| scholarly article | Q13442814 |
| P50 | author | Matteo Pellegrini | Q41172848 |
| P2093 | author name string | D. Eisenberg | |
| E. M. Marcotte | |||
| M. J. Thompson | |||
| T. O. Yeates | |||
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| P433 | issue | 8 | |
| P407 | language of work or name | English | Q1860 |
| P921 | main subject | phylogenetics | Q171184 |
| P304 | page(s) | 4285-4288 | |
| P577 | publication date | 1999-04-13 | |
| P1433 | published in | Proceedings of the National Academy of Sciences of the United States of America | Q1146531 |
| P1476 | title | Assigning protein functions by comparative genome analysis: protein phylogenetic profiles | |
| P478 | volume | 96 |
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| Q33503883 | Gene networks in Drosophila melanogaster: integrating experimental data to predict gene function |
| Q52895002 | Gene selection and cloning approaches for co-expression and production of recombinant protein-protein complexes. |
| Q24646439 | GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function |
| Q28601833 | Generation of open biomedical datasets through ontology-driven transformation and integration processes |
| Q34083028 | Genes linked by fusion events are generally of the same functional category: a systematic analysis of 30 microbial genomes |
| Q39196143 | Genetic Bases of Fungal White Rot Wood Decay Predicted by Phylogenomic Analysis of Correlated Gene-Phenotype Evolution. |
| Q29346651 | Genetic and computational identification of a conserved bacterial metabolic module |
| Q28478625 | Genetic co-occurrence network across sequenced microbes |
| Q31746728 | Genome data: what do we learn? |
| Q34787866 | Genome evolution reveals biochemical networks and functional modules |
| Q22065753 | Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea |
| Q24811434 | Genome trees from conservation profiles |
| Q33244710 | Genome wide prediction of protein function via a generic knowledge discovery approach based on evidence integration. |
| Q48226881 | Genome-Wide Inference of Protein-Protein Interaction Networks Identifies Crosstalk in Abscisic Acid Signaling |
| Q35018620 | Genome-scale identification and characterization of moonlighting proteins |
| Q33826880 | Genome-wide discovery of missing genes in biological pathways of prokaryotes |
| Q35130251 | Genome-wide identification of genes likely to be involved in human genetic disease |
| Q36188504 | Genome-wide protein-protein interactions and protein function exploration in cyanobacteria |
| Q40414926 | Genomewide function conservation and phylogeny in the Herpesviridae |
| Q35666138 | Genomic Comparison of Non-Typhoidal Salmonella enterica Serovars Typhimurium, Enteritidis, Heidelberg, Hadar and Kentucky Isolates from Broiler Chickens |
| Q33884928 | Genomic analysis |
| Q21144925 | Genomic analysis of the hydrocarbon-producing, cellulolytic, endophytic fungus Ascocoryne sarcoides |
| Q30341468 | Genomic biodiversity, phylogenetics and coevolution in proteins |
| Q36218064 | Genomic context analysis reveals dense interaction network between vertebrate ultraconserved non-coding elements |
| Q24793609 | Genomic functional annotation using co-evolution profiles of gene clusters |
| Q21146404 | Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath) |
| Q21090163 | Getting started in gene orthology and functional analysis |
| Q21145830 | Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins |
| Q24671999 | Global gene expression of Prochlorococcus ecotypes in response to changes in nitrogen availability |
| Q36968159 | Global probabilistic annotation of metabolic networks enables enzyme discovery. |
| Q30977956 | Global protein function annotation through mining genome-scale data in yeast Saccharomyces cerevisiae |
| Q47921995 | Global protein function prediction from protein-protein interaction networks |
| Q35012998 | Graemlin: general and robust alignment of multiple large interaction networks |
| Q30408206 | Graph pyramids for protein function prediction |
| Q33410275 | HPC2 and ubinuclein define a novel family of histone chaperones conserved throughout eukaryotes |
| Q25256829 | Hierarchical clustering algorithm for comprehensive orthologous-domain classification in multiple genomes |
| Q34173517 | High similarity of phylogenetic profiles of rate-limiting enzymes with inhibitory relation in Human, Mouse, Rat, budding Yeast and E. coli |
| Q33321071 | High-precision high-coverage functional inference from integrated data sources |
| Q33289001 | High-throughput identification of interacting protein-protein binding sites |
| Q34136223 | High-throughput, pooled sequencing identifies mutations in NUBPL and FOXRED1 in human complex I deficiency |
| Q34063510 | Highways of gene sharing in prokaryotes |
| Q42212125 | Homology modelling of protein-protein complexes: a simple method and its possibilities and limitations. |
| Q41847575 | Horizontally transferred genes cluster spatially and metabolically |
| Q24790990 | How biologically relevant are interaction-based modules in protein networks? |
| Q21134980 | How did the spider cross the river? Behavioral adaptations for river-bridging webs in Caerostris darwini (Araneae: Araneidae) |
| Q36766852 | How to comprehensively analyse proteins and how this influences nutritional research |
| Q43460248 | Human protein-protein interaction prediction by a novel sequence-based co-evolution method: co-evolutionary divergence |
| Q33368056 | Identification and analysis of co-occurrence networks with NetCutter. |
| Q30002330 | Identification and analysis of evolutionarily cohesive functional modules in protein networks |
| Q112312969 | Identification and characterization of genes related to salt stress tolerance within segregation distortion regions of genetic map in F2 population of upland cotton |
| Q34326112 | Identification and functional analysis of 'hypothetical' genes expressed in Haemophilus influenzae |
| Q33359587 | Identification and functional characterization of gene components of Type VI Secretion system in bacterial genomes |
| Q91806556 | Identification of Moonlighting Proteins in Genomes Using Text Mining Techniques |
| Q34645119 | Identification of a fourth family of lycopene cyclases in photosynthetic bacteria |
| Q46843737 | Identification of fungal sphingolipid C9-methyltransferases by phylogenetic profiling |
| Q24630006 | Identification of genes encoding tRNA modification enzymes by comparative genomics |
| Q35192752 | Identification of host-microbe interaction factors in the genomes of soft rot-associated pathogens Dickeya dadantii 3937 and Pectobacterium carotovorum WPP14 with supervised machine learning. |
| Q39175163 | Identification of hub proteins from sequence |
| Q35037874 | Identification of potential interaction networks using sequence-based searches for conserved protein-protein interactions or "interologs". |
| Q34525141 | Identification of putative rhamnogalacturonan-II specific glycosyltransferases in Arabidopsis using a combination of bioinformatics approaches |
| Q42584215 | Identification of small RNA pathway genes using patterns of phylogenetic conservation and divergence |
| Q28473568 | Identifying cognate binding pairs among a large set of paralogs: the case of PE/PPE proteins of Mycobacterium tuberculosis |
| Q44518986 | Identifying functional links between genes by evolutionary transcriptomics. |
| Q77876822 | Identifying functional links between genes using conserved chromosomal proximity |
| Q33237950 | Identifying metabolic enzymes with multiple types of association evidence |
| Q33582802 | Identifying overrepresented concepts in gene lists from literature: a statistical approach based on Poisson mixture model |
| Q54690940 | Immunohistochemical detection of Ki67 in breast cancer correlates with transcriptional regulation of genes related to apoptosis and cell death. |
| Q24796982 | Implications for domain fusion protein-protein interactions based on structural information |
| Q36089866 | Improvement in Protein Domain Identification Is Reached by Breaking Consensus, with the Agreement of Many Profiles and Domain Co-occurrence |
| Q33673805 | Improvement of domain-level ortholog clustering by optimizing domain-specific sum-of-pairs score |
| Q50420865 | Improving prediction of heterodimeric protein complexes using combination with pairwise kernel. |
| Q33328326 | Improving protein function prediction methods with integrated literature data |
| Q47266675 | Improving protein protein interaction prediction based on phylogenetic information using a least-squares support vector machine |
| Q24811498 | Improving the precision of the structure-function relationship by considering phylogenetic context |
| Q42064841 | Improving the prediction of yeast protein function using weighted protein-protein interactions |
| Q33281129 | In silico pathway reconstruction: Iron-sulfur cluster biogenesis in Saccharomyces cerevisiae. |
| Q45967003 | In silico prediction of the peroxisomal proteome in fungi, plants and animals. |
| Q33418943 | In silico prioritisation of candidate genes for prokaryotic gene function discovery: an application of phylogenetic profiles. |
| Q54547905 | In silico two-hybrid system for the selection of physically interacting protein pairs. |
| Q42687787 | In vivo interaction between the polyprenol phosphate mannose synthase Ppm1 and the integral membrane protein Ppm2 from Mycobacterium smegmatis revealed by a bacterial two-hybrid system |
| Q33304043 | InPrePPI: an integrated evaluation method based on genomic context for predicting protein-protein interactions in prokaryotic genomes |
| Q33550772 | Inference of functional relations in predicted protein networks with a machine learning approach |
| Q24797198 | Inference of protein function and protein linkages in Mycobacterium tuberculosis based on prokaryotic genome organization: a combined computational approach |
| Q39023260 | Inferring Trees |
| Q35806010 | Inferring domain-domain interactions from protein-protein interactions |
| Q46880217 | Inferring functional information from domain co-evolution |
| Q33893320 | Inferring functional modules of protein families with probabilistic topic models. |
| Q40619848 | Inferring gene function from evolutionary change in signatures of translation efficiency |
| Q31104442 | Inferring genome-wide functional linkages in E. coli by combining improved genome context methods: comparison with high-throughput experimental data |
| Q34569064 | Inferring homologous protein-protein interactions through pair position specific scoring matrix |
| Q21045419 | Inferring horizontal gene transfer |
| Q30482747 | Inferring modules of functionally interacting proteins using the Bond Energy Algorithm. |
| Q24796950 | Information assessment on predicting protein-protein interactions |
| Q37748492 | Innovative bioinformatic approaches for developing peptide-based vaccines against hypervariable viruses |
| Q42509091 | Insights into Ciliary Genes and Evolution from Multi-Level Phylogenetic Profiling |
| Q34883678 | Insights into the species-specific TLR4 signaling mechanism in response to Rhodobacter sphaeroides lipid A detection |
| Q33247445 | Integrated assessment and prediction of transcription factor binding |
| Q21284254 | Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks |
| Q33609193 | Integrating physical and genetic maps: from genomes to interaction networks |
| Q30628119 | Integration of genome data and protein structures: prediction of protein folds, protein interactions and "molecular phenotypes" of single nucleotide polymorphisms |
| Q37169808 | Integration of phenotypic metadata and protein similarity in Archaea using a spectral bipartitioning approach |
| Q24306825 | Integrative genomics identifies MCU as an essential component of the mitochondrial calcium uniporter |
| Q34514384 | Inter-Protein Sequence Co-Evolution Predicts Known Physical Interactions in Bacterial Ribosomes and the Trp Operon |
| Q47442338 | Inter-residue, inter-protein and inter-family coevolution: bridging the scales. |
| Q30399514 | InterPred: A pipeline to identify and model protein-protein interactions. |
| Q39535240 | Interaction generality, a measurement to assess the reliability of a protein-protein interaction |
| Q29615776 | Interaction network containing conserved and essential protein complexes in Escherichia coli |
| Q54311731 | Interaction network in cyanobacterial nitrogen regulation: PipX, a protein that interacts in a 2-oxoglutarate dependent manner with PII and NtcA. |
| Q31162634 | Interactome data and databases: different types of protein interaction |
| Q38010411 | Interactome mapping for analysis of complex phenotypes: insights from benchmarking binary interaction assays |
| Q36257382 | Interactome: gateway into systems biology |
| Q33294540 | Interplay between network structures, regulatory modes and sensing mechanisms of transcription factors in the transcriptional regulatory network of E. coli |
| Q34027140 | Interrogating protein interaction networks through structural biology |
| Q92267126 | Interspecies association mapping links reduced CG to TG substitution rates to the loss of gene-body methylation |
| Q89489979 | Into the wild: new yeast genomes from natural environments and new tools for their analysis |
| Q40918605 | Investigating Moorella thermoacetica metabolism with a genome-scale constraint-based metabolic model. |
| Q87370078 | Investigating co-evolution of functionally associated phosphosites in human |
| Q33304236 | Investigation of factors affecting prediction of protein-protein interaction networks by phylogenetic profiling |
| Q36531717 | Investigation of glycan evolution based on a comprehensive analysis of glycosyltransferases using phylogenetic profiling. |
| Q41018971 | Itinerary profiling to analyze a large number of protein-folding trajectories |
| Q42690307 | Joint learning of gene functions--a Bayesian network model approach |
| Q38460563 | KEGG OC: a large-scale automatic construction of taxonomy-based ortholog clusters |
| Q24817122 | Kernel-based machine learning protocol for predicting DNA-binding proteins |
| Q30364926 | Large Scale Chemical Cross-linking Mass Spectrometry Perspectives. |
| Q57007326 | Large-Scale Comparative Genomic Analyses of Cytoplasmic Membrane Transport Systems in Prokaryotes |
| Q34294587 | Large-scale analysis of microRNA evolution |
| Q37827559 | Lateral genetic transfer and the construction of genetic exchange communities |
| Q21145276 | Life in hot carbon monoxide: the complete genome sequence of Carboxydothermus hydrogenoformans Z-2901 |
| Q24675220 | Lineage-specific loss and divergence of functionally linked genes in eukaryotes |
| Q33921865 | Localizing proteins in the cell from their phylogenetic profiles. |
| Q46080127 | Locally defined protein phylogenetic profiles reveal previously missed protein interactions and functional relationships |
| Q33992757 | Long-chain N-acyl amino acid synthases are linked to the putative PEP-CTERM/exosortase protein-sorting system in Gram-negative bacteria |
| Q37746962 | Loss and gain of GroEL in the Mollicutes. |
| Q38295261 | LysM domains from Pteris ryukyuensis chitinase-A: a stability study and characterization of the chitin-binding site |
| Q33600892 | MBGD update 2010: toward a comprehensive resource for exploring microbial genome diversity |
| Q35159357 | MBGD: microbial genome database for comparative analysis |
| Q40586801 | MIRAGE: a functional genomics-based approach for metabolic network model reconstruction and its application to cyanobacteria networks |
| Q47304411 | MOCASSIN-prot: A Multi-Objective Clustering Approach for Protein Similarity Networks |
| Q25257010 | MaGe: a microbial genome annotation system supported by synteny results |
| Q33780899 | Making connections between novel transcription factors and their DNA motifs. |
| Q36742805 | Making the connections--the crucial role of metabolite transporters at the interface between chloroplast and cytosol. |
| Q43920334 | Mammalian selenoprotein gene signature: identification and functional analysis of selenoprotein genes using bioinformatics methods |
| Q64387955 | Mapping global and local coevolution across 600 species to identify novel homologous recombination repair genes |
| Q28752683 | Massive comparative genomic analysis reveals convergent evolution of specialized bacteria |
| Q42082146 | Meta-analysis of general bacterial subclades in whole-genome phylogenies using tree topology profiling |
| Q45943697 | Metabolic Pathway Assignment of Plant Genes based on Phylogenetic Profiling-A Feasibility Study. |
| Q30279122 | Metabolic network modeling of microbial communities |
| Q41949939 | Metabolic pathway reconstruction of eugenol to vanillin bioconversion in Aspergillus niger. |
| Q28074539 | Metabolic pathway reconstruction strategies for central metabolism and natural product biosynthesis |
| Q34937774 | Metagenomic guilt by association: an operonic perspective |
| Q30578902 | MicroScope--an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data |
| Q33531416 | MicroScope: a platform for microbial genome annotation and comparative genomics |
| Q33333213 | Microbial genotype-phenotype mapping by class association rule mining |
| Q34094923 | Mining bacterial genomes for antimicrobial targets |
| Q38149723 | Minireview: applied structural bioinformatics in proteomics |
| Q33705060 | Mitochondrial p32 protein is a critical regulator of tumor metabolism via maintenance of oxidative phosphorylation |
| Q30030541 | Model-enabled gene search (MEGS) allows fast and direct discovery of enzymatic and transport gene functions in the marine bacterium Vibrio fischeri. |
| Q33371821 | Modifying the DPClus algorithm for identifying protein complexes based on new topological structures |
| Q74431979 | Modularity in the gain and loss of genes: applications for function prediction |
| Q51735031 | Modules of co-occurrence in the cyanobacterial pan-genome reveal functional associations between groups of ortholog genes. |
| Q47792928 | Molecular evolution of lysin motif-type receptor-like kinases in plants |
| Q29568187 | Molecular insights into the binding of coenzyme F420 to the conserved protein Rv1155 from Mycobacterium tuberculosis |
| Q30764897 | Motif-based fold assignment |
| Q36434721 | MouseNet v2: a database of gene networks for studying the laboratory mouse and eight other model vertebrates. |
| Q33490835 | Multi-level learning: improving the prediction of protein, domain and residue interactions by allowing information flow between levels |
| Q33499113 | MultiLoc2: integrating phylogeny and Gene Ontology terms improves subcellular protein localization prediction |
| Q40829773 | Multimeric threading-based prediction of protein-protein interactions on a genomic scale: application to the Saccharomyces cerevisiae proteome |
| Q34280166 | Multiple alignment of complete sequences (MACS) in the post-genomic era. |
| Q41338172 | Multiple biomarker tissue arrays: A computational approach to identifying protein-protein interactions in the EGFR/ERK signalling pathway |
| Q30370660 | Multiple sequence alignments as tools for protein structure and function prediction. |
| Q35965216 | Mycobacterium tuberculosis and Clostridium difficille interactomes: demonstration of rapid development of computational system for bacterial interactome prediction |
| Q24620084 | NAPP: the Nucleic Acid Phylogenetic Profile Database |
| Q24796432 | Nebulon: a system for the inference of functional relationships of gene products from the rearrangement of predicted operons |
| Q38447168 | Network analysis and cross species comparison of protein-protein interaction networks of human, mouse and rat cytochrome P450 proteins that degrade xenobiotics. |
| Q21560992 | Network compression as a quality measure for protein interaction networks |
| Q35015314 | Network genomics--a novel approach for the analysis of biological systems in the post-genomic era. |
| Q38815372 | Network-Based Gene Function Prediction in Mouse and Other Model Vertebrates Using MouseNet Server |
| Q37775135 | Network-based function prediction and interactomics: the case for metabolic enzymes |
| Q61811426 | Network-based microsynteny analysis identifies major differences and genomic outliers in mammalian and angiosperm genomes |
| Q38914293 | Networks of ProteinProtein Interactions: From Uncertainty to Molecular Details. |
| Q62689583 | New Long-Term Memory Genes Revealed by Assessing Computational Function Prediction Methods |
| Q45801913 | New genetic associations in thiopurine-related bone marrow toxicity among inflammatory bowel disease patients. |
| Q30705590 | Nitrogen assimilation in Escherichia coli: putting molecular data into a systems perspective |
| Q30559749 | Novel cardiovascular gene functions revealed via systematic phenotype prediction in zebrafish |
| Q34613793 | Novel genes exhibit distinct patterns of function acquisition and network integration |
| Q92675086 | Novel phylogenetic methods are needed for understanding gene function in the era of mega-scale genome sequencing |
| Q92999345 | OMA standalone: orthology inference among public and custom genomes and transcriptomes |
| Q33302712 | On the detection of functionally coherent groups of protein domains with an extension to protein annotation |
| Q41847454 | Open source tool for prediction of genome wide protein-protein interaction network based on ortholog information |
| Q42940094 | Operon prediction for sequenced bacterial genomes without experimental information |
| Q35646651 | Operon prediction using both genome-specific and general genomic information |
| Q36511729 | Orphan SelD proteins and selenium-dependent molybdenum hydroxylases |
| Q34039734 | Ortho2ExpressMatrix--a web server that interprets cross-species gene expression data by gene family information |
| Q58090462 | OrthoInspector 3.0: open portal for comparative genomics |
| Q50602540 | Orthogenomics of photosynthetic organisms: bioinformatic and experimental analysis of chloroplast proteins of endosymbiont origin in Arabidopsis and their counterparts in Synechocystis. |
| Q38815377 | Ortholog Identification and Comparative Analysis of Microbial Genomes Using MBGD and RECOG. |
| Q36361689 | Orthoscape: a cytoscape application for grouping and visualization KEGG based gene networks by taxonomy and homology principles. |
| Q30859106 | Overview of software options for processing, analysis and interpretation of mass spectrometric proteomic data |
| Q48118907 | Oxidative stress gene expression profile in inbred mouse after ischemia/reperfusion small bowel injury |
| Q24791114 | PCOGR: phylogenetic COG ranking as an online tool to judge the specificity of COGs with respect to freely definable groups of organisms |
| Q36204412 | PPCM: Combing Multiple Classifiers to Improve Protein-Protein Interaction Prediction |
| Q37245673 | PPISearch: a web server for searching homologous protein-protein interactions across multiple species. |
| Q33901481 | PRIN: a predicted rice interactome network |
| Q24796893 | PartiGeneDB--collating partial genomes |
| Q36479565 | PatchSurfers: Two methods for local molecular property-based binding ligand prediction |
| Q42619738 | Pathogen profiling for disease management and surveillance. |
| Q30375382 | Pathogenic or not? And if so, then how? Studying the effects of missense mutations using bioinformatics methods. |
| Q33313510 | Persistence drives gene clustering in bacterial genomes |
| Q35194747 | Pharmacophylogenomics: genes, evolution and drug targets |
| Q35127370 | Pharmacoproteomics in drug development |
| Q24815778 | Phydbac "Gene Function Predictor": a gene annotation tool based on genomic context analysis |
| Q39804537 | Phydbac (phylogenomic display of bacterial genes): An interactive resource for the annotation of bacterial genomes |
| Q41010528 | Phydbac2: improved inference of gene function using interactive phylogenomic profiling and chromosomal location analysis |
| Q34544393 | Phyletic profiling with cliques of orthologs is enhanced by signatures of paralogy relationships |
| Q35630176 | PhyloFacts: an online structural phylogenomic encyclopedia for protein functional and structural classification |
| Q39015302 | PhyloPro2.0: a database for the dynamic exploration of phylogenetically conserved proteins and their domain architectures across the Eukarya |
| Q41613516 | Phylo_dCor: distance correlation as a novel metric for phylogenetic profiling |
| Q58733687 | Phylogenetic Clustering of Genes Reveals Shared Evolutionary Trajectories and Putative Gene Functions |
| Q30157037 | Phylogenetic Profiles Reveal Structural and Functional Determinants of Lipid-binding |
| Q28074488 | Phylogenetic Profiling for Probing the Modular Architecture of the Human Genome |
| Q47280089 | Phylogenetic Profiling of Mitochondrial Proteins and Integration Analysis of Bacterial Transcription Units Suggest Evolution of F1Fo ATP Synthase from Multiple Modules |
| Q33411072 | Phylogenetic diversity of stress signalling pathways in fungi |
| Q37079528 | Phylogenetic portrait of the Saccharomyces cerevisiae functional genome |
| Q36858814 | Phylogenetic profiles reveal evolutionary relationships within the "twilight zone" of sequence similarity |
| Q24797489 | Phylogenetic profiling of the Arabidopsis thaliana proteome: what proteins distinguish plants from other organisms? |
| Q30892241 | Phylogenetic profiling: how much input data is enough? |
| Q33268698 | Phylogenetic tree information aids supervised learning for predicting protein-protein interaction based on distance matrices |
| Q34102051 | Phylogenetically informed logic relationships improve detection of biological network organization |
| Q47209968 | Phylogenomic Synteny Network Analysis of MADS-Box Transcription Factor Genes Reveals Lineage-Specific Transpositions, Ancient Tandem Duplications, and Deep Positional Conservation |
| Q21563646 | Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements |
| Q30394741 | Phylogeny vs genome reshuffling: horizontal gene transfer |
| Q33516895 | Phylogeny-guided interaction mapping in seven eukaryotes |
| Q34842519 | Physical protein-protein interactions predicted from microarrays |
| Q30388661 | PoGO: Prediction of Gene Ontology terms for fungal proteins. |
| Q37169034 | PoplarGene: poplar gene network and resource for mining functional information for genes from woody plants |
| Q35658253 | Positional clustering improves computational binding site detection and identifies novel cis-regulatory sites in mammalian GABAA receptor subunit genes |
| Q33186645 | Potential genomic determinants of hyperthermophily |
| Q36834546 | Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution |
| Q37024705 | Practical applications of bacterial functional genomics. |
| Q34391358 | Practical aspects of protein co-evolution |
| Q24806232 | Practical lessons from protein structure prediction |
| Q41575762 | PrePhyloPro: phylogenetic profile-based prediction of whole proteome linkages |
| Q41274007 | Predicted networks of protein-protein interactions in Stegodyphus mimosarum by cross-species comparisons |
| Q38654083 | Predicting Functional Interactions Among Genes in Prokaryotes by Genomic Context. |
| Q30002397 | Predicting biological networks from genomic data |
| Q24811440 | Predicting functional gene links from phylogenetic-statistical analyses of whole genomes |
| Q35050912 | Predicting gene function using similarity learning |
| Q43227038 | Predicting genes for orphan metabolic activities using phylogenetic profiles |
| Q34018348 | Predicting genetic modifier loci using functional gene networks |
| Q51952704 | Predicting interactions in protein networks by completing defective cliques. |
| Q33702746 | Predicting phenotypic traits of prokaryotes from protein domain frequencies |
| Q40414366 | Predicting protein function by genomic context: quantitative evaluation and qualitative inferences |
| Q37014089 | Predicting protein function from sequence and structure |
| Q33308257 | Predicting protein function with hierarchical phylogenetic profiles: the Gene3D Phylo-Tuner method applied to eukaryotic genomes |
| Q38386937 | Predicting protein interface residues using easily accessible on-line resources. |
| Q33371800 | Predicting protein linkages in bacteria: which method is best depends on task |
| Q34204567 | Predicting protein-ATP binding sites from primary sequence through fusing bi-profile sampling of multi-view features |
| Q33217293 | Predicting protein-protein interaction by searching evolutionary tree automorphism space |
| Q37660067 | Predicting protein-protein interactions in the context of protein evolution |
| Q33548907 | Predicting protein-protein interactions in unbalanced data using the primary structure of proteins |
| Q39601005 | Predicting regulons and their cis-regulatory motifs by comparative genomics |
| Q33528207 | Predicting the protein-protein interactions using primary structures with predicted protein surface |
| Q35837549 | Prediction and characterization of protein-protein interaction networks in swine |
| Q28974902 | Prediction and identification of sequences coding for orphan enzymes using genomic and metagenomic neighbours |
| Q34580039 | Prediction and redesign of protein-protein interactions |
| Q30002391 | Prediction of Human Protein Function from Post-translational Modifications and Localization Features |
| Q39541532 | Prediction of Protein-Protein Interaction via co-occurring Aligned Pattern Clusters |
| Q28078131 | Prediction of Protein-Protein Interactions by Evidence Combining Methods |
| Q40273038 | Prediction of Protein-Protein Interactions with Physicochemical Descriptors and Wavelet Transform via Random Forests |
| Q45943145 | Prediction of Protein-Protein Interactions. |
| Q34366898 | Prediction of RNA-binding proteins from primary sequence by a support vector machine approach |
| Q48150110 | Prediction of enzymatic pathways by integrative pathway mapping. |
| Q33374636 | Prediction of evolutionarily conserved interologs in Mus musculus. |
| Q24527323 | Prediction of functional modules based on comparative genome analysis and Gene Ontology application |
| Q35607697 | Prediction of host - pathogen protein interactions between Mycobacterium tuberculosis and Homo sapiens using sequence motifs |
| Q41184191 | Prediction of interacting proteins from homology-modeled complex structures using sequence and structure scores. |
| Q28492567 | Prediction of missing enzyme genes in a bacterial metabolic network. Reconstruction of the lysine-degradation pathway of Pseudomonas aeruginosa |
| Q30002328 | Prediction of novel archaeal enzymes from sequence-derived features |
| Q47637567 | Prediction of protein-protein interaction networks. |
| Q38520195 | Prediction of protein-protein interactions using distant conservation of sequence patterns and structure relationships |
| Q47919853 | Prediction of protein-protein interactions using protein signature profiling |
| Q33241224 | Prediction of yeast protein-protein interaction network: insights from the Gene Ontology and annotations |
| Q78482210 | Prediction, assessment and validation of protein interaction maps in bacteria |
| Q34010645 | Predictome: a database of putative functional links between proteins |
| Q34070720 | ProPhylo: partial phylogenetic profiling to guide protein family construction and assignment of biological process |
| Q33290139 | Probabilistic prediction and ranking of human protein-protein interactions |
| Q31107612 | Probabilistic protein function prediction from heterogeneous genome-wide data |
| Q24801555 | Prolinks: a database of protein functional linkages derived from coevolution |
| Q22065755 | Properties of overlapping genes are conserved across microbial genomes |
| Q40958767 | ProtPhylo: identification of protein-phenotype and protein-protein functional associations via phylogenetic profiling. |
| Q33771019 | Protease-Inhibitor Interaction Predictions: Lessons on the Complexity of Protein-Protein Interactions |
| Q57747933 | Protein Interaction Networks and Their Statistical Analysis |
| Q35223658 | Protein annotation from protein interaction networks and Gene Ontology |
| Q36914675 | Protein co-evolution, co-adaptation and interactions |
| Q33911778 | Protein coalitions in a core mammalian biochemical network linked by rapidly evolving proteins |
| Q38681085 | Protein complex analysis: From raw protein lists to protein interaction networks |
| Q33693902 | Protein complex prediction based on k-connected subgraphs in protein interaction network. |
| Q42092310 | Protein content of minimal and ancestral ribosome |
| Q33318470 | Protein function assignment through mining cross-species protein-protein interactions |
| Q33906809 | Protein function in the post-genomic era. |
| Q38460064 | Protein function prediction using guilty by association from interaction networks. |
| Q29616048 | Protein interaction maps for complete genomes based on gene fusion events |
| Q34286374 | Protein interaction maps for model organisms |
| Q36168366 | Protein interaction networks |
| Q73256714 | Protein networks-built by association |
| Q34669644 | Protein-interaction networks: from experiments to analysis |
| Q41961515 | Protein-protein interaction based on pairwise similarity. |
| Q38272993 | Protein-protein interaction networks (PPI) and complex diseases. |
| Q34450771 | Protein-protein interaction predictions using text mining methods |
| Q62492646 | Protein-protein interaction sites prediction by ensemble random forests with synthetic minority oversampling technique |
| Q28469024 | Protein-protein interactions more conserved within species than across species |
| Q30002405 | Protein-protein interactions: analysis and prediction |
| Q34325454 | ProteinHistorian: tools for the comparative analysis of eukaryote protein origin |
| Q38254995 | Proteogenomics in microbiology: taking the right turn at the junction of genomics and proteomics |
| Q34315933 | Proteome-wide prediction of protein-protein interactions from high-throughput data |
| Q34642328 | Proteomic tools for biomedicine |
| Q34575441 | Proteomics: posttranslational modifications, immune responses and current analytical tools |
| Q36482021 | Quantification of ortholog losses in insects and vertebrates. |
| Q40622623 | Quantifying modularity in the evolution of biomolecular systems |
| Q30002368 | Quantitative assessment of protein function prediction from metagenomics shotgun sequences |
| Q28473198 | Quantitative comparison of catalytic mechanisms and overall reactions in convergently evolved enzymes: implications for classification of enzyme function |
| Q33801141 | Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana |
| Q34448299 | Recent advances in computational genomics |
| Q34020017 | Recent developments and future directions in computational genomics |
| Q33251431 | Reciprocal illumination in the gene content tree of life |
| Q60921530 | Recombination of ecologically and evolutionarily significant loci maintains genetic cohesion in the Pseudomonas syringae species complex |
| Q33284271 | Reconstruction of human protein interolog network using evolutionary conserved network |
| Q33641446 | Reconstruction of the core and extended regulons of global transcription factors |
| Q52047756 | Recurrence quantification analysis reveals interaction partners in paramyxoviridae envelope glycoproteins. |
| Q34664857 | Redefining bacterial populations: a post-genomic reformation |
| Q33450610 | Relationship between phylogenetic distribution and genomic features in Neurospora crassa |
| Q24791625 | Relative predicted protein levels of functionally associated proteins are conserved across organisms |
| Q34081467 | Representing and analysing molecular and cellular function using the computer |
| Q36854674 | Resolving the network of cell signaling pathways using the evolving yeast two-hybrid system |
| Q36251286 | Revisiting operons: an analysis of the landscape of transcriptional units in E. coli |
| Q28611186 | Ribosylnicotinamide kinase domain of NadR protein: identification and implications in NAD biosynthesis |
| Q33619990 | Role for protein-protein interaction databases in human genetics |
| Q42012920 | Role-similarity based functional prediction in networked systems: application to the yeast proteome |
| Q34538669 | Roundup: a multi-genome repository of orthologs and evolutionary distances |
| Q25255876 | SIMAP: the similarity matrix of proteins |
| Q34146561 | SPPS: a sequence-based method for predicting probability of protein-protein interaction partners |
| Q24675384 | STRING 7--recent developments in the integration and prediction of protein interactions |
| Q24681946 | STRING: a database of predicted functional associations between proteins |
| Q24523893 | STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene |
| Q30002354 | SVD-phy: improved prediction of protein functional associations through singular value decomposition of phylogenetic profiles |
| Q30621056 | Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data |
| Q64251780 | Selecting Near-Native Protein Structures from Predicted Decoy Sets Using Ordered Graphlet Degree Similarity |
| Q34017079 | Selection of organisms for the co-evolution-based study of protein interactions |
| Q33334075 | Sequence similarity network reveals common ancestry of multidomain proteins |
| Q39625557 | Sequence-based prediction of protein-protein interactions by means of codon usage. |
| Q34845004 | Shared protein complex subunits contribute to explaining disrupted co-occurrence |
| Q55035526 | Similarity of phylogenetic trees as indicator of protein-protein interaction. |
| Q30477519 | Similarity searches in genome-wide numerical data sets |
| Q34328058 | Simulated evolution of protein-protein interaction networks with realistic topology |
| Q30394016 | Simultaneous identification of specifically interacting paralogs and interprotein contacts by direct coupling analysis. |
| Q24648002 | Single-pass classification of all noncoding sequences in a bacterial genome using phylogenetic profiles |
| Q33526650 | Sites Inferred by Metabolic Background Assertion Labeling (SIMBAL): adapting the Partial Phylogenetic Profiling algorithm to scan sequences for signatures that predict protein function |
| Q33463453 | SpaK/SpaR two-component system characterized by a structure-driven domain-fusion method and in vitro phosphorylation studies |
| Q33513755 | Steps toward broad-spectrum therapeutics: discovering virulence-associated genes present in diverse human pathogens |
| Q24683633 | Stepwise formation of the bacterial flagellar system |
| Q37037777 | Strategies for reliable exploitation of evolutionary concepts in high throughput biology. |
| Q33513017 | Stratification of co-evolving genomic groups using ranked phylogenetic profiles |
| Q30489524 | Streamlining and large ancestral genomes in Archaea inferred with a phylogenetic birth-and-death model |
| Q30363264 | Structural bioinformatics of the interactome. |
| Q47588542 | Structural characterization of FlgE2 protein from Helicobacter pylori hook |
| Q52938509 | Structural genomics analysis: characteristics of atypical, common, and horizontally transferred folds. |
| Q46253521 | Sugar Lego: gene composition of bacterial carbohydrate metabolism genomic loci |
| Q35100906 | Supervised learning and prediction of physical interactions between human and HIV proteins |
| Q37571299 | Supra-operonic clusters of functionally related genes (SOCs) are a source of horizontal gene co-transfers |
| Q33393419 | SynteBase/SynteView: a tool to visualize gene order conservation in prokaryotic genomes |
| Q41046461 | Systematic Discovery of Human Gene Function and Principles of Modular Organization through Phylogenetic Profiling |
| Q24806114 | Systematic association of genes to phenotypes by genome and literature mining |
| Q36098282 | Systematic condition-dependent annotation of metabolic genes |
| Q44470521 | Systematic discovery of analogous enzymes in thiamin biosynthesis |
| Q36061303 | Systematic identification and analysis of frequent gene fusion events in metabolic pathways |
| Q64124619 | Systematic prediction of genes functionally linked to CRISPR-Cas systems by gene neighborhood analysis |
| Q37030590 | Systematic screens for human disease genes, from yeast to human and back |
| Q35058632 | Systematizing the generation of missing metabolic knowledge |
| Q36372378 | Systems analysis of host-parasite interactions |
| Q37860613 | Systems biology of tuberculosis |
| Q30276470 | Systems level analysis of the Chlamydomonas reinhardtii metabolic network reveals variability in evolutionary co-conservation |
| Q34342155 | Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1 |
| Q38678916 | Systems-wide Studies Uncover Commander, a Multiprotein Complex Essential to Human Development. |
| Q34314590 | TIGRFAMs and Genome Properties in 2013. |
| Q24683561 | TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes |
| Q38559450 | Template-based identification of protein-protein interfaces using eFindSitePPI. |
| Q37037798 | Testing the accuracy of eukaryotic phylogenetic profiles for prediction of biological function |
| Q36994374 | The Biosynthetic pathway for synechoxanthin, an aromatic carotenoid synthesized by the euryhaline, unicellular cyanobacterium Synechococcus sp. strain PCC 7002 |
| Q21184023 | The CRIT framework for identifying cross patterns in systems biology and application to chemogenomics |
| Q28484023 | The CanOE strategy: integrating genomic and metabolic contexts across multiple prokaryote genomes to find candidate genes for orphan enzymes |
| Q92134796 | The Comparison Between the Mutated HuIFN-β 27-101 and the Wild Type Interferon β: the Comprehensive In Silico Study to Evaluate the Effect of Mutations on IFN-β |
| Q37738644 | The Effects of Increasing the Number of Taxa on Inferences of Molecular Convergence |
| Q44876881 | The MORPH algorithm: ranking candidate genes for membership in Arabidopsis and tomato pathways. |
| Q35427460 | The Mitochondrial Proteome and Human Disease |
| Q35157897 | The PEDANT genome database |
| Q24793731 | The SYSTERS Protein Family Database in 2005 |
| Q33468705 | The Symbiosis Interactome: a computational approach reveals novel components, functional interactions and modules in Sinorhizobium meliloti |
| Q35846941 | The TB Structural Genomics Consortium: a decade of progress |
| Q28775893 | The balance of driving forces during genome evolution in prokaryotes |
| Q37508088 | The chlamydiales pangenome revisited: structural stability and functional coherence |
| Q22066260 | The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacterium |
| Q42641021 | The conservation and evolutionary modularity of metabolism |
| Q42103322 | The crucial role of PNPase in the degradation of small RNAs that are not associated with Hfq. |
| Q27701107 | The crystal structure of Helicobacter pylori HP1029 highlights the functional diversity of the sialic acid-related DUF386 family |
| Q28487146 | The crystal structure of Rv1347c, a putative antibiotic resistance protein from Mycobacterium tuberculosis, reveals a GCN5-related fold and suggests an alternative function in siderophore biosynthesis |
| Q42047417 | The distinctive signatures of promoter regions and operon junctions across prokaryotes |
| Q21202786 | The diversity and evolution of cell cycle regulation in alpha-proteobacteria: a comparative genomic analysis |
| Q42286183 | The evolutionary dynamics of functional modules and the extraordinary plasticity of regulons: the Escherichia coli perspective |
| Q57127814 | The evolutionary signal in metagenome phyletic profiles predicts many gene functions |
| Q44981604 | The genes and enzymes for the catabolism of galactitol, D-tagatose, and related carbohydrates in Klebsiella oxytoca M5a1 and other enteric bacteria display convergent evolution |
| Q49912618 | The genes of the sulphoquinovose catabolism in Escherichia coli are also associated with a previously unknown pathway of lactose degradation. |
| Q24814780 | The genomics of disulfide bonding and protein stabilization in thermophiles |
| Q28755465 | The global landscape of sequence diversity |
| Q37395221 | The human protein coevolution network. |
| Q40562890 | The identification of an integral membrane, cytochrome c urate oxidase completes the catalytic repertoire of a therapeutic enzyme |
| Q34027115 | The identification of functional modules from the genomic association of genes |
| Q34997450 | The language of genes |
| Q24551006 | The nitrilase superfamily: classification, structure and function |
| Q24681035 | The origins and early evolution of DNA mismatch repair genes--multiple horizontal gene transfers and co-evolution |
| Q24673696 | The origins and evolution of functional modules: lessons from protein complexes |
| Q34503048 | The origins of the evolutionary signal used to predict protein-protein interactions |
| Q34977461 | The outcomes of pathway database computations depend on pathway ontology |
| Q24303932 | The periplasmic serine protease inhibitor ecotin protects bacteria against neutrophil elastase |
| Q40949739 | The phylogenetic extent of metabolic enzymes and pathways |
| Q80485545 | The plant-specific database. Classification of Arabidopsis proteins based on their phylogenetic profile |
| Q34733596 | The post-genomic era of interactive proteomics: facts and perspectives |
| Q26801105 | The power of operon rearrangements for predicting functional associations |
| Q33268914 | The relationship between protein sequences and their gene ontology functions |
| Q35051909 | The role of indirect connections in gene networks in predicting function |
| Q24793719 | The society of genes: networks of functional links between genes from comparative genomics |
| Q33347894 | The topology of the bacterial co-conserved protein network and its implications for predicting protein function |
| Q33369980 | The use of Gene Ontology terms for predicting highly-connected 'hub' nodes in protein-protein interaction networks |
| Q49222848 | Time-consistent reconciliation maps and forbidden time travel. |
| Q34980439 | Topological structure analysis of the protein-protein interaction network in budding yeast |
| Q34023960 | Toward an efficient method of identifying core genes for evolutionary and functional microbial phylogenies |
| Q27860789 | Toward the structural genomics of complexes: Crystal structure of a PE/PPE protein complex from Mycobacterium tuberculosis |
| Q38446542 | Towards Consensus Gene Ages |
| Q36689026 | Towards a universal group B Streptococcus vaccine using multistrain genome analysis |
| Q36371202 | Towards multidimensional genome annotation |
| Q36282643 | Towards quantitative biology: integration of biological information to elucidate disease pathways and to guide drug discovery |
| Q34715175 | Towards the prediction of protein interaction partners using physical docking |
| Q33307860 | Towards validating the hypothesis of phylogenetic profiling |
| Q34794275 | Tracing evolutionary footprints to identify novel gene functional linkages |
| Q52023850 | Trait-to-gene: a computational method for predicting the function of uncharacterized genes. |
| Q33696515 | Trees on networks: resolving statistical patterns of phylogenetic similarities among interacting proteins |
| Q37213785 | Uncovering metabolic pathways relevant to phenotypic traits of microbial genomes |
| Q41878629 | Uncovering the co-evolutionary network among prokaryotic genes |
| Q28731026 | Understanding communication signals during mycobacterial latency through predicted genome-wide protein interactions and boolean modeling |
| Q36168349 | Understanding the yeast proteome: a bioinformatics perspective |
| Q34334118 | Unique transcriptome signature of Mycobacterium tuberculosis in pulmonary tuberculosis. |
| Q92837710 | Up-regulated FSTL5 inhibits invasion of hepatocellular carcinoma through the Wnt/β-catenin/YAP pathway |
| Q33381173 | Update of KDBI: Kinetic Data of Bio-molecular Interaction database. |
| Q43633753 | Using bioinformatics in gene and drug discovery |
| Q92237101 | Using discriminative vector machine model with 2DPCA to predict interactions among proteins |
| Q30479593 | Using indirect protein interactions for the prediction of Gene Ontology functions |
| Q30479591 | Using structural motif descriptors for sequence-based binding site prediction |
| Q36676452 | Using support vector machine combined with auto covariance to predict protein-protein interactions from protein sequences |
| Q37328570 | Utility of computational methods to identify the apoptosis machinery in unicellular eukaryotes |
| Q62111548 | Utilization of selenocysteine in early-branching fungal phyla |
| Q31010780 | Utilizing logical relationships in genomic data to decipher cellular processes |
| Q24800519 | VisANT: an online visualization and analysis tool for biological interaction data |
| Q24796237 | Visualisation and graph-theoretic analysis of a large-scale protein structural interactome |
| Q34054057 | Visualization and interpretation of protein networks in Mycobacterium tuberculosis based on hierarchical clustering of genome-wide functional linkage maps |
| Q28708807 | What we can learn about Escherichia coli through application of Gene Ontology |
| Q24804052 | Whither genomics? |
| Q30874386 | Who's your neighbor? New computational approaches for functional genomics |
| Q36852724 | Whole-genome annotation by using evidence integration in functional-linkage networks |
| Q37037782 | Why should we care about molecular coevolution? |
| Q39080836 | Xenolog classification |
| Q34139029 | YibK is the 2'-O-methyltransferase TrmL that modifies the wobble nucleotide in Escherichia coli tRNA(Leu) isoacceptors |
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