Access the full text.
Sign up today, get DeepDyve free for 14 days.
Pavel (2022)
Network analysis of microarray dataMethods Mol Biol, 2401
Chen (2004)
Global protein function annotation through mining genome-scale data in yeast Saccharomyces cerevisiaeNucleic Acids Res, 32
Cao (2014)
The central role of EED in the orchestration of polycomb group complexesNature Commun, 5
Kiemer (2007)
WI-PHI: a weighted yeast interactome enriched for direct physical interactionsProteomics, 7
Trewavas (2006)
A brief history of systems biologyPlant Cell, 18
Kariithi (2016)
A proteomics approach reveals molecular manipulators of distinct cellular processes in the salivary glands of Glossina m. morsitans in response to Trypanosoma b. brucei infectionsParasit Vectors, 9
Itzhaki (2006)
Evolutionary conservation of domain-domain interactionsGenome Biol, 7
Marcotte (1999)
Detecting protein function and protein-protein interactions from genome sequencesScience, 285
Huang (2007)
Reconstruction of human protein interolog network using evolutionary conserved networkBMC Bioinformatics, 8
Barabasi (1999)
Emergence of scaling in random networksScience, 286
Goll (2006)
The elusive yeast interactomeGenome Biol, 7
Gavin (2006)
Proteome survey reveals modularity of the yeast cell machineryNature, 440
Konieczka (2009)
BioNetBuilder2.0: bringing systems biology to chicken and other model organismsBMC Genomics, 10
Xu (2015)
Transcriptome profiling and molecular pathway analysis of genes in association with salinity adaptation in nile tilapia Oreochromis niloticusPloS One, 10
Seo (2011)
Towards establishment of a rice stress response interactomePLoS Genet, 7
James (2009)
Integration of full-coverage probabilistic functional networks with relevance to specific biological processesData Integr Life Sci, 5647
Zhu (2011)
Computational identification of protein-protein interactions in rice based on the predicted rice interactome networkGenomics Proteomics Bioinformatics
Fletcher (2015)
Aging in the wild: insights from free-living and non-model organismsExp Gerontol, 71
LaCount (2005)
A protein interaction network of the malaria parasite plasmodium falciparumNature, 438
Fukuyama (2013)
Landscape of protein-protein interactions in drosophila immune deficiency signaling during bacterial challengeProc Natl Acad Sci U S A, 110
Watanabe Costa (2020)
Comparative analysis of the secretome and interactome of Trypanosoma cruzi and Trypanosoma rangeli reveals species specific immune response modulating proteinsFront Immunol, 11
Stuart (2003)
A gene-coexpression network for global discovery of conserved genetic modulesScience, 302
Velázquez-Lizárraga (2019)
Transcriptomic analysis of Pacific white shrimp (Litopenaeus vannamei, Boone 1931) in response to acute hepatopancreatic necrosis disease caused by Vibrio parahaemolyticusPloS One, 14
Millan-Cubillo (2019)
Proteomic characterization of primary cultured myocytes in a fish model at different myogenesis stagesSci Rep, 9
Mason (2007)
Graph theory and networks in biologyIET Syst Biol, 1
Chang (2016)
Field guide to plant model systemsCell, 167
Fromont-Racine (1997)
Toward a functional analysis of the yeast genome through exhaustive two-hybrid screensNat Genet, 16
Sumathy (2014)
In silico identification of protein-protein interactions in silkwormBombyxmori Bioinformation, 10
Albert (2005)
Scale-free networks in cell biologyJJ Cell Sci, 118
Sato (2005)
The inference of protein-protein interactions by co-evolutionary analysis is improved by excluding the information about the phylogenetic relationshipsBioinformatics, 21
Ito (2001)
A comprehensive two-hybrid analysis to explore the yeast protein interactomeProc Natl Acad Sci U S A, 98
Strogatz (2001)
Exploring complex networksNature, 410
Goh (2002)
Co-evolutionary analysis reveals insights into protein-protein interactionsJ Mol Biol, 324
Karaoz (2004)
Whole-genome annotation by using evidence integration in functional-linkage networksProc Natl Acad Sci U S A, 101
Koch (2012)
Conserved rules govern genetic interaction degree across speciesGenome Biol, 13
Braun (2013)
Plant protein interactomesAnnu Rev Plant Biol, 64
Morsy (2008)
Charting plant interactomes: possibilities and challengesTrends Plant Sci, 13
Waiho (2020)
Protein-protein interaction network: an emerging tool for understanding fish disease in aquacultureRev Aquac, 13
Li (2017)
Spatiotemporal profile of postsynaptic interactomes integrates components of complex brain disordersNat Neurosci, 20
Scott (2007)
Probabilistic prediction and ranking of human protein-protein interactionsBMC Bioinformatics, 8
Guruharsha (2011)
A protein complex network of Drosophila melanogasterCell, 147
Liang (2006)
Comparison of protein interaction networks reveals species conservation and divergenceBMC Bioinformatics, 7
Yu (2008)
High-quality binary protein interaction map of the yeast interactome networkScience, 322
Huang (2004)
POINT: a database for the prediction of protein-protein interactions based on the orthologous interactomeBioinformatics, 20
Franzosa (2009)
Computational reconstruction of protein-protein interaction networks: algorithms and issuesMethods Mol Biol, 541
Musungu (2015)
A predicted protein interactome identifies conserved global networks and disease resistance subnetworks in maizeFront Genet, 6
Raghavachari (2008)
Domine: a database of protein domain interactionsNucleic Acids Res, 36
Cusick (2005)
Interactome: gateway into systems biologyHum Mol Genet, 14
Joyce (2006)
The model organism as a system: integrating ‘omics’ data setsNat Rev Mol Cell Biol, 7
Wang (2012)
Prediction and characterization of protein-protein interaction networks in swineProteome Sci, 10
Matthews (2001)
Identification of potential interaction networks using sequence-based searches for conserved protein-protein interactions or “interologs”Genome Res, 11
Ogris (2018)
FunCoup 4: new species, data, and visualizationNucleic Acids Res, 46
Lee (2011)
Genetic dissection of the biotic stress response using a genome-scale gene network for riceProc Natl Acad Sci U S A, 108
Singh (2020)
Genome-wide interologous interactome map (TeaGPIN) of Camellia sinensisGenomics, S0888-7543
Lo (2005)
Effect of training datasets on support vector machine prediction of protein-protein interactionsProteomics, 5
Tagu (2014)
Genomic data integration for ecological and evolutionary traits in non-model organismsBMC Genomics, 15
Lee (2007)
An improved, bias-reduced probabilistic functional gene network of baker’s yeast, Saccharomyces cerevisiaePloS One, 2
Altman (2001)
Whole-genome expression analysis: challenges beyond clusteringCurr Opin Struct Biol, 11
Sharan (2006)
Modeling cellular machinery through biological network comparisonNat Biotechnol, 24
Yue (2016)
PTIR: predicted tomato interactome resourceSci Rep, 6
Wang (2016)
Prediction and analysis of the protein-protein interaction networks for chickens, cattle, dogs, horses and rabbitsCurr Bioinform, 11
Koorman (2016)
A combined binary interaction and phenotypic map of C. elegans cell polarity proteinsNat Cell Biol, 18
Qian (2001)
Beyond synexpression relationships: local clustering of time-shifted and inverted gene expression profiles identifies new, biologically relevant interactionsJ Mol Biol, 314
Yanai (2001)
Genes linked by fusion events are generally of the same functional category: a systematic analysis of 30 microbial genomesProc Natl Acad Sci U S A, 98
Liu (2009)
Knowledge-guided inference of domain-domain interactions from incomplete protein-protein interaction networksBioinformatics, 25
O’Rourke (2007)
Dynein modifiers in C. elegans: light chains suppress conditional heavy chain mutantsPLoS Genet, 3
Huang (2016)
An integrative C. elegans protein–protein interaction network with reliability assessment based on a probabilistic graphical modelMol Biosyst, 12
Kuo (2013)
Identification of infection- and defense-related genes via a dynamic host-pathogen interaction network using a Candida albicans-zebrafish infection modelJ Innate Immun, 5
Mitrofanova (2010)
Predicting malaria interactome classifications from time-course transcriptomic data along the intraerythrocytic developmental cycleArtif Intell Med, 49
González-Fernández (2010)
Proteomics of plant pathogenic fungiJ Biomed Biotechnol, 2010
Alanis-Lobato (2020)
MIPPIE: the mouse integrated protein-protein interaction referenceDatabase (Oxford), 2020
Guillemin (2011)
Functional analysis of beef tendernessJ Proteomics, 75
Diezmann (2012)
Mapping the Hsp90 genetic interaction network in Candida albicans reveals environmental contingency and rewired circuitryPLoS Genet, 8
Pazos (2002)
In silico two-hybrid system for the selection of physically interacting protein pairsProteins, 47
Carrera (2013)
The sarcoplasmic fish proteome: pathways, metabolic networks and potential bioactive peptides for nutritional inferencesJ Proteomics, 78
Lee (2006)
An integrated approach to the prediction of domain-domain interactionsBMC Bioinformatics, 7
Howick (2019)
The malaria cell atlas: single parasite transcriptomes across the complete plasmodium life cycleScience, 365
Boltz (2019)
Collective influencers in protein interaction networksSci Rep, 9
Singh (2019)
Construction and analysis of an interologous protein-protein interaction network of Camellia sinensis leaf (TeaLIPIN) from rna-seq data setsPlant Cell Rep, 38
Raposo (2020)
Protein changes as robust signatures of fish chronic stress: a proteomics approach to fish welfare researchBMC Genomics, 21
Taylor (2011)
Targeting protein-protein interactions for parasite controlPloS One, 6
Alborzi (2021)
Ppidomainminer: inferring domain-domain interactions from multiple sources of protein-protein interactionsPLoS Comput Biol, 17
Chen (2020)
Predicted functional interactome of Caenorhabditis elegans and a web tool for the functional interpretation of differentially expressed genesBiol Direct, 15
Lu (2006)
Integrated analysis of multiple data sources reveals modular structure of biological networksBiochem Biophys Res Commun, 345
Collins (2007)
Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiaeMol Cell Proteomics, 6
Sprague (2006)
The zebrafish information network: the zebrafish model organism databaseNucleic Acids Res, 34
Pellegrini (1999)
Assigning protein functions by comparative genome analysis: protein phylogenetic profilesProc Natl Acad Sci U S A, 96
Schoeters (2018)
C d’Enfert, and P Van Dijck. A high-throughput Candida albicans two-hybrid systemmSphere, 3
Koonin (2006)
Evolutionary systems biology: links between gene evolution and functionCurr Opin Biotechnol, 17
Jothi (2005)
Predicting protein-protein interaction by searching evolutionary tree automorphism spaceBioinformatics, 21
Li (2016)
AraPPISite: a database of fine-grained protein-protein interaction site annotations for Arabidopsis thalianaPlant Mol Biol, 92
Sci Signal, 6
Hartwell (1999)
From molecular to modular cell biologyNature, 402
Alexeyenko (2010)
Dynamic zebrafish interactome reveals transcriptional mechanisms of dioxin toxicityPloS One, 5
Pourhaghighi (2020)
BraInMap elucidates the macromolecular connectivity landscape of mammalian brainCell Syst, 10
Geisler-Lee (2007)
A predicted interactome for ArabidopsisPlant Physiol
Stegeman (2016)
The spliceosomal protein SF3B5 is a novel component of drosophila SAGA that functions in gene expression independent of splicingJ Mol Biol, 428
Bertin (2007)
Confirmation of organized modularity in the yeast interactomePLoS Biol, 5
Giot (2003)
A protein interaction map of Drosophila melanogasterScience, 302
Xin (2009)
Shifted transversal design smart-pooling for high coverage interactome mappingGenome Res, 19
Vandereyken (2018)
Hub protein controversy: taking a closer look at plant stress response hubsFront Plant Sci, 9
Sahu (2014)
Predicting genome-scale Arabidopsis-pseudomonas syringae interactome using domain and interolog-based approachesBMC Bioinformatics, 15
Beyer (2007)
Integrating physical and genetic maps: from genomes to interaction networksNat Rev Genet, 8
Skinnider (2021)
An atlas of protein-protein interactions across mouse tissuesCell, 184
Yu (2019)
Big data in yeast systems biologyFEMS Yeast Res, 19
Gilchrist (2004)
A statistical framework for combining and interpreting proteomic datasetsBioinformatics, 20
Rhind (2011)
Comparative functional genomics of the fission yeastsScience, 332
Lee (2008)
Ortholog-based protein-protein interaction prediction and its application to inter-species interactionsBMC Bioinformatics, 9
Huber (2007)
Graphs in molecular biologyBMC Bioinformatics, 8
Pang (2020)
Analytical guidelines for co-fractionation mass spectrometry obtained through global profiling of gold standard Saccharomyces cerevisiae protein complexesMol Cell Proteomics, 19
Espadaler (2005)
Prediction of protein-protein interactions using distant conservation of sequence patterns and structure relationshipsBioinformatics, 21
Dandekar (1998)
Conservation of gene order: a fingerprint of proteins that physically interactTrends Biochem Sci, 23
Wiles (2010)
Building and analyzing protein interactome networks by cross-species comparisonsBMC Syst Biol, 4
Arabidopsis Interactome Mapping Consortium (2011)
Evidence for network evolution in an Arabidopsis interactome mapScience, 333
Stanyon (2004)
A drosophila protein-interaction map centered on cell-cycle regulatorsGenome Biol, 5
Li (2016)
Identification of the interactome between fish plasma proteins and Edwardsiella tarda reveals tissue-specific strategies against bacterial infectionInt J Biochem Cell Biol, 78
Rees (2011)
In vivo analysis of proteomes and interactomes using parallel affinity capture (iPAC) coupled to mass spectrometryMol Cell Proteomics, 10
Liu (2010)
A network approach to predict pathogenic genes for Fusarium graminearumPloS One, 5
Tao (2020)
Predicted rat interactome database and gene set linkage analysisDatabase (Oxford), 2020
Ewing (2007)
Large-scale mapping of human protein-protein interactions by mass spectrometryMol Syst Biol, 3
Li (2010)
A mouse protein interactome through combined literature mining with multiple sources of interaction evidenceAmino Acids, 38
Yu (2004)
Annotation transfer between genomes: protein-protein interologs and protein-dna regulogsGenome Res, 14
Shin (2009)
Towards the mammalian interactome: inference of a core mammalian interaction set in mouseProteomics, 9
Carruthers (2018)
De novo transcriptome assembly, annotation and comparison of four ecological and evolutionary model salmonid fish speciesBMC Genomics, 19
Kelley (2003)
Conserved pathways within bacteria and yeast as revealed by global protein network alignmentProc Natl Acad Sci U S A, 100
Jeong (2000)
The large-scale organization of metabolic networksNature, 407
Zhang (2018)
Complementary proteomics strategies capture an ataxin-1 interactome in neuro-2a cellsSci Data, 5
Guo (2010)
Response of the mosquito protein interaction network to dengue infectionBMC Genomics, 11
Rao (2010)
Cerebral malaria: insights from host-parasite protein-protein interactionsMalar J, 9
Rodgers-Melnick (2013)
Predicting whole genome protein interaction networks from primary sequence data in model and non-model organisms using ENTSBMC Genomics, 14
Koonin (2005)
Systemic determinants of gene evolution and functionMol Syst Biol, 1
Suratanee (2020)
Heterogeneous network model to identify potential associations between plasmodium vivax and human proteinsInt J Mol Sci, 21
Yamanishi (2004)
Protein network inference from multiple genomic data: a supervised approachBioinformatics, 20
Formstecher (2005)
Protein interaction mapping: a drosophila case studyGenome Res, 15
Patil (2005)
Filtering high-throughput protein-protein interaction data using a combination of genomic featuresBMC Bioinformatics, 6
Kim (2008)
Inferring mouse gene functions from genomic-scale data using a combined functional network/classification strategyGenome Biol, 9
Yanai (2002)
The society of genes: networks of functional links between genes from comparative genomicsGenome Biol, 3
Fraser (2004)
A probabilistic view of gene functionNat Genet, 36
Lee (2007)
Coimmunoprecipitation assayMethods Mol Biol, 362
Lee (2008)
A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegansNat Genet, 40
Cai (2014)
Identification of a genetic interaction between the tumor suppressor EAF2 and the retinoblastoma protein (Rb) signaling pathway in C. elegans and prostate cancer cellsBiochem Biophys Res Commun, 447
Kovács (2019)
Network-based prediction of protein interactionsNat Commun, 10
Kann (2007)
Protein interactions and disease: computational approaches to uncover the etiology of diseasesBrief Bioinform, 8
Aho (2010)
Reconstruction and validation of RefRec: a global model for the yeast molecular interaction networkPLoS One, 5
Lv (2017)
AtPID: a genome-scale resource for genotype-phenotype associations in ArabidopsisNucleic Acids Res, 45
Zhao (2019)
AraPPINet: an updated interactome for the analysis of hormone signaling crosstalk in Arabidopsis thalianaFront Plant Sci, 10
García-Jiménez (2010)
Inference of functional relations in predicted protein networks with a machine learning approachPLoS One, 5
Ungaro (2017)
Challenges and advances for transcriptome assembly in non-model speciesPloS One, 12
Moné (2010)
A large repertoire of parasite epitopes matched by a large repertoire of host immune receptors in an invertebrate host/parasite modelPLoS Negl Trop Dis, 4
Ji (2014)
Protein-protein interaction network of the marine microalga Tetraselmis subcordiformis: prediction and application for starch metabolism analysisJ Ind Microbiol Biotechnol, 41
Tang (2009)
Chemical cross-linking for protein-protein interaction studiesMethods Mol Biol, 492
Wuchty (2006)
Stable evolutionary signal in a yeast protein interaction networkBMC Evol Biol, 6
Murali (2011)
DroID 2011: a comprehensive, integrated resource for protein, transcription factor, rna and gene interactions for drosophilaNucleic Acids Res, 39
Gerstein (2002)
Integrating interactomesScience, 295
Gunsalus (2008)
A Caenorhabditis elegans genetic-interaction map wiggles into viewJ Biol, 7
Lee (2020)
BarleyNet: a network-based functional omics analysis server for cultivated barley, Hordeum vulgare lFront Plant Sci, 11
Suthram (2005)
The plasmodium protein network diverges from those of other eukaryotesNature, 438
Kim (2002)
Large scale statistical prediction of protein-protein interaction by potentially interacting domain (PID) pairGenome Inform, 13
Daraselia (2004)
Extracting human protein interactions from MEDLINE using a full-sentence parserBioinformatics, 20
Shoemaker (2007)
Deciphering protein-protein interactions. Part II. Computational methods to predict protein and domain interaction partnersPLoS Comput Biol, 3
Ryan (2012)
Hierarchical modularity and the evolution of genetic interactomes across speciesMol Cell, 46
Kim (2020)
BiomeNet: a database for construction and analysis of functional interaction networks for any species with a sequenced genomeBioinformatics, 36
Shokri (2019)
A comprehensive Drosophila melanogaster transcription factor interactomeCell Rep, 27
Overbeek (1999)
The use of gene clusters to infer functional couplingProc Natl Acad Sci U S A, 96
van Noort (2003)
Predicting gene function by conserved co-expressionTrends Genet, 19
Loewe (2009)
A framework for evolutionary systems biologyBMC Syst Biol, 3
Chaiboonchoe (2016)
Systems level analysis of the Chlamydomonas reinhardtii metabolic network reveals variability in evolutionary co-conservationMol Biosyst, 12
Sapkota (2011)
DIPOS: database of interacting proteins in Oryza sativaMol Biosyst, 7
Deng (2002)
Inferring domain-domain interactions from protein-protein interactionsGenome Res, 12
Thanasomboon (2017)
Prediction of cassava protein interactome based on interolog methodSci Rep, 7
Lehner (2006)
Systematic mapping of genetic interactions in Caenorhabditis elegans identifies common modifiers of diverse signaling pathwaysNat Genet, 38
O’Meara (2019)
Global proteomic analyses define an environmentally contingent Hsp90 interactome and reveal chaperone-dependent regulation of stress granule proteins and the R2TP complex in a fungal pathogenPLoS Biol, 17
Gunsalus (2011)
Networks in Caenorhabditis elegansCurr Opin Genet Dev, 21
Cuesta-Astroz (2019)
Analysis of predicted host-parasite interactomes reveals commonalities and specificities related to parasitic lifestyle and tissues tropismFront Immunol, 10
Lee (2015)
RiceNet v2: an improved network prioritization server for rice genesNucleic Acids Res, 43
Sun (2007)
Construction of phylogenetic profiles based on the genetic distance of hundreds of genomesBiochem Biophys Res Commun, 355
LaCount (2012)
Interactome mapping in malaria parasites: challenges and opportunitiesMethods Mol Biol, 812
Mairiang (2013)
Identification of new protein interactions between dengue fever virus and its hosts, human and mosquitoPloS One, 8
Hart (2007)
A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentialityBMC Bioinformatics, 8
Stynen (2010)
A CUG codon adapted two-hybrid system for the pathogenic fungus Candida albicansNucleic Acids Res, 38
Van Leene (2010)
Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thalianaMol Syst Biol, 6
Popescu (2007)
Differential binding of calmodulin-related proteins to their targets revealed through high-density Arabidopsis protein microarraysProc Natl Acad Sci U S A, 104
Yang (2020)
PlaPPISite: a comprehensive resource for plant protein-protein interaction sitesBMC Plant Biol, 20
Bowers (2004)
Prolinks: a database of protein functional linkages derived from coevolutionGenome Biol, 5
Han (2004)
Evidence for dynamically organized modularity in the yeast protein-protein interaction networkNature, 430
Berriman (2009)
The genome of the blood fluke Schistosoma mansoniNature, 460
Van Leene (2011)
A kaleidoscopic view of the Arabidopsis core cell cycle interactomeTrends Plant Sci, 16
Wan (2015)
Panorama of ancient metazoan macromolecular complexesNature, 525
Nguyen (2013)
Identifying conserved protein complexes between species by constructing interolog networksBMC Bioinformatics, 14
Jansen (2002)
Integration of genomic datasets to predict protein complexes in yeastJ Struct Funct Genomics, 2
Segura (2016)
3diana: 3d domain interaction analysis: a toolbox for quaternary structure modelingBiophys J, 110
Özkan (2013)
An extracellular interactome of immunoglobulin and lrr proteins reveals receptor-ligand networksCell, 154
Ceron (2007)
Large-scale RNAi screens identify novel genes that interact with the C. elegans retinoblastoma pathway as well as splicing-related components with synMuv B activityBMC Dev Biol, 7
Barabási (2004)
Network biology: understanding the cell’s functional organizationNat Rev Genet, 5
Batada (2006)
Evolutionary and physiological importance of hub proteinsPLoS Comput Biol, 2
Vo (2016)
A proteome-wide fission yeast interactome reveals network evolution principles from yeasts to humanCell, 164
Tong (2001)
Systematic genetic analysis with ordered arrays of yeast deletion mutantsScience, 294
Dyer (2007)
Computational prediction of host-pathogen protein-protein interactionsBioinformatics, 23
Ge (2003)
Integrating ‘omic’ information: a bridge between genomics and systems biologyTrends Genet, 19
Yu (2006)
Computational approaches for predicting protein-protein interactions: a surveyJ Med Syst, 30
Sharan (2005)
Conserved patterns of protein interaction in multiple speciesProc Natl Acad Sci U S A, 102
Ravasz (2002)
Hierarchical organization of modularity in metabolic networksScience, 297
Pazos (2001)
Similarity of phylogenetic trees as indicator of protein-protein interactionProtein Eng, 14
Yang (2019)
Critical assessment and performance improvement of plant-pathogen protein-protein interaction prediction methodsBrief Bioinform, 20
Ding (2009)
A rice kinase-protein interaction mapPlant Physiol, 149
Bar-Joseph (2012)
Studying and modelling dynamic biological processes using time-series gene expression dataNat Rev Genet, 13
Ding (2020)
Predicted drosophila Interactome resource and web tool for functional interpretation of differentially expressed genesDatabase (Oxford), 2020
Zhao (2009)
FPPI: Fusarium graminearum protein-protein interaction databaseJ Proteome Res, 8
Cui (2008)
AtPID: Arabidopsis thaliana protein interactome database–an integrative platform for plant systems biologyNucleic Acids Res, 36
Lu (2002)
MULTIPROSPECTOR: an algorithm for the prediction of protein-protein interactions by multimeric threadingProteins, 49
Simonis (2009)
Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome networkNat Methods, 6
Kirk (2017)
The impact of the protein interactome on the syntenic structure of mammalian genomesPloS One, 12
Ponte-Sucre (2016)
An overview of Trypanosoma brucei infections: an intense host-parasite interactionFront Microbiol, 7
Ekblom (2011)
Applications of next generation sequencing in molecular ecology of non-model organismsHeredity (Edinb), 107
Sprinzak (2003)
How reliable are experimental protein-protein interaction data?J Mol Biol, 327
Lee (2010)
Rational association of genes with traits using a genome-scale gene network for Arabidopsis thalianaNat Biotechnol, 28
Bader (2002)
Analyzing yeast protein-protein interaction data obtained from different sourcesNat Biotechnol, 20
De Bodt (2009)
Predicting protein-protein interactions in Arabidopsis thaliana through integration of orthology, gene ontology and co-expressionBMC Genomics, 10
Erten (2009)
Phylogenetic analysis of modularity in protein interaction networksBMC Bioinformatics, 10
Schuldiner (2005)
Exploration of the function and organization of the yeast early secretory pathway through an epistatic miniarray profileCell, 123
Jafari (2013)
Evolutionarily conserved motifs and modules in mitochondrial protein-protein interaction networksMitochondrion, 13
Asthana (2004)
Predicting protein complex membership using probabilistic network reliabilityGenome Res, 14
Liu (2017)
A computational interactome for prioritizing genes associated with complex agronomic traits in rice (Oryza sativa)Plant J, 90
Hao (2019)
The protein-protein interaction network of, Litopenaeus vannamei haemocytesFront Physiol, 10
James (2020)
The tapeworm interactome: inferring confidence scored protein-protein interactions from the proteome of Hymenolepis microstomaBMC Genomics, 21
Wuchty (2009)
A comprehensive plasmodium falciparum protein interaction map reveals a distinct architecture of a core interactomeProteomics, 9
Ding (2014)
Prediction and functional analysis of the sweet orange protein-protein interaction networkBMC Plant Biol, 14
Lee (2019)
MaizeNet: a co-functional network for network-assisted systems genetics in Zea maysPlant Jy, 99
Finn (2014)
iPfam: a database of protein family and domain interactions found in the protein data BankNucleic Acids Res, 42
Ma (2019)
Prediction of protein-protein interactions between fungus (Magnaporthe grisea) and rice (Oryza sativa l.)Briefings Bioinform, 20
Vinayagam (2016)
An integrative analysis of the InR/PI3K/Akt network identifies the dynamic response to insulin signalingCell Rep, 16
Bock (2003)
Whole-proteome interaction miningBioinformatics, 19
Tseng (2014)
New classes of mind bomb-interacting proteins identified from yeast two-hybrid screensPLoS One, 9
Smith (2011)
Resolving the evolutionary relationships of molluscs with phylogenomic toolsNature, 480
Wang (2011)
A predicted protein-protein interaction network of the filamentous fungus Neurospora crassaMol Biosyst, 7
Gupta (2020)
Genome-wide inference of the Camponotus floridanus protein-protein interaction network using homologous mapping and interacting domain profile pairsSci Rep, 10
Brun (2004)
Clustering proteins from interaction networks for the prediction of cellular functionsBMC Bioinformatics, 5
Marcotte (2001)
Exploiting big biology: integrating large-scale biological data for function inferenceBrief Bioinform, 2
Bhardwaj (2016)
Global de novo protein-protein interactome elucidates interactions of drought-responsive proteins in horse gram (Macrotyloma uniflorum)J Proteome Res, 15
Turinsky (2010)
Literature curation of protein interactions: measuring agreement across major public databasesDatabase, 2010
Huang (2004)
Evolutionary conservation and selection of human disease gene orthologs in the rat and mouse genomesGenome Biol, 5
Brehme (2010)
A global protein-lipid interactome mapMol Syst Biol, 6
Ho (2012)
A predicted protein interactome for riceRice (N Y), 5
Dreher (2012)
Construction of a pig physical interactome using sequence homology and a comprehensive reference human interactomeEvol Bioinform Online, 8
Gow (2017)
Microbe profile: Candida albicans: a shape-changing, opportunistic pathogenic fungus of humansMicrobiology (Reading), 163
Caby (2017)
Analysis of the interactome of Schistosoma mansoni histone deacetylase 8PLoS Negl Trop Dis, 11
Lee (2004)
A probabilistic functional network of yeast genesScience, 306
Browne (2009)
GRIP: a web-based system for constructing gold standard datasets for protein-protein interaction predictionSource Code Biol Med, 4
Wang (2014)
Genome-wide identification of heat shock proteins (Hsps) and Hsp interactors in rice: Hsp70s as a case studyBMC Genomics, 15
Castillo-Lara (2020)
PlanExp: intuitive integration of complex RNA-seq datasets with planarian omics resourcesBioinformatics, 36
Wu (2003)
Identification of functional links between genes using phylogenetic profilesBioinformatics, 19
Wolf (2001)
Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic contextGenome Res, 11
Lu (2005)
Assessing the limits of genomic data integration for predicting protein networksGenome Res, 15
Mohr (2010)
Genomic screening with RNAi: results and challengesAnnu Rev Biochem, 79
Gunsalus (2005)
Predictive models of molecular machines involved in Caenorhabditis elegans early embryogenesisNature, 436
Jeong (2001)
Lethality and centrality in protein networksNature, 411
Jones (2014)
Border control–a membrane-linked interactome of ArabidopsisScience, 344
Roguev (2008)
Conservation and rewiring of functional modules revealed by an epistasis map in fission yeastScience, 322
Gazestani (2017)
TrypsNetDB: an integrated framework for the functional characterization of trypanosomatid proteinsPLoS Negl Trop Dis, 11
Berg (2004)
Structure and evolution of protein interaction networks: a statistical model for link dynamics and gene duplicationsBMC Evol Biol, 4
Boulton (2002)
Combined functional genomic maps of the C. elegans dna damage responseScience, 295
Juan (2008)
High-confidence prediction of global interactomes based on genome-wide coevolutionary networksProc Natl Acad Sci U S A, 105
Ben-Hur (2005)
Kernel methods for predicting protein-protein interactionsBioinformatics, 21
Zhang (2018)
Bradyrhizobium diazoefficiens usda 110-Glycine max interactome provides candidate proteins associated with symbiosisJ Proteome Res, 17
Ravasi (2010)
An atlas of combinatorial transcriptional regulation in mouse and manCell, 140
Zhu (2007)
Getting connected: analysis and principles of biological networksGenes Dev, 21
Zhang (2017)
Fancd2 in vivo interaction network reveals a non-canonical role in mitochondrial functionSci Rep, 7
Müller (2010)
Model organisms–a historical perspectiveJ Proteomics, 73
Qi (2006)
Evaluation of different biological data and computational classification methods for use in protein interaction predictionProteins, 63
Kaneva (2019)
Proteins that physically interact with the phosphatase Cdc14 in Candida albicans have diverse roles in the cell cycleSci Rep, 9
dos Santos Vasconcelos (2018)
Building protein-protein interaction networks for Leishmania species through protein structural informationBMC Bioinformatics, 19
Huh (2003)
Global analysis of protein localization in budding yeastNature, 425
Wickett (2014)
Phylotranscriptomic analysis of the origin and early diversification of land plantsProc Natl Acad Sci U S A, 111
von Mering (2003)
STRING: a database of predicted functional associations between proteinsNucleic Acids Res, 31
Dheilly (2014)
No more non-model species: the promise of next generation sequencing for comparative immunologyDev Comp Immunol, 45
Krogan (2006)
Global landscape of protein complexes in the yeast Saccharomyces cerevisiaeNature, 440
Schuette (2015)
Predicted protein-protein interactions in the moss Physcomitrella patens: a new bioinformatic resourceBMC Bioinformatics, 16
Pan (2004)
A robust toolkit for functional profiling of the yeast genomeMol Cell, 16
von Mering (2002)
Comparative assessment of large-scale data sets of protein-protein interactionsNature, 417
Rachlin (2006)
Biological context networks: a mosaic view of the interactomeMol Syst Biol, 2
Schoeters (2019)
Protein-protein interactions in Candida albicansFront Microbiol, 10
Beltrao (2009)
Evolution of phosphoregulation: comparison of phosphorylation patterns across yeast speciesPLoS Biol, 7
Slabodnick (2017)
The macronuclear genome of Stentor coeruleus reveals tiny introns in a giant cellCurr Biol, 27
Yook (2004)
Functional and topological characterization of protein interaction networksProteomics, 4
Pesch (2013)
Complementing the eukaryotic protein interactomePloS One, 8
Yu (2008)
Construction of a chloroplast protein interaction network and functional mining of photosynthetic proteins in Arabidopsis thalianaCell Res, 18
Uhrig (2006)
Protein interaction networks in plantsPlanta, 224
Milo (2004)
Superfamilies of evolved and designed networksScience, 303
Byrne (2007)
A global analysis of genetic interactions in Caenorhabditis elegansJ Biol, 6
Mosca (2014)
3did: a catalog of domain-based interactions of known three-dimensional structureNucleic Acids Res, 42
Li (2018)
The interactomic analysis reveals pathogenic protein networks in Phomopsis longicolla underlying seed decay of soybeanFront Genet, 9
Kim (2016)
MouseNet v2: a database of gene networks for studying the laboratory mouse and eight other model vertebratesNucleic Acids Res, 44
Müller (2004)
Textpresso: an ontology-based information retrieval and extraction system for biological literaturePLoS Biol, 2
Ho (2002)
Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometryNature, 415
Xu (2017)
The first succinylome profile of Trichophyton rubrum reveals lysine succinylation on proteins involved in various key cellular processesBMC Genomics, 18
Gu (2011)
PRIN: a predicted rice interactome networkBMC Bioinformatics, 12
Tong (2004)
Global mapping of the yeast genetic interaction networkScience, 303
Han (2004)
Prespi: a domain combination based prediction system for protein-protein interactionNucleic Acids Res, 32
Lo (2010)
3D-interologs: an evolution database of physical protein-protein interactions across multiple genomesBMC Genomics, 11
Pérez-Molina (2018)
Chagas diseaseLancet, 391
Milo (2002)
Network motifs: simple building blocks of complex networksScience, 298
Futschik (2007)
Comparison of human protein-protein interaction mapsBioinformatics, 23
Pazos (2005)
Assessing protein co-evolution in the context of the tree of life assists in the prediction of the interactomeJ Mol Biol, 352
Kumar (2002)
Subcellular localization of the yeast proteomeGenes Dev, 16
Riley (2005)
Inferring protein domain interactions from databases of interacting proteinsGenome Biol, 6
Scholtens (2005)
Local modeling of global interactome networksBioinformatics, 21
Mishra (2006)
Human protein reference database–2006 updateNucleic Acids Res, 34
Bock (2001)
Predicting protein–protein interactions from primary structureBioinformatics, 17
Lu (2003)
Multimeric threading-based prediction of protein-protein interactions on a genomic scale: application to the Saccharomyces cerevisiae proteomeGenome Res, 13
Ohue (2013)
Highly precise protein-protein interaction prediction based on consensus between template-based and de novo docking methodsBMC Proc, 7
Marcotte (1999)
A combined algorithm for genome-wide prediction of protein functionNature, 402
Tsaparas (2006)
Global similarity and local divergence in human and mouse gene co-expression networksBMC Evol Biol, 6
Titz (2004)
What do we learn from high-throughput protein interaction data?Expert Rev Proteomics, 1
Pagel (2007)
Assembly rules for protein networks derived from phylogenetic-statistical analysis of whole genomesBMC Evol Biol, 7
Ideker (2001)
A new approach to decoding life: systems biologyAnnu Rev Genomics Hum Genet, 2
Arbogast (2019)
ATG5 is required for b cell polarization and presentation of particulate antigensAutophagy, 15
Boxem (2008)
A protein domain-based interactome network for C. elegans early embryogenesisCell, 134
Mohamed (2010)
Active learning for human protein-protein interaction predictionBMC Bioinformatics, 11
Trigg (2017)
CrY2H-seq: a massively multiplexed assay for deep-coverage interactome mappingNat Methods, 14
Said (2004)
Global network analysis of phenotypic effects: protein networks and toxicity modulation in Saccharomyces cerevisiaeProc Natl Acad Sci U S A, 101
Wuchty (2003)
Evolutionary conservation of motif constituents in the yeast protein interaction networkNat Genet, 35
Friedman (2011)
Proteomic and functional genomic landscape of receptor tyrosine kinase and Ras to extracellular signal-regulated kinase signalingSci Signal, 4
Betel (2007)
Structure-templated predictions of novel protein interactions from sequence informationPLoS Comput Biol, 3
Soong (2008)
Physical protein-protein interactions predicted from microarraysBioinformatics, 24
Huynen (2000)
Predicting protein function by genomic context: quantitative evaluation and qualitative inferencesGenome Res, 10
Yellaboina (2008)
Prediction of evolutionarily conserved interologs in Mus musculusBMC Genomics, 9
Xu (2003)
BTB proteins are substrate-specific adaptors in an SCF-like modular ubiquitin ligase containing CUL-3Nature, 425
Huttenhower (2008)
Assessing the functional structure of genomic dataBioinformatics, 24
Liu (2008)
Protein interaction predictions from diverse sourcesDrug Discov Today, 13
Altmann (2020)
Extensive signal integration by the phytohormone protein networkNature, 583
Aloy (2003)
InterPreTS: protein interaction prediction through tertiary structureBioinformatics, 19
Date (2006)
Computational modeling of the plasmodium falciparum interactome reveals protein function on a genome-wide scaleGenome Res, 16
He (2008)
The prediction of protein-protein interaction networks in rice blast fungusBMC Genomics, 9
Doolittle (2011)
Mapping protein interactions between dengue virus and its human and insect hostsPLoS Negl Trop Dis, 5
Snel (2004)
Gene co-regulation is highly conserved in the evolution of eukaryotes and prokaryotesNucleic Acids Res, 32
Aloy (2002)
Interrogating protein interaction networks through structural biologyProc Natl Acad Sci U S A, 99
Rual (2005)
Towards a proteome-scale map of the human protein-protein interaction networkNature, 437
Spirin (2003)
Protein complexes and functional modules in molecular networksProc Natl Acad Sci U S A, 100
Wang (2017)
Big data mining powers fungal research: recent advances in fission yeast systems biology approachesCurr Genet, 63
Reinke (2013)
Networks of bZIP protein-protein interactions diversified over a billion years of evolutionScience, 340
Ng (2003)
Integrative approach for computationally inferring protein domain interactionsBioinformatics, 19
Wagner (2003)
How the global structure of protein interaction networks evolvesProc Biol Sci, 270
da Fonseca (2016)
Next-generation biology: sequencing and data analysis approaches for non-model organismsMar Genomics, 30
Li (2004)
A map of the interactome network of the metazoan C. elegansScience, 303
Fraser (2002)
Evolutionary rate in the protein interaction networkScience, 296
Myers (2006)
Finding function: evaluation methods for functional genomic dataBMC Genomics, 7
Ou-Yang (2016)
Protein complex detection based on partially shared multi-view clusteringBMC Bioinformatics, 17
Biswal (2019)
The nucleotide-dependent interactome of rice heterotrimeric G-protein $\alpha $-subunitProteomics, 19
Randhawa (2020)
Advancing from protein interactomes and gene co-expression networks towards multi-omics-based composite networks: approaches for predicting and extracting biological knowledgeBrief Funct Genomics, 19
Brohée (2008)
NeAT: a toolbox for the analysis of biological networks, clusters, classes and pathwaysNucleic Acids Res, 36
Bu (2003)
Topological structure analysis of the protein-protein interaction network in budding yeastNucleic Acids Res, 31
Aloy (2004)
Structure-based assembly of protein complexes in yeastScience, 303
Clauset (2008)
Hierarchical structure and the prediction of missing links in networksNature, 453
Yang (2012)
Inferring the Brassica rapa interactome using protein-protein interaction data from Arabidopsis thalianaFront Plant Sci, 3
Kitano (2002)
Systems biology: a brief overviewScience, 295
Vázquez (2004)
The topological relationship between the large-scale attributes and local interaction patterns of complex networksProc Natl Acad Sci U S A, 101
Suthram (2006)
A direct comparison of protein interaction confidence assignment schemesBMC Bioinformatics, 7
Gaasterland (1998)
Microbial genescapes: phyletic and functional patterns of ORF distribution among prokaryotesMicrob Comp Genomics, 3
Wang (2014)
Essential functional modules for pathogenic and defensive mechanisms in Candida albicans infectionsBiomed Res Int, 2014
Reece-Hoyes (2013)
Extensive rewiring and complex evolutionary dynamics in a C. elegans multiparameter transcription factor networkMol Cell, 51
Zhang (2017)
Pathogenicity genes in Ustilaginoidea virens revealed by a predicted protein-protein interaction networkJ Proteome Res, 16
Koh (2012)
Analyzing protein-protein interaction networksJ Proteome Res, 11
Klopffleisch (2011)
Arabidopsis G-protein interactome reveals connections to cell wall carbohydrates and morphogenesisMol Syst Biol, 7
Sprinzak (2001)
Correlated sequence-signatures as markers of protein-protein interactionJ Mol Biol, 311
Nguyen (2008)
An integrative domain-based approach to predicting protein-protein interactionsJ Bioinform Comput Biol, 6
Ramírez (2007)
Computational analysis of human protein interaction networksProteomics, 7
Chen (2012)
Inferring domain-domain interactions from protein-protein interactions in the complex network conformationBMC Syst Biol, 6
Enright (1999)
Protein interaction maps for complete genomes based on gene fusion eventsNature, 402
Chua (2007)
Using indirect protein interactions for the prediction of gene ontology functionsBMC Bioinformatics, 8
Albert (2000)
Error and attack tolerance of complex networksNature, 406
Jansen (2004)
Analyzing protein function on a genomic scale: the importance of gold-standard positives and negatives for network predictionCurr Opin Microbiol, 7
Chen (2014)
The architecture of a scrambled genome reveals massive levels of genomic rearrangement during developmentCell, 158
Thanasomboon (2020)
Exploring dynamic protein-protein interactions in cassava through the integrative interactome networkSci Rep, 10
Ding (2019)
Computational identification of protein-protein interactions in model plant proteomesSci Rep, 9
Muriithi (2018)
In silico prediction of protein-protein interaction between Glossina m. morsitans (Westwood, 1851) and Trypanosoma brucei (kinetoplastida: Trypanosomatidae)Bioscience Horizons, 11
Shen (2007)
Predicting protein-protein interactions based only on sequences informationProc Natl Acad Sci U S A, 104
Piovesan (2015)
INGA: protein function prediction combining interaction networks, domain assignments and sequence similarityNucleic Acids Res, 43
Zhu (2016)
PPIM: a protein-protein interaction database for maizePlant Physiol, 170
Ba (2012)
Proteome-wide discovery of evolutionary conserved sequences in disordered regionsSci Signal, 5
Dixon (2008)
Significant conservation of synthetic lethal genetic interaction networks between distantly related eukaryotesProc Natl Acad Sci U S A, 105
Smith (2002)
Prediction of protein-protein interactions by docking methodsCurr Opin Struct Biol, 12
Lin (2011)
PAIR: the predicted Arabidopsis interactome resourceNucleic Acids Res, 39
Guo (2017)
Comparative proteomic analysis of lysine acetylation in fish CIK cells infected with aquareovirusInt J Mol Sci, 18
Yu (2008)
DroID: the drosophila interactions database, a comprehensive resource for annotated gene and protein interactionsBMC Genomics, 9
Singh (2020)
TulsiPIN: an interologous protein interactome of Ocimum tenuiflorumJ Proteome Res, 19
Zhu (2016)
Plants in silico: why, why now and what?–an integrative platform for plant systems biology researchPlant Cell Environ, 39
Science, 282
Jiao (2020)
Transcriptome analysis of the hepatopancreas in the Litopenaeus vannamei responding to the lead stressBiol Trace Elem Res, 199
Popescu (2009)
MAPK target networks in Arabidopsis thaliana revealed using functional protein microarraysGenes Dev, 23
Friedel (2006)
Inferring topology from clustering coefficients in protein-protein interaction networksBMC Bioinformatics, 7
Janin (2003)
CAPRI: a critical assessment of PRedicted interactionsProteins, 52
Kumar (2018)
Proteome analysis reveals a role of rainbow trout lymphoid organs during Yersinia ruckeri infection processSci Rep, 8
Brown (2007)
Unequal evolutionary conservation of human protein interactions in interologous networksGenome Biol, 8
Hao (2014)
The protein-protein interaction network of eyestalk, Y-organ and hepatopancreas in Chinese mitten crab Eriocheir sinensisBMC Syst Biol, 8
Tebbji (2014)
A functional portrait of Med7 and the mediator complex in Candida albicansPLoS Genet, 10
Flórez (2010)
Protein network prediction and topological analysis in Leishmania major as a tool for drug target selectionBMC Bioinformatics, 11
Tao (2007)
Information theory applied to the sparse gene ontology annotation network to predict novel gene functionBioinformatics, 23
Matthews (2005)
Research resources for drosophila: the expanding universeNat Rev Genet, 6
Stelzl (2005)
A human protein-protein interaction network: a resource for annotating the proteomeCell, 122
Dror (2008)
Structural similarity of genetically interacting proteinsBMC Syst Biol, 2
Skrabanek (2008)
Computational prediction of protein-protein interactionsMol Biotechnol, 38
Deane (2002)
Protein interactions: two methods for assessment of the reliability of high throughput observationsMol Cell Proteomics, 1
Banky (2009)
NASCENT: an automatic protein interaction network generation tool for non-model organismsBioinformation, 3
Rezende (2012)
Computational prediction of protein-protein interactions in Leishmania predicted proteomesPloS One, 7
Zitnik (2019)
Evolution of resilience in protein interactomes across the tree of lifeProc Natl Acad Sci U S A, 116
Lo (2015)
Reconstructing genome-wide protein-protein interaction networks using multiple strategies with homologous mappingPloS One, 10
He (2006)
Higher duplicability of less important genes in yeast genomesMol Biol Evol, 23
Urban (2019)
PHI-nets: a network resource for ascomycete fungal pathogens to annotate and identify putative virulence interacting proteins and siRNAsFrontiers Microbiol, 10
Folador (2014)
An improved interolog mapping-based computational prediction of protein-protein interactions with increased network coverageIntegr Biol (Camb), 6
Liu (2012)
Determination of the heterogeneous interactome between Edwardsiella tarda and fish gillsJ Proteomics, 75
Gavin (2002)
Functional organization of the yeast proteome by systematic analysis of protein complexesNature, 415
Enright (2002)
An efficient algorithm for large-scale detection of protein familiesNucleic Acids Res, 30
Remmelzwaal (2019)
Protein interactome mapping in Caenorhabditis elegansCurr Opin Syst Biol, 13
Li (2012)
Prediction of protein-protein interaction sites by random forest algorithm with mRMR and IFSPloS One, 7
Rhee (2014)
Transcription factor networks in Drosophila melanogasterCell Rep, 8
Pavithra (2007)
Systems analysis of chaperone networks in the malarial parasite plasmodium falciparumPLoS Comput Biol, 3
Foote (2015)
Convergent evolution of the genomes of marine mammalsNat Genet, 47
Ogmen (2005)
PRISM: protein interactions by structural matchingNucleic Acids Res, 33
Huo (2015)
Prediction of host - pathogen protein interactions between mycobacterium tuberculosis and Homo sapiens using sequence motifsBMC Bioinformatics, 16
Park (2001)
Mapping protein family interactions: intramolecular and intermolecular protein family interaction repertoires in the PDB and yeastJ Mol Biol, 307
Gupta (2021)
Pathogen and host-pathogen protein interactions provide a key to identify novel drug targets
Lenfant (2010)
A genome-wide study of PDZ-domain interactions in C. elegans reveals a high frequency of non-canonical bindingBMC Genomics, 11
White Bear (2018)
Predictions of novel Schistosoma mansoni - human protein interactions consistent with experimental dataSci Rep, 8
Richards (2015)
It’s more than stamp collecting: how genome sequencing can unify biological researchTrends Genet, 31
Cirrone (2020)
Outpredict: multiple datasets can improve prediction of expression and inference of causalitySci Rep, 10
Lei (2014)
Global protein-protein interaction network of rice sheath blight pathogenJ Proteome Res, 13
Zhao (2016)
Multi-tissue transcriptomics for construction of a comprehensive gene resource for the terrestrial snail Theba pisanaSci Rep, 6
Aytuna (2005)
Prediction of protein-protein interactions by combining structure and sequence conservation in protein interfacesBioinformatics, 21
Hu (2019)
EPIC: software toolkit for elution profile-based inference of protein complexesNat Methods, 16
Russell (2017)
Non-model model organismsBMC Biol, 15
Rain (2001)
The protein-protein interaction map of helicobacter pyloriNature, 409
Doerks (2002)
Systematic identification of novel protein domain families associated with nuclear functionsGenome Res, 12
Ryan (2013)
All or nothing: protein complexes flip essentiality between distantly related eukaryotesGenome Biol Evol, 5
McWhite (2020)
A pan-plant protein complex map reveals deep conservation and novel assembliesCell, 181
Wang (2017)
Predicted networks of protein-protein interactions in Stegodyphus mimosarum by cross-species comparisonsBMC Genomics, 18
Lemberger (2007)
Systems biology in human health and diseaseMol Syst Biol, 3
Kamau (2016)
Prediction of protein–protein interactions between Theileria parva and Bos taurus based on sequence homologyBioscience Horizons, 9
Yeung (2004)
From co-expression to co-regulation: how many microarray experiments do we need?Genome Biol, 5
Fitzek (2011)
A predicted interactome for coffee (Coffea canephora var robusta)J Plant Mol Biol Biotechnol, 2
Latgé (1999)
Aspergillus fumigatus and aspergillosisClin Microbiol Rev, 12
Li (2017)
Interactome of E. piscicida and grouper liver proteins reveals strategies of bacterial infection and host immune responseSci Rep, 7
Troyanskaya (2003)
A bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae)Proc Natl Acad Sci U S A, 100
Chen (2009)
Happi: an online database of comprehensive human annotated and predicted protein interactionsBMC Genomics, 10
Parry (1995)
Fusarium ear blight (scab) in small grain cereals-a reviewPlant Pathol, 44
Pancaldi (2012)
Predicting the fission yeast protein interaction networkG3 (Bethesda), 2
Camacho (2018)
Next-generation machine learning for biological networksCell, 173
Struk (2019)
Exploring the protein-protein interaction landscape in plantsPlant Cell Environ, 42
Newman (2003)
The structure and function of complex networksSIAM Rev Soc Ind Appl Math, 45
Hue (2010)
Large-scale prediction of protein-protein interactions from structuresBMC Bioinformatics, 11
Wang (2013)
Interspecies protein-protein interaction network construction for characterization of host-pathogen interactions: a Candida albicans-zebrafish interaction studyBMC Syst Biol, 7
Jansen (2003)
A bayesian networks approach for predicting protein-protein interactions from genomic dataScience, 302
Hillier (2019)
Landscape of the plasmodium interactome reveals both conserved and species-specific functionalityCell Rep, 28
Mellor (2002)
Predictome: a database of putative functional links between proteinsNucleic Acids Res, 30
Sun (2007)
Phylogenetic profiles for the prediction of protein-protein interactions: how to select reference organisms?Biochem Biophys Res Commun, 353
Asensio (2017)
Centrality in the host-pathogen interactome is associated with pathogen fitness during infectionNat Commun, 8
Di Silvestre (2018)
Large scale proteomic data and network-based systems biology approaches to explore the plant worldProteomes, 6
Hase (2010)
Difference in gene duplicability may explain the difference in overall structure of protein-protein interaction networks among eukaryotesBMC Evol Biol, 10
Li (2018)
Transcriptome profiling based on protein-protein interaction networks provides a core set of genes for understanding blood immune response mechanisms against Edwardsiella tarda infection in japanese flounder (Paralichthys olivaceus)Dev Comp Immunol, 78
Wagner (2001)
The yeast protein interaction network evolves rapidly and contains few redundant duplicate genesMol Biol Evol, 18
Myers (2007)
Context-sensitive data integration and prediction of biological networksBioinformatics, 23
Eisenberg (2000)
Protein function in the post-genomic eraNature, 405
Murray (2005)
Advances in leishmaniasisLancet, 366
Ramani (2005)
Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactomeGenome Biol, 6
Wuchty (2011)
Computational prediction of host-parasite protein interactions between P. falciparum and H. sapiensPloS One, 6
Zhang (2016)
Genome-wide inference of protein-protein interaction networks identifies crosstalk in abscisic acid signalingPlant Physiol, 171
Luo (2019)
An improved genome assembly of the fluke Schistosoma japonicumPLoS Negl Trop Dis, 13
Chen (2008)
Protein function assignment through mining cross-species protein-protein interactionsPLoS One, 3
Lunardi (2010)
A genome-scale protein interaction profile of drosophila p53 uncovers additional nodes of the human p53 networkProc Natl Acad Sci U S A, 107
Remmele (2015)
Integrated inference and evaluation of host-fungi interaction networksFront Microbiol, 6
Castillo-Lara (2018)
PlanNET: homology-based predicted interactome for multiple planarian transcriptomesBioinformatics, 34
Michaut (2008)
InteroPorc: automated inference of highly conserved protein interaction networksBioinformatics, 24
von Mering (2003)
Genome evolution reveals biochemical networks and functional modulesProc Natl Acad Sci U S A, 100
Gong (2005)
PSIbase: a database of protein structural interactome map (PSIMAP)Bioinformatics, 21
Uetz (2000)
A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiaeNature, 403
Kwon (2013)
The hippo signaling pathway interactomeScience, 342
Gillingham (2014)
Toward a comprehensive map of the effectors of Rab GTPasesDev Cell, 31
Interactome analyses have traditionally been applied to yeast, human and other model organisms due to the availability of protein–protein interaction data for these species. Recently, these techniques have been applied to more diverse species using computational interaction prediction from genome sequence and other data types. This review describes the various types of computational interactome networks that can be created and how they have been used in diverse eukaryotic species, highlighting some of the key interactome studies in non-model organisms.
Briefings in Functional Genomics – Oxford University Press
Published: May 12, 2022
Keywords: systems biology; integrative bioinformatics; interactomics; eukaryotes; non-models; network biology
Read and print from thousands of top scholarly journals.
Already have an account? Log in
Bookmark this article. You can see your Bookmarks on your DeepDyve Library.
To save an article, log in first, or sign up for a DeepDyve account if you don’t already have one.
Copy and paste the desired citation format or use the link below to download a file formatted for EndNote
Access the full text.
Sign up today, get DeepDyve free for 14 days.
All DeepDyve websites use cookies to improve your online experience. They were placed on your computer when you launched this website. You can change your cookie settings through your browser.