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Literature DB >> 25788543

Refinement of whole-genome multilocus sequence typing analysis by addressing gene paralogy.

Ji Zhang¹, Jani Halkilahti², Marja-Liisa Hänninen³, Mirko Rossi¹.

Abstract

We developed a user-friendly program, Genome Profiler (GeP), to refine whole-genome multilocus sequence typing analysis by addressing gene paralogy with conserved gene neighborhoods. In comparison to similar programs, GeP produced overall the best results in terms of accuracy and is thus a useful alternative to resolve relationships of bacterial isolates.

Mesh：

Year: 2015 PMID： 25788543 PMCID： PMC4400783 DOI： 10.1128/JCM.00051-15

Source DB: PubMed Journal: J Clin Microbiol ISSN： 0095-1137 Impact factor: 5.948

11 in total

1. Galaxy: a platform for interactive large-scale genome analysis.

Authors: Belinda Giardine; Cathy Riemer; Ross C Hardison; Richard Burhans; Laura Elnitski; Prachi Shah; Yi Zhang; Daniel Blankenberg; Istvan Albert; James Taylor; Webb Miller; W James Kent; Anton Nekrutenko
Journal: Genome Res Date: 2005-09-16 Impact factor: 9.043

Review 2. Turning a hobby into a job: how duplicated genes find new functions.

Authors: Gavin C Conant; Kenneth H Wolfe
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3. Whole-genome-based Mycobacterium tuberculosis surveillance: a standardized, portable, and expandable approach.

Authors: Thomas A Kohl; Roland Diel; Dag Harmsen; Jörg Rothgänger; Karen Meywald Walter; Matthias Merker; Thomas Weniger; Stefan Niemann
Journal: J Clin Microbiol Date: 2014-04-30 Impact factor: 5.948

4. PanOCT: automated clustering of orthologs using conserved gene neighborhood for pan-genomic analysis of bacterial strains and closely related species.

Authors: Derrick E Fouts; Lauren Brinkac; Erin Beck; Jason Inman; Granger Sutton
Journal: Nucleic Acids Res Date: 2012-08-16 Impact factor: 16.971

5. Genetic heterogeneity of Campylobacter jejuni NCTC 11168 upon human infection.

Authors: Joana Revez; Thomas Schott; Ann-Katrin Llarena; Mirko Rossi; Marja-Liisa Hänninen
Journal: Infect Genet Evol Date: 2013-03-20 Impact factor: 3.342

6. CmeABC functions as a multidrug efflux system in Campylobacter jejuni.

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Journal: Antimicrob Agents Chemother Date: 2002-07 Impact factor: 5.191

7. BIGSdb: Scalable analysis of bacterial genome variation at the population level.

Authors: Keith A Jolley; Martin C J Maiden
Journal: BMC Bioinformatics Date: 2010-12-10 Impact factor: 3.169

8. SyntTax: a web server linking synteny to prokaryotic taxonomy.

Authors: Jacques Oberto
Journal: BMC Bioinformatics Date: 2013-01-16 Impact factor: 3.169

9. The RAST Server: rapid annotations using subsystems technology.

Authors: Ramy K Aziz; Daniela Bartels; Aaron A Best; Matthew DeJongh; Terrence Disz; Robert A Edwards; Kevin Formsma; Svetlana Gerdes; Elizabeth M Glass; Michael Kubal; Folker Meyer; Gary J Olsen; Robert Olson; Andrei L Osterman; Ross A Overbeek; Leslie K McNeil; Daniel Paarmann; Tobias Paczian; Bruce Parrello; Gordon D Pusch; Claudia Reich; Rick Stevens; Olga Vassieva; Veronika Vonstein; Andreas Wilke; Olga Zagnitko
Journal: BMC Genomics Date: 2008-02-08 Impact factor: 3.969

10. Genome analysis of Campylobacter jejuni strains isolated from a waterborne outbreak.

Authors: Joana Revez; Ann-Katrin Llarena; Thomas Schott; Markku Kuusi; Marjaana Hakkinen; Rauni Kivistö; Marja-Liisa Hänninen; Mirko Rossi
Journal: BMC Genomics Date: 2014-09-08 Impact factor: 3.969

11 in total

Review 1. Whole-Genome Sequencing in Epidemiology of Campylobacter jejuni Infections.

Authors: Ann-Katrin Llarena; Eduardo Taboada; Mirko Rossi
Journal: J Clin Microbiol Date: 2017-03-01 Impact factor: 5.948

2. Identification and pathogenomic analysis of an Escherichia coli strain producing a novel Shiga toxin 2 subtype.

Authors: Xiangning Bai; Shanshan Fu; Ji Zhang; Ruyue Fan; Yanmei Xu; Hui Sun; Xiaohua He; Jianguo Xu; Yanwen Xiong
Journal: Sci Rep Date: 2018-04-30 Impact factor: 4.379

3. Fast hierarchical Bayesian analysis of population structure.

Authors: Gerry Tonkin-Hill; John A Lees; Stephen D Bentley; Simon D W Frost; Jukka Corander
Journal: Nucleic Acids Res Date: 2019-06-20 Impact factor: 16.971

4. Population Genetics and Antimicrobial Susceptibility of Canine Campylobacter Isolates Collected before and after a Raw Feeding Experiment.

Authors: Satu Olkkola; Sara Kovanen; Johanna Roine; Marja-Liisa Hänninen; Anna Hielm-Björkman; Rauni Kivistö
Journal: PLoS One Date: 2015-07-14 Impact factor: 3.240

5. Updating the genomic taxonomy and epidemiology of Campylobacter hyointestinalis.

Authors: David A Wilkinson; Andrew J O'Donnell; Rukhshana N Akhter; Ahmed Fayaz; Hamish J Mack; Lynn E Rogers; Patrick J Biggs; Nigel P French; Anne C Midwinter
Journal: Sci Rep Date: 2018-02-05 Impact factor: 4.379

Review 6. Food Safety in the Age of Next Generation Sequencing, Bioinformatics, and Open Data Access.

Authors: Eduardo N Taboada; Morag R Graham; João A Carriço; Gary Van Domselaar
Journal: Front Microbiol Date: 2017-05-23 Impact factor: 5.640

7. Monomorphic genotypes within a generalist lineage of Campylobacter jejuni show signs of global dispersion.

Authors: Ann-Katrin Llarena; Ji Zhang; Minna Vehkala; Niko Välimäki; Marjaana Hakkinen; Marja-Liisa Hänninen; Mati Roasto; Mihkel Mäesaar; Eduardo Taboada; Dillon Barker; Giuliano Garofolo; Cesare Cammà; Elisabetta Di Giannatale; Jukka Corander; Mirko Rossi
Journal: Microb Genom Date: 2016-10-21