Assessing protein co-evolution in the context of the tree of life assists in the prediction of the interactome.

[1]  Martin Bland,et al.  An Introduction to Medical Statistics , 1987 .

[2]  S. Fields,et al.  A novel genetic system to detect protein–protein interactions , 1989, Nature.

[3]  W. Doolittle,et al.  Root of the universal tree of life based on ancient aminoacyl-tRNA synthetase gene duplications. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[4]  K. J. Fryxell,et al.  The coevolution of gene family trees. , 1996, Trends in genetics : TIG.

[5]  J. Lawrence Selfish operons and speciation by gene transfer. , 1997, Trends in microbiology.

[6]  E. Bayer,et al.  Species‐specificity of the cohesin‐dockerin interaction between Clostridium thermocellum and Clostridium cellulolyticum: Prediction of specificity determinants of the dockerin domain , 1997, Proteins.

[7]  P. Schimmel,et al.  Maintaining genetic code through adaptations of tRNA synthetases to taxonomic domains. , 1997, Trends in biochemical sciences.

[8]  Gapped BLAST and PSI-BLAST: A new , 1997 .

[9]  Mark D'Souza,et al.  Use of contiguity on the chromosome to predict functional coupling , 1998, Silico Biol..

[10]  B. Snel,et al.  Conservation of gene order: a fingerprint of proteins that physically interact. , 1998, Trends in biochemical sciences.

[11]  D. Eisenberg,et al.  Detecting protein function and protein-protein interactions from genome sequences. , 1999, Science.

[12]  D. Eisenberg,et al.  Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[13]  Anton J. Enright,et al.  Protein interaction maps for complete genomes based on gene fusion events , 1999, Nature.

[14]  James R. Knight,et al.  A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae , 2000, Nature.

[15]  Gary J. Olsen,et al.  Aminoacyl-tRNA Synthetases, the Genetic Code, and the Evolutionary Process , 2000, Microbiology and Molecular Biology Reviews.

[16]  F. Cohen,et al.  Co-evolution of proteins with their interaction partners. , 2000, Journal of molecular biology.

[17]  A. Valencia,et al.  Similarity of phylogenetic trees as indicator of protein-protein interaction. , 2001, Protein engineering.

[18]  A. Barabasi,et al.  Lethality and centrality in protein networks , 2001, Nature.

[19]  J. Wojcik,et al.  The protein–protein interaction map of Helicobacter pylori , 2001, Nature.

[20]  Gary D Bader,et al.  Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry , 2002, Nature.

[21]  Ioannis Xenarios,et al.  DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions , 2002, Nucleic Acids Res..

[22]  A. Valencia,et al.  In silico two‐hybrid system for the selection of physically interacting protein pairs , 2002, Proteins.

[23]  P. Bork,et al.  Functional organization of the yeast proteome by systematic analysis of protein complexes , 2002, Nature.

[24]  B. Bukau,et al.  Protein folding and degradation in bacteria:¶To degrade or not to degrade? That is the question , 2002, Cellular and Molecular Life Sciences CMLS.

[25]  B. Snel,et al.  Comparative assessment of large-scale data sets of protein–protein interactions , 2002, Nature.

[26]  Howard Ochman,et al.  Reconciling the many faces of lateral gene transfer. , 2002, Trends in microbiology.

[27]  A. E. Hirsh,et al.  Evolutionary Rate in the Protein Interaction Network , 2002, Science.

[28]  A. Valencia,et al.  Computational methods for the prediction of protein interactions. , 2002, Current opinion in structural biology.

[29]  M. Ragan,et al.  Inferring Genome Trees by Using a Filter To Eliminate Phylogenetically Discordant Sequences and a Distance Matrix Based on Mean Normalized BLASTP Scores , 2002, Journal of bacteriology.

[30]  Chern-Sing Goh,et al.  Co-evolutionary analysis reveals insights into protein-protein interactions. , 2002, Journal of molecular biology.

[31]  Bruce Rothschild,et al.  Inferring protein interactions from phylogenetic distance matrices , 2003, Bioinform..

[32]  Gene Ontology Consortium The Gene Ontology (GO) database and informatics resource , 2003 .

[33]  R. Karp,et al.  Conserved pathways within bacteria and yeast as revealed by global protein network alignment , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[34]  Z N Oltvai,et al.  Evolutionary conservation of motif constituents in the yeast protein interaction network , 2003, Nature Genetics.

[35]  B. Snel,et al.  Function prediction and protein networks. , 2003, Current opinion in cell biology.

[36]  D. Eisenberg,et al.  Computational methods of analysis of protein-protein interactions. , 2003, Current opinion in structural biology.

[37]  E. Koonin,et al.  Evolution of mosaic operons by horizontal gene transfer and gene displacement in situ , 2003, Genome Biology.

[38]  James R. Brown Ancient horizontal gene transfer , 2003, Nature Reviews Genetics.

[39]  A. Grigoriev On the number of protein-protein interactions in the yeast proteome. , 2003, Nucleic acids research.

[40]  Wen-Hsiung Li,et al.  Evolution of the yeast protein interaction network , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[41]  Christos A. Ouzounis,et al.  GeneTRACE - Reconstruction of Gene Content of Ancestral Species , 2003, Bioinform..

[42]  James R. Knight,et al.  A Protein Interaction Map of Drosophila melanogaster , 2003, Science.

[43]  Arun K. Ramani,et al.  Exploiting the co-evolution of interacting proteins to discover interaction specificity. , 2003, Journal of molecular biology.

[44]  D. Bu,et al.  Topological structure analysis of the protein-protein interaction network in budding yeast. , 2003, Nucleic acids research.

[45]  Rodrigo Lopez,et al.  Multiple sequence alignment with the Clustal series of programs , 2003, Nucleic Acids Res..

[46]  Eileen Kraemer,et al.  RED-T: utilizing the Ratios of Evolutionary Distances for determination of alternative phylogenetic events , 2003, Bioinform..

[47]  Hanah Margalit,et al.  Detection of regulatory circuits by integrating the cellular networks of protein-protein interactions and transcription regulation. , 2003, Nucleic acids research.

[48]  N. Moran,et al.  Phylogenetics and the Cohesion of Bacterial Genomes , 2003, Science.

[49]  Edward M Marcotte,et al.  Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages , 2003, Nature Biotechnology.

[50]  Alessandro Vespignani,et al.  Global protein function prediction from protein-protein interaction networks , 2003, Nature Biotechnology.

[51]  M. Samanta,et al.  Predicting protein functions from redundancies in large-scale protein interaction networks , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[52]  Hervé Philippe,et al.  Horizontal gene transfer and phylogenetics. , 2003, Current opinion in microbiology.

[53]  M. Kanehisa,et al.  Prediction of Protein-Protein Interactions from Phylogenetic Trees Using Partial Correlation Coefficient , 2003 .

[54]  M. Gerstein,et al.  A Bayesian Networks Approach for Predicting Protein-Protein Interactions from Genomic Data , 2003, Science.

[55]  Dan M. Bolser,et al.  Large-scale co-evolution analysis of protein structural interlogues using the global protein structural interactome map (PSIMAP) , 2004, Bioinform..

[56]  See-Kiong Ng,et al.  ADVICE: Automated Detection and Validation of Interaction by Co-Evolution , 2004, Nucleic Acids Res..

[57]  Guy Perrière,et al.  The European ribosomal RNA database , 2004, Nucleic Acids Res..

[58]  S. L. Wong,et al.  A Map of the Interactome Network of the Metazoan C. elegans , 2004, Science.

[59]  L. Holm,et al.  Unraveling protein interaction networks with near-optimal efficiency , 2004, Nature Biotechnology.

[60]  A. E. Hirsh,et al.  Coevolution of gene expression among interacting proteins , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[61]  H Matsuda,et al.  Corrigendum: Biased biological functions of horizontally transfered genes in prokaryotic genomes , 2004, Nature Genetics.

[62]  Kiheung Kim,et al.  Ko Kuei Chen: a pioneer of modern pharmacological research in China , 2022, Protein & cell.