R3QS4R last accessed: 2022-11-04

metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:13.752584

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

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

intact
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:13.752584

Other names: IntAct, IntAct Molecular Interaction Database, intact

IntAct provides a database system and analysis tools for molecular interaction data. All interactions are derived from literature curation or direct user submissions. IntAct (with MINT) is a Core Data Resource of ELIXIR. IntAct contains data from all organisations belonging to The IMEx Consortium.

Webpage:

https://www.ebi.ac.uk/intact

Licence:

Name: Apache v2.0
URL: https://www.ebi.ac.uk/intact/downloads

Publications: (6)

Publications
More detailed information about this field from each metasource.

The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases
PMID: 24234451
metasource: Fairsharing.org
version: FAIRsharing.org: IntAct; IntAct molecular interaction database; DOI: https://doi.org/10.25504/FAIRsharing.d05nwx; Last edited: Feb. 8, 2021, 1:21 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

IntAct: an open source molecular interaction database
PMID: 14681455
metasource: Fairsharing.org
version: FAIRsharing.org: IntAct; IntAct molecular interaction database; DOI: https://doi.org/10.25504/FAIRsharing.d05nwx; Last edited: Feb. 8, 2021, 1:21 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

The IntAct molecular interaction database in 2010
PMID: 19850723
metasource: Fairsharing.org
version: FAIRsharing.org: IntAct; IntAct molecular interaction database; DOI: https://doi.org/10.25504/FAIRsharing.d05nwx; Last edited: Feb. 8, 2021, 1:21 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

PSICQUIC and PSISCORE: accessing and scoring molecular interactions
PMID: 21716279
metasource: Fairsharing.org
version: FAIRsharing.org: IntAct; IntAct molecular interaction database; DOI: https://doi.org/10.25504/FAIRsharing.d05nwx; Last edited: Feb. 8, 2021, 1:21 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions
PMID: 17925023
metasource: Fairsharing.org
version: FAIRsharing.org: IntAct; IntAct molecular interaction database; DOI: https://doi.org/10.25504/FAIRsharing.d05nwx; Last edited: Feb. 8, 2021, 1:21 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

http://dx.doi.org/10.1093/nar/gkt1115
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:13.752584

The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases PubMed citations: 757.

757 articles citing: The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases

The Landscape of Virus-Host Protein-Protein Interaction Databases. PMID:35910656
Daily Reports on Phage-Host Interactions. PMID:35910653
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
Single-cell network biology characterizes cell type gene regulation for drug repurposing and phenotype prediction in Alzheimer's disease. PMID:35849618
HumanMine: advanced data searching, analysis and cross-species comparison. PMID:35820040
Molecular Modelling Hurdle in the Next-Generation Sequencing Era. PMID:35806177
Calpain-mediated cleavage generates a ZBTB18 N-terminal product that regulates HIF1A signaling and glioblastoma metabolism. PMID:35800763
PHILM2Web: A high-throughput database of macromolecular host-pathogen interactions on the Web. PMID:35776535
A Role of the TEX101 Interactome in the Common Aetiology Behind Male Subfertility and Testicular Germ Cell Tumor. PMID:35774118
Inferring functional communities from partially observed biological networks exploiting geometric topology and side information. PMID:35760826
Systems Drug Discovery for Diffuse Large B Cell Lymphoma Based on Pathogenic Molecular Mechanism via Big Data Mining and Deep Learning Method. PMID:35743172
Identification of the Potential Molecular Mechanisms Linking RUNX1 Activity with Nonalcoholic Fatty Liver Disease, by Means of Systems Biology. PMID:35740337
PCfun: a hybrid computational framework for systematic characterization of protein complex function. PMID:35724564
Identifying Candidate Flavonoids for Non-Alcoholic Fatty Liver Disease by Network-Based Strategy. PMID:35721123
A Hybrid Protocol for Identifying Comorbidity-Based Potential Drugs for COVID-19 Using Biomedical Literature Mining, Network Analysis, and Deep Learning. PMID:35713866
Network approaches for modeling the effect of drugs and diseases. PMID:35704883
Repurposing Histaminergic Drugs in Multiple Sclerosis. PMID:35683024
A comprehensive SARS-CoV-2-human protein-protein interactome network identifies pathobiology and host-targeting therapies for COVID-19. PMID:35677070
An approach to cellular tropism of SARS-CoV-2 through protein-protein interaction and enrichment analysis. PMID:35672403
Network assisted analysis of de novo variants using protein-protein interaction information identified 46 candidate genes for congenital heart disease. PMID:35671298
Dissecting Meta-Analysis in GWAS Era: Bayesian Framework for Gene/Subnetwork-Specific Meta-Analysis. PMID:35664319
PEPPI: Whole-proteome Protein-protein Interaction Prediction through Structure and Sequence Similarity, Functional Association, and Machine Learning. PMID:35662463
GWYRE: A Resource for Mapping Variants onto Experimental and Modeled Structures of Human Protein Complexes. PMID:35662458
Identification of candidate biomarkers and pathways associated with type 1 diabetes mellitus using bioinformatics analysis. PMID:35650387
OmicsNet 2.0: a web-based platform for multi-omics integration and network visual analytics. PMID:35639733
Proteome-wide prediction and analysis of the Cryptosporidium parvum protein-protein interaction network through integrative methods. PMID:35615014
A Data Science Approach for the Identification of Molecular Signatures of Aggressive Cancers. PMID:35565454
Representing Normal and Abnormal Physiology as Routes of Flow in ApiNATOMY. PMID:35547570
Degron masking outlines degronons, co-degrading functional modules in the proteome. PMID:35545699
Mapping the epithelial-immune cell interactome upon infection in the gut and the upper airways. PMID:35501398
Membranome 3.0: Database of single-pass membrane proteins with AlphaFold models. PMID:35481632
Superoxide dismutase 6 is required during metamorphosis for the development of properly movable legs in Tribolium castaneum. PMID:35477951
Prioritization of Candidate Biomarkers for Degenerative Aortic Stenosis through a Systems Biology-Based In-Silico Approach. PMID:35455758
αα-hub coregulator structure and flexibility determine transcription factor binding and selection in regulatory interactomes. PMID:35452682
The Human Myelin Proteome and Sub-Metalloproteome Interaction Map: Relevance to Myelin-Related Neurological Diseases. PMID:35447967
Comprehensive network medicine-based drug repositioning via integration of therapeutic efficacy and side effects. PMID:35443763
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
Are transient protein-protein interactions more dispensable? PMID:35404956
FKBP52 and FKBP51 differentially regulate the stability of estrogen receptor in breast cancer. PMID:35394865
Predicted mouse interactome and network-based interpretation of differentially expressed genes. PMID:35390003
Physical and functional interactome atlas of human receptor tyrosine kinases. PMID:35384245
The D2R-DISC1 protein complex and associated proteins are altered in schizophrenia and normalized with antipsychotic treatment. PMID:35361701
Functional Impact and Regulation of Alternative Splicing in Mouse Heart Development and Disease. PMID:35355220
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
Finding New Ways How to Control BACE1. PMID:35305135
Exploration of the DARTable Genome- a Resource Enabling Data-Driven NAMs for Developmental and Reproductive Toxicity Prediction. PMID:35295108
Function of SYDE C2-RhoGAP family as signaling hubs for neuronal development deduced by computational analysis. PMID:35279680
Improved prediction of protein-protein interactions using AlphaFold2. PMID:35273146
A Bioinformatics Approach Toward Unravelling the Synaptic Molecular Crosstalk Between Alzheimer's Disease and Diabetes. PMID:35253743
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
Antifungal activity of an artificial peptide aptamer SNP-D4 against Fusarium oxysporum. PMID:35223198
Effective drug combinations in breast, colon and pancreatic cancer cells. PMID:35197630
Investigating the Role of Obesity in Prostate Cancer and Identifying Biomarkers for Drug Discovery: Systems Biology and Deep Learning Approaches. PMID:35164166
Unravelling Mechanisms of Doxorubicin-Induced Toxicity in 3D Human Intestinal Organoids. PMID:35163210
Multi-Omics Profiling to Assess Signaling Changes upon VHL Restoration and Identify Putative VHL Substrates in Clear Cell Renal Cell Carcinoma Cell Lines. PMID:35159281
An Integrated In Silico, In Vitro and Tumor Tissues Study Identified Selenoprotein S (SELENOS) and Valosin-Containing Protein (VCP/p97) as Novel Potential Associated Prognostic Biomarkers in Triple Negative Breast Cancer. PMID:35158912
The Landscape of Aminoacyl-tRNA Synthetases Involved in Severe Acute Respiratory Syndrome Coronavirus 2 Infection. PMID:35153822
14-3-3 Proteins are Potential Regulators of Liquid-Liquid Phase Separation. PMID:35142991
Human transcription factor protein interaction networks. PMID:35140242
Interactomes: Experimental and In Silico Approaches. PMID:35113398
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
Experimental Evidence of Intrinsic Disorder and Amyloid Formation by the Henipavirus W Proteins. PMID:35055108
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
How Far Are We from the Completion of the Human Protein Interactome Reconstruction? PMID:35053288
Proteome-scale mapping of binding sites in the unstructured regions of the human proteome. PMID:35044719
Plant Reactome and PubChem: The Plant Pathway and (Bio)Chemical Entity Knowledgebases. PMID:35037224
Defining the interactomes of proteins involved in cytoskeletal dynamics using high-throughput proximity-dependent biotinylation in cellulo. PMID:35036956
Potential Molecular Mechanisms and Remdesivir Treatment for Acute Respiratory Syndrome Corona Virus 2 Infection/COVID 19 Through RNA Sequencing and Bioinformatics Analysis. PMID:34992355
Large-scale protein-protein post-translational modification extraction with distant supervision and confidence calibrated BioBERT. PMID:34983371
Trojan horse treatment based on PEG-coated extracellular vesicles to deliver doxorubicin to melanoma in vitro and in vivo. PMID:34964693
GRWD1-WDR5-MLL2 Epigenetic Complex Mediates H3K4me3 Mark and Is Essential for Kaposi's Sarcoma-Associated Herpesvirus-Induced Cellular Transformation. PMID:34933446
Targeting uPA-uPAR interaction to improve intestinal epithelial barrier integrity in inflammatory bowel disease. PMID:34933179
ENTREP/FAM189A2 encodes a new ITCH ubiquitin ligase activator that is downregulated in breast cancer. PMID:34927784
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
A Network-Centric Framework for the Evaluation of Mutual Exclusivity Tests on Cancer Drivers. PMID:34899838
The methyltransferase METTL3 negatively regulates nonalcoholic steatohepatitis (NASH) progression. PMID:34893641
Prediction of Protein-Protein Binding Affinities from Unbound Protein Structures. PMID:34888728
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
Homodimeric and Heterodimeric Interactions among Vertebrate Basic Helix-Loop-Helix Transcription Factors. PMID:34884664
Interpretation of network-based integration from multi-omics longitudinal data. PMID:34883510
GFI1 tethers the NuRD complex to open and transcriptionally active chromatin in myeloid progenitors. PMID:34857890
TissueNexus: a database of human tissue functional gene networks built with a large compendium of curated RNA-seq data. PMID:34850130
ConsensusPathDB 2022: molecular interactions update as a resource for network biology. PMID:34850110
In silico Methods for Identification of Potential Therapeutic Targets. PMID:34826045
Interactome analysis illustrates diverse gene regulatory processes associated with LIN28A in human iPS cell-derived neural progenitor cells. PMID:34816099
Limits and potential of combined folding and docking. PMID:34788800
Computationally Reconstructed Interactome of Bradyrhizobium diazoefficiens USDA110 Reveals Novel Functional Modules and Protein Hubs for Symbiotic Nitrogen Fixation. PMID:34769335
Systematic Analysis of FASTK Gene Family Alterations in Cancer. PMID:34768773
Elucidation of the Translation Initiation Factor Interaction Network of Haloferax volcanii Reveals Coupling of Transcription and Translation in Haloarchaea. PMID:34764944
The IntAct database: efficient access to fine-grained molecular interaction data. PMID:34761267
IID 2021: towards context-specific protein interaction analyses by increased coverage, enhanced annotation and enrichment analysis. PMID:34755877
Co-evolution based machine-learning for predicting functional interactions between human genes. PMID:34753957
GPRuler: Metabolic gene-protein-reaction rules automatic reconstruction. PMID:34748537
HumanNet v3: an improved database of human gene networks for disease research. PMID:34747468
Hymenoptera Genome Database: new genomes and annotation datasets for improved go enrichment and orthologue analyses. PMID:34747465
Cross-platform transcriptomic profiling of the response to recombinant human erythropoietin. PMID:34737331
Network-based protein-protein interaction prediction method maps perturbations of cancer interactome. PMID:34727106
Complex Portal 2022: new curation frontiers. PMID:34718729
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
Computational repurposing of therapeutic small molecules from cancer to pulmonary hypertension. PMID:34669463
Drug repurposing improves disease targeting 11-fold and can be augmented by network module targeting, applied to COVID-19. PMID:34667255
SYNBIP: synthetic binding proteins for research, diagnosis and therapy. PMID:34664670
A Systematic Analysis Identifies Key Regulators Involved in Cell Proliferation and Potential Drugs for the Treatment of Human Lung Adenocarcinoma. PMID:34650921
Regulation of ER Composition and Extent, and Putative Action in Protein Networks by ER/NE Protein TMEM147. PMID:34638576
SignaLink3: a multi-layered resource to uncover tissue-specific signaling networks. PMID:34634810
OnTheFly2.0: a text-mining web application for automated biomedical entity recognition, document annotation, network and functional enrichment analysis. PMID:34632381
Getting to know each other: PPIMem, a novel approach for predicting transmembrane protein-protein complexes. PMID:34630938
DNArepairK: An Interactive Database for Exploring the Impact of Anticancer Drugs onto the Dynamics of DNA Repair Proteins. PMID:34572428
PncsHub: a platform for annotating and analyzing non-classically secreted proteins in Gram-positive bacteria. PMID:34551435
Transcriptional Profile of the Industrial Hybrid Saccharomyces pastorianus Reveals Temperature-Dependent Allele Expression Bias and Preferential Orthologous Protein Assemblies. PMID:34550394
Finding functional associations between prokaryotic virus orthologous groups: a proof of concept. PMID:34525942
OGT Protein Interaction Network (OGT-PIN): A Curated Database of Experimentally Identified Interaction Proteins of OGT. PMID:34502531
Tau Protein Interaction Partners and Their Roles in Alzheimer's Disease and Other Tauopathies. PMID:34502116
Mitochondria-localized AMPK responds to local energetics and contributes to exercise and energetic stress-induced mitophagy. PMID:34493662
A machine learning framework for predicting drug-drug interactions. PMID:34475500
Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review. PMID:34439912
A global map of associations between types of protein posttranslational modifications and human genetic diseases. PMID:34430807
Ten simple rules for creating reusable pathway models for computational analysis and visualization. PMID:34411100
Mechanism-Centric Approaches for Biomarker Detection and Precision Therapeutics in Cancer. PMID:34408770
Exploring the Pharmacological Mechanism of Liuwei Dihuang Decoction for Diabetic Retinopathy: A Systematic Biological Strategy-Based Research. PMID:34394383
PPIDomainMiner: Inferring domain-domain interactions from multiple sources of protein-protein interactions. PMID:34370723
Predicting Protein-Protein Interactions Between Rice and Blast Fungus Using Structure-Based Approaches. PMID:34367213
Global effects of RAB3GAP1 dysexpression on the proteome of mouse cortical neurons. PMID:34363538
Multimodal single-cell omics analysis identifies epithelium-immune cell interactions and immune vulnerability associated with sex differences in COVID-19. PMID:34330889
Functionathon: a manual data mining workflow to generate functional hypotheses for uncharacterized human proteins and its application by undergraduate students. PMID:34318869
CFTR Lifecycle Map-A Systems Medicine Model of CFTR Maturation to Predict Possible Active Compound Combinations. PMID:34299207
Targeted capture sequencing identifies genetic variations of GRK4 and RDH8 in Han Chinese with essential hypertension in Xinjiang. PMID:34297769
TIDB: a comprehensive database of trained immunity. PMID:34244719
Databases for Protein-Protein Interactions. PMID:34236665
Integrated analysis of Shank1 PDZ interactions with C-terminal and internal binding motifs. PMID:34235485
Identification of Diagnostic Markers for Major Depressive Disorder Using Machine Learning Methods. PMID:34220416
Applications and analytical tools of cell communication based on ligand-receptor interactions at single cell level. PMID:34217372
Towards a global investigation of transcriptomic signatures through co-expression networks and pathway knowledge for the identification of disease mechanisms. PMID:34197603
Assembling Disease Networks From Causal Interaction Resources. PMID:34178043
FINER: enhancing the prediction of tissue-specific functions of isoforms by refining isoform interaction networks. PMID:34169280
Unraveling the surface glycoprotein interaction network by integrating chemical crosslinking with MS-based proteomics. PMID:34163979
Network-based analysis of virulence factors for uncovering Aeromonas veronii pathogenesis. PMID:34162325
mPPI: a database extension to visualize structural interactome in a one-to-many manner. PMID:34156447
DGLinker: flexible knowledge-graph prediction of disease-gene associations. PMID:34125897
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
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
Proteomimetic surface fragments distinguish targets by function. PMID:34094300
A proximity-dependent biotinylation map of a human cell. PMID:34079125
Mechnetor: a web server for exploring protein mechanism and the functional context of genetic variants. PMID:34076240
The COVID-19 Data Portal: accelerating SARS-CoV-2 and COVID-19 research through rapid open access data sharing. PMID:34048576
emiRIT: a text-mining-based resource for microRNA information. PMID:34048547
Computational Biology and Machine Learning Approaches to Understand Mechanistic Microbiome-Host Interactions. PMID:34046017
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
Structural Profiling of Bacterial Effectors Reveals Enrichment of Host-Interacting Domains and Motifs. PMID:34012977
Drug Repurposing: A Network-based Approach to Amyotrophic Lateral Sclerosis. PMID:33987813
METTL13 inhibits progression of clear cell renal cell carcinoma with repression on PI3K/AKT/mTOR/HIF-1α pathway and c-Myc expression. PMID:33985542
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
IntAct App: a Cytoscape application for molecular interaction network visualisation and analysis. PMID:33961020
Employing core regulatory circuits to define cell identity. PMID:33934382
Discovery-Versus Hypothesis-Driven Detection of Protein-Protein Interactions and Complexes. PMID:33923221
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
Prediction of host-pathogen protein interactions by extended network model. PMID:33907496
The VRNetzer platform enables interactive network analysis in Virtual Reality. PMID:33893283
Effect of HPV 16 E6 Oncoprotein Variants on the Alterations of the Proteome of C33A Cells. PMID:33893080
Identification of IFN-Induced Transmembrane Protein 1 With Prognostic Value in Pancreatic Cancer Using Network Module-Based Analysis. PMID:33869009
Triple SILAC identified progestin-independent and dependent PRA and PRB interacting partners in breast cancer. PMID:33846359
Multilevel proteomics reveals host perturbations by SARS-CoV-2 and SARS-CoV. PMID:33845483
Network-based modeling of herb combinations in traditional Chinese medicine. PMID:33834186
Peptide location fingerprinting reveals modification-associated biomarker candidates of ageing in human tissue proteomes. PMID:33830638
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
Mutations of Intrinsically Disordered Protein Regions Can Drive Cancer but Lack Therapeutic Strategies. PMID:33806614
Quantitative Proteomic Approach Reveals Altered Metabolic Pathways in Response to the Inhibition of Lysine Deacetylases in A549 Cells under Normoxia and Hypoxia. PMID:33806075
Network medicine links SARS-CoV-2/COVID-19 infection to brain microvascular injury and neuroinflammation in dementia-like cognitive impairment. PMID:33791705
Genome-wide RNAi screen for regulators of UPRmt in Caenorhabditis elegans mutants with defects in mitochondrial fusion. PMID:33784383
Cardiovascular informatics: building a bridge to data harmony. PMID:33751044
Integrated intra- and intercellular signaling knowledge for multicellular omics analysis. PMID:33749993
Integrating 3D structural information into systems biology. PMID:33744294
Short loop functional commonality identified in leukaemia proteome highlights crucial protein sub-networks. PMID:33709075
Identification of potential and novel target genes in pituitary prolactinoma by bioinformatics analysis. PMID:33709028
Analysing the yeast complexome-the Complex Portal rising to the challenge. PMID:33677561
HIR V2: a human interactome resource for the biological interpretation of differentially expressed genes via gene set linkage analysis. PMID:33677507
DbStRiPs: Database of structural repeats in proteins. PMID:33641184
Proximity-dependent Mapping of the Androgen Receptor Identifies Kruppel-like Factor 4 as a Functional Partner. PMID:33640491
Exploring the conservation of Alzheimer-related pathways between H. sapiens and C. elegans: a network alignment approach. PMID:33633188
Comparative Genomics and Integrated Network Approach Unveiled Undirected Phylogeny Patterns, Co-mutational Hot Spots, Functional Cross Talk, and Regulatory Interactions in SARS-CoV-2. PMID:33622851
A systems-based method to repurpose marketed therapeutics for antiviral use: a SARS-CoV-2 case study. PMID:33593923
Genome-wide meta-analysis, fine-mapping and integrative prioritization implicate new Alzheimer's disease risk genes. PMID:33589840
UniProt-Related Documents (UniReD): assisting wet lab biologists in their quest on finding novel counterparts in a protein network. PMID:33575553
Ranking cancer drivers via betweenness-based outlier detection and random walks. PMID:33568049
Bioinformatics analyses of significant genes, related pathways, and candidate diagnostic biomarkers and molecular targets in SARS-CoV-2/COVID-19. PMID:33553808
CausalBuilder: bringing the MI2CAST causal interaction annotation standard to the curator. PMID:33547799
ViralLink: An integrated workflow to investigate the effect of SARS-CoV-2 on intracellular signalling and regulatory pathways. PMID:33534793
Role of Antizyme Inhibitor Proteins in Cancers and Beyond. PMID:33531815
Pan-cancer detection of driver genes at the single-patient resolution. PMID:33517897
Integrative analysis of transcriptomic data for identification of T-cell activation-related mRNA signatures indicative of preterm birth. PMID:33504832
NLPEI: A Novel Self-Interacting Protein Prediction Model Based on Natural Language Processing and Evolutionary Information. PMID:33488064
Multiplexed MRM-Based Proteomics Identified Multiple Biomarkers of Disease Severity in Human Heart Failure. PMID:33467687
Combined RNA/tissue profiling identifies novel Cancer/testis genes. PMID:33426787
A network-based deep learning methodology for stratification of tumor mutations. PMID:33416857
Bioinformatics: new tools and applications in life science and personalized medicine. PMID:33404829
The Interactome of Cancer-Related Lysyl Oxidase and Lysyl Oxidase-Like Proteins. PMID:33383846
PICKLE 3.0: Enriching the human Meta-database with the mouse protein interactome extended via mouse-human orthology. PMID:33367505
SECAT: Quantifying Protein Complex Dynamics across Cell States by Network-Centric Analysis of SEC-SWATH-MS Profiles. PMID:33333029
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
Alignment of virus-host protein-protein interaction networks by integer linear programming: SARS-CoV-2. PMID:33284827
Drug2ways: Reasoning over causal paths in biological networks for drug discovery. PMID:33264280
Towards a unified open access dataset of molecular interactions. PMID:33262342
What Can Machine Learning Approaches in Genomics Tell Us about the Molecular Basis of Amyotrophic Lateral Sclerosis? PMID:33256133
A ligand-based computational drug repurposing pipeline using KNIME and Programmatic Data Access: case studies for rare diseases and COVID-19. PMID:33250934
EffectorK, a comprehensive resource to mine for Ralstonia, Xanthomonas, and other published effector interactors in the Arabidopsis proteome. PMID:33245626
Expression of Pro-Angiogenic Markers Is Enhanced by Blue Light in Human RPE Cells. PMID:33233546
PINA 3.0: mining cancer interactome. PMID:33231689
Predicted rat interactome database and gene set linkage analysis. PMID:33216897
The ATPase ATP6V1A facilitates rabies virus replication by promoting virion uncoating and interacting with the viral matrix protein. PMID:33208464
The IMEx coronavirus interactome: an evolving map of Coronaviridae-host molecular interactions. PMID:33206959
TREM2 Alzheimer's variant R47H causes similar transcriptional dysregulation to knockout, yet only subtle functional phenotypes in human iPSC-derived macrophages. PMID:33198789
KG-COVID-19: A Framework to Produce Customized Knowledge Graphs for COVID-19 Response. PMID:33196056
Comprehensive mapping of the human cytokine gene regulatory network. PMID:33179750
RNA-seq analysis identifies cytoskeletal structural genes and pathways for meat quality in beef. PMID:33175867
Gramene 2021: harnessing the power of comparative genomics and pathways for plant research. PMID:33170273
Triage of documents containing protein interactions affected by mutations using an NLP based machine learning approach. PMID:33167858
EpiGraphDB: a database and data mining platform for health data science. PMID:33165574
A network medicine approach to investigation and population-based validation of disease manifestations and drug repurposing for COVID-19. PMID:33156843
IHP-PING-generating integrated human protein-protein interaction networks on-the-fly. PMID:33129201
FFAT motif phosphorylation controls formation and lipid transfer function of inter-organelle contacts. PMID:33124732
The MemMoRF database for recognizing disordered protein regions interacting with cellular membranes. PMID:33119751
RNAcentral 2021: secondary structure integration, improved sequence search and new member databases. PMID:33106848
Whole Genome Sequence Data Provides Novel Insights Into the Genetic Architecture of Meat Quality Traits in Beef. PMID:33101375
BastionHub: a universal platform for integrating and analyzing substrates secreted by Gram-negative bacteria. PMID:33084862
Predicted functional interactome of Caenorhabditis elegans and a web tool for the functional interpretation of differentially expressed genes. PMID:33076954
VRK1 Phosphorylates Tip60/KAT5 and Is Required for H4K16 Acetylation in Response to DNA Damage. PMID:33076429
LRRK2 mediates microglial neurotoxicity via NFATc2 in rodent models of synucleinopathies. PMID:33055242
Tumor Microenvironment-Associated Immune-Related Genes for the Prognosis of Malignant Pleural Mesothelioma. PMID:33042835
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
Hyperconserved Elements in Human 5'UTRs Shape Essential Post-transcriptional Regulatory Networks. PMID:33005630
Affinity proteomic dissection of the human nuclear cap-binding complex interactome. PMID:32960270
MasterPATH: network analysis of functional genomics screening data. PMID:32928103
The Pathophysiological Significance of Fibulin-3. PMID:32911658
A functionally defined high-density NRF2 interactome reveals new conditional regulators of ARE transactivation. PMID:32911434
ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis. PMID:32907876
Cholesterol sensing by CD81 is important for hepatitis C virus entry. PMID:32900848
Investigating Core Signaling Pathways of Hepatitis B Virus Pathogenesis for Biomarkers Identification and Drug Discovery via Systems Biology and Deep Learning Method. PMID:32878239
Determining the interaction status and evolutionary fate of duplicated homomeric proteins. PMID:32853212
Systems Biology Approaches to Understanding the Human Immune System. PMID:32849587
KG-COVID-19: a framework to produce customized knowledge graphs for COVID-19 response. PMID:32839776
Zooming into the Dark Side of Human Annexin-S100 Complexes: Dynamic Alliance of Flexible Partners. PMID:32824294
A Human IgSF Cell-Surface Interactome Reveals a Complex Network of Protein-Protein Interactions. PMID:32822567
Using collections of structural models to predict changes of binding affinity caused by mutations in protein-protein interactions. PMID:32797645
Population-scale proteome variation in human induced pluripotent stem cells. PMID:32773033
A Molecular Signal Integration Network Underpinning Arabidopsis Seed Germination. PMID:32763174
Piggybacking on Classical Import and Other Non-Classical Mechanisms of Nuclear Import Appear Highly Prevalent within the Human Proteome. PMID:32718019
A Coordinated Approach by Public Domain Bioinformatics Resources to Aid the Fight Against Alzheimer's Disease Through Expert Curation of Key Protein Targets. PMID:32716361
Analyzing IDPs in Interactomes. PMID:32696395
How to Annotate and Submit a Short Linear Motif to the Eukaryotic Linear Motif Resource. PMID:32696353
Heatr9 is an infection responsive gene that affects cytokine production in alveolar epithelial cells. PMID:32678841
Harnessing endophenotypes and network medicine for Alzheimer's drug repurposing. PMID:32656864
The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST). PMID:32637990
Pushing myelination - developmental regulation of myosin expression drives oligodendrocyte morphological differentiation. PMID:32620697
Seq-ing answers: Current data integration approaches to uncover mechanisms of transcriptional regulation. PMID:32612756
Extensive signal integration by the phytohormone protein network. PMID:32612234
Proteomics of Sentinel Lymph Nodes in Early Breast Cancer for Identification of Thymidylate Synthase as a Potential Biomarker to Flag Metastasis: A Preliminary Study. PMID:32606973
Selective Neuronal Vulnerability in Alzheimer's Disease: A Network-Based Analysis. PMID:32603655
The IMEx Coronavirus interactome: an evolving map of Coronaviridae-Host molecular interactions. PMID:32587962
Prediction of the Secretome and the Surfaceome: A Strategy to Decipher the Crosstalk between Adipose Tissue and Muscle during Fetal Growth. PMID:32575512
A Knowledge-Based Machine Learning Approach to Gene Prioritisation in Amyotrophic Lateral Sclerosis. PMID:32575372
Multilevel regulation of muscle-specific transcription factor hlh-1 during Caenorhabditis elegans embryogenesis. PMID:32556563
Predicting Self-Interacting Proteins Using a Recurrent Neural Network and Protein Evolutionary Information. PMID:32550764
Kir2.1 Interactome Mapping Uncovers PKP4 as a Modulator of the Kir2.1-Regulated Inward Rectifier Potassium Currents. PMID:32541000
A flexible network-based imputing-and-fusing approach towards the identification of cell types from single-cell RNA-seq data. PMID:32527285
Omics Integration Analyses Reveal the Early Evolution of Malignancy in Breast Cancer. PMID:32512721
Guilt-by-Association - Functional Insights Gained From Studying the LRRK2 Interactome. PMID:32508578
Integrated omics in Drosophila uncover a circadian kinome. PMID:32483184
Repurposed Analog of GLP-1 Ameliorates Hyperglycemia in Type 1 Diabetic Mice Through Pancreatic Cell Reprogramming. PMID:32477262
G2G: A web-server for the prediction of human synthetic lethal interactions. PMID:32419903
Gene Ontology Curation of Neuroinflammation Biology Improves the Interpretation of Alzheimer's Disease Gene Expression Data. PMID:32417785
Mutation severity spectrum of rare alleles in the human genome is predictive of disease type. PMID:32413045
Ellagic acid and human cancers: a systems pharmacology and docking study to identify principal hub genes and main mechanisms of action. PMID:32410114
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
MyoMiner: explore gene co-expression in normal and pathological muscle. PMID:32393257
BraInMap Elucidates the Macromolecular Connectivity Landscape of Mammalian Brain. PMID:32325033
Characterization of Signaling Pathways Associated with Pancreatic β-cell Adaptive Flexibility in Compensation of Obesity-linked Diabetes in db/db Mice. PMID:32265294
WeiBI (web-based platform): Enriching integrated interaction network with increased coverage and functional proteins from genome-wide experimental OMICS data. PMID:32221380
Systems analysis of RhoGEF and RhoGAP regulatory proteins reveals spatially organized RAC1 signalling from integrin adhesions. PMID:32203420
Predicted Drosophila Interactome Resource and web tool for functional interpretation of differentially expressed genes. PMID:32103267
Exploring Integrative Analysis Using the BioMedical Evidence Graph. PMID:32097025
Exploration of databases and methods supporting drug repurposing: a comprehensive survey. PMID:32055842
In-silico simulated prototype-patients using TPMS technology to study a potential adverse effect of sacubitril and valsartan. PMID:32053711
Improving Identification of In-organello Protein-Protein Interactions Using an Affinity-enrichable, Isotopically Coded, and Mass Spectrometry-cleavable Chemical Crosslinker. PMID:32051233
Genome-wide inference of the Camponotus floridanus protein-protein interaction network using homologous mapping and interacting domain profile pairs. PMID:32047225
Discovering the genes mediating the interactions between chronic respiratory diseases in the human interactome. PMID:32041952
Classification of Trispanins: A Diverse Group of Proteins That Function in Membrane Synthesis and Transport Mechanisms. PMID:32039202
A Bipartite Network Module-Based Project to Predict Pathogen-Host Association. PMID:32038713
The plant MBF1 protein family: a bridge between stress and transcription. PMID:32037452
PlaPPISite: a comprehensive resource for plant protein-protein interaction sites. PMID:32028878
Use of a Systematic Pharmacological Methodology to Explore the Mechanism of Shengmai Powder in Treating Diabetic Cardiomyopathy. PMID:32023237
Localized Inhibition of Protein Phosphatase 1 by NUAK1 Promotes Spliceosome Activity and Reveals a MYC-Sensitive Feedback Control of Transcription. PMID:32006464
Mechanical forces induce an asthma gene signature in healthy airway epithelial cells. PMID:31969610
Hepatitis Delta Virus histone mimicry drives the recruitment of chromatin remodelers for viral RNA replication. PMID:31964889
In silico unravelling pathogen-host signaling cross-talks via pathogen mimicry and human protein-protein interaction networks. PMID:31956393
Machine learning approaches and databases for prediction of drug-target interaction: a survey paper. PMID:31950972
Biophysical prediction of protein-peptide interactions and signaling networks using machine learning. PMID:31907444
Two-hybrid screening of FAM13A protein partners in lung epithelial cells. PMID:31900205
Substrate specificity of thioredoxins and glutaredoxins - towards a functional classification. PMID:31890941
A novel algorithm for alignment of multiple PPI networks based on simulated annealing. PMID:31881842
Identification of self-interacting proteins by integrating random projection classifier and finite impulse response filter. PMID:31881833
Human cytomegalovirus interactome analysis identifies degradation hubs, domain associations and viral protein functions. PMID:31873071
CrRLK1L receptor-like kinases HERK1 and ANJEA are female determinants of pollen tube reception. PMID:31867824
PHI-Nets: A Network Resource for Ascomycete Fungal Pathogens to Annotate and Identify Putative Virulence Interacting Proteins and siRNA Targets. PMID:31866958
The human DEPhOsphorylation Database DEPOD: 2019 update. PMID:31836896
An intrinsically disordered proteins community for ELIXIR. PMID:31824649
Sequence-Derived Markers of Drug Targets and Potentially Druggable Human Proteins. PMID:31803227
Integrating protein localization with automated signaling pathway reconstruction. PMID:31787091
Protein Interactions Network of Hepatitis E Virus RNA and Polymerase With Host Proteins. PMID:31736926
The Architecture of the Human RNA-Binding Protein Regulatory Network. PMID:31733516
Global Vectors Representation of Protein Sequences and Its Application for Predicting Self-Interacting Proteins with Multi-Grained Cascade Forest Model. PMID:31726752
The neXtProt knowledgebase in 2020: data, tools and usability improvements. PMID:31724716
A Computational Framework for Predicting Direct Contacts and Substructures within Protein Complexes. PMID:31717703
The Cytoscape BioGateway App: explorative network building from the BioGateway triple store. PMID:31710663
Mitochondrial dysfunction in rheumatoid arthritis: A comprehensive analysis by integrating gene expression, protein-protein interactions and gene ontology data. PMID:31703070
AppleMDO: A Multi-Dimensional Omics Database for Apple Co-Expression Networks and Chromatin States. PMID:31695717
Co-regulation map of the human proteome enables identification of protein functions. PMID:31690884
Plant Reactome: a knowledgebase and resource for comparative pathway analysis. PMID:31680153
Systematic Pharmacological Methodology to Explore the Pharmacological Mechanism of Siwu Decoction for Osteoporosis. PMID:31666500
FKBP4 connects mTORC2 and PI3K to activate the PDK1/Akt-dependent cell proliferation signaling in breast cancer. PMID:31660083
Bovine Genome Database: new annotation tools for a new reference genome. PMID:31647100
Pathway Commons 2019 Update: integration, analysis and exploration of pathway data. PMID:31647099
Disorder-to-order transition in PE-PPE proteins of Mycobacterium tuberculosis augments the pro-pathogen immune response. PMID:31643141
Neglog: Homology-Based Negative Data Sampling Method for Genome-Scale Reconstruction of Human Protein-Protein Interaction Networks. PMID:31614890
Biological Network Approaches and Applications in Rare Disease Studies. PMID:31614842
pathfindR: An R Package for Comprehensive Identification of Enriched Pathways in Omics Data Through Active Subnetworks. PMID:31608109
Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices. PMID:31602618
Conserved Central Intraviral Protein Interactome of the Herpesviridae Family. PMID:31575665
Quantitative Proteomics of Uukuniemi Virus-host Cell Interactions Reveals GBF1 as Proviral Host Factor for Phleboviruses. PMID:31570497
Tissue-specific mouse mRNA isoform networks. PMID:31562339
Paralog dependency indirectly affects the robustness of human cells. PMID:31556487
The RNA-mediated estrogen receptor α interactome of hormone-dependent human breast cancer cell nuclei. PMID:31527615
CSF1R inhibitor JNJ-40346527 attenuates microglial proliferation and neurodegeneration in P301S mice. PMID:31504240
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
Discovering human transcription factor physical interactions with genetic variants, novel DNA motifs, and repetitive elements using enhanced yeast one-hybrid assays. PMID:31481462
Measuring rank robustness in scored protein interaction networks. PMID:31462221
The role of structural pleiotropy and regulatory evolution in the retention of heteromers of paralogs. PMID:31454312
Deep Protein Methylation Profiling by Combined Chemical and Immunoaffinity Approaches Reveals Novel PRMT1 Targets. PMID:31451547
Precise Prediction of Calpain Cleavage Sites and Their Aberrance Caused by Mutations in Cancer. PMID:31440276
Epistatic Analysis of the Contribution of Rabs and Kifs to CATCHR Family Dependent Golgi Organization. PMID:31428608
Large-effect flowering time mutations reveal conditionally adaptive paths through fitness landscapes in Arabidopsis thaliana. PMID:31420516
In silico evidence of de novo interactions between ribosomal and Epstein - Barr virus proteins. PMID:31416416
HENA, heterogeneous network-based data set for Alzheimer's disease. PMID:31413325
MiR-574-5p: A Circulating Marker of Thoracic Aortic Aneurysm. PMID:31409059
Quantifying the impact of public omics data. PMID:31383865
A genome-wide positioning systems network algorithm for in silico drug repurposing. PMID:31375661
Using distant supervision to augment manually annotated data for relation extraction. PMID:31361753
Benchmark and integration of resources for the estimation of human transcription factor activities. PMID:31340985
AraPPINet: An Updated Interactome for the Analysis of Hormone Signaling Crosstalk in Arabidopsis thaliana. PMID:31333706
Estimating dispensable content in the human interactome. PMID:31324802
Identification of important invasion and proliferation related genes in adrenocortical carcinoma. PMID:31321566
Exploring the Molecular Mechanism of the Drug-Treated Breast Cancer Based on Gene Expression Microarray. PMID:31311202
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
Protein interaction networks revealed by proteome coevolution. PMID:31296772
Uncovering biomarker genes with enriched classification potential from Hallmark gene sets. PMID:31278367
Inferring Interaction Networks From Multi-Omics Data. PMID:31249591
Identification of a Multiplex Biomarker Panel for Hypertrophic Cardiomyopathy Using Quantitative Proteomics and Machine Learning. PMID:31243064
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
Gene Information eXtension (GIX): effortless retrieval of gene product information on any website. PMID:31217594
Protein interactions and consensus clustering analysis uncover insights into herpesvirus virion structure and function relationships. PMID:31199794
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
Identification of Endogenous Adenomatous Polyposis Coli Interaction Partners and β-Catenin-Independent Targets by Proteomics. PMID:31160382
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
Protein Melting Temperature Cannot Fully Assess Whether Protein Folding Free Energy Underlies the Universal Abundance-Evolutionary Rate Correlation Seen in Proteins. PMID:31093676
PhyreRisk: A Dynamic Web Application to Bridge Genomics, Proteomics and 3D Structural Data to Guide Interpretation of Human Genetic Variants. PMID:31075275
Parkinson's disease-associated LRRK2-G2019S mutant acts through regulation of SERCA activity to control ER stress in astrocytes. PMID:31046837
Autism risk genes are evolutionarily ancient and maintain a unique feature landscape that echoes their function. PMID:31025836
Identification of Important Invasion-Related Genes in Non-functional Pituitary Adenomas. PMID:30982163
Quantitative in situ proximity ligation assays examining protein interactions and phosphorylation during smooth muscle contractions. PMID:30981700
Mining Featured Biomarkers Linked with Epithelial Ovarian CancerBased on Bioinformatics. PMID:30970615
Crystal structure of the SH3 domain of human Lyn non-receptor tyrosine kinase. PMID:30969999
croFGD: Catharanthus roseus Functional Genomics Database. PMID:30967897
Network reconstruction from infection cascades. PMID:30958195
Downregulation of CENPF Remodels Prostate Cancer Cells and Alters Cellular Metabolism. PMID:30957416
Structural and Computational Characterization of Disease-Related Mutations Involved in Protein-Protein Interfaces. PMID:30934865
A Network Module for the Perseus Software for Computational Proteomics Facilitates Proteome Interaction Graph Analysis. PMID:30931570
Novel binding partners for Prenylated Rab Acceptor 1 identified by a split-ubiquitin yeast two-hybrid screen. PMID:30925931
Network-based prediction of protein interactions. PMID:30886144
An Improved Deep Forest Model for Predicting Self-Interacting Proteins From Protein Sequence Using Wavelet Transformation. PMID:30881376
Infrastructures of systems biology that facilitate functional genomic study in rice. PMID:30874968
Identification of Novel Interaction Partners of Ets-1: Focus on DNA Repair. PMID:30857266
Compendium of synovial signatures identifies pathologic characteristics for predicting treatment response in rheumatoid arthritis patients. PMID:30831253
Map of physical interactions between extracellular domains of Arabidopsis leucine-rich repeat receptor kinases. PMID:30806640
Gene-Specific Intron Retention Serves as Molecular Signature that Distinguishes Melanoma from Non-Melanoma Cancer Cells in Greek Patients. PMID:30795533
Prediction of Self-Interacting Proteins from Protein Sequence Information Based on Random Projection Model and Fast Fourier Transform. PMID:30795499
CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination. PMID:30793173
HN1L-mediated transcriptional axis AP-2γ/METTL13/TCF3-ZEB1 drives tumor growth and metastasis in hepatocellular carcinoma. PMID:30778199
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
MDH1 and MPP7 Regulate Autophagy in Pancreatic Ductal Adenocarcinoma. PMID:30765601
Convergent perturbation of the human domain-resolved interactome by viruses and mutations inducing similar disease phenotypes. PMID:30759076
Integration of macromolecular complex data into the Saccharomyces Genome Database. PMID:30715277
APID database: redefining protein-protein interaction experimental evidences and binary interactomes. PMID:30715274
Overview of the BioCreative VI Precision Medicine Track: mining protein interactions and mutations for precision medicine. PMID:30689846
Representing dynamic biological networks with multi-scale probabilistic models. PMID:30675519
Optimising orbit counting of arbitrary order by equation selection. PMID:30646859
The Network of Cancer Genes (NCG): a comprehensive catalogue of known and candidate cancer genes from cancer sequencing screens. PMID:30606230
Exploring the underlying biology of intrinsic cardiorespiratory fitness through integrative analysis of genomic variants and muscle gene expression profiling. PMID:30605401
Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set. PMID:30602777
Integrating node embeddings and biological annotations for genes to predict disease-gene associations. PMID:30598097
The RTK Interactome: Overview and Perspective on RTK Heterointeractions. PMID:30589534
Identification of genes required for eye development by high-throughput screening of mouse knockouts. PMID:30588515
Prediction of protein self-interactions using stacked long short-term memory from protein sequences information. PMID:30577794
Role of oxidative stress in Retinitis pigmentosa: new involved pathways by an RNA-Seq analysis. PMID:30569795
Integrating molecular networks with genetic variant interpretation for precision medicine. PMID:30548534
Systems biology analysis reveals new insights into invasive lung cancer. PMID:30547817
Mitoproteomics: Tackling Mitochondrial Dysfunction in Human Disease. PMID:30533169
Embracing the Dark Side: Computational Approaches to Unveil the Functionality of Genes Lacking Biological Annotation in Drug-Induced Liver Injury. PMID:30515189
Improving the Gene Ontology Resource to Facilitate More Informative Analysis and Interpretation of Alzheimer's Disease Data. PMID:30501127
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
Gears-In-Motion: The Interplay of WW and PPIase Domains in Pin1. PMID:30460195
Structural disorder in the proteome and interactome of Alkhurma virus (ALKV). PMID:30443749
IID 2018 update: context-specific physical protein-protein interactions in human, model organisms and domesticated species. PMID:30407591
The pervasive effects of recombinant Fasciola gigantica Ras-related protein Rab10 on the functions of goat peripheral blood mononuclear cells. PMID:30400957
The protein interaction networks of mucolipins and two-pore channels. PMID:30395881
Characterization of Squamous Cell Lung Cancers from Appalachian Kentucky. PMID:30377206
MatrixDB: integration of new data with a focus on glycosaminoglycan interactions. PMID:30371822
Establishment of stably expandable induced myogenic stem cells by four transcription factors. PMID:30361642
Heterogeneous network embedding for identifying symptom candidate genes. PMID:30357378
CORUM: the comprehensive resource of mammalian protein complexes-2019. PMID:30357367
An integrative tissue-network approach to identify and test human disease genes. PMID:30346941
Affinity capture of polyribosomes followed by RNAseq (ACAPseq), a discovery platform for protein-protein interactions. PMID:30345971
Domain architecture of BAF250a reveals the ARID and ARM-repeat domains with implication in function and assembly of the BAF remodeling complex. PMID:30307988
PlaD: A Transcriptomics Database for Plant Defense Responses to Pathogens, Providing New Insights into Plant Immune System. PMID:30266409
Viruses.STRING: A Virus-Host Protein-Protein Interaction Database. PMID:30249048
PTMD: A Database of Human Disease-associated Post-translational Modifications. PMID:30244175
A comprehensive manually-curated compendium of bovine transcription factors. PMID:30213987
Proteome-wide analysis of phospho-regulated PDZ domain interactions. PMID:30126976
Factors Associated with Heritable Pulmonary Arterial Hypertension Exert Convergent Actions on the miR-130/301-Vascular Matrix Feedback Loop. PMID:30081553
Structural Analysis of Hippocampal Kinase Signal Transduction. PMID:30053369
Leveraging Experimental Details for an Improved Understanding of Host-Pathogen Interactome. PMID:30040202
Protein-protein interactions of human viruses. PMID:30031213
Hepatitis C virus enters liver cells using the CD81 receptor complex proteins calpain-5 and CBLB. PMID:30024968
Histone Interaction Landscapes Visualized by Crosslinking Mass Spectrometry in Intact Cell Nuclei. PMID:30021884
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
LuTHy: a double-readout bioluminescence-based two-hybrid technology for quantitative mapping of protein-protein interactions in mammalian cells. PMID:29997244
Identifying a panel of genes/proteins/miRNAs modulated by arsenicals in bladder, prostate, kidney cancers. PMID:29991691
Improving Prediction of Self-interacting Proteins Using Stacked Sparse Auto-Encoder with PSSM profiles. PMID:29989064
Positional specificity of different transcription factor classes within enhancers. PMID:29987030
A genome-wide scan for correlated mutations detects macromolecular and chromatin interactions in Arabidopsis thaliana. PMID:29986106
In silico approach in reveal traditional medicine plants pharmacological material basis. PMID:29946351
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
Hub Protein Controversy: Taking a Closer Look at Plant Stress Response Hubs. PMID:29922309
Developments in toxicogenomics: understanding and predicting compound-induced toxicity from gene expression data. PMID:29917034
Towards a functional definition of the mitochondrial human proteome. PMID:29900096
Stratification of candidate genes for Parkinson's disease using weighted protein-protein interaction network analysis. PMID:29898659
OmicsNet: a web-based tool for creation and visual analysis of biological networks in 3D space. PMID:29878180
Identification of Central Regulators of Calcium Signaling and ECM-Receptor Interaction Genetically Associated With the Progression and Recurrence of Atrial Fibrillation. PMID:29868113
KIAA0100 Modulates Cancer Cell Aggression Behavior of MDA-MB-231 through Microtubule and Heat Shock Proteins. PMID:29867023
Landscape of transcriptional deregulation in lung cancer. PMID:29866045
Predicting Interactions between Virus and Host Proteins Using Repeat Patterns and Composition of Amino Acids. PMID:29854357
Systematic detection of positive selection in the human-pathogen interactome and lasting effects on infectious disease susceptibility. PMID:29799843
Mistimed food intake and sleep alters 24-hour time-of-day patterns of the human plasma proteome. PMID:29784788
A Primer for the Rat Genome Database (RGD). PMID:29761460
Xpo7 is a broad-spectrum exportin and a nuclear import receptor. PMID:29748336
ProteomeVis: a web app for exploration of protein properties from structure to sequence evolution across organisms' proteomes. PMID:29741573
Role of duplicate genes in determining the tissue-selectivity of hereditary diseases. PMID:29723191
PDZscape: a comprehensive PDZ-protein database. PMID:29699484
An epistatic effect of KRT25 on SP6 is involved in curly coat in horses. PMID:29686323
Biogeography and environmental conditions shape bacteriophage-bacteria networks across the human microbiome. PMID:29668682
JAMI: a Java library for molecular interactions and data interoperability. PMID:29642846
A Multi-Parameter Analysis of Cellular Coordination of Major Transcriptome Regulation Mechanisms. PMID:29636505
Systematic Evaluation of Molecular Networks for Discovery of Disease Genes. PMID:29605183
An AP-MS- and BioID-compatible MAC-tag enables comprehensive mapping of protein interactions and subcellular localizations. PMID:29568061
The striatal kinase DCLK3 produces neuroprotection against mutant huntingtin. PMID:29534157
A recombinant Fasciola gigantica 14-3-3 epsilon protein (rFg14-3-3e) modulates various functions of goat peripheral blood mononuclear cells. PMID:29510740
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
The dynamic life of the glycogen granule. PMID:29483195
Network analysis of coronary artery disease risk genes elucidates disease mechanisms and druggable targets. PMID:29467471
Network Analysis of UBE3A/E6AP-Associated Proteins Provides Connections to Several Distinct Cellular Processes. PMID:29426014
Moonlighting with WDR5: A Cellular Multitasker. PMID:29385767
PhenoRank: reducing study bias in gene prioritization through simulation. PMID:29360927
Robust phenotype prediction from gene expression data using differential shrinkage of co-regulated genes. PMID:29352257
VRK1 and AURKB form a complex that cross inhibit their kinase activity and the phosphorylation of histone H3 in the progression of mitosis. PMID:29340707
Biosystems Study of the Molecular Networks Underlying Hippocampal Aging Progression and Anti-aging Treatment in Mice. PMID:29311893
Characterizing ZC3H18, a Multi-domain Protein at the Interface of RNA Production and Destruction Decisions. PMID:29298432
Functional Analysis of Human Hub Proteins and Their Interactors Involved in the Intrinsic Disorder-Enriched Interactions. PMID:29257115
Interactome Mapping Uncovers a General Role for Numb in Protein Kinase Regulation. PMID:29217616
The Ink4a/Arf locus operates as a regulator of the circadian clock modulating RAS activity. PMID:29216180
Uncovering the Pharmacological Mechanism of Astragalus Salvia Compound on Pregnancy-Induced Hypertension Syndrome by a Network Pharmacology Approach. PMID:29203792
A network pharmacology approach to investigate the pharmacological effects of Guizhi Fuling Wan on uterine fibroids. PMID:29201170
Nbeal2 interacts with Dock7, Sec16a, and Vac14. PMID:29187380
The European Bioinformatics Institute in 2017: data coordination and integration. PMID:29186510
The OncoPPi Portal: an integrative resource to explore and prioritize protein-protein interactions for cancer target discovery. PMID:29186335
Virus-host protein-protein interactions of mycobacteriophage Giles. PMID:29184079
Global landscape of cell envelope protein complexes in Escherichia coli. PMID:29176613
Graph-theoretical comparison of normal and tumor networks in identifying BRCA genes. PMID:29166896
Protein complex scaffolding predicted as a prevalent function of long non-coding RNAs. PMID:29165713
FunCoup 4: new species, data, and visualization. PMID:29165593
THANATOS: an integrative data resource of proteins and post-translational modifications in the regulation of autophagy. PMID:29157087
Molecular Interaction Search Tool (MIST): an integrated resource for mining gene and protein interaction data. PMID:29155944
Chronic oxidative stress promotes GADD34-mediated phosphorylation of the TAR DNA-binding protein TDP-43, a modification linked to neurodegeneration. PMID:29109149
The UCSC Genome Browser database: 2018 update. PMID:29106570
Computational methods using weighed-extreme learning machine to predict protein self-interactions with protein evolutionary information. PMID:29086182
Critical assessment of methods of protein structure prediction (CASP)-Round XII. PMID:29082672
Affinity proteomics reveals extensive phosphorylation of the Brassica chromosome axis protein ASY1 and a network of associated proteins at prophase I of meiosis. PMID:29078019
SalmoNet, an integrated network of ten Salmonella enterica strains reveals common and distinct pathways to host adaptation. PMID:29057095
The SSU processome interactome in Saccharomyces cerevisiae reveals novel protein subcomplexes. PMID:29054886
The online Tabloid Proteome: an annotated database of protein associations. PMID:29040688
ComplexViewer: visualization of curated macromolecular complexes. PMID:29036573
Environment and bladder cancer: molecular analysis by interaction networks. PMID:29029427
Rapamycin-induced miR-21 promotes mitochondrial homeostasis and adaptation in mTORC1 activated cells. PMID:29029388
PICKLE 2.0: A human protein-protein interaction meta-database employing data integration via genetic information ontology. PMID:29023571
A transcriptome-based protein network that identifies new therapeutic targets in colorectal cancer. PMID:28962550
High rate of adaptation of mammalian proteins that interact with Plasmodium and related parasites. PMID:28957326
Molecular mechanisms underlying gliomas and glioblastoma pathogenesis revealed by bioinformatics analysis of microarray data. PMID:28952134
SciLite: a platform for displaying text-mined annotations as a means to link research articles with biological data. PMID:28948232
MCbiclust: a novel algorithm to discover large-scale functionally related gene sets from massive transcriptomics data collections. PMID:28911113
Exploring the Human-Nipah Virus Protein-Protein Interactome. PMID:28904190
Predicting multicellular function through multi-layer tissue networks. PMID:28881986
Cadherin complexes recruit mRNAs and RISC to regulate epithelial cell signaling. PMID:28877994
Modeling protein quaternary structure of homo- and hetero-oligomers beyond binary interactions by homology. PMID:28874689
Surface PD-L1, E-cadherin, CD24, and VEGFR2 as markers of epithelial cancer stem cells associated with rapid tumorigenesis. PMID:28851898
Comprehensive Analyses of Tissue-Specific Networks with Implications to Psychiatric Diseases. PMID:28849569
Domain-based prediction of the human isoform interactome provides insights into the functional impact of alternative splicing. PMID:28846689
An integrated bioinformatics platform for investigating the human E3 ubiquitin ligase-substrate interaction network. PMID:28839186
Type 1 Diabetes: Urinary Proteomics and Protein Network Analysis Support Perturbation of Lysosomal Function. PMID:28819457
OLS Client and OLS Dialog: Open Source Tools to Annotate Public Omics Datasets. PMID:28792687
Dynamic scaffolds for neuronal signaling: in silico analysis of the TANC protein family. PMID:28754924
MINERVA-a platform for visualization and curation of molecular interaction networks. PMID:28725475
Centriolar Satellites Control GABARAP Ubiquitination and GABARAP-Mediated Autophagy. PMID:28712572
HDNetDB: A Molecular Interaction Database for Network-Oriented Investigations into Huntington's Disease. PMID:28701700
The yeast noncoding RNA interaction network. PMID:28701522
Strength of functional signature correlates with effect size in autism. PMID:28687074
CausalR: extracting mechanistic sense from genome scale data. PMID:28666369
Network Analysis Reveals a Common Host-Pathogen Interaction Pattern in Arabidopsis Immune Responses. PMID:28611808
Inhibition of Avian Influenza A Virus Replication in Human Cells by Host Restriction Factor TUFM Is Correlated with Autophagy. PMID:28611246
Knowledge Discovery in Biological Databases for Revealing Candidate Genes Linked to Complex Phenotypes. PMID:28609292
Neighbours of cancer-related proteins have key influence on pathogenesis and could increase the drug target space for anticancer therapies. PMID:28603644
Characterization of developmental defects in the forebrain resulting from hyperactivated mTOR signaling by integrative analysis of transcriptomic and proteomic data. PMID:28588230
RalBP1 and p19-VHL play an oncogenic role, and p30-VHL plays a tumor suppressor role during the blebbishield emergency program. PMID:28580172
Genetic association study of exfoliation syndrome identifies a protective rare variant at LOXL1 and five new susceptibility loci. PMID:28553957
CLMSVault: A Software Suite for Protein Cross-Linking Mass-Spectrometry Data Analysis and Visualization. PMID:28537071
A computational framework for distinguishing direct versus indirect interactions in human functional protein-protein interaction networks. PMID:28524201
Unbiased Protein Association Study on the Public Human Proteome Reveals Biological Connections between Co-Occurring Protein Pairs. PMID:28480704
The Bologna Annotation Resource (BAR 3.0): improving protein functional annotation. PMID:28453653
Identification of protein features encoded by alternative exons using Exon Ontology. PMID:28420690
The role of CRKL in breast cancer metastasis: insights from systems biology. PMID:28392847
Bioinformatics analysis of the proteins interacting with LASP-1 and their association with HBV-related hepatocellular carcinoma. PMID:28266596
Integrated systems biology analysis of KSHV latent infection reveals viral induction and reliance on peroxisome mediated lipid metabolism. PMID:28257516
Drug voyager: a computational platform for exploring unintended drug action. PMID:28241745
CLK-dependent exon recognition and conjoined gene formation revealed with a novel small molecule inhibitor. PMID:28232751
A Comprehensive Gene Expression Meta-analysis Identifies Novel Immune Signatures in Rheumatoid Arthritis Patients. PMID:28210261
The OncoPPi network of cancer-focused protein-protein interactions to inform biological insights and therapeutic strategies. PMID:28205554
How can functional annotations be derived from profiles of phenotypic annotations? PMID:28183267
The CIA Targeting Complex Is Highly Regulated and Provides Two Distinct Binding Sites for Client Iron-Sulfur Proteins. PMID:28178521
Comparative influenza protein interactomes identify the role of plakophilin 2 in virus restriction. PMID:28169297
Deep-proteome mapping of WM-266-4 human metastatic melanoma cells: From oncogenic addiction to druggable targets. PMID:28158294
Protein Bioinformatics Databases and Resources. PMID:28150231
Thrombospondin-1 and microRNA-1 expression in response to multiwalled carbon nanotubes in alveolar epithelial cells. PMID:28128526
Epigenetic profiling of human brain differential DNA methylation networks in schizophrenia. PMID:28117656
Non-interacting proteins may resemble interacting proteins: prevalence and implications. PMID:28084410
A Network Pharmacology Approach to Explore the Pharmacological Mechanism of Xiaoyao Powder on Anovulatory Infertility. PMID:28074099
Identifying Candidate Reprogramming Genes in Mouse Induced Pluripotent Stem Cells. PMID:28063063
Plant genome and transcriptome annotations: from misconceptions to simple solutions. PMID:28062412
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
Selecting optimal combinations of transcription factors to promote axon regeneration: Why mechanisms matter. PMID:28025113
Weighted Protein Interaction Network Analysis of Frontotemporal Dementia. PMID:28004582
Interactomic analysis of REST/NRSF and implications of its functional links with the transcription suppressor TRIM28 during neuronal differentiation. PMID:27976729
PluriPred: AWeb server for predicting proteins involved in pluripotent network. PMID:27966493
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
Co-expression network analyses identify functional modules associated with development and stress response in Gossypium arboreum. PMID:27922095
Differential variation patterns between hubs and bottlenecks in human protein-protein interaction networks. PMID:27903259
Glycosaminoglycanomics: where we are. PMID:27900575
The neXtProt knowledgebase on human proteins: 2017 update. PMID:27899619
The TissueNet v.2 database: A quantitative view of protein-protein interactions across human tissues. PMID:27899616
A scored human protein-protein interaction network to catalyze genomic interpretation. PMID:27892958
Genome, transcriptome and proteome: the rise of omics data and their integration in biomedical sciences. PMID:27881428
Increasing Role of Titin Mutations in Neuromuscular Disorders. PMID:27854229
EphA2 proteomics in human keratinocytes reveals a novel association with afadin and epidermal tight junctions. PMID:27815408
HIPPIE v2.0: enhancing meaningfulness and reliability of protein-protein interaction networks. PMID:27794551
A Systems Biology Comparison of Ovarian Cancers Implicates Putative Somatic Driver Mutations through Protein-Protein Interaction Models. PMID:27788148
Mapping wild-type and R345W fibulin-3 intracellular interactomes. PMID:27777122
Identification of self-interacting proteins by exploring evolutionary information embedded in PSI-BLAST-constructed position specific scoring matrix. PMID:27732957
Simultaneous identification of specifically interacting paralogs and interprotein contacts by direct coupling analysis. PMID:27729520
The fractal heart - embracing mathematics in the cardiology clinic. PMID:27708281
Prediction and validation of protein-protein interactors from genome-wide DNA-binding data using a knowledge-based machine-learning approach. PMID:27683156
The application of transcriptomic data in the authentication of beef derived from contrasting production systems. PMID:27654331
Systems Medicine as an Emerging Tool for Cardiovascular Genetics. PMID:27626034
Implication of Terminal Residues at Protein-Protein and Protein-DNA Interfaces. PMID:27611671
A Novel Role for Progesterone Receptor Membrane Component 1 (PGRMC1): A Partner and Regulator of Ferrochelatase. PMID:27599036
Automated detection of discourse segment and experimental types from the text of cancer pathway results sections. PMID:27580922
Fusing literature and full network data improves disease similarity computation. PMID:27578323
A protein network descriptor server and its use in studying protein, disease, metabolic and drug targeted networks. PMID:27542402
Functional characterization of EI24-induced autophagy in the degradation of RING-domain E3 ligases. PMID:27541728
Robust de novo pathway enrichment with KeyPathwayMiner 5. PMID:27540470
Membranome: a database for proteome-wide analysis of single-pass membrane proteins. PMID:27510400
Modelling the Structure and Dynamics of Biological Pathways. PMID:27509052
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
AraPPISite: a database of fine-grained protein-protein interaction site annotations for Arabidopsis thaliana. PMID:27338257
Oncogenic Sox2 regulates and cooperates with VRK1 in cell cycle progression and differentiation. PMID:27334688
The LIM domain protein nTRIP6 acts as a co-repressor for the transcription factor MEF2C in myoblasts. PMID:27292777
Gene regulation knowledge commons: community action takes care of DNA binding transcription factors. PMID:27270715
Data set of interactomes and metabolic pathways of proteins differentially expressed in brains with Alzheimer׳s disease. PMID:27257613
CoopTFD: a repository for predicted yeast cooperative transcription factor pairs. PMID:27242036
Endocytosis and serpentine filopodia drive blebbishield-mediated resurrection of apoptotic cancer stem cells. PMID:27226900
Computational Framework for Prediction of Peptide Sequences That May Mediate Multiple Protein Interactions in Cancer-Associated Hub Proteins. PMID:27218803
Genome-Wide Inference of Protein-Protein Interaction Networks Identifies Crosstalk in Abscisic Acid Signaling. PMID:27208273
Reactome from a WikiPathways Perspective. PMID:27203685
Controllability of protein-protein interaction phosphorylation-based networks: Participation of the hub 14-3-3 protein family. PMID:27195976
Systematic Protein-Protein Interaction Analysis Reveals Intersubcomplex Contacts in the Nuclear Pore Complex. PMID:27194810
Practical Approaches for Mining Frequent Patterns in Molecular Datasets. PMID:27168722
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
Identification of the BRD1 interaction network and its impact on mental disorder risk. PMID:27142060
APID interactomes: providing proteome-based interactomes with controlled quality for multiple species and derived networks. PMID:27131791
Candidate gene prioritization with Endeavour. PMID:27131783
A Protein Domain and Family Based Approach to Rare Variant Association Analysis. PMID:27128313
PTIR: Predicted Tomato Interactome Resource. PMID:27121261
HIPPO-Integrin-linked Kinase Cross-Talk Controls Self-Sustaining Proliferation and Survival in Pulmonary Hypertension. PMID:27119551
A Network Pharmacology Approach to Uncover the Pharmacological Mechanism of XuanHuSuo Powder on Osteoarthritis. PMID:27110264
An inter-species protein-protein interaction network across vast evolutionary distance. PMID:27107014
Pooled-matrix protein interaction screens using Barcode Fusion Genetics. PMID:27107012
The interactome of Streptococcus pneumoniae and its bacteriophages show highly specific patterns of interactions among bacteria and their phages. PMID:27103053
APP Is a Context-Sensitive Regulator of the Hippocampal Presynaptic Active Zone. PMID:27092780
Uncovering disease mechanisms through network biology in the era of Next Generation Sequencing. PMID:27080396
Novel PKC-ζ to p47 phox interaction is necessary for transformation from blebbishields. PMID:27040869
Systems psychopharmacology: A network approach to developing novel therapies. PMID:27014599
Proteomics-Based Analysis of Protein Complexes in Pluripotent Stem Cells and Cancer Biology. PMID:27011181
FlyOde - a platform for community curation and interactive visualization of dynamic gene regulatory networks in Drosophila eye development. PMID:26998229
PIPINO: A Software Package to Facilitate the Identification of Protein-Protein Interactions from Affinity Purification Mass Spectrometry Data. PMID:26966684
Identification of Toxic Pyrrolizidine Alkaloids and Their Common Hepatotoxicity Mechanism. PMID:26959016
Comparing Alzheimer's and Parkinson's diseases networks using graph communities structure. PMID:26935435
Key Immune Events of the Pathomechanisms of Early Cardioembolic Stroke: Multi-Database Mining and Systems Biology Approach. PMID:26927091
Bacterial Interactomes: Interacting Protein Partners Share Similar Function and Are Validated in Independent Assays More Frequently Than Previously Reported. PMID:26873250
Inositol 1,4,5-trisphosphate receptors and their protein partners as signalling hubs. PMID:26830355
Proteomic approaches to uncovering virus-host protein interactions during the progression of viral infection. PMID:26817613
Lamina Associated Polypeptide 1 (LAP1) Interactome and Its Functional Features. PMID:26784240
Correlative Gene Expression to Protective Seroconversion in Rift Valley Fever Vaccinates. PMID:26783758
A combined binary interaction and phenotypic map of C. elegans cell polarity proteins. PMID:26780296
FIH Regulates Cellular Metabolism through Hydroxylation of the Deubiquitinase OTUB1. PMID:26752685
HitPredict version 4: comprehensive reliability scoring of physical protein-protein interactions from more than 100 species. PMID:26708988
Prediction of Druggable Proteins Using Machine Learning and Systems Biology: A Mini-Review. PMID:26696900
Forward Individualized Medicine from Personal Genomes to Interactomes. PMID:26696898
SLiMScape 3.x: a Cytoscape 3 app for discovery of Short Linear Motifs in protein interaction networks. PMID:26674271
A deep proteomics perspective on CRM1-mediated nuclear export and nucleocytoplasmic partitioning. PMID:26673895
freeQuant: A Mass Spectrometry Label-Free Quantification Software Tool for Complex Proteome Analysis. PMID:26665161
Integrated analysis of global proteome, phosphoproteome, and glycoproteome enables complementary interpretation of disease-related protein networks. PMID:26657352
Kiwifruit Information Resource (KIR): a comparative platform for kiwifruit genomics. PMID:26656885
A simple feature construction method for predicting upstream/downstream signal flow in human protein-protein interaction networks. PMID:26648121
PPIM: A Protein-Protein Interaction Database for Maize. PMID:26620522
NDEx, the Network Data Exchange. PMID:26594663
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
An Effective Method to Identify Shared Pathways and Common Factors among Neurodegenerative Diseases. PMID:26575483
MAPanalyzer: a novel online tool for analyzing microtubule-associated proteins. PMID:26568329
Deciphering Supramolecular Structures with Protein-Protein Interaction Network Modeling. PMID:26549015
Host-Microbe Protein Interactions during Bacterial Infection. PMID:26548613
Tools and data services registry: a community effort to document bioinformatics resources. PMID:26538599
NCG 5.0: updates of a manually curated repository of cancer genes and associated properties from cancer mutational screenings. PMID:26516186
Bioinformatics Knowledge Map for Analysis of Beta-Catenin Function in Cancer. PMID:26509276
A Glimpse to Background and Characteristics of Major Molecular Biological Networks. PMID:26491677
An integrative systems genetics approach reveals potential causal genes and pathways related to obesity. PMID:26482556
DIDA: A curated and annotated digenic diseases database. PMID:26481352
SIGNOR: a database of causal relationships between biological entities. PMID:26467481
The Hepatitis E virus intraviral interactome. PMID:26463011
Global multiple protein-protein interaction network alignment by combining pairwise network alignments. PMID:26423128
Mammalian splicing factor SF1 interacts with SURP domains of U2 snRNP-associated proteins. PMID:26420826
Detecting modules in biological networks by edge weight clustering and entropy significance. PMID:26379697
Decoding protein networks during virus entry by quantitative proteomics. PMID:26365680
Reconstructed Ancestral Enzymes Impose a Fitness Cost upon Modern Bacteria Despite Exhibiting Favourable Biochemical Properties. PMID:26349578
In vivo hematopoietic Myc activation directs a transcriptional signature in endothelial cells within the bone marrow microenvironment. PMID:26308666
Integrated inference and evaluation of host-fungi interaction networks. PMID:26300851
Identification of the Mitochondrial Heme Metabolism Complex. PMID:26287972
Identifying and characterising key alternative splicing events in Drosophila development. PMID:26275604
Prediction of problematic complexes from PPI networks: sparse, embedded, and small complexes. PMID:26231465
Quantitative Proteomics Identifies Serum Response Factor Binding Protein 1 as a Host Factor for Hepatitis C Virus Entry. PMID:26212323
Extracting biomedical events from pairs of text entities. PMID:26201478
Comprehensive Protein Interactome Analysis of a Key RNA Helicase: Detection of Novel Stress Granule Proteins. PMID:26184334
Acquisition of estrogen independence induces TOB1-related mechanisms supporting breast cancer cell proliferation. PMID:26165839
A reproducible approach to high-throughput biological data acquisition and integration. PMID:26157642
EpiFactors: a comprehensive database of human epigenetic factors and complexes. PMID:26153137
Surfing the Protein-Protein Interaction Surface Using Docking Methods: Application to the Design of PPI Inhibitors. PMID:26111183
Computational methods and resources for the interpretation of genomic variants in cancer. PMID:26111056
Predicting and exploring network components involved in pathogenesis in the malaria parasite via novel subnetwork alignments. PMID:26100579
By the company they keep: interaction networks define the binding ability of transcription factors. PMID:26089389
Proteins interaction network and modeling of IGVH mutational status in chronic lymphocytic leukemia. PMID:26088082
Integrated web visualizations for protein-protein interaction databases. PMID:26077899
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
SPECTRA: An Integrated Knowledge Base for Comparing Tissue and Tumor-Specific PPI Networks in Human. PMID:26005672
Dynamic network-based relevance score reveals essential proteins and functional modules in directed differentiation. PMID:25977693
Improving the Understanding of Pathogenesis of Human Papillomavirus 16 via Mapping Protein-Protein Interaction Network. PMID:25961044
Global alterations of the transcriptional landscape during yeast growth and development in the absence of Ume6-dependent chromatin modification. PMID:25957495
ProtPhylo: identification of protein-phenotype and protein-protein functional associations via phylogenetic profiling. PMID:25956654
A review on computational systems biology of pathogen-host interactions. PMID:25914674
CellWhere: graphical display of interaction networks organized on subcellular localizations. PMID:25883154
ANDSystem: an Associative Network Discovery System for automated literature mining in the field of biology. PMID:25881313
A protein interaction map of the LSU processome. PMID:25877921
Biochemical functional predictions for protein structures of unknown or uncertain function. PMID:25848497
Shared resources, shared costs--leveraging biocuration resources. PMID:25776020
The Open Physiology workflow: modeling processes over physiology circuitboards of interoperable tissue units. PMID:25759670
Development of data representation standards by the human proteome organization proteomics standards initiative. PMID:25726569
FR database 1.0: a resource focused on fruit development and ripening. PMID:25725058
Systems biology analysis of the proteomic alterations induced by MPP(+), a Parkinson's disease-related mitochondrial toxin. PMID:25698928
The functional interactome of PYHIN immune regulators reveals IFIX is a sensor of viral DNA. PMID:25665578
Huntingtin-associated protein 1 (HAP1) is a cGMP-dependent kinase anchoring protein (GKAP) specific for the cGMP-dependent protein kinase Iβ isoform. PMID:25653285
Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study. PMID:25652942
A visual review of the interactome of LRRK2: Using deep-curated molecular interaction data to represent biology. PMID:25648416
Quantitative and logic modelling of molecular and gene networks. PMID:25645874
Autophagy Regulatory Network - a systems-level bioinformatics resource for studying the mechanism and regulation of autophagy. PMID:25635527
Network representations of immune system complexity. PMID:25625853
Virus-host interactomics: new insights and opportunities for antiviral drug discovery. PMID:25593595
A highly efficient approach to protein interactome mapping based on collaborative filtering framework. PMID:25572661
Proceedings of the Thirteenth Annual UT- KBRIN Bioinformatics Summit 2014. PMID:25571995
Transcript co-variance with Nestin in two mouse genetic reference populations identifies Lef1 as a novel candidate regulator of neural precursor cell proliferation in the adult hippocampus. PMID:25565948
Discovery of small protein complexes from PPI networks with size-specific supervised weighting. PMID:25559663
DCDB 2.0: a major update of the drug combination database. PMID:25539768
The EHEC-host interactome reveals novel targets for the translocated intimin receptor. PMID:25519916
Comprehensive discovery of DNA motifs in 349 human cells and tissues reveals new features of motifs. PMID:25505144
The InterPro protein families database: the classification resource after 15 years. PMID:25428371
Araport: the Arabidopsis information portal. PMID:25414324
Using biological networks to improve our understanding of infectious diseases. PMID:25379138
MatrixDB, the extracellular matrix interaction database: updated content, a new navigator and expanded functionalities. PMID:25378329
Protein-tyrosine phosphorylation interaction network in Bacillus subtilis reveals new substrates, kinase activators and kinase cross-talk. PMID:25374563
PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins. PMID:25361965
STRING v10: protein-protein interaction networks, integrated over the tree of life. PMID:25352553
ComPPI: a cellular compartment-specific database for protein-protein interaction network analysis. PMID:25348397
ImmuCo: a database of gene co-expression in immune cells. PMID:25326331
The complex portal--an encyclopaedia of macromolecular complexes. PMID:25313161
Linear motif-mediated interactions have contributed to the evolution of modularity in complex protein interaction networks. PMID:25299147
Analysis of the expression patterns, subcellular localisations and interaction partners of Drosophila proteins using a pigP protein trap library. PMID:25294943
Affinity purification-mass spectrometry and network analysis to understand protein-protein interactions. PMID:25275790
SANTA: quantifying the functional content of molecular networks. PMID:25210953
esyN: network building, sharing and publishing. PMID:25181461
Toward a systems-level understanding of gene regulatory, protein interaction, and metabolic networks in cyanobacteria. PMID:25071821
A quantitative chaperone interaction network reveals the architecture of cellular protein homeostasis pathways. PMID:25036637
Robust clinical outcome prediction based on Bayesian analysis of transcriptional profiles and prior causal networks. PMID:24932007
A framework for application of metabolic modeling in yeast to predict the effects of nsSNV in human orthologs. PMID:24894379
Biophysical constraints on the evolution of tissue structure and function. PMID:24882821
NetworkAnalyst--integrative approaches for protein-protein interaction network analysis and visual exploration. PMID:24861621
BioCreative-IV virtual issue. PMID:24852177
Analysis pipeline for the epistasis search - statistical versus biological filtering. PMID:24817878
What's that gene (or protein)? Online resources for exploring functions of genes, transcripts, and proteins. PMID:24723265
IntAct: an open source molecular interaction database PubMed citations: 356.

356 articles citing: IntAct: an open source molecular interaction database

Mutations in SORL1 and MTHFDL1 possibly contribute to the development of Alzheimer's disease in a multigenerational Colombian Family. PMID:35905044
Challenges and Limitations of Biological Network Analysis. PMID:35892929
Integrating multi-omics data reveals function and therapeutic potential of deubiquitinating enzymes. PMID:35737447
Integration of Protein-Protein Interaction Networks and Gene Expression Profiles Helps Detect Pancreatic Adenocarcinoma Candidate Genes. PMID:35711911
Bioinformatics-Based Approaches to Study Virus-Host Interactions During SARS-CoV-2 Infection. PMID:35554909
A hybrid approach unveils drug repurposing candidates targeting an Alzheimer pathophysiology mechanism. PMID:35510183
Mapping the epithelial-immune cell interactome upon infection in the gut and the upper airways. PMID:35501398
ImitateDB: A database for domain and motif mimicry incorporating host and pathogen protein interactions. PMID:35487995
An atlas of posttranslational modifications on RNA binding proteins. PMID:35438783
LPInsider: a webserver for lncRNA-protein interaction extraction from the literature. PMID:35428172
Integrating protein copy numbers with interaction networks to quantify stoichiometry in clathrin-mediated endocytosis. PMID:35354856
Alpha B-Crystallin in Muscle Disease Prevention: The Role of Physical Activity. PMID:35164412
Network analysis of host-pathogen protein interactions in microbe induced cardiovascular diseases. PMID:35001887
A full-proteome, interaction-specific characterization of mutational hotspots across human cancers. PMID:34963661
Intellectual disability genomics: current state, pitfalls and future challenges. PMID:34930158
Protein network analysis to prioritize key genes in amyotrophic lateral sclerosis. PMID:34918006
Navigating Multi-Scale Cancer Systems Biology Towards Model-Driven Clinical Oncology and Its Applications in Personalized Therapeutics. PMID:34900668
Self-Attention-Based Models for the Extraction of Molecular Interactions from Biological Texts. PMID:34827589
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
Centrality of drug targets in protein networks. PMID:34715787
Proteomic Tools for the Analysis of Cytoskeleton Proteins. PMID:34542864
The protein-protein interaction network alignment using recurrent neural network. PMID:34529185
The chemical biology of coronavirus host-cell interactions. PMID:34458775
Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review. PMID:34439912
Looking for pathways related to COVID-19: confirmation of pathogenic mechanisms by SARS-CoV-2-host interactome. PMID:34385425
Revealing protein-protein interactions at the transcriptome scale by sequencing. PMID:34348091
DGLinker: flexible knowledge-graph prediction of disease-gene associations. PMID:34125897
Detecting Protein Communities in Native Cell Extracts by Machine Learning: A Structural Biologist's Perspective. PMID:33937337
Genome-wide identification of MIKC-type genes related to stamen and gynoecium development in Liriodendron. PMID:33753780
Integration of single-cell datasets reveals novel transcriptomic signatures of β-cells in human type 2 diabetes. PMID:33575641
ViralLink: An integrated workflow to investigate the effect of SARS-CoV-2 on intracellular signalling and regulatory pathways. PMID:33534793
TROAP switches DYRK1 activity to drive hepatocellular carcinoma progression. PMID:33500384
An Integrative Computational Approach for the Prediction of Human-Plasmodium Protein-Protein Interactions. PMID:33426052
Elucidating the network features and evolutionary attributes of intra- and interspecific protein-protein interactions between human and pathogenic bacteria. PMID:33420198
Systems Approach to Pathogenic Mechanism of Type 2 Diabetes and Drug Discovery Design Based on Deep Learning and Drug Design Specifications. PMID:33375269
Applications and advancements of FT-ICR-MS for interactome studies. PMID:33289940
The European Bioinformatics Institute: empowering cooperation in response to a global health crisis. PMID:33245775
Conjoint Feature Representation of GO and Protein Sequence for PPI Prediction Based on an Inception RNN Attention Network. PMID:33230427
H-RACS: a handy tool to rank anti-cancer synergistic drugs. PMID:33173014
Deciphering cell-cell interactions and communication from gene expression. PMID:33168968
Determinants of correlated expression of transcription factors and their target genes. PMID:33104784
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
Comparative Genomic Analysis of Rapidly Evolving SARS-CoV-2 Reveals Mosaic Pattern of Phylogeographical Distribution. PMID:32723797
A RIPOR2 in-frame deletion is a frequent and highly penetrant cause of adult-onset hearing loss. PMID:32631815
Detecting Prognosis Risk Biomarkers for Colon Cancer Through Multi-Omics-Based Prognostic Analysis and Target Regulation Simulation Modeling. PMID:32528533
Post-translational Modification Crosstalk and Hotspots in Sirtuin Interactors Implicated in Cardiovascular Diseases. PMID:32425973
Essential gene prediction in Drosophila melanogaster using machine learning approaches based on sequence and functional features. PMID:32257045
Cell Type-Specific Intralocus Interactions Reveal Oligodendrocyte Mechanisms in MS. PMID:32246942
Understanding of Zaire ebolavirus-human protein interaction for drug repurposing. PMID:32206696
A Guide to Conquer the Biological Network Era Using Graph Theory. PMID:32083072
Improving Identification of In-organello Protein-Protein Interactions Using an Affinity-enrichable, Isotopically Coded, and Mass Spectrometry-cleavable Chemical Crosslinker. PMID:32051233
Identification of cancer driver genes based on nucleotide context. PMID:32015527
MASS SPECTROMETRY IN VIROLOGICAL SCIENCES. PMID:31876329
Leveraging User-Friendly Network Approaches to Extract Knowledge From High-Throughput Omics Datasets. PMID:31798629
CSF1R inhibitor JNJ-40346527 attenuates microglial proliferation and neurodegeneration in P301S mice. PMID:31504240
Hamiltonian energy as an efficient approach to identify the significant key regulators in biological networks. PMID:31442253
The endosomal sorting adaptor HD-PTP is required for ephrin-B:EphB signalling in cellular collapse and spinal motor axon guidance. PMID:31420572
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
MorCVD: A Unified Database for Host-Pathogen Protein-Protein Interactions of Cardiovascular Diseases Related to Microbes. PMID:30858555
Host Vesicle Fusion Protein VAPB Contributes to the Nuclear Egress Stage of Herpes Simplex Virus Type-1 (HSV-1) Replication. PMID:30717447
Molecular subtyping of cancer and nomination of kinase candidates for inhibition with phosphoproteomics: Reanalysis of CPTAC ovarian cancer. PMID:30594550
The RTK Interactome: Overview and Perspective on RTK Heterointeractions. PMID:30589534
iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data. PMID:30567491
Search of Allosteric Inhibitors and Associated Proteins of an AKT-like Kinase from Trypanosoma cruzi. PMID:30544836
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
Chromosome 17 Missing Proteins: Recent Progress and Future Directions as Part of the neXt-MP50 Challenge. PMID:30280577
Launching the C-HPP neXt-CP50 Pilot Project for Functional Characterization of Identified Proteins with No Known Function. PMID:30269496
Prediction of Novel Drugs and Diseases for Hepatocellular Carcinoma Based on Multi-Source Simulated Annealing Based Random Walk. PMID:30173379
PPInS: a repository of protein-protein interaction sitesbase. PMID:30127348
Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken. PMID:30086717
Evolution of In Silico Strategies for Protein-Protein Interaction Drug Discovery. PMID:30082644
Tissue-specific Network Analysis of Genetic Variants Associated with Coronary Artery Disease. PMID:30065343
An unsupervised machine learning method for discovering patient clusters based on genetic signatures. PMID:30016722
Leveraging prior knowledge for protein-protein interaction extraction with memory network. PMID:30010731
Prediction of human-Bacillus anthracis protein-protein interactions using multi-layer neural network. PMID:29945178
Systems-Based Interactome Analysis for Hematopoiesis Effect of Angelicae sinensis Radix: Regulated Network of Cell Proliferation towards Hemopoiesis. PMID:29943236
Proteome-wide analysis of human motif-domain interactions mapped on influenza a virus. PMID:29940841
Computational Methods for Predicting Protein-Protein Interactions Using Various Protein Features. PMID:29927082
An interactome perturbation framework prioritizes damaging missense mutations for developmental disorders. PMID:29892012
Network-based machine learning and graph theory algorithms for precision oncology. PMID:29872707
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
Systematic Evaluation of Molecular Networks for Discovery of Disease Genes. PMID:29605183
Gastric cancer biomarkers; A systems biology approach. PMID:29556568
Predicted Arabidopsis Interactome Resource and Gene Set Linkage Analysis: A Transcriptomic Analysis Resource. PMID:29530937
Cholangiocarcinoma‑associated genes identified by integrative analysis of gene expression data. PMID:29436659
Evaluation of epidermal growth factor receptor signaling effects in gastric cancer cell lines by detailed motility-focused phenotypic characterization linked with molecular analysis. PMID:29237412
In-Cardiome: integrated knowledgebase for coronary artery disease enabling translational research. PMID:29220465
Predicting new indications of compounds with a network pharmacology approach: Liuwei Dihuang Wan as a case study. PMID:29212201
The Eukaryotic Elongation Factor 1 Alpha (eEF1α) from the Parasite Leishmania infantum Is Modified with the Immunomodulatory Substituent Phosphorylcholine (PC). PMID:29186074
Xenbase: a genomic, epigenomic and transcriptomic model organism database. PMID:29059324
Report and Application of a Tool Compound Data Set. PMID:29035535
A novel network analysis approach reveals DNA damage, oxidative stress and calcium/cAMP homeostasis-associated biomarkers in frontotemporal dementia. PMID:29020091
Integrated transcriptomics and metabolomics analysis to characterize cold stress responses in Nicotiana tabacum. PMID:28662642
Endothelium-Independent Primitive Myxoid Vascularization Creates Invertebrate-Like Channels to Maintain Blood Supply in Optic Gliomas. PMID:28606795
GeMSTONE: orchestrated prioritization of human germline mutations in the cloud. PMID:28521008
Bioinformatics in translational drug discovery. PMID:28487472
Transcriptional regulatory networks underlying the reprogramming of spermatogonial stem cells to multipotent stem cells. PMID:28408750
The amyloid interactome: Exploring protein aggregation. PMID:28249044
The post-genomic era of biological network alignment. PMID:28194172
Binding of small molecules at interface of protein-protein complex - A newer approach to rational drug design. PMID:28149177
Automatic query generation using word embeddings for retrieving passages describing experimental methods. PMID:28077568
Improving protein complex prediction by reconstructing a high-confidence protein-protein interaction network of Escherichia coli from different physical interaction data sources. PMID:28049415
Non-Coding RNAs in Lung Cancer: Contribution of Bioinformatics Analysis to the Development of Non-Invasive Diagnostic Tools. PMID:28035947
PROPER: global protein interaction network alignment through percolation matching. PMID:27955623
The role of charged surface residues in the binding ability of small hubs in protein-protein interaction networks. PMID:27857564
HINT: a database of annotated protein-protein interactions and their homologs. PMID:27857549
In silico identification of essential proteins in Corynebacterium pseudotuberculosis based on protein-protein interaction networks. PMID:27814699
Integrating network, sequence and functional features using machine learning approaches towards identification of novel Alzheimer genes. PMID:27756223
The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. PMID:27374120
SorghumFDB: sorghum functional genomics database with multidimensional network analysis. PMID:27352859
APP Is a Context-Sensitive Regulator of the Hippocampal Presynaptic Active Zone. PMID:27092780
A Network of Splice Isoforms for the Mouse. PMID:27079421
Computational Reconstruction of NFκB Pathway Interaction Mechanisms during Prostate Cancer. PMID:27078000
Biomolecular Relationships Discovered from Biological Labyrinth and Lost in Ocean of Literature: Community Efforts Can Rescue Until Automated Artificial Intelligence Takes Over. PMID:27066067
libChEBI: an API for accessing the ChEBI database. PMID:26933452
Comparative analysis of housekeeping and tissue-selective genes in human based on network topologies and biological properties. PMID:26897376
Prediction and characterization of protein-protein interaction network in Bacillus licheniformis WX-02. PMID:26782814
Rsite2: an efficient computational method to predict the functional sites of noncoding RNAs. PMID:26751501
Use of the BioGRID Database for Analysis of Yeast Protein and Genetic Interactions. PMID:26729909
Bioinformatics Mining and Modeling Methods for the Identification of Disease Mechanisms in Neurodegenerative Disorders. PMID:26690135
Application of Gene Expression Trajectories Initiated from ErbB Receptor Activation Highlights the Dynamics of Divergent Promoter Usage. PMID:26658111
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
Predicting Pharmacodynamic Drug-Drug Interactions through Signaling Propagation Interference on Protein-Protein Interaction Networks. PMID:26469276
Genome-wide prediction of prokaryotic two-component system networks using a sequence-based meta-predictor. PMID:26384938
Network Modules of the Cross-Species Genotype-Phenotype Map Reflect the Clinical Severity of Human Diseases. PMID:26301634
KnowEnG: a knowledge engine for genomics. PMID:26205246
Self-Organizing Feature Maps Identify Proteins Critical to Learning in a Mouse Model of Down Syndrome. PMID:26111164
Publisher’s Note:Abstraction for data integration:Fusing mammalian molecular, cellular and phenotype big datasets for better knowledge extraction. PMID:26101093
Improving 3D Genome Reconstructions Using Orthologous and Functional Constraints. PMID:26000633
Urothelial cancer gene regulatory networks inferred from large-scale RNAseq, Bead and Oligo gene expression data. PMID:25971253
CEMTDD: The database for elucidating the relationships among herbs, compounds, targets and related diseases for Chinese ethnic minority traditional drugs. PMID:25970778
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
Identifying module biomarker in type 2 diabetes mellitus by discriminative area of functional activity. PMID:25888350
Computational analysis of the LRRK2 interactome. PMID:25737818
Pathway mapping and development of disease-specific biomarkers: protein-based network biomarkers. PMID:25560835
MicroRNA Dysregulation, Gene Networks, and Risk for Schizophrenia in 22q11.2 Deletion Syndrome. PMID:25484875
OntoGene web services for biomedical text mining. PMID:25472638
Diffusion of information throughout the host interactome reveals gene expression variations in network proximity to target proteins of hepatitis C virus. PMID:25461596
Community structure detection for overlapping modules through mathematical programming in protein interaction networks. PMID:25412367
GroupRank: rank candidate genes in PPI network by differentially expressed gene groups. PMID:25330105
Gene expression profiles on predicting protein interaction network and exploring of new treatments for lung cancer. PMID:25205123
Lean Big Data integration in systems biology and systems pharmacology. PMID:25109570
Proteome-wide analysis of human disease mutations in short linear motifs: neglected players in cancer? PMID:25057855
The human plasma membrane peripherome: visualization and analysis of interactions. PMID:25057483
Interaction networks of prion, prionogenic and prion-like proteins in budding yeast, and their role in gene regulation. PMID:24972093
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
Stringent homology-based prediction of H. sapiens-M. tuberculosis H37Rv protein-protein interactions. PMID:24708540
Protein-protein interaction detection: methods and analysis. PMID:24693427
Modelling the yeast interactome. PMID:24589662
Corbi: a new R package for biological network alignment and querying. PMID:24565104
Stringent DDI-based prediction of H. sapiens-M. tuberculosis H37Rv protein-protein interactions. PMID:24564941
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
Methods and approaches in the topology-based analysis of biological pathways. PMID:24133454
A probabilistic model of neutral and selective dynamics of protein network evolution. PMID:23931333
Shared protein complex subunits contribute to explaining disrupted co-occurrence. PMID:23874172
Module-based breast cancer classification. PMID:23819260
Mining breast cancer genes with a network based noise-tolerant approach. PMID:23799982
Structure and non-structure of centrosomal proteins. PMID:23671615
An integrated approach to uncover driver genes in breast cancer methylation genomes. PMID:23579546
The potential of text mining in data integration and network biology for plant research: a case study on Arabidopsis. PMID:23532071
Using the OntoGene pipeline for the triage task of BioCreative 2012. PMID:23396322
Visualization of protein interaction networks: problems and solutions. PMID:23368786
PCDq: human protein complex database with quality index which summarizes different levels of evidences of protein complexes predicted from h-invitational protein-protein interactions integrative dataset. PMID:23282181
Wiki-pi: a web-server of annotated human protein-protein interactions to aid in discovery of protein function. PMID:23209562
Proteomics-based methods for discovery, quantification, and validation of protein-protein interactions. PMID:23157382
Protein stickiness, rather than number of functional protein-protein interactions, predicts expression noise and plasticity in yeast. PMID:23017156
An integrated approach to identify causal network modules of complex diseases with application to colorectal cancer. PMID:22967703
Multiple biomarker tissue arrays: A computational approach to identifying protein-protein interactions in the EGFR/ERK signalling pathway. PMID:22937740
Sets2Networks: network inference from repeated observations of sets. PMID:22824380
Detecting mutually exclusive interactions in protein-protein interaction maps. PMID:22715412
DroPNet: a web portal for integrated analysis of Drosophila protein-protein interaction networks. PMID:22641854
Functional and topological properties in hepatocellular carcinoma transcriptome. PMID:22539975
Network- and attribute-based classifiers can prioritize genes and pathways for autism spectrum disorders and intellectual disability. PMID:22499558
Bayesian integration of networks without gold standards. PMID:22492647
PrionHome: a database of prions and other sequences relevant to prion phenomena. PMID:22363733
An integer linear programming approach for finding deregulated subgraphs in regulatory networks. PMID:22210863
Dynamical analysis of yeast protein interaction network during the sake brewing process. PMID:22203560
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
Identification of dysfunctional modules and disease genes in congenital heart disease by a network-based approach. PMID:22136190
Network analysis of microRNAs and their regulation in human ovarian cancer. PMID:22050994
Chronic morphine alters the presynaptic protein profile: identification of novel molecular targets using proteomics and network analysis. PMID:22043286
Proteomic analysis of Col11a1-associated protein complexes. PMID:22038862
An interaction network predicted from public data as a discovery tool: application to the Hsp90 molecular chaperone machine. PMID:22022502
Meta-analysis and genome-wide interpretation of genetic susceptibility to drug addiction. PMID:21999673
Network-based prediction and analysis of HIV dependency factors. PMID:21966263
A physical interaction network of dengue virus and human proteins. PMID:21911577
Application of computational systems biology to explore environmental toxicity hazards. PMID:21846611
Computational simulations to predict creatine kinase-associated factors: protein-protein interaction studies of brain and muscle types of creatine kinases. PMID:21826261
Computational approach to identify enzymes that are potential therapeutic candidates for psoriasis. PMID:21822480
The cytoplasmic cyclophilin from Azotobacter vinelandii interacts with phosphate acetyltransferase isoforms enhancing their in vitro activity. PMID:21773943
Reactome pathway analysis to enrich biological discovery in proteomics data sets. PMID:21751369
Integrative computational biology for cancer research. PMID:21691773
Noise reduction in protein-protein interaction graphs by the implementation of a novel weighting scheme. PMID:21679454
PRIN: a predicted rice interactome network. PMID:21575196
Network-based pipeline for analyzing MS data: an application toward liver cancer. PMID:21410269
Supervised learning and prediction of physical interactions between human and HIV proteins. PMID:21382517
Connectedness of PPI network neighborhoods identifies regulatory hub proteins. PMID:21367871
GeneRanker: An Online System for Predicting Gene-Disease Associations for Translational Research. PMID:21347122
Comparative analysis of protein interaction networks reveals that conserved pathways are susceptible to HIV-1 interception. PMID:21342548
A machine learning approach for genome-wide prediction of morbid and druggable human genes based on systems-level data. PMID:21210975
SIDEKICK: Genomic data driven analysis and decision-making framework. PMID:21192813
Literature curation of protein interactions: measuring agreement across major public databases. PMID:21183497
Combining modularity, conservation, and interactions of proteins significantly increases precision and coverage of protein function prediction. PMID:21171995
Features analysis for identification of date and party hubs in protein interaction network of Saccharomyces Cerevisiae. PMID:21167069
Extending pathways and processes using molecular interaction networks to analyse cancer genome data. PMID:21144022
A comparative study of cancer proteins in the human protein-protein interaction network. PMID:21143787
KUPS: constructing datasets of interacting and non-interacting protein pairs with associated attributions. PMID:20952400
iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence. PMID:20940177
ChemProt: a disease chemical biology database. PMID:20935044
Protein network prediction and topological analysis in Leishmania major as a tool for drug target selection. PMID:20875130
Identifying dysfunctional crosstalk of pathways in various regions of Alzheimer's disease brains. PMID:20840725
The BioPAX community standard for pathway data sharing. PMID:20829833
The human-bacterial pathogen protein interaction networks of Bacillus anthracis, Francisella tularensis, and Yersinia pestis. PMID:20711500
Open source tool for prediction of genome wide protein-protein interaction network based on ortholog information. PMID:20684769
Mitochondrial-nuclear epistasis: implications for human aging and longevity. PMID:20601194
PPLook: an automated data mining tool for protein-protein interaction. PMID:20550717
Deciphering the Arabidopsis floral transition process by integrating a protein-protein interaction network and gene expression data. PMID:20530214
Functional features, biological pathways, and protein interaction networks of addiction-related genes. PMID:20491072
Construction of a large scale integrated map of macrophage pathogen recognition and effector systems. PMID:20470404
Molecular signaling in zebrafish development and the vertebrate phylotypic period. PMID:20433455
SZGR: a comprehensive schizophrenia gene resource. PMID:20424623
Reconstruction of gene regulatory modules in cancer cell cycle by multi-source data integration. PMID:20422009
Inference of functional relations in predicted protein networks with a machine learning approach. PMID:20376314
Building and analyzing protein interactome networks by cross-species comparisons. PMID:20353594
TopoGSA: network topological gene set analysis. PMID:20335277
Dosage sensitivity shapes the evolution of copy-number varied regions. PMID:20224824
Towards the integration of mouse databases - definition and implementation of solutions to two use-cases in mouse functional genomics. PMID:20205870
Predicting highly-connected hubs in protein interaction networks by QSAR and biological data descriptors. PMID:20198194
High-throughput discovery and characterization of fetal protein trafficking in the blood of pregnant women. PMID:20186258
Xenopus meiotic microtubule-associated interactome. PMID:20174651
Expander: from expression microarrays to networks and functions. PMID:20134430
Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana. PMID:20118918
CORNET: a user-friendly tool for data mining and integration. PMID:20053712
AtPIN: Arabidopsis thaliana protein interaction network. PMID:20043823
Expression-based network biology identifies alteration in key regulatory pathways of type 2 diabetes and associated risk/complications. PMID:19997558
MitoInteractome: mitochondrial protein interactome database, and its application in 'aging network' analysis. PMID:19958484
PutidaNET: interactome database service and network analysis of Pseudomonas putida KT2440. PMID:19958481
Phylogeny-guided interaction mapping in seven eukaryotes. PMID:19948065
Novel protein-protein interactions inferred from literature context. PMID:19924298
NAViGaTOR: Network Analysis, Visualization and Graphing Toronto. PMID:19837718
Protopia: a protein-protein interaction tool. PMID:19828077
Towards a systems biology approach to mammalian cell cycle: modeling the entrance into S phase of quiescent fibroblasts after serum stimulation. PMID:19828076
HPD: an online integrated human pathway database enabling systems biology studies. PMID:19811689
Pushing structural information into the yeast interactome by high-throughput protein docking experiments. PMID:19714207
Gastric Cancer (Biomarkers) Knowledgebase (GCBKB): A Curated and Fully Integrated Knowledgebase of Putative Biomarkers Related to Gastric Cancer. PMID:19690644
Yeast two-hybrid, a powerful tool for systems biology. PMID:19582228
BowTieBuilder: modeling signal transduction pathways. PMID:19566957
Predicting protein-protein interactions in Arabidopsis thaliana through integration of orthology, gene ontology and co-expression. PMID:19563678
Large-scale assessment of the effect of popularity on the reliability of research. PMID:19551148
Bioinformatics resources for cancer research with an emphasis on gene function and structure prediction tools. PMID:19458756
Protein-protein interaction databases: keeping up with growing interactomes. PMID:19403463
Rich can get poor: conversion of hub to non-hub proteins. PMID:19399641
Identifying disease-specific genes based on their topological significance in protein networks. PMID:19309513
Protein-protein interaction as a predictor of subcellular location. PMID:19243629
A survey of available tools and web servers for analysis of protein-protein interactions and interfaces. PMID:19240123
Enumeration of condition-dependent dense modules in protein interaction networks. PMID:19213739
High throughput interaction data reveals degree conservation of hub proteins. PMID:19209717
Dissecting the interface between signaling and transcriptional regulation in human B cells. PMID:19209707
Improved homology-driven computational validation of protein-protein interactions motivated by the evolutionary gene duplication and divergence hypothesis. PMID:19152684
Ortholog-based protein-protein interaction prediction and its application to inter-species interactions. PMID:19091010
An empirical framework for binary interactome mapping. PMID:19060904
Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome. PMID:19054114
Network integration and graph analysis in mammalian molecular systems biology. PMID:19045817
A survey of visualization tools for biological network analysis. PMID:19040716
PIG--the pathogen interaction gateway. PMID:18984614
Michigan molecular interactions r2: from interacting proteins to pathways. PMID:18978014
TCMGeneDIT: a database for associated traditional Chinese medicine, gene and disease information using text mining. PMID:18854039
The interactome: predicting the protein-protein interactions in cells. PMID:18839074
Gene mention normalization and interaction extraction with context models and sentence motifs. PMID:18834492
Mining physical protein-protein interactions from the literature. PMID:18834490
PID: the Pathway Interaction Database. PMID:18832364
iRefIndex: a consolidated protein interaction database with provenance. PMID:18823568
The use of Gene Ontology terms for predicting highly-connected 'hub' nodes in protein-protein interaction networks. PMID:18796161
Modeling synthetic lethality. PMID:18789146
Integrating protein-protein interactions and text mining for protein function prediction. PMID:18673526
Construction of a cancer-perturbed protein-protein interaction network for discovery of apoptosis drug targets. PMID:18590547
Meta-analysis approach identifies candidate genes and associated molecular networks for type-2 diabetes mellitus. PMID:18590522
Calling on a million minds for community annotation in WikiProteins. PMID:18507872
Defining a modular signalling network from the fly interactome. PMID:18489752
Inferring the role of transcription factors in regulatory networks. PMID:18460200
MassNet: a functional annotation service for protein mass spectrometry data. PMID:18448467
Cytoscape ESP: simple search of complex biological networks. PMID:18445605
Prediction of phosphotyrosine signaling networks using a scoring matrix-assisted ligand identification approach. PMID:18424801
Exploiting likely-positive and unlabeled data to improve the identification of protein-protein interaction articles. PMID:18315856
The landscape of human proteins interacting with viruses and other pathogens. PMID:18282095
Genome-wide inference of protein interaction sites: lessons from the yeast high-quality negative protein-protein interaction dataset. PMID:18281313
OpenDMAP: an open source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-type-specific gene expression. PMID:18237434
Predicting the interactome of Xanthomonas oryzae pathovar oryzae for target selection and DB service. PMID:18215330
Protein interactions in human genetic diseases. PMID:18199329
MeInfoText: associated gene methylation and cancer information from text mining. PMID:18194557
Computational prediction of protein-protein interactions. PMID:18095187
Integrative analysis for finding genes and networks involved in diabetes and other complex diseases. PMID:18045462
Assessing and combining reliability of protein interaction sources. PMID:17990508
Construction, visualisation, and clustering of transcription networks from microarray expression data. PMID:17967053
Integration of biological networks and gene expression data using Cytoscape. PMID:17947979
BNDB - the Biochemical Network Database. PMID:17910766
Structure-templated predictions of novel protein interactions from sequence information. PMID:17892321
Computation of significance scores of unweighted Gene Set Enrichment Analyses. PMID:17683603
A data integration approach for cell cycle analysis oriented to model simulation in systems biology. PMID:17678529
Natively unstructured loops differ from other loops. PMID:17658943
Reuse of structural domain-domain interactions in protein networks. PMID:17640363
Not all scale-free networks are born equal: the role of the seed graph in PPI network evolution. PMID:17616981
Transcript-level annotation of Affymetrix probesets improves the interpretation of gene expression data. PMID:17559689
GeneTrail--advanced gene set enrichment analysis. PMID:17526521
Reconstruction of human protein interolog network using evolutionary conserved network. PMID:17493278
Analysing protein-protein interaction networks of human liver cancer cell lines with diverse metastasis potential. PMID:17458561
Deciphering protein-protein interactions. Part I. Experimental techniques and databases. PMID:17397251
A cheminformatic toolkit for mining biomedical knowledge. PMID:17385012
Reactome: a knowledge base of biologic pathways and processes. PMID:17367534
An evaluation of human protein-protein interaction data in the public domain. PMID:17254303
SNAPPI-DB: a database and API of Structures, iNterfaces and Alignments for Protein-Protein Interactions. PMID:17202171
New developments in the InterPro database. PMID:17202162
Evolutionary conservation of domain-domain interactions. PMID:17184549
IntAct--open source resource for molecular interaction data. PMID:17145710
CellCircuits: a database of protein network models. PMID:17135207
MINT: the Molecular INTeraction database. PMID:17135203
DOMINO: a database of domain-peptide interactions. PMID:17135199
Michigan Molecular Interactions (MiMI): putting the jigsaw puzzle together. PMID:17130145
Parameter estimate of signal transduction pathways. PMID:17118160
cPath: open source software for collecting, storing, and querying biological pathways. PMID:17101041
Protein-protein interactions more conserved within species than across species. PMID:16854211
VIRGO: computational prediction of gene functions. PMID:16845022
APID: Agile Protein Interaction DataAnalyzer. PMID:16845013
The HUPO Brain Proteome Project--no need to hurry? PMID:16835694
Dry work in a wet world: computation in systems biology. PMID:16820781
The cognitive phenotype of Down syndrome: insights from intracellular network analysis. PMID:16815222
The interaction map of yeast: terra incognita? PMID:16762048
Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae. PMID:16762047
A database and tool, IM Browser, for exploring and integrating emerging gene and protein interaction data for Drosophila. PMID:16603075
Protein protein interactions, evolutionary rate, abundance and age. PMID:16533385
The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries. PMID:16507094
GenoLink: a graph-based querying and browsing system for investigating the function of genes and proteins. PMID:16417636
PRIDE: a public repository of protein and peptide identifications for the proteomics community. PMID:16381953
BioGRID: a general repository for interaction datasets. PMID:16381927
pSTIING: a 'systems' approach towards integrating signalling pathways, interaction and transcriptional regulatory networks in inflammation and cancer. PMID:16381926
SCOPPI: a structural classification of protein-protein interfaces. PMID:16381874
NPInter: the noncoding RNAs and protein related biomacromolecules interaction database. PMID:16381834
EMBL Nucleotide Sequence Database: developments in 2005. PMID:16381823
HomoMINT: an inferred human network based on orthology mapping of protein interactions discovered in model organisms. PMID:16351748
Data mining for protein-protein interactions in invertebrate model organisms. PMID:16158290
Text-mining and information-retrieval services for molecular biology. PMID:15998455
Filtering high-throughput protein-protein interaction data using a combination of genomic features. PMID:15833142
Atlas - a data warehouse for integrative bioinformatics. PMID:15723693
The European Bioinformatics Institute's data resources: towards systems biology. PMID:15608238
STRING: known and predicted protein-protein associations, integrated and transferred across organisms. PMID:15608232
The Biomolecular Interaction Network Database and related tools 2005 update. PMID:15608229
The EMBL Nucleotide Sequence Database. PMID:15608199
E-MSD: an integrated data resource for bioinformatics. PMID:15608192
The IntAct molecular interaction database in 2010 PubMed citations: 343.

343 articles citing: The IntAct molecular interaction database in 2010

HAUS5 Is A Potential Prognostic Biomarker With Functional Significance in Breast Cancer. PMID:35280773
An Integrative Network Approach to Identify Common Genes for the Therapeutics in Tuberculosis and Its Overlapping Non-Communicable Diseases. PMID:35153741
Locally Adjust Networks Based on Connectivity and Semantic Similarities for Disease Module Detection. PMID:34759955
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
Databases for Protein-Protein Interactions. PMID:34236665
An overview of graph databases and their applications in the biomedical domain. PMID:34003247
Genome analyses of 174 strains of Mycobacterium tuberculosis provide insight into the evolution of drug resistance and reveal potential drug targets. PMID:33750515
Structure and dynamics of membrane protein in SARS-CoV-2. PMID:33353499
MICA enhances sensitivity to cisplatin in patients with extensive small cell lung cancer via downregulation of ABCG2. PMID:32724354
Network-principled deep generative models for designing drug combinations as graph sets. PMID:32657357
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
Dissecting the Role of NF-κb Protein Family and Its Regulators in Rheumatoid Arthritis Using Weighted Gene Co-Expression Network. PMID:31824568
Qualitative transcriptional signature for predicting pathological response of colorectal cancer to FOLFOX therapy. PMID:31785020
Computer aided analysis of disease linked protein networks. PMID:31485137
Membrane protein-regulated networks across human cancers. PMID:31311925
Quantitative proteomic analysis of sperm in unexplained recurrent pregnancy loss. PMID:31288842
ResponseNet v.3: revealing signaling and regulatory pathways connecting your proteins and genes across human tissues. PMID:31114913
A Comprehensive Drosophila melanogaster Transcription Factor Interactome. PMID:30995488
Analysis of Topological Parameters of Complex Disease Genes Reveals the Importance of Location in a Biomolecular Network. PMID:30769902
Context-enriched interactome powered by proteomics helps the identification of novel regulators of macrophage activation. PMID:30303482
Evolution of In Silico Strategies for Protein-Protein Interaction Drug Discovery. PMID:30082644
MiRNA-BD: an evidence-based bioinformatics model and software tool for microRNA biomarker discovery. PMID:30081733
Automatic extraction of protein-protein interactions using grammatical relationship graph. PMID:30066644
A systems immunology approach identifies the collective impact of 5 miRs in Th2 inflammation. PMID:29875322
Systematic detection of positive selection in the human-pathogen interactome and lasting effects on infectious disease susceptibility. PMID:29799843
Determining the minimum number of protein-protein interactions required to support known protein complexes. PMID:29698482
Systematic Evaluation of Molecular Networks for Discovery of Disease Genes. PMID:29605183
A homologous mapping method for three-dimensional reconstruction of protein networks reveals disease-associated mutations. PMID:29560828
Tau Phosphorylation is Impacted by Rare AKAP9 Mutations Associated with Alzheimer Disease in African Americans. PMID:29516269
Protein-protein interaction analysis to identify biomarker networks for endometriosis. PMID:29201163
The DifferentialNet database of differential protein-protein interactions in human tissues. PMID:29069447
Protein-Protein Interactions in Virus-Host Systems. PMID:28861068
Main active constituent identification in Guanxinjing capsule, a traditional Chinese medicine, for the treatment of coronary heart disease complicated with depression. PMID:28858293
The effect of Bu Zhong Yi Qi decoction on simulated weightlessness‑induced muscle atrophy and its mechanisms. PMID:28849026
Docking-based modeling of protein-protein interfaces for extensive structural and functional characterization of missense mutations. PMID:28841721
A network pharmacology-based strategy deciphers the underlying molecular mechanisms of Qixuehe Capsule in the treatment of menstrual disorders. PMID:28835770
sgnesR: An R package for simulating gene expression data from an underlying real gene network structure considering delay parameters. PMID:28676075
Study of intra-inter species protein-protein interactions for potential drug targets identification and subsequent drug design for Escherichia coli O104:H4 C277-11. PMID:28401513
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
Improved method for prioritization of disease associated lncRNAs based on ceRNA theory and functional genomics data. PMID:27992375
Bisdemethoxycurcumin exerts pro-apoptotic effects in human pancreatic adenocarcinoma cells through mitochondrial dysfunction and a GRP78-dependent pathway. PMID:27845899
Effective comparative analysis of protein-protein interaction networks by measuring the steady-state network flow using a Markov model. PMID:27766938
A Shortest Dependency Path Based Convolutional Neural Network for Protein-Protein Relation Extraction. PMID:27493967
Entropy-based divergent and convergent modular pattern reveals additive and synergistic anticerebral ischemia mechanisms. PMID:27480252
Quantitative Determination of Flexible Pharmacological Mechanisms Based On Topological Variation in Mice Anti-Ischemic Modular Networks. PMID:27383195
Reconstruction and Application of Protein-Protein Interaction Network. PMID:27338356
Endophenotype Network Models: Common Core of Complex Diseases. PMID:27278246
Guizhi-Shaoyao-Zhimu decoction attenuates rheumatoid arthritis partially by reversing inflammation-immune system imbalance. PMID:27277474
Review on Graph Clustering and Subgraph Similarity Based Analysis of Neurological Disorders. PMID:27258269
Systematic analysis of the molecular mechanism underlying atherosclerosis using a text mining approach. PMID:27251057
MicroRNA-140-5p and SMURF1 regulate pulmonary arterial hypertension. PMID:27214554
Revealing the Effects of the Herbal Pair of Euphorbia kansui and Glycyrrhiza on Hepatocellular Carcinoma Ascites with Integrating Network Target Analysis and Experimental Validation. PMID:27143956
A Network of Splice Isoforms for the Mouse. PMID:27079421
Systems psychopharmacology: A network approach to developing novel therapies. PMID:27014599
Dissecting dysfunctional crosstalk pathways regulated by miRNAs during glioma progression. PMID:27013589
The Impact of Mass Spectrometry-Based Proteomics on Fundamental Discoveries in Virology. PMID:26958735
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
Topological characteristics of target genes regulated by abiotic-stress-responsible miRNAs in a rice interactome network. PMID:26830287
Proteomics and bioinformatics analysis of mouse hypothalamic neurogenesis with or without EPHX2 gene deletion. PMID:26722453
Inferring plant microRNA functional similarity using a weighted protein-protein interaction network. PMID:26538106
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
A predicted protein interactome identifies conserved global networks and disease resistance subnetworks in maize. PMID:26089837
Tools for visualization and analysis of molecular networks, pathways, and -omics data. PMID:26082651
A systematic investigation based on microRNA-mediated gene regulatory network reveals that dysregulation of microRNA-19a/Cyclin D1 axis confers an oncogenic potential and a worse prognosis in human hepatocellular carcinoma. PMID:25985117
Deciphering the pharmacological mechanism of the Chinese formula huanglian-jie-du decoction in the treatment of ischemic stroke using a systems biology-based strategy. PMID:25937634
Predicted protein-protein interactions in the moss Physcomitrella patens: a new bioinformatic resource. PMID:25885037
A DIseAse MOdule Detection (DIAMOnD) algorithm derived from a systematic analysis of connectivity patterns of disease proteins in the human interactome. PMID:25853560
Uncovering pharmacological mechanisms of Wu-tou decoction acting on rheumatoid arthritis through systems approaches: drug-target prediction, network analysis and experimental validation. PMID:25820382
Module organization and variance in protein-protein interaction networks. PMID:25797237
The identification of specific methylation patterns across different cancers. PMID:25774687
Efficient prediction of progesterone receptor interactome using a support vector machine model. PMID:25741764
cisPath: an R/Bioconductor package for cloud users for visualization and management of functional protein interaction networks. PMID:25708840
Accurate multiple network alignment through context-sensitive random walk. PMID:25707987
IIIDB: a database for isoform-isoform interactions and isoform network modules. PMID:25707505
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
Network-based association of hypoxia-responsive genes with cardiovascular diseases. PMID:25530704
Systems Medicine: from molecular features and models to the clinic in COPD. PMID:25471042
Comprehensive analysis of microRNA-regulated protein interaction network reveals the tumor suppressive role of microRNA-149 in human hepatocellular carcinoma via targeting AKT-mTOR pathway. PMID:25424347
A systems biology strategy to identify molecular mechanisms of action and protein indicators of traumatic brain injury. PMID:25399920
Comparative study of computational methods for reconstructing genetic networks of cancer-related pathways. PMID:25288880
Proteome-wide subcellular topologies of E. coli polypeptides database (STEPdb). PMID:25210196
Transcriptome sequencing of a large human family identifies the impact of rare noncoding variants. PMID:25192044
Revealing molecular mechanisms by integrating high-dimensional functional screens with protein interaction data. PMID:25188415
Construction and analysis of the protein-protein interaction networks based on gene expression profiles of Parkinson's disease. PMID:25170921
A systems biology-based approach to uncovering the molecular mechanisms underlying the effects of dragon's blood tablet in colitis, involving the integration of chemical analysis, ADME prediction, and network pharmacology. PMID:25068885
Functional gene groups are concentrated within chromosomes, among chromosomes and in the nuclear space of the human genome. PMID:25056310
Large Scale Chemical Cross-linking Mass Spectrometry Perspectives. PMID:25045217
Building a hierarchical organization of protein complexes out of protein association data. PMID:24978199
Comparative analysis of human tissue interactomes reveals factors leading to tissue-specific manifestation of hereditary diseases. PMID:24921629
Increasing the precision of orthology-based complex prediction through network alignment. PMID:24918034
Plant systems biology: insights, advances and challenges. PMID:24671625
M-Finder: Uncovering functionally associated proteins from interactome data integrated with GO annotations. PMID:24565382
Genome-wide structural modelling of TCR-pMHC interactions. PMID:24564684
A systems biology-based investigation into the therapeutic effects of Gansui Banxia Tang on reversing the imbalanced network of hepatocellular carcinoma. PMID:24561634
Proteomic strategies for the discovery of novel diagnostic and therapeutic targets for infectious diseases. PMID:24488789
Computational Prediction of Protein-Protein Interaction Networks: Algo-rithms and Resources. PMID:24396273
Identification of GRB2 and GAB1 coexpression as an unfavorable prognostic factor for hepatocellular carcinoma by a combination of expression profile and network analysis. PMID:24391994
Interaction proteome of human Hippo signaling: modular control of the co-activator YAP1. PMID:24366813
Signatures of pleiotropy, economy and convergent evolution in a domain-resolved map of human-virus protein-protein interaction networks. PMID:24339775
Molecular signatures of antibody responses derived from a systems biology study of five human vaccines. PMID:24336226
A predicted protein interactome for rice. PMID:24279740
Specialized Dynamical Properties of Promiscuous Residues Revealed by Simulated Conformational Ensembles. PMID:24250278
Annotating cancer variants and anti-cancer therapeutics in reactome. PMID:24213504
Simple topological features reflect dynamics and modularity in protein interaction networks. PMID:24130468
Identification of small exonic CNV from whole-exome sequence data and application to autism spectrum disorder. PMID:24094742
Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals. PMID:24092820
Detecting non-uniform clusters in large-scale interaction graphs. PMID:24050498
Stable isotope metabolic labeling-based quantitative phosphoproteomic analysis of Arabidopsis mutants reveals ethylene-regulated time-dependent phosphoproteins and putative substrates of constitutive triple response 1 kinase. PMID:24043427
PainNetworks: a web-based resource for the visualisation of pain-related genes in the context of their network associations. PMID:24036287
Learning a Markov Logic network for supervised gene regulatory network inference. PMID:24028533
Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology. PMID:23895341
Network-based analysis of genome wide association data provides novel candidate genes for lipid and lipoprotein traits. PMID:23882023
Cloud-based uniform ChIP-Seq processing tools for modENCODE and ENCODE. PMID:23875683
Target essentiality and centrality characterize drug side effects. PMID:23874169
GoSynthetic database tool to analyse natural and engineered molecular processes. PMID:23813641
A context-sensitive framework for the analysis of human signalling pathways in molecular interaction networks. PMID:23812986
iBIG: an integrative network tool for supporting human disease mechanism studies. PMID:23809576
Arabidopsis MSI1 connects LHP1 to PRC2 complexes. PMID:23778966
ResponseNet2.0: Revealing signaling and regulatory pathways connecting your proteins and genes--now with human data. PMID:23761447
The functional interactome landscape of the human histone deacetylase family. PMID:23752268
Hypoxamirs in Pulmonary Hypertension: Breathing New Life into Pulmonary Vascular Research. PMID:23745175
Glutathione S-transferases interact with AMP-activated protein kinase: evidence for S-glutathionylation and activation in vitro. PMID:23741294
Integrated analysis of recurrent properties of cancer genes to identify novel drivers. PMID:23718799
β1- and αv-class integrins cooperate to regulate myosin II during rigidity sensing of fibronectin-based microenvironments. PMID:23708002
A systems biology-based investigation into the pharmacological mechanisms of wu tou tang acting on rheumatoid arthritis by integrating network analysis. PMID:23690848
Maternal factors required for oocyte developmental competence in mice: transcriptome analysis of non-surrounded nucleolus (NSN) and surrounded nucleolus (SN) oocytes. PMID:23673344
Interfacing cellular networks of S. cerevisiae and E. coli: connecting dynamic and genetic information. PMID:23663484
Gene expression analysis distinguishes tissue-specific and gender-related functions among adult Ascaris suum tissues. PMID:23572074
Alternative splicing and protein interaction data sets. PMID:23563420
SH3 interactome conserves general function over specific form. PMID:23549480
Network pharmacology strategies toward multi-target anticancer therapies: from computational models to experimental design principles. PMID:23530504
Novel semantic similarity measure improves an integrative approach to predicting gene functional associations. PMID:23497449
Proteome-wide prediction of self-interacting proteins based on multiple properties. PMID:23422585
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
Identification of additional proteins in differential proteomics using protein interaction networks. PMID:23386401
Equal opportunity for low-degree network nodes: a PageRank-based method for protein target identification in metabolic graphs. PMID:23382878
Predicting PDZ domain mediated protein interactions from structure. PMID:23336252
mirTarPri: improved prioritization of microRNA targets through incorporation of functional genomics data. PMID:23326485
PPInterFinder--a mining tool for extracting causal relations on human proteins from literature. PMID:23325628
Importance of different types of prior knowledge in selecting genome-wide findings for follow-up. PMID:23307621
Inferring the Brassica rapa Interactome Using Protein-Protein Interaction Data from Arabidopsis thaliana. PMID:23293649
TranSeqAnnotator: large-scale analysis of transcriptomic data. PMID:23282024
Discovering pathway cross-talks based on functional relations between pathways. PMID:23282018
Toward a three-dimensional view of protein networks between species. PMID:23267356
Computational prediction of protein-protein interactions in Leishmania predicted proteomes. PMID:23251492
GWIDD: a comprehensive resource for genome-wide structural modeling of protein-protein interactions. PMID:23245398
The Escherichia coli peripheral inner membrane proteome. PMID:23230279
Identification and analysis of biomarkers for mismatch repair proteins: A bioinformatic approach. PMID:23225975
BioCreative-2012 virtual issue. PMID:23221175
Identification of pharmacological targets in amyotrophic lateral sclerosis through genomic analysis of deregulated genes and pathways. PMID:23204922
The TissueNet database of human tissue protein-protein interactions. PMID:23193266
Holding our breath: The emerging and anticipated roles of microRNA in pulmonary hypertension. PMID:23130098
Activity-dependent protein dynamics define interconnected cores of co-regulated postsynaptic proteins. PMID:23035237
Tissue-specific functional networks for prioritizing phenotype and disease genes. PMID:23028291
A simple knowledge-based mining method for exploring hidden key molecules in a human biomolecular network. PMID:22979956
A network-based maximum link approach towards MS identifies potentially important roles for undetected ARRB1/2 and ACTB in liver cancer progression. PMID:22961449
Searching for Hif1-α interacting proteins in renal cell carcinoma. PMID:22926943
Dissecting the gene network of dietary restriction to identify evolutionarily conserved pathways and new functional genes. PMID:22912585
Identifying novel drug indications through automated reasoning. PMID:22911721
Protein-protein-interaction network organization of the hypusine modification system. PMID:22888148
A high-throughput approach for measuring temporal changes in the interactome. PMID:22863883
Discovering the hidden sub-network component in a ranked list of genes or proteins derived from genomic experiments. PMID:22844098
Function prediction and analysis of mycobacterium tuberculosis hypothetical proteins. PMID:22837694
atBioNet--an integrated network analysis tool for genomics and biomarker discovery. PMID:22817640
A strategy based on protein-protein interface motifs may help in identifying drug off-targets. PMID:22817115
Crowd sourcing a new paradigm for interactome driven drug target identification in Mycobacterium tuberculosis. PMID:22808064
Cancer develops, progresses and responds to therapies through restricted perturbation of the protein-protein interaction network. PMID:22806580
Combinatorial drug therapy for cancer in the post-genomic era. PMID:22781697
Integration of biological networks and pathways with genetic association studies. PMID:22777728
Viral perturbations of host networks reflect disease etiology. PMID:22761553
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
Proteome-wide prediction of protein-protein interactions from high-throughput data. PMID:22729399
Dynamical systems approach to endothelial heterogeneity. PMID:22723222
Network compression as a quality measure for protein interaction networks. PMID:22719828
DEFOG: discrete enrichment of functionally organized genes. PMID:22706384
Network-induced classification kernels for gene expression profile analysis. PMID:22697242
Tackling drought stress: receptor-like kinases present new approaches. PMID:22693282
MoNetFamily: a web server to infer homologous modules and module-module interaction networks in vertebrates. PMID:22689643
ROCS: a reproducibility index and confidence score for interaction proteomics studies. PMID:22682516
MAGNET: MicroArray Gene expression and Network Evaluation Toolkit. PMID:22669910
A topology-based metric for measuring term similarity in the gene ontology. PMID:22666244
NetAligner--a network alignment server to compare complexes, pathways and whole interactomes. PMID:22618871
Cis-acting polymorphisms affect complex traits through modifications of microRNA regulation pathways. PMID:22606281
IRView: a database and viewer for protein interacting regions. PMID:22592381
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
A framework for mapping, visualisation and automatic model creation of signal-transduction networks. PMID:22531118
Methods for visual mining of genomic and proteomic data atlases. PMID:22524279
Context-specific protein network miner--an online system for exploring context-specific protein interaction networks from the literature. PMID:22493694
System approaches reveal the molecular networks involved in neural stem cell differentiation. PMID:22492180
Integrated inference and analysis of regulatory networks from multi-level measurements. PMID:22482944
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
Protein interaction data curation: the International Molecular Exchange (IMEx) consortium. PMID:22453911
How to link ontologies and protein-protein interactions to literature: text-mining approaches and the BioCreative experience. PMID:22438567
Biocurators and biocuration: surveying the 21st century challenges. PMID:22434828
Coordination of the transcriptome and metabolome by the circadian clock. PMID:22431615
PINALOG: a novel approach to align protein interaction networks--implications for complex detection and function prediction. PMID:22419782
An Interspecies Regulatory Network Inferred from Simultaneous RNA-seq of Candida albicans Invading Innate Immune Cells. PMID:22416242
The role of structural disorder in the rewiring of protein interactions through evolution. PMID:22389433
Comparative analysis and assessment of M. tuberculosis H37Rv protein-protein interaction datasets. PMID:22369691
Prioritizing disease candidate genes by a gene interconnectedness-based approach. PMID:22369140
A classification scoring schema to validate protein interactors. PMID:22359432
Drug-target network in myocardial infarction reveals multiple side effects of unrelated drugs. PMID:22355571
HIPPIE: Integrating protein interaction networks with experiment based quality scores. PMID:22348130
ANAP: an integrated knowledge base for Arabidopsis protein interaction network analysis. PMID:22345505
Identifying gene interaction networks. PMID:22307715
TranscriptomeBrowser 3.0: introducing a new compendium of molecular interactions and a new visualization tool for the study of gene regulatory networks. PMID:22292669
A dynamic view of domain-motif interactions. PMID:22253583
Three-dimensional reconstruction of protein networks provides insight into human genetic disease. PMID:22252508
Differential network biology. PMID:22252388
IMID: integrated molecular interaction database. PMID:22238258
Channelpedia: an integrative and interactive database for ion channels. PMID:22232598
Constructing a robust protein-protein interaction network by integrating multiple public databases. PMID:22165958
Advances in omics and bioinformatics tools for systems analyses of plant functions. PMID:22156726
The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text. PMID:22151929
Classifying protein-protein interaction articles using word and syntactic features. PMID:22151252
Benchmarking of the 2010 BioCreative Challenge III text-mining competition by the BioGRID and MINT interaction databases. PMID:22151178
Minimotif Miner 3.0: database expansion and significantly improved reduction of false-positive predictions from consensus sequences. PMID:22146221
The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. PMID:22140109
Gene3D: a domain-based resource for comparative genomics, functional annotation and protein network analysis. PMID:22139938
MetaBase--the wiki-database of biological databases. PMID:22139927
Nematode.net update 2011: addition of data sets and tools featuring next-generation sequencing data. PMID:22139919
neXtProt: a knowledge platform for human proteins. PMID:22139911
A comprehensive manually curated protein-protein interaction database for the Death Domain superfamily. PMID:22135292
The UniProt-GO Annotation database in 2011. PMID:22123736
iRefR: an R package to manipulate the iRefIndex consolidated protein interaction database. PMID:22115179
Comparative interactomics with Funcoup 2.0. PMID:22110034
i-ADHoRe 3.0--fast and sensitive detection of genomic homology in extremely large data sets. PMID:22102584
InterPro in 2011: new developments in the family and domain prediction database. PMID:22096229
MINT, the molecular interaction database: 2012 update. PMID:22096227
Functional coupling analysis suggests link between the obesity gene FTO and the BDNF-NTRK2 signaling pathway. PMID:22087873
modMine: flexible access to modENCODE data. PMID:22080565
Network of Cancer Genes (NCG 3.0): integration and analysis of genetic and network properties of cancer genes. PMID:22080562
Modularity and hormone sensitivity of the Drosophila melanogaster insulin receptor/target of rapamycin interaction proteome. PMID:22068330
PINA v2.0: mining interactome modules. PMID:22067443
InterEvol database: exploring the structure and evolution of protein complex interfaces. PMID:22053089
An integrated approach to elucidate the intra-viral and viral-cellular protein interaction networks of a gamma-herpesvirus. PMID:22028648
Proteomic and functional genomic landscape of receptor tyrosine kinase and ras to extracellular signal-regulated kinase signaling. PMID:22028469
canSAR: an integrated cancer public translational research and drug discovery resource. PMID:22013161
iRefScape. A Cytoscape plug-in for visualization and data mining of protein interaction data from iRefIndex. PMID:21975162
Quantification of protein group coherence and pathway assignment using functional association. PMID:21929787
The representation of protein complexes in the Protein Ontology (PRO). PMID:21929785
Systems biology and the future of medicine. PMID:21928407
Proteomic analysis of virus-host interactions in an infectious context using recombinant viruses. PMID:21911578
A physical interaction network of dengue virus and human proteins. PMID:21911577
PATRIC: the comprehensive bacterial bioinformatics resource with a focus on human pathogenic species. PMID:21896772
ppiTrim: constructing non-redundant and up-to-date interactomes. PMID:21873645
Prediction of body fluids where proteins are secreted into based on protein interaction network. PMID:21829572
Bio::Homology::InterologWalk--a Perl module to build putative protein-protein interaction networks through interolog mapping. PMID:21767381
HelmCoP: an online resource for helminth functional genomics and drug and vaccine targets prioritization. PMID:21760913
Domain-domain interactions underlying herpesvirus-human protein-protein interaction networks. PMID:21760902
Information encoded in a network of inflammation proteins predicts clinical outcome after myocardial infarction. PMID:21756327
Reactome pathway analysis to enrich biological discovery in proteomics data sets. PMID:21751369
Simplified method to predict mutual interactions of human transcription factors based on their primary structure. PMID:21750739
Integrated bio-entity network: a system for biological knowledge discovery. PMID:21738677
An evolutionary trade-off between protein turnover rate and protein aggregation favors a higher aggregation propensity in fast degrading proteins. PMID:21731483
Visualization and biochemical analyses of the emerging mammalian 14-3-3-phosphoproteome. PMID:21725060
InterMitoBase: an annotated database and analysis platform of protein-protein interactions for human mitochondria. PMID:21718467
Pathway annotation and analysis with Reactome: the solute carrier class of membrane transporters. PMID:21712192
Mapping protein interactions by combining antibody affinity maturation and mass spectrometry. PMID:21704603
Structural principles within the human-virus protein-protein interaction network. PMID:21680884
IFIT1 is an antiviral protein that recognizes 5'-triphosphate RNA. PMID:21642987
Assessing the functional coherence of modules found in multiple-evidence networks from Arabidopsis. PMID:21612636
BioProfiling.de: analytical web portal for high-throughput cell biology. PMID:21609949
Constructing de novo biosynthetic pathways for chemical synthesis inside living cells. PMID:21591680
PRIN: a predicted rice interactome network. PMID:21575196
Protein annotation from protein interaction networks and Gene Ontology. PMID:21571095
Transcriptional landscape of bone marrow-derived very small embryonic-like stem cells during hypoxia. PMID:21569252
The multiple-specificity landscape of modular peptide recognition domains. PMID:21525870
The Protein Data Bank in Europe (PDBe): bringing structure to biology. PMID:21460450
UniProt Knowledgebase: a hub of integrated protein data. PMID:21447597
Predictive integration of gene functional similarity and co-expression defines treatment response of endothelial progenitor cells. PMID:21447198
The predicted Arabidopsis interactome resource and network topology-based systems biology analyses. PMID:21441435
Assembling a protein-protein interaction map of the SSU processome from existing datasets. PMID:21423703
Sig2BioPAX: Java tool for converting flat files to BioPAX Level 3 format. PMID:21418653
Network-based pipeline for analyzing MS data: an application toward liver cancer. PMID:21410269
Omics-based molecular target and biomarker identification. PMID:21370102
Mass spectrometry-based immuno-precipitation proteomics - the user's guide. PMID:21365760
Mapping protein interactions between Dengue virus and its human and insect hosts. PMID:21358811
Integrating multiple protein-protein interaction networks to prioritize disease genes: a Bayesian regression approach. PMID:21342540
Dynamic programming re-ranking for PPI interactor and pair extraction in full-text articles. PMID:21342534
BioGRID REST Service, BiogridPlugin2 and BioGRID WebGraph: new tools for access to interaction data at BioGRID. PMID:21300700
Predicting functions of proteins in mouse based on weighted protein-protein interaction network and protein hybrid properties. PMID:21283518
Dengue-2 structural proteins associate with human proteins to produce a coagulation and innate immune response biased interactome. PMID:21281507
PNAC: a protein nucleolar association classifier. PMID:21272300
Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology. PMID:21249183
Discovering networks of perturbed biological processes in hepatocyte cultures. PMID:21245926
A stele-enriched gene regulatory network in the Arabidopsis root. PMID:21245844
The Biomolecular Interaction Network Database in PSI-MI 2.5. PMID:21233089
Literature curation of protein interactions: measuring agreement across major public databases. PMID:21183497
Interactome mapping suggests new mechanistic details underlying Alzheimer's disease. PMID:21163940
GermOnline 4.0 is a genomics gateway for germline development, meiosis and the mitotic cell cycle. PMID:21149299
Revealing the molecular relationship between type 2 diabetes and the metabolic changes induced by a very-low-carbohydrate low-fat ketogenic diet. PMID:21143928
A computational approach to analyze the mechanism of action of the kinase inhibitor bafetinib. PMID:21124949
Computational biology for ageing. PMID:21115530
Discovering pathways by orienting edges in protein interaction networks. PMID:21109539
MIPS: curated databases and comprehensive secondary data resources in 2010. PMID:21109531
DIMA 3.0: Domain Interaction Map. PMID:21097782
SPIKE: a database of highly curated human signaling pathways. PMID:21097778
dictyBase update 2011: web 2.0 functionality and the initial steps towards a genome portal for the Amoebozoa. PMID:21087999
Genetic associations of variants in genes encoding HIV-dependency factors required for HIV-1 infection. PMID:21083371
BISC: binary subcomplexes in proteins database. PMID:21081561
ConsensusPathDB: toward a more complete picture of cell biology. PMID:21071422
Pathway Commons, a web resource for biological pathway data. PMID:21071392
Reactome: a database of reactions, pathways and biological processes. PMID:21067998
Concept and application of a computational vaccinology workflow. PMID:21067549
CPLA 1.0: an integrated database of protein lysine acetylation. PMID:21059677
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. PMID:21045058
DroID 2011: a comprehensive, integrated resource for protein, transcription factor, RNA and gene interactions for Drosophila. PMID:21036869
TcoF-DB: dragon database for human transcription co-factors and transcription factor interacting proteins. PMID:20965969
PAIR: the predicted Arabidopsis interactome resource. PMID:20952401
HitPredict: a database of quality assessed protein-protein interactions in nine species. PMID:20947562
HPIDB--a unified resource for host-pathogen interactions. PMID:20946599
Prediction of human protein-protein interaction by a mixed Bayesian model and its application to exploring underlying cancer-related pathway crosstalk. PMID:20943681
A computational tool for identifying minimotifs in protein-protein interactions and improving the accuracy of minimotif predictions. PMID:20938975
Human protein reference database and human proteinpedia as discovery resources for molecular biotechnology. PMID:20927658
DAnCER: disease-annotated chromatin epigenetics resource. PMID:20876685
Synthetic lethal screen of an EGFR-centered network to improve targeted therapies. PMID:20858866
MatrixDB, the extracellular matrix interaction database. PMID:20852260
TRIP Database: a manually curated database of protein-protein interactions for mammalian TRP channels. PMID:20851834
Candidate gene prioritization by network analysis of differential expression using machine learning approaches. PMID:20840752
Viral organization of human proteins. PMID:20827298
Molecular mechanistic associations of human diseases. PMID:20815942
The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*. PMID:20727200
Minimum information about a protein affinity reagent (MIAPAR). PMID:20622827
Protein-protein interactions essentials: key concepts to building and analyzing interactome networks. PMID:20589078
The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function. PMID:20576703
Stress signaling by Tec tyrosine kinase in the ischemic myocardium. PMID:20543088
Improved microarray-based decision support with graph encoded interactome data. PMID:20419106
Mapping plant interactomes using literature curated and predicted protein-protein interaction data sets. PMID:20371643
Construction and analysis of protein-protein interaction networks. PMID:20334628
Visualization of omics data for systems biology. PMID:20195258
The 2010 Nucleic Acids Research Database Issue and online Database Collection: a community of data resources. PMID:19965766
The European Bioinformatics Institute's data resources. PMID:19934258
PSICQUIC and PSISCORE: accessing and scoring molecular interactions PubMed citations: 141.

141 articles citing: PSICQUIC and PSISCORE: accessing and scoring molecular interactions

PEPPI: Whole-proteome Protein-protein Interaction Prediction through Structure and Sequence Similarity, Functional Association, and Machine Learning. PMID:35662463
HOX Protein Activity Regulation by Cellular Localization. PMID:34940503
Obsessive-Compulsive Disorder Interactome Profile Analysis: A Perspective From Molecular Mechanism. PMID:34925715
A multitask transfer learning framework for the prediction of virus-human protein-protein interactions. PMID:34837942
Gene Ontology curation of the blood-brain barrier to improve the analysis of Alzheimer's and other neurological diseases. PMID:34697638
Interactome of human and SARS-CoV-2 proteins to identify human hub proteins associated with comorbidities. PMID:34655901
Looking for pathways related to COVID-19: confirmation of pathogenic mechanisms by SARS-CoV-2-host interactome. PMID:34385425
Contextualized Protein-Protein Interactions. PMID:33511361
Towards a unified open access dataset of molecular interactions. PMID:33262342
IHP-PING-generating integrated human protein-protein interaction networks on-the-fly. PMID:33129201
The BioGRID database: A comprehensive biomedical resource of curated protein, genetic, and chemical interactions. PMID:33070389
PINOT: an intuitive resource for integrating protein-protein interactions. PMID:32527260
COVID-19: viral-host interactome analyzed by network based-approach model to study pathogenesis of SARS-CoV-2 infection. PMID:32522207
The role of 3'UTR-protein complexes in the regulation of protein multifunctionality and subcellular localization. PMID:32484544
The human DEPhOsphorylation Database DEPOD: 2019 update. PMID:31836896
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
Reconstructing signaling pathways using regular language constrained paths. PMID:31510694
The Methods Employed in Mass Spectrometric Analysis of Posttranslational Modifications (PTMs) and Protein-Protein Interactions (PPIs). PMID:31347048
Protein-Protein Interaction Analysis of Common Top Genes in Obsessive-Compulsive Disorder (OCD) and Schizophrenia: Towards New Drug Approach Obsessive-Compulsive disorder (OCD) and Schizophrenia Comorbidity Gene Analysis. PMID:31086558
CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination. PMID:30793173
APID database: redefining protein-protein interaction experimental evidences and binary interactomes. PMID:30715274
Proteome-wide, Structure-Based Prediction of Protein-Protein Interactions/New Molecular Interactions Viewer. PMID:30679268
Modulation of auxin and cytokinin responses by early steps of the phenylpropanoid pathway. PMID:30419822
Leveraging Experimental Details for an Improved Understanding of Host-Pathogen Interactome. PMID:30040202
Protein-protein interactions of human viruses. PMID:30031213
Identification of Antifungal Targets Based on Computer Modeling. PMID:29973534
Host lipidome analysis during rhinovirus replication in HBECs identifies potential therapeutic targets. PMID:29946055
Identification of Central Regulators of Calcium Signaling and ECM-Receptor Interaction Genetically Associated With the Progression and Recurrence of Atrial Fibrillation. PMID:29868113
Aberration hubs in protein interaction networks highlight actionable targets in cancer. PMID:29861861
Low-level laser irradiation induces a transcriptional myotube-like profile in C2C12 myoblasts. PMID:29717386
New perspectives: systems medicine in cardiovascular disease. PMID:29699591
Mapping the tumour human leukocyte antigen (HLA) ligandome by mass spectrometry. PMID:29658117
SPV: a JavaScript Signaling Pathway Visualizer. PMID:29590303
Comparative Protein Interaction Network Analysis Identifies Shared and Distinct Functions for the Human ROCO Proteins. PMID:29513927
Network modeling of kinase inhibitor polypharmacology reveals pathways targeted in chemical screens. PMID:29023490
Protein-Protein Interactions in Virus-Host Systems. PMID:28861068
Proteomics Standards Initiative: Fifteen Years of Progress and Future Work. PMID:28849660
Perturbed human sub-networks by Fusobacterium nucleatum candidate virulence proteins. PMID:28793925
Unraveling a tumor type-specific regulatory core underlying E2F1-mediated epithelial-mesenchymal transition to predict receptor protein signatures. PMID:28775339
Integration of miRNA and mRNA expression profiles reveals microRNA-regulated networks during muscle wasting in cardiac cachexia. PMID:28765595
Exploring the cross talk between ER stress and inflammation in age-related macular degeneration. PMID:28742151
MINERVA-a platform for visualization and curation of molecular interaction networks. PMID:28725475
Pathways on demand: automated reconstruction of human signaling networks. PMID:28725467
Endothelium-Independent Primitive Myxoid Vascularization Creates Invertebrate-Like Channels to Maintain Blood Supply in Optic Gliomas. PMID:28606795
Protein-Protein Interactions: Gene Acronym Redundancies and Current Limitations Precluding Automated Data Integration. PMID:28250396
Protein Bioinformatics Databases and Resources. PMID:28150231
Glycosaminoglycanomics: where we are. PMID:27900575
Genome, transcriptome and proteome: the rise of omics data and their integration in biomedical sciences. PMID:27881428
Coupling an EML4-ALK-centric interactome with RNA interference identifies sensitizers to ALK inhibitors. PMID:27811184
Path2enet: generation of human pathway-derived networks in an expression specific context. PMID:27801297
HIPPIE v2.0: enhancing meaningfulness and reliability of protein-protein interaction networks. PMID:27794551
Revealing disease-associated pathways by network integration of untargeted metabolomics. PMID:27479327
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
Gene regulation knowledge commons: community action takes care of DNA binding transcription factors. PMID:27270715
Tyrosine Kinase Signaling in Clear Cell and Papillary Renal Cell Carcinoma Revealed by Mass Spectrometry-Based Phosphotyrosine Proteomics. PMID:27220961
Reactome from a WikiPathways Perspective. PMID:27203685
APID interactomes: providing proteome-based interactomes with controlled quality for multiple species and derived networks. PMID:27131791
Using biological networks to integrate, visualize and analyze genomics data. PMID:27036106
MONGKIE: an integrated tool for network analysis and visualization for multi-omics data. PMID:26987515
Fundamentals of protein interaction network mapping. PMID:26681426
Drug target prioritization by perturbed gene expression and network information. PMID:26615774
A Pan-Cancer Catalogue of Cancer Driver Protein Interaction Interfaces. PMID:26485003
BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology. PMID:26481362
Exploring novel mechanistic insights in Alzheimer's disease by assessing reliability of protein interactions. PMID:26346705
Integrated inference and evaluation of host-fungi interaction networks. PMID:26300851
The MI bundle: enabling network and structural biology in genome visualization tools. PMID:26209801
A Comprehensive Inter-Tissue Crosstalk Analysis Underlying Progression and Control of Obesity and Diabetes. PMID:26202695
Relationships between predicted moonlighting proteins, human diseases, and comorbidities from a network perspective. PMID:26157390
PrOnto database : GO term functional dissimilarity inferred from biological data. PMID:26089836
Tools for visualization and analysis of molecular networks, pathways, and -omics data. PMID:26082651
Extreme multifunctional proteins identified from a human protein interaction network. PMID:26054620
ProteINSIDE to Easily Investigate Proteomics Data from Ruminants: Application to Mine Proteome of Adipose and Muscle Tissues in Bovine Foetuses. PMID:26000831
MyProteinNet: build up-to-date protein interaction networks for organisms, tissues and user-defined contexts. PMID:25990735
Visualisation of BioPAX Networks using BioLayout Express (3D). PMID:25949802
A review on computational systems biology of pathogen-host interactions. PMID:25914674
Inbreeding Affects Gene Expression Differently in Two Self-Incompatible Arabidopsis lyrata Populations with Similar Levels of Inbreeding Depression. PMID:25855783
Comprehensive data resources and analytical tools for pathological association of aminoacyl tRNA synthetases with cancer. PMID:25824651
Harnessing the heart of big data. PMID:25814682
Shared resources, shared costs--leveraging biocuration resources. PMID:25776020
Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study. PMID:25652942
A visual review of the interactome of LRRK2: Using deep-curated molecular interaction data to represent biology. PMID:25648416
The BioJS article collection of open source components for biological data visualisation. PMID:25580221
The BioGRID interaction database: 2015 update. PMID:25428363
MatrixDB, the extracellular matrix interaction database: updated content, a new navigator and expanded functionalities. PMID:25378329
The human DEPhOsphorylation database DEPOD: a 2015 update. PMID:25332398
Affinity purification-mass spectrometry and network analysis to understand protein-protein interactions. PMID:25275790
VirusMentha: a new resource for virus-host protein interactions. PMID:25217587
PsicquicGraph, a BioJS component to visualize molecular interactions from PSICQUIC servers. PMID:25075287
Pogo-like transposases have been repeatedly domesticated into CENP-B-related proteins. PMID:25062917
Using in vivo biotinylated ubiquitin to describe a mitotic exit ubiquitome from human cells. PMID:24857844
R-based software for the integration of pathway data into bioinformatic algorithms. PMID:24833336
A method for predicting protein-protein interaction types. PMID:24625764
BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains. PMID:24495517
Computational Prediction of Protein-Protein Interaction Networks: Algo-rithms and Resources. PMID:24396273
Differential expression of serum/plasma proteins in various infectious diseases: specific or nonspecific signatures. PMID:24293340
Profiling of Parkin-binding partners using tandem affinity purification. PMID:24244333
The Reactome pathway knowledgebase. PMID:24243840
PATRIC, the bacterial bioinformatics database and analysis resource. PMID:24225323
Simple topological features reflect dynamics and modularity in protein interaction networks. PMID:24130468
Pathways of Toxicity. PMID:24127042
yApoptosis: yeast apoptosis database. PMID:24082050
Capturing cooperative interactions with the PSI-MI format. PMID:24067240
mentha: a resource for browsing integrated protein-interaction networks. PMID:23900247
GeneMANIA prediction server 2013 update. PMID:23794635
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
A new reference implementation of the PSICQUIC web service. PMID:23671334
Towards the collaborative curation of the registry underlying Identifiers.org. PMID:23584831
Novel semantic similarity measure improves an integrative approach to predicting gene functional associations. PMID:23497449
Linking proteomic and transcriptional data through the interactome and epigenome reveals a map of oncogene-induced signaling. PMID:23408876
The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies. PMID:23398680
'Omics' approaches to understanding interstitial cystitis/painful bladder syndrome/bladder pain syndrome. PMID:23346481
Visual data mining of biological networks: one size does not fit all. PMID:23341759
Adding protein context to the human protein-protein interaction network to reveal meaningful interactions. PMID:23300433
Teaching the fundamentals of biological data integration using classroom games. PMID:23300402
Inferring the Brassica rapa Interactome Using Protein-Protein Interaction Data from Arabidopsis thaliana. PMID:23293649
The Disease and Gene Annotations (DGA): an annotation resource for human disease. PMID:23197658
InnateDB: systems biology of innate immunity and beyond--recent updates and continuing curation. PMID:23180781
The ConsensusPathDB interaction database: 2013 update. PMID:23143270
A travel guide to Cytoscape plugins. PMID:23132118
TRIP database 2.0: a manually curated information hub for accessing TRP channel interaction network. PMID:23071747
Popular computational methods to assess multiprotein complexes derived from label-free affinity purification and mass spectrometry (AP-MS) experiments. PMID:23071097
SAMNet: a network-based approach to integrate multi-dimensional high throughput datasets. PMID:23060147
Ten years of standardizing proteomic data: a report on the HUPO-PSI Spring Workshop: April 12-14th, 2012, San Diego, USA. PMID:22969026
Analyzing protein-protein interactions from affinity purification-mass spectrometry data with SAINT. PMID:22948729
Public domain databases for medicinal chemistry. PMID:22731701
IntScore: a web tool for confidence scoring of biological interactions. PMID:22649056
Computational and informatics strategies for identification of specific protein interaction partners in affinity purification mass spectrometry experiments. PMID:22611043
Swimming upstream: identifying proteomic signals that drive transcriptional changes using the interactome and multiple "-omics" datasets. PMID:22482945
Protein interaction data curation: the International Molecular Exchange (IMEx) consortium. PMID:22453911
HIPPIE: Integrating protein interaction networks with experiment based quality scores. PMID:22348130
The IntAct molecular interaction database in 2012. PMID:22121220
iRefR: an R package to manipulate the iRefIndex consolidated protein interaction database. PMID:22115179
TopFIND 2.0--linking protein termini with proteolytic processing and modifications altering protein function. PMID:22102574
MINT, the molecular interaction database: 2012 update. PMID:22096227
canSAR: an integrated cancer public translational research and drug discovery resource. PMID:22013161
ChEMBL: a large-scale bioactivity database for drug discovery. PMID:21948594
Minimum information about a bioactive entity (MIABE). PMID:21878981
Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions PubMed citations: 139.

139 articles citing: Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions

The Landscape of Virus-Host Protein-Protein Interaction Databases. PMID:35910656
The Intricacy of the Viral-Human Protein Interaction Networks: Resources, Data, and Analyses. PMID:35531299
Harmonizing model organism data in the Alliance of Genome Resources. PMID:35380658
Interactomes: Experimental and In Silico Approaches. PMID:35113398
ECO: the Evidence and Conclusion Ontology, an update for 2022. PMID:34986598
The protein-protein interaction ontology: for better representing and capturing the biological context of protein interaction. PMID:34789143
The IntAct database: efficient access to fine-grained molecular interaction data. PMID:34761267
Databases for Protein-Protein Interactions. PMID:34236665
CausalBuilder: bringing the MI2CAST causal interaction annotation standard to the curator. PMID:33547799
Towards a unified open access dataset of molecular interactions. PMID:33262342
How to Annotate and Submit a Short Linear Motif to the Eukaryotic Linear Motif Resource. PMID:32696353
Pathway Commons 2019 Update: integration, analysis and exploration of pathway data. PMID:31647099
Conserved Central Intraviral Protein Interactome of the Herpesviridae Family. PMID:31575665
The Methods Employed in Mass Spectrometric Analysis of Posttranslational Modifications (PTMs) and Protein-Protein Interactions (PPIs). PMID:31347048
Membrane protein-regulated networks across human cancers. PMID:31311925
CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination. PMID:30793173
The BioGRID interaction database: 2019 update. PMID:30476227
Complex Portal 2018: extended content and enhanced visualization tools for macromolecular complexes. PMID:30357405
Leveraging Experimental Details for an Improved Understanding of Host-Pathogen Interactome. PMID:30040202
A network map of thrombopoietin signaling. PMID:30039510
JAMI: a Java library for molecular interactions and data interoperability. PMID:29642846
Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions. PMID:29642841
The eukaryotic linear motif resource - 2018 update. PMID:29136216
DiffSLC: A graph centrality method to detect essential proteins of a protein-protein interaction network. PMID:29121073
ComplexViewer: visualization of curated macromolecular complexes. PMID:29036573
Proteomics Standards Initiative: Fifteen Years of Progress and Future Work. PMID:28849660
The amyloid interactome: Exploring protein aggregation. PMID:28249044
The use of gene interaction networks to improve the identification of cancer driver genes. PMID:28149674
Automatic query generation using word embeddings for retrieving passages describing experimental methods. PMID:28077568
The BioGRID interaction database: 2017 update. PMID:27980099
Glycosaminoglycanomics: where we are. PMID:27900575
Genome, transcriptome and proteome: the rise of omics data and their integration in biomedical sciences. PMID:27881428
DBSecSys 2.0: a database of Burkholderia mallei and Burkholderia pseudomallei secretion systems. PMID:27650316
Automated detection of discourse segment and experimental types from the text of cancer pathway results sections. PMID:27580922
HVint: A Strategy for Identifying Novel Protein-Protein Interactions in Herpes Simplex Virus Type 1. PMID:27384951
APID interactomes: providing proteome-based interactomes with controlled quality for multiple species and derived networks. PMID:27131791
Using biological networks to integrate, visualize and analyze genomics data. PMID:27036106
BioGRID: A Resource for Studying Biological Interactions in Yeast. PMID:26729913
Fundamentals of protein interaction network mapping. PMID:26681426
ELM 2016--data update and new functionality of the eukaryotic linear motif resource. PMID:26615199
Experimental detection of short regulatory motifs in eukaryotic proteins: tips for good practice as well as for bad. PMID:26581338
Tools for visualization and analysis of molecular networks, pathways, and -omics data. PMID:26082651
Development of data representation standards by the human proteome organization proteomics standards initiative. PMID:25726569
Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study. PMID:25652942
A visual review of the interactome of LRRK2: Using deep-curated molecular interaction data to represent biology. PMID:25648416
Virus-host interactomics: new insights and opportunities for antiviral drug discovery. PMID:25593595
Finding gene regulatory network candidates using the gene expression knowledge base. PMID:25490885
The BioGRID interaction database: 2015 update. PMID:25428363
VirHostNet 2.0: surfing on the web of virus/host molecular interactions data. PMID:25392406
The role of the interactome in the maintenance of deleterious variability in human populations. PMID:25261458
PsicquicGraph, a BioJS component to visualize molecular interactions from PSICQUIC servers. PMID:25075287
The human plasma membrane peripherome: visualization and analysis of interactions. PMID:25057483
DBSecSys: a database of Burkholderia mallei secretion systems. PMID:25030112
The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience. PMID:24980485
R-based software for the integration of pathway data into bioinformatic algorithms. PMID:24833336
Guidelines for managing data and processes in bone and cartilage tissue engineering. PMID:24564199
Variation ontology: annotator guide. PMID:24533660
Computational Prediction of Protein-Protein Interaction Networks: Algo-rithms and Resources. PMID:24396273
The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases. PMID:24234451
Negatome 2.0: a database of non-interacting proteins derived by literature mining, manual annotation and protein structure analysis. PMID:24214996
The eukaryotic linear motif resource ELM: 10 years and counting. PMID:24214962
Variation Ontology for annotation of variation effects and mechanisms. PMID:24162187
Using biological pathway data with paxtools. PMID:24068901
Capturing cooperative interactions with the PSI-MI format. PMID:24067240
A new reference implementation of the PSICQUIC web service. PMID:23671334
From Peptidome to PRIDE: public proteomics data migration at a large scale. PMID:23533138
Access guide to human proteinpedia. PMID:23504933
Controlled vocabularies and ontologies in proteomics: overview, principles and practice. PMID:23429179
Interactome3D: adding structural details to protein networks. PMID:23399932
Visual data mining of biological networks: one size does not fit all. PMID:23341759
Inferring the Brassica rapa Interactome Using Protein-Protein Interaction Data from Arabidopsis thaliana. PMID:23293649
The BioGRID interaction database: 2013 update. PMID:23203989
InnateDB: systems biology of innate immunity and beyond--recent updates and continuing curation. PMID:23180781
PhosPhAt goes kinases--searchable protein kinase target information in the plant phosphorylation site database PhosPhAt. PMID:23172287
Proteomics-based methods for discovery, quantification, and validation of protein-protein interactions. PMID:23157382
Popular computational methods to assess multiprotein complexes derived from label-free affinity purification and mass spectrometry (AP-MS) experiments. PMID:23071097
PRD: A protein-RNA interaction database. PMID:23055619
Data management strategies for multinational large-scale systems biology projects. PMID:23047157
Minireview: progress and challenges in proteomics data management, sharing, and integration. PMID:22902541
Discovering the hidden sub-network component in a ranked list of genes or proteins derived from genomic experiments. PMID:22844098
A Bioinformatics Resource for TWEAK-Fn14 Signaling Pathway. PMID:22649723
IRView: a database and viewer for protein interacting regions. PMID:22592381
DIPSBC--data integration platform for systems biology collaborations. PMID:22568834
Bayesian integration of networks without gold standards. PMID:22492647
Protein interaction data curation: the International Molecular Exchange (IMEx) consortium. PMID:22453911
How to link ontologies and protein-protein interactions to literature: text-mining approaches and the BioCreative experience. PMID:22438567
The mzIdentML data standard for mass spectrometry-based proteomics results. PMID:22375074
Benchmarking of the 2010 BioCreative Challenge III text-mining competition by the BioGRID and MINT interaction databases. PMID:22151178
The IntAct molecular interaction database in 2012. PMID:22121220
INOH: ontology-based highly structured database of signal transduction pathways. PMID:22120663
iRefR: an R package to manipulate the iRefIndex consolidated protein interaction database. PMID:22115179
Structural and functional protein network analyses predict novel signaling functions for rhodopsin. PMID:22108793
MINT, the molecular interaction database: 2012 update. PMID:22096227
modMine: flexible access to modENCODE data. PMID:22080565
PINA v2.0: mining interactome modules. PMID:22067443
Proteomic and functional genomic landscape of receptor tyrosine kinase and ras to extracellular signal-regulated kinase signaling. PMID:22028469
BioPAX support in CellDesigner. PMID:22021903
ChEMBL: a large-scale bioactivity database for drug discovery. PMID:21948594
Minimum information about a bioactive entity (MIABE). PMID:21878981
ppiTrim: constructing non-redundant and up-to-date interactomes. PMID:21873645
Bio::Homology::InterologWalk--a Perl module to build putative protein-protein interaction networks through interolog mapping. PMID:21767381
PSICQUIC and PSISCORE: accessing and scoring molecular interactions. PMID:21716279
Data standards for Omics data: the basis of data sharing and reuse. PMID:21370078
BioGRID REST Service, BiogridPlugin2 and BioGRID WebGraph: new tools for access to interaction data at BioGRID. PMID:21300700
Literature curation of protein interactions: measuring agreement across major public databases. PMID:21183497
ConsensusPathDB: toward a more complete picture of cell biology. PMID:21071422
The BioGRID Interaction Database: 2011 update. PMID:21071413
Pathway Commons, a web resource for biological pathway data. PMID:21071392
Reactome: a database of reactions, pathways and biological processes. PMID:21067998
DroID 2011: a comprehensive, integrated resource for protein, transcription factor, RNA and gene interactions for Drosophila. PMID:21036869
iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence. PMID:20940177
Human protein reference database and human proteinpedia as discovery resources for molecular biotechnology. PMID:20927658
MatrixDB, the extracellular matrix interaction database. PMID:20852260
The BioPAX community standard for pathway data sharing. PMID:20829833
Curating the innate immunity interactome. PMID:20727158
Minimum information about a protein affinity reagent (MIAPAR). PMID:20622827
Ontologies in quantitative biology: a basis for comparison, integration, and discovery. PMID:20520843
MINT, the molecular interaction database: 2009 update. PMID:19897547
The IntAct molecular interaction database in 2010. PMID:19850723
XMPP for cloud computing in bioinformatics supporting discovery and invocation of asynchronous web services. PMID:19732427
A community standard format for the representation of protein affinity reagents. PMID:19674966
Pathway databases and tools for their exploitation: benefits, current limitations and challenges. PMID:19638971
BioNetBuilder2.0: bringing systems biology to chicken and other model organisms. PMID:19607657
Computational identification of potential molecular interactions in Arabidopsis. PMID:19592425
DASMIweb: online integration, analysis and assessment of distributed protein interaction data. PMID:19502495
DASMI: exchanging, annotating and assessing molecular interaction data. PMID:19420069
Nucleoside diphosphate kinase (NDPK, NM23, AWD): recent regulatory advances in endocytosis, metastasis, psoriasis, insulin release, fetal erythroid lineage and heart failure; translational medicine exemplified. PMID:19415463
Protein-protein interaction databases: keeping up with growing interactomes. PMID:19403463
A general pipeline for quality and statistical assessment of protein interaction data using R and Bioconductor. PMID:19325550
MatrixDB, a database focused on extracellular protein-protein and protein-carbohydrate interactions. PMID:19147664
Literature-curated protein interaction datasets. PMID:19116613
Genome and proteome annotation: organization, interpretation and integration. PMID:19019817
VirHostNet: a knowledge base for the management and the analysis of proteome-wide virus-host interaction networks. PMID:18984613
VirusMINT: a viral protein interaction database. PMID:18974184
The Protein Feature Ontology: a tool for the unification of protein feature annotations. PMID:18936051
MINT and IntAct contribute to the Second BioCreative challenge: serving the text-mining community with high quality molecular interaction data. PMID:18834496
iRefIndex: a consolidated protein interaction database with provenance. PMID:18823568
MPI-LIT: a literature-curated dataset of microbial binary protein--protein interactions. PMID:18786976
MPIDB: the microbial protein interaction database. PMID:18556668

http://dx.doi.org/10.1093/nar/gkt1115

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binding
metasource: Fairsharing.org
version: FAIRsharing.org: IntAct; IntAct molecular interaction database; DOI: https://doi.org/10.25504/FAIRsharing.d05nwx; Last edited: Feb. 8, 2021, 1:21 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

citation
metasource: Fairsharing.org
version: FAIRsharing.org: IntAct; IntAct molecular interaction database; DOI: https://doi.org/10.25504/FAIRsharing.d05nwx; Last edited: Feb. 8, 2021, 1:21 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

experimental measurement
metasource: Fairsharing.org
version: FAIRsharing.org: IntAct; IntAct molecular interaction database; DOI: https://doi.org/10.25504/FAIRsharing.d05nwx; Last edited: Feb. 8, 2021, 1:21 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

experimentally determined
metasource: Fairsharing.org
version: FAIRsharing.org: IntAct; IntAct molecular interaction database; DOI: https://doi.org/10.25504/FAIRsharing.d05nwx; Last edited: Feb. 8, 2021, 1:21 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

free text
metasource: Fairsharing.org
version: FAIRsharing.org: IntAct; IntAct molecular interaction database; DOI: https://doi.org/10.25504/FAIRsharing.d05nwx; Last edited: Feb. 8, 2021, 1:21 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

gene ontology enrichment
metasource: Fairsharing.org
version: FAIRsharing.org: IntAct; IntAct molecular interaction database; DOI: https://doi.org/10.25504/FAIRsharing.d05nwx; Last edited: Feb. 8, 2021, 1:21 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

gene name
metasource: Fairsharing.org
version: FAIRsharing.org: IntAct; IntAct molecular interaction database; DOI: https://doi.org/10.25504/FAIRsharing.d05nwx; Last edited: Feb. 8, 2021, 1:21 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

molecular interaction
metasource: Fairsharing.org
version: FAIRsharing.org: IntAct; IntAct molecular interaction database; DOI: https://doi.org/10.25504/FAIRsharing.d05nwx; Last edited: Feb. 8, 2021, 1:21 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

protein
metasource: Fairsharing.org
version: FAIRsharing.org: IntAct; IntAct molecular interaction database; DOI: https://doi.org/10.25504/FAIRsharing.d05nwx; Last edited: Feb. 8, 2021, 1:21 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

metasource: re3data.org
version: re3data.org: IntAct; editing status 2021-09-07; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3QS4R last accessed: 2022-11-04

protein domain
metasource: Fairsharing.org
version: FAIRsharing.org: IntAct; IntAct molecular interaction database; DOI: https://doi.org/10.25504/FAIRsharing.d05nwx; Last edited: Feb. 8, 2021, 1:21 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

protein interaction
metasource: Fairsharing.org
version: FAIRsharing.org: IntAct; IntAct molecular interaction database; DOI: https://doi.org/10.25504/FAIRsharing.d05nwx; Last edited: Feb. 8, 2021, 1:21 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

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

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

alzheimer
metasource: re3data.org
version: re3data.org: IntAct; editing status 2021-09-07; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3QS4R last accessed: 2022-11-04

covid-19
metasource: re3data.org
version: re3data.org: IntAct; editing status 2021-09-07; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3QS4R last accessed: 2022-11-04

parkinson
metasource: re3data.org
version: re3data.org: IntAct; editing status 2021-09-07; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3QS4R last accessed: 2022-11-04

affinomics
metasource: re3data.org
version: re3data.org: IntAct; editing status 2021-09-07; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3QS4R last accessed: 2022-11-04

cancer
metasource: re3data.org
version: re3data.org: IntAct; editing status 2021-09-07; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3QS4R last accessed: 2022-11-04

canobacteria
metasource: re3data.org
version: re3data.org: IntAct; editing status 2021-09-07; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3QS4R last accessed: 2022-11-04

diabetes
metasource: re3data.org
version: re3data.org: IntAct; editing status 2021-09-07; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3QS4R last accessed: 2022-11-04

human
metasource: re3data.org
version: re3data.org: IntAct; editing status 2021-09-07; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3QS4R last accessed: 2022-11-04

protein interactions
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:13.752584

binding citation experimental measurement experimentally determined free text gene ontology enrichment gene name molecular interaction protein protein domain protein interaction metabolic and signaling pathways protein-protein interactions alzheimer covid-19 parkinson affinomics cancer canobacteria diabetes human protein interaction

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