{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,18]],"date-time":"2026-06-18T05:51:55Z","timestamp":1781761915572,"version":"3.54.5"},"reference-count":28,"publisher":"Public Library of Science (PLoS)","issue":"8","license":[{"start":{"date-parts":[[2009,8,14]],"date-time":"2009-08-14T00:00:00Z","timestamp":1250208000000},"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.1000465","type":"journal-article","created":{"date-parts":[[2009,8,13]],"date-time":"2009-08-13T22:05:24Z","timestamp":1250201124000},"page":"e1000465","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":572,"title":["A Parsimony Approach to Biological Pathway Reconstruction\/Inference for Genomes and Metagenomes"],"prefix":"10.1371","volume":"5","author":[{"given":"Yuzhen","family":"Ye","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas G.","family":"Doak","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2009,8,14]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1016\/j.ygeno.2008.07.001","article-title":"Applications of next-generation sequencing technologies in functional genomics.","volume":"92","author":"O Morozova","year":"2008","journal-title":"Genomics"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1093\/nar\/28.1.27","article-title":"KEGG: kyoto encyclopedia of genes and genomes.","volume":"28","author":"M Kanehisa","year":"2000","journal-title":"Nucleic Acids Res"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"5691","DOI":"10.1093\/nar\/gki866","article-title":"The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes.","volume":"33","author":"R Overbeek","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"W182","DOI":"10.1093\/nar\/gkm321","article-title":"KAAS: an automatic genome annotation and pathway reconstruction server.","volume":"35","author":"Y Moriya","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1186\/1471-2164-9-75","article-title":"The RAST Server: rapid annotations using subsystems technology.","volume":"9","author":"RK Aziz","year":"2008","journal-title":"BMC Genomics"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"386","DOI":"10.1186\/1471-2105-9-386","article-title":"The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes.","volume":"9","author":"F Meyer","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1016\/S1367-5931(03)00027-9","article-title":"Missing genes in metabolic pathways: a comparative genomics approach.","volume":"7","author":"A Osterman","year":"2003","journal-title":"Curr Opin Chem Biol"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"i478","DOI":"10.1093\/bioinformatics\/bti1052","article-title":"Automatic detection of subsystem\/pathway variants in genome analysis.","volume":"21","author":"Y Ye","year":"2005","journal-title":"Bioinformatics"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"335","DOI":"10.6026\/97320630001335","article-title":"Functional annotation of hypothetical proteins - A review.","volume":"1","author":"S Sivashankari","year":"2006","journal-title":"Bioinformation"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"1527","DOI":"10.1110\/ps.062158406","article-title":"New avenues in protein function prediction.","volume":"15","author":"I Friedberg","year":"2006","journal-title":"Protein Sci"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"1108","DOI":"10.1126\/science.1165578","article-title":"Genome of an endosymbiont coupling N2 fixation to cellulolysis within protist cells in termite gut.","volume":"322","author":"Y Hongoh","year":"2008","journal-title":"Science"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"1265","DOI":"10.1016\/j.cell.2006.10.036","article-title":"Quantitative proteomics analysis of the secretory pathway.","volume":"127","author":"A Gilchrist","year":"2006","journal-title":"Cell"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"11969","DOI":"10.1073\/pnas.172183199","article-title":"Proteomic survey of metabolic pathways in rice.","volume":"99","author":"A Koller","year":"2002","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"543","DOI":"10.1111\/j.1462-2920.2004.00652.x","article-title":"Metagenomics: from acid mine to shining sea.","volume":"6","author":"M Galperin","year":"2004","journal-title":"Environ Microbiol"},{"key":"ref15","article-title":"Proteomics by Mass Spectrometry: Approaches, Advances, and Applications.","author":"J Yates","year":"2009","journal-title":"Annu Rev Biomed Eng Epub ahead of print"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"480","DOI":"10.1038\/nature07540","article-title":"A core gut microbiome in obese and lean twins.","volume":"457","author":"PJ Turnbaugh","year":"2009","journal-title":"Nature"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"629","DOI":"10.1038\/nature06810","article-title":"Functional metagenomic profiling of nine biomes.","volume":"452","author":"EA Dinsdale","year":"2008","journal-title":"Nature"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"W423","DOI":"10.1093\/nar\/gkn282","article-title":"KEGG Atlas mapping for global analysis of metabolic pathways.","volume":"36","author":"S Okuda","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"516","DOI":"10.1016\/j.tplants.2005.09.002","article-title":"Moonlighting vacuolar protease: multiple jobs for a busy protein.","volume":"10","author":"FM Rosin","year":"2005","journal-title":"Trends Plant Sci"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1016\/j.tim.2005.09.001","article-title":"Reconstructing the metabolic network of a bacterium from its genome.","volume":"13","author":"C Francke","year":"2005","journal-title":"Trends Microbiol"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"2790","DOI":"10.1128\/JB.01583-07","article-title":"Genome-scale metabolic network analysis of the opportunistic pathogen Pseudomonas aeruginosa PAO1.","volume":"190","author":"MA Oberhardt","year":"2008","journal-title":"J Bacteriol"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"i359","DOI":"10.1093\/bioinformatics\/btm170","article-title":"SPINE: a framework for signaling-regulatory pathway inference from cause-effect experiments.","volume":"23","author":"O Ourfali","year":"2007","journal-title":"Bioinformatics"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"1374","DOI":"10.1073\/pnas.0808022106","article-title":"Quantifying environmental adaptation of metabolic pathways in metagenomics.","volume":"106","author":"TA Gianoulis","year":"2009","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref24","article-title":"Introduction to Linear Optimization","author":"D Bertsimas","year":"1997"},{"key":"ref25","article-title":"Combinatorial Optimization","author":"WJ Cook","year":"1998"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1089\/106652704773416876","article-title":"1001 optimal PDB structure alignments: integer programming methods for finding the maximum contact map overlap.","volume":"11","author":"A Caprara","year":"2004","journal-title":"J Comput Biol"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1142\/S0219720003000186","article-title":"RAPTOR: optimal protein threading by linear programming.","volume":"1","author":"J Xu","year":"2004","journal-title":"J Bioinform Comput Biol"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"i186","DOI":"10.1093\/bioinformatics\/bth936","article-title":"Optimal robust non-unique probe selection using Integer Linear Programming.","volume":"20","author":"GW Klau","year":"2004","journal-title":"Bioinformatics"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1000465","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,10,23]],"date-time":"2018-10-23T20:55:19Z","timestamp":1540328119000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1000465"}},"subtitle":[],"editor":[{"given":"Christos A.","family":"Ouzounis","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2009,8,14]]},"references-count":28,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2009,8,14]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1000465","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2009,8,14]]}}}