R3VG8D last accessed: 2022-11-04

Database of interacting proteins (DIP)
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:10.100293

dip
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:10.100293

Other names: DIP, Database of interacting proteins (DIP), dip

The database of interacting protein (DIP) database stores experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions. The data stored within the DIP database were curated, both manually by expert curators and automatically using computational approaches that utilize the the knowledge about the protein-protein interaction networks extracted from the core DIP data.

Webpage:

https://dip.doe-mbi.ucla.edu

Licence:

Name: Creative Commons Attribution-NoDerivs 3.0 Unported (CC BY-ND 3.0)
URL: https://creativecommons.org/licenses/by-nd/3.0/

Publications:

Publications
More detailed information about this field from each metasource.

The Database of Interacting Proteins: 2004 update
PMID: 14681454
metasource: Fairsharing.org
version: FAIRsharing.org: DIP; Database of Interacting Proteins; DOI: https://doi.org/10.25504/FAIRsharing.qje0v8; Last edited: June 23, 2021, 2 p.m.; Last accessed: Jan 03 2022 7:09 p.m.

metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:10.100293

DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions
PMID: 11752321
metasource: Fairsharing.org
version: FAIRsharing.org: DIP; Database of Interacting Proteins; DOI: https://doi.org/10.25504/FAIRsharing.qje0v8; Last edited: June 23, 2021, 2 p.m.; Last accessed: Jan 03 2022 7:09 p.m.

metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:10.100293

DIP: the database of interacting proteins
PMID: 10592249
metasource: Fairsharing.org
version: FAIRsharing.org: DIP; Database of Interacting Proteins; DOI: https://doi.org/10.25504/FAIRsharing.qje0v8; Last edited: June 23, 2021, 2 p.m.; Last accessed: Jan 03 2022 7:09 p.m.

DIP: The Database of Interacting Proteins: 2001 update
PMID: 11125102
metasource: Fairsharing.org
version: FAIRsharing.org: DIP; Database of Interacting Proteins; DOI: https://doi.org/10.25504/FAIRsharing.qje0v8; Last edited: June 23, 2021, 2 p.m.; Last accessed: Jan 03 2022 7:09 p.m.

metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:10.100293

The Database of Interacting Proteins: 2004 update PubMed citations: 853.

853 articles citing: The Database of Interacting Proteins: 2004 update

The Landscape of Virus-Host Protein-Protein Interaction Databases. PMID:35910656
SIPGCN: A Novel Deep Learning Model for Predicting Self-Interacting Proteins from Sequence Information Using Graph Convolutional Networks. PMID:35884848
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
Systems Drug Discovery for Diffuse Large B Cell Lymphoma Based on Pathogenic Molecular Mechanism via Big Data Mining and Deep Learning Method. PMID:35743172
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
Protein-Protein Interaction (PPI) Network of Zebrafish Oestrogen Receptors: A Bioinformatics Workflow. PMID:35629318
A Novel Ensemble Learning-Based Computational Method to Predict Protein-Protein Interactions from Protein Primary Sequences. PMID:35625503
Proteome-wide prediction and analysis of the Cryptosporidium parvum protein-protein interaction network through integrative methods. PMID:35615014
IMEx Databases: Displaying Molecular Interactions into a Single, Standards-Compliant Dataset. PMID:35507258
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
Antifungal activity of an artificial peptide aptamer SNP-D4 against Fusarium oxysporum. PMID:35223198
Using Surface Hydrophobicity Together with Empirical Potentials to Identify Protein-Protein Binding Sites: Application to the Interactions of E-cadherins. PMID:35167069
Investigating the Role of Obesity in Prostate Cancer and Identifying Biomarkers for Drug Discovery: Systems Biology and Deep Learning Approaches. PMID:35164166
Interactome of Arabidopsis Thaliana. PMID:35161331
The Landscape of Aminoacyl-tRNA Synthetases Involved in Severe Acute Respiratory Syndrome Coronavirus 2 Infection. PMID:35153822
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
How Far Are We from the Completion of the Human Protein Interactome Reconstruction? PMID:35053288
Potential Molecular Mechanisms and Remdesivir Treatment for Acute Respiratory Syndrome Corona Virus 2 Infection/COVID 19 Through RNA Sequencing and Bioinformatics Analysis. PMID:34992355
A full-proteome, interaction-specific characterization of mutational hotspots across human cancers. PMID:34963661
Protein-protein interactions: Methods, databases, and applications in virus-host study. PMID:34909403
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
Multiscale interactome analysis coupled with off-target drug predictions reveals drug repurposing candidates for human coronavirus disease. PMID:34857794
ConsensusPathDB 2022: molecular interactions update as a resource for network biology. PMID:34850110
A Network-Based Methodology to Identify Subnetwork Markers for Diagnosis and Prognosis of Colorectal Cancer. PMID:34790220
A Deep Learning and XGBoost-Based Method for Predicting Protein-Protein Interaction Sites. PMID:34764983
ATRX regulates glial identity and the tumor microenvironment in IDH-mutant glioma. PMID:34763709
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
An Ebola, Neisseria and Trypanosoma human protein interaction census reveals a conserved human protein cluster targeted by various human pathogens. PMID:34745452
DeepTrio: a ternary prediction system for protein-protein interaction using mask multiple parallel convolutional neural networks. PMID:34694333
Alternative Splicing Mechanisms Underlying Opioid-Induced Hyperalgesia. PMID:34680965
Computational repurposing of therapeutic small molecules from cancer to pulmonary hypertension. PMID:34669463
Protein-protein interaction prediction based on ordinal regression and recurrent convolutional neural networks. PMID:34625020
PncsHub: a platform for annotating and analyzing non-classically secreted proteins in Gram-positive bacteria. PMID:34551435
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
Robust and accurate prediction of protein-protein interactions by exploiting evolutionary information. PMID:34413375
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
alfaNET: A Database of Alfalfa-Bacterial Stem Blight Protein-Protein Interactions Revealing the Molecular Features of the Disease-causing Bacteria. PMID:34361108
Overlapping Structures Detection in Protein-Protein Interaction Networks Using Community Detection Algorithm Based on Neighbor Clustering Coefficient. PMID:34249104
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
KEA3: improved kinase enrichment analysis via data integration. PMID:34019655
An overview of graph databases and their applications in the biomedical domain. PMID:34003247
scConnect: a method for exploratory analysis of cell-cell communication based on single cell RNA sequencing data. PMID:33974001
In silico comparative analysis of LRRK2 interactomes from brain, kidney and lung. PMID:33915162
Identification of IFN-Induced Transmembrane Protein 1 With Prognostic Value in Pancreatic Cancer Using Network Module-Based Analysis. PMID:33869009
Identification of disease treatment mechanisms through the multiscale interactome. PMID:33741907
Identification of potential and novel target genes in pituitary prolactinoma by bioinformatics analysis. PMID:33709028
Bioinformatics analyses of significant genes, related pathways, and candidate diagnostic biomarkers and molecular targets in SARS-CoV-2/COVID-19. PMID:33553808
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
Classification and prediction of protein-protein interaction interface using machine learning algorithm. PMID:33469042
Functions of Essential Genes and a Scale-Free Protein Interaction Network Revealed by Structure-Based Function and Interaction Prediction for a Minimal Genome. PMID:33393786
PICKLE 3.0: Enriching the human Meta-database with the mouse protein interactome extended via mouse-human orthology. PMID:33367505
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
Conjoint Feature Representation of GO and Protein Sequence for PPI Prediction Based on an Inception RNN Attention Network. PMID:33230427
ClusterM: a scalable algorithm for computational prediction of conserved protein complexes across multiple protein interaction networks. PMID:33208103
FunRes: resolving tissue-specific functional cell states based on a cell-cell communication network model. PMID:33179736
Human Gene Functional Network-Informed Prediction of HIV-1 Host Dependency Factors. PMID:33144314
IHP-PING-generating integrated human protein-protein interaction networks on-the-fly. PMID:33129201
Cell Development Deficiency and Gene Expression Dysregulation of Trisomy 21 Retina Revealed by Single-Nucleus RNA Sequencing. PMID:33072724
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
A review of protein-protein interaction network alignment: From pathway comparison to global alignment. PMID:33033584
De novo missense variants disrupting protein-protein interactions affect risk for autism through gene co-expression and protein networks in neuronal cell types. PMID:33032641
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
Determining the interaction status and evolutionary fate of duplicated homomeric proteins. PMID:32853212
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
Flexible model selection for mechanistic network models. PMID:32765880
Analyzing IDPs in Interactomes. PMID:32696395
DPCT: A Dynamic Method for Detecting Protein Complexes From TAP-Aware Weighted PPI Network. PMID:32676097
Using Random Forest Model Combined With Gabor Feature to Predict Protein-Protein Interaction From Protein Sequence. PMID:32655275
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
Dynamic rewiring of the human interactome by interferon signaling. PMID:32539747
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
Ellagic acid and human cancers: a systems pharmacology and docking study to identify principal hub genes and main mechanisms of action. PMID:32410114
Comprehensive gene and pathway analysis of cervical cancer progression. PMID:32256826
WeiBI (web-based platform): Enriching integrated interaction network with increased coverage and functional proteins from genome-wide experimental OMICS data. PMID:32221380
Circular RNA expression profile in blood according to ischemic stroke etiology. PMID:32175077
Exploring Integrative Analysis Using the BioMedical Evidence Graph. PMID:32097025
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
Identification of a Two-Gene (PML-EPB41) Signature With Independent Prognostic Value in Osteosarcoma. PMID:32039036
In Silico Strategies in Tuberculosis Drug Discovery. PMID:32033144
PlaPPISite: a comprehensive resource for plant protein-protein interaction sites. PMID:32028878
Unraveling the role of salt-sensitivity genes in obesity with integrated network biology and co-expression analysis. PMID:32027667
Bioinformatics for Renal and Urinary Proteomics: Call for Aggrandization. PMID:32024005
Identification of self-interacting proteins by integrating random projection classifier and finite impulse response filter. PMID:31881833
Analysis of Differentially Expressed Genes in Coronary Artery Disease by Integrated Microarray Analysis. PMID:31881747
MaXLinker: Proteome-wide Cross-link Identifications with High Specificity and Sensitivity. PMID:31839598
Sequence-Derived Markers of Drug Targets and Potentially Druggable Human Proteins. PMID:31803227
Leveraging User-Friendly Network Approaches to Extract Knowledge From High-Throughput Omics Datasets. PMID:31798629
Qualitative transcriptional signature for predicting pathological response of colorectal cancer to FOLFOX therapy. PMID:31785020
Global Vectors Representation of Protein Sequences and Its Application for Predicting Self-Interacting Proteins with Multi-Grained Cascade Forest Model. PMID:31726752
A Bootstrap Method for Goodness of Fit and Model Selection with a Single Observed Network. PMID:31723196
Mitochondrial dysfunction in rheumatoid arthritis: A comprehensive analysis by integrating gene expression, protein-protein interactions and gene ontology data. PMID:31703070
Therapeutic target database 2020: enriched resource for facilitating research and early development of targeted therapeutics. PMID:31691823
Dissecting the Shared and Context-Dependent Pathways Mediated by the p140Cap Adaptor Protein in Cancer and in Neurons. PMID:31681758
Pathway Commons 2019 Update: integration, analysis and exploration of pathway data. PMID:31647099
Neglog: Homology-Based Negative Data Sampling Method for Genome-Scale Reconstruction of Human Protein-Protein Interaction Networks. PMID:31614890
Identifying Protein Complexes from Dynamic Temporal Interval Protein-Protein Interaction Networks. PMID:31531351
Multifaceted protein-protein interaction prediction based on Siamese residual RCNN. PMID:31510705
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
Protein-Protein Interactions in Candida albicans. PMID:31440220
Differential network analysis and protein-protein interaction study reveals active protein modules in glucocorticoid resistance for infant acute lymphoblastic leukemia. PMID:31370801
The Methods Employed in Mass Spectrometric Analysis of Posttranslational Modifications (PTMs) and Protein-Protein Interactions (PPIs). PMID:31347048
PS-MCL: parallel shotgun coarsened Markov clustering of protein interaction networks. PMID:31337329
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
Patient-specific cancer genes contribute to recurrently perturbed pathways and establish therapeutic vulnerabilities in esophageal adenocarcinoma. PMID:31308377
Genome-wide functional association networks: background, data & state-of-the-art resources. PMID:31281921
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
Protein-protein interaction prediction using a hybrid feature representation and a stacked generalization scheme. PMID:31182027
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
Multi-Omic Data Interpretation to Repurpose Subtype Specific Drug Candidates for Breast Cancer. PMID:31134131
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
A Comprehensive Drosophila melanogaster Transcription Factor Interactome. PMID:30995488
Understanding Human-Virus Protein-Protein Interactions Using a Human Protein Complex-Based Analysis Framework. PMID:30984872
Identification of Important Invasion-Related Genes in Non-functional Pituitary Adenomas. PMID:30982163
Mining Featured Biomarkers Linked with Epithelial Ovarian CancerBased on Bioinformatics. PMID:30970615
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 Comprehensive Survey of Tools and Software for Active Subnetwork Identification. PMID:30891064
An Improved Deep Forest Model for Predicting Self-Interacting Proteins From Protein Sequence Using Wavelet Transformation. PMID:30881376
BGFE: A Deep Learning Model for ncRNA-Protein Interaction Predictions Based on Improved Sequence Information. PMID:30813451
Prediction of Self-Interacting Proteins from Protein Sequence Information Based on Random Projection Model and Fast Fourier Transform. PMID:30795499
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
Detecting protein complexes based on a combination of topological and biological properties in protein-protein interaction network. PMID:30647725
ACCBN: ant-Colony-clustering-based bipartite network method for predicting long non-coding RNA-protein interactions. PMID:30626319
The Network of Cancer Genes (NCG): a comprehensive catalogue of known and candidate cancer genes from cancer sequencing screens. PMID:30606230
Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set. PMID:30602777
Predicting protein-protein interactions using high-quality non-interacting pairs. PMID:30598096
The RTK Interactome: Overview and Perspective on RTK Heterointeractions. PMID:30589534
Classifying mild traumatic brain injuries with functional network analysis. PMID:30577783
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
STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. PMID:30476243
Structural disorder in the proteome and interactome of Alkhurma virus (ALKV). PMID:30443749
Predicting protein-protein interactions through sequence-based deep learning. PMID:30423091
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
Antiviral activity of the mineralocorticoid receptor NR3C2 against Herpes simplex virus Type 1 (HSV-1) infection. PMID:30367157
Establishment of stably expandable induced myogenic stem cells by four transcription factors. PMID:30361642
Genomic data integration systematically biases interactome mapping. PMID:30332399
Single-cell RNA-seq reveals dynamic transcriptome profiling in human early neural differentiation. PMID:30239706
Gene Ontology Enrichment Improves Performances of Functional Similarity of Genes. PMID:30108262
Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken. PMID:30086717
Evolution of In Silico Strategies for Protein-Protein Interaction Drug Discovery. PMID:30082644
MiRNA-BD: an evidence-based bioinformatics model and software tool for microRNA biomarker discovery. PMID:30081733
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
Automatic extraction of protein-protein interactions using grammatical relationship graph. PMID:30066644
Identification of drug target candidates of the swine pathogen Actinobacillus pleuropneumoniae by construction of protein-protein interaction network. PMID:30047117
Protein-protein interactions of human viruses. PMID:30031213
Integrating Rio1 activities discloses its nutrient-activated network in Saccharomyces cerevisiae. PMID:30011030
Identification of Antifungal Targets Based on Computer Modeling. PMID:29973534
An interactome perturbation framework prioritizes damaging missense mutations for developmental disorders. PMID:29892012
Construction of a specific SVM classifier and identification of molecular markers for lung adenocarcinoma based on lncRNA-miRNA-mRNA network. PMID:29872324
Identification of Central Regulators of Calcium Signaling and ECM-Receptor Interaction Genetically Associated With the Progression and Recurrence of Atrial Fibrillation. PMID:29868113
Discovering novel SNPs that are correlated with patient outcome in a Singaporean cancer patient cohort treated with gemcitabine-based chemotherapy. PMID:29751792
Functional signaling and gene regulatory networks between the oocyte and the surrounding cumulus cells. PMID:29747587
PPI network analyses of human WD40 protein family systematically reveal their tendency to assemble complexes and facilitate the complex predictions. PMID:29745845
NIPS, a 3D network-integrated predictor of deleterious protein SAPs, and its application in cancer prognosis. PMID:29662108
JAMI: a Java library for molecular interactions and data interoperability. PMID:29642846
Systematic Evaluation of Molecular Networks for Discovery of Disease Genes. PMID:29605183
Completing sparse and disconnected protein-protein network by deep learning. PMID:29566671
Gastric cancer biomarkers; A systems biology approach. PMID:29556568
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
Protein complex finding and ranking: An application to Alzheimer's disease. PMID:29358552
Interactome INSIDER: a structural interactome browser for genomic studies. PMID:29355848
Investigation and identification of functional post-translational modification sites associated with drug binding and protein-protein interactions. PMID:29322920
Revealing protein functions based on relationships of interacting proteins and GO terms. PMID:29297388
A systematic atlas of chaperome deregulation topologies across the human cancer landscape. PMID:29293508
The integration of weighted gene association networks based on information entropy. PMID:29272314
Functional Analysis of Human Hub Proteins and Their Interactors Involved in the Intrinsic Disorder-Enriched Interactions. PMID:29257115
A multi-network clustering method for detecting protein complexes from multiple heterogeneous networks. PMID:29219066
FunCoup 4: new species, data, and visualization. PMID:29165593
Molecular Interaction Search Tool (MIST): an integrated resource for mining gene and protein interaction data. PMID:29155944
SPRINT: ultrafast protein-protein interaction prediction of the entire human interactome. PMID:29141584
DiffSLC: A graph centrality method to detect essential proteins of a protein-protein interaction network. PMID:29121073
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
The DifferentialNet database of differential protein-protein interactions in human tissues. PMID:29069447
Systems biology: An emerging strategy for discovering novel pathogenetic mechanisms that promote cardiovascular disease. PMID:29043273
Anti-CRISPRdb: a comprehensive online resource for anti-CRISPR proteins. PMID:29036676
Rapamycin-induced miR-21 promotes mitochondrial homeostasis and adaptation in mTORC1 activated cells. PMID:29029388
Review of computational methods for virus-host protein interaction prediction: a case study on novel Ebola-human interactions. PMID:29028879
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
Evolutionary analysis and interaction prediction for protein-protein interaction network in geometric space. PMID:28886027
Protein Complexes Prediction Method Based on Core-Attachment Structure and Functional Annotations. PMID:28878201
Modeling protein quaternary structure of homo- and hetero-oligomers beyond binary interactions by homology. PMID:28874689
The effect of Bu Zhong Yi Qi decoction on simulated weightlessness‑induced muscle atrophy and its mechanisms. PMID:28849026
Identifying protein complexes in PPI network using non-cooperative sequential game. PMID:28827597
Knowledge-guided gene prioritization reveals new insights into the mechanisms of chemoresistance. PMID:28800781
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
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
A computational framework for distinguishing direct versus indirect interactions in human functional protein-protein interaction networks. PMID:28524201
LncRNAs2Pathways: Identifying the pathways influenced by a set of lncRNAs of interest based on a global network propagation method. PMID:28425476
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
Finding low-conductance sets with dense interactions (FLCD) for better protein complex prediction. PMID:28361714
A Review of Recent Advancement in Integrating Omics Data with Literature Mining towards Biomedical Discoveries. PMID:28331849
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
Understanding the roles of intrinsic disorder in subunits of hemoglobin and the disease process of sickle cell anemia. PMID:28232898
A Comprehensive Gene Expression Meta-analysis Identifies Novel Immune Signatures in Rheumatoid Arthritis Patients. PMID:28210261
How can functional annotations be derived from profiles of phenotypic annotations? PMID:28183267
Protein Bioinformatics Databases and Resources. PMID:28150231
Binding of small molecules at interface of protein-protein complex - A newer approach to rational drug design. PMID:28149177
Minimal amino acids in the I/LWEQ domain required for anterior/posterior localization in Dictyostelium. PMID:28124777
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
Genomic expression differences between cutaneous cells from red hair color individuals and black hair color individuals based on bioinformatic analysis. PMID:28030792
CanProVar 2.0: An Updated Database of Human Cancer Proteome Variation. PMID:27977206
Specificity of broad protein interaction surfaces for proteins with multiple binding partners. PMID:27924264
The TissueNet v.2 database: A quantitative view of protein-protein interactions across human tissues. PMID:27899616
Prediction of Protein-Protein Interactions by Evidence Combining Methods. PMID:27879651
Prediction of interacting proteins from homology-modeled complex structures using sequence and structure scores. PMID:27857563
HINT: a database of annotated protein-protein interactions and their homologs. PMID:27857549
Bisdemethoxycurcumin exerts pro-apoptotic effects in human pancreatic adenocarcinoma cells through mitochondrial dysfunction and a GRP78-dependent pathway. PMID:27845899
Intrinsic disorder in proteins involved in amyotrophic lateral sclerosis. PMID:27838743
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
Approaches to modernize the combination drug development paradigm. PMID:27793177
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
Effective comparative analysis of protein-protein interaction networks by measuring the steady-state network flow using a Markov model. PMID:27766938
Identification of self-interacting proteins by exploring evolutionary information embedded in PSI-BLAST-constructed position specific scoring matrix. PMID:27732957
Exploring the interactions of the RAS family in the human protein network and their potential implications in RAS-directed therapies. PMID:27713118
Predicting protein-protein interactions via multivariate mutual information of protein sequences. PMID:27677692
Identification of Protein-Protein Interactions via a Novel Matrix-Based Sequence Representation Model with Amino Acid Contact Information. PMID:27669239
BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID. PMID:27589962
Functional characterization of EI24-induced autophagy in the degradation of RING-domain E3 ligases. PMID:27541728
BiCAMWI: A Genetic-Based Biclustering Algorithm for Detecting Dynamic Protein Complexes. PMID:27462706
Unfoldomics of prostate cancer: on the abundance and roles of intrinsically disordered proteins in prostate cancer. PMID:27453073
Multi-omics landscapes of colorectal cancer subtypes discriminated by an individualized prognostic signature for 5-fluorouracil-based chemotherapy. PMID:27429074
Protein function in precision medicine: deep understanding with machine learning. PMID:27423136
Clinical significance of mitofusin-2 and its signaling pathways in hepatocellular carcinoma. PMID:27389277
Comparison of large networks with sub-sampling strategies. PMID:27380992
Systematic Identification of Anti-Fungal Drug Targets by a Metabolic Network Approach. PMID:27379244
HPIDB 2.0: a curated database for host-pathogen interactions. PMID:27374121
The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. PMID:27374120
Reconstruction and Application of Protein-Protein Interaction Network. PMID:27338356
Challenges in structural approaches to cell modeling. PMID:27255863
Systematic analysis of the molecular mechanism underlying atherosclerosis using a text mining approach. PMID:27251057
Genome-Wide Inference of Protein-Protein Interaction Networks Identifies Crosstalk in Abscisic Acid Signaling. PMID:27208273
Controllability of protein-protein interaction phosphorylation-based networks: Participation of the hub 14-3-3 protein family. PMID:27195976
Characterizing gene sets using discriminative random walks with restart on heterogeneous biological networks. PMID:27153592
APID interactomes: providing proteome-based interactomes with controlled quality for multiple species and derived networks. PMID:27131791
PTIR: Predicted Tomato Interactome Resource. PMID:27121261
A Quantitative Approach to Analyzing Genome Reductive Evolution Using Protein-Protein Interaction Networks: A Case Study of Mycobacterium leprae. PMID:27066064
Proteomics-Based Analysis of Protein Complexes in Pluripotent Stem Cells and Cancer Biology. PMID:27011181
Identification of Toxic Pyrrolizidine Alkaloids and Their Common Hepatotoxicity Mechanism. PMID:26959016
Inference of protein-protein interaction networks from multiple heterogeneous data. PMID:26941784
Comparing Alzheimer's and Parkinson's diseases networks using graph communities structure. PMID:26935435
Discovering communities in complex networks by edge label propagation. PMID:26926830
A two-layer integration framework for protein complex detection. PMID:26911324
Complementary Post Transcriptional Regulatory Information is Detected by PUNCH-P and Ribosome Profiling. PMID:26898226
Bayesian module identification from multiple noisy networks. PMID:26893596
Predicting physiologically relevant SH3 domain mediated protein-protein interactions in yeast. PMID:26861823
Topological characteristics of target genes regulated by abiotic-stress-responsible miRNAs in a rice interactome network. PMID:26830287
Proteomic approaches to uncovering virus-host protein interactions during the progression of viral infection. PMID:26817613
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
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
CancerNet: a database for decoding multilevel molecular interactions across diverse cancer types. PMID:26690544
Fundamentals of protein interaction network mapping. PMID:26681426
LENS: web-based lens for enrichment and network studies of human proteins. PMID:26680011
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
dbPTM 2016: 10-year anniversary of a resource for post-translational modification of proteins. PMID:26578568
CD36 Is a Matrix Metalloproteinase-9 Substrate That Stimulates Neutrophil Apoptosis and Removal During Cardiac Remodeling. PMID:26578544
Protein-protein interaction site prediction in Homo sapiens and E. coli using an interaction-affinity based membership function in fuzzy SVM. PMID:26564981
PharmDB-K: Integrated Bio-Pharmacological Network Database for Traditional Korean Medicine. PMID:26555441
The Transporter Classification Database (TCDB): recent advances. PMID:26546518
Integrated interactions database: tissue-specific view of the human and model organism interactomes. PMID:26516188
NCG 5.0: updates of a manually curated repository of cancer genes and associated properties from cancer mutational screenings. PMID:26516186
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
Integrative analysis of human protein, function and disease networks. PMID:26399914
Tyrosine Kinase Ligand-Receptor Pair Prediction by Using Support Vector Machine. PMID:26347773
Large-scale extraction of gene interactions from full-text literature using DeepDive. PMID:26338771
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
A computational framework for the prioritization of disease-gene candidates. PMID:26330267
Integrated inference and evaluation of host-fungi interaction networks. PMID:26300851
Computational analysis of protein interaction networks for infectious diseases. PMID:26261187
Systematic Analysis of the Molecular Mechanism Underlying Decidualization Using a Text Mining Approach. PMID:26222155
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
PrOnto database : GO term functional dissimilarity inferred from biological data. PMID:26089836
By the company they keep: interaction networks define the binding ability of transcription factors. PMID:26089389
Protein flexibility in the light of structural alphabets. PMID:26075209
TRRUST: a reference database of human transcriptional regulatory interactions. PMID:26066708
Identifying diabetes-related important protein targets with few interacting partners with the PageRank algorithm. PMID:26064627
Extreme multifunctional proteins identified from a human protein interaction network. PMID:26054620
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
MyProteinNet: build up-to-date protein interaction networks for organisms, tissues and user-defined contexts. PMID:25990735
Predicting protein-protein interactions from primary protein sequences using a novel multi-scale local feature representation scheme and the random forest. PMID:25946106
A review on computational systems biology of pathogen-host interactions. PMID:25914674
Identifying module biomarker in type 2 diabetes mellitus by discriminative area of functional activity. PMID:25888350
Predicted protein-protein interactions in the moss Physcomitrella patens: a new bioinformatic resource. PMID:25885037
REGULATOR: a database of metazoan transcription factors and maternal factors for developmental studies. PMID:25880930
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
Computational approaches for prediction of pathogen-host protein-protein interactions. PMID:25759684
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
Prediction of protein-protein interactions related to protein complexes based on protein interaction networks. PMID:25722972
cisPath: an R/Bioconductor package for cloud users for visualization and management of functional protein interaction networks. PMID:25708840
Network tuned multiple rank aggregation and applications to gene ranking. PMID:25708095
Accurate multiple network alignment through context-sensitive random walk. PMID:25707987
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
Comparison of human cell signaling pathway databases--evolution, drawbacks and challenges. PMID:25632107
Virus-host interactomics: new insights and opportunities for antiviral drug discovery. PMID:25593595
cytoHubba: identifying hub objects and sub-networks from complex interactome. PMID:25521941
Comprehensive discovery of DNA motifs in 349 human cells and tissues reveals new features of motifs. PMID:25505144
Protein structure annotation resources. PMID:25502191
MicroRNA Dysregulation, Gene Networks, and Risk for Schizophrenia in 22q11.2 Deletion Syndrome. PMID:25484875
In silico prediction of synthetic lethality by meta-analysis of genetic interactions, functions, and pathways in yeast and human cancer. PMID:25452682
A proteome-scale map of the human interactome network. PMID:25416956
A systems biology strategy to identify molecular mechanisms of action and protein indicators of traumatic brain injury. PMID:25399920
Text mining in cancer gene and pathway prioritization. PMID:25392685
Mechismo: predicting the mechanistic impact of mutations and modifications on molecular interactions. PMID:25392414
MatrixDB, the extracellular matrix interaction database: updated content, a new navigator and expanded functionalities. PMID:25378329
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
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
Detecting temporal protein complexes from dynamic protein-protein interaction networks. PMID:25282536
Drug-Like Protein-Protein Interaction Modulators: Challenges and Opportunities for Drug Discovery and Chemical Biology. PMID:25254076
Integration strategy is a key step in network-based analysis and dramatically affects network topological properties and inferring outcomes. PMID:25243127
VirusMentha: a new resource for virus-host protein interactions. PMID:25217587
Finding trans-regulatory genes and protein complexes modulating meiotic recombination hotspots of human, mouse and yeast. PMID:25208583
Alignment-free protein interaction network comparison. PMID:25161230
Functional and genomic context in pathway analysis of GWAS data. PMID:25154796
Network biology in medicine and beyond. PMID:25140061
Toward a systems-level understanding of gene regulatory, protein interaction, and metabolic networks in cyanobacteria. PMID:25071821
Proteome-wide analysis of human disease mutations in short linear motifs: neglected players in cancer? PMID:25057855
Detecting communities based on network topology. PMID:25033828
The domain landscape of virus-host interactomes. PMID:24991570
Building a hierarchical organization of protein complexes out of protein association data. PMID:24978199
Exploring function prediction in protein interaction networks via clustering methods. PMID:24972109
Correlating information contents of gene ontology terms to infer semantic similarity of gene products. PMID:24963342
Detecting overlapping protein complexes based on a generative model with functional and topological properties. PMID:24928559
Comparative analysis of human tissue interactomes reveals factors leading to tissue-specific manifestation of hereditary diseases. PMID:24921629
NetworkAnalyst--integrative approaches for protein-protein interaction network analysis and visual exploration. PMID:24861621
GeneSense: a new approach for human gene annotation integrated with protein-protein interaction networks. PMID:24667292
pZMO7-Derived shuttle vectors for heterologous protein expression and proteomic applications in the ethanol-producing bacterium Zymomonas mobilis. PMID:24629064
A second-generation protein-protein interaction network of Helicobacter pylori. PMID:24627523
A systematic in silico mining of the mechanistic implications and therapeutic potentials of estrogen receptor (ER)-α in breast cancer. PMID:24614816
NCG 4.0: the network of cancer genes in the era of massive mutational screenings of cancer genomes. PMID:24608173
Protein-protein interactions prediction based on iterative clique extension with gene ontology filtering. PMID:24578640
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
Joint clustering of protein interaction networks through Markov random walk. PMID:24565376
Detection of type 2 diabetes related modules and genes based on epigenetic networks. PMID:24565181
Prediction of protein interaction types based on sequence and network features. PMID:24564924
A combined approach for genome wide protein function annotation/prediction. PMID:24564915
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
Computational Prediction of Protein-Protein Interaction Networks: Algo-rithms and Resources. PMID:24396273
A Module Analysis Approach to Investigate Molecular Mechanism of TCM Formula: A Trial on Shu-feng-jie-du Formula. PMID:24376467
A predicted protein interactome for rice. PMID:24279740
Integrating structure to protein-protein interaction networks that drive metastasis to brain and lung in breast cancer. PMID:24278371
KBDOCK 2013: a spatial classification of 3D protein domain family interactions. PMID:24271397
Prediction of protein essentiality by the support vector machine with statistical tests. PMID:24250217
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
Integrating in silico resources to map a signaling network. PMID:24233784
PATRIC, the bacterial bioinformatics database and analysis resource. PMID:24225323
UniHI 7: an enhanced database for retrieval and interactive analysis of human molecular interaction networks. PMID:24214987
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
Functional module identification in protein interaction networks by interaction patterns. PMID:24085567
Capturing cooperative interactions with the PSI-MI format. PMID:24067240
Optimizing a global alignment of protein interaction networks. PMID:24048352
Stable isotope metabolic labeling-based quantitative phosphoproteomic analysis of Arabidopsis mutants reveals ethylene-regulated time-dependent phosphoproteins and putative substrates of constitutive triple response 1 kinase. PMID:24043427
PainNetworks: a web-based resource for the visualisation of pain-related genes in the context of their network associations. PMID:24036287
Computational analysis of virus-host interactomes. PMID:23996253
A systematic analysis of host factors reveals a Med23-interferon-λ regulatory axis against herpes simplex virus type 1 replication. PMID:23950709
A probabilistic model of neutral and selective dynamics of protein network evolution. PMID:23931333
Automatic extraction of biomolecular interactions: an empirical approach. PMID:23883165
Genes dysregulated to different extent or oppositely in estrogen receptor-positive and estrogen receptor-negative breast cancers. PMID:23875016
SMETANA: accurate and scalable algorithm for probabilistic alignment of large-scale biological networks. PMID:23874484
JBioWH: an open-source Java framework for bioinformatics data integration. PMID:23846595
DBATE: database of alternative transcripts expression. PMID:23842462
Link clustering reveals structural characteristics and biological contexts in signed molecular networks. PMID:23826198
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 context-sensitive framework for the analysis of human signalling pathways in molecular interaction networks. PMID:23812986
Revealing the hidden relationship by sparse modules in complex networks with a large-scale analysis. PMID:23762457
ResponseNet2.0: Revealing signaling and regulatory pathways connecting your proteins and genes--now with human data. PMID:23761447
Optimization criteria and biological process enrichment in homologous multiprotein modules. PMID:23757502
PPIcons: identification of protein-protein interaction sites in selected organisms. PMID:23729008
Integrated analysis of recurrent properties of cancer genes to identify novel drivers. PMID:23718799
Human monogenic disease genes have frequently functionally redundant paralogs. PMID:23696728
Cross-species protein interactome mapping reveals species-specific wiring of stress response pathways. PMID:23695164
Proteome-wide discovery of mislocated proteins in cancer. PMID:23674306
INstruct: a database of high-quality 3D structurally resolved protein interactome networks. PMID:23599502
An integrated approach to uncover driver genes in breast cancer methylation genomes. PMID:23579546
Improved method for protein complex detection using bottleneck proteins. PMID:23566214
The potential of text mining in data integration and network biology for plant research: a case study on Arabidopsis. PMID:23532071
Network pharmacology strategies toward multi-target anticancer therapies: from computational models to experimental design principles. PMID:23530504
The evolutionary dynamics of protein-protein interaction networks inferred from the reconstruction of ancient networks. PMID:23526967
Protein complex-based analysis framework for high-throughput data sets. PMID:23443684
Proteome-wide prediction of self-interacting proteins based on multiple properties. PMID:23422585
Interactome3D: adding structural details to protein networks. PMID:23399932
Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review. PMID:23384594
Identification of ovarian cancer associated genes using an integrated approach in a Boolean framework. PMID:23383610
A novel subgradient-based optimization algorithm for blockmodel functional module identification. PMID:23368964
Inferring homologous protein-protein interactions through pair position specific scoring matrix. PMID:23367879
Partial AUC maximization for essential gene prediction using genetic algorithms. PMID:23351383
Predicting PDZ domain mediated protein interactions from structure. PMID:23336252
PPInterFinder--a mining tool for extracting causal relations on human proteins from literature. PMID:23325628
NeuroDNet - an open source platform for constructing and analyzing neurodegenerative disease networks. PMID:23286825
TranSeqAnnotator: large-scale analysis of transcriptomic data. PMID:23282024
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
Protein interaction network of Arabidopsis thaliana female gametophyte development identifies novel proteins and relations. PMID:23239973
Identification of pharmacological targets in amyotrophic lateral sclerosis through genomic analysis of deregulated genes and pathways. PMID:23204922
STRING v9.1: protein-protein interaction networks, with increased coverage and integration. PMID:23203871
The TissueNet database of human tissue protein-protein interactions. PMID:23193266
PrePPI: a structure-informed database of protein-protein interactions. PMID:23193263
Systems biology of pathogen-host interaction: networks of protein-protein interaction within pathogens and pathogen-human interactions in the post-genomic era. PMID:23193100
Proteomics-based methods for discovery, quantification, and validation of protein-protein interactions. PMID:23157382
SpliceAid-F: a database of human splicing factors and their RNA-binding sites. PMID:23118479
Systems analysis of plant functional, transcriptional, physical interaction, and metabolic networks. PMID:23110892
Combing the hairball with BioFabric: a new approach for visualization of large networks. PMID:23102059
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
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
A Systems Biology Approach to Deciphering the Etiology of Steatosis Employing Patient-Derived Dermal Fibroblasts and iPS Cells. PMID:22969728
RhesusBase: a knowledgebase for the monkey research community. PMID:22965133
Identifying functional modules in interaction networks through overlapping Markov clustering. PMID:22962469
Biological function through network topology: a survey of the human diseasome. PMID:22962330
Multiple biomarker tissue arrays: A computational approach to identifying protein-protein interactions in the EGFR/ERK signalling pathway. PMID:22937740
A network synthesis model for generating protein interaction network families. PMID:22912671
CDA: combinatorial drug discovery using transcriptional response modules. PMID:22905152
DTome: a web-based tool for drug-target interactome construction. PMID:22901092
HINT: High-quality protein interactomes and their applications in understanding human disease. PMID:22846459
Effect of reference genome selection on the performance of computational methods for genome-wide protein-protein interaction prediction. PMID:22844541
Differentially co-expressed interacting protein pairs discriminate samples under distinct stages of HIV type 1 infection. PMID:22784566
Combinatorial drug therapy for cancer in the post-genomic era. PMID:22781697
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
Protein interface remodeling in a chemically induced protein dimer. PMID:22733548
Proteome-wide prediction of protein-protein interactions from high-throughput data. PMID:22729399
AlignNemo: a local network alignment method to integrate homology and topology. PMID:22719866
Detecting mutually exclusive interactions in protein-protein interaction maps. PMID:22715412
BIPS: BIANA Interolog Prediction Server. A tool for protein-protein interaction inference. PMID:22689642
Templates are available to model nearly all complexes of structurally characterized proteins. PMID:22645367
The evolutionary dynamics of functional modules and the extraordinary plasticity of regulons: the Escherichia coli perspective. PMID:22618875
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
Prediction and comparison of Salmonella-human and Salmonella-Arabidopsis interactomes. PMID:22589098
Inferring high-confidence human protein-protein interactions. PMID:22558947
Revisiting the variation of clustering coefficient of biological networks suggests new modular structure. PMID:22548803
A comparative analysis of protein targets of withdrawn cardiovascular drugs in human and mouse. PMID:22548699
MOfinder: a novel algorithm for detecting overlapping modules from protein-protein interaction network. PMID:22500072
System approaches reveal the molecular networks involved in neural stem cell differentiation. PMID:22492180
Swimming upstream: identifying proteomic signals that drive transcriptional changes using the interactome and multiple "-omics" datasets. PMID:22482945
Integrated inference and analysis of regulatory networks from multi-level measurements. PMID:22482944
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
How to link ontologies and protein-protein interactions to literature: text-mining approaches and the BioCreative experience. PMID:22438567
Information flow in interaction networks II: channels, path lengths, and potentials. PMID:22409812
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
A classification scoring schema to validate protein interactors. PMID:22359432
Drug-target network in myocardial infarction reveals multiple side effects of unrelated drugs. PMID:22355571
HIPPIE: Integrating protein interaction networks with experiment based quality scores. PMID:22348130
Infection Strategies of Bacterial and Viral Pathogens through Pathogen-Human Protein-Protein Interactions. PMID:22347880
Rewiring of PDZ domain-ligand interaction network contributed to eukaryotic evolution. PMID:22346764
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
Modularity in protein complex and drug interactions reveals new polypharmacological properties. PMID:22279562
Fast and accurate modeling of protein-protein interactions by combining template-interface-based docking with flexible refinement. PMID:22275112
A dynamic view of domain-motif interactions. PMID:22253583
IMID: integrated molecular interaction database. PMID:22238258
Prediction and characterization of protein-protein interaction networks in swine. PMID:22230699
An integer linear programming approach for finding deregulated subgraphs in regulatory networks. PMID:22210863
Evolution of biological interaction networks: from models to real data. PMID:22204388
Dynamical analysis of yeast protein interaction network during the sake brewing process. PMID:22203560
Novel search method for the discovery of functional relationships. PMID:22180409
Protein complex detection with semi-supervised learning in protein interaction networks. PMID:22165896
NWE: Node-weighted expansion for protein complex prediction using random walk distances. PMID:22165822
The dichotomy in degree correlation of biological networks. PMID:22164269
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
BinTree seeking: a novel approach to mine both bi-sparse and cohesive modules in protein interaction networks. PMID:22140454
Gene3D: a domain-based resource for comparative genomics, functional annotation and protein network analysis. PMID:22139938
MetaBase--the wiki-database of biological databases. PMID:22139927
A comprehensive manually curated protein-protein interaction database for the Death Domain superfamily. PMID:22135292
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
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
Tools used to study how protein complexes are assembled in signaling cascades. PMID:22002082
Prioritizing cancer-related genes with aberrant methylation based on a weighted protein-protein interaction network. PMID:21985575
iRefScape. A Cytoscape plug-in for visualization and data mining of protein interaction data from iRefIndex. PMID:21975162
Network-based prediction and analysis of HIV dependency factors. PMID:21966263
Quantification of protein group coherence and pathway assignment using functional association. PMID:21929787
Revisiting the negative example sampling problem for predicting protein-protein interactions. PMID:21908540
Dominating biological networks. PMID:21887225
ppiTrim: constructing non-redundant and up-to-date interactomes. PMID:21873645
Exploiting bounded signal flow for graph orientation based on cause-effect pairs. PMID:21867496
Application of computational systems biology to explore environmental toxicity hazards. PMID:21846611
Prediction of body fluids where proteins are secreted into based on protein interaction network. PMID:21829572
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
Integrated bio-entity network: a system for biological knowledge discovery. PMID:21738677
An organogenesis network-based comparative transcriptome analysis for understanding early human development in vivo and in vitro. PMID:21733158
InterMitoBase: an annotated database and analysis platform of protein-protein interactions for human mitochondria. PMID:21718467
BioGraph: unsupervised biomedical knowledge discovery via automated hypothesis generation. PMID:21696594
Conditional random field approach to prediction of protein-protein interactions using domain information. PMID:21689483
Generative probabilistic models for protein-protein interaction networks--the biclique perspective. PMID:21685063
Noise reduction in protein-protein interaction graphs by the implementation of a novel weighting scheme. PMID:21679454
A gene-phenotype network for the laboratory mouse and its implications for systematic phenotyping. PMID:21625554
Evidence for the additions of clustered interacting nodes during the evolution of protein interaction networks from network motifs. PMID:21595981
CASCADE_SCAN: mining signal transduction network from high-throughput data based on steepest descent method. PMID:21575263
PRIN: a predicted rice interactome network. PMID:21575196
Protein annotation from protein interaction networks and Gene Ontology. PMID:21571095
Transcriptional robustness and protein interactions are associated in yeast. PMID:21545728
Modification of gene duplicability during the evolution of protein interaction network. PMID:21490719
The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods. PMID:21472436
A systems biology approach for the investigation of the heparin/heparan sulfate interactome. PMID:21454685
Predictive integration of gene functional similarity and co-expression defines treatment response of endothelial progenitor cells. PMID:21447198
Assembling a protein-protein interaction map of the SSU processome from existing datasets. PMID:21423703
Assessing the biological significance of gene expression signatures and co-expression modules by studying their network properties. PMID:21408226
Supervised learning and prediction of physical interactions between human and HIV proteins. PMID:21382517
Comparative analysis of protein interaction networks reveals that conserved pathways are susceptible to HIV-1 interception. PMID:21342548
BioGRID REST Service, BiogridPlugin2 and BioGRID WebGraph: new tools for access to interaction data at BioGRID. PMID:21300700
Integrative features of the yeast phosphoproteome and protein-protein interaction map. PMID:21298081
Discovering networks of perturbed biological processes in hepatocyte cultures. PMID:21245926
A machine learning approach for genome-wide prediction of morbid and druggable human genes based on systems-level data. PMID:21210975
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Understanding protein evolutionary rate by integrating gene co-expression with protein interactions. PMID:21190591
Novel genes exhibit distinct patterns of function acquisition and network integration. PMID:21187012
Literature curation of protein interactions: measuring agreement across major public databases. PMID:21183497
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Combining modularity, conservation, and interactions of proteins significantly increases precision and coverage of protein function prediction. PMID:21171995
Features analysis for identification of date and party hubs in protein interaction network of Saccharomyces Cerevisiae. PMID:21167069
Interactome mapping suggests new mechanistic details underlying Alzheimer's disease. PMID:21163940
Using biological knowledge to uncover the mystery in the search for epistasis in genome-wide association studies. PMID:21158748
A comparative study of cancer proteins in the human protein-protein interaction network. PMID:21143787
A computational approach to analyze the mechanism of action of the kinase inhibitor bafetinib. PMID:21124949
Network analysis of human protein location. PMID:21106131
Integrating diverse biological and computational sources for reliable protein-protein interactions. PMID:21106130
Modularity of Escherichia coli sRNA regulation revealed by sRNA-target and protein network analysis. PMID:21106118
Functional genomics complements quantitative genetics in identifying disease-gene associations. PMID:21085640
ConsensusPathDB: toward a more complete picture of cell biology. PMID:21071422
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
Global protein interactome exploration through mining genome-scale data in Arabidopsis thaliana. PMID:21047383
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. PMID:21045058
Inference of surface membrane factors of HIV-1 infection through functional interaction networks. PMID:20967291
Discover protein complexes in protein-protein interaction networks using parametric local modularity. PMID:20958996
HitPredict: a database of quality assessed protein-protein interactions in nine species. PMID:20947562
HPIDB--a unified resource for host-pathogen interactions. PMID:20946599
Prediction of human protein-protein interaction by a mixed Bayesian model and its application to exploring underlying cancer-related pathway crosstalk. PMID:20943681
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
Mapping the self-interacting domains of TuMV HC-Pro and the subcellular localization of the protein. PMID:20938729
Structural polymorphism in F-actin. PMID:20935633
ChemProt: a disease chemical biology database. PMID:20935044
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
Candidate gene prioritization by network analysis of differential expression using machine learning approaches. PMID:20840752
Diffusion model based spectral clustering for protein-protein interaction networks. PMID:20830307
The BioPAX community standard for pathway data sharing. PMID:20829833
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
The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*. PMID:20727200
Curating the innate immunity interactome. PMID:20727158
The human-bacterial pathogen protein interaction networks of Bacillus anthracis, Francisella tularensis, and Yersinia pestis. PMID:20711500
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
Development of a novel bioinformatics tool for in silico validation of protein interactions. PMID:20625507
PROFESS: a PROtein function, evolution, structure and sequence database. PMID:20624718
Protein-protein interactions essentials: key concepts to building and analyzing interactome networks. PMID:20589078
PPLook: an automated data mining tool for protein-protein interaction. PMID:20550717
Composite functional module inference: detecting cooperation between transcriptional regulation and protein interaction by mantel test. PMID:20534172
dockYard--a repository to assist modeling of protein-protein docking. PMID:20524020
A quick guide to large-scale genomic data mining. PMID:20523745
PCFamily: a web server for searching homologous protein complexes. PMID:20511590
Functional features, biological pathways, and protein interaction networks of addiction-related genes. PMID:20491072
DynaMod: dynamic functional modularity analysis. PMID:20460468
Profiling of protein interaction networks of protein complexes using affinity purification and quantitative mass spectrometry. PMID:20445003
Detection of gene orthology from gene co-expression and protein interaction networks. PMID:20438654
Identification of functional hubs and modules by converting interactome networks into hierarchical ordering of proteins. PMID:20438650
SZGR: a comprehensive schizophrenia gene resource. PMID:20424623
Reconstruction of gene regulatory modules in cancer cell cycle by multi-source data integration. PMID:20422009
Improved microarray-based decision support with graph encoded interactome data. PMID:20419106
Systems pharmacology of arrhythmias. PMID:20407125
Inference of functional relations in predicted protein networks with a machine learning approach. PMID:20376314
Protein Bioinformatics Infrastructure for the Integration and Analysis of Multiple High-Throughput "omics" Data. PMID:20369061
Predicting protein-protein interactions in unbalanced data using the primary structure of proteins. PMID:20361868
Visualization of omics data for systems biology. PMID:20195258
Xenopus meiotic microtubule-associated interactome. PMID:20174651
BisoGenet: a new tool for gene network building, visualization and analysis. PMID:20163717
Global approaches to study protein-protein interactions among viruses and hosts. PMID:20143950
Biana: a software framework for compiling biological interactions and analyzing networks. PMID:20105306
Transcriptomic analysis identifies phosphatases as novel targets for adenotonsillar hypertrophy of pediatric obstructive sleep apnea. PMID:20093640
Network-free inference of knockout effects in yeast. PMID:20066032
Deciphering chemotaxis pathways using cross species comparisons. PMID:20064255
CORNET: a user-friendly tool for data mining and integration. PMID:20053712
Of mice and men: comparative proteomics of bronchoalveolar fluid. PMID:20032019
Comparison of phylogenetic trees through alignment of embedded evolutionary distances. PMID:20003527
Critical assessment of sequence-based protein-protein interaction prediction methods that do not require homologous protein sequences. PMID:20003442
'Unknown' proteins and 'orphan' enzymes: the missing half of the engineering parts list--and how to find it. PMID:20001958
Chromatin regulation and gene centrality are essential for controlling fitness pleiotropy in yeast. PMID:19956643
Phylogeny-guided interaction mapping in seven eukaryotes. PMID:19948065
Recurated protein interaction datasets. PMID:19935838
Role for protein-protein interaction databases in human genetics. PMID:19929610
Novel protein-protein interactions inferred from literature context. PMID:19924298
Network of Cancer Genes: a web resource to analyze duplicability, orthology and network properties of cancer genes. PMID:19906700
GWIDD: Genome-wide protein docking database. PMID:19900970
MINT, the molecular interaction database: 2009 update. PMID:19897547
Looking at cerebellar malformations through text-mined interactomes of mice and humans. PMID:19893633
Evolution of biomolecular networks: lessons from metabolic and protein interactions. PMID:19851337
The IntAct molecular interaction database in 2010. PMID:19850723
Predicting meiotic pathways in human fetal oogenesis. PMID:19846598
PathBinder--text empirics and automatic extraction of biomolecular interactions. PMID:19811683
The Modular Organization of Protein Interactions in Escherichia coli. PMID:19798435
Detection of molecular paths associated with insulitis and type 1 diabetes in non-obese diabetic mouse. PMID:19798418
Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network. PMID:19728866
NASCENT: an automatic protein interaction network generation tool for non-model organisms. PMID:19707301
Knowledge-guided inference of domain-domain interactions from incomplete protein-protein interaction networks. PMID:19667081
Multi-level learning: improving the prediction of protein, domain and residue interactions by allowing information flow between levels. PMID:19656385
A survey of the population genetic variation in the human kinome. PMID:19644514
Discovery: an interactive resource for the rational selection and comparison of putative drug target proteins in malaria. PMID:19642978
PathBuilder--open source software for annotating and developing pathway resources. PMID:19628504
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
RNAiCut: automated detection of significant genes from functional genomic screens. PMID:19564846
Predicting protein-protein interactions in Arabidopsis thaliana through integration of orthology, gene ontology and co-expression. PMID:19563678
A network of conserved damage survival pathways revealed by a genomic RNAi screen. PMID:19543366
The Symbiosis Interactome: a computational approach reveals novel components, functional interactions and modules in Sinorhizobium meliloti. PMID:19531251
PIAS proteins: pleiotropic interactors associated with SUMO. PMID:19526197
SpaK/SpaR two-component system characterized by a structure-driven domain-fusion method and in vitro phosphorylation studies. PMID:19503843
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
Network-based prediction of metabolic enzymes' subcellular localization. PMID:19477995
Bioinformatics resources for cancer research with an emphasis on gene function and structure prediction tools. PMID:19458756
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
Deciphering peculiar protein-protein interacting modules in Deinococcus radiodurans. PMID:19356244
Biomedical discovery acceleration, with applications to craniofacial development. PMID:19325874
A general pipeline for quality and statistical assessment of protein interaction data using R and Bioconductor. PMID:19325550
Uncovering new signaling proteins and potential drug targets through the interactome analysis of Mycobacterium tuberculosis. PMID:19298676
Using biological networks to search for interacting loci in genome-wide association studies. PMID:19277065
Noninjurious mechanical ventilation activates a proinflammatory transcriptional program in the lung. PMID:19276240
Protein-protein interaction as a predictor of subcellular location. PMID:19243629
Protein function annotation by homology-based inference. PMID:19226439
An innovative approach for testing bioinformatics programs using metamorphic testing. PMID:19152705
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
Effects of binding factors on structural elements in F-actin. PMID:19113841
An evolutionary and structural characterization of mammalian protein complex organization. PMID:19108706
Precision and recall estimates for two-hybrid screens. PMID:19091773
POLAR MAPPER: a computational tool for integrated visualization of protein interaction networks and mRNA expression data. PMID:19091689
Ortholog-based protein-protein interaction prediction and its application to inter-species interactions. PMID:19091010
Integrated network analysis platform for protein-protein interactions. PMID:19079255
An experimentally derived confidence score for binary protein-protein interactions. PMID:19060903
Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome. PMID:19054114
Network integration and graph analysis in mammalian molecular systems biology. PMID:19045817
PIPs: human protein-protein interaction prediction database. PMID:18988626
UniHI 4: new tools for query, analysis and visualization of the human protein-protein interactome. PMID:18984619
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
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
DroID: the Drosophila Interactions Database, a comprehensive resource for annotated gene and protein interactions. PMID:18840285
The interactome: predicting the protein-protein interactions in cells. PMID:18839074
Physical protein-protein interactions predicted from microarrays. PMID:18829707
iRefIndex: a consolidated protein interaction database with provenance. PMID:18823568
A genomewide functional network for the laboratory mouse. PMID:18818725
The information highways of a biotechnological workhorse--signal transduction in Hypocrea jecorina. PMID:18803869
A probabilistic framework to predict protein function from interaction data integrated with semantic knowledge. PMID:18801191
The use of Gene Ontology terms for predicting highly-connected 'hub' nodes in protein-protein interaction networks. PMID:18796161
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
Automated clustering of probe molecules from solvent mapping of protein surfaces: new algorithms applied to hot-spot mapping and structure-based drug design. PMID:18679808
Integrating protein-protein interactions and text mining for protein function prediction. PMID:18673526
Visualizing global properties of large complex networks. PMID:18648531
The molecule role ontology: an ontology for annotation of signal transduction pathway molecules in the scientific literature. PMID:18629146
Deducing topology of protein-protein interaction networks from experimentally measured sub-networks. PMID:18598366
The topology of the bacterial co-conserved protein network and its implications for predicting protein function. PMID:18590549
The effects of protein interactions, gene essentiality and regulatory regions on expression variation. PMID:18582382
Human Proteinpedia as a resource for clinical proteomics. PMID:18573810
Probabilistic cross-species inference of orthologous genomic regions created by whole-genome duplication in yeast. PMID:18562662
Inferring modules of functionally interacting proteins using the Bond Energy Algorithm. PMID:18559112
Ensemble non-negative matrix factorization methods for clustering protein-protein interactions. PMID:18556670
MPIDB: the microbial protein interaction database. PMID:18556668
Exploiting the proteome to improve the genome-wide genetic analysis of epistasis in common human diseases. PMID:18551320
Discovering functional interaction patterns in protein-protein interaction networks. PMID:18547430
ENDEAVOUR update: a web resource for gene prioritization in multiple species. PMID:18508807
Prediction of enzyme function by combining sequence similarity and protein interactions. PMID:18505562
Beyond tissueInfo: functional prediction using tissue expression profile similarity searches. PMID:18483083
Protein interaction predictions from diverse sources. PMID:18468558
GPS 2.0, a tool to predict kinase-specific phosphorylation sites in hierarchy. PMID:18463090
The MoVIN server for the analysis of protein interaction networks. PMID:18387199
Walking the interactome for prioritization of candidate disease genes. PMID:18371930
Predicting cancer involvement of genes from heterogeneous data. PMID:18371197
Interrogating domain-domain interactions with parsimony based approaches. PMID:18366803
Topological comparison of methods for predicting transcriptional cooperativity in yeast. PMID:18366726
A systems-level approach to mapping the telomere length maintenance gene circuitry. PMID:18319724
The landscape of human proteins interacting with viruses and other pathogens. PMID:18282095
Prediction of protein-protein interactions using protein signature profiling. PMID:18267299
Protein function assignment through mining cross-species protein-protein interactions. PMID:18253506
The evolutionary dynamics of the Saccharomyces cerevisiae protein interaction network after duplication. PMID:18199840
Modeling the regulatory network of histone acetylation in Saccharomyces cerevisiae. PMID:18091724
EndoNet: an information resource about regulatory networks of cell-to-cell communication. PMID:18045786
Where have all the interactions gone? Estimating the coverage of two-hybrid protein interaction maps. PMID:18039026
Transcriptional profiling of non-small cell lung cancer cells with activating EGFR somatic mutations. PMID:18030354
Functional pathways shared by liver and lung metastases: a mitochondrial chaperone machine is up-regulated in soft-tissue breast cancer metastasis. PMID:18008173
The BioGRID Interaction Database: 2008 update. PMID:18000002
AtPID: Arabidopsis thaliana protein interactome database--an integrative platform for plant systems biology. PMID:17962307
Bacteriome.org--an integrated protein interaction database for E. coli. PMID:17942431
Characterization of protein hubs by inferring interacting motifs from protein interactions. PMID:17941705
Analysis on multi-domain cooperation for predicting protein-protein interactions. PMID:17937822
Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions. PMID:17925023
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
Semantic integration to identify overlapping functional modules in protein interaction networks. PMID:17650343
Reuse of structural domain-domain interactions in protein networks. PMID:17640363
Not all scale-free networks are born equal: the role of the seed graph in PPI network evolution. PMID:17616981
Probabilistic prediction and ranking of human protein-protein interactions. PMID:17615067
In search of the biological significance of modular structures in protein networks. PMID:17542644
bZIPDB: a database of regulatory information for human bZIP transcription factors. PMID:17535445
GeneTrail--advanced gene set enrichment analysis. PMID:17526521
FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments. PMID:17478504
In silico pathway reconstruction: Iron-sulfur cluster biogenesis in Saccharomyces cerevisiae. PMID:17408500
Deciphering protein-protein interactions. Part I. Experimental techniques and databases. PMID:17397251
BioInfer: a corpus for information extraction in the biomedical domain. PMID:17291334
An evaluation of human protein-protein interaction data in the public domain. PMID:17254303
SPIDer: Saccharomyces protein-protein interaction database. PMID:17254300
Evolutionary conservation of domain-domain interactions. PMID:17184549
UniHI: an entry gate to the human protein interactome. PMID:17158159
IntAct--open source resource for molecular interaction data. PMID:17145710
MINT: the Molecular INTeraction database. PMID:17135203
DOMINO: a database of domain-peptide interactions. PMID:17135199
Parameter estimate of signal transduction pathways. PMID:17118160
A correlated motif approach for finding short linear motifs from protein interaction networks. PMID:17107624
cPath: open source software for collecting, storing, and querying biological pathways. PMID:17101041
STRING 7--recent developments in the integration and prediction of protein interactions. PMID:17098935
Predicting domain-domain interactions using a parsimony approach. PMID:17094802
Co-evolutionary analysis of domains in interacting proteins reveals insights into domain-domain interactions mediating protein-protein interactions. PMID:16949097
PIPE: a protein-protein interaction prediction engine based on the re-occurring short polypeptide sequences between known interacting protein pairs. PMID:16872538
Free-energy distribution of binary protein-protein binding suggests cross-species interactome differences. PMID:16861299
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
APID: Agile Protein Interaction DataAnalyzer. PMID:16845013
Global topological features of cancer proteins in the human interactome. PMID:16844706
BBP: Brucella genome annotation with literature mining and curation. PMID:16842628
The cognitive phenotype of Down syndrome: insights from intracellular network analysis. PMID:16815222
What properties characterize the hub proteins of the protein-protein interaction network of Saccharomyces cerevisiae? PMID:16780599
Network motif identification in stochastic networks. PMID:16769903
Accelerated evolutionary rate may be responsible for the emergence of lineage-specific genes in ascomycota. PMID:16755356
Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks. PMID:16749936
Protein complex compositions predicted by structural similarity. PMID:16738133
An integrated approach to the prediction of domain-domain interactions. PMID:16725050
Exploration of biological network centralities with CentiBiN. PMID:16630347
Predicting disease genes using protein-protein interactions. PMID:16611749
QPath: a method for querying pathways in a protein-protein interaction network. PMID:16606460
A database and tool, IM Browser, for exploring and integrating emerging gene and protein interaction data for Drosophila. PMID:16603075
Functional partitioning of yeast co-expression networks after genome duplication. PMID:16555924
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
Computational modeling of the Plasmodium falciparum interactome reveals protein function on a genome-wide scale. PMID:16520460
A pooling-deconvolution strategy for biological network elucidation. PMID:16489335
Djinn Lite: a tool for customised gene transcript modelling, annotation-data enrichment and exploration. PMID:16426464
Cluster analysis of networks generated through homology: automatic identification of important protein communities involved in cancer metastasis. PMID:16398927
EndoNet: an information resource about endocrine networks. PMID:16381928
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
PINT: Protein-protein Interactions Thermodynamic Database. PMID:16381844
Refining protein subcellular localization. PMID:16322766
Discover protein sequence signatures from protein-protein interaction data. PMID:16305745
The yeast kinome displays scale free topology with functional hub clusters. PMID:16283924
Alternative splicing and protein function. PMID:16274476
Inferring protein domain interactions from databases of interacting proteins. PMID:16207360
Bcl-x(L)-mediated changes in metabolic pathways of breast cancer cells: from survival in the blood stream to organ-specific metastasis. PMID:16192647
Effect of dataset selection on the topological interpretation of protein interaction networks. PMID:16174296
Large-scale identification of yeast integral membrane protein interactions. PMID:16093310
Tools enabling the elucidation of molecular pathways active in human disease: application to Hepatitis C virus infection. PMID:15967031
Detecting remotely related proteins by their interactions and sequence similarity. PMID:15883372
Confirmation of human protein interaction data by human expression data. PMID:15877815
Nebulon: a system for the inference of functional relationships of gene products from the rearrangement of predicted operons. PMID:15867197
Filtering high-throughput protein-protein interaction data using a combination of genomic features. PMID:15833142
Comparative analysis of the Saccharomyces cerevisiae and Caenorhabditis elegans protein interaction networks. PMID:15777474
BioAfrica's HIV-1 proteomics resource: combining protein data with bioinformatics tools. PMID:15757512
Atlas - a data warehouse for integrative bioinformatics. PMID:15723693
The European Bioinformatics Institute's data resources: towards systems biology. PMID:15608238
STRING: known and predicted protein-protein associations, integrated and transferred across organisms. PMID:15608232
The Biomolecular Interaction Network Database and related tools 2005 update. PMID:15608229
Biomedical term mapping databases. PMID:15608198
ProtoNet 4.0: a hierarchical classification of one million protein sequences. PMID:15608180
The topological relationship between the large-scale attributes and local interaction patterns of complex networks. PMID:15598746
PreSPI: a domain combination based prediction system for protein-protein interaction. PMID:15576357
'Conserved hypothetical' proteins: prioritization of targets for experimental study. PMID:15479782
PathBLAST: a tool for alignment of protein interaction networks. PMID:15215356
Charting gene regulatory networks: strategies, challenges and perspectives. PMID:15080794
DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions PubMed citations: 527.

527 articles citing: DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions

lncRNA-miRNA-mRNA ceRNA Network Involved in Sheep Prolificacy: An Integrated Approach. PMID:35893032
A supervised protein complex prediction method with network representation learning and gene ontology knowledge. PMID:35879648
Deep learning frameworks for protein-protein interaction prediction. PMID:35832624
Protein-protein interaction and non-interaction predictions using gene sequence natural vector. PMID:35780196
PHILM2Web: A high-throughput database of macromolecular host-pathogen interactions on the Web. PMID:35776535
Computational identification of protein complexes from network interactions: Present state, challenges, and the way forward. PMID:35685359
A tensor-based bi-random walks model for protein function prediction. PMID:35637427
Bioinformatics-Based Approaches to Study Virus-Host Interactions During SARS-CoV-2 Infection. PMID:35554909
An Ensemble Learning Framework for Detecting Protein Complexes From PPI Networks. PMID:35281831
Predicting Protein-Protein Interactions via Random Ferns with Evolutionary Matrix Representation. PMID:35242211
An Iterative Method for Predicting Essential Proteins Based on Multifeature Fusion and Linear Neighborhood Similarity. PMID:35140599
The DOMINO web-server for active module identification analysis. PMID:35139202
Super.Complex: A supervised machine learning pipeline for molecular complex detection in protein-interaction networks. PMID:34972161
An Improved Memetic Algorithm for Detecting Protein Complexes in Protein Interaction Networks. PMID:34970305
Computational methods for protein localization prediction. PMID:34765098
A Novel Collaborative Filtering Model-Based Method for Identifying Essential Proteins. PMID:34745230
DeepTrio: a ternary prediction system for protein-protein interaction using mask multiple parallel convolutional neural networks. PMID:34694333
Convolutional neural network for human cancer types prediction by integrating protein interaction networks and omics data. PMID:34667236
An iteration model for identifying essential proteins by combining comprehensive PPI network with biological information. PMID:34496745
A Novel Method for Identifying Essential Proteins Based on Non-negative Matrix Tri-Factorization. PMID:34422014
Robust and accurate prediction of protein-protein interactions by exploiting evolutionary information. PMID:34413375
A Novel Model for Identifying Essential Proteins Based on Key Target Convergence Sets. PMID:34394201
Computational Phosphorylation Network Reconstruction: An Update on Methods and Resources. PMID:34270057
Method for Identifying Essential Proteins by Key Features of Proteins in a Novel Protein-Domain Network. PMID:34267785
A protein interactions map of multiple organ systems associated with COVID-19 disease. PMID:34261299
Databases for Protein-Protein Interactions. PMID:34236665
Super.Complex: A supervised machine learning pipeline for molecular complex detection in protein-interaction networks. PMID:34189530
mPPI: a database extension to visualize structural interactome in a one-to-many manner. PMID:34156447
Protein functional module identification method combining topological features and gene expression data. PMID:34103008
Predicting Protein-Protein Interactions via Gated Graph Attention Signed Network. PMID:34071437
A unified resource and configurable model of the synapse proteome and its role in disease. PMID:33976238
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
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
Pathogenic missense protein variants affect different functional pathways and proteomic features than healthy population variants. PMID:33909605
Centrality Analysis of Protein-Protein Interaction Networks and Molecular Docking Prioritize Potential Drug-Targets in Type 1 Diabetes. PMID:33841528
Editor's introduction to this issue (G&I 19:1, 2021). PMID:33840165
Predicting Protein-Protein Interactions Using Symmetric Logistic Matrix Factorization. PMID:33831302
Method for Essential Protein Prediction Based on a Novel Weighted Protein-Domain Interaction Network. PMID:33815480
Systems Medicine Design for Triple-Negative Breast Cancer and Non-Triple-Negative Breast Cancer Based on Systems Identification and Carcinogenic Mechanisms. PMID:33802957
CEGSO: Boosting Essential Proteins Prediction by Integrating Protein Complex, Gene Expression, Gene Ontology, Subcellular Localization and Orthology Information. PMID:33772722
Short loop functional commonality identified in leukaemia proteome highlights crucial protein sub-networks. PMID:33709075
Overexpression of miR-1306-5p, miR-3195, and miR-3914 Inhibits Ameloblast Differentiation through Suppression of Genes Associated with Human Amelogenesis Imperfecta. PMID:33672174
DOMINO: a network-based active module identification algorithm with reduced rate of false calls. PMID:33471440
Elucidating the network features and evolutionary attributes of intra- and interspecific protein-protein interactions between human and pathogenic bacteria. PMID:33420198
Delayed Comparison and Apriori Algorithm (DCAA): A Tool for Discovering Protein-Protein Interactions From Time-Series Phosphoproteomic Data. PMID:33363212
The IMEx coronavirus interactome: an evolving map of Coronaviridae-host molecular interactions. PMID:33206959
H-RACS: a handy tool to rank anti-cancer synergistic drugs. PMID:33173014
Evolution of Sequence-based Bioinformatics Tools for Protein-protein Interaction Prediction. PMID:33093807
Integrating Single-Step GWAS and Bipartite Networks Reconstruction Provides Novel Insights into Yearling Weight and Carcass Traits in Hanwoo Beef Cattle. PMID:33050182
SARS-CoV-2-human protein-protein interaction network. PMID:32838020
The IMEx Coronavirus interactome: an evolving map of Coronaviridae-Host molecular interactions. PMID:32587962
Omics Integration Analyses Reveal the Early Evolution of Malignancy in Breast Cancer. PMID:32512721
A Novel Computational Approach for Identifying Essential Proteins From Multiplex Biological Networks. PMID:32373163
Ginkgolic acid inhibits the growth of renal cell carcinoma cells via inactivation of the EGFR signaling pathway. PMID:32256780
A novel method to predict essential proteins based on tensor and HITS algorithm. PMID:32252824
Systematic analysis of ovarian cancer platinum-resistance mechanisms via text mining. PMID:32160916
FCTP-WSRC: Protein-Protein Interactions Prediction via Weighted Sparse Representation Based Classification. PMID:32117437
Identification of common key genes and pathways between type 1 diabetes and multiple sclerosis using transcriptome and interactome analysis. PMID:31912409
Using discriminative vector machine model with 2DPCA to predict interactions among proteins. PMID:31874626
Detecting overlapping protein complexes in weighted PPI network based on overlay network chain in quotient space. PMID:31874605
AppleMDO: A Multi-Dimensional Omics Database for Apple Co-Expression Networks and Chromatin States. PMID:31695717
An Efficient Feature Extraction Technique Based on Local Coding PSSM and Multifeatures Fusion for Predicting Protein-Protein Interactions. PMID:31619921
Biclustering-based association rule mining approach for predicting cancer-associated protein interactions. PMID:31538957
Identifying protein complexes based on an edge weight algorithm and core-attachment structure. PMID:31521132
Machine-learning techniques for the prediction of protein-protein interactions. PMID:31502581
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
A seed-extended algorithm for detecting protein complexes based on density and modularity with topological structure and GO annotations. PMID:31390979
Detection of dynamic protein complexes through Markov Clustering based on Elephant Herd Optimization Approach. PMID:31366992
The Methods Employed in Mass Spectrometric Analysis of Posttranslational Modifications (PTMs) and Protein-Protein Interactions (PPIs). PMID:31347048
An Ensemble Classifier to Predict Protein-Protein Interactions by Combining PSSM-based Evolutionary Information with Local Binary Pattern Model. PMID:31319578
Membrane protein-regulated networks across human cancers. PMID:31311925
An integration of deep learning with feature embedding for protein-protein interaction prediction. PMID:31245182
An iteration method for identifying yeast essential proteins from heterogeneous network. PMID:31234779
Molecular mechanisms involved in drug-induced liver injury caused by urate-lowering Chinese herbs: A network pharmacology study and biology experiments. PMID:31141540
Sequence-based Prediction of Protein-Protein Interactions Using Gray Wolf Optimizer-Based Relevance Vector Machine. PMID:31080346
Protein complex detection based on flower pollination mechanism in multi-relation reconstructed dynamic protein networks. PMID:30925866
Using Machine Learning to Measure Relatedness Between Genes: A Multi-Features Model. PMID:30862804
Analysis of Topological Parameters of Complex Disease Genes Reveals the Importance of Location in a Biomolecular Network. PMID:30769902
A common neighbor based technique to detect protein complexes in PPI networks. PMID:30647726
A Novel Method for Identifying Essential Genes by Fusing Dynamic Protein⁻Protein Interactive Networks. PMID:30626157
Molecular subtyping of cancer and nomination of kinase candidates for inhibition with phosphoproteomics: Reanalysis of CPTAC ovarian cancer. PMID:30594550
Protein complexes identification based on go attributed network embedding. PMID:30572820
WebNetCoffee: a web-based application to identify functionally conserved proteins from Multiple PPI networks. PMID:30419809
Homodimerization regulates an endothelial specific signature of the SOX18 transcription factor. PMID:30335167
Viruses.STRING: A Virus-Host Protein-Protein Interaction Database. PMID:30249048
PTMD: A Database of Human Disease-associated Post-translational Modifications. PMID:30244175
Identifying protein complexes based on node embeddings obtained from protein-protein interaction networks. PMID:30241459
Using Two-dimensional Principal Component Analysis and Rotation Forest for Prediction of Protein-Protein Interactions. PMID:30150728
Investigating genetic-and-epigenetic networks, and the cellular mechanisms occurring in Epstein-Barr virus-infected human B lymphocytes via big data mining and genome-wide two-sided NGS data identification. PMID:30133498
Reconstruction of the Protein-Protein Interaction Network for Protein Complexes Identification by Walking on the Protein Pair Fingerprints Similarity Network. PMID:30087694
Regional Diversity in the Postsynaptic Proteome of the Mouse Brain. PMID:30071621
ProfPPIdb: Pairs of physical protein-protein interactions predicted for entire proteomes. PMID:30020956
Computational Methods for Predicting Protein-Protein Interactions Using Various Protein Features. PMID:29927082
Griffiths phases in infinite-dimensional, non-hierarchical modular networks. PMID:29904065
A new method for predicting essential proteins based on participation degree in protein complex and subgraph density. PMID:29894517
Multiple Testing of Submatrices of a Precision Matrix with Applications to Identification of Between Pathway Interactions. PMID:29881130
Network-based machine learning and graph theory algorithms for precision oncology. PMID:29872707
MGOGP: a gene module-based heuristic algorithm for cancer-related gene prioritization. PMID:29871590
INTERSPIA: a web application for exploring the dynamics of protein-protein interactions among multiple species. PMID:29746660
Detecting complexes from edge-weighted PPI networks via genes expression analysis. PMID:29745859
Role of duplicate genes in determining the tissue-selectivity of hereditary diseases. PMID:29723191
MTGO: PPI Network Analysis Via Topological and Functional Module Identification. PMID:29615773
Systematic Evaluation of Molecular Networks for Discovery of Disease Genes. PMID:29605183
PCLPred: A Bioinformatics Method for Predicting Protein-Protein Interactions by Combining Relevance Vector Machine Model with Low-Rank Matrix Approximation. PMID:29596363
Key genes and regulatory networks involved in the initiation, progression and invasion of colorectal cancer. PMID:29568567
A homologous mapping method for three-dimensional reconstruction of protein networks reveals disease-associated mutations. PMID:29560828
Predicting protein complexes using a supervised learning method combined with local structural information. PMID:29554120
Overlapping functional modules detection in PPI network with pair-wise constrained non-negative matrix tri-factorisation. PMID:29533217
An uncertain model-based approach for identifying dynamic protein complexes in uncertain protein-protein interaction networks. PMID:29513194
An Integrated Lipidomics and Phenotype Study Reveals Protective Effect and Biochemical Mechanism of Traditionally Used Alisma orientale Juzepzuk in Chronic Kidney Disease. PMID:29472858
iOPTICS-GSO for identifying protein complexes from dynamic PPI networks. PMID:29297344
The node-weighted Steiner tree approach to identify elements of cancer-related signaling pathways. PMID:29297291
Evaluating the associations between human circadian rhythms and dysregulated genes in liver cancer cells. PMID:29250165
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
Predicting new indications of compounds with a network pharmacology approach: Liuwei Dihuang Wan as a case study. PMID:29212201
Repository corticotrophin injection exerts direct acute effects on human B cell gene expression distinct from the actions of glucocorticoids. PMID:29205315
Uncovering the relationship and mechanisms of Tartary buckwheat (Fagopyrum tataricum) and Type II diabetes, hypertension, and hyperlipidemia using a network pharmacology approach. PMID:29177114
NemoProfile as an efficient approach to network motif analysis with instance collection. PMID:29072139
Identifying protein complex by integrating characteristic of core-attachment into dynamic PPI network. PMID:29045465
Protein-Protein Interactions in Virus-Host Systems. PMID:28861068
Integrated transcriptomics and metabolomics analysis to characterize cold stress responses in Nicotiana tabacum. PMID:28662642
A review of active learning approaches to experimental design for uncovering biological networks. PMID:28570593
Geometric explanation of the rich-club phenomenon in complex networks. PMID:28496187
Accurate prediction of protein-protein interactions by integrating potential evolutionary information embedded in PSSM profile and discriminative vector machine classifier. PMID:28423569
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
Net2Align: An Algorithm For Pairwise Global Alignment of Biological Networks. PMID:28356678
Deficiency in Sperm-Egg Protein Interaction as a Major Cause of Fertilization Failure. PMID:28280854
The post-genomic era of biological network alignment. PMID:28194172
Systematic analysis of molecular mechanisms for HCC metastasis via text mining approach. PMID:28108733
Automatic query generation using word embeddings for retrieving passages describing experimental methods. PMID:28077568
ccNET: Database of co-expression networks with functional modules for diploid and polyploid Gossypium. PMID:28053168
Improving protein complex prediction by reconstructing a high-confidence protein-protein interaction network of Escherichia coli from different physical interaction data sources. PMID:28049415
An ensemble approach for large-scale identification of protein- protein interactions using the alignments of multiple sequences. PMID:28029645
Network-based analysis of differentially expressed genes in cerebrospinal fluid (CSF) and blood reveals new candidate genes for multiple sclerosis. PMID:28028462
Co-expression network analyses identify functional modules associated with development and stress response in Gossypium arboreum. PMID:27922095
A scored human protein-protein interaction network to catalyze genomic interpretation. PMID:27892958
Biomolecular Network-Based Synergistic Drug Combination Discovery. PMID:27891522
Prediction of Protein-Protein Interactions by Evidence Combining Methods. PMID:27879651
A Systems Biology Comparison of Ovarian Cancers Implicates Putative Somatic Driver Mutations through Protein-Protein Interaction Models. PMID:27788148
Celecoxib exhibits an anti-gastric cancer effect by targeting focal adhesion and leukocyte transendothelial migration-associated genes. PMID:27698798
Statistical Approaches for the Construction and Interpretation of Human Protein-Protein Interaction Network. PMID:27648447
Predicting essential proteins based on subcellular localization, orthology and PPI networks. PMID:27586883
Highly Accurate Prediction of Protein-Protein Interactions via Incorporating Evolutionary Information and Physicochemical Characteristics. PMID:27571061
Improving protein-protein interactions prediction accuracy using protein evolutionary information and relevance vector machine model. PMID:27452983
Small-molecule binding sites to explore protein-protein interactions in the cancer proteome. PMID:27452673
Ens-PPI: A Novel Ensemble Classifier for Predicting the Interactions of Proteins Using Autocovariance Transformation from PSSM. PMID:27437399
Multi-OMICs and Genome Editing Perspectives on Liver Cancer Signaling Networks. PMID:27403431
HPIDB 2.0: a curated database for host-pathogen interactions. PMID:27374121
BioTriangle: a web-accessible platform for generating various molecular representations for chemicals, proteins, DNAs/RNAs and their interactions. PMID:27330567
Identification of the key regulating genes of diminished ovarian reserve (DOR) by network and gene ontology analysis. PMID:27324248
Using the Relevance Vector Machine Model Combined with Local Phase Quantization to Predict Protein-Protein Interactions from Protein Sequences. PMID:27314023
Construction of dynamic probabilistic protein interaction networks for protein complex identification. PMID:27117946
Mining Temporal Protein Complex Based on the Dynamic PIN Weighted with Connected Affinity and Gene Co-Expression. PMID:27100396
A Network of Splice Isoforms for the Mouse. PMID:27079421
Graph theory and stability analysis of protein complex interaction networks. PMID:26997661
PIPINO: A Software Package to Facilitate the Identification of Protein-Protein Interactions from Affinity Purification Mass Spectrometry Data. PMID:26966684
Key Immune Events of the Pathomechanisms of Early Cardioembolic Stroke: Multi-Database Mining and Systems Biology Approach. PMID:26927091
Regulatory consequences of neuronal ELAV-like protein binding to coding and non-coding RNAs in human brain. PMID:26894958
Using contrast patterns between true complexes and random subgraphs in PPI networks to predict unknown protein complexes. PMID:26868667
Identification of Novel Pathways in Plant Lectin-Induced Cancer Cell Apoptosis. PMID:26867193
Correlative Gene Expression to Protective Seroconversion in Rift Valley Fever Vaccinates. PMID:26783758
Prediction and characterization of protein-protein interaction network in Bacillus licheniformis WX-02. PMID:26782814
Use of the BioGRID Database for Analysis of Yeast Protein and Genetic Interactions. PMID:26729909
Forward Individualized Medicine from Personal Genomes to Interactomes. PMID:26696898
Inference of gene interaction networks using conserved subsequential patterns from multiple time course gene expression datasets. PMID:26681650
Detecting Protein Complexes in Protein Interaction Networks Modeled as Gene Expression Biclusters. PMID:26641660
Using Weighted Sparse Representation Model Combined with Discrete Cosine Transformation to Predict Protein-Protein Interactions from Protein Sequence. PMID:26634213
MIPCE: an MI-based protein complex extraction technique. PMID:26564972
BioDB extractor: customized data extraction system for commonly used bioinformatics databases. PMID:26516349
Discovering distinct functional modules of specific cancer types using protein-protein interaction networks. PMID:26495282
A Glimpse to Background and Characteristics of Major Molecular Biological Networks. PMID:26491677
Biconnectivity of the cellular metabolism: A cross-species study and its implication for human diseases. PMID:26490723
An overview of bioinformatics methods for modeling biological pathways in yeast. PMID:26476430
Genome-wide prediction of prokaryotic two-component system networks using a sequence-based meta-predictor. PMID:26384938
Human protein interaction networks across tissues and diseases. PMID:26347769
Data integration in biological research: an overview. PMID:26336651
Integration of 'omics' data in aging research: from biomarkers to systems biology. PMID:26331998
Protein complex detection in PPI networks based on data integration and supervised learning method. PMID:26329886
Identification of Aberrant Chromosomal Regions in Human Breast Cancer Using Gene Expression Data and Related Gene Information. PMID:26319982
Algorithms for modeling global and context-specific functional relationship networks. PMID:26254431
LK6/Mnk2a is a new kinase of alpha synuclein phosphorylation mediating neurodegeneration. PMID:26220523
Acquisition of estrogen independence induces TOB1-related mechanisms supporting breast cancer cell proliferation. PMID:26165839
Detecting conserved protein complexes using a dividing-and-matching algorithm and unequally lenient criteria for network comparison. PMID:26136815
A density-based clustering approach for identifying overlapping protein complexes with functional preferences. PMID:26013799
A BAYESIAN NONPARAMETRIC MIXTURE MODEL FOR SELECTING GENES AND GENE SUBNETWORKS. PMID:25984253
CEMTDD: The database for elucidating the relationships among herbs, compounds, targets and related diseases for Chinese ethnic minority traditional drugs. PMID:25970778
Prediction of host - pathogen protein interactions between Mycobacterium tuberculosis and Homo sapiens using sequence motifs. PMID:25887594
Systems biology network-based discovery of a small molecule activator BL-AD008 targeting AMPK/ZIPK and inducing apoptosis in cervical cancer. PMID:25797270
Module organization and variance in protein-protein interaction networks. PMID:25797237
Computational prediction and experimental validation of a novel synthesized pan-PIM inhibitor PI003 and its apoptosis-inducing mechanisms in cervical cancer. PMID:25749522
The relative vertex clustering value--a new criterion for the fast discovery of functional modules in protein interaction networks. PMID:25734691
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
Biological databases for human research. PMID:25712261
Identifying essential proteins from active PPI networks constructed with dynamic gene expression. PMID:25707432
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
Amyloid precursor protein interaction network in human testis: sentinel proteins for male reproduction. PMID:25591988
A survey of computational intelligence techniques in protein function prediction. PMID:25574395
Pathway mapping and development of disease-specific biomarkers: protein-based network biomarkers. PMID:25560835
FGF8 promotes colorectal cancer growth and metastasis by activating YAP1. PMID:25473897
Pin-Align: a new dynamic programming approach to align protein-protein interaction networks. PMID:25435900
Integrating PPI datasets with the PPI data from biomedical literature for protein complex detection. PMID:25350598
Predicting genome-scale Arabidopsis-Pseudomonas syringae interactome using domain and interolog-based approaches. PMID:25350354
Predicting protein complex in protein interaction network - a supervised learning based method. PMID:25349902
Integrated analysis of microarray data of atherosclerotic plaques: modulation of the ubiquitin-proteasome system. PMID:25333956
Comparative study of computational methods for reconstructing genetic networks of cancer-related pathways. PMID:25288880
Identification of essential proteins based on ranking edge-weights in protein-protein interaction networks. PMID:25268881
MAE-FMD: multi-agent evolutionary method for functional module detection in protein-protein interaction networks. PMID:25265982
Identifying hierarchical and overlapping protein complexes based on essential protein-protein interactions and "seed-expanding" method. PMID:25143945
Prediction and functional analysis of the sweet orange protein-protein interaction network. PMID:25091279
Large Scale Chemical Cross-linking Mass Spectrometry Perspectives. PMID:25045217
Proteome-wide remodeling of protein location and function by stress. PMID:25028499
Quantification of biological network perturbations for mechanistic insight and diagnostics using two-layer causal models. PMID:25015298
Construction and analysis of microRNA-transcription factor regulation network in Arabidopsis. PMID:25014374
Bioinformatic prediction of WSSV-host protein-protein interaction. PMID:24982879
Pathway reconstruction of airway remodeling in chronic lung diseases: a systems biology approach. PMID:24978043
Identifying dynamic protein complexes based on gene expression profiles and PPI networks. PMID:24963481
Nanoinformatics knowledge infrastructures: bringing efficient information management to nanomedical research. PMID:24932210
Large scale analysis of signal reachability. PMID:24932011
New directions for diffusion-based network prediction of protein function: incorporating pathways with confidence. PMID:24931987
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
Network-based identification of key proteins involved in apoptosis and cell cycle regulation. PMID:24889965
Genome-wide identification of heat shock proteins (Hsps) and Hsp interactors in rice: Hsp70s as a case study. PMID:24884676
Protein-protein interaction network of the marine microalga Tetraselmis subcordiformis: prediction and application for starch metabolism analysis. PMID:24879479
Protein-protein interface detection using the energy centrality relationship (ECR) characteristic of proteins. PMID:24830938
Unraveling human protein interaction networks underlying co-occurrences of diseases and pathological conditions. PMID:24731539
Building and exploring an integrated human kinase network: global organization and medical entry points. PMID:24704859
Protein-protein interaction detection: methods and analysis. PMID:24693427
Plant systems biology: insights, advances and challenges. PMID:24671625
The organisational structure of protein networks: revisiting the centrality-lethality hypothesis. PMID:24592293
Integrating systems biology sources illuminates drug action. PMID:24577151
Identifying protein complexes with fuzzy machine learning model. PMID:24565338
Detecting protein complexes from active protein interaction networks constructed with dynamic gene expression profiles. PMID:24565281
Identifying protein complexes based on density and modularity in protein-protein interaction network. PMID:24565048
PLW: Probabilistic Local Walks for detecting protein complexes from protein interaction networks. PMID:24564427
Analysis of schizophrenia and hepatocellular carcinoma genetic network with corresponding modularity and pathways: novel insights to the immune system. PMID:24564241
Computational developments in microRNA-regulated protein-protein interactions. PMID:24507415
Computational Prediction of Protein-Protein Interaction Networks: Algo-rithms and Resources. PMID:24396273
Protein interaction network for Alzheimer's disease using computational approach. PMID:24391359
Protein complex identification by integrating protein-protein interaction evidence from multiple sources. PMID:24386289
Predicting protein-protein interaction by the mirrortree method: possibilities and limitations. PMID:24349035
Prediction of essential proteins based on gene expression programming. PMID:24267033
Toward better drug repositioning: prioritizing and integrating existing methods into efficient pipelines. PMID:24239728
The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases. PMID:24234451
Perturbation centrality and turbine: a novel centrality measure obtained using a versatile network dynamics tool. PMID:24205090
Predicting whole genome protein interaction networks from primary sequence data in model and non-model organisms using ENTS. PMID:24015873
Navigating traditional chinese medicine network pharmacology and computational tools. PMID:23983798
Experimental characterization of the human non-sequence-specific nucleic acid interactome. PMID:23902751
Predicting and analyzing interactions between Mycobacterium tuberculosis and its human host. PMID:23844013
Module-based breast cancer classification. PMID:23819260
iBIG: an integrative network tool for supporting human disease mechanism studies. PMID:23809576
Silicon era of carbon-based life: application of genomics and bioinformatics in crop stress research. PMID:23759993
β1- and αv-class integrins cooperate to regulate myosin II during rigidity sensing of fibronectin-based microenvironments. PMID:23708002
Structure and non-structure of centrosomal proteins. PMID:23671615
Interfacing cellular networks of S. cerevisiae and E. coli: connecting dynamic and genetic information. PMID:23663484
A web-based comparative genomics tutorial for investigating microbial genomes. PMID:23653555
Construction of ontology augmented networks for protein complex prediction. PMID:23650509
Chapter 15: disease gene prioritization. PMID:23633938
Protein-protein interactions: switch from classical methods to proteomics and bioinformatics-based approaches. PMID:23579629
An effective method for refining predicted protein complexes based on protein activity and the mechanism of protein complex formation. PMID:23537347
Functional site plasticity in domain superfamilies. PMID:23499848
Predicting the binding patterns of hub proteins: a study using yeast protein interaction networks. PMID:23431393
A survey of protein interaction data and multigenic inherited disorders. PMID:23398688
Equal opportunity for low-degree network nodes: a PageRank-based method for protein target identification in metabolic graphs. PMID:23382878
Allele-specific behavior of molecular networks: understanding small-molecule drug response in yeast. PMID:23308257
Chapter 2: Data-driven view of disease biology. PMID:23300408
Inferring the Brassica rapa Interactome Using Protein-Protein Interaction Data from Arabidopsis thaliana. PMID:23293649
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
Helminth secretome database (HSD): a collection of helminth excretory/secretory proteins predicted from expressed sequence tags (ESTs). PMID:23281827
Managing biological complexity across orthologs with a visual knowledgebase of documented biomolecular interactions. PMID:23264875
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
SpermatogenesisOnline 1.0: a resource for spermatogenesis based on manual literature curation and genome-wide data mining. PMID:23193286
Investigation of stable and transient protein-protein interactions: Past, present, and future. PMID:23193082
Effects of protein interaction data integration, representation and reliability on the use of network properties for drug target prediction. PMID:23146171
A network-based maximum link approach towards MS identifies potentially important roles for undetected ARRB1/2 and ACTB in liver cancer progression. PMID:22961449
An overview of computational life science databases & exchange formats of relevance to chemical biology research. PMID:22934944
Dissecting the gene network of dietary restriction to identify evolutionarily conserved pathways and new functional genes. PMID:22912585
Functional annotation from the genome sequence of the giant panda. PMID:22865348
Prediction and analysis of the protein interactome in Pseudomonas aeruginosa to enable network-based drug target selection. PMID:22848443
Embryonic stem cell interactomics: the beginning of a long road to biological function. PMID:22847281
Effect of reference genome selection on the performance of computational methods for genome-wide protein-protein interaction prediction. PMID:22844541
Iteration method for predicting essential proteins based on orthology and protein-protein interaction networks. PMID:22808943
INDI: a computational framework for inferring drug interactions and their associated recommendations. PMID:22806140
Integration of biological networks and pathways with genetic association studies. PMID:22777728
Filtering Gene Ontology semantic similarity for identifying protein complexes in large protein interaction networks. PMID:22759576
Seed selection strategy in global network alignment without destroying the entire structures of functional modules. PMID:22759574
Efficient and accurate Greedy Search Methods for mining functional modules in protein interaction networks. PMID:22759424
A methodology for detecting the orthology signal in a PPI network at a functional complex level. PMID:22759423
Computational analysis of interactomes: current and future perspectives for bioinformatics approaches to model the host-pathogen interaction space. PMID:22750305
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
Towards the identification of protein complexes and functional modules by integrating PPI network and gene expression data. PMID:22621308
Inferring a protein interaction map of Mycobacterium tuberculosis based on sequences and interologs. PMID:22595003
Graph spectral analysis of protein interaction network evolution. PMID:22552917
LDGIdb: a database of gene interactions inferred from long-range strong linkage disequilibrium between pairs of SNPs. PMID:22551073
Scalable global alignment for multiple biological networks. PMID:22536895
A framework for mapping, visualisation and automatic model creation of signal-transduction networks. PMID:22531118
"Guilt by association" is the exception rather than the rule in gene networks. PMID:22479173
Host-pathogen interactome mapping for HTLV-1 and -2 retroviruses. PMID:22458338
Protein interaction data curation: the International Molecular Exchange (IMEx) consortium. PMID:22453911
MUCHA: multiple chemical alignment algorithm to identify building block substructures of orphan secondary metabolites. PMID:22373367
ANAP: an integrated knowledge base for Arabidopsis protein interaction network analysis. PMID:22345505
Large-scale elucidation of drug response pathways in humans. PMID:22300318
Tools for protein-protein interaction network analysis in cancer research. PMID:22262713
Differential network biology. PMID:22252388
IMID: integrated molecular interaction database. PMID:22238258
A searchable cross-platform gene expression database reveals connections between drug treatments and disease. PMID:22233519
Recovering protein-protein and domain-domain interactions from aggregation of IP-MS proteomics of coregulator complexes. PMID:22219718
A binary matrix factorization algorithm for protein complex prediction. PMID:22166008
Minimotif Miner 3.0: database expansion and significantly improved reduction of false-positive predictions from consensus sequences. PMID:22146221
Aberrant epigenetic grooming of miRNAs in pancreatic cancer: a systems biology perspective. PMID:22126293
iRefR: an R package to manipulate the iRefIndex consolidated protein interaction database. PMID:22115179
A novel method of transcriptional response analysis to facilitate drug repositioning for cancer therapy. PMID:22108825
Systems-biology approaches to discover anti-viral effectors of the human innate immune response. PMID:21994773
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
Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM. PMID:21886100
GPS-Prot: a web-based visualization platform for integrating host-pathogen interaction data. PMID:21777475
Proteomic patterns of cervical cancer cell lines, a network perspective. PMID:21696634
An enhanced Petri-net model to predict synergistic effects of pairwise drug combinations from gene microarray data. PMID:21685086
PREDICT: a method for inferring novel drug indications with application to personalized medicine. PMID:21654673
Knowledge-driven multi-locus analysis reveals gene-gene interactions influencing HDL cholesterol level in two independent EMR-linked biobanks. PMID:21589926
CASCADE_SCAN: mining signal transduction network from high-throughput data based on steepest descent method. PMID:21575263
The role of indirect connections in gene networks in predicting function. PMID:21551147
DomainRBF: a Bayesian regression approach to the prioritization of candidate domains for complex diseases. PMID:21504591
Network-based pipeline for analyzing MS data: an application toward liver cancer. PMID:21410269
The impact of multifunctional genes on "guilt by association" analysis. PMID:21364756
Interaction site prediction by structural similarity to neighboring clusters in protein-protein interaction networks. PMID:21342570
Landscape mapping of functional proteins in insulin signal transduction and insulin resistance: a network-based protein-protein interaction analysis. PMID:21305025
Dengue-2 structural proteins associate with human proteins to produce a coagulation and innate immune response biased interactome. PMID:21281507
Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology. PMID:21249183
The role of exon shuffling in shaping protein-protein interaction networks. PMID:21210967
Cross-species Functionome analysis identifies proteins associated with DNA repair, translation and aerobic respiration as conserved modulators of UV-toxicity. PMID:21195161
Extending pathways and processes using molecular interaction networks to analyse cancer genome data. PMID:21144022
Protein complex forming ability is favored over the features of interacting partners in determining the evolutionary rates of proteins in the yeast protein-protein interaction networks. PMID:21073713
Global protein interactome exploration through mining genome-scale data in Arabidopsis thaliana. PMID:21047383
Integrative systems biology for data-driven knowledge discovery. PMID:21044756
RegPhos: a system to explore the protein kinase-substrate phosphorylation network in humans. PMID:21037261
Predicting direct protein interactions from affinity purification mass spectrometry data. PMID:21034440
Quantitative trait loci mapping reveals candidate pathways regulating cell cycle duration in Plasmodium falciparum. PMID:20955606
ATHENA: A knowledge-based hybrid backpropagation-grammatical evolution neural network algorithm for discovering epistasis among quantitative trait Loci. PMID:20875103
Trees on networks: resolving statistical patterns of phylogenetic similarities among interacting proteins. PMID:20854660
In silico models of cancer. PMID:20836040
The BioPAX community standard for pathway data sharing. PMID:20829833
PRED_PPI: a server for predicting protein-protein interactions based on sequence data with probability assignment. PMID:20500905
Visual integration of quantitative proteomic data, pathways, and protein interactions. PMID:20467059
Low-complexity regions within protein sequences have position-dependent roles. PMID:20385029
Building and analyzing protein interactome networks by cross-species comparisons. PMID:20353594
High-throughput discovery and characterization of fetal protein trafficking in the blood of pregnant women. PMID:20186258
Computational approaches for detecting protein complexes from protein interaction networks: a survey. PMID:20158874
Synthetic biology: tools to design, build, and optimize cellular processes. PMID:20150964
Protein interactions and ligand binding: from protein subfamilies to functional specificity. PMID:20133844
Gene prioritization in Type 2 Diabetes using domain interactions and network analysis. PMID:20122255
An ontology-based search engine for protein-protein interactions. PMID:20122195
A temporal precedence based clustering method for gene expression microarray data. PMID:20113513
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
Covariation of branch lengths in phylogenies of functionally related genes. PMID:20041191
Effective identification of conserved pathways in biological networks using hidden Markov models. PMID:19997609
Inferring protein function by domain context similarities in protein-protein interaction networks. PMID:19954509
Reconstructing ancestral gene content by coevolution. PMID:19948819
Integrating diverse information to gain more insight into microarray analysis. PMID:19834567
Phylogenetic analysis of modularity in protein interaction networks. PMID:19828041
The Modular Organization of Protein Interactions in Escherichia coli. PMID:19798435
Functionally guided alignment of protein interaction networks for module detection. PMID:19797409
Gene networks in Drosophila melanogaster: integrating experimental data to predict gene function. PMID:19758432
Automatic parameter learning for multiple local network alignment. PMID:19645599
A genome-wide screen in Saccharomyces cerevisiae reveals pathways affected by arsenic toxicity. PMID:19631266
A core-attachment based method to detect protein complexes in PPI networks. PMID:19486541
IsoRankN: spectral methods for global alignment of multiple protein networks. PMID:19477996
Domain-oriented edge-based alignment of protein interaction networks. PMID:19477994
A complex-centric view of protein network evolution. PMID:19465379
Perturbation of interaction networks for application to cancer therapy. PMID:19390668
Biological process linkage networks. PMID:19390589
Tissue specificity and the human protein interaction network. PMID:19357639
A comprehensive Plasmodium falciparum protein interaction map reveals a distinct architecture of a core interactome. PMID:19333996
Biomedical discovery acceleration, with applications to craniofacial development. PMID:19325874
Identifying disease-specific genes based on their topological significance in protein networks. PMID:19309513
Genomic landscape of developing male germ cells. PMID:19306351
Toward accurate reconstruction of functional protein networks. PMID:19293828
Uncovering biological network function via graphlet degree signatures. PMID:19259413
Energetic determinants of protein binding specificity: insights into protein interaction networks. PMID:19253304
A survey of available tools and web servers for analysis of protein-protein interactions and interfaces. PMID:19240123
Co-expression among constituents of a motif in the protein-protein interaction network. PMID:19226657
Tuberculosis drug resistance mutation database. PMID:19209951
Biofilter: a knowledge-integration system for the multi-locus analysis of genome-wide association studies. PMID:19209715
Dissecting the interface between signaling and transcriptional regulation in human B cells. PMID:19209707
Querying pathways in protein interaction networks based on hidden Markov models. PMID:19193142
A complex-based reconstruction of the Saccharomyces cerevisiae interactome. PMID:19176519
A rice kinase-protein interaction map. PMID:19109415
A Two-Step Approach for Clustering Proteins based on Protein Interaction Profile. PMID:19081747
An empirical framework for binary interactome mapping. PMID:19060904
Hepatitis C virus infection protein network. PMID:18985028
Michigan molecular interactions r2: from interacting proteins to pathways. PMID:18978014
The prediction of protein-protein interaction networks in rice blast fungus. PMID:18976500
Protein networks markedly improve prediction of subcellular localization in multiple eukaryotic species. PMID:18836191
Systems based mapping demonstrates that recovery from alkylation damage requires DNA repair, RNA processing, and translation associated networks. PMID:18824089
ProteoLens: a visual analytic tool for multi-scale database-driven biological network data mining. PMID:18793469
Modeling synthetic lethality. PMID:18789146
Automated clustering of probe molecules from solvent mapping of protein surfaces: new algorithms applied to hot-spot mapping and structure-based drug design. PMID:18679808
In silico identification of functional protein interfaces. PMID:18629079
TRANSPATH--a high quality database focused on signal transduction. PMID:18629064
Interactome data and databases: different types of protein interaction. PMID:18629062
PRISM: protein-protein interaction prediction by structural matching. PMID:18592198
Global investigation of protein-protein interactions in yeast Saccharomyces cerevisiae using re-occurring short polypeptide sequences. PMID:18586826
Protein complex identification by supervised graph local clustering. PMID:18586722
Biomolecular network motif counting and discovery by color coding. PMID:18586721
Inferring modules of functionally interacting proteins using the Bond Energy Algorithm. PMID:18559112
Natural selection against protein aggregation on self-interacting and essential proteins in yeast, fly, and worm. PMID:18503047
Targeting the human cancer pathway protein interaction network by structural genomics. PMID:18487680
Cytoscape ESP: simple search of complex biological networks. PMID:18445605
Global transcriptome and deletome profiles of yeast exposed to transition metals. PMID:18437200
Improving protein function prediction methods with integrated literature data. PMID:18412966
Uncovering signal transduction networks from high-throughput data by integer linear programming. PMID:18411207
Using support vector machine combined with auto covariance to predict protein-protein interactions from protein sequences. PMID:18390576
An integrated genetic, genomic and systems approach defines gene networks regulated by the interaction of light and carbon signaling pathways in Arabidopsis. PMID:18387196
SynechoNET: integrated protein-protein interaction database of a model cyanobacterium Synechocystis sp. PCC 6803. PMID:18315852
Two different classes of co-occurring motif pairs found by a novel visualization method in human promoter regions. PMID:18312685
A mixture of feature experts approach for protein-protein interaction prediction. PMID:18269700
GraphCrunch: a tool for large network analyses. PMID:18230190
The evolutionary dynamics of the Saccharomyces cerevisiae protein interaction network after duplication. PMID:18199840
High-confidence prediction of global interactomes based on genome-wide coevolutionary networks. PMID:18199838
PARPs database: a LIMS systems for protein-protein interaction data mining or laboratory information management system. PMID:18093328
Denoising inferred functional association networks obtained by gene fusion analysis. PMID:18081932
Broad network-based predictability of Saccharomyces cerevisiae gene loss-of-function phenotypes. PMID:18053250
DIMA 2.0--predicted and known domain interactions. PMID:17999995
Assessing and combining reliability of protein interaction sources. PMID:17990508
An improved, bias-reduced probabilistic functional gene network of baker's yeast, Saccharomyces cerevisiae. PMID:17912365
InSite: a computational method for identifying protein-protein interaction binding sites on a proteome-wide scale. PMID:17868464
Statistical analysis of physical-chemical properties and prediction of protein-protein interfaces. PMID:17828612
Design of multi-specificity in protein interfaces. PMID:17722975
Influence of degree correlations on network structure and stability in protein-protein interaction networks. PMID:17688687
PepBank--a database of peptides based on sequence text mining and public peptide data sources. PMID:17678535
Automating document classification for the Immune Epitope Database. PMID:17655769
Not all scale-free networks are born equal: the role of the seed graph in PPI network evolution. PMID:17616981
Exploiting residue-level and profile-level interface propensities for usage in binding sites prediction of proteins. PMID:17480235
The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics. PMID:17447836
Epstein-Barr virus and virus human protein interaction maps. PMID:17446270
Evolution of protein complexes by duplication of homomeric interactions. PMID:17411433
In silico pathway reconstruction: Iron-sulfur cluster biogenesis in Saccharomyces cerevisiae. PMID:17408500
From genes to functional classes in the study of biological systems. PMID:17407596
Rich-club phenomenon in the interactome of P. falciparum--artifact or signature of a parasitic life style? PMID:17389924
Fly-DPI: database of protein interactomes for D. melanogaster in the approach of systems biology. PMID:17254302
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
Inferring topology from clustering coefficients in protein-protein interaction networks. PMID:17137490
CellCircuits: a database of protein network models. PMID:17135207
DOMINO: a database of domain-peptide interactions. PMID:17135199
Biological context networks: a mosaic view of the interactome. PMID:17130868
Michigan Molecular Interactions (MiMI): putting the jigsaw puzzle together. PMID:17130145
IntNetDB v1.0: an integrated protein-protein interaction network database generated by a probabilistic model. PMID:17112386
Comparison of protein interaction networks reveals species conservation and divergence. PMID:17044912
Genomic analysis of the hierarchical structure of regulatory networks. PMID:17003135
Characterization and prediction of protein-protein interactions within and between complexes. PMID:17003128
Computational analysis of tissue-specific combinatorial gene regulation: predicting interaction between transcription factors in human tissues. PMID:16982645
Cataloging the relationships between proteins: a review of interaction databases. PMID:16943573
Graemlin: general and robust alignment of multiple large interaction networks. PMID:16899655
A direct comparison of protein interaction confidence assignment schemes. PMID:16872496
Design principles of molecular networks revealed by global comparisons and composite motifs. PMID:16859507
Protein-protein interactions more conserved within species than across species. PMID:16854211
Network motif identification in stochastic networks. PMID:16769903
Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae. PMID:16762047
Choosing negative examples for the prediction of protein-protein interactions. PMID:16723005
Topology and weights in a protein domain interaction network--a novel way to predict protein interactions. PMID:16716232
A systems approach to mapping DNA damage response pathways. PMID:16709784
A computational framework for the topological analysis and targeted disruption of signal transduction networks. PMID:16617070
Benchmarking ortholog identification methods using functional genomics data. PMID:16613613
SCOWLP: a web-based database for detailed characterization and visualization of protein interfaces. PMID:16512892
Systematic identification of functional orthologs based on protein network comparison. PMID:16510899
In search of functional association from time-series microarray data based on the change trend and level of gene expression. PMID:16478547
Computational inference and experimental validation of the nitrogen assimilation regulatory network in cyanobacterium Synechococcus sp. WH 8102. PMID:16473855
Genome-wide prediction and characterization of interactions between transcription factors in Saccharomyces cerevisiae. PMID:16464824
Evaluation of different biological data and computational classification methods for use in protein interaction prediction. PMID:16450363
Stable evolutionary signal in a yeast protein interaction network. PMID:16441898
NPInter: the noncoding RNAs and protein related biomacromolecules interaction database. PMID:16381834
HomoMINT: an inferred human network based on orthology mapping of protein interactions discovered in model organisms. PMID:16351748
A data integration methodology for systems biology: experimental verification. PMID:16301536
The Plasmodium protein network diverges from those of other eukaryotes. PMID:16267557
L2L: a simple tool for discovering the hidden significance in microarray expression data. PMID:16168088
Data mining for protein-protein interactions in invertebrate model organisms. PMID:16158290
High-betweenness proteins in the yeast protein interaction network. PMID:16046814
Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome. PMID:15892868
Systematic interpretation of genetic interactions using protein networks. PMID:15877074
Relative predicted protein levels of functionally associated proteins are conserved across organisms. PMID:15718304
Conserved patterns of protein interaction in multiple species. PMID:15687504
The Genomes of Oryza sativa: a history of duplications. PMID:15685292
A database for G proteins and their interaction with GPCRs. PMID:15619328
Global network analysis of phenotypic effects: protein networks and toxicity modulation in Saccharomyces cerevisiae. PMID:15608068
Integrating phenotypic and expression profiles to map arsenic-response networks. PMID:15575969
How biologically relevant are interaction-based modules in protein networks? PMID:15535869
A computational approach for ordering signal transduction pathway components from genomics and proteomics Data. PMID:15504238
Information assessment on predicting protein-protein interactions. PMID:15491499
Nucleocapsid protein of SARS coronavirus tightly binds to human cyclophilin A. PMID:15358143
Molecular dimension explored in evolution to promote proteomic complexity. PMID:15347802
Evolution and topology in the yeast protein interaction network. PMID:15231746
InterWeaver: interaction reports for discovering potential protein interaction partners with online evidence. PMID:15215354
Computational approaches to protein-protein interaction. PMID:15185965
Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. PMID:15173116
Predicting protein complex membership using probabilistic network reliability. PMID:15140827
Prolinks: a database of protein functional linkages derived from coevolution. PMID:15128449
Identification and functional analysis of 'hypothetical' genes expressed in Haemophilus influenzae. PMID:15121896
Interaction networks in yeast define and enumerate the signaling steps of the vertebrate aryl hydrocarbon receptor. PMID:15024417
The nonconserved wrapping of conserved protein folds reveals a trend toward increasing connectivity in proteomic networks. PMID:14978274
TopNet: a tool for comparing biological sub-networks, correlating protein properties with topological statistics. PMID:14724320
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
Visualization and interpretation of protein networks in Mycobacterium tuberculosis based on hierarchical clustering of genome-wide functional linkage maps. PMID:14654685
Expressionview: visualization of quantitative trait loci and gene-expression data in Ensembl. PMID:14611663
Conserved pathways within bacteria and yeast as revealed by global protein network alignment. PMID:14504397
Determining the basis of channel-tetramerization specificity by x-ray crystallography and a sequence-comparison algorithm: Family Values (FamVal). PMID:12835418
Bioverse: Functional, structural and contextual annotation of proteins and proteomes. PMID:12824406
ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins. PMID:12824381
The mammalian protein-protein interaction database and its viewing system that is linked to the main FANTOM2 viewer. PMID:12819152
Kinase pathway database: an integrated protein-kinase and NLP-based protein-interaction resource. PMID:12799355
Domain fusion analysis by applying relational algebra to protein sequence and domain databases. PMID:12734020
Novel functions of the phosphatidylinositol metabolic pathway discovered by a chemical genomics screen with wortmannin. PMID:12615994
An automated method for finding molecular complexes in large protein interaction networks. PMID:12525261
KDBI: Kinetic Data of Bio-molecular Interactions database. PMID:12519995
InterDom: a database of putative interacting protein domains for validating predicted protein interactions and complexes. PMID:12519994
BIND: the Biomolecular Interaction Network Database. PMID:12519993
TRANSPATH: an integrated database on signal transduction and a tool for array analysis. PMID:12519957
DIP: the database of interacting proteins PubMed citations: 304.

304 articles citing: DIP: the database of interacting proteins

Challenges and Limitations of Biological Network Analysis. PMID:35892929
Analyzing the Systems Biology Effects of COVID-19 mRNA Vaccines to Assess Their Safety and Putative Side Effects. PMID:35889989
Transcriptomic analysis reveals pathophysiological relationship between chronic obstructive pulmonary disease (COPD) and periodontitis. PMID:35676670
Network Pharmacology Approach for Medicinal Plants: Review and Assessment. PMID:35631398
ImitateDB: A database for domain and motif mimicry incorporating host and pathogen protein interactions. PMID:35487995
Predicting Essential Proteins Based on Integration of Local Fuzzy Fractal Dimension and Subcellular Location Information. PMID:35205217
Network analysis of host-pathogen protein interactions in microbe induced cardiovascular diseases. PMID:35001887
Computational modeling of human-nCoV protein-protein interaction network. PMID:34902553
Navigating Multi-Scale Cancer Systems Biology Towards Model-Driven Clinical Oncology and Its Applications in Personalized Therapeutics. PMID:34900668
Shared Molecular Mechanisms between Atherosclerosis and Periodontitis by Analyzing the Transcriptomic Alterations of Peripheral Blood Monocytes. PMID:34899963
Interpretation of network-based integration from multi-omics longitudinal data. PMID:34883510
In silico Methods for Identification of Potential Therapeutic Targets. PMID:34826045
Computationally Reconstructed Interactome of Bradyrhizobium diazoefficiens USDA110 Reveals Novel Functional Modules and Protein Hubs for Symbiotic Nitrogen Fixation. PMID:34769335
An Ebola, Neisseria and Trypanosoma human protein interaction census reveals a conserved human protein cluster targeted by various human pathogens. PMID:34745452
Centrality of drug targets in protein networks. PMID:34715787
Investigating Pathogenetic Mechanisms of Alzheimer's Disease by Systems Biology Approaches for Drug Discovery. PMID:34681938
GreeningDB: A Database of Host-Pathogen Protein-Protein Interactions and Annotation Features of the Bacteria Causing Huanglongbing HLB Disease. PMID:34639237
Identification of Novel Choroidal Neovascularization-Related Genes Using Laplacian Heat Diffusion Algorithm. PMID:34532497
The chemical biology of coronavirus host-cell interactions. PMID:34458775
Drug Discovery of Spinal Muscular Atrophy (SMA) from the Computational Perspective: A Comprehensive Review. PMID:34445667
Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review. PMID:34439912
Classification of protein-protein association rates based on biophysical informatics. PMID:34404340
Revealing protein-protein interactions at the transcriptome scale by sequencing. PMID:34348091
Databases for Protein-Protein Interactions. PMID:34236665
Applications and analytical tools of cell communication based on ligand-receptor interactions at single cell level. PMID:34217372
A computational model for GPCR-ligand interaction prediction. PMID:34171942
Evolving scenario of big data and Artificial Intelligence (AI) in drug discovery. PMID:34159484
Multiple-Molecule Drug Design Based on Systems Biology Approaches and Deep Neural Network to Mitigate Human Skin Aging. PMID:34073305
Shared Molecular Mechanisms between Alzheimer's Disease and Periodontitis Revealed by Transcriptomic Analysis. PMID:33869630
Integrated intra- and intercellular signaling knowledge for multicellular omics analysis. PMID:33749993
Systems Approach to Pathogenic Mechanism of Type 2 Diabetes and Drug Discovery Design Based on Deep Learning and Drug Design Specifications. PMID:33375269
Chemocentric Informatics Analysis: Dexamethasone Versus Combination Therapy for COVID-19. PMID:33251412
Biological network analysis with deep learning. PMID:33169146
Systematic elucidation of neuron-astrocyte interaction in models of amyotrophic lateral sclerosis using multi-modal integrated bioinformatics workflow. PMID:33149111
Determinants of correlated expression of transcription factors and their target genes. PMID:33104784
BastionHub: a universal platform for integrating and analyzing substrates secreted by Gram-negative bacteria. PMID:33084862
Identification of Latent Oncogenes with a Network Embedding Method and Random Forest. PMID:33029511
A Systems Biology Workflow for Drug and Vaccine Repurposing: Identifying Small-Molecule BCG Mimics to Reduce or Prevent COVID-19 Mortality. PMID:33025261
Identification of COVID-19 Infection-Related Human Genes Based on a Random Walk Model in a Virus-Human Protein Interaction Network. PMID:32685484
Using Coarse-Grained Simulations to Characterize the Mechanisms of Protein-Protein Association. PMID:32679892
A flexible network-based imputing-and-fusing approach towards the identification of cell types from single-cell RNA-seq data. PMID:32527285
Mutation severity spectrum of rare alleles in the human genome is predictive of disease type. PMID:32413045
A massively parallel barcoded sequencing pipeline enables generation of the first ORFeome and interactome map for rice. PMID:32398372
A network analysis to identify pathophysiological pathways distinguishing ischaemic from non-ischaemic heart failure. PMID:32243695
Hierarchy and levels: analysing networks to study mechanisms in molecular biology. PMID:32089112
A Guide to Conquer the Biological Network Era Using Graph Theory. PMID:32083072
Long-term survivors of early breast cancer treated with chemotherapy are characterized by a pro-inflammatory biomarker profile compared to matched controls. PMID:32078215
Identification of cancer driver genes based on nucleotide context. PMID:32015527
NAPAbench 2: A network synthesis algorithm for generating realistic protein-protein interaction (PPI) network families. PMID:31986158
Ligands, Receptors, and Transcription Factors that Mediate Inter-Cellular and Intra-Cellular Communication during Ovarian Follicle Development. PMID:31939199
MASS SPECTROMETRY IN VIROLOGICAL SCIENCES. PMID:31876329
Dissecting the Role of NF-κb Protein Family and Its Regulators in Rheumatoid Arthritis Using Weighted Gene Co-Expression Network. PMID:31824568
Leveraging User-Friendly Network Approaches to Extract Knowledge From High-Throughput Omics Datasets. PMID:31798629
Measurement of Conditional Relatedness Between Genes Using Fully Convolutional Neural Network. PMID:31695723
Synchronized replication of genes encoding the same protein complex in fast-proliferating cells. PMID:31662304
HMNPPID-human malignant neoplasm protein-protein interaction database. PMID:31639057
CavBench: A benchmark for protein cavity detection methods. PMID:31609980
Conserved Central Intraviral Protein Interactome of the Herpesviridae Family. PMID:31575665
Hamiltonian energy as an efficient approach to identify the significant key regulators in biological networks. PMID:31442253
A comprehensive study on genome-wide coexpression network of KHDRBS1/Sam68 reveals its cancer and patient-specific association. PMID:31366900
Protein interaction networks revealed by proteome coevolution. PMID:31296772
In Silico Toxicology Data Resources to Support Read-Across and (Q)SAR. PMID:31244651
Protein interactions and consensus clustering analysis uncover insights into herpesvirus virion structure and function relationships. PMID:31199794
Network Medicine in the Age of Biomedical Big Data. PMID:31031797
Single cell RNA sequencing reveals regional heterogeneity of hepatobiliary innate lymphoid cells in a tissue-enriched fashion. PMID:31022195
Disease association of human tumor suppressor genes. PMID:30945018
MorCVD: A Unified Database for Host-Pathogen Protein-Protein Interactions of Cardiovascular Diseases Related to Microbes. PMID:30858555
Computational studies of protein-protein dissociation by statistical potential and coarse-grained simulations: a case study on interactions between colicin E9 endonuclease and immunity proteins. PMID:30652698
Network spectra for drug-target identification in complex diseases: new guns against old foes. PMID:30596144
Identification of essential proteins based on a new combination of topological and biological features in weighted protein-protein interaction networks. PMID:30472688
Strategies for Pathway Analysis Using GWAS and WGS Data. PMID:30387919
Computational discovery of dynamic cell line specific Boolean networks from multiplex time-course data. PMID:30372442
Use of Laplacian Heat Diffusion Algorithm to Infer Novel Genes With Functions Related to Uveitis. PMID:30349554
Context-specific interactions in literature-curated protein interaction databases. PMID:30340458
CASS: A distributed network clustering algorithm based on structure similarity for large-scale network. PMID:30303961
PPInS: a repository of protein-protein interaction sitesbase. PMID:30127348
Feature Selection via Swarm Intelligence for Determining Protein Essentiality. PMID:29958434
Improved flower pollination algorithm for identifying essential proteins. PMID:29745838
An improved approach to infer protein-protein interaction based on a hierarchical vector space model. PMID:29699476
Determining the minimum number of protein-protein interactions required to support known protein complexes. PMID:29698482
Prediction of Protein-Protein Interactions from Amino Acid Sequences Based on Continuous and Discrete Wavelet Transform Features. PMID:29617272
Systematic Evaluation of Molecular Networks for Discovery of Disease Genes. PMID:29605183
Integrated analysis of microarray data to identify the genes critical for the rupture of intracranial aneurysm. PMID:29552131
Deciphering the Relationship between Obesity and Various Diseases from a Network Perspective. PMID:29258237
A multigene support vector machine predictor for metastasis of cutaneous melanoma. PMID:29257259
Protein-protein interaction analysis to identify biomarker networks for endometriosis. PMID:29201163
DiffSLC: A graph centrality method to detect essential proteins of a protein-protein interaction network. PMID:29121073
Protein-Protein Interactions Prediction Using a Novel Local Conjoint Triad Descriptor of Amino Acid Sequences. PMID:29117139
PICKLE 2.0: A human protein-protein interaction meta-database employing data integration via genetic information ontology. PMID:29023571
Network-Based Method for Identifying Co- Regeneration Genes in Bone, Dentin, Nerve and Vessel Tissues. PMID:28974058
A support vector machine classifier for the prediction of osteosarcoma metastasis with high accuracy. PMID:28901446
Detection of Interactions between Proteins by Using Legendre Moments Descriptor to Extract Discriminatory Information Embedded in PSSM. PMID:28820478
A new computational strategy for identifying essential proteins based on network topological properties and biological information. PMID:28753682
Across-proteome modeling of dimer structures for the bottom-up assembly of protein-protein interaction networks. PMID:28499419
A new two-stage method for revealing missing parts of edges in protein-protein interaction networks. PMID:28493910
Predicting Protein-protein Association Rates using Coarse-grained Simulation and Machine Learning. PMID:28418043
Transcriptional regulatory networks underlying the reprogramming of spermatogonial stem cells to multipotent stem cells. PMID:28408750
The post-genomic era of biological network alignment. PMID:28194172
Protein complex prediction for large protein protein interaction networks with the Core&Peel method. PMID:28185552
Differential variation patterns between hubs and bottlenecks in human protein-protein interaction networks. PMID:27903259
In silico identification of essential proteins in Corynebacterium pseudotuberculosis based on protein-protein interaction networks. PMID:27814699
An efficient method for protein function annotation based on multilayer protein networks. PMID:27678214
inFRank: a ranking-based identification of influential genes in biological networks. PMID:27623074
An ensemble framework for identifying essential proteins. PMID:27557880
Interaction Between Peroxisome Proliferator Activated Receptor δ and Epithelial Membrane Protein 2 Polymorphisms Influences HDL-C Levels in the Chinese Population. PMID:27530449
A New Method for Identifying Essential Proteins Based on Network Topology Properties and Protein Complexes. PMID:27529423
Identification of protein complexes from multi-relationship protein interaction networks. PMID:27461193
FOXR2 Interacts with MYC to Promote Its Transcriptional Activities and Tumorigenesis. PMID:27346356
Using the Relevance Vector Machine Model Combined with Local Phase Quantization to Predict Protein-Protein Interactions from Protein Sequences. PMID:27314023
Penicimenolides A-F, Resorcylic Acid Lactones from Penicillium sp., isolated from the Rhizosphere Soil of Panax notoginseng. PMID:27271722
Review on Graph Clustering and Subgraph Similarity Based Analysis of Neurological Disorders. PMID:27258269
The Use of Protein-Protein Interactions for the Analysis of the Associations between PM2.5 and Some Diseases. PMID:27243032
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
Biomolecular Relationships Discovered from Biological Labyrinth and Lost in Ocean of Literature: Community Efforts Can Rescue Until Automated Artificial Intelligence Takes Over. PMID:27066067
Rsite2: an efficient computational method to predict the functional sites of noncoding RNAs. PMID:26751501
Identifying novel protein phenotype annotations by hybridizing protein-protein interactions and protein sequence similarities. PMID:26728152
PPCM: Combing Multiple Classifiers to Improve Protein-Protein Interaction Prediction. PMID:26539460
Indexing a protein-protein interaction network expedites network alignment. PMID:26453444
PPCheck: A Webserver for the Quantitative Analysis of Protein-Protein Interfaces and Prediction of Residue Hotspots. PMID:26448684
Identification of Essential Proteins Based on a New Combination of Local Interaction Density and Protein Complexes. PMID:26125187
Proteins interaction network and modeling of IGVH mutational status in chronic lymphocytic leukemia. PMID:26088082
Integrative random forest for gene regulatory network inference. PMID:26072483
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
Predicting peptide-mediated interactions on a genome-wide scale. PMID:25938916
Follicle Online: an integrated database of follicle assembly, development and ovulation. PMID:25931457
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
A hybrid computational method for the discovery of novel reproduction-related genes. PMID:25768094
Identification of hybrid node and link communities in complex networks. PMID:25728010
An integrative approach for a network based meta-analysis of viral RNAi screens. PMID:25691914
Spatial features for Escherichia coli genome organization. PMID:25652224
Proteomic analyses reveal distinct chromatin-associated and soluble transcription factor complexes. PMID:25609649
Decomposing the space of protein quaternary structures with the interface fragment pair library. PMID:25592649
Using biological networks to improve our understanding of infectious diseases. PMID:25379138
Prediction of disease-related genes based on weighted tissue-specific networks by using DNA methylation. PMID:25350763
GroupRank: rank candidate genes in PPI network by differentially expressed gene groups. PMID:25330105
Comparative study of computational methods for reconstructing genetic networks of cancer-related pathways. PMID:25288880
Gene expression profiles on predicting protein interaction network and exploring of new treatments for lung cancer. PMID:25205123
Symbolic regression of generative network models. PMID:25190000
Construction and analysis of the protein-protein interaction networks based on gene expression profiles of Parkinson's disease. PMID:25170921
From pathways to networks: connecting dots by establishing protein-protein interaction networks in signaling pathways using affinity purification and mass spectrometry. PMID:25137225
The human plasma membrane peripherome: visualization and analysis of interactions. PMID:25057483
Proteogenomic convergence for understanding cancer pathways and networks. PMID:24994965
In silico analysis and experimental validation of azelastine hydrochloride (N4) targeting sodium taurocholate co-transporting polypeptide (NTCP) in HBV therapy. PMID:24965018
Correlating information contents of gene ontology terms to infer semantic similarity of gene products. PMID:24963342
Proteomics analysis of the non-muscle myosin heavy chain IIa-enriched actin-myosin complex reveals multiple functions within the podocyte. PMID:24949636
IIS--Integrated Interactome System: a web-based platform for the annotation, analysis and visualization of protein-metabolite-gene-drug interactions by integrating a variety of data sources and tools. PMID:24949626
Analysis pipeline for the epistasis search - statistical versus biological filtering. PMID:24817878
Using systems biology approaches to understand cardiac inflammation and extracellular matrix remodeling in the setting of myocardial infarction. PMID:24741709
RNA-Seq and microarrays analyses reveal global differential transcriptomes of Mesorhizobium huakuii 7653R between bacteroids and free-living cells. PMID:24695521
Improving protein function prediction using domain and protein complexes in PPI networks. PMID:24655481
in silico identification of protein-protein interactions in Silkworm, Bombyx mori. PMID:24616555
Modelling the yeast interactome. PMID:24589662
Detecting overlapping protein complexes in PPI networks based on robustness. PMID:24565162
Corbi: a new R package for biological network alignment and querying. PMID:24565104
RRHGE: a novel approach to classify the estrogen receptor based breast cancer subtypes. PMID:24563630
Link community detection using generative model and nonnegative matrix factorization. PMID:24489803
Computational Prediction of Protein-Protein Interaction Networks: Algo-rithms and Resources. PMID:24396273
The transporter classification database. PMID:24225317
High-throughput RNA interference screens integrative analysis: Towards a comprehensive understanding of the virus-host interplay. PMID:24175227
Methods and approaches in the topology-based analysis of biological pathways. PMID:24133454
Identifying overlapping communities as well as hubs and outliers via nonnegative matrix factorization. PMID:24129402
Evolution after whole-genome duplication: a network perspective. PMID:24048644
A miniaturized chemical proteomic approach for target profiling of clinical kinase inhibitors in tumor biopsies. PMID:23901793
Complementing the Eukaryotic Protein Interactome. PMID:23825550
Improving the measurement of semantic similarity between gene ontology terms and gene products: insights from an edge- and IC-based hybrid method. PMID:23741529
A new method for the discovery of essential proteins. PMID:23555595
Identification of MFS proteins in sorghum using semantic similarity. PMID:23299296
Mining functional subgraphs from cancer protein-protein interaction networks. PMID:23282132
Computational prediction of protein-protein interactions in Leishmania predicted proteomes. PMID:23251492
GWIDD: a comprehensive resource for genome-wide structural modeling of protein-protein interactions. PMID:23245398
Identifying complexes from protein interaction networks according to different types of neighborhood density. PMID:23210476
Interactogeneous: disease gene prioritization using heterogeneous networks and full topology scores. PMID:23185389
Inferring domain-domain interactions from protein-protein interactions in the complex network conformation. PMID:23046795
Discovering protein complexes in protein interaction networks via exploring the weak ties effect. PMID:23046740
Protein stickiness, rather than number of functional protein-protein interactions, predicts expression noise and plasticity in yeast. PMID:23017156
ReLiance: a machine learning and literature-based prioritization of receptor--ligand pairings. PMID:22962483
Identification of microRNA-regulated autophagic pathways in plant lectin-induced cancer cell death. PMID:22882626
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
atBioNet--an integrated network analysis tool for genomics and biomarker discovery. PMID:22817640
Biological network motif detection and evaluation. PMID:22784624
Assessing and predicting protein interactions by combining manifold embedding with multiple information integration. PMID:22595000
Exploring statistical and population aspects of network complexity. PMID:22590495
Pathway detection from protein interaction networks and gene expression data using color-coding methods and A∗ search algorithms. PMID:22577352
Network- and attribute-based classifiers can prioritize genes and pathways for autism spectrum disorders and intellectual disability. PMID:22499558
A new essential protein discovery method based on the integration of protein-protein interaction and gene expression data. PMID:22405054
ANAP: an integrated knowledge base for Arabidopsis protein interaction network analysis. PMID:22345505
Systems Biology Reveals MicroRNA-Mediated Gene Regulation. PMID:22303325
SAFE Software and FED Database to Uncover Protein-Protein Interactions using Gene Fusion Analysis. PMID:22267904
Which clustering algorithm is better for predicting protein complexes? PMID:22185599
Constructing a robust protein-protein interaction network by integrating multiple public databases. PMID:22165958
Aberrant epigenetic grooming of miRNAs in pancreatic cancer: a systems biology perspective. PMID:22126293
Chronic morphine alters the presynaptic protein profile: identification of novel molecular targets using proteomics and network analysis. PMID:22043286
Proteomic analysis of Col11a1-associated protein complexes. PMID:22038862
An interaction network predicted from public data as a discovery tool: application to the Hsp90 molecular chaperone machine. PMID:22022502
Tools used to study how protein complexes are assembled in signaling cascades. PMID:22002082
Computer applications for prediction of protein-protein interactions and rational drug design. PMID:21918619
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
Processes of fungal proteome evolution and gain of function: gene duplication and domain rearrangement. PMID:21572172
Using graph theory to analyze biological networks. PMID:21527005
Unexpected complexity of the reef-building coral Acropora millepora transcription factor network. PMID:21526989
Network-based pipeline for analyzing MS data: an application toward liver cancer. PMID:21410269
Predicting functions of proteins in mouse based on weighted protein-protein interaction network and protein hybrid properties. PMID:21283518
Finding undetected protein associations in cell signaling by belief propagation. PMID:21187432
New insights into protein-protein interaction data lead to increased estimates of the S. cerevisiae interactome size. PMID:21176124
3D-interologs: an evolution database of physical protein- protein interactions across multiple genomes. PMID:21143789
An improved method for scoring protein-protein interactions using semantic similarity within the gene ontology. PMID:21078182
Global protein interactome exploration through mining genome-scale data in Arabidopsis thaliana. PMID:21047383
Protein network prediction and topological analysis in Leishmania major as a tool for drug target selection. PMID:20875130
Yeast proteomics and protein microarrays. PMID:20728591
An information-flow-based model with dissipation, saturation and direction for active pathway inference. PMID:20504374
TopoGSA: network topological gene set analysis. PMID:20335277
Large-scale prediction of protein-protein interactions from structures. PMID:20298601
DmsD, a Tat system specific chaperone, interacts with other general chaperones and proteins involved in the molybdenum cofactor biosynthesis. PMID:20153451
Lists2Networks: integrated analysis of gene/protein lists. PMID:20152038
Investigating topological and functional features of multimodular proteins. PMID:20069113
Expression-based network biology identifies alteration in key regulatory pathways of type 2 diabetes and associated risk/complications. PMID:19997558
MitoInteractome: mitochondrial protein interactome database, and its application in 'aging network' analysis. PMID:19958484
PutidaNET: interactome database service and network analysis of Pseudomonas putida KT2440. PMID:19958481
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
Protopia: a protein-protein interaction tool. PMID:19828077
Evidence of highly regulated genes (in-Hubs) in gene networks of Saccharomyces cerevisiae. PMID:19812784
An integrated systems analysis implicates EGR1 downregulation in simian immunodeficiency virus encephalitis-induced neural dysfunction. PMID:19812322
Proteomics data repositories. PMID:19795424
BowTieBuilder: modeling signal transduction pathways. PMID:19566957
Large-scale assessment of the effect of popularity on the reliability of research. PMID:19551148
GIBA: a clustering tool for detecting protein complexes. PMID:19534736
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
Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PMID:19402753
POINeT: protein interactome with sub-network analysis and hub prioritization. PMID:19379523
FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions. PMID:19374773
Deciphering peculiar protein-protein interacting modules in Deinococcus radiodurans. PMID:19356244
Enumeration of condition-dependent dense modules in protein interaction networks. PMID:19213739
Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome. PMID:19054114
Network integration and graph analysis in mammalian molecular systems biology. PMID:19045817
The integrated analysis of metabolic and protein interaction networks reveals novel molecular organizing principles. PMID:19032748
Evaluation of GO-based functional similarity measures using S. cerevisiae protein interaction and expression profile data. PMID:18986551
Impacts of protein-protein interaction domains on organism and network complexity. PMID:18687879
Predicting and validating protein interactions using network structure. PMID:18654616
Website review: protein-protein interactions on the web. PMID:18629244
Extracting information automatically from biological literature. PMID:18629239
Can bibliographic pointers for known biological data be found automatically? Protein interactions as a case study. PMID:18628915
Probabilistic cross-species inference of orthologous genomic regions created by whole-genome duplication in yeast. PMID:18562662
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
Genome-wide inference of protein interaction sites: lessons from the yeast high-quality negative protein-protein interaction dataset. PMID:18281313
Protein databases on the internet. PMID:18265344
Predicting the interactome of Xanthomonas oryzae pathovar oryzae for target selection and DB service. PMID:18215330
The evolutionary dynamics of the Saccharomyces cerevisiae protein interaction network after duplication. PMID:18199840
The SeqFEATURE library of 3D functional site models: comparison to existing methods and applications to protein function annotation. PMID:18197987
Computational prediction of protein-protein interactions. PMID:18095187
Novel roles for selected genes in meiotic DNA processing. PMID:18069899
Generating confidence intervals on biological networks. PMID:18053130
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
Genes2Networks: connecting lists of gene symbols using mammalian protein interactions databases. PMID:17916244
Functional atlas of the integrin adhesome. PMID:17671451
A proteome-wide protein interaction map for Campylobacter jejuni. PMID:17615063
Comprehensive analysis of co-occurring domain sets in yeast proteins. PMID:17562021
Unequal evolutionary conservation of human protein interactions in interologous networks. PMID:17535438
Analysis of intraviral protein-protein interactions of the SARS coronavirus ORFeome. PMID:17520018
Reconstruction of human protein interolog network using evolutionary conserved network. PMID:17493278
Phylogenetic tree information aids supervised learning for predicting protein-protein interaction based on distance matrices. PMID:17212819
SNAPPI-DB: a database and API of Structures, iNterfaces and Alignments for Protein-Protein Interactions. PMID:17202171
cPath: open source software for collecting, storing, and querying biological pathways. PMID:17101041
Towards the identification of essential genes using targeted genome sequencing and comparative analysis. PMID:17052348
Stratus not altocumulus: a new view of the yeast protein interaction network. PMID:16984220
Cataloging the relationships between proteins: a review of interaction databases. PMID:16943573
Finding function: evaluation methods for functional genomic data. PMID:16869964
The Escherichia coli proteome: past, present, and future prospects. PMID:16760308
Large-scale identification of protein-protein interaction of Escherichia coli K-12. PMID:16606699
Functional partitioning of yeast co-expression networks after genome duplication. PMID:16555924
INTEGRATOR: interactive graphical search of large protein interactomes over the Web. PMID:16542421
Ulysses - an application for the projection of molecular interactions across species. PMID:16356269
The yeast kinome displays scale free topology with functional hub clusters. PMID:16283924
Comparative genomics and disorder prediction identify biologically relevant SH3 protein interactions. PMID:16110343
Gene essentiality and the topology of protein interaction networks. PMID:16087428
Are scale-free networks robust to measurement errors? PMID:15904487
Nebulon: a system for the inference of functional relationships of gene products from the rearrangement of predicted operons. PMID:15867197
Content-rich biological network constructed by mining PubMed abstracts. PMID:15473905
The Database of Interacting Proteins: 2004 update. PMID:14681454
Visualisation and graph-theoretic analysis of a large-scale protein structural interactome. PMID:14531933
Development of human protein reference database as an initial platform for approaching systems biology in humans. PMID:14525934
Interrogating protein interaction networks through structural biology. PMID:11972061
Relating whole-genome expression data with protein-protein interactions. PMID:11779829
Predictome: a database of putative functional links between proteins. PMID:11752322
DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. PMID:11752321
Probabilistic prediction of unknown metabolic and signal-transduction networks. PMID:11729170
SPINE: an integrated tracking database and data mining approach for identifying feasible targets in high-throughput structural proteomics. PMID:11433035
PartsList: a web-based system for dynamically ranking protein folds based on disparate attributes, including whole-genome expression and interaction information. PMID:11292848
A comprehensive two-hybrid analysis to explore the yeast protein interactome. PMID:11283351
BIND--The Biomolecular Interaction Network Database. PMID:11125103
DIP: The Database of Interacting Proteins: 2001 update. PMID:11125102
DIP: The Database of Interacting Proteins: 2001 update PubMed citations: 55.

55 articles citing: DIP: The Database of Interacting Proteins: 2001 update

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
Protein network analysis to prioritize key genes in amyotrophic lateral sclerosis. PMID:34918006
Tumor relevant protein functional interactions identified using bipartite graph analyses. PMID:34728699
Network-based protein-protein interaction prediction method maps perturbations of cancer interactome. PMID:34727106
MetaCancer: A deep learning-based pan-cancer metastasis prediction model developed using multi-omics data. PMID:34429856
Databases for Protein-Protein Interactions. PMID:34236665
UniProt-Related Documents (UniReD): assisting wet lab biologists in their quest on finding novel counterparts in a protein network. PMID:33575553
Towards a unified open access dataset of molecular interactions. PMID:33262342
Network Modeling Approaches and Applications to Unravelling Non-Alcoholic Fatty Liver Disease. PMID:31771247
Identification of drug target candidates of the swine pathogen Actinobacillus pleuropneumoniae by construction of protein-protein interaction network. PMID:30047117
Improving Prediction of Self-interacting Proteins Using Stacked Sparse Auto-Encoder with PSSM profiles. PMID:29989064
Systematic Evaluation of Molecular Networks for Discovery of Disease Genes. PMID:29605183
Network Biomarkers Constructed from Gene Expression and Protein-Protein Interaction Data for Accurate Prediction of Leukemia. PMID:28243332
BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID. PMID:27589962
PIPE: a protein-protein interaction passage extraction module for BioCreative challenge. PMID:27524807
HVint: A Strategy for Identifying Novel Protein-Protein Interactions in Herpes Simplex Virus Type 1. PMID:27384951
Novel Neuroprotective Multicomponent Therapy for Amyotrophic Lateral Sclerosis Designed by Networked Systems. PMID:26807587
PPIM: A Protein-Protein Interaction Database for Maize. PMID:26620522
Network Modules of the Cross-Species Genotype-Phenotype Map Reflect the Clinical Severity of Human Diseases. PMID:26301634
GECluster: a novel protein complex prediction method. PMID:26019559
Aberrant gene expression in mucosa adjacent to tumor reveals a molecular crosstalk in colon cancer. PMID:24597571
Computational Prediction of Protein-Protein Interaction Networks: Algo-rithms and Resources. PMID:24396273
Integration of proteomics, bioinformatics, and systems biology in traumatic brain injury biomarker discovery. PMID:23750150
Relaxation response induces temporal transcriptome changes in energy metabolism, insulin secretion and inflammatory pathways. PMID:23650531
Crowd sourcing a new paradigm for interactome driven drug target identification in Mycobacterium tuberculosis. PMID:22808064
ANAP: an integrated knowledge base for Arabidopsis protein interaction network analysis. PMID:22345505
Modularity analysis based on predicted protein-protein interactions provides new insights into pathogenicity and cellular process of Escherichia coli O157:H7. PMID:22188601
Aberrant epigenetic grooming of miRNAs in pancreatic cancer: a systems biology perspective. PMID:22126293
Chronic morphine alters the presynaptic protein profile: identification of novel molecular targets using proteomics and network analysis. PMID:22043286
Network-based pipeline for analyzing MS data: an application toward liver cancer. PMID:21410269
Defining the antigen receptor-dependent regulatory network that induces arrest of cycling immature B-lymphocytes. PMID:21143896
Global protein interactome exploration through mining genome-scale data in Arabidopsis thaliana. PMID:21047383
RegPhos: a system to explore the protein kinase-substrate phosphorylation network in humans. PMID:21037261
Construction and analysis of protein-protein interaction networks. PMID:20334628
Human cancer protein-protein interaction network: a structural perspective. PMID:20011507
Mutation of SHOC2 promotes aberrant protein N-myristoylation and causes Noonan-like syndrome with loose anagen hair. PMID:19684605
Design logic of a cannabinoid receptor signaling network that triggers neurite outgrowth. PMID:18487186
The evolutionary dynamics of the Saccharomyces cerevisiae protein interaction network after duplication. PMID:18199840
Increasing the power to detect causal associations by combining genotypic and expression data in segregating populations. PMID:17432931
Prediction of phenotype and gene expression for combinations of mutations. PMID:17389876
SNAPPI-DB: a database and API of Structures, iNterfaces and Alignments for Protein-Protein Interactions. PMID:17202171
VIRGO: computational prediction of gene functions. PMID:16845022
The cognitive phenotype of Down syndrome: insights from intracellular network analysis. PMID:16815222
BIOZON: a system for unification, management and analysis of heterogeneous biological data. PMID:16480510
Hubs of knowledge: using the functional link structure in Biozon to mine for biologically significant entities. PMID:16480496
BIOZON: a hub of heterogeneous biological data. PMID:16381854
Toward predictive models of mammalian cells. PMID:15869393
Identification and functional analysis of 'hypothetical' genes expressed in Haemophilus influenzae. PMID:15121896
Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction. PMID:15079056
VisANT: an online visualization and analysis tool for biological interaction data. PMID:15028117
From gene networks to gene function. PMID:14656964
Detection of regulatory circuits by integrating the cellular networks of protein-protein interactions and transcription regulation. PMID:14530453
Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs. PMID:12824383
Inferring higher functional information for RIKEN mouse full-length cDNA clones with FACTS. PMID:12819151
DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. PMID:11752321

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high-throughput screening
metasource: Fairsharing.org
version: FAIRsharing.org: DIP; Database of Interacting Proteins; DOI: https://doi.org/10.25504/FAIRsharing.qje0v8; Last edited: June 23, 2021, 2 p.m.; Last accessed: Jan 03 2022 7:09 p.m.

network model
metasource: Fairsharing.org
version: FAIRsharing.org: DIP; Database of Interacting Proteins; DOI: https://doi.org/10.25504/FAIRsharing.qje0v8; Last edited: June 23, 2021, 2 p.m.; Last accessed: Jan 03 2022 7:09 p.m.

protein
metasource: Fairsharing.org
version: FAIRsharing.org: DIP; Database of Interacting Proteins; DOI: https://doi.org/10.25504/FAIRsharing.qje0v8; Last edited: June 23, 2021, 2 p.m.; Last accessed: Jan 03 2022 7:09 p.m.

protein interaction
metasource: Fairsharing.org
version: FAIRsharing.org: DIP; Database of Interacting Proteins; DOI: https://doi.org/10.25504/FAIRsharing.qje0v8; Last edited: June 23, 2021, 2 p.m.; Last accessed: Jan 03 2022 7:09 p.m.

caenorhabditis elegans
metasource: re3data.org
version: re3data.org: Database of Interacting Proteins; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3VG8D last accessed: 2022-11-04

helicobacter pylori
metasource: re3data.org
version: re3data.org: Database of Interacting Proteins; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3VG8D last accessed: 2022-11-04

norway rat
metasource: re3data.org
version: re3data.org: Database of Interacting Proteins; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3VG8D last accessed: 2022-11-04

baker's yeast
metasource: re3data.org
version: re3data.org: Database of Interacting Proteins; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3VG8D last accessed: 2022-11-04

cow
metasource: re3data.org
version: re3data.org: Database of Interacting Proteins; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3VG8D last accessed: 2022-11-04

escherichia coli
metasource: re3data.org
version: re3data.org: Database of Interacting Proteins; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3VG8D last accessed: 2022-11-04

fruit fly
metasource: re3data.org
version: re3data.org: Database of Interacting Proteins; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3VG8D last accessed: 2022-11-04

human
metasource: re3data.org
version: re3data.org: Database of Interacting Proteins; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3VG8D last accessed: 2022-11-04

mouse
metasource: re3data.org
version: re3data.org: Database of Interacting Proteins; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3VG8D last accessed: 2022-11-04

thale cress
metasource: re3data.org
version: re3data.org: Database of Interacting Proteins; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3VG8D last accessed: 2022-11-04

protein interactions
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:10.100293

protein interaction experiment
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:10.100293

molecular interactions, pathways and networks
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:10.100293

proteins
metasource: bio.tools
version: extracted_at: 2022-11-04T11:36:10.100293

high-throughput screening network model protein protein interaction caenorhabditis elegans helicobacter pylori norway rat baker's yeast cow escherichia coli fruit fly human mouse thale cress protein interaction protein interaction experiment molecular interactions, pathways and networks proteins

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PSIQUIC (DIP)

Negatome

Bacterial Protein Interaction Database

Human Protein-Protein Interaction rEference

Molecular INTeraction database

KUPS

DroID - Drosophila Interactions Database

TRIP

Human protein-protein interaction network database search

STRING

Protein Protein Interaction Inhibition Database

HitPredict

mentha

Biological General Repository for Interaction Datasets

Agile Protein Interactomes Dataserver

The Protein Database

Protein Interaction Network Analysis platform

Compartmentalized Protein-Protein Interaction

VirusMentha

AtPID