R38S3B last accessed: 2022-11-04

mint
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:36.893430

Other names: MINT, Molecular INTeraction Database, mint

MINT focuses on experimentally verified protein-protein interactions mined from the scientific literature by expert curators. This resource uses the IntAct database framework to help reduce the effort of scientists and improve on IT development. MINT is an ELIXIR Core Resource.

Webpage:

http://mint.bio.uniroma2.it

Licence:

Name: Creative Commons Attribution 2.5 Generic (CC BY 2.5)
URL: https://creativecommons.org/licenses/by/2.5/

Publications: (7)

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: bio.tools
version: extracted_at: 2022-11-04T11:29:36.893430

MINT, the molecular interaction database: 2012 update
PMID: 22096227
metasource: Fairsharing.org
version: FAIRsharing.org: MINT; Molecular INTeraction database; DOI: https://doi.org/10.25504/FAIRsharing.2bdvmk; Last edited: March 19, 2021, 11:16 a.m.; Last accessed: Jan 03 2022 7:06 p.m.

metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:36.893430

MINT: the Molecular INTeraction database
PMID: 17135203
metasource: Fairsharing.org
version: FAIRsharing.org: MINT; Molecular INTeraction database; DOI: https://doi.org/10.25504/FAIRsharing.2bdvmk; Last edited: March 19, 2021, 11:16 a.m.; Last accessed: Jan 03 2022 7:06 p.m.

MINT: a Molecular INTeraction database
PMID: 11911893
metasource: Fairsharing.org
version: FAIRsharing.org: MINT; Molecular INTeraction database; DOI: https://doi.org/10.25504/FAIRsharing.2bdvmk; Last edited: March 19, 2021, 11:16 a.m.; Last accessed: Jan 03 2022 7:06 p.m.

MINT, the molecular interaction database: 2009 update
PMID: 19897547
metasource: Fairsharing.org
version: FAIRsharing.org: MINT; Molecular INTeraction database; DOI: https://doi.org/10.25504/FAIRsharing.2bdvmk; Last edited: March 19, 2021, 11:16 a.m.; Last accessed: Jan 03 2022 7:06 p.m.

http://dx.doi.org/10.1093/nar/GKR930
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

http://dx.doi.org/10.1002/cpbi.93
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:36.893430

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
MINT, the molecular interaction database: 2012 update PubMed citations: 450.

450 articles citing: MINT, the molecular interaction database: 2012 update

BioAlign: An Accurate Global PPI Network Alignment Algorithm. PMID:35898232
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
Deep learning frameworks for protein-protein interaction prediction. PMID:35832624
TritiKBdb: A Functional Annotation Resource for Deciphering the Complete Interaction Networks in Wheat-Karnal Bunt Pathosystem. PMID:35806459
Deciphering the Crosstalk Mechanisms of Wheat-Stem Rust Pathosystem: Genome-Scale Prediction Unravels Novel Host Targets. PMID:35800602
PHILM2Web: A high-throughput database of macromolecular host-pathogen interactions on the Web. PMID:35776535
Systems Drug Discovery for Diffuse Large B Cell Lymphoma Based on Pathogenic Molecular Mechanism via Big Data Mining and Deep Learning Method. PMID:35743172
Repurposing Histaminergic Drugs in Multiple Sclerosis. PMID:35683024
A comprehensive SARS-CoV-2-human protein-protein interactome network identifies pathobiology and host-targeting therapies for COVID-19. PMID:35677070
Transcriptomic analysis reveals pathophysiological relationship between chronic obstructive pulmonary disease (COPD) and periodontitis. PMID:35676670
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
WeCoNET: a host-pathogen interactome database for deciphering crucial molecular networks of wheat-common bunt cross-talk mechanisms. PMID:35658913
Proteome-wide prediction and analysis of the Cryptosporidium parvum protein-protein interaction network through integrative methods. PMID:35615014
Identification of Potential Muscle Biomarkers in McArdle Disease: Insights from Muscle Proteome Analysis. PMID:35563042
Bioinformatics-Based Approaches to Study Virus-Host Interactions During SARS-CoV-2 Infection. PMID:35554909
Comprehensive network medicine-based drug repositioning via integration of therapeutic efficacy and side effects. PMID:35443763
An atlas of posttranslational modifications on RNA binding proteins. PMID:35438783
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
Deciphering the Host-Pathogen Interactome of the Wheat-Common Bunt System: A Step towards Enhanced Resilience in Next Generation Wheat. PMID:35269732
Computational Systems Biology of Alfalfa - Bacterial Blight Host-Pathogen Interactions: Uncovering the Complex Molecular Networks for Developing Durable Disease Resistant Crop. PMID:35251063
Predicting Protein-Protein Interactions via Random Ferns with Evolutionary Matrix Representation. PMID:35242211
Antifungal activity of an artificial peptide aptamer SNP-D4 against Fusarium oxysporum. PMID:35223198
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
The Landscape of Aminoacyl-tRNA Synthetases Involved in Severe Acute Respiratory Syndrome Coronavirus 2 Infection. PMID:35153822
Interactomes: Experimental and In Silico Approaches. PMID:35113398
Simple But Efficacious Enrichment of Integral Membrane Proteins and Their Interactions for In-Depth Membrane Proteomics. PMID:35085786
How Far Are We from the Completion of the Human Protein Interactome Reconstruction? PMID:35053288
Plant Reactome and PubChem: The Plant Pathway and (Bio)Chemical Entity Knowledgebases. PMID:35037224
Potential Molecular Mechanisms and Remdesivir Treatment for Acute Respiratory Syndrome Corona Virus 2 Infection/COVID 19 Through RNA Sequencing and Bioinformatics Analysis. PMID:34992355
Protein-protein interactions: Methods, databases, and applications in virus-host study. PMID:34909403
Metabolic endophenotype associated with right ventricular glucose uptake in pulmonary hypertension. PMID:34888034
Interpretation of network-based integration from multi-omics longitudinal data. PMID:34883510
Computational Network Pharmacology-Based Strategy to Capture Key Functional Components and Decode the Mechanism of Chai-Hu-Shu-Gan-San in Treating Depression. PMID:34867413
ConsensusPathDB 2022: molecular interactions update as a resource for network biology. PMID:34850110
In silico Methods for Identification of Potential Therapeutic Targets. PMID:34826045
A Network-Based Methodology to Identify Subnetwork Markers for Diagnosis and Prognosis of Colorectal Cancer. PMID:34790220
Computational methods for protein localization prediction. PMID:34765098
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
Network-driven analysis of human-Plasmodium falciparum interactome: processes for malaria drug discovery and extracting in silico targets. PMID:34702263
Alternative Splicing Mechanisms Underlying Opioid-Induced Hyperalgesia. PMID:34680965
Text Mining for Building Biomedical Networks Using Cancer as a Case Study. PMID:34680062
Computational repurposing of therapeutic small molecules from cancer to pulmonary hypertension. PMID:34669463
GreeningDB: A Database of Host-Pathogen Protein-Protein Interactions and Annotation Features of the Bacteria Causing Huanglongbing HLB Disease. PMID:34639237
Getting to know each other: PPIMem, a novel approach for predicting transmembrane protein-protein complexes. PMID:34630938
PncsHub: a platform for annotating and analyzing non-classically secreted proteins in Gram-positive bacteria. PMID:34551435
The protein-protein interaction network alignment using recurrent neural network. PMID:34529185
Identifying Protein Complexes With Clear Module Structure Using Pairwise Constraints in Protein Interaction Networks. PMID:34512712
Tau Protein Interaction Partners and Their Roles in Alzheimer's Disease and Other Tauopathies. PMID:34502116
Drug Discovery of Spinal Muscular Atrophy (SMA) from the Computational Perspective: A Comprehensive Review. PMID:34445667
Enzymes in the Cholesterol Synthesis Pathway: Interactomics in the Cancer Context. PMID:34440098
Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review. PMID:34439912
Robust and accurate prediction of protein-protein interactions by exploiting evolutionary information. PMID:34413375
alfaNET: A Database of Alfalfa-Bacterial Stem Blight Protein-Protein Interactions Revealing the Molecular Features of the Disease-causing Bacteria. PMID:34361108
Revealing protein-protein interactions at the transcriptome scale by sequencing. PMID:34348091
Multimodal single-cell omics analysis identifies epithelium-immune cell interactions and immune vulnerability associated with sex differences in COVID-19. PMID:34330889
CFTR Lifecycle Map-A Systems Medicine Model of CFTR Maturation to Predict Possible Active Compound Combinations. PMID:34299207
Utilizing image and caption information for biomedical document classification. PMID:34252939
Databases for Protein-Protein Interactions. PMID:34236665
A comprehensive review of integrative pharmacology-based investigation: A paradigm shift in traditional Chinese medicine. PMID:34221858
Identification of Diagnostic Markers for Major Depressive Disorder Using Machine Learning Methods. PMID:34220416
Applications and analytical tools of cell communication based on ligand-receptor interactions at single cell level. PMID:34217372
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
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
KEA3: improved kinase enrichment analysis via data integration. PMID:34019655
Drug Repurposing: A Network-based Approach to Amyotrophic Lateral Sclerosis. PMID:33987813
A New Sequential Forward Feature Selection (SFFS) Algorithm for Mining Best Topological and Biological Features to Predict Protein Complexes from Protein-Protein Interaction Networks (PPINs). PMID:33959851
Prioritizing Molecular Biomarkers in Asthma and Respiratory Allergy Using Systems Biology. PMID:33936056
Identification of the Key Role of NF-κB Signaling Pathway in the Treatment of Osteoarthritis With Bushen Zhuangjin Decoction, a Verification Based on Network Pharmacology Approach. PMID:33912052
An integrative drug repositioning framework discovered a potential therapeutic agent targeting COVID-19. PMID:33895786
Identification of IFN-Induced Transmembrane Protein 1 With Prognostic Value in Pancreatic Cancer Using Network Module-Based Analysis. PMID:33869009
Centrality Analysis of Protein-Protein Interaction Networks and Molecular Docking Prioritize Potential Drug-Targets in Type 1 Diabetes. PMID:33841528
Network-based modeling of herb combinations in traditional Chinese medicine. PMID:33834186
Predicting Protein-Protein Interactions Using Symmetric Logistic Matrix Factorization. PMID:33831302
Bioinformatic Analysis of Structure and Function of LIM Domains of Human Zyxin Family Proteins. PMID:33808029
Network medicine links SARS-CoV-2/COVID-19 infection to brain microvascular injury and neuroinflammation in dementia-like cognitive impairment. PMID:33791705
Identification of potential and novel target genes in pituitary prolactinoma by bioinformatics analysis. PMID:33709028
A systems-based method to repurpose marketed therapeutics for antiviral use: a SARS-CoV-2 case study. PMID:33593923
UniProt-Related Documents (UniReD): assisting wet lab biologists in their quest on finding novel counterparts in a protein network. PMID:33575553
Bioinformatics analyses of significant genes, related pathways, and candidate diagnostic biomarkers and molecular targets in SARS-CoV-2/COVID-19. PMID:33553808
Human pathways in animal models: possibilities and limitations. PMID:33524155
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
A network-based deep learning methodology for stratification of tumor mutations. PMID:33416857
Systems Approach to Pathogenic Mechanism of Type 2 Diabetes and Drug Discovery Design Based on Deep Learning and Drug Design Specifications. PMID:33375269
Neuronal-Glial Interaction in a Triple-Transgenic Mouse Model of Alzheimer's Disease: Gene Ontology and Lithium Pathways. PMID:33335468
Differential Co-Expression Analyses Allow the Identification of Critical Signalling Pathways Altered during Tumour Transformation and Progression. PMID:33322692
Applications and advancements of FT-ICR-MS for interactome studies. PMID:33289940
PINA 3.0: mining cancer interactome. PMID:33231689
The IMEx coronavirus interactome: an evolving map of Coronaviridae-host molecular interactions. PMID:33206959
Biological network analysis with deep learning. PMID:33169146
A network medicine approach to investigation and population-based validation of disease manifestations and drug repurposing for COVID-19. PMID:33156843
IHP-PING-generating integrated human protein-protein interaction networks on-the-fly. PMID:33129201
BastionHub: a universal platform for integrating and analyzing substrates secreted by Gram-negative bacteria. PMID:33084862
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
Molecular dynamics of the histamine H3 membrane receptor reveals different mechanisms of GPCR signal transduction. PMID:33037273
Structure-based validation can drastically underestimate error rate in proteome-wide cross-linking mass spectrometry studies. PMID:32994567
MasterPATH: network analysis of functional genomics screening data. PMID:32928103
Investigating Core Signaling Pathways of Hepatitis B Virus Pathogenesis for Biomarkers Identification and Drug Discovery via Systems Biology and Deep Learning Method. PMID:32878239
Systems Biology Approaches to Understanding the Human Immune System. PMID:32849587
Lasting and Sex-Dependent Impact of Maternal Immune Activation on Molecular Pathways of the Amygdala. PMID:32848554
Network-based modeling of drug effects on disease module in systemic sclerosis. PMID:32770109
Analyzing IDPs in Interactomes. PMID:32696395
Harnessing endophenotypes and network medicine for Alzheimer's drug repurposing. PMID:32656864
Using Random Forest Model Combined With Gabor Feature to Predict Protein-Protein Interaction From Protein Sequence. PMID:32655275
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
Multilevel regulation of muscle-specific transcription factor hlh-1 during Caenorhabditis elegans embryogenesis. PMID:32556563
Network Medicine Framework for Identifying Drug Repurposing Opportunities for COVID-19. PMID:32550253
Dynamic rewiring of the human interactome by interferon signaling. PMID:32539747
PINOT: an intuitive resource for integrating protein-protein interactions. PMID:32527260
MIPPIE: the mouse integrated protein-protein interaction reference. PMID:32496562
Integrated omics in Drosophila uncover a circadian kinome. PMID:32483184
Ellagic acid and human cancers: a systems pharmacology and docking study to identify principal hub genes and main mechanisms of action. PMID:32410114
A massively parallel barcoded sequencing pipeline enables generation of the first ORFeome and interactome map for rice. PMID:32398372
WeiBI (web-based platform): Enriching integrated interaction network with increased coverage and functional proteins from genome-wide experimental OMICS data. PMID:32221380
Systematic analysis of ovarian cancer platinum-resistance mechanisms via text mining. PMID:32160916
Exploration of databases and methods supporting drug repurposing: a comprehensive survey. PMID:32055842
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
PlaPPISite: a comprehensive resource for plant protein-protein interaction sites. PMID:32028878
Bioinformatics for Renal and Urinary Proteomics: Call for Aggrandization. PMID:32024005
Structure-Guided Design and In-Cell Target Profiling of a Cell-Active Target Engagement Probe for PARP Inhibitors. PMID:32017532
Identification of cancer driver genes based on nucleotide context. PMID:32015527
Mechanical forces induce an asthma gene signature in healthy airway epithelial cells. PMID:31969610
Machine learning approaches and databases for prediction of drug-target interaction: a survey paper. PMID:31950972
Identification of common key genes and pathways between type 1 diabetes and multiple sclerosis using transcriptome and interactome analysis. PMID:31912409
Analysis of Differentially Expressed Genes in Coronary Artery Disease by Integrated Microarray Analysis. PMID:31881747
Human cytomegalovirus interactome analysis identifies degradation hubs, domain associations and viral protein functions. PMID:31873071
MaXLinker: Proteome-wide Cross-link Identifications with High Specificity and Sensitivity. PMID:31839598
The human DEPhOsphorylation Database DEPOD: 2019 update. PMID:31836896
Sequence-Derived Markers of Drug Targets and Potentially Druggable Human Proteins. PMID:31803227
AppleMDO: A Multi-Dimensional Omics Database for Apple Co-Expression Networks and Chromatin States. PMID:31695717
CSF1R inhibitor JNJ-40346527 attenuates microglial proliferation and neurodegeneration in P301S mice. PMID:31504240
A Survey of Gene Prioritization Tools for Mendelian and Complex Human Diseases. PMID:31494632
Computer aided analysis of disease linked protein networks. PMID:31485137
Analyzing the regulation of miRNAs on protein-protein interaction network in Hodgkin lymphoma. PMID:31477006
Transcriptome and Network Dissection of Microsatellite Stable and Highly Instable Colorectal Cancer. PMID:31450919
Protein-Protein Interactions in Candida albicans. PMID:31440220
A genome-wide positioning systems network algorithm for in silico drug repurposing. PMID:31375661
Differential network analysis and protein-protein interaction study reveals active protein modules in glucocorticoid resistance for infant acute lymphoblastic leukemia. PMID:31370801
AraPPINet: An Updated Interactome for the Analysis of Hormone Signaling Crosstalk in Arabidopsis thaliana. PMID:31333706
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
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
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 Crucial Candidate Genes and Pathways in Glioblastoma Multiform by Bioinformatics Analysis. PMID:31137733
Opioid-Induced Hyperalgesia Is Associated with Dysregulation of Circadian Rhythm and Adaptive Immune Pathways in the Mouse Trigeminal Ganglia and Nucleus Accumbens. PMID:31129808
Identification of LIFR, PIK3R1, and MMP12 as Novel Prognostic Signatures in Gallbladder Cancer Using Network-Based Module Analysis. PMID:31119098
Downregulated UCHL1 Accelerates Gentamicin-Induced Auditory Cell Death via Autophagy. PMID:31041655
Identification of Important Invasion-Related Genes in Non-functional Pituitary Adenomas. PMID:30982163
Mining Featured Biomarkers Linked with Epithelial Ovarian CancerBased on Bioinformatics. PMID:30970615
Structural and Computational Characterization of Disease-Related Mutations Involved in Protein-Protein Interfaces. PMID:30934865
An Improved Deep Forest Model for Predicting Self-Interacting Proteins From Protein Sequence Using Wavelet Transformation. PMID:30881376
PIMKL: Pathway-Induced Multiple Kernel Learning. PMID:30854223
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
Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set. PMID:30602777
Molecular subtyping of cancer and nomination of kinase candidates for inhibition with phosphoproteomics: Reanalysis of CPTAC ovarian cancer. PMID:30594550
Integrating molecular networks with genetic variant interpretation for precision medicine. PMID:30548534
Interpretation of an individual functional genomics experiment guided by massive public data. PMID:30478325
Network Pharmacology to Unveil the Biological Basis of Health-Strengthening Herbal Medicine in Cancer Treatment. PMID:30469422
Structural disorder in the proteome and interactome of Alkhurma virus (ALKV). PMID:30443749
A Network Pharmacology Approach to Uncover the Molecular Mechanisms of Herbal Formula Ban-Xia-Xie-Xin-Tang. PMID:30410554
IID 2018 update: context-specific physical protein-protein interactions in human, model organisms and domesticated species. PMID:30407591
Network pharmacology-based strategy to investigate pharmacological mechanisms of Zuojinwan for treatment of gastritis. PMID:30382864
Establishment of stably expandable induced myogenic stem cells by four transcription factors. PMID:30361642
An integrative tissue-network approach to identify and test human disease genes. PMID:30346941
Genomic data integration systematically biases interactome mapping. PMID:30332399
Modeling and Simulating the Aerobic Carbon Metabolism of a Green Microalga Using Petri Nets and New Concepts of VANESA. PMID:30218605
Prediction of Novel Drugs and Diseases for Hepatocellular Carcinoma Based on Multi-Source Simulated Annealing Based Random Walk. PMID:30173379
Evolution of In Silico Strategies for Protein-Protein Interaction Drug Discovery. PMID:30082644
Factors Associated with Heritable Pulmonary Arterial Hypertension Exert Convergent Actions on the miR-130/301-Vascular Matrix Feedback Loop. PMID:30081553
Brain region-dependent gene networks associated with selective breeding for increased voluntary wheel-running behavior. PMID:30071007
Protein-protein interactions of human viruses. PMID:30031213
An unsupervised machine learning method for discovering patient clusters based on genetic signatures. PMID:30016722
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
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
Computational Methods for Predicting Protein-Protein Interactions Using Various Protein Features. PMID:29927082
Hub Protein Controversy: Taking a Closer Look at Plant Stress Response Hubs. PMID:29922309
Identification of Central Regulators of Calcium Signaling and ECM-Receptor Interaction Genetically Associated With the Progression and Recurrence of Atrial Fibrillation. PMID:29868113
Urinary Proteome Analysis Identified Neprilysin and VCAM as Proteins Involved in Diabetic Nephropathy. PMID:29854824
Network-Based Disease Module Discovery by a Novel Seed Connector Algorithm with Pathobiological Implications. PMID:29791871
Functional signaling and gene regulatory networks between the oocyte and the surrounding cumulus cells. PMID:29747587
In silico epigenetics of metal exposure and subclinical atherosclerosis in middle aged men: pilot results from the Aragon Workers Health Study. PMID:29685964
NIPS, a 3D network-integrated predictor of deleterious protein SAPs, and its application in cancer prognosis. PMID:29662108
Gastric cancer biomarkers; A systems biology approach. PMID:29556568
Comparative Protein Interaction Network Analysis Identifies Shared and Distinct Functions for the Human ROCO Proteins. PMID:29513927
Brain-specific functional relationship networks inform autism spectrum disorder gene prediction. PMID:29507298
Identification of Shared Molecular Signatures Indicate the Susceptibility of Endometriosis to Multiple Sclerosis. PMID:29503661
Cholangiocarcinoma‑associated genes identified by integrative analysis of gene expression data. PMID:29436659
Interactome INSIDER: a structural interactome browser for genomic studies. PMID:29355848
ksrMKL: a novel method for identification of kinase-substrate relationships using multiple kernel learning. PMID:29340231
Investigation and identification of functional post-translational modification sites associated with drug binding and protein-protein interactions. PMID:29322920
A Novel Phosphorylation Site-Kinase Network-Based Method for the Accurate Prediction of Kinase-Substrate Relationships. PMID:29312990
Predicting drug-disease interactions by semi-supervised graph cut algorithm and three-layer data integration. PMID:29297383
A systematic atlas of chaperome deregulation topologies across the human cancer landscape. PMID:29293508
Functional Analysis of Human Hub Proteins and Their Interactors Involved in the Intrinsic Disorder-Enriched Interactions. PMID:29257115
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
Repository corticotrophin injection exerts direct acute effects on human B cell gene expression distinct from the actions of glucocorticoids. PMID:29205315
Protein-protein interaction analysis to identify biomarker networks for endometriosis. PMID:29201163
Computational systems biology approaches for Parkinson's disease. PMID:29185073
Uncovering the relationship and mechanisms of Tartary buckwheat (Fagopyrum tataricum) and Type II diabetes, hypertension, and hyperlipidemia using a network pharmacology approach. PMID:29177114
THANATOS: an integrative data resource of proteins and post-translational modifications in the regulation of autophagy. PMID:29157087
The UCSC Genome Browser database: 2018 update. PMID:29106570
Rapamycin-induced miR-21 promotes mitochondrial homeostasis and adaptation in mTORC1 activated cells. PMID:29029388
Molecular mechanisms underlying gliomas and glioblastoma pathogenesis revealed by bioinformatics analysis of microarray data. PMID:28952134
HTS-Net: An integrated regulome-interactome approach for establishing network regulation models in high-throughput screenings. PMID:28949986
Modeling protein quaternary structure of homo- and hetero-oligomers beyond binary interactions by homology. PMID:28874689
Protein-Protein Interactions in Virus-Host Systems. PMID:28861068
Enriching Traditional Protein-protein Interaction Networks with Alternative Conformations of Proteins. PMID:28775330
Genetic and functional characterization of disease associations explains comorbidity. PMID:28740175
HDNetDB: A Molecular Interaction Database for Network-Oriented Investigations into Huntington's Disease. PMID:28701700
Drug Target Protein-Protein Interaction Networks: A Systematic Perspective. PMID:28691014
Mechanisms of action of sacubitril/valsartan on cardiac remodeling: a systems biology approach. PMID:28649439
Characterization of developmental defects in the forebrain resulting from hyperactivated mTOR signaling by integrative analysis of transcriptomic and proteomic data. PMID:28588230
Architecture of the human interactome defines protein communities and disease networks. PMID:28514442
PCVMZM: Using the Probabilistic Classification Vector Machines Model Combined with a Zernike Moments Descriptor to Predict Protein-Protein Interactions from Protein Sequences. PMID:28492483
LncRNAs2Pathways: Identifying the pathways influenced by a set of lncRNAs of interest based on a global network propagation method. PMID:28425476
Using structural knowledge in the protein data bank to inform the search for potential host-microbe protein interactions in sequence space: application to Mycobacterium tuberculosis. PMID:28376709
Finding low-conductance sets with dense interactions (FLCD) for better protein complex prediction. PMID:28361714
Drug voyager: a computational platform for exploring unintended drug action. PMID:28241745
Understanding the roles of intrinsic disorder in subunits of hemoglobin and the disease process of sickle cell anemia. PMID:28232898
Protein Bioinformatics Databases and Resources. PMID:28150231
Systematic analysis of molecular mechanisms for HCC metastasis via text mining approach. PMID:28108733
Non-interacting proteins may resemble interacting proteins: prevalence and implications. PMID:28084410
A Global Analysis of the Receptor Tyrosine Kinase-Protein Phosphatase Interactome. PMID:28065597
Identifying Candidate Reprogramming Genes in Mouse Induced Pluripotent Stem Cells. PMID:28063063
ccNET: Database of co-expression networks with functional modules for diploid and polyploid Gossypium. PMID:28053168
Genomic expression differences between cutaneous cells from red hair color individuals and black hair color individuals based on bioinformatic analysis. PMID:28030792
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
PROPER: global protein interaction network alignment through percolation matching. PMID:27955623
Specificity of broad protein interaction surfaces for proteins with multiple binding partners. PMID:27924264
Co-expression network analyses identify functional modules associated with development and stress response in Gossypium arboreum. PMID:27922095
The TissueNet v.2 database: A quantitative view of protein-protein interactions across human tissues. PMID:27899616
XTalkDB: a database of signaling pathway crosstalk. PMID:27899583
Prediction of Protein-Protein Interactions by Evidence Combining Methods. PMID:27879651
Intrinsic disorder in proteins involved in amyotrophic lateral sclerosis. PMID:27838743
Local Action with Global Impact: Highly Similar Infection Patterns of Human Viruses and Bacteriophages. PMID:27822522
Gene expression profiles and protein-protein interaction networks in amyotrophic lateral sclerosis patients with C9orf72 mutation. PMID:27814735
WORMHOLE: Novel Least Diverged Ortholog Prediction through Machine Learning. PMID:27812085
HIPPIE v2.0: enhancing meaningfulness and reliability of protein-protein interaction networks. PMID:27794551
TcoF-DB v2: update of the database of human and mouse transcription co-factors and transcription factor interactions. PMID:27789689
A Systems Biology Comparison of Ovarian Cancers Implicates Putative Somatic Driver Mutations through Protein-Protein Interaction Models. PMID:27788148
Identification of lncRNA functions in lung cancer based on associated protein-protein interaction modules. PMID:27786280
A computational interactome and functional annotation for the human proteome. PMID:27770567
In Vivo Analysis of Protein-Protein Interactions with Bioluminescence Resonance Energy Transfer (BRET): Progress and Prospects. PMID:27727181
Exploring the interactions of the RAS family in the human protein network and their potential implications in RAS-directed therapies. PMID:27713118
The epichaperome is an integrated chaperome network that facilitates tumour survival. PMID:27706135
DenHunt - A Comprehensive Database of the Intricate Network of Dengue-Human Interactions. PMID:27618709
DNA-binding protects p53 from interactions with cofactors involved in transcription-independent functions. PMID:27604871
Unfoldomics of prostate cancer: on the abundance and roles of intrinsically disordered proteins in prostate cancer. PMID:27453073
Small-molecule binding sites to explore protein-protein interactions in the cancer proteome. PMID:27452673
Clinical significance of mitofusin-2 and its signaling pathways in hepatocellular carcinoma. PMID:27389277
Reconstruction and Application of Protein-Protein Interaction Network. PMID:27338356
Yeast two-hybrid screening identified WDR77 as a novel interacting partner of TSC22D2. PMID:27337956
MicroRNA-140-5p and SMURF1 regulate pulmonary arterial hypertension. PMID:27214554
Genome-Wide Inference of Protein-Protein Interaction Networks Identifies Crosstalk in Abscisic Acid Signaling. PMID:27208273
APID interactomes: providing proteome-based interactomes with controlled quality for multiple species and derived networks. PMID:27131791
Hepatitis C Virus Protein Interaction Network Analysis Based on Hepatocellular Carcinoma. PMID:27115606
A Network Pharmacology Approach to Uncover the Pharmacological Mechanism of XuanHuSuo Powder on Osteoarthritis. PMID:27110264
Network-Based Interpretation of Diverse High-Throughput Datasets through the Omics Integrator Software Package. PMID:27096930
A Network of Splice Isoforms for the Mouse. PMID:27079421
A Quantitative Approach to Analyzing Genome Reductive Evolution Using Protein-Protein Interaction Networks: A Case Study of Mycobacterium leprae. PMID:27066064
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
An Atlas of the Human Kinome Reveals the Mutational Landscape Underlying Dysregulated Phosphorylation Cascades in Cancer. PMID:26921330
Correlative Gene Expression to Protective Seroconversion in Rift Valley Fever Vaccinates. PMID:26783758
Use of the BioGRID Database for Analysis of Yeast Protein and Genetic Interactions. PMID:26729909
Proteomics and bioinformatics analysis of mouse hypothalamic neurogenesis with or without EPHX2 gene deletion. PMID:26722453
HitPredict version 4: comprehensive reliability scoring of physical protein-protein interactions from more than 100 species. PMID:26708988
Forward Individualized Medicine from Personal Genomes to Interactomes. PMID:26696898
NERI: network-medicine based integrative approach for disease gene prioritization by relative importance. PMID:26696568
CancerNet: a database for decoding multilevel molecular interactions across diverse cancer types. PMID:26690544
Fundamentals of protein interaction network mapping. PMID:26681426
Application of Gene Expression Trajectories Initiated from ErbB Receptor Activation Highlights the Dynamics of Divergent Promoter Usage. PMID:26658111
Integrated analysis of global proteome, phosphoproteome, and glycoproteome enables complementary interpretation of disease-related protein networks. PMID:26657352
PPIM: A Protein-Protein Interaction Database for Maize. PMID:26620522
Lynx: a knowledge base and an analytical workbench for integrative medicine. PMID:26590263
Transcriptator: An Automated Computational Pipeline to Annotate Assembled Reads and Identify Non Coding RNA. PMID:26581084
dbPTM 2016: 10-year anniversary of a resource for post-translational modification of proteins. PMID:26578568
Exploring potential new floral organ morphogenesis genes of Arabidopsis thaliana using systems biology approach. PMID:26528302
BioDB extractor: customized data extraction system for commonly used bioinformatics databases. PMID:26516349
Integrated interactions database: tissue-specific view of the human and model organism interactomes. PMID:26516188
Discovering distinct functional modules of specific cancer types using protein-protein interaction networks. PMID:26495282
Identification of shared and unique susceptibility pathways among cancers of the lung, breast, and prostate from genome-wide association studies and tissue-specific protein interactions. PMID:26483192
PlantPAN 2.0: an update of plant promoter analysis navigator for reconstructing transcriptional regulatory networks in plants. PMID:26476450
An overview of bioinformatics methods for modeling biological pathways in yeast. PMID:26476430
SIGNOR: a database of causal relationships between biological entities. PMID:26467481
Indexing a protein-protein interaction network expedites network alignment. PMID:26453444
Recent findings and technological advances in phosphoproteomics for cells and tissues. PMID:26400465
Human protein interaction networks across tissues and diseases. PMID:26347769
Exploring novel mechanistic insights in Alzheimer's disease by assessing reliability of protein interactions. PMID:26346705
Meta-Analysis of Large-Scale Toxicogenomic Data Finds Neuronal Regeneration Related Protein and Cathepsin D to Be Novel Biomarkers of Drug-Induced Toxicity. PMID:26335687
Advances in computational approaches for prioritizing driver mutations and significantly mutated genes in cancer genomes. PMID:26307061
Integrated inference and evaluation of host-fungi interaction networks. PMID:26300851
Dissecting ancestry genomic background in substance dependence genome-wide association studies. PMID:26267224
Computational analysis of protein interaction networks for infectious diseases. PMID:26261187
Prediction of problematic complexes from PPI networks: sparse, embedded, and small complexes. PMID:26231465
Identification of putative drug targets for human sperm-egg interaction defect using protein network approach. PMID:26187737
The BioPlex Network: A Systematic Exploration of the Human Interactome. PMID:26186194
Acquisition of estrogen independence induces TOB1-related mechanisms supporting breast cancer cell proliferation. PMID:26165839
Publisher’s Note:Abstraction for data integration:Fusing mammalian molecular, cellular and phenotype big datasets for better knowledge extraction. PMID:26101093
Integrated web visualizations for protein-protein interaction databases. PMID:26077899
TRRUST: a reference database of human transcriptional regulatory interactions. PMID:26066708
The hierarchical organization of natural protein interaction networks confers self-organization properties on pseudocells. PMID:26050708
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
Biology-Driven Gene-Gene Interaction Analysis of Age-Related Cataract in the eMERGE Network. PMID:25982363
IMP 2.0: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks. PMID:25969450
Improving the Understanding of Pathogenesis of Human Papillomavirus 16 via Mapping Protein-Protein Interaction Network. PMID:25961044
NetworkAnalyst for statistical, visual and network-based meta-analysis of gene expression data. PMID:25950236
FNTM: a server for predicting functional networks of tissues in mouse. PMID:25940632
NOD-Like Receptor Signaling in Cholesteatoma. PMID:25922834
Understanding multicellular function and disease with human tissue-specific networks. PMID:25915600
A review on computational systems biology of pathogen-host interactions. PMID:25914674
ANDSystem: an Associative Network Discovery System for automated literature mining in the field of biology. PMID:25881313
REGULATOR: a database of metazoan transcription factors and maternal factors for developmental studies. PMID:25880930
CD4 T-cell transcriptome analysis reveals aberrant regulation of STAT3 and Wnt signaling pathways in rheumatoid arthritis: evidence from a case-control study. PMID:25880754
Inbreeding Affects Gene Expression Differently in Two Self-Incompatible Arabidopsis lyrata Populations with Similar Levels of Inbreeding Depression. PMID:25855783
Network-based proteomic approaches reveal the neurodegenerative, neuroprotective and pain-related mechanisms involved after retrograde axonal damage. PMID:25784190
The identification of specific methylation patterns across different cancers. PMID:25774687
FR database 1.0: a resource focused on fruit development and ripening. PMID:25725058
cisPath: an R/Bioconductor package for cloud users for visualization and management of functional protein interaction networks. PMID:25708840
EcoliNet: a database of cofunctional gene network for Escherichia coli. PMID:25650278
A visual review of the interactome of LRRK2: Using deep-curated molecular interaction data to represent biology. PMID:25648416
Amyloid precursor protein interaction network in human testis: sentinel proteins for male reproduction. PMID:25591988
Identification of caveolar resident proteins in ventricular myocytes using a quantitative proteomic approach: dynamic changes in caveolar composition following adrenoceptor activation. PMID:25561500
Discovery of small protein complexes from PPI networks with size-specific supervised weighting. PMID:25559663
β-Catenin is central to DUX4-driven network rewiring in facioscapulohumeral muscular dystrophy. PMID:25551153
Comprehensive discovery of DNA motifs in 349 human cells and tissues reveals new features of motifs. PMID:25505144
A proteome-scale map of the human interactome network. PMID:25416956
Characterization of age signatures of DNA methylation in normal and cancer tissues from multiple studies. PMID:25406591
Mechismo: predicting the mechanistic impact of mutations and modifications on molecular interactions. PMID:25392414
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
Reconstruction of metabolic pathways by combining probabilistic graphical model-based and knowledge-based methods. PMID:25374614
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
Expression profiling of mitochondrial voltage-dependent anion channel-1 associated genes predicts recurrence-free survival in human carcinomas. PMID:25333947
The human DEPhOsphorylation database DEPOD: a 2015 update. PMID:25332398
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
The role of the interactome in the maintenance of deleterious variability in human populations. PMID:25261458
Drug-Like Protein-Protein Interaction Modulators: Challenges and Opportunities for Drug Discovery and Chemical Biology. PMID:25254076
A random set scoring model for prioritization of disease candidate genes using protein complexes and data-mining of GeneRIF, OMIM and PubMed records. PMID:25253562
Integration strategy is a key step in network-based analysis and dramatically affects network topological properties and inferring outcomes. PMID:25243127
VirusMentha: a new resource for virus-host protein interactions. PMID:25217587
Identifying candidate genes for discrimination of ulcerative colitis and Crohn's disease. PMID:25182475
Functional and genomic context in pathway analysis of GWAS data. PMID:25154796
An integrative omics strategy to assess the germ cell secretome and to decipher sertoli-germ cell crosstalk in the Mammalian testis. PMID:25111155
Lean Big Data integration in systems biology and systems pharmacology. PMID:25109570
Prediction and functional analysis of the sweet orange protein-protein interaction network. PMID:25091279
PPI layouts: BioJS components for the display of Protein-Protein Interactions. PMID:25075288
Toward a systems-level understanding of gene regulatory, protein interaction, and metabolic networks in cyanobacteria. PMID:25071821
The domain landscape of virus-host interactomes. PMID:24991570
The emerging era of genomic data integration for analyzing splice isoform function. PMID:24951248
Lynx web services for annotations and systems analysis of multi-gene disorders. PMID:24948611
New directions for diffusion-based network prediction of protein function: incorporating pathways with confidence. PMID:24931987
NetworkAnalyst--integrative approaches for protein-protein interaction network analysis and visual exploration. PMID:24861621
Screening of critical genes in lung adenocarcinoma via network analysis of gene expression profile. PMID:24859971
Identification of gene expression changes from colitis to CRC in the mouse CAC model. PMID:24743346
Unraveling human protein interaction networks underlying co-occurrences of diseases and pathological conditions. PMID:24731539
Plant systems biology: insights, advances and challenges. PMID:24671625
GeneSense: a new approach for human gene annotation integrated with protein-protein interaction networks. PMID:24667292
Systems-level analysis of innate immunity. PMID:24655298
A second-generation protein-protein interaction network of Helicobacter pylori. PMID:24627523
PARK2 and proinflammatory/anti-inflammatory cytokine gene interactions contribute to the susceptibility to leprosy: a case-control study of North Indian population. PMID:24578538
Computational prediction of the human-microbial oral interactome. PMID:24576332
Detection of type 2 diabetes related modules and genes based on epigenetic networks. PMID:24565181
RRHGE: a novel approach to classify the estrogen receptor based breast cancer subtypes. PMID:24563630
VarWalker: personalized mutation network analysis of putative cancer genes from next-generation sequencing data. PMID:24516372
Review of biological network data and its applications. PMID:24465231
Systematic large-scale study of the inheritance mode of Mendelian disorders provides new insight into human diseasome. PMID:24448549
Low frequency variants, collapsed based on biological knowledge, uncover complexity of population stratification in 1000 genomes project data. PMID:24385916
Genomic analyses with biofilter 2.0: knowledge driven filtering, annotation, and model development. PMID:24378202
Integrating structure to protein-protein interaction networks that drive metastasis to brain and lung in breast cancer. PMID:24278371
Lynx: a database and knowledge extraction engine for integrative medicine. PMID:24270788
P³DB 3.0: From plant phosphorylation sites to protein networks. PMID:24243849
Integrating protein-protein interaction networks with phenotypes reveals signs of interactions. PMID:24240319
The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases. PMID:24234451
Integrating in silico resources to map a signaling network. PMID:24233784
High-resolution network biology: connecting sequence with function. PMID:24197012
Widespread aggregation and neurodegenerative diseases are associated with supersaturated proteins. PMID:24183671
Exploring mechanisms of human disease through structurally resolved protein interactome networks. PMID:24096645
Reconstruction of the experimentally supported human protein interactome: what can we learn? PMID:24088582
Capturing cooperative interactions with the PSI-MI format. PMID:24067240
Computational analysis of virus-host interactomes. PMID:23996253
mentha: a resource for browsing integrated protein-interaction networks. PMID:23900247
DBATE: database of alternative transcripts expression. PMID:23842462
BioBin: a bioinformatics tool for automating the binning of rare variants using publicly available biological knowledge. PMID:23819467
Evolutionary rate heterogeneity of core and attachment proteins in yeast protein complexes. PMID:23814130
A nutrigenomic framework to identify time-resolving responses of hepatic genes in diet-induced obese mice. PMID:23813319
A graph kernel approach for alignment-free domain-peptide interaction prediction with an application to human SH3 domains. PMID:23813002
GeneMANIA prediction server 2013 update. PMID:23794635
Optimization criteria and biological process enrichment in homologous multiprotein modules. PMID:23757502
Human monogenic disease genes have frequently functionally redundant paralogs. PMID:23696728
Interfacing cellular networks of S. cerevisiae and E. coli: connecting dynamic and genetic information. PMID:23663484
PCorral--interactive mining of protein interactions from MEDLINE. PMID:23640984
INstruct: a database of high-quality 3D structurally resolved protein interactome networks. PMID:23599502
Protein-protein interactions: switch from classical methods to proteomics and bioinformatics-based approaches. PMID:23579629
The SH2 domain interaction landscape. PMID:23545499
The evolutionary dynamics of protein-protein interaction networks inferred from the reconstruction of ancient networks. PMID:23526967
Functional knowledge transfer for high-accuracy prediction of under-studied biological processes. PMID:23516347
The human gene connectome as a map of short cuts for morbid allele discovery. PMID:23509278
Functional site plasticity in domain superfamilies. PMID:23499848
Protein complex-based analysis framework for high-throughput data sets. PMID:23443684
Using BioBin to explore rare variant population stratification. PMID:23424138
Next-generation analysis of cataracts: determining knowledge driven gene-gene interactions using Biofilter, and gene-environment interactions using the PhenX Toolkit. PMID:23424120
STOP using just GO: a multi-ontology hypothesis generation tool for high throughput experimentation. PMID:23409969
Interactome3D: adding structural details to protein networks. PMID:23399932
Novel genes underlying beta cell survival in metabolic stress. PMID:23390342
Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review. PMID:23384594
Evidence classification of high-throughput protocols and confidence integration in RegulonDB. PMID:23327937
Adding protein context to the human protein-protein interaction network to reveal meaningful interactions. PMID:23300433
Identification of novel cholesteatoma-related gene expression signatures using full-genome microarrays. PMID:23285167
Supervised maximum-likelihood weighting of composite protein networks for complex prediction. PMID:23281936
Managing biological complexity across orthologs with a visual knowledgebase of documented biomolecular interactions. PMID:23264875
STRING v9.1: protein-protein interaction networks, with increased coverage and integration. PMID:23203871
The Disease and Gene Annotations (DGA): an annotation resource for human disease. PMID:23197658
SpermatogenesisOnline 1.0: a resource for spermatogenesis based on manual literature curation and genome-wide data mining. PMID:23193286
Systems biology of pathogen-host interaction: networks of protein-protein interaction within pathogens and pathogen-human interactions in the post-genomic era. PMID:23193100
Text-mining solutions for biomedical research: enabling integrative biology. PMID:23150036
Effects of protein interaction data integration, representation and reliability on the use of network properties for drug target prediction. PMID:23146171
Transcriptional alterations related to neuropathology and clinical manifestation of Alzheimer's disease. PMID:23144955
SpliceAid-F: a database of human splicing factors and their RNA-binding sites. PMID:23118479
ValidNESs: a database of validated leucine-rich nuclear export signals. PMID:23093589
Popular computational methods to assess multiprotein complexes derived from label-free affinity purification and mass spectrometry (AP-MS) experiments. PMID:23071097
Protein stickiness, rather than number of functional protein-protein interactions, predicts expression noise and plasticity in yeast. PMID:23017156
Using ProHits to store, annotate, and analyze affinity purification-mass spectrometry (AP-MS) data. PMID:22948730
A network synthesis model for generating protein interaction network families. PMID:22912671
HINT: High-quality protein interactomes and their applications in understanding human disease. PMID:22846459
Computational analysis of interactomes: current and future perspectives for bioinformatics approaches to model the host-pathogen interaction space. PMID:22750305
BIPS: BIANA Interolog Prediction Server. A tool for protein-protein interaction inference. PMID:22689642
IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks. PMID:22684505
IntScore: a web tool for confidence scoring of biological interactions. PMID:22649056
CombFunc: predicting protein function using heterogeneous data sources. PMID:22641853
Methods for visual mining of genomic and proteomic data atlases. PMID:22524279
MINT: the Molecular INTeraction database PubMed citations: 368.

368 articles citing: MINT: the Molecular INTeraction database

Analyzing the Systems Biology Effects of COVID-19 mRNA Vaccines to Assess Their Safety and Putative Side Effects. PMID:35889989
ImitateDB: A database for domain and motif mimicry incorporating host and pathogen protein interactions. PMID:35487995
Mapping oncogenic protein interactions for precision medicine. PMID:35113472
Network analysis of host-pathogen protein interactions in microbe induced cardiovascular diseases. PMID:35001887
Protein network analysis to prioritize key genes in amyotrophic lateral sclerosis. PMID:34918006
Shared Molecular Mechanisms between Atherosclerosis and Periodontitis by Analyzing the Transcriptomic Alterations of Peripheral Blood Monocytes. PMID:34899963
Tumor relevant protein functional interactions identified using bipartite graph analyses. PMID:34728699
Centrality of drug targets in protein networks. PMID:34715787
Proteomics: Concepts and applications in human medicine. PMID:34630910
The chemical biology of coronavirus host-cell interactions. PMID:34458775
Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review. PMID:34439912
Bioinformatics Analysis Reveals Crosstalk Among Platelets, Immune Cells, and the Glomerulus That May Play an Important Role in the Development of Diabetic Nephropathy. PMID:34249963
DGLinker: flexible knowledge-graph prediction of disease-gene associations. PMID:34125897
Multiple-Molecule Drug Design Based on Systems Biology Approaches and Deep Neural Network to Mitigate Human Skin Aging. PMID:34073305
Proteomic Analyses of Vitreous in Proliferative Diabetic Retinopathy: Prior Studies and Future Outlook. PMID:34070658
In silico comparative analysis of LRRK2 interactomes from brain, kidney and lung. PMID:33915162
Exploring the Imbalance of Periodontitis Immune System From the Cellular to Molecular Level. PMID:33841510
Systems Medicine Design for Triple-Negative Breast Cancer and Non-Triple-Negative Breast Cancer Based on Systems Identification and Carcinogenic Mechanisms. PMID:33802957
Overexpression of miR-1306-5p, miR-3195, and miR-3914 Inhibits Ameloblast Differentiation through Suppression of Genes Associated with Human Amelogenesis Imperfecta. PMID:33672174
Structural similarity-based prediction of host factors associated with SARS-CoV-2 infection and pathogenesis. PMID:33506741
Comparative analysis on the anti-inflammatory/immune effect of mesenchymal stem cell therapy for the treatment of pulmonary arterial hypertension. PMID:33479312
Classification and prediction of protein-protein interaction interface using machine learning algorithm. PMID:33469042
Elucidating the network features and evolutionary attributes of intra- and interspecific protein-protein interactions between human and pathogenic bacteria. PMID:33420198
Chemocentric Informatics Analysis: Dexamethasone Versus Combination Therapy for COVID-19. PMID:33251412
Conjoint Feature Representation of GO and Protein Sequence for PPI Prediction Based on an Inception RNN Attention Network. PMID:33230427
In silico and in vitro studies reveal complement system drives coagulation cascade in SARS-CoV-2 pathogenesis. PMID:33200027
Determinants of correlated expression of transcription factors and their target genes. PMID:33104784
A Systems Biology Workflow for Drug and Vaccine Repurposing: Identifying Small-Molecule BCG Mimics to Reduce or Prevent COVID-19 Mortality. PMID:33025261
Omics Integration Analyses Reveal the Early Evolution of Malignancy in Breast Cancer. PMID:32512721
Exploring dynamic protein-protein interactions in cassava through the integrative interactome network. PMID:32300157
Comprehensive gene and pathway analysis of cervical cancer progression. PMID:32256826
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
Contents, Construction Methods, Data Resources, and Functions Comparative Analysis of Bacteria Databases. PMID:32071553
NAPAbench 2: A network synthesis algorithm for generating realistic protein-protein interaction (PPI) network families. PMID:31986158
Machine learning approaches and databases for prediction of drug-target interaction: a survey paper. PMID:31950972
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
Network Modeling Approaches and Applications to Unravelling Non-Alcoholic Fatty Liver Disease. PMID:31771247
Mitochondrial dysfunction in rheumatoid arthritis: A comprehensive analysis by integrating gene expression, protein-protein interactions and gene ontology data. PMID:31703070
Cerebrospinal Fluid Proteomics For Identification Of α2-Macroglobulin As A Potential Biomarker To Monitor Pharmacological Therapeutic Efficacy In Dopamine Dictated Disease States Of Parkinson's Disease And Schizophrenia. PMID:31632033
Disjoint motif discovery in biological network using pattern join method. PMID:31538955
Hamiltonian energy as an efficient approach to identify the significant key regulators in biological networks. PMID:31442253
Evaluation of α-synuclein and apolipoprotein E as potential biomarkers in cerebrospinal fluid to monitor pharmacotherapeutic efficacy in dopamine dictated disease states of Parkinson's disease and schizophrenia. PMID:31410011
PS-MCL: parallel shotgun coarsened Markov clustering of protein interaction networks. PMID:31337329
Application of dynamic expansion tree for finding large network motifs in biological networks. PMID:31149400
DeepTACT: predicting 3D chromatin contacts via bootstrapping deep learning. PMID:30869141
MorCVD: A Unified Database for Host-Pathogen Protein-Protein Interactions of Cardiovascular Diseases Related to Microbes. PMID:30858555
Analysis of Topological Parameters of Complex Disease Genes Reveals the Importance of Location in a Biomolecular Network. PMID:30769902
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
Systems biology analysis reveals new insights into invasive lung cancer. PMID:30547817
Antiviral activity of the mineralocorticoid receptor NR3C2 against Herpes simplex virus Type 1 (HSV-1) infection. PMID:30367157
Context-specific interactions in literature-curated protein interaction databases. PMID:30340458
Evaluation of Serum Apolipoprotein E as a Potential Biomarker for Pharmacological Therapeutic Efficacy Monitoring in Dopamine Dictated Disease Spectrum of Schizophrenia and Parkinson's disease: A Preliminary Study. PMID:30327579
A mitochondrial proteome profile indicative of type 2 diabetes mellitus in skeletal muscles. PMID:30266947
Insights into archaeal chaperone machinery: a network-based approach. PMID:30178307
Loss of the E3 ubiquitin ligase MKRN1 represses diet-induced metabolic syndrome through AMPK activation. PMID:30143610
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
Automatic extraction of protein-protein interactions using grammatical relationship graph. PMID:30066644
A cytokine protein-protein interaction network for identifying key molecules in rheumatoid arthritis. PMID:29928007
Stratification of candidate genes for Parkinson's disease using weighted protein-protein interaction network analysis. PMID:29898659
Network-based machine learning and graph theory algorithms for precision oncology. PMID:29872707
Discovering novel SNPs that are correlated with patient outcome in a Singaporean cancer patient cohort treated with gemcitabine-based chemotherapy. PMID:29751792
INTERSPIA: a web application for exploring the dynamics of protein-protein interactions among multiple species. PMID:29746660
Determining the minimum number of protein-protein interactions required to support known protein complexes. PMID:29698482
PCLPred: A Bioinformatics Method for Predicting Protein-Protein Interactions by Combining Relevance Vector Machine Model with Low-Rank Matrix Approximation. PMID:29596363
The integration of weighted gene association networks based on information entropy. PMID:29272314
Prediction of cassava protein interactome based on interolog method. PMID:29222529
Systems Bioinformatics: increasing precision of computational diagnostics and therapeutics through network-based approaches. PMID:29186305
SPRINT: ultrafast protein-protein interaction prediction of the entire human interactome. PMID:29141584
Review of computational methods for virus-host protein interaction prediction: a case study on novel Ebola-human interactions. PMID:29028879
Multi-dimensional histone methylations for coordinated regulation of gene expression under hypoxia. PMID:28977425
Integrated transcriptomics and metabolomics analysis to characterize cold stress responses in Nicotiana tabacum. PMID:28662642
Use of Graph Database for the Integration of Heterogeneous Biological Data. PMID:28416946
Transcriptional regulatory networks underlying the reprogramming of spermatogonial stem cells to multipotent stem cells. PMID:28408750
Disease Risk Assessment Using a Voronoi-Based Network Analysis of Genes and Variants Scores. PMID:28326099
Automatic query generation using word embeddings for retrieving passages describing experimental methods. PMID:28077568
An ensemble approach for large-scale identification of protein- protein interactions using the alignments of multiple sequences. PMID:28029645
Improved method for prioritization of disease associated lncRNAs based on ceRNA theory and functional genomics data. PMID:27992375
A computational interactome and functional annotation for the human proteome. PMID:27770567
Integrating network, sequence and functional features using machine learning approaches towards identification of novel Alzheimer genes. PMID:27756223
Identification of large disjoint motifs in biological networks. PMID:27716036
Comprehensive Proteome Profiling of Platelet Identified a Protein Profile Predictive of Responses to An Antiplatelet Agent Sarpogrelate. PMID:27601597
Automated detection of discourse segment and experimental types from the text of cancer pathway results sections. PMID:27580922
Functional characterization of EI24-induced autophagy in the degradation of RING-domain E3 ligases. PMID:27541728
Multi-OMICs and Genome Editing Perspectives on Liver Cancer Signaling Networks. PMID:27403431
Review on Graph Clustering and Subgraph Similarity Based Analysis of Neurological Disorders. PMID:27258269
Network-Based Protein Biomarker Discovery Platforms. PMID:27103885
Proteomics-Based Analysis of Protein Complexes in Pluripotent Stem Cells and Cancer Biology. PMID:27011181
Comparative Proteomic Analysis of Advanced Ovarian Cancer Tissue to Identify Potential Biomarkers of Responders and Nonresponders to First-Line Chemotherapy of Carboplatin and Paclitaxel. PMID:26997873
Differential network analysis reveals the genome-wide landscape of estrogen receptor modulation in hormonal cancers. PMID:26972162
Topological characteristics of target genes regulated by abiotic-stress-responsible miRNAs in a rice interactome network. PMID:26830287
Prediction and characterization of protein-protein interaction network in Bacillus licheniformis WX-02. PMID:26782814
Largescale Transcriptomics Analysis Suggests Over-Expression of BGH3, MMP9 and PDIA3 in Oral Squamous Cell Carcinoma. PMID:26745629
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
LENS: web-based lens for enrichment and network studies of human proteins. PMID:26680011
Data integration in biological research: an overview. PMID:26336651
A computational framework for the prioritization of disease-gene candidates. PMID:26330267
Identification of Aberrant Chromosomal Regions in Human Breast Cancer Using Gene Expression Data and Related Gene Information. PMID:26319982
An integrated network platform for contextual prioritization of drugs and pathways. PMID:26315485
Network Modules of the Cross-Species Genotype-Phenotype Map Reflect the Clinical Severity of Human Diseases. PMID:26301634
Correcting for the study bias associated with protein-protein interaction measurements reveals differences between protein degree distributions from different cancer types. PMID:26300911
NET-GE: a novel NETwork-based Gene Enrichment for detecting biological processes associated to Mendelian diseases. PMID:26110971
A predicted protein interactome identifies conserved global networks and disease resistance subnetworks in maize. PMID:26089837
Identifying diabetes-related important protein targets with few interacting partners with the PageRank algorithm. PMID:26064627
Improving 3D Genome Reconstructions Using Orthologous and Functional Constraints. PMID:26000633
An improved method for completely uncertain biological network alignment. PMID:26000284
Dynamic network-based relevance score reveals essential proteins and functional modules in directed differentiation. PMID:25977693
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
Application of centrality measures in the identification of critical genes in diabetes mellitus. PMID:25848169
Comprehensive data resources and analytical tools for pathological association of aminoacyl tRNA synthetases with cancer. PMID:25824651
An integrative approach for a network based meta-analysis of viral RNAi screens. PMID:25691914
A systems biology strategy to identify molecular mechanisms of action and protein indicators of traumatic brain injury. PMID:25399920
Expression profiling of mitochondrial voltage-dependent anion channel-1 associated genes predicts recurrence-free survival in human carcinomas. PMID:25333947
Computational survey of peptides derived from disulphide-bonded protein loops that may serve as mediators of protein-protein interactions. PMID:25231912
Transcriptome sequencing of a large human family identifies the impact of rare noncoding variants. PMID:25192044
Proteome-wide analysis of human disease mutations in short linear motifs: neglected players in cancer? PMID:25057855
GWAS and drug targets. PMID:25057111
Bioinformatic analysis of proteomics data. PMID:25033288
Quantification of biological network perturbations for mechanistic insight and diagnostics using two-layer causal models. PMID:25015298
Predicting disease-related proteins based on clique backbone in protein-protein interaction network. PMID:25013377
Proteogenomic convergence for understanding cancer pathways and networks. PMID:24994965
Exploring function prediction in protein interaction networks via clustering methods. PMID:24972109
Proteomics analysis of the non-muscle myosin heavy chain IIa-enriched actin-myosin complex reveals multiple functions within the podocyte. PMID:24949636
Improving functional annotation for industrial microbes: a case study with Pichia pastoris. PMID:24929579
Event-based text mining for biology and functional genomics. PMID:24907365
Protein-protein interaction network of the marine microalga Tetraselmis subcordiformis: prediction and application for starch metabolism analysis. PMID:24879479
Analysis pipeline for the epistasis search - statistical versus biological filtering. PMID:24817878
Protein-protein interaction detection: methods and analysis. PMID:24693427
Identification of novel kinase inhibitors by targeting a kinase-related apoptotic protein-protein interaction network in HeLa cells. PMID:24645986
Integrating systems biology sources illuminates drug action. PMID:24577151
A protein profile of visceral adipose tissues linked to early pathogenesis of type 2 diabetes mellitus. PMID:24403596
Computational Prediction of Protein-Protein Interaction Networks: Algo-rithms and Resources. PMID:24396273
Protein interaction network for Alzheimer's disease using computational approach. PMID:24391359
PATRIC, the bacterial bioinformatics database and analysis resource. PMID:24225323
High-throughput RNA interference screens integrative analysis: Towards a comprehensive understanding of the virus-host interplay. PMID:24175227
Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals. PMID:24092820
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
A systematic analysis of host factors reveals a Med23-interferon-λ regulatory axis against herpes simplex virus type 1 replication. PMID:23950709
Searching for synergies: matrix algebraic approaches for efficient pair screening. PMID:23935877
A probabilistic model of neutral and selective dynamics of protein network evolution. PMID:23931333
A miniaturized chemical proteomic approach for target profiling of clinical kinase inhibitors in tumor biopsies. PMID:23901793
JBioWH: an open-source Java framework for bioinformatics data integration. PMID:23846595
PhosphoChain: a novel algorithm to predict kinase and phosphatase networks from high-throughput expression data. PMID:23832245
Complementing the Eukaryotic Protein Interactome. PMID:23825550
Module-based breast cancer classification. PMID:23819260
Construction of protein phosphorylation networks by data mining, text mining and ontology integration: analysis of the spindle checkpoint. PMID:23749465
An efficient weighted graph strategy to identify differentiation associated genes in embryonic stem cells. PMID:23638139
Use of the protein ontology for multi-faceted analysis of biological processes: a case study of the spindle checkpoint. PMID:23637705
The SH2 domain interaction landscape. PMID:23545499
The potential of text mining in data integration and network biology for plant research: a case study on Arabidopsis. PMID:23532071
Using existing drugs as leads for broad spectrum anthelmintics targeting protein kinases. PMID:23459584
Module cover - a new approach to genotype-phenotype studies. PMID:23424119
mirTarPri: improved prioritization of microRNA targets through incorporation of functional genomics data. PMID:23326485
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
Mining functional subgraphs from cancer protein-protein interaction networks. PMID:23282132
Genome-wide meta-analysis of genetic susceptible genes for Type 2 Diabetes. PMID:23281828
Identification and analysis of biomarkers for mismatch repair proteins: A bioinformatic approach. PMID:23225975
Wiki-pi: a web-server of annotated human protein-protein interactions to aid in discovery of protein function. PMID:23209562
DbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications. PMID:23193290
PrePPI: a structure-informed database of protein-protein interactions. PMID:23193263
Proteomics-based methods for discovery, quantification, and validation of protein-protein interactions. PMID:23157382
Systems analysis of plant functional, transcriptional, physical interaction, and metabolic networks. PMID:23110892
Identification of significant pathways in gastric cancer based on protein-protein interaction networks and cluster analysis. PMID:23055812
What evidence is there for the homology of protein-protein interactions? PMID:23028270
Protein stickiness, rather than number of functional protein-protein interactions, predicts expression noise and plasticity in yeast. PMID:23017156
SRC Homology 2 Domain Binding Sites in Insulin, IGF-1 and FGF receptor mediated signaling networks reveal an extensive potential interactome. PMID:22974441
Biological function through network topology: a survey of the human diseasome. PMID:22962330
DTome: a web-based tool for drug-target interactome construction. PMID:22901092
Robust co-regulation of tyrosine phosphorylation sites on proteins reveals novel protein interactions. PMID:22851037
Sets2Networks: network inference from repeated observations of sets. PMID:22824380
Crowd sourcing a new paradigm for interactome driven drug target identification in Mycobacterium tuberculosis. PMID:22808064
NetWalker: a contextual network analysis tool for functional genomics. PMID:22732065
Proteome-wide prediction of protein-protein interactions from high-throughput data. PMID:22729399
Detecting mutually exclusive interactions in protein-protein interaction maps. PMID:22715412
Prediction and comparison of Salmonella-human and Salmonella-Arabidopsis interactomes. PMID:22589098
Inferring high-confidence human protein-protein interactions. PMID:22558947
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
Swimming upstream: identifying proteomic signals that drive transcriptional changes using the interactome and multiple "-omics" datasets. PMID:22482945
Interactomic and pharmacological insights on human sirt-1. PMID:22470339
Host-pathogen interactome mapping for HTLV-1 and -2 retroviruses. PMID:22458338
Information flow in interaction networks II: channels, path lengths, and potentials. PMID:22409812
Bioinformatics and systems biology. PMID:22377422
A novel framework for the comparative analysis of biological networks. PMID:22363585
Fast and accurate modeling of protein-protein interactions by combining template-interface-based docking with flexible refinement. PMID:22275112
IMID: integrated molecular interaction database. PMID:22238258
Genome-wide expression profiling of schizophrenia using a large combined cohort. PMID:22212594
Modeling community-wide molecular networks of multicellular systems. PMID:22210865
Novel search method for the discovery of functional relationships. PMID:22180409
Simple and efficient machine learning frameworks for identifying protein-protein interaction relevant articles and experimental methods used to study the interactions. PMID:22151701
Gene3D: a domain-based resource for comparative genomics, functional annotation and protein network analysis. PMID:22139938
Computational prediction of host-parasite protein interactions between P. falciparum and H. sapiens. PMID:22114664
A novel method of transcriptional response analysis to facilitate drug repositioning for cancer therapy. PMID:22108825
Structural and functional protein network analyses predict novel signaling functions for rhodopsin. PMID:22108793
An integrated approach to elucidate the intra-viral and viral-cellular protein interaction networks of a gamma-herpesvirus. PMID:22028648
iRefScape. A Cytoscape plug-in for visualization and data mining of protein interaction data from iRefIndex. PMID:21975162
Structural analysis of hubs in human NR-RTK network. PMID:21974810
A physical interaction network of dengue virus and human proteins. PMID:21911577
Insight into bacterial virulence mechanisms against host immune response via the Yersinia pestis-human protein-protein interaction network. PMID:21911467
Integrating GPCR-specific information with full text articles. PMID:21910883
Computational approaches to selecting and optimising targets for structural biology. PMID:21906678
GPS-Prot: a web-based visualization platform for integrating host-pathogen interaction data. PMID:21777475
Domain-domain interactions underlying herpesvirus-human protein-protein interaction networks. PMID:21760902
Integrated bio-entity network: a system for biological knowledge discovery. PMID:21738677
In silico gene prioritization by integrating multiple data sources. PMID:21731658
BioGraph: unsupervised biomedical knowledge discovery via automated hypothesis generation. PMID:21696594
An enhanced Petri-net model to predict synergistic effects of pairwise drug combinations from gene microarray data. PMID:21685086
Noise reduction in protein-protein interaction graphs by the implementation of a novel weighting scheme. PMID:21679454
Shared molecular strategies of the malaria parasite P. falciparum and the human virus HIV-1. PMID:21586753
PRIN: a predicted rice interactome network. PMID:21575196
The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods. PMID:21472436
Assessing the biological significance of gene expression signatures and co-expression modules by studying their network properties. PMID:21408226
Identifying causal genes and dysregulated pathways in complex diseases. PMID:21390271
The draft genome of the parasitic nematode Trichinella spiralis. PMID:21336279
Initial characterization of the human central proteome. PMID:21269460
Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology. PMID:21249183
Context-dependent transcriptional regulations between signal transduction pathways. PMID:21232126
A knowledge-based weighting framework to boost the power of genome-wide association studies. PMID:21217833
A machine learning approach for genome-wide prediction of morbid and druggable human genes based on systems-level data. PMID:21210975
The role of exon shuffling in shaping protein-protein interaction networks. PMID:21210967
Literature curation of protein interactions: measuring agreement across major public databases. PMID:21183497
Combining modularity, conservation, and interactions of proteins significantly increases precision and coverage of protein function prediction. PMID:21171995
Extending pathways and processes using molecular interaction networks to analyse cancer genome data. PMID:21144022
Defining the antigen receptor-dependent regulatory network that induces arrest of cycling immature B-lymphocytes. PMID:21143896
Discovering pathways by orienting edges in protein interaction networks. PMID:21109539
Network analysis of human protein location. PMID:21106131
Patterns of human gene expression variance show strong associations with signaling network hierarchy. PMID:21073694
The BioGRID Interaction Database: 2011 update. PMID:21071413
CPLA 1.0: an integrated database of protein lysine acetylation. PMID:21059677
Multi-level reproducibility of signature hubs in human interactome for breast cancer metastasis. PMID:21059271
RegPhos: a system to explore the protein kinase-substrate phosphorylation network in humans. PMID:21037261
Characterising and predicting haploinsufficiency in the human genome. PMID:20976243
Inference of surface membrane factors of HIV-1 infection through functional interaction networks. PMID:20967291
iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence. PMID:20940177
Toward a complete in silico, multi-layered embryonic stem cell regulatory network. PMID:20890967
Finding the "dark matter" in human and yeast protein network prediction and modelling. PMID:20885791
Evidence mining and novelty assessment of protein-protein interactions with the ConsensusPathDB plugin for Cytoscape. PMID:20847220
The BioPAX community standard for pathway data sharing. PMID:20829833
The FEBS Letters/BioCreative II.5 experiment: making biological information accessible. PMID:20829821
Gene pathways and subnetworks distinguish between major glioma subtypes and elucidate potential underlying biology. PMID:20828632
Utopia documents: linking scholarly literature with research data. PMID:20823323
Improving disease gene prioritization using the semantic similarity of Gene Ontology terms. PMID:20823322
A yeast's eye view of mammalian reproduction: cross-species gene co-expression in meiotic prophase. PMID:20819218
Use of data-biased random walks on graphs for the retrieval of context-specific networks from genomic data. PMID:20808879
Measuring the physical cohesiveness of proteins using physical interaction enrichment. PMID:20798171
Curating the innate immunity interactome. PMID:20727158
Encoding the states of interacting proteins to facilitate biological pathways reconstruction. PMID:20707925
Open source tool for prediction of genome wide protein-protein interaction network based on ortholog information. PMID:20684769
A genome-wide siRNA screen reveals multiple mTORC1 independent signaling pathways regulating autophagy under normal nutritional conditions. PMID:20627085
A comprehensive benchmark of kernel methods to extract protein-protein interactions from literature. PMID:20617200
Differential proteome and phosphoproteome signatures in human T-lymphoblast cells induced by sirolimus. PMID:20590665
PPLook: an automated data mining tool for protein-protein interaction. PMID:20550717
Predicting genetic modifier loci using functional gene networks. PMID:20538624
A quick guide to large-scale genomic data mining. PMID:20523745
Struct2Net: a web service to predict protein-protein interactions using a structure-based approach. PMID:20513650
PCFamily: a web server for searching homologous protein complexes. PMID:20511590
Novel peptide-mediated interactions derived from high-resolution 3-dimensional structures. PMID:20502673
Functional features, biological pathways, and protein interaction networks of addiction-related genes. PMID:20491072
Profiling of protein interaction networks of protein complexes using affinity purification and quantitative mass spectrometry. PMID:20445003
Identification of functional hubs and modules by converting interactome networks into hierarchical ordering of proteins. PMID:20438650
Systems pharmacology of arrhythmias. PMID:20407125
Low-complexity regions within protein sequences have position-dependent roles. PMID:20385029
Construction and analysis of protein-protein interaction networks. PMID:20334628
Comparative evolutionary analysis of protein complexes in E. coli and yeast. PMID:20122144
Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana. PMID:20118918
Relationship between operon preference and functional properties of persistent genes in bacterial genomes. PMID:20109203
Biana: a software framework for compiling biological interactions and analyzing networks. PMID:20105306
CORNET: a user-friendly tool for data mining and integration. PMID:20053712
CanProVar: a human cancer proteome variation database. PMID:20052754
From protein sequences to 3D-structures and beyond: the example of the UniProt knowledgebase. PMID:20043185
Expression-based network biology identifies alteration in key regulatory pathways of type 2 diabetes and associated risk/complications. PMID:19997558
Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction. PMID:19953085
Phylogeny-guided interaction mapping in seven eukaryotes. PMID:19948065
Recurated protein interaction datasets. PMID:19935838
Calling International Rescue: knowledge lost in literature and data landslide! PMID:19929850
Role for protein-protein interaction databases in human genetics. PMID:19929610
Novel protein-protein interactions inferred from literature context. PMID:19924298
ELM: the status of the 2010 eukaryotic linear motif resource. PMID:19920119
Gene3D: merging structure and function for a Thousand genomes. PMID:19906693
MINT, the molecular interaction database: 2009 update. PMID:19897547
pISTil: a pipeline for yeast two-hybrid Interaction Sequence Tags identification and analysis. PMID:19874608
The IntAct molecular interaction database in 2010. PMID:19850723
Predicting meiotic pathways in human fetal oogenesis. PMID:19846598
Detection of molecular paths associated with insulitis and type 1 diabetes in non-obese diabetic mouse. PMID:19798418
Defining elastic fiber interactions by molecular fishing: an affinity purification and mass spectrometry approach. PMID:19755719
Pushing structural information into the yeast interactome by high-throughput protein docking experiments. PMID:19714207
NASCENT: an automatic protein interaction network generation tool for non-model organisms. PMID:19707301
Mutation of SHOC2 promotes aberrant protein N-myristoylation and causes Noonan-like syndrome with loose anagen hair. PMID:19684605
Discovery: an interactive resource for the rational selection and comparison of putative drug target proteins in malaria. PMID:19642978
BioNetBuilder2.0: bringing systems biology to chicken and other model organisms. PMID:19607657
HAPPI: an online database of comprehensive human annotated and predicted protein interactions. PMID:19594875
Computational identification of potential molecular interactions in Arabidopsis. PMID:19592425
Towards inferring time dimensionality in protein-protein interaction networks by integrating structures: the p53 example. PMID:19585003
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
Interactome for auxiliary splicing factor U2AF(65) suggests diverse roles. PMID:19540372
PIAS proteins: pleiotropic interactors associated with SUMO. PMID:19526197
DASMIweb: online integration, analysis and assessment of distributed protein interaction data. PMID:19502495
myGRN: a database and visualisation system for the storage and analysis of developmental genetic regulatory networks. PMID:19500400
Tumor suppressor density-enhanced phosphatase-1 (DEP-1) inhibits the RAS pathway by direct dephosphorylation of ERK1/2 kinases. PMID:19494114
Public databases and software for the pathway analysis of cancer genomes. PMID:19455256
SNOW, a web-based tool for the statistical analysis of protein-protein interaction networks. PMID:19454602
MedlineRanker: flexible ranking of biomedical literature. PMID:19429696
DASMI: exchanging, annotating and assessing molecular interaction data. PMID:19420069
PPISearch: a web server for searching homologous protein-protein interactions across multiple species. PMID:19417070
Rich can get poor: conversion of hub to non-hub proteins. PMID:19399641
Bayesian inference of protein-protein interactions from biological literature. PMID:19369495
ModLink+: improving fold recognition by using protein-protein interactions. PMID:19357100
A novel hybrid yeast-human network analysis reveals an essential role for FNBP1L in antibacterial autophagy. PMID:19342671
A general pipeline for quality and statistical assessment of protein interaction data using R and Bioconductor. PMID:19325550
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
Dynamic modularity in protein interaction networks predicts breast cancer outcome. PMID:19182785
Next generation tools for the annotation of human SNPs. PMID:19181721
KEA: kinase enrichment analysis. PMID:19176546
Improved homology-driven computational validation of protein-protein interactions motivated by the evolutionary gene duplication and divergence hypothesis. PMID:19152684
MatrixDB, a database focused on extracellular protein-protein and protein-carbohydrate interactions. PMID:19147664
Literature-curated protein interaction datasets. PMID:19116613
An evolutionary and structural characterization of mammalian protein complex organization. PMID:19108706
Integrated network analysis platform for protein-protein interactions. PMID:19079255
An experimentally derived confidence score for binary protein-protein interactions. PMID:19060903
Network integration and graph analysis in mammalian molecular systems biology. PMID:19045817
Combining multiple positive training sets to generate confidence scores for protein-protein interactions. PMID:19010802
EcID. A database for the inference of functional interactions in E. coli. PMID:19004873
PIPs: human protein-protein interaction prediction database. PMID:18988626
MoKCa database--mutations of kinases in cancer. PMID:18986996
Hepatitis C virus infection protein network. PMID:18985028
VirHostNet: a knowledge base for the management and the analysis of proteome-wide virus-host interaction networks. PMID:18984613
Michigan molecular interactions r2: from interacting proteins to pathways. PMID:18978014
VirusMINT: a viral protein interaction database. PMID:18974184
ConsensusPathDB--a database for integrating human functional interaction networks. PMID:18940869
STRING 8--a global view on proteins and their functional interactions in 630 organisms. PMID:18940858
Human immunodeficiency virus type 1, human protein interaction database at NCBI. PMID:18927109
Selected reaction monitoring for quantitative proteomics: a tutorial. PMID:18854821
Prediction of evolutionarily conserved interologs in Mus musculus. PMID:18842131
DroID: the Drosophila Interactions Database, a comprehensive resource for annotated gene and protein interactions. PMID:18840285
Multiplexed isobaric tagging protocols for quantitative mass spectrometry approaches to auditory research. PMID:18839358
The interactome: predicting the protein-protein interactions in cells. PMID:18839074
MINT and IntAct contribute to the Second BioCreative challenge: serving the text-mining community with high quality molecular interaction data. PMID:18834496
Overview of the protein-protein interaction annotation extraction task of BioCreative II. PMID:18834495
Uncovering protein interaction in abstracts and text using a novel linear model and word proximity networks. PMID:18834489
PID: the Pathway Interaction Database. PMID:18832364
iRefIndex: a consolidated protein interaction database with provenance. PMID:18823568
MPI-LIT: a literature-curated dataset of microbial binary protein--protein interactions. PMID:18786976
Probing the extent of randomness in protein interaction networks. PMID:18769589
InnateDB: facilitating systems-level analyses of the mammalian innate immune response. PMID:18766178
Global sequencing of proteolytic cleavage sites in apoptosis by specific labeling of protein N termini. PMID:18722006
Human Proteinpedia as a resource for clinical proteomics. PMID:18573810
Exploiting the proteome to improve the genome-wide genetic analysis of epistasis in common human diseases. PMID:18551320
ENDEAVOUR update: a web resource for gene prioritization in multiple species. PMID:18508807
Design logic of a cannabinoid receptor signaling network that triggers neurite outgrowth. PMID:18487186
Beyond tissueInfo: functional prediction using tissue expression profile similarity searches. PMID:18483083
Network-based global inference of human disease genes. PMID:18463613
Protein networks in disease. PMID:18381899
Predicting cancer involvement of genes from heterogeneous data. PMID:18371197
Topological comparison of methods for predicting transcriptional cooperativity in yeast. PMID:18366726
The Annotation, Mapping, Expression and Network (AMEN) suite of tools for molecular systems biology. PMID:18254954
Gene3D: comprehensive structural and functional annotation of genomes. PMID:18032434
The BioGRID Interaction Database: 2008 update. PMID:18000002
DIMA 2.0--predicted and known domain interactions. PMID:17999995
Phospho.ELM: a database of phosphorylation sites--update 2008. PMID:17962309
Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions. PMID:17925023
PepBank--a database of peptides based on sequence text mining and public peptide data sources. PMID:17678535
MINT: a Molecular INTeraction database PubMed citations: 263.

263 articles citing: MINT: a Molecular INTeraction database

Challenges and Limitations of Biological Network Analysis. PMID:35892929
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
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
Investigating Pathogenetic Mechanisms of Alzheimer's Disease by Systems Biology Approaches for Drug Discovery. PMID:34681938
Drug Discovery of Spinal Muscular Atrophy (SMA) from the Computational Perspective: A Comprehensive Review. PMID:34445667
Targeted capture sequencing identifies genetic variations of GRK4 and RDH8 in Han Chinese with essential hypertension in Xinjiang. PMID:34297769
Databases for Protein-Protein Interactions. PMID:34236665
Shared Molecular Mechanisms between Alzheimer's Disease and Periodontitis Revealed by Transcriptomic Analysis. PMID:33869630
Detecting Prognosis Risk Biomarkers for Colon Cancer Through Multi-Omics-Based Prognostic Analysis and Target Regulation Simulation Modeling. PMID:32528533
Metabolic reprogramming of fibro/adipogenic progenitors facilitates muscle regeneration. PMID:32019766
Machine learning approaches and databases for prediction of drug-target interaction: a survey paper. PMID:31950972
A comprehensive study on genome-wide coexpression network of KHDRBS1/Sam68 reveals its cancer and patient-specific association. PMID:31366900
The Methods Employed in Mass Spectrometric Analysis of Posttranslational Modifications (PTMs) and Protein-Protein Interactions (PPIs). PMID:31347048
Disease association of human tumor suppressor genes. PMID:30945018
Network Pharmacology Databases for Traditional Chinese Medicine: Review and Assessment. PMID:30846939
Computational discovery of dynamic cell line specific Boolean networks from multiplex time-course data. PMID:30372442
Tissue-specific Network Analysis of Genetic Variants Associated with Coronary Artery Disease. PMID:30065343
ProfPPIdb: Pairs of physical protein-protein interactions predicted for entire proteomes. PMID:30020956
PPI network analyses of human WD40 protein family systematically reveal their tendency to assemble complexes and facilitate the complex predictions. PMID:29745845
Prediction of Protein-Protein Interactions from Amino Acid Sequences Based on Continuous and Discrete Wavelet Transform Features. PMID:29617272
Key genes and regulatory networks involved in the initiation, progression and invasion of colorectal cancer. PMID:29568567
Improving prediction of heterodimeric protein complexes using combination with pairwise kernel. PMID:29504897
Predicting new indications of compounds with a network pharmacology approach: Liuwei Dihuang Wan as a case study. PMID:29212201
Systems biology: An emerging strategy for discovering novel pathogenetic mechanisms that promote cardiovascular disease. PMID:29043273
A novel network analysis approach reveals DNA damage, oxidative stress and calcium/cAMP homeostasis-associated biomarkers in frontotemporal dementia. PMID:29020091
Accurate prediction of protein-protein interactions by integrating potential evolutionary information embedded in PSSM profile and discriminative vector machine classifier. PMID:28423569
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
A Review of Recent Advancement in Integrating Omics Data with Literature Mining towards Biomedical Discoveries. PMID:28331849
Binding of small molecules at interface of protein-protein complex - A newer approach to rational drug design. PMID:28149177
Multichannel Convolutional Neural Network for Biological Relation Extraction. PMID:28053977
Bisdemethoxycurcumin exerts pro-apoptotic effects in human pancreatic adenocarcinoma cells through mitochondrial dysfunction and a GRP78-dependent pathway. PMID:27845899
Automated detection of discourse segment and experimental types from the text of cancer pathway results sections. PMID:27580922
A Shortest Dependency Path Based Convolutional Neural Network for Protein-Protein Relation Extraction. PMID:27493967
Improving protein-protein interactions prediction accuracy using protein evolutionary information and relevance vector machine model. PMID:27452983
Using the Relevance Vector Machine Model Combined with Local Phase Quantization to Predict Protein-Protein Interactions from Protein Sequences. PMID:27314023
Sequence-based prediction of protein-protein interactions using weighted sparse representation model combined with global encoding. PMID:27112932
APP Is a Context-Sensitive Regulator of the Hippocampal Presynaptic Active Zone. PMID:27092780
Controllability analysis of the directed human protein interaction network identifies disease genes and drug targets. PMID:27091990
A Network of Splice Isoforms for the Mouse. PMID:27079421
Biomolecular Relationships Discovered from Biological Labyrinth and Lost in Ocean of Literature: Community Efforts Can Rescue Until Automated Artificial Intelligence Takes Over. PMID:27066067
Using Weighted Sparse Representation Model Combined with Discrete Cosine Transformation to Predict Protein-Protein Interactions from Protein Sequence. PMID:26634213
Computing interaction probabilities in signaling networks. PMID:26587014
PharmDB-K: Integrated Bio-Pharmacological Network Database for Traditional Korean Medicine. PMID:26555441
Genome-wide prediction of prokaryotic two-component system networks using a sequence-based meta-predictor. PMID:26384938
Surfing the Protein-Protein Interaction Surface Using Docking Methods: Application to the Design of PPI Inhibitors. PMID:26111183
Publisher’s Note:Abstraction for data integration:Fusing mammalian molecular, cellular and phenotype big datasets for better knowledge extraction. PMID:26101093
By the company they keep: interaction networks define the binding ability of transcription factors. PMID:26089389
Integrative random forest for gene regulatory network inference. PMID:26072483
Urothelial cancer gene regulatory networks inferred from large-scale RNAseq, Bead and Oligo gene expression data. PMID:25971253
Follicle Online: an integrated database of follicle assembly, development and ovulation. PMID:25931457
Pathway mapping and development of disease-specific biomarkers: protein-based network biomarkers. PMID:25560835
INTEGRATING COMPUTATIONAL PROTEIN FUNCTION PREDICTION INTO DRUG DISCOVERY INITIATIVES. PMID:25530654
Pathway crosstalk analysis of microarray gene expression profile in human hepatocellular carcinoma. PMID:25480734
Construction and analysis of the protein-protein interaction networks based on gene expression profiles of Parkinson's disease. PMID:25170921
The development and application of a quantitative peptide microarray based approach to protein interaction domain specificity space. PMID:25135669
Lean Big Data integration in systems biology and systems pharmacology. PMID:25109570
The human plasma membrane peripherome: visualization and analysis of interactions. PMID:25057483
An unsupervised text mining method for relation extraction from biomedical literature. PMID:25036529
Construction and analysis of microRNA-transcription factor regulation network in Arabidopsis. PMID:25014374
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
Protein-protein interface detection using the energy centrality relationship (ECR) characteristic of proteins. PMID:24830938
Impact of vitamin D on immune function: lessons learned from genome-wide analysis. PMID:24795646
Controllability in protein interaction networks. PMID:24778220
Stringent homology-based prediction of H. sapiens-M. tuberculosis H37Rv protein-protein interactions. PMID:24708540
DAWN: a framework to identify autism genes and subnetworks using gene expression and genetics. PMID:24602502
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
A predicted protein interactome for rice. PMID:24279740
Gentrepid V2.0: a web server for candidate disease gene prediction. PMID:23947436
Prediction of heterodimeric protein complexes from weighted protein-protein interaction networks using novel features and kernel functions. PMID:23776458
Structure and non-structure of centrosomal proteins. PMID:23671615
Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. PMID:23586463
An integrated approach to uncover driver genes in breast cancer methylation genomes. PMID:23579546
Novel semantic similarity measure improves an integrative approach to predicting gene functional associations. PMID:23497449
BiNoM 2.0, a Cytoscape plugin for accessing and analyzing pathways using standard systems biology formats. PMID:23453054
Equal opportunity for low-degree network nodes: a PageRank-based method for protein target identification in metabolic graphs. PMID:23382878
PPInterFinder--a mining tool for extracting causal relations on human proteins from literature. PMID:23325628
Identification of MFS proteins in sorghum using semantic similarity. PMID:23299296
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
ReLiance: a machine learning and literature-based prioritization of receptor--ligand pairings. PMID:22962483
Multiple biomarker tissue arrays: A computational approach to identifying protein-protein interactions in the EGFR/ERK signalling pathway. PMID:22937740
Large scale genotype comparison of human papillomavirus E2-host interaction networks provides new insights for e2 molecular functions. PMID:22761572
DroPNet: a web portal for integrated analysis of Drosophila protein-protein interaction networks. PMID:22641854
High-throughput analysis of peptide-binding modules. PMID:22610655
LDGIdb: a database of gene interactions inferred from long-range strong linkage disequilibrium between pairs of SNPs. PMID:22551073
A comparative analysis of protein targets of withdrawn cardiovascular drugs in human and mouse. PMID:22548699
Progressive dry-core-wet-rim hydration trend in a nested-ring topology of protein binding interfaces. PMID:22452998
An integer linear programming approach for finding deregulated subgraphs in regulatory networks. PMID:22210863
Which clustering algorithm is better for predicting protein complexes? PMID:22185599
Detection of interaction articles and experimental methods in biomedical literature. PMID:22151872
Structural and functional protein network analyses predict novel signaling functions for rhodopsin. PMID:22108793
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
Proteome-wide detection of Abl1 SH3-binding peptides by integrating computational prediction and peptide microarray. PMID:22023807
An interaction network predicted from public data as a discovery tool: application to the Hsp90 molecular chaperone machine. PMID:22022502
Systems-biology approaches to discover anti-viral effectors of the human innate immune response. PMID:21994773
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
NETGEM: Network Embedded Temporal GEnerative Model for gene expression data. PMID:21824426
Computational approach to identify enzymes that are potential therapeutic candidates for psoriasis. PMID:21822480
Reactome pathway analysis to enrich biological discovery in proteomics data sets. PMID:21751369
Integrative computational biology for cancer research. PMID:21691773
PRIN: a predicted rice interactome network. PMID:21575196
Using graph theory to analyze biological networks. PMID:21527005
Gene expression profiles in rat mesenteric lymph nodes upon supplementation with conjugated linoleic acid during gestation and suckling. PMID:21481241
Sig2BioPAX: Java tool for converting flat files to BioPAX Level 3 format. PMID:21418653
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
Virus interactions with human signal transduction pathways. PMID:21330695
SIDEKICK: Genomic data driven analysis and decision-making framework. PMID:21192813
A comparative study of cancer proteins in the human protein-protein interaction network. PMID:21143787
HPIDB--a unified resource for host-pathogen interactions. PMID:20946599
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
Candidate gene prioritization by network analysis of differential expression using machine learning approaches. PMID:20840752
Identifying dysfunctional crosstalk of pathways in various regions of Alzheimer's disease brains. PMID:20840725
In silico models of cancer. PMID:20836040
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
The function of communities in protein interaction networks at multiple scales. PMID:20649971
Literature-based discovery of IFN-gamma and vaccine-mediated gene interaction networks. PMID:20625487
Visual integration of quantitative proteomic data, pathways, and protein interactions. PMID:20467059
Coordinated modular functionality and prognostic potential of a heart failure biomarker-driven interaction network. PMID:20462429
SZGR: a comprehensive schizophrenia gene resource. PMID:20424623
Interactome mapping of the phosphatidylinositol 3-kinase-mammalian target of rapamycin pathway identifies deformed epidermal autoregulatory factor-1 as a new glycogen synthase kinase-3 interactor. PMID:20368287
High-throughput discovery and characterization of fetal protein trafficking in the blood of pregnant women. PMID:20186258
Walk-weighted subsequence kernels for protein-protein interaction extraction. PMID:20184736
Xenopus meiotic microtubule-associated interactome. PMID:20174651
BisoGenet: a new tool for gene network building, visualization and analysis. PMID:20163717
Lists2Networks: integrated analysis of gene/protein lists. PMID:20152038
A manually curated network of the PML nuclear body interactome reveals an important role for PML-NBs in SUMOylation dynamics. PMID:20087442
Biomedical text mining and its applications. PMID:20041219
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
GWIDD: Genome-wide protein docking database. PMID:19900970
Evaluation of linguistic features useful in extraction of interactions from PubMed; application to annotating known, high-throughput and predicted interactions in I2D. PMID:19850753
NAViGaTOR: Network Analysis, Visualization and Graphing Toronto. PMID:19837718
Towards a systems biology approach to mammalian cell cycle: modeling the entrance into S phase of quiescent fibroblasts after serum stimulation. PMID:19828076
Networking of differentially expressed genes in human cancer cells resistant to methotrexate. PMID:19732436
Building disease-specific drug-protein connectivity maps from molecular interaction networks and PubMed abstracts. PMID:19649302
Pathway databases and tools for their exploitation: benefits, current limitations and challenges. PMID:19638971
Yeast two-hybrid, a powerful tool for systems biology. PMID:19582228
Proteome-wide prediction of signal flow direction in protein interaction networks based on interacting domains. PMID:19502588
Protein-protein interaction databases: keeping up with growing interactomes. PMID:19403463
POINeT: protein interactome with sub-network analysis and hub prioritization. PMID:19379523
Reconstructing the ubiquitin network: cross-talk with other systems and identification of novel functions. PMID:19331687
Biomedical discovery acceleration, with applications to craniofacial development. PMID:19325874
Protein-protein interaction as a predictor of subcellular location. PMID:19243629
High throughput interaction data reveals degree conservation of hub proteins. PMID:19209717
Literature-curated protein interaction datasets. PMID:19116613
Ortholog-based protein-protein interaction prediction and its application to inter-species interactions. PMID:19091010
An empirical framework for binary interactome mapping. PMID:19060904
Network integration and graph analysis in mammalian molecular systems biology. PMID:19045817
PIG--the pathogen interaction gateway. PMID:18984614
VirHostNet: a knowledge base for the management and the analysis of proteome-wide virus-host interaction networks. PMID:18984613
Update of KDBI: Kinetic Data of Bio-molecular Interaction database. PMID:18971255
OntoGene in BioCreative II. PMID:18834491
Mining physical protein-protein interactions from the literature. PMID:18834490
TRANSPATH--a high quality database focused on signal transduction. PMID:18629064
Interactome data and databases: different types of protein interaction. PMID:18629062
Identifying gene-disease associations using centrality on a literature mined gene-interaction network. PMID:18586725
MPIDB: the microbial protein interaction database. PMID:18556668
Targeting the human cancer pathway protein interaction network by structural genomics. PMID:18487680
VisANT: an integrative framework for networks in systems biology. PMID:18463131
GPS 2.0, a tool to predict kinase-specific phosphorylation sites in hierarchy. PMID:18463090
Inferring the role of transcription factors in regulatory networks. PMID:18460200
MassNet: a functional annotation service for protein mass spectrometry data. PMID:18448467
Exploiting likely-positive and unlabeled data to improve the identification of protein-protein interaction articles. PMID:18315856
DBMLoc: a Database of proteins with multiple subcellular localizations. PMID:18304364
Adaptations to climate in candidate genes for common metabolic disorders. PMID:18282109
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
Protein function assignment through mining cross-species protein-protein interactions. PMID:18253506
Predicting the interactome of Xanthomonas oryzae pathovar oryzae for target selection and DB service. PMID:18215330
High-confidence prediction of global interactomes based on genome-wide coevolutionary networks. PMID:18199838
Linking the ovarian cancer transcriptome and immunome. PMID:18173842
Computational prediction of protein-protein interactions. PMID:18095187
A new computational approach to analyze human protein complexes and predict novel protein interactions. PMID:18053208
Integrative analysis for finding genes and networks involved in diabetes and other complex diseases. PMID:18045462
Hubs with network motifs organize modularity dynamically in the protein-protein interaction network of yeast. PMID:18030341
Discovery of protein interaction networks shared by diseases. PMID:17992746
Integration of biological networks and gene expression data using Cytoscape. PMID:17947979
Genes2Networks: connecting lists of gene symbols using mammalian protein interactions databases. PMID:17916244
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
Functional atlas of the integrin adhesome. PMID:17671451
Not all scale-free networks are born equal: the role of the seed graph in PPI network evolution. PMID:17616981
Characterization of protein-interaction networks in tumors. PMID:17597514
Unequal evolutionary conservation of human protein interactions in interologous networks. PMID:17535438
GeneTrail--advanced gene set enrichment analysis. PMID:17526521
Reconstruction of human protein interolog network using evolutionary conserved network. PMID:17493278
Epstein-Barr virus and virus human protein interaction maps. PMID:17446270
ProtNet: a tool for stochastic simulations of protein interaction networks dynamics. PMID:17430571
Deciphering protein-protein interactions. Part I. Experimental techniques and databases. PMID:17397251
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
RINGdb: an integrated database for G protein-coupled receptors and regulators of G protein signaling. PMID:17173697
T1DBase: integration and presentation of complex data for type 1 diabetes research. PMID:17169983
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
Snap: an integrated SNP annotation platform. PMID:17135198
Parameter estimate of signal transduction pathways. PMID:17118160
cPath: open source software for collecting, storing, and querying biological pathways. PMID:17101041
STRING 7--recent developments in the integration and prediction of protein interactions. PMID:17098935
MAPU: Max-Planck Unified database of organellar, cellular, tissue and body fluid proteomes. PMID:17090601
Comparison of protein interaction networks reveals species conservation and divergence. PMID:17044912
Analysis of protein sequence and interaction data for candidate disease gene prediction. PMID:17020920
Stratus not altocumulus: a new view of the yeast protein interaction network. PMID:16984220
Modelling protein-protein interaction networks via a stickiness index. PMID:16971339
Cataloging the relationships between proteins: a review of interaction databases. PMID:16943573
Protein-protein interactions more conserved within species than across species. PMID:16854211
ProKware: integrated software for presenting protein structural properties in protein tertiary structures. PMID:16845116
VIRGO: computational prediction of gene functions. PMID:16845022
APID: Agile Protein Interaction DataAnalyzer. PMID:16845013
The cognitive phenotype of Down syndrome: insights from intracellular network analysis. PMID:16815222
The Autoimmune Disease Database: a dynamically compiled literature-derived database. PMID:16803617
The interaction map of yeast: terra incognita? PMID:16762048
Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae. PMID:16762047
Phosphotyrosine interactome of the ErbB-receptor kinase family. PMID:16729043
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
Exploiting protein structure data to explore the evolution of protein function and biological complexity. PMID:16524831
SCOWLP: a web-based database for detailed characterization and visualization of protein interfaces. PMID:16512892
PhosphoregDB: the tissue and sub-cellular distribution of mammalian protein kinases and phosphatases. PMID:16504016
Computational analysis and prediction of the binding motif and protein interacting partners of the Abl SH3 domain. PMID:16446784
Djinn Lite: a tool for customised gene transcript modelling, annotation-data enrichment and exploration. PMID:16426464
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
MPact: the MIPS protein interaction resource on yeast. PMID:16381906
Gene3D: modelling protein structure, function and evolution. PMID:16381865
Ulysses - an application for the projection of molecular interactions across species. PMID:16356269
HomoMINT: an inferred human network based on orthology mapping of protein interactions discovered in model organisms. PMID:16351748
Comparative genomics and disorder prediction identify biologically relevant SH3 protein interactions. PMID:16110343
VisANT: data-integrating visual framework for biological networks and modules. PMID:15980487
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
PASBio: predicate-argument structures for event extraction in molecular biology. PMID:15494078
Phospho.ELM: a database of experimentally verified phosphorylation sites in eukaryotic proteins. PMID:15212693
Computational approaches to protein-protein interaction. PMID:15185965
Charting gene regulatory networks: strategies, challenges and perspectives. PMID:15080794
VisANT: an online visualization and analysis tool for biological interaction data. PMID:15028117
MitoProteome: mitochondrial protein sequence database and annotation system. PMID:14681458
IntAct: an open source molecular interaction database. PMID:14681455
The Database of Interacting Proteins: 2004 update. PMID:14681454
The aMAZE LightBench: a web interface to a relational database of cellular processes. PMID:14681453
SURFACE: a database of protein surface regions for functional annotation. PMID:14681403
From gene networks to gene function. PMID:14656964
Expressionview: visualization of quantitative trait loci and gene-expression data in Ensembl. PMID:14611663
Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs. PMID:12824383
ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins. PMID:12824381
BIND: the Biomolecular Interaction Network Database. PMID:12519993
TRANSPATH: an integrated database on signal transduction and a tool for array analysis. PMID:12519957
MINT, the molecular interaction database: 2009 update PubMed citations: 258.

258 articles citing: MINT, the molecular interaction database: 2009 update

An Integrative Network Approach to Identify Common Genes for the Therapeutics in Tuberculosis and Its Overlapping Non-Communicable Diseases. PMID:35153741
TissueNexus: a database of human tissue functional gene networks built with a large compendium of curated RNA-seq data. PMID:34850130
Network-based protein-protein interaction prediction method maps perturbations of cancer interactome. PMID:34727106
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
Genome analyses of 174 strains of Mycobacterium tuberculosis provide insight into the evolution of drug resistance and reveal potential drug targets. PMID:33750515
Integrating 3D structural information into systems biology. PMID:33744294
H-RACS: a handy tool to rank anti-cancer synergistic drugs. PMID:33173014
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
Identification of a Two-Gene (PML-EPB41) Signature With Independent Prognostic Value in Osteosarcoma. PMID:32039036
Machine learning approaches and databases for prediction of drug-target interaction: a survey paper. PMID:31950972
UNIPred-Web: a web tool for the integration and visualization of biomolecular networks for protein function prediction. PMID:31412768
Membrane protein-regulated networks across human cancers. PMID:31311925
Quantitative proteomic analysis of sperm in unexplained recurrent pregnancy loss. PMID:31288842
Molecular mechanisms involved in drug-induced liver injury caused by urate-lowering Chinese herbs: A network pharmacology study and biology experiments. PMID:31141540
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
Network spectra for drug-target identification in complex diseases: new guns against old foes. PMID:30596144
Shortest path counting in probabilistic biological networks. PMID:30514202
Context-enriched interactome powered by proteomics helps the identification of novel regulators of macrophage activation. PMID:30303482
Prediction of Novel Drugs and Diseases for Hepatocellular Carcinoma Based on Multi-Source Simulated Annealing Based Random Walk. PMID:30173379
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
ProMotE: an efficient algorithm for counting independent motifs in uncertain network topologies. PMID:29940838
Proximal Pathway Enrichment Analysis for Targeting Comorbid Diseases via Network Endopharmacology. PMID:29932108
A systems immunology approach identifies the collective impact of 5 miRs in Th2 inflammation. PMID:29875322
A homologous mapping method for three-dimensional reconstruction of protein networks reveals disease-associated mutations. PMID:29560828
The DifferentialNet database of differential protein-protein interactions in human tissues. PMID:29069447
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
A network pharmacology-based strategy deciphers the underlying molecular mechanisms of Qixuehe Capsule in the treatment of menstrual disorders. PMID:28835770
From protein-protein interactions to protein co-expression networks: a new perspective to evaluate large-scale proteomic data. PMID:28477207
ANKRD54 preferentially selects Bruton's Tyrosine Kinase (BTK) from a Human Src-Homology 3 (SH3) domain library. PMID:28369144
Net2Align: An Algorithm For Pairwise Global Alignment of Biological Networks. PMID:28356678
Integrated systems biology analysis of KSHV latent infection reveals viral induction and reliance on peroxisome mediated lipid metabolism. PMID:28257516
Network Biomarkers Constructed from Gene Expression and Protein-Protein Interaction Data for Accurate Prediction of Leukemia. PMID:28243332
Both Intrinsic Substrate Preference and Network Context Contribute to Substrate Selection of Classical Tyrosine Phosphatases. PMID:28159843
Network pharmacology-based identification of key pharmacological pathways of Yin-Huang-Qing-Fei capsule acting on chronic bronchitis. PMID:28053519
Network-based analysis of differentially expressed genes in cerebrospinal fluid (CSF) and blood reveals new candidate genes for multiple sclerosis. PMID:28028462
CanProVar 2.0: An Updated Database of Human Cancer Proteome Variation. PMID:27977206
Effective comparative analysis of protein-protein interaction networks by measuring the steady-state network flow using a Markov model. PMID:27766938
inFRank: a ranking-based identification of influential genes in biological networks. PMID:27623074
Mining biomedical images towards valuable information retrieval in biomedical and life sciences. PMID:27538578
Entropy-based divergent and convergent modular pattern reveals additive and synergistic anticerebral ischemia mechanisms. PMID:27480252
Multi-omics landscapes of colorectal cancer subtypes discriminated by an individualized prognostic signature for 5-fluorouracil-based chemotherapy. PMID:27429074
Quantitative Determination of Flexible Pharmacological Mechanisms Based On Topological Variation in Mice Anti-Ischemic Modular Networks. PMID:27383195
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
Systematic analysis of the molecular mechanism underlying atherosclerosis using a text mining approach. PMID:27251057
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
Comparative analysis of housekeeping and tissue-selective genes in human based on network topologies and biological properties. PMID:26897376
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
Signal reachability facilitates characterization of probabilistic signaling networks. PMID:26679404
Sphingosine kinase 2 is a chikungunya virus host factor co-localized with the viral replication complex. PMID:26576339
Integrative analysis of human protein, function and disease networks. PMID:26399914
Algorithms for modeling global and context-specific functional relationship networks. PMID:26254431
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
Ferret: a sentence-based literature scanning system. PMID:26091670
PrOnto database : GO term functional dissimilarity inferred from biological data. PMID:26089836
Extreme multifunctional proteins identified from a human protein interaction network. PMID:26054620
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
Prediction of host - pathogen protein interactions between Mycobacterium tuberculosis and Homo sapiens using sequence motifs. PMID:25887594
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
Network-based proteomic approaches reveal the neurodegenerative, neuroprotective and pain-related mechanisms involved after retrograde axonal damage. PMID:25784190
Expression profile of mitrogen-activated protein kinase (MAPK) signaling genes in the skeletal muscle & liver of rat with type 2 diabetes: role in disease pathology. PMID:25758573
Efficient prediction of progesterone receptor interactome using a support vector machine model. PMID:25741764
Biological databases for human research. PMID:25712261
Accurate multiple network alignment through context-sensitive random walk. PMID:25707987
Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study. PMID:25652942
Reconstructing genome-wide protein-protein interaction networks using multiple strategies with homologous mapping. PMID:25602759
The neXtProt knowledgebase on human proteins: current status. PMID:25593349
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
Protein interaction networks reveal novel autism risk genes within GWAS statistical noise. PMID:25409314
Prediction of disease-related genes based on weighted tissue-specific networks by using DNA methylation. PMID:25350763
Hope for GWAS: relevant risk genes uncovered from GWAS statistical noise. PMID:25268625
Network biology in medicine and beyond. PMID:25140061
Modeling dynamic functional relationship networks and application to ex vivo human erythroid differentiation. PMID:25115705
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
Intercellular network structure and regulatory motifs in the human hematopoietic system. PMID:25028490
Building a hierarchical organization of protein complexes out of protein association data. PMID:24978199
Large scale analysis of signal reachability. PMID:24932011
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
Integrating the interactome and the transcriptome of Drosophila. PMID:24913703
GASOLINE: a Greedy And Stochastic algorithm for optimal Local multiple alignment of Interaction NEtworks. PMID:24911103
Protein-protein interactions and genetic diseases: The interactome. PMID:24892209
BioCreative-IV virtual issue. PMID:24852177
Identification of functional modules by integration of multiple data sources using a Bayesian network classifier. PMID:24736851
NCG 4.0: the network of cancer genes in the era of massive mutational screenings of cancer genomes. PMID:24608173
A framework for biomedical figure segmentation towards image-based document retrieval. PMID:24565394
M-Finder: Uncovering functionally associated proteins from interactome data integrated with GO annotations. PMID:24565382
Prediction of protein interaction types based on sequence and network features. PMID:24564924
A systems biology-based investigation into the therapeutic effects of Gansui Banxia Tang on reversing the imbalanced network of hepatocellular carcinoma. PMID:24561634
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
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
Network cluster analysis of protein-protein interaction network identified biomarker for early onset colorectal cancer. PMID:24197691
Identification of small exonic CNV from whole-exome sequence data and application to autism spectrum disorder. PMID:24094742
PainNetworks: a web-based resource for the visualisation of pain-related genes in the context of their network associations. PMID:24036287
Network-based analysis of genome wide association data provides novel candidate genes for lipid and lipoprotein traits. PMID:23882023
Genes dysregulated to different extent or oppositely in estrogen receptor-positive and estrogen receptor-negative breast cancers. PMID:23875016
Inferring potential microRNA-microRNA associations based on targeting propensity and connectivity in the context of protein interaction network. PMID:23874989
Target essentiality and centrality characterize drug side effects. PMID:23874169
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
Trinucleotide repeats: a structural perspective. PMID:23801983
Cancer missense mutations alter binding properties of proteins and their interaction networks. PMID:23799087
ResponseNet2.0: Revealing signaling and regulatory pathways connecting your proteins and genes--now with human data. PMID:23761447
Hypoxamirs in Pulmonary Hypertension: Breathing New Life into Pulmonary Vascular Research. PMID:23745175
Protein-Protein Interactions Inferred from Domain-Domain Interactions in Genogroup II Genotype 4 Norovirus Sequences. PMID:23738320
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
Cross-species protein interactome mapping reveals species-specific wiring of stress response pathways. PMID:23695164
A systems biology-based investigation into the pharmacological mechanisms of wu tou tang acting on rheumatoid arthritis by integrating network analysis. PMID:23690848
The SH2 domain interaction landscape. PMID:23545499
Network pharmacology strategies toward multi-target anticancer therapies: from computational models to experimental design principles. PMID:23530504
Vitexicarpin acts as a novel angiogenesis inhibitor and its target network. PMID:23476684
Proteome-wide prediction of self-interacting proteins based on multiple properties. PMID:23422585
Linking proteomic and transcriptional data through the interactome and epigenome reveals a map of oncogene-induced signaling. PMID:23408876
Interactome3D: adding structural details to protein networks. PMID:23399932
A survey of protein interaction data and multigenic inherited disorders. PMID:23398688
The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies. PMID:23398680
Identification of ovarian cancer associated genes using an integrated approach in a Boolean framework. PMID:23383610
Predicting PDZ domain mediated protein interactions from structure. PMID:23336252
Identification of new protein interactions between dengue fever virus and its hosts, human and mosquito. PMID:23326450
NeuroDNet - an open source platform for constructing and analyzing neurodegenerative disease networks. PMID:23286825
Revealing functionally coherent subsets using a spectral clustering and an information integration approach. PMID:23282411
Discovering pathway cross-talks based on functional relations between pathways. PMID:23282018
GWIDD: a comprehensive resource for genome-wide structural modeling of protein-protein interactions. PMID:23245398
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
Popular computational methods to assess multiprotein complexes derived from label-free affinity purification and mass spectrometry (AP-MS) experiments. PMID:23071097
Tissue-specific functional networks for prioritizing phenotype and disease genes. PMID:23028291
Quantitative dynamics of phosphoproteome: the devil is in the details. PMID:23020125
A simple knowledge-based mining method for exploring hidden key molecules in a human biomolecular network. PMID:22979956
An integrated approach to identify causal network modules of complex diseases with application to colorectal cancer. PMID:22967703
An overview of computational life science databases & exchange formats of relevance to chemical biology research. PMID:22934944
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
CDA: combinatorial drug discovery using transcriptional response modules. PMID:22905152
Discovering the hidden sub-network component in a ranked list of genes or proteins derived from genomic experiments. PMID:22844098
atBioNet--an integrated network analysis tool for genomics and biomarker discovery. PMID:22817640
A strategy based on protein-protein interface motifs may help in identifying drug off-targets. PMID:22817115
Combinatorial drug therapy for cancer in the post-genomic era. PMID:22781697
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
Rational drug repositioning guided by an integrated pharmacological network of protein, disease and drug. PMID:22748168
Genes2FANs: connecting genes through functional association networks. PMID:22748121
Involvement of microRNA families in cancer. PMID:22743268
Network compression as a quality measure for protein interaction networks. PMID:22719828
BioContext: an integrated text mining system for large-scale extraction and contextualization of biomolecular events. PMID:22711795
DEFOG: discrete enrichment of functionally organized genes. PMID:22706384
MoNetFamily: a web server to infer homologous modules and module-module interaction networks in vertebrates. PMID:22689643
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
Computational and informatics strategies for identification of specific protein interaction partners in affinity purification mass spectrometry experiments. PMID:22611043
Context-specific protein network miner--an online system for exploring context-specific protein interaction networks from the literature. PMID:22493694
Integrated inference and analysis of regulatory networks from multi-level measurements. PMID:22482944
"Guilt by association" is the exception rather than the rule in gene networks. PMID:22479173
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
Coordination of the transcriptome and metabolome by the circadian clock. PMID:22431615
The role of structural disorder in the rewiring of protein interactions through evolution. PMID:22389433
Prioritizing disease candidate genes by a gene interconnectedness-based approach. PMID:22369140
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
Infection Strategies of Bacterial and Viral Pathogens through Pathogen-Human Protein-Protein Interactions. PMID:22347880
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
Large-scale mapping of human protein interactome using structural complexes. PMID:22261719
A dynamic view of domain-motif interactions. PMID:22253583
Three-dimensional reconstruction of protein networks provides insight into human genetic disease. PMID:22252508
Prediction and characterization of protein-protein interaction networks in swine. PMID:22230699
Recovering protein-protein and domain-domain interactions from aggregation of IP-MS proteomics of coregulator complexes. PMID:22219718
Evolution of biological interaction networks: from models to real data. PMID:22204388
RefNetBuilder: a platform for construction of integrated reference gene regulatory networks from expressed sequence tags. PMID:22166047
Constructing a robust protein-protein interaction network by integrating multiple public databases. PMID:22165958
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
IPAVS: Integrated Pathway Resources, Analysis and Visualization System. PMID:22140115
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
Identification of dysfunctional modules and disease genes in congenital heart disease by a network-based approach. PMID:22136190
A comprehensive manually curated protein-protein interaction database for the Death Domain superfamily. PMID:22135292
The IntAct molecular interaction database in 2012. PMID:22121220
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
Network of Cancer Genes (NCG 3.0): integration and analysis of genetic and network properties of cancer genes. PMID:22080562
PINA v2.0: mining interactome modules. PMID:22067443
Network analysis of microRNAs and their regulation in human ovarian cancer. PMID:22050994
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
Systems-biology approaches to discover anti-viral effectors of the human innate immune response. PMID:21994773
Prioritizing cancer-related genes with aberrant methylation based on a weighted protein-protein interaction network. PMID:21985575
Systems biology and the future of medicine. PMID:21928407
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
GPS-Prot: a web-based visualization platform for integrating host-pathogen interaction data. PMID:21777475
Bio::Homology::InterologWalk--a Perl module to build putative protein-protein interaction networks through interolog mapping. PMID:21767381
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
Systematic approaches towards the development of host-directed antiviral therapeutics. PMID:21747723
Visualization and biochemical analyses of the emerging mammalian 14-3-3-phosphoproteome. PMID:21725060
Proteomic patterns of cervical cancer cell lines, a network perspective. PMID:21696634
MINE: Module Identification in Networks. PMID:21605434
PRIN: a predicted rice interactome network. PMID:21575196
Transcriptional landscape of bone marrow-derived very small embryonic-like stem cells during hypoxia. PMID:21569252
Targeting protein-protein interactions for parasite control. PMID:21556146
The role of indirect connections in gene networks in predicting function. PMID:21551147
Predictive integration of gene functional similarity and co-expression defines treatment response of endothelial progenitor cells. PMID:21447198
Omics-based molecular target and biomarker identification. PMID:21370102
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
Discovering networks of perturbed biological processes in hepatocyte cultures. PMID:21245926
Immunogenomics and systems biology of vaccines. PMID:21198673
Interactome mapping suggests new mechanistic details underlying Alzheimer's disease. PMID:21163940
A computational approach to analyze the mechanism of action of the kinase inhibitor bafetinib. PMID:21124949
Identification of new substrates of the protein-tyrosine phosphatase PTP1B by Bayesian integration of proteome evidence. PMID:21123182
SPIKE: a database of highly curated human signaling pathways. PMID:21097778
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
Phospho.ELM: a database of phosphorylation sites--update 2011. PMID:21062810
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
KUPS: constructing datasets of interacting and non-interacting protein pairs with associated attributions. PMID:20952400
HitPredict: a database of quality assessed protein-protein interactions in nine species. PMID:20947562
Prediction of human protein-protein interaction by a mixed Bayesian model and its application to exploring underlying cancer-related pathway crosstalk. PMID:20943681
iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence. PMID:20940177
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
MatrixDB, the extracellular matrix interaction database. PMID:20852260
TRIP Database: a manually curated database of protein-protein interactions for mammalian TRP channels. PMID:20851834
Curating the innate immunity interactome. PMID:20727158
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
DynaMod: dynamic functional modularity analysis. PMID:20460468
Improved microarray-based decision support with graph encoded interactome data. PMID:20419106

http://dx.doi.org/10.1093/nar/GKR930

http://dx.doi.org/10.1002/cpbi.93

Tags:

Tags
More detailed information about this field from each metasource.

molecular interaction
metasource: Fairsharing.org
version: FAIRsharing.org: MINT; Molecular INTeraction database; DOI: https://doi.org/10.25504/FAIRsharing.2bdvmk; Last edited: March 19, 2021, 11:16 a.m.; Last accessed: Jan 03 2022 7:06 p.m.

metasource: re3data.org
version: re3data.org: Molecular INTeraction Database; editing status 2022-10-25; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R38S3B last accessed: 2022-11-04

protein interaction
metasource: Fairsharing.org
version: FAIRsharing.org: MINT; Molecular INTeraction database; DOI: https://doi.org/10.25504/FAIRsharing.2bdvmk; Last edited: March 19, 2021, 11:16 a.m.; Last accessed: Jan 03 2022 7:06 p.m.

metasource: re3data.org
version: re3data.org: Molecular INTeraction Database; editing status 2022-10-25; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R38S3B last accessed: 2022-11-04

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

genetic interaction
metasource: re3data.org
version: re3data.org: Molecular INTeraction Database; editing status 2022-10-25; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R38S3B last accessed: 2022-11-04

human proteins
metasource: re3data.org
version: re3data.org: Molecular INTeraction Database; editing status 2022-10-25; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R38S3B last accessed: 2022-11-04

peptide interaction
metasource: re3data.org
version: re3data.org: Molecular INTeraction Database; editing status 2022-10-25; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R38S3B last accessed: 2022-11-04

protein interacting partners
metasource: re3data.org
version: re3data.org: Molecular INTeraction Database; editing status 2022-10-25; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R38S3B last accessed: 2022-11-04

protein-protein interaction
metasource: re3data.org
version: re3data.org: Molecular INTeraction Database; editing status 2022-10-25; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R38S3B last accessed: 2022-11-04

viral proteins
metasource: re3data.org
version: re3data.org: Molecular INTeraction Database; editing status 2022-10-25; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R38S3B last accessed: 2022-11-04

protein interactions
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:36.893430

molecular interactions, pathways and networks
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:36.893430

data integration and warehousing
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:36.893430

rare diseases
metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:36.893430

molecular interaction protein interaction metabolic and signaling pathways protein-protein interactions genetic interaction human proteins peptide interaction protein interacting partners protein-protein interaction viral proteins protein interaction molecular interactions, pathways and networks data integration and warehousing rare diseases

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IntAct molecular interaction database

DOMINO

Molecular Interaction eXtensible Markup Language

HPID - Human Protein Interaction database

Human Protein-Protein Interaction rEference

PespotDB

Bacterial Protein Interaction Database

Interaction Reference Index Web Interface

Biological General Repository for Interaction Datasets

Microbial Protein Interaction Database

mentha

Protein Interaction Network Analysis platform

VirusMentha

I2D - Interologous Interaction Database

DroID - Drosophila Interactions Database

PSI Molecular Interaction Controlled Vocabulary

Interologous Interaction Database

Negatome

Database of Interacting Proteins

Complex Portal