Literature DB >> 23839141

Read and assembly metrics inconsequential for clinical utility of whole-genome sequencing in mapping outbreaks.

Simon R Harris, M E Török, Edward J P Cartwright, Michael A Quail, Sharon J Peacock, Julian Parkhill.   

Abstract

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Year:  2013        PMID： 23839141      PMCID： PMC4335133          DOI： 10.1038/nbt.2616

Source DB:  PubMed          Journal:  Nat Biotechnol        ISSN： 1087-0156            Impact factor:   54.908


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  12 in total

1.  Performance comparison of benchtop high-throughput sequencing platforms.

Authors:  Nicholas J Loman; Raju V Misra; Timothy J Dallman; Chrystala Constantinidou; Saheer E Gharbia; John Wain; Mark J Pallen
Journal:  Nat Biotechnol       Date:  2012-05       Impact factor: 54.908

2.  The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.

Authors:  Aaron McKenna; Matthew Hanna; Eric Banks; Andrey Sivachenko; Kristian Cibulskis; Andrew Kernytsky; Kiran Garimella; David Altshuler; Stacey Gabriel; Mark Daly; Mark A DePristo
Journal:  Genome Res       Date:  2010-07-19       Impact factor: 9.043

3.  Rapid whole-genome sequencing for investigation of a suspected tuberculosis outbreak.

Authors:  M Estée Török; Sandra Reuter; Josephine Bryant; Claudio U Köser; Sian V Stinchcombe; Bernadette Nazareth; Matthew J Ellington; Stephen D Bentley; Geoffrey P Smith; Julian Parkhill; Sharon J Peacock
Journal:  J Clin Microbiol       Date:  2012-11-21       Impact factor: 5.948

4.  Whole-genome sequencing and social-network analysis of a tuberculosis outbreak.

Authors:  Jennifer L Gardy; James C Johnston; Shannan J Ho Sui; Victoria J Cook; Lena Shah; Elizabeth Brodkin; Shirley Rempel; Richard Moore; Yongjun Zhao; Robert Holt; Richard Varhol; Inanc Birol; Marcus Lem; Meenu K Sharma; Kevin Elwood; Steven J M Jones; Fiona S L Brinkman; Robert C Brunham; Patrick Tang
Journal:  N Engl J Med       Date:  2011-02-24       Impact factor: 91.245

5.  The Sequence Alignment/Map format and SAMtools.

Authors:  Heng Li; Bob Handsaker; Alec Wysoker; Tim Fennell; Jue Ruan; Nils Homer; Gabor Marth; Goncalo Abecasis; Richard Durbin
Journal:  Bioinformatics       Date:  2009-06-08       Impact factor: 6.937

6.  Tracking a hospital outbreak of carbapenem-resistant Klebsiella pneumoniae with whole-genome sequencing.

Authors:  Evan S Snitkin; Adrian M Zelazny; Pamela J Thomas; Frida Stock; David K Henderson; Tara N Palmore; Julia A Segre
Journal:  Sci Transl Med       Date:  2012-08-22       Impact factor: 17.956

7.  Rapid whole-genome sequencing for investigation of a neonatal MRSA outbreak.

Authors:  Claudio U Köser; Matthew T G Holden; Matthew J Ellington; Edward J P Cartwright; Nicholas M Brown; Amanda L Ogilvy-Stuart; Li Yang Hsu; Claire Chewapreecha; Nicholas J Croucher; Simon R Harris; Mandy Sanders; Mark C Enright; Gordon Dougan; Stephen D Bentley; Julian Parkhill; Louise J Fraser; Jason R Betley; Ole B Schulz-Trieglaff; Geoffrey P Smith; Sharon J Peacock
Journal:  N Engl J Med       Date:  2012-06-14       Impact factor: 91.245

Review 8.  Routine use of microbial whole genome sequencing in diagnostic and public health microbiology.

Authors:  Claudio U Köser; Matthew J Ellington; Edward J P Cartwright; Stephen H Gillespie; Nicholas M Brown; Mark Farrington; Matthew T G Holden; Gordon Dougan; Stephen D Bentley; Julian Parkhill; Sharon J Peacock
Journal:  PLoS Pathog       Date:  2012-08-02       Impact factor: 6.823

9.  A pilot study of rapid benchtop sequencing of Staphylococcus aureus and Clostridium difficile for outbreak detection and surveillance.

Authors:  David W Eyre; Tanya Golubchik; N Claire Gordon; Rory Bowden; Paolo Piazza; Elizabeth M Batty; Camilla L C Ip; Daniel J Wilson; Xavier Didelot; Lily O'Connor; Rochelle Lay; David Buck; Angela M Kearns; Angela Shaw; John Paul; Mark H Wilcox; Peter J Donnelly; Tim E A Peto; A Sarah Walker; Derrick W Crook
Journal:  BMJ Open       Date:  2012-06-06       Impact factor: 2.692

10.  Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study.

Authors:  Simon R Harris; Edward J P Cartwright; M Estée Török; Matthew T G Holden; Nicholas M Brown; Amanda L Ogilvy-Stuart; Matthew J Ellington; Michael A Quail; Stephen D Bentley; Julian Parkhill; Sharon J Peacock
Journal:  Lancet Infect Dis       Date:  2012-11-14       Impact factor: 25.071
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  14 in total

Review 1.  Clinical microbiology informatics.

Authors:  Daniel D Rhoads; Vitali Sintchenko; Carol A Rauch; Liron Pantanowitz
Journal:  Clin Microbiol Rev       Date:  2014-10       Impact factor: 26.132

Review 2.  The implications of whole-genome sequencing in the control of tuberculosis.

Authors:  Robyn S Lee; Marcel A Behr
Journal:  Ther Adv Infect Dis       Date:  2015-12-30

Review 3.  Whole-genome sequencing targets drug-resistant bacterial infections.

Authors:  N V Punina; N M Makridakis; M A Remnev; A F Topunov
Journal:  Hum Genomics       Date:  2015-08-05       Impact factor: 4.639

4.  The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes.

Authors:  Todd J Treangen; Brian D Ondov; Sergey Koren; Adam M Phillippy
Journal:  Genome Biol       Date:  2014       Impact factor: 13.583

Review 5.  Whole genome sequencing in clinical and public health microbiology.

Authors:  J C Kwong; N McCallum; V Sintchenko; B P Howden
Journal:  Pathology       Date:  2015-04       Impact factor: 5.306

Review 6.  Next-generation sequencing technologies and their application to the study and control of bacterial infections.

Authors:  J Besser; H A Carleton; P Gerner-Smidt; R L Lindsey; E Trees
Journal:  Clin Microbiol Infect       Date:  2017-10-23       Impact factor: 8.067

Review 7.  Best practices for evaluating single nucleotide variant calling methods for microbial genomics.

Authors:  Nathan D Olson; Steven P Lund; Rebecca E Colman; Jeffrey T Foster; Jason W Sahl; James M Schupp; Paul Keim; Jayne B Morrow; Marc L Salit; Justin M Zook
Journal:  Front Genet       Date:  2015-07-07       Impact factor: 4.599

8.  Early insights into the potential of the Oxford Nanopore MinION for the detection of antimicrobial resistance genes.

Authors:  Kim Judge; Simon R Harris; Sandra Reuter; Julian Parkhill; Sharon J Peacock
Journal:  J Antimicrob Chemother       Date:  2015-07-28       Impact factor: 5.790

9.  Rapid single-colony whole-genome sequencing of bacterial pathogens.

Authors:  Claudio U Köser; Louise J Fraser; Avgousta Ioannou; Jennifer Becq; Matthew J Ellington; Matthew T G Holden; Sandra Reuter; M Estée Török; Stephen D Bentley; Julian Parkhill; Niall A Gormley; Geoffrey P Smith; Sharon J Peacock
Journal:  J Antimicrob Chemother       Date:  2013-12-25       Impact factor: 5.790

Review 10.  Whole-genome sequencing to control antimicrobial resistance.

Authors:  Claudio U Köser; Matthew J Ellington; Sharon J Peacock
Journal:  Trends Genet       Date:  2014-08-03       Impact factor: 11.639
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