{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,4]],"date-time":"2024-08-04T17:54:54Z","timestamp":1722794094739},"reference-count":49,"publisher":"Springer Science and Business Media LLC","issue":"3","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Stand. Genomic Sci."],"DOI":"10.4056\/sigs.3286690","type":"journal-article","created":{"date-parts":[[2013,3,12]],"date-time":"2013-03-12T16:43:29Z","timestamp":1363106609000},"page":"483-496","source":"Crossref","is-referenced-by-count":6,"title":["The Genomic Blueprint of Salmonella enterica subspecies enterica serovar Typhi P-stx-12"],"prefix":"10.4056","volume":"7","author":[{"given":"Su Yean","family":"Ong","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chandra Bhan","family":"Pratap","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xuehua","family":"Wan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shaobin","family":"Hou","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ahmad Yamin Abdul","family":"Rahman","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jennifer A.","family":"Saito","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gopal","family":"Nath","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Maqsudul","family":"Alam","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2013,1,20]]},"reference":[{"key":"key20130312114550245_r1","doi-asserted-by":"crossref","first-page":"1770","DOI":"10.1056\/NEJMra020201","article-title":"Typhoid fever.","volume":"347","author":"Parry","year":"2002","journal-title":"N Engl J Med"},{"key":"key20130312114550245_r2","doi-asserted-by":"crossref","first-page":"686","DOI":"10.1056\/NEJM197009242831306","article-title":"Typhoid fever: pathogenesis and immunologic control.","volume":"283","author":"Hornick","year":"1970","journal-title":"N Engl J Med"},{"key":"key20130312114550245_r3","doi-asserted-by":"crossref","first-page":"S29","DOI":"10.1086\/518143","article-title":"The genome of Salmonella enterica serovar Typhi.","volume":"45","author":"Baker","year":"2007","journal-title":"Clin Infect Dis"},{"key":"key20130312114550245_r4","first-page":"346","article-title":"The global burden of typhoid fever.","volume":"82","author":"Crump","year":"2004","journal-title":"Bull World Health Organ"},{"key":"key20130312114550245_r5","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1038\/cmi.2008.11","article-title":"Salmonella typhi: from a human pathogen to a vaccine vector.","volume":"5","author":"Zhang","year":"2008","journal-title":"Cell Mol Immunol"},{"key":"key20130312114550245_r6"},{"key":"key20130312114550245_r7","doi-asserted-by":"crossref","first-page":"5341","DOI":"10.1128\/IAI.00786-08","article-title":"Identification of a bile-induced exopolysaccharide required for Salmonella biofilm formation on gallstone surfaces.","volume":"76","author":"Crawford","year":"2008","journal-title":"Infect Immun"},{"key":"key20130312114550245_r8","doi-asserted-by":"crossref","first-page":"267","DOI":"10.3855\/jidc.220","article-title":"SPI-7: Salmonella's Vi-encoding Pathogenicity Island.","volume":"2","author":"Seth-Smith","year":"2008","journal-title":"J Infect Dev Ctries"},{"key":"key20130312114550245_r9","doi-asserted-by":"crossref","first-page":"2330","DOI":"10.1128\/JB.185.7.2330-2337.2003","article-title":"Comparative genomics of Salmonella enterica serovar Typhi strains Ty2 and CT18.","volume":"185","author":"Deng","year":"2003","journal-title":"J Bacteriol"},{"key":"key20130312114550245_r10","doi-asserted-by":"crossref","first-page":"2115","DOI":"10.1128\/JB.00121-12","article-title":"Complete genome sequence of Salmonella enterica subsp. enterica serovar Typhi P-stx-12.","volume":"194","author":"Ong","year":"2012","journal-title":"J Bacteriol"},{"key":"key20130312114550245_r11","doi-asserted-by":"crossref","first-page":"D141","DOI":"10.1093\/nar\/gkn879","article-title":"The Ribosomal Database Project: improved alignments and new tools for rRNA analysis.","volume":"37","author":"Cole","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"key20130312114550245_r12","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1093\/oxfordjournals.molbev.a026231","article-title":"Weighted neighbor joining: a likelihood-based approach to distance-based phylogeny reconstruction.","volume":"17","author":"Bruno","year":"2000","journal-title":"Mol Biol Evol"},{"key":"key20130312114550245_r13","doi-asserted-by":"crossref","first-page":"4576","DOI":"10.1073\/pnas.87.12.4576","article-title":"Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.","volume":"87","author":"Woese","year":"1990","journal-title":"Proc Natl Acad Sci USA"},{"key":"key20130312114550245_r14"},{"key":"key20130312114550245_r15","doi-asserted-by":"crossref","first-page":"2235","DOI":"10.1099\/ijs.0.64108-0","article-title":"Validation of publication of new names and new combinations previously effectively published outside the IJSEM. List no. 106.","volume":"55","year":"2005","journal-title":"Int J Syst Evol Microbiol"},{"key":"key20130312114550245_r16"},{"key":"key20130312114550245_r17"},{"key":"key20130312114550245_r18","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1099\/00207713-30-1-225","article-title":"Approved lists of bacterial names.","volume":"30","author":"Skerman","year":"1980","journal-title":"Int J Syst Bacteriol"},{"key":"key20130312114550245_r19","first-page":"273","article-title":"New principles for the classification of bacteria.","volume":"96","author":"Rahn","year":"1937","journal-title":"Zentralbl Bakteriol Parasitenkd Infektionskr Hyg"},{"key":"key20130312114550245_r20","first-page":"73","article-title":"Conservation of the family name Enterobacteriaceae, of the name of the type genus, and designation of the type species. Opinion No. 15.","volume":"8","author":"Judicial Commission of the International Committee on Bacteriological Nomenclature","year":"1958","journal-title":"Int Bull Bacteriol Nomencl Taxon"},{"key":"key20130312114550245_r21","first-page":"389","article-title":"Maladies du porc.","volume":"18","author":"Lignieres","year":"1900","journal-title":"Bulletin of the Society for Central Medical Veterinarians"},{"key":"key20130312114550245_r22"},{"key":"key20130312114550245_r23","doi-asserted-by":"crossref","first-page":"519","DOI":"10.1099\/ijs.0.63579-0","article-title":"The type species of the genus Salmonella Lignieres 1900 is Salmonella enterica (ex Kauffmann and Edwards 1952) Le Minor and Popoff 1987, with the type strain LT2T, and conservation of the epithet enterica in Salmonella enterica over all earlier epithets that may be applied to this species. Opinion 80.","volume":"55","author":"Judicial Commission of the International Committee on Systematics of Prokaryotes","year":"2005","journal-title":"Int J Syst Evol Microbiol"},{"key":"key20130312114550245_r24","doi-asserted-by":"crossref","first-page":"465","DOI":"10.1099\/00207713-37-4-465","article-title":"Request for an opinion. Designation of Salmonella enterica sp. nov., nom. rev., as the type and only species of the genus Salmonella.","volume":"37","author":"Le Minor","year":"1987","journal-title":"Int J Syst Bacteriol"},{"key":"key20130312114550245_r25"},{"key":"key20130312114550245_r26","unstructured":"WHO. Background document: the diagnosis, treatment and prevention of typhoid fever. http:\/\/www.who.int\/vaccines-documents. WHO; 2003."},{"key":"key20130312114550245_r27","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.","volume":"25","author":"Ashburner","year":"2000","journal-title":"Nat Genet"},{"key":"key20130312114550245_r28"},{"key":"key20130312114550245_r29","doi-asserted-by":"crossref","first-page":"1439","DOI":"10.1128\/JCM.31.6.1439-1443.1993","article-title":"Detection of Salmonella typhi in the blood of patients with typhoid fever by polymerase chain reaction.","volume":"31","author":"Song","year":"1993","journal-title":"J Clin Microbiol"},{"key":"key20130312114550245_r30","doi-asserted-by":"crossref","first-page":"1415","DOI":"10.1128\/JCM.32.5.1415-.1994","article-title":"Detection of Salmonella typhi by PCR.","volume":"32","author":"Frankel","year":"1994","journal-title":"J Clin Microbiol"},{"key":"key20130312114550245_r31","doi-asserted-by":"crossref","first-page":"1753","DOI":"10.1128\/JCM.38.5.1753-1757.2000","article-title":"Detection of and discrimination between Gram-positive and Gram-negative bacteria in intraocular samples by using nested PCR.","volume":"38","author":"Carroll","year":"2000","journal-title":"J Clin Microbiol"},{"key":"key20130312114550245_r32","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows-Wheeler transform.","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"key20130312114550245_r33","doi-asserted-by":"crossref","first-page":"1122","DOI":"10.1093\/bioinformatics\/btq090","article-title":"An Ergatis-based prokaryotic genome annotation web server.","volume":"26","author":"Hemmerich","year":"2010","journal-title":"Bioinformatics"},{"key":"key20130312114550245_r34","doi-asserted-by":"crossref","first-page":"962","DOI":"10.1093\/bioinformatics\/btp097","article-title":"DIYA: a bacterial annotation pipeline for any genomics lab.","volume":"25","author":"Stewart","year":"2009","journal-title":"Bioinformatics"},{"key":"key20130312114550245_r35","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":"Delcher","year":"2007","journal-title":"Bioinformatics"},{"key":"key20130312114550245_r36","doi-asserted-by":"crossref","first-page":"955","DOI":"10.1093\/nar\/25.5.0955","article-title":"tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence.","volume":"25","author":"Lowe","year":"1997","journal-title":"Nucleic Acids Res"},{"key":"key20130312114550245_r37","doi-asserted-by":"crossref","first-page":"3100","DOI":"10.1093\/nar\/gkm160","article-title":"RNAmmer: consistent and rapid annotation of ribosomal RNA genes.","volume":"35","author":"Lagesen","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"key20130312114550245_r38","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool.","volume":"215","author":"Altschul","year":"1990","journal-title":"J Mol Biol"},{"key":"key20130312114550245_r39","doi-asserted-by":"crossref","first-page":"2593","DOI":"10.1002\/cbdv.200790212","article-title":"Automated system for gene annotation and metabolic pathway reconstruction using general sequence databases.","volume":"4","author":"Alves","year":"2007","journal-title":"Chem Biodivers"},{"key":"key20130312114550245_r40","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":"Altschul","year":"1997","journal-title":"Nucleic Acids Res"},{"key":"key20130312114550245_r41"},{"key":"key20130312114550245_r42"},{"key":"key20130312114550245_r43","doi-asserted-by":"crossref","first-page":"664","DOI":"10.1093\/bioinformatics\/btp030","article-title":"IslandViewer: an integrated interface for computational identification and visualization of genomic islands.","volume":"25","author":"Langille","year":"2009","journal-title":"Bioinformatics"},{"key":"key20130312114550245_r44","doi-asserted-by":"crossref","first-page":"e11147","DOI":"10.1371\/journal.pone.0011147","article-title":"progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement.","volume":"5","author":"Darling","year":"2010","journal-title":"PLoS ONE"},{"key":"key20130312114550245_r45","doi-asserted-by":"crossref","first-page":"537","DOI":"10.1093\/bioinformatics\/bti054","article-title":"Circular genome visualization and exploration using CGView.","volume":"21","author":"Stothard","year":"2005","journal-title":"Bioinformatics"},{"key":"key20130312114550245_r46","doi-asserted-by":"crossref","first-page":"2155","DOI":"10.1093\/bioinformatics\/btg290","article-title":"Pathway studio-the analysis and navigation of molecular networks.","volume":"19","author":"Nikitin","year":"2003","journal-title":"Bioinformatics"},{"key":"key20130312114550245_r47","doi-asserted-by":"crossref","first-page":"848","DOI":"10.1038\/35101607","article-title":"Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18.","volume":"413","author":"Parkhill","year":"2001","journal-title":"Nature"},{"key":"key20130312114550245_r48","first-page":"272","article-title":"IncHI plasmids, a dynamic link between resistance and pathogenicity.","volume":"2","author":"Phan","year":"2008","journal-title":"J Infect Dev Ctries"},{"key":"key20130312114550245_r49","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1038\/nrg2749","article-title":"CRISPR interference: RNA-directed adaptive immunity in Bacteria and Archaea.","volume":"11","author":"Marraffini","year":"2010","journal-title":"Nat Rev Genet"}],"container-title":["Standards in Genomic Sciences"],"original-title":[],"language":"en","deposited":{"date-parts":[[2024,4,9]],"date-time":"2024-04-09T19:56:38Z","timestamp":1712692598000},"score":1,"resource":{"primary":{"URL":"https:\/\/environmentalmicrobiome.biomedcentral.com\/articles\/10.4056\/sigs.3286690"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,1,20]]},"references-count":49,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2013,1,20]]}},"alternative-id":["10.4056\/sigs.3286690"],"URL":"https:\/\/doi.org\/10.4056\/sigs.3286690","relation":{},"ISSN":["1944-3277"],"issn-type":[{"value":"1944-3277","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,1,20]]}}}