Receptor (FGFR) 1 Activity and Influences Sensitivity to FGFR Kinase Inhibitors. PMID:29371290
Using genetic buffering relationships identified in fission yeast to reveal susceptibilities in cells lacking hamartin or tuberin function. PMID:29343513
Systemic bioinformatics analysis of recurrent aphthous stomatitis gene expression profiles. PMID:29340037
Aux/IAA Gene Family in Plants: Molecular Structure, Regulation, and Function. PMID:29337875
Feature genes in metastatic breast cancer identified by MetaDE and SVM classifier methods. PMID:29328377
Circulating microRNA (miRNA) Expression Profiling in Plasma of Patients with Gestational Diabetes Mellitus Reveals Upregulation of miRNA miR-330-3p. PMID:29312141
Biosystems Study of the Molecular Networks Underlying Hippocampal Aging Progression and Anti-aging Treatment in Mice. PMID:29311893
TRANSPARENT TESTA GLABRA 1-Dependent Regulation of Flavonoid Biosynthesis. PMID:29261137
Functional Analysis of Human Hub Proteins and Their Interactors Involved in the Intrinsic Disorder-Enriched Interactions. PMID:29257115
Weighted Gene Co-expression Network Analysis Identifies FKBP11 as a Key Regulator in Acute Aortic Dissection through a NF-kB Dependent Pathway. PMID:29255427
Constructing a comprehensive gene co-expression based interactome in Bos taurus. PMID:29226034
MiRIAD update: using alternative polyadenylation, protein interaction network analysis and additional species to enhance exploration of the role of intragenic miRNAs and their host genes. PMID:29220447
Extended Linkers Improve the Detection of Protein-protein Interactions (PPIs) by Dihydrofolate Reductase Protein-fragment Complementation Assay (DHFR PCA) in Living Cells. PMID:29203496
Systems Bioinformatics: increasing precision of computational diagnostics and therapeutics through network-based approaches. PMID:29186305
FunCoup 4: new species, data, and visualization. PMID:29165593
Molecular Interaction Search Tool (MIST): an integrated resource for mining gene and protein interaction data. PMID:29155944
Constructing Genetic Networks using Biomedical Literature and Rare Event Classification. PMID:29150626
ANAT 2.0: reconstructing functional protein subnetworks. PMID:29145805
Saccharomyces genome database informs human biology. PMID:29140510
Protein Moonlighting Revealed by Noncatalytic Phenotypes of Yeast Enzymes. PMID:29127264
The UCSC Genome Browser database: 2018 update. PMID:29106570
The DifferentialNet database of differential protein-protein interactions in human tissues. PMID:29069447
The online Tabloid Proteome: an annotated database of protein associations. PMID:29040688
A Compendium of Co-regulated Protein Complexes in Breast Cancer Reveals Collateral Loss Events. PMID:29032073
PICKLE 2.0: A human protein-protein interaction meta-database employing data integration via genetic information ontology. PMID:29023571
A Unique TGFB1-Driven Genomic Program Links Astrocytosis, Low-Grade Inflammation and Partial Demyelination in Spinal Cord Periplaques from Progressive Multiple Sclerosis Patients. PMID:28981455
Molecular mechanisms underlying gliomas and glioblastoma pathogenesis revealed by bioinformatics analysis of microarray data. PMID:28952134
Detecting gene subnetworks under selection in biological pathways. PMID:28934485
Digoxin-induced anemia among patients with atrial fibrillation and heart failure: clinical data analysis and drug-gene interaction network. PMID:28915649
Knowledge-guided gene prioritization reveals new insights into the mechanisms of chemoresistance. PMID:28800781
CytoMCS: A Multiple Maximum Common Subgraph Detection Tool for Cytoscape. PMID:28731857
HDNetDB: A Molecular Interaction Database for Network-Oriented Investigations into Huntington's Disease. PMID:28701700
NetNorM: Capturing cancer-relevant information in somatic exome mutation data with gene networks for cancer stratification and prognosis. PMID:28650955
Agonist-specific Protein Interactomes of Glucocorticoid and Androgen Receptor as Revealed by Proximity Mapping. PMID:28611094
Comparative analysis of genes frequently regulated by drugs based on connectivity map transcriptome data. PMID:28575118
GLADIATOR: a global approach for elucidating disease modules. PMID:28549478
CLMSVault: A Software Suite for Protein Cross-Linking Mass-Spectrometry Data Analysis and Visualization. PMID:28537071
Unbiased Protein Association Study on the Public Human Proteome Reveals Biological Connections between Co-Occurring Protein Pairs. PMID:28480704
WebGestalt 2017: a more comprehensive, powerful, flexible and interactive gene set enrichment analysis toolkit. PMID:28472511
Mapping the Synthetic Dosage Lethality Network of CDK1/CDC28. PMID:28428242
Diagnostic and prognostic relevance of CP2c and YY1 expression in hepatocellular carcinoma. PMID:28412749
Cancer/Testis Antigens: "Smart" Biomarkers for Diagnosis and Prognosis of Prostate and Other Cancers. PMID:28362316
Protein Kinase CK2: Intricate Relationships within Regulatory Cellular Networks. PMID:28273877
Emerging Roles for Ciz1 in Cell Cycle Regulation and as a Driver of Tumorigenesis. PMID:28036012 -
The BioGRID Interaction Database: 2011 update
PubMed citations: 422.
422 articles citing: The BioGRID Interaction Database: 2011 update
DEMA: a distance-bounded energy-field minimization algorithm to model and layout biomolecular networks with quantitative features. PMID:35758816
Contribution of Model Organisms to Investigating the Far-Reaching Consequences of PRPP Metabolism on Human Health and Well-Being. PMID:35741038
Protein-Protein Interaction (PPI) Network of Zebrafish Oestrogen Receptors: A Bioinformatics Workflow. PMID:35629318
Uncompensated mitochondrial oxidative stress underlies heart failure in an iPSC-derived model of congenital heart disease. PMID:35395180
Integrating protein copy numbers with interaction networks to quantify stoichiometry in clathrin-mediated endocytosis. PMID:35354856
Protein interaction networks provide insight into fetal origins of chronic obstructive pulmonary disease. PMID:35331221
Correlation Imputation for Single-Cell RNA-seq. PMID:35325552
Identifying large-scale interaction atlases using probabilistic graphs and external knowledge. PMID:35321220
Protein Function Prediction Based on PPI Networks: Network Reconstruction vs Edge Enrichment. PMID:34970299
The Hippo Signaling Pathway in Cancer: A Cell Cycle Perspective. PMID:34944834
Convolutional neural network for human cancer types prediction by integrating protein interaction networks and omics data. PMID:34667236
LncTx: A network-based method to repurpose drugs acting on the survival-related lncRNAs in lung cancer. PMID:34377365
Correlation Imputation in Single cell RNA-seq using Auxiliary Information and Ensemble Learning. PMID:34278382
Environmental robustness of the global yeast genetic interaction network. PMID:33958448
The contributions from the progenitor genomes of the mesopolyploid Brassiceae are evolutionarily distinct but functionally compatible. PMID:33863805
Genome analyses of 174 strains of Mycobacterium tuberculosis provide insight into the evolution of drug resistance and reveal potential drug targets. PMID:33750515
Chemical-Genetic Interactions of Bacopa monnieri Constituents in Cells Deficient for the DNA Repair Endonuclease RAD1 Appear Linked to Vacuolar Disruption. PMID:33668176
A large accessory protein interactome is rewired across environments. PMID:32924934
Network-principled deep generative models for designing drug combinations as graph sets. PMID:32657357
Predicting Self-Interacting Proteins Using a Recurrent Neural Network and Protein Evolutionary Information. PMID:32550764
Systematic analysis of ovarian cancer platinum-resistance mechanisms via text mining. PMID:32160916
The Need for SMN-Independent Treatments of Spinal Muscular Atrophy (SMA) to Complement SMN-Enhancing Drugs. PMID:32117013
Systematic genetics and single-cell imaging reveal widespread morphological pleiotropy and cell-to-cell variability. PMID:32064787
Genome-wide inference of the Camponotus floridanus protein-protein interaction network using homologous mapping and interacting domain profile pairs. PMID:32047225
A comparative study of topology-based pathway enrichment analysis methods. PMID:31684881
Speeding up the drug discovery process: structural similarity searches using molecular surfaces. PMID:31440460
Membrane protein-regulated networks across human cancers. PMID:31311925
Gnal haploinsufficiency causes genomic instability and increased sensitivity to haloperidol. PMID:31034808
A Comprehensive Drosophila melanogaster Transcription Factor Interactome. PMID:30995488
Analysis of Predicted Host-Parasite Interactomes Reveals Commonalities and Specificities Related to Parasitic Lifestyle and Tissues Tropism. PMID:30815000
Molecular subtyping of cancer and nomination of kinase candidates for inhibition with phosphoproteomics: Reanalysis of CPTAC ovarian cancer. PMID:30594550
A Network Pharmacology Approach to Uncover the Molecular Mechanisms of Herbal Formula Ban-Xia-Xie-Xin-Tang. PMID:30410554
Context-enriched interactome powered by proteomics helps the identification of novel regulators of macrophage activation. PMID:30303482
Evidence that RNA Viruses Drove Adaptive Introgression between Neanderthals and Modern Humans. PMID:30290142
MiRNA-BD: an evidence-based bioinformatics model and software tool for microRNA biomarker discovery. PMID:30081733
Automatic extraction of protein-protein interactions using grammatical relationship graph. PMID:30066644
Proximal Pathway Enrichment Analysis for Targeting Comorbid Diseases via Network Endopharmacology. PMID:29932108
A systems immunology approach identifies the collective impact of 5 miRs in Th2 inflammation. PMID:29875322
Systematic Evaluation of Molecular Networks for Discovery of Disease Genes. PMID:29605183
Preferential retention of genes from one parental genome after polyploidy illustrates the nature and scope of the genomic conflicts induced by hybridization. PMID:29590103
Key genes and regulatory networks involved in the initiation, progression and invasion of colorectal cancer. PMID:29568567
A homologous mapping method for three-dimensional reconstruction of protein networks reveals disease-associated mutations. PMID:29560828
Prediction of Disordered Regions and Their Roles in the Anti-Pathogenic and Immunomodulatory Functions of Butyrophilins. PMID:29401697
Co-complex protein membership evaluation using Maximum Entropy on GO ontology and InterPro annotation. PMID:29390084
Support vector machine classifier for prediction of the metastasis of colorectal cancer. PMID:29328363
Protein-protein interaction analysis to identify biomarker networks for endometriosis. PMID:29201163
SPRINT: ultrafast protein-protein interaction prediction of the entire human interactome. PMID:29141584
CRISPR/Cas9-Based Engineering of the Epigenome. PMID:28985525
High rate of adaptation of mammalian proteins that interact with Plasmodium and related parasites. PMID:28957326
Genome wide host gene expression analysis in mice experimentally infected with Pasteurella multocida. PMID:28704394
Application of a systems approach to study developmental gene regulation. PMID:28510076
iTRAQ-based quantitative proteomic analysis of Yamanaka factors reprogrammed breast cancer cells. PMID:28423718
RNA Seq analysis for transcriptome profiling in response to classical swine fever vaccination in indigenous and crossbred pigs. PMID:28361233
Gene Expression, Protein Function and Pathways of Arabidopsis thaliana Responding to Silver Nanoparticles in Comparison to Silver Ions, Cold, Salt, Drought, and Heat. PMID:28347022
Downstream targets of GWAS-detected genes for breast, lung, and prostate and colon cancer converge to G1/S transition pathway. PMID:28334950
IODNE: An integrated optimization method for identifying the deregulated subnetwork for precision medicine in cancer. PMID:28266149
Systematic analysis of molecular mechanisms for HCC metastasis via text mining approach. PMID:28108733
Properties of human disease genes and the role of genes linked to Mendelian disorders in complex disease aetiology. PMID:28053046
CanProVar 2.0: An Updated Database of Human Cancer Proteome Variation. PMID:27977206
Personalized anticancer therapy selection using molecular landscape topology and thermodynamics. PMID:27793055
Protein folding, binding, and droplet formation in cell-like conditions. PMID:27771543
A computational interactome and functional annotation for the human proteome. PMID:27770567
A global genetic interaction network maps a wiring diagram of cellular function. PMID:27708008
Systems Medicine as an Emerging Tool for Cardiovascular Genetics. PMID:27626034
Entropy-based divergent and convergent modular pattern reveals additive and synergistic anticerebral ischemia mechanisms. PMID:27480252
Identification of key target genes and pathways in laryngeal carcinoma. PMID:27446427
Mining Functional Modules in Heterogeneous Biological Networks Using Multiplex PageRank Approach. PMID:27446133
Relational Network for Knowledge Discovery through Heterogeneous Biomedical and Clinical Features. PMID:27427091
Network analysis and juvenile idiopathic arthritis (JIA): a new horizon for the understanding of disease pathogenesis and therapeutic target identification. PMID:27411317
Quantitative Determination of Flexible Pharmacological Mechanisms Based On Topological Variation in Mice Anti-Ischemic Modular Networks. PMID:27383195
BcCluster: A Bladder Cancer Database at the Molecular Level. PMID:27376128
Endophenotype Network Models: Common Core of Complex Diseases. PMID:27278246
Systematic analysis of the molecular mechanism underlying atherosclerosis using a text mining approach. PMID:27251057
Viruses are a dominant driver of protein adaptation in mammals. PMID:27187613
A Network of Splice Isoforms for the Mouse. PMID:27079421
Dissecting dysfunctional crosstalk pathways regulated by miRNAs during glioma progression. PMID:27013589
Regulatory consequences of neuronal ELAV-like protein binding to coding and non-coding RNAs in human brain. PMID:26894958
Network-based in silico drug efficacy screening. PMID:26831545
Identification of miRNA-mRNA regulatory modules by exploring collective group relationships. PMID:26817421
CSGene: a literature-based database for cell senescence genes and its application to identify critical cell aging pathways and associated diseases. PMID:26775705
BioGRID: A Resource for Studying Biological Interactions in Yeast. PMID:26729913
Scope and limitations of yeast as a model organism for studying human tissue-specific pathways. PMID:26714768
Transcriptome analysis in calorie-restricted rats implicates epigenetic and post-translational mechanisms in neuroprotection and aging. PMID:26694192
CancerNet: a database for decoding multilevel molecular interactions across diverse cancer types. PMID:26690544
Properly defining the targets of a transcription factor significantly improves the computational identification of cooperative transcription factor pairs in yeast. PMID:26679776
YAGM: a web tool for mining associated genes in yeast based on diverse biological associations. PMID:26678566
PCTFPeval: a web tool for benchmarking newly developed algorithms for predicting cooperative transcription factor pairs in yeast. PMID:26677932
A network pharmacology approach reveals new candidate caloric restriction mimetics in C. elegans. PMID:26676933
Application of Gene Expression Trajectories Initiated from ErbB Receptor Activation Highlights the Dynamics of Divergent Promoter Usage. PMID:26658111
NDEx, the Network Data Exchange. PMID:26594663
Interpreting functional effects of coding variants: challenges in proteome-scale prediction, annotation and assessment. PMID:26494363
Integrative analysis of human protein, function and disease networks. PMID:26399914
Systematic Analysis of the Molecular Mechanism Underlying Decidualization Using a Text Mining Approach. PMID:26222155
Genes Caught In Flagranti: Integrating Renal Transcriptional Profiles With Genotypes and Phenotypes. PMID:26215861
The BioPlex Network: A Systematic Exploration of the Human Interactome. PMID:26186194
Transcriptomic-Wide Discovery of Direct and Indirect HuR RNA Targets in Activated CD4+ T Cells. PMID:26162078
A reproducible approach to high-throughput biological data acquisition and integration. PMID:26157642
Biology-Driven Gene-Gene Interaction Analysis of Age-Related Cataract in the eMERGE Network. PMID:25982363
FNTM: a server for predicting functional networks of tissues in mouse. PMID:25940632
Follicle Online: an integrated database of follicle assembly, development and ovulation. PMID:25931457
Lineage-specific sequence evolution and exon edge conservation partially explain the relationship between evolutionary rate and expression level in A. thaliana. PMID:25930165
Predicted protein-protein interactions in the moss Physcomitrella patens: a new bioinformatic resource. PMID:25885037
Inhibition of cathepsin proteases attenuates migration and sensitizes aggressive N-Myc amplified human neuroblastoma cells to doxorubicin. PMID:25883214
A DIseAse MOdule Detection (DIAMOnD) algorithm derived from a systematic analysis of connectivity patterns of disease proteins in the human interactome. PMID:25853560
Recent positive selection has acted on genes encoding proteins with more interactions within the whole human interactome. PMID:25840415
Genomic analysis of host - Peste des petits ruminants vaccine viral transcriptome uncovers transcription factors modulating immune regulatory pathways. PMID:25827022
The pentameric nucleoplasmin fold is present in Drosophila FKBP39 and a large number of chromatin-related proteins. PMID:25813344
MDM2 turnover and expression of ATRX determine the choice between quiescence and senescence in response to CDK4 inhibition. PMID:25803170
Module organization and variance in protein-protein interaction networks. PMID:25797237
Network-based proteomic approaches reveal the neurodegenerative, neuroprotective and pain-related mechanisms involved after retrograde axonal damage. PMID:25784190
LC-MS/MS-based serum proteomics for identification of candidate biomarkers for hepatocellular carcinoma. PMID:25778709
The identification of specific methylation patterns across different cancers. PMID:25774687
Expression profile of mitrogen-activated protein kinase (MAPK) signaling genes in the skeletal muscle & liver of rat with type 2 diabetes: role in disease pathology. PMID:25758573
Efficient prediction of progesterone receptor interactome using a support vector machine model. PMID:25741764
Network tuned multiple rank aggregation and applications to gene ranking. PMID:25708095
An integrative approach for a network based meta-analysis of viral RNAi screens. PMID:25691914
Reconstructing genome-wide protein-protein interaction networks using multiple strategies with homologous mapping. PMID:25602759
The molecular genetic architecture of attention deficit hyperactivity disorder. PMID:25600112
Protein interactome of muscle invasive bladder cancer. PMID:25569276
Integrated systems analysis reveals a molecular network underlying autism spectrum disorders. PMID:25549968
Network-based association of hypoxia-responsive genes with cardiovascular diseases. PMID:25530704
Complex-based analysis of dysregulated cellular processes in cancer. PMID:25521701
A comprehensive performance evaluation on the prediction results of existing cooperative transcription factors identification algorithms. PMID:25521604
A proteomic analysis reveals that Snail regulates the expression of the nuclear orphan receptor Nuclear Receptor Subfamily 2 Group F Member 6 (Nr2f6) and interleukin 17 (IL-17) to inhibit adipocyte differentiation. PMID:25505127
Pathway crosstalk analysis of microarray gene expression profile in human hepatocellular carcinoma. PMID:25480734
Systems Medicine: from molecular features and models to the clinic in COPD. PMID:25471042
In silico prediction of synthetic lethality by meta-analysis of genetic interactions, functions, and pathways in yeast and human cancer. PMID:25452682
Tissue-aware data integration approach for the inference of pathway interactions in metazoan organisms. PMID:25431329
Systematic identification of cell size regulators in budding yeast. PMID:25411401
Spotlite: web application and augmented algorithms for predicting co-complexed proteins from affinity purification--mass spectrometry data. PMID:25300367
Identification of essential proteins based on ranking edge-weights in protein-protein interaction networks. PMID:25268881
Characterizing protein interactions employing a genome-wide siRNA cellular phenotyping screen. PMID:25255318
Drug-Like Protein-Protein Interaction Modulators: Challenges and Opportunities for Drug Discovery and Chemical Biology. PMID:25254076
Integration strategy is a key step in network-based analysis and dramatically affects network topological properties and inferring outcomes. PMID:25243127
Finding trans-regulatory genes and protein complexes modulating meiotic recombination hotspots of human, mouse and yeast. PMID:25208583
Unbiased functional clustering of gene variants with a phenotypic-linkage network. PMID:25166029
Bioinformatics analysis of biomarkers and transcriptional factor motifs in Down syndrome. PMID:25118625
Modeling dynamic functional relationship networks and application to ex vivo human erythroid differentiation. PMID:25115705
An integrative omics strategy to assess the germ cell secretome and to decipher sertoli-germ cell crosstalk in the Mammalian testis. PMID:25111155
Prediction and functional analysis of the sweet orange protein-protein interaction network. PMID:25091279
A dedicated database system for handling multi-level data in systems biology. PMID:25053973
Large Scale Chemical Cross-linking Mass Spectrometry Perspectives. PMID:25045217
Construction and analysis of microRNA-transcription factor regulation network in Arabidopsis. PMID:25014374
The domain landscape of virus-host interactomes. PMID:24991570
Building a hierarchical organization of protein complexes out of protein association data. PMID:24978199
Correlating information contents of gene ontology terms to infer semantic similarity of gene products. PMID:24963342
Scale-space measures for graph topology link protein network architecture to function. PMID:24931989
Improving functional annotation for industrial microbes: a case study with Pichia pastoris. PMID:24929579
Comparative analysis of human tissue interactomes reveals factors leading to tissue-specific manifestation of hereditary diseases. PMID:24921629
Essential functional modules for pathogenic and defensive mechanisms in Candida albicans infections. PMID:24757665
Stringent homology-based prediction of H. sapiens-M. tuberculosis H37Rv protein-protein interactions. PMID:24708540
Tissue-specific expression and regulatory networks of pig microRNAome. PMID:24699212
A second-generation protein-protein interaction network of Helicobacter pylori. PMID:24627523
Modelling the yeast interactome. PMID:24589662
Protein-protein interactions prediction based on iterative clique extension with gene ontology filtering. PMID:24578640
M-Finder: Uncovering functionally associated proteins from interactome data integrated with GO annotations. PMID:24565382
Stringent DDI-based prediction of H. sapiens-M. tuberculosis H37Rv protein-protein interactions. PMID:24564941
Identifying conserved protein complexes between species by constructing interolog networks. PMID:24564762
RRHGE: a novel approach to classify the estrogen receptor based breast cancer subtypes. PMID:24563630
Navigating the multilayered organization of eukaryotic signaling: a new trend in data integration. PMID:24550716
A Network Approach to Wound Healing. PMID:24527361
Discovery and characterization of two Nimrod superfamily members in Anopheles gambiae. PMID:24428830
Dynamics of regulatory networks in gastrin-treated adenocarcinoma cells. PMID:24416123
Computational Prediction of Protein-Protein Interaction Networks: Algo-rithms and Resources. PMID:24396273
Identifying functional transcription factor binding sites in yeast by considering their positional preference in the promoters. PMID:24386279
Low frequency variants, collapsed based on biological knowledge, uncover complexity of population stratification in 1000 genomes project data. PMID:24385916
Reverse engineering molecular hypergraphs. PMID:24384702
An association-adjusted consensus deleterious scheme to classify homozygous Mis-sense mutations for personal genome interpretation. PMID:24365473
Identification of unstable network modules reveals disease modules associated with the progression of Alzheimer's disease. PMID:24348898
Causal inference of gene regulation with subnetwork assembly from genetical genomics data. PMID:24322297
SysBioCube: A Data Warehouse and Integrative Data Analysis Platform Facilitating Systems Biology Studies of Disorders of Military Relevance. PMID:24303294
Expression of integrin alpha 10 is transcriptionally activated by pRb in mouse osteoblasts and is downregulated in multiple solid tumors. PMID:24287699
Integrating structure to protein-protein interaction networks that drive metastasis to brain and lung in breast cancer. PMID:24278371
Protein function prediction by collective classification with explicit and implicit edges in protein-protein interaction networks. PMID:24267980
P³DB 3.0: From plant phosphorylation sites to protein networks. PMID:24243849
Integrating protein-protein interaction networks with phenotypes reveals signs of interactions. PMID:24240319
Genotype to phenotype via network analysis. PMID:24238873
Integrating in silico resources to map a signaling network. PMID:24233784
Discovering disease-disease associations by fusing systems-level molecular data. PMID:24232732
Bayesian network prior: network analysis of biological data using external knowledge. PMID:24215027
Synthetic genetic targeting of genome instability in cancer. PMID:24202319
High-resolution network biology: connecting sequence with function. PMID:24197012
Conserved versatile master regulators in signalling pathways in response to stress in plants. PMID:24147216
Systematic identification of transcriptional regulatory modules from protein-protein interaction networks. PMID:24137002
NP-MuScL: unsupervised global prediction of interaction networks from multiple data sources. PMID:24134391
Simple topological features reflect dynamics and modularity in protein interaction networks. PMID:24130468
Protein kinase PKN1 represses Wnt/β-catenin signaling in human melanoma cells. PMID:24114839
Exploring mechanisms of human disease through structurally resolved protein interactome networks. PMID:24096645
Identification of small exonic CNV from whole-exome sequence data and application to autism spectrum disorder. PMID:24094742
Integration of new genes into cellular networks, and their structural maturation. PMID:24056411
Detecting non-uniform clusters in large-scale interaction graphs. PMID:24050498
PainNetworks: a web-based resource for the visualisation of pain-related genes in the context of their network associations. PMID:24036287
IQdb: an intelligence quotient score-associated gene resource for human intelligence. PMID:24030781
Predicting whole genome protein interaction networks from primary sequence data in model and non-model organisms using ENTS. PMID:24015873
ExoCarta as a resource for exosomal research. PMID:24009883
Inferring the effective TOR-dependent network: a computational study in yeast. PMID:24005029
Research prioritization through prediction of future impact on biomedical science: a position paper on inference-analytics. PMID:24001106
Computational analysis of virus-host interactomes. PMID:23996253
Network clusters analysis based on protein-protein interaction network constructed in phosgene-induced acute lung injury. PMID:23963411
Ultrasensitivity in phosphorylation-dephosphorylation cycles with little substrate. PMID:23950701
Human growth is associated with distinct patterns of gene expression in evolutionarily conserved networks. PMID:23941278
Association study of 167 candidate genes for schizophrenia selected by a multi-domain evidence-based prioritization algorithm and neurodevelopmental hypothesis. PMID:23922650
Cloud-based uniform ChIP-Seq processing tools for modENCODE and ENCODE. PMID:23875683
SMETANA: accurate and scalable algorithm for probabilistic alignment of large-scale biological networks. PMID:23874484
Genome evolution predicts genetic interactions in protein complexes and reveals cancer drug targets. PMID:23851603
Widespread evidence of cooperative DNA binding by transcription factors in Drosophila development. PMID:23847101
DBATE: database of alternative transcripts expression. PMID:23842462
PhosphoChain: a novel algorithm to predict kinase and phosphatase networks from high-throughput expression data. PMID:23832245
Mapping the functional yeast ABC transporter interactome. PMID:23831759
Link clustering reveals structural characteristics and biological contexts in signed molecular networks. PMID:23826198
BioBin: a bioinformatics tool for automating the binning of rare variants using publicly available biological knowledge. PMID:23819467
A nutrigenomic framework to identify time-resolving responses of hepatic genes in diet-induced obese mice. PMID:23813319
Integrating sequence, expression and interaction data to determine condition-specific miRNA regulation. PMID:23813013
A context-sensitive framework for the analysis of human signalling pathways in molecular interaction networks. PMID:23812986
Arbor: comparative analysis workflows for the tree of life. PMID:23811960
Mining breast cancer genes with a network based noise-tolerant approach. PMID:23799982
Integrative approaches for predicting protein function and prioritizing genes for complex phenotypes using protein interaction networks. PMID:23788799
ResponseNet2.0: Revealing signaling and regulatory pathways connecting your proteins and genes--now with human data. PMID:23761447
Optimization criteria and biological process enrichment in homologous multiprotein modules. PMID:23757502
Construction of protein phosphorylation networks by data mining, text mining and ontology integration: analysis of the spindle checkpoint. PMID:23749465
The development of a universal in silico predictor of protein-protein interactions. PMID:23741499
Comparison of modules of wild type and mutant Huntingtin and TP53 protein interaction networks: implications in biological processes and functions. PMID:23741403
Passing messages between biological networks to refine predicted interactions. PMID:23741402
Integrated analysis of recurrent properties of cancer genes to identify novel drivers. PMID:23718799
NRF2-ome: an integrated web resource to discover protein interaction and regulatory networks of NRF2. PMID:23710289
Genome-wide methylated DNA immunoprecipitation analysis of patients with polycystic ovary syndrome. PMID:23705014
Evolutionary pressure on the topology of protein interface interaction networks. PMID:23701316
A genome-wide resource of cell cycle and cell shape genes of fission yeast. PMID:23697806
A "candidate-interactome" aggregate analysis of genome-wide association data in multiple sclerosis. PMID:23696811
Human monogenic disease genes have frequently functionally redundant paralogs. PMID:23696728
Interface-resolved network of protein-protein interactions. PMID:23696724
Cross-species protein interactome mapping reveals species-specific wiring of stress response pathways. PMID:23695164
Adjusting for High-dimensional Covariates in Sparse Precision Matrix Estimation by ℓ1-Penalization. PMID:23687392
The PhosphoGRID Saccharomyces cerevisiae protein phosphorylation site database: version 2.0 update. PMID:23674503
All or nothing: protein complexes flip essentiality between distantly related eukaryotes. PMID:23661563
Protein complex detection via weighted ensemble clustering based on Bayesian nonnegative matrix factorization. PMID:23658709
Genotype to phenotype mapping and the fitness landscape of the E. coli lac promoter. PMID:23650500
Top-down network analysis to drive bottom-up modeling of physiological processes. PMID:23641868
PCorral--interactive mining of protein interactions from MEDLINE. PMID:23640984
Use of the protein ontology for multi-faceted analysis of biological processes: a case study of the spindle checkpoint. PMID:23637705
Chapter 15: disease gene prioritization. PMID:23633938
Genome-wide association study of sleep in Drosophila melanogaster. PMID:23617951
Large-scale event extraction from literature with multi-level gene normalization. PMID:23613707
INstruct: a database of high-quality 3D structurally resolved protein interactome networks. PMID:23599502
Interplay between chromatin state, regulator binding, and regulatory motifs in six human cell types. PMID:23595227
Evolutionary capacitance and control of protein stability in protein-protein interaction networks. PMID:23592969
Physical and genetic-interaction density reveals functional organization and informs significance cutoffs in genome-wide screens. PMID:23589890
Endometrial receptivity: a revisit to functional genomics studies on human endometrium and creation of HGEx-ERdb. PMID:23555582
Comparison of hepatocellular carcinoma (HCC), cholangiocarcinoma (CC), and combined HCC-CC (CHC) with each other based on microarray dataset. PMID:23532688
Network pharmacology strategies toward multi-target anticancer therapies: from computational models to experimental design principles. PMID:23530504
Functional knowledge transfer for high-accuracy prediction of under-studied biological processes. PMID:23516347
Functional site plasticity in domain superfamilies. PMID:23499848
Preferential duplication of intermodular hub genes: an evolutionary signature in eukaryotes genome networks. PMID:23468868
Predicting the binding patterns of hub proteins: a study using yeast protein interaction networks. PMID:23431393
Using BioBin to explore rare variant population stratification. PMID:23424138
Next-generation analysis of cataracts: determining knowledge driven gene-gene interactions using Biofilter, and gene-environment interactions using the PhenX Toolkit. PMID:23424120
Epigenetic epistatic interactions constrain the evolution of gene expression. PMID:23423319
Quantitative analysis of chaperone network throughput in budding yeast. PMID:23420633
A genomic toolkit to investigate kinesin and myosin motor function in cells. PMID:23417121
Linking proteomic and transcriptional data through the interactome and epigenome reveals a map of oncogene-induced signaling. PMID:23408876
Benchmarking human protein complexes to investigate drug-related systems and evaluate predicted protein complexes. PMID:23405067
Interactome3D: adding structural details to protein networks. PMID:23399932
A survey of protein interaction data and multigenic inherited disorders. PMID:23398688
The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies. PMID:23398680
The YeastGenome app: the Saccharomyces Genome Database at your fingertips. PMID:23396302
Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review. PMID:23384594
Identification of ovarian cancer associated genes using an integrated approach in a Boolean framework. PMID:23383610
Turning gold into 'junk': transposable elements utilize central proteins of cellular networks. PMID:23341038
Predicting PDZ domain mediated protein interactions from structure. PMID:23336252
SignaLink 2 - a signaling pathway resource with multi-layered regulatory networks. PMID:23331499
Identification of new protein interactions between dengue fever virus and its hosts, human and mosquito. PMID:23326450
Systems biology approach reveals genome to phenome correlation in type 2 diabetes. PMID:23308243
Evidence for the robustness of protein complexes to inter-species hybridization. PMID:23300466
Adding protein context to the human protein-protein interaction network to reveal meaningful interactions. PMID:23300433
Distinct transcriptional regulatory modules underlie STAT3's cell type-independent and cell type-specific functions. PMID:23295670
Supervised maximum-likelihood weighting of composite protein networks for complex prediction. PMID:23281936
Helminth secretome database (HSD): a collection of helminth excretory/secretory proteins predicted from expressed sequence tags (ESTs). PMID:23281827
GWIDD: a comprehensive resource for genome-wide structural modeling of protein-protein interactions. PMID:23245398
A gene ontology inferred from molecular networks. PMID:23242164
A novel link prediction algorithm for reconstructing protein-protein interaction networks by topological similarity. PMID:23235927
Building an efficient curation workflow for the Arabidopsis literature corpus. PMID:23221298
Mitotic exit and separation of mother and daughter cells. PMID:23212898
An evolutionarily conserved innate immunity protein interaction network. PMID:23209288
Identification of pharmacological targets in amyotrophic lateral sclerosis through genomic analysis of deregulated genes and pathways. PMID:23204922
The BioGRID interaction database: 2013 update. PMID:23203989
STRING v9.1: protein-protein interaction networks, with increased coverage and integration. PMID:23203871
The Disease and Gene Annotations (DGA): an annotation resource for human disease. PMID:23197658
SpermatogenesisOnline 1.0: a resource for spermatogenesis based on manual literature curation and genome-wide data mining. PMID:23193286
The TissueNet database of human tissue protein-protein interactions. PMID:23193266
Systems biology of pathogen-host interaction: networks of protein-protein interaction within pathogens and pathogen-human interactions in the post-genomic era. PMID:23193100
Evolutionary rate and duplicability in the Arabidopsis thaliana protein-protein interaction network. PMID:23160177
Proteomics-based methods for discovery, quantification, and validation of protein-protein interactions. PMID:23157382
Discovery of cell compartment specific protein-protein interactions using affinity purification combined with tandem mass spectrometry. PMID:23157168
Effects of protein interaction data integration, representation and reliability on the use of network properties for drug target prediction. PMID:23146171
The ConsensusPathDB interaction database: 2013 update. PMID:23143270
A travel guide to Cytoscape plugins. PMID:23132118
Spliceosome database: a tool for tracking components of the spliceosome. PMID:23118483
SpliceAid-F: a database of human splicing factors and their RNA-binding sites. PMID:23118479
Identifying novel protein complexes in cancer cells using epitope-tagging of endogenous human genes and affinity-purification mass spectrometry. PMID:23106643
Popular computational methods to assess multiprotein complexes derived from label-free affinity purification and mass spectrometry (AP-MS) experiments. PMID:23071097
Dr. PIAS 2.0: an update of a database of predicted druggable protein-protein interactions. PMID:23060433
Aminopropyltransferases involved in polyamine biosynthesis localize preferentially in the nucleus of plant cells. PMID:23056524
Identification of significant pathways in gastric cancer based on protein-protein interaction networks and cluster analysis. PMID:23055812
PRD: A protein-RNA interaction database. PMID:23055619
Cluster-based assessment of protein-protein interaction confidence. PMID:23050565
Evaluating caveolin interactions: do proteins interact with the caveolin scaffolding domain through a widespread aromatic residue-rich motif? PMID:23028656
Tissue-specific functional networks for prioritizing phenotype and disease genes. PMID:23028291
Protein stickiness, rather than number of functional protein-protein interactions, predicts expression noise and plasticity in yeast. PMID:23017156
Fungal Hsp90: a biological transistor that tunes cellular outputs to thermal inputs. PMID:22976491
RhesusBase: a knowledgebase for the monkey research community. PMID:22965133
Identifying functional modules in interaction networks through overlapping Markov clustering. PMID:22962469
Architecture of the human regulatory network derived from ENCODE data. PMID:22955619
Feature Identification of Compensatory Gene Pairs without Sequence Homology in Yeast. PMID:22952430
Using ProHits to store, annotate, and analyze affinity purification-mass spectrometry (AP-MS) data. PMID:22948730
Analyzing protein-protein interactions from affinity purification-mass spectrometry data with SAINT. PMID:22948729
A network-based approach for predicting missing pathway interactions. PMID:22916002
A network synthesis model for generating protein interaction network families. PMID:22912671
A SPARSE CONDITIONAL GAUSSIAN GRAPHICAL MODEL FOR ANALYSIS OF GENETICAL GENOMICS DATA. PMID:22905077
Minireview: progress and challenges in proteomics data management, sharing, and integration. PMID:22902541
Identifying biologically interpretable transcription factor knockout targets by jointly analyzing the transcription factor knockout microarray and the ChIP-chip data. PMID:22898448
Screening of candidate genes for primary open angle glaucoma. PMID:22876139
HINT: High-quality protein interactomes and their applications in understanding human disease. PMID:22846459
Computational framework for analysis of prey-prey associations in interaction proteomics identifies novel human protein-protein interactions and networks. PMID:22845868
Discovering the hidden sub-network component in a ranked list of genes or proteins derived from genomic experiments. PMID:22844098
atBioNet--an integrated network analysis tool for genomics and biomarker discovery. PMID:22817640
INDI: a computational framework for inferring drug interactions and their associated recommendations. PMID:22806140
Endosomal crosstalk: meeting points for signaling pathways. PMID:22796207
The core regulation module of stress-responsive regulatory networks in yeast. PMID:22784859
Combinatorial drug therapy for cancer in the post-genomic era. PMID:22781697
Integrating genome and functional genomics data to reveal perturbed signaling pathways in ovarian cancers. PMID:22779056
Posterior association networks and functional modules inferred from rich phenotypes of gene perturbations. PMID:22761558
Accuracy improvement in protein complex prediction from protein interaction networks by refining cluster overlaps. PMID:22759580
Genes2FANs: connecting genes through functional association networks. PMID:22748121
MC EMiNEM maps the interaction landscape of the Mediator. PMID:22737066
Detecting mutually exclusive interactions in protein-protein interaction maps. PMID:22715412
Beyond hairballs: The use of quantitative mass spectrometry data to understand protein-protein interactions. PMID:22710165
DEFOG: discrete enrichment of functionally organized genes. PMID:22706384
Dynamic network of transcription and pathway crosstalk to reveal molecular mechanism of MGd-treated human lung cancer cells. PMID:22693540
MoNetFamily: a web server to infer homologous modules and module-module interaction networks in vertebrates. PMID:22689643
BIPS: BIANA Interolog Prediction Server. A tool for protein-protein interaction inference. PMID:22689642
IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks. PMID:22684505
Hierarchical modularity and the evolution of genetic interactomes across species. PMID:22681890
MAGNET: MicroArray Gene expression and Network Evaluation Toolkit. PMID:22669910
A topology-based metric for measuring term similarity in the gene ontology. PMID:22666244
An interaction map of endoplasmic reticulum chaperones and foldases. PMID:22665516
Integrated analysis of transcriptome and lipid profiling reveals the co-influences of inositol-choline and Snf1 in controlling lipid biosynthesis in yeast. PMID:22622761
MGEx-Udb: a mammalian uterus database for expression-based cataloguing of genes across conditions, including endometriosis and cervical cancer. PMID:22606288
Prediction and comparison of Salmonella-human and Salmonella-Arabidopsis interactomes. PMID:22589098
Mycobacterium tuberculosis and Clostridium difficille interactomes: demonstration of rapid development of computational system for bacterial interactome prediction. PMID:22587966
The human proteome - a scientific opportunity for transforming diagnostics, therapeutics, and healthcare. PMID:22583803
M-Track: detecting short-lived protein-protein interactions in vivo. PMID:22581371
Exploring the yeast acetylome using functional genomics. PMID:22579291
Functional and topological characterization of transcriptional cooperativity in yeast. PMID:22574744
Linking proteins to signaling pathways for experiment design and evaluation. PMID:22558382
System approaches reveal the molecular networks involved in neural stem cell differentiation. PMID:22492180
Swimming upstream: identifying proteomic signals that drive transcriptional changes using the interactome and multiple "-omics" datasets. PMID:22482945
Integrated inference and analysis of regulatory networks from multi-level measurements. PMID:22482944
Network-based functional enrichment. PMID:22479706
The protein expression landscape of the Arabidopsis root. PMID:22447775
A systematic analysis of cell cycle regulators in yeast reveals that most factors act independently of cell size to control initiation of division. PMID:22438835
How to link ontologies and protein-protein interactions to literature: text-mining approaches and the BioCreative experience. PMID:22438567
An Interspecies Regulatory Network Inferred from Simultaneous RNA-seq of Candida albicans Invading Innate Immune Cells. PMID:22416242
Protein misinteraction avoidance causes highly expressed proteins to evolve slowly. PMID:22416125
Purification of the COP9 signalosome complex and binding partners from human T cells. PMID:22414063
Reducing false-positive prediction of minimotifs with a genetic interaction filter. PMID:22403687
AtPAN: an integrated system for reconstructing transcriptional regulatory networks in Arabidopsis thaliana. PMID:22397531
The role of structural disorder in the rewiring of protein interactions through evolution. PMID:22389433
Transparent mediation-based access to multiple yeast data sources using an ontology driven interface. PMID:22372975
Detection of interacting transcription factors in human tissues using predicted DNA binding affinity. PMID:22369666
Transcriptional activity and nuclear localization of Cabut, the Drosophila ortholog of vertebrate TGF-β-inducible early-response gene (TIEG) proteins. PMID:22359651
Short Co-occurring Polypeptide Regions Can Predict Global Protein Interaction Maps. PMID:22355752
HIPPIE: Integrating protein interaction networks with experiment based quality scores. PMID:22348130
Infection Strategies of Bacterial and Viral Pathogens through Pathogen-Human Protein-Protein Interactions. PMID:22347880
Rewiring of PDZ domain-ligand interaction network contributed to eukaryotic evolution. PMID:22346764
ANAP: an integrated knowledge base for Arabidopsis protein interaction network analysis. PMID:22345505
The identification of short linear motif-mediated interfaces within the human interactome. PMID:22328783
Functional dissection of lysine deacetylases reveals that HDAC1 and p300 regulate AMPK. PMID:22318606
Evolution and function of CAG/polyglutamine repeats in protein-protein interaction networks. PMID:22287626
Putting the pieces together: integrative modeling platform software for structure determination of macromolecular assemblies. PMID:22272186
Differential network biology. PMID:22252388
The genetic control of growth rate: a systems biology study in yeast. PMID:22244311
IMID: integrated molecular interaction database. PMID:22238258
Systems pharmacology: network analysis to identify multiscale mechanisms of drug action. PMID:22235860
Prediction and characterization of protein-protein interaction networks in swine. PMID:22230699
Tramtrack is genetically upstream of genes controlling tracheal tube size in Drosophila. PMID:22216153
Evolution of biological interaction networks: from models to real data. PMID:22204388
Molecular links between cellular senescence, longevity and age-related diseases - a systems biology perspective. PMID:22184282
RefNetBuilder: a platform for construction of integrated reference gene regulatory networks from expressed sequence tags. PMID:22166047
The dichotomy in degree correlation of biological networks. PMID:22164269
The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text. PMID:22151929
Benchmarking of the 2010 BioCreative Challenge III text-mining competition by the BioGRID and MINT interaction databases. PMID:22151178
The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. PMID:22140109
AutismKB: an evidence-based knowledgebase of autism genetics. PMID:22139918
iRefR: an R package to manipulate the iRefIndex consolidated protein interaction database. PMID:22115179
modMine: flexible access to modENCODE data. PMID:22080565
AnimalTFDB: a comprehensive animal tra