{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,6]],"date-time":"2026-05-06T07:51:51Z","timestamp":1778053911939,"version":"3.51.4"},"reference-count":20,"publisher":"Public Library of Science (PLoS)","issue":"1","license":[{"start":{"date-parts":[[2010,1,29]],"date-time":"2010-01-29T00:00:00Z","timestamp":1264723200000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1000621","type":"journal-article","created":{"date-parts":[[2010,1,28]],"date-time":"2010-01-28T22:33:48Z","timestamp":1264718028000},"page":"e1000621","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":16,"title":["Getting Started in Structural Phylogenomics"],"prefix":"10.1371","volume":"6","author":[{"given":"Kimmen","family":"Sj\u00f6lander","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2010,1,29]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"361","DOI":"10.1038\/nrg1603","article-title":"Phylogenomics and the reconstruction of the tree of life.","volume":"6","author":"F Delsuc","year":"2005","journal-title":"Nat Rev Genet"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1101\/gr.8.3.163","article-title":"Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis.","volume":"8","author":"JA Eisen","year":"1998","journal-title":"Genome Res"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"170","DOI":"10.1093\/bioinformatics\/bth021","article-title":"Phylogenomic inference of protein molecular function: advances and challenges.","volume":"20","author":"K Sj\u00f6lander","year":"2004","journal-title":"Bioinformatics"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"e77","DOI":"10.1371\/journal.pcbi.0020077","article-title":"Functional classification using phylogenomic inference.","volume":"2","author":"D Brown","year":"2006","journal-title":"PLoS Comput Biol"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"55","DOI":"10.3233\/ISB-00007","article-title":"Sources of systematic error in functional annotation of genomes: domain rearrangement, non-orthologous gene displacement and operon disruption.","volume":"1","author":"MY Galperin","year":"1998","journal-title":"In Silico Biol"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1016\/S0168-9525(99)01706-0","article-title":"Errors in genome annotation.","volume":"15","author":"SE Brenner","year":"1999","journal-title":"Trends Genet"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"4035","DOI":"10.1093\/nar\/gki711","article-title":"Genome annotation errors in pathway databases due to semantic ambiguity in partial EC numbers.","volume":"33","author":"ML Green","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"170","DOI":"10.1186\/1471-2105-8-170","article-title":"Estimating the annotation error rate of curated GO database sequence annotations.","volume":"8","author":"CE Jones","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"S12","DOI":"10.1186\/1471-2148-7-S1-S12","article-title":"FlowerPower: Clustering proteins into domain architecture classes for phylogenomic inference of protein function.","volume":"7","author":"N Krishnamurthy","year":"2007","journal-title":"BMC Evol Biol"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"e49","DOI":"10.1371\/journal.pcbi.0010049","article-title":"Structural evolution of the protein kinase-like superfamily.","volume":"1","author":"ED Scheeff","year":"2005","journal-title":"PLoS Comput Biol"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"R83","DOI":"10.1186\/gb-2006-7-9-r83","article-title":"PhyloFacts: An online structural phylogenomic encyclopedia for protein functional and structural classification.","volume":"7","author":"N Krishnamurthy","year":"2006","journal-title":"Genome Biol"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1186\/1471-2105-3-14","article-title":"RIO: Analyzing proteomes by automated phylogenomics using resampled inference of orthologs.","volume":"3","author":"CM Zmasek","year":"2002","journal-title":"BMC Bioinformatics"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"588","DOI":"10.1080\/10635150290102339","article-title":"Increased taxon sampling greatly reduces phylogenetic error.","volume":"51","author":"DJ Zwickl","year":"2002","journal-title":"Syst Biol"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1126\/science.1065659","article-title":"Protein structure prediction and structural genomics.","volume":"294","author":"D Baker","year":"2001","journal-title":"Science"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"1404","DOI":"10.1093\/bioinformatics\/btg158","article-title":"SATCHMO: Sequence alignment and tree construction using hidden Markov models.","volume":"19","author":"RC Edgar","year":"2003","journal-title":"Bioinformatics"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"D323","DOI":"10.1093\/nar\/gkn822","article-title":"The ConSurf-DB: Pre-calculated evolutionary conservation profiles of protein structures.","volume":"37","author":"O Goldenberg","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"2445","DOI":"10.1093\/bioinformatics\/btn474","article-title":"INTREPID\u2013INformation-theoretic TREe traversal for Protein functional site IDentification.","volume":"24","author":"S Sankararaman","year":"2008","journal-title":"Bioinformatics"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"196","DOI":"10.1006\/jmbi.1996.0569","article-title":"Using evolutionary trees in protein secondary structure prediction and other comparative sequence analyses.","volume":"263","author":"N Goldman","year":"1996","journal-title":"J Mol Biol"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"446","DOI":"10.1002\/prot.10373","article-title":"Detecting distant homologs using phylogenetic tree-based HMMs.","volume":"52","author":"B Qian","year":"2003","journal-title":"Proteins"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1093\/bib\/bbl004","article-title":"Automated protein function prediction\u2013the genomic challenge.","volume":"7","author":"I Friedberg","year":"2006","journal-title":"Brief Bioinform"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1000621","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,2,17]],"date-time":"2025-02-17T01:45:53Z","timestamp":1739756753000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1000621"}},"subtitle":[],"editor":[{"given":"Olga","family":"Troyanskaya","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2010,1,29]]},"references-count":20,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2010,1,29]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1000621","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2010,1,29]]}}}