{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T05:43:33Z","timestamp":1772171013963,"version":"3.50.1"},"reference-count":34,"publisher":"Public Library of Science (PLoS)","issue":"9","license":[{"start":{"date-parts":[[2008,9,26]],"date-time":"2008-09-26T00:00:00Z","timestamp":1222387200000},"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.1000186","type":"journal-article","created":{"date-parts":[[2008,9,25]],"date-time":"2008-09-25T18:14:24Z","timestamp":1222366464000},"page":"e1000186","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":44,"title":["Gene-Boosted Assembly of a Novel Bacterial Genome from Very Short Reads"],"prefix":"10.1371","volume":"4","author":[{"given":"Steven L.","family":"Salzberg","sequence":"first","affiliation":[]},{"given":"Daniel D.","family":"Sommer","sequence":"additional","affiliation":[]},{"given":"Daniela","family":"Puiu","sequence":"additional","affiliation":[]},{"given":"Vincent T.","family":"Lee","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2008,9,26]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"1767","DOI":"10.1101\/gr.3770505","article-title":"Emerging technologies in DNA sequencing.","volume":"15","author":"ML Metzker","year":"2005","journal-title":"Genome Res"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1016\/j.tig.2007.12.007","article-title":"The impact of next-generation sequencing technology on genetics.","volume":"24","author":"ER Mardis","year":"2008","journal-title":"Trends Genet"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"324","DOI":"10.1101\/gr.7088808","article-title":"Short read fragment assembly of bacterial genomes.","volume":"18","author":"MJ Chaisson","year":"2008","journal-title":"Genome Res"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"376","DOI":"10.1038\/nature03959","article-title":"Genome sequencing in microfabricated high-density picolitre reactors.","volume":"437","author":"M Margulies","year":"2005","journal-title":"Nature"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"e171","DOI":"10.1093\/nar\/gni170","article-title":"An analysis of the feasibility of short read sequencing.","volume":"33","author":"N Whiteford","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"601","DOI":"10.1101\/gad.1510307","article-title":"New insights into Acinetobacter baumannii pathogenesis revealed by high-density pyrosequencing and transposon mutagenesis.","volume":"21","author":"MG Smith","year":"2007","journal-title":"Genes Dev"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"11240","DOI":"10.1073\/pnas.0604351103","article-title":"A Sanger\/pyrosequencing hybrid approach for the generation of high-quality draft assemblies of marine microbial genomes.","volume":"103","author":"SM Goldberg","year":"2006","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1038\/nmeth.1179","article-title":"Whole-genome sequencing and variant discovery in C. elegans.","volume":"5","author":"LW Hillier","year":"2008","journal-title":"Nat Methods"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"651","DOI":"10.1038\/nmeth1068","article-title":"Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing.","volume":"4","author":"G Robertson","year":"2007","journal-title":"Nat Methods"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1101\/gr.208902","article-title":"ARACHNE: a whole-genome shotgun assembler.","volume":"12","author":"S Batzoglou","year":"2002","journal-title":"Genome Res"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1101\/gr.828403","article-title":"Whole-genome sequence assembly for Mammalian genomes: Arachne 2.","volume":"13","author":"DB Jaffe","year":"2003","journal-title":"Genome Res"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"2196","DOI":"10.1126\/science.287.5461.2196","article-title":"A whole-genome assembly of Drosophila.","volume":"287","author":"EW Myers","year":"2000","journal-title":"Science"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"500","DOI":"10.1093\/bioinformatics\/btl629","article-title":"Assembling millions of short DNA sequences using SSAKE.","volume":"23","author":"RL Warren","year":"2007","journal-title":"Bioinformatics"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"821","DOI":"10.1101\/gr.074492.107","article-title":"Velvet: algorithms for de novo short read assembly using de Bruijn graphs.","volume":"18","author":"D Zerbino","year":"2008","journal-title":"Genome Res"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"802","DOI":"10.1101\/gr.072033.107","article-title":"De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer.","volume":"18","author":"D Hernandez","year":"2008","journal-title":"Genome Res"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"810","DOI":"10.1101\/gr.7337908","article-title":"ALLPATHS: de novo assembly of whole-genome shotgun microreads.","volume":"18","author":"J Butler","year":"2008","journal-title":"Genome Res"},{"key":"ref17","article-title":"Harrison&apos;s Principles of Internal Medicine","author":"DL Kasper","year":"2005"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"470","DOI":"10.1016\/j.ajic.2004.10.001","article-title":"National Nosocomial Infections Surveillance (NNIS) System Report, data summary from January 1992 through June 2004, issued October 2004.","volume":"32","year":"2004","journal-title":"Am J Infect Control"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"959","DOI":"10.1038\/35023079","article-title":"Complete genome sequence of Pseudomonas aeruginosa PA01, an opportunistic pathogen.","volume":"406","author":"CK Stover","year":"2000","journal-title":"Nature"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"R90","DOI":"10.1186\/gb-2006-7-10-r90","article-title":"Genomic analysis reveals that Pseudomonas aeruginosa virulence is combinatorial.","volume":"7","author":"DG Lee","year":"2006","journal-title":"Genome Biol"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1093\/bib\/5.3.237","article-title":"Comparative genome assembly.","volume":"5","author":"M Pop","year":"2004","journal-title":"Brief Bioinform"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"R12","DOI":"10.1186\/gb-2004-5-2-r12","article-title":"Versatile and open software for comparing large genomes.","volume":"5","author":"S Kurtz","year":"2004","journal-title":"Genome Biol"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"64","DOI":"10.1186\/1471-2105-8-64","article-title":"Minimus: a fast, lightweight genome assembler.","volume":"8","author":"DD Sommer","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"673","DOI":"10.1093\/bioinformatics\/btm009","article-title":"Identifying bacterial genes and endosymbiont DNA with Glimmer.","volume":"23","author":"AL Delcher","year":"2007","journal-title":"Bioinformatics"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.","volume":"25","author":"SF Altschul","year":"1997","journal-title":"Nucleic Acids Res"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"809","DOI":"10.1046\/j.1365-2958.2003.03740.x","article-title":"A four-tiered transcriptional regulatory circuit controls flagellar biogenesis in Pseudomonas aeruginosa.","volume":"50","author":"N Dasgupta","year":"2003","journal-title":"Mol Microbiol"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"218","DOI":"10.1016\/j.mib.2006.02.010","article-title":"Cyclic di-GMP as a second messenger.","volume":"9","author":"U Romling","year":"2006","journal-title":"Curr Opin Microbiol"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"1113","DOI":"10.1126\/science.1121357","article-title":"Bacterial small-molecule signaling pathways.","volume":"311","author":"A Camilli","year":"2006","journal-title":"Science"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"2839","DOI":"10.1073\/pnas.0511090103","article-title":"Analysis of Pseudomonas aeruginosa diguanylate cyclases and phosphodiesterases reveals a role for bis-(3\u2032-5\u2032)-cyclic-GMP in virulence.","volume":"103","author":"H Kulasakara","year":"2006","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"876","DOI":"10.1111\/j.1365-2958.2007.05817.x","article-title":"The second messenger bis-(3\u2032-5\u2032)-cyclic-GMP and its PilZ domain-containing receptor Alg44 are required for alginate biosynthesis in Pseudomonas aeruginosa.","volume":"65","author":"M Merighi","year":"2007","journal-title":"Mol Microbiol"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"1474","DOI":"10.1111\/j.1365-2958.2007.05879.x","article-title":"A cyclic-di-GMP receptor required for bacterial exopolysaccharide production.","volume":"65","author":"VT Lee","year":"2007","journal-title":"Mol Microbiol"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"1171","DOI":"10.1038\/nature03912","article-title":"Aminoglycoside antibiotics induce bacterial biofilm formation.","volume":"436","author":"LR Hoffman","year":"2005","journal-title":"Nature"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"740","DOI":"10.1038\/416740a","article-title":"Pseudomonas biofilm formation and antibiotic resistance are linked to phenotypic variation.","volume":"416","author":"E Drenkard","year":"2002","journal-title":"Nature"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"276","DOI":"10.1016\/S0168-9525(00)02024-2","article-title":"EMBOSS: the European Molecular Biology Open Software Suite.","volume":"16","author":"P Rice","year":"2000","journal-title":"Trends Genet"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1000186","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,5,14]],"date-time":"2019-05-14T02:09:42Z","timestamp":1557799782000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1000186"}},"subtitle":[],"editor":[{"given":"William Stafford","family":"Noble","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2008,9,26]]},"references-count":34,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2008,9,26]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1000186","relation":{"has-review":[{"id-type":"doi","id":"10.3410\/f.1128888.585988","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2008,9,26]]}}}