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Literature DB >> 23979431

What has high-throughput sequencing ever done for us?

Abstract

This month's Genome Watch looks back over the past 10 years and highlights how the incredible advances in sequencing technologies have transformed research into microbial genomes.

Mesh：

Year: 2013 PMID： 23979431 DOI： 10.1038/nrmicro3112

Source DB: PubMed Journal: Nat Rev Microbiol ISSN： 1740-1526 Impact factor: 60.633

10 in total

1. Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica.

Authors: Julian Parkhill; Mohammed Sebaihia; Andrew Preston; Lee D Murphy; Nicholas Thomson; David E Harris; Matthew T G Holden; Carol M Churcher; Stephen D Bentley; Karen L Mungall; Ana M Cerdeño-Tárraga; Louise Temple; Keith James; Barbara Harris; Michael A Quail; Mark Achtman; Rebecca Atkin; Steven Baker; David Basham; Nathalie Bason; Inna Cherevach; Tracey Chillingworth; Matthew Collins; Anne Cronin; Paul Davis; Jonathan Doggett; Theresa Feltwell; Arlette Goble; Nancy Hamlin; Heidi Hauser; Simon Holroyd; Kay Jagels; Sampsa Leather; Sharon Moule; Halina Norberczak; Susan O'Neil; Doug Ormond; Claire Price; Ester Rabbinowitsch; Simon Rutter; Mandy Sanders; David Saunders; Katherine Seeger; Sarah Sharp; Mark Simmonds; Jason Skelton; Robert Squares; Steven Squares; Kim Stevens; Louise Unwin; Sally Whitehead; Bart G Barrell; Duncan J Maskell
Journal: Nat Genet Date: 2003-08-10 Impact factor: 38.330

2. Community structure and metabolism through reconstruction of microbial genomes from the environment.

Authors: Gene W Tyson; Jarrod Chapman; Philip Hugenholtz; Eric E Allen; Rachna J Ram; Paul M Richardson; Victor V Solovyev; Edward M Rubin; Daniel S Rokhsar; Jillian F Banfield
Journal: Nature Date: 2004-02-01 Impact factor: 49.962

3. Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli.

Authors: R A Welch; V Burland; G Plunkett; P Redford; P Roesch; D Rasko; E L Buckles; S-R Liou; A Boutin; J Hackett; D Stroud; G F Mayhew; D J Rose; S Zhou; D C Schwartz; N T Perna; H L T Mobley; M S Donnenberg; F R Blattner
Journal: Proc Natl Acad Sci U S A Date: 2002-12-05 Impact factor: 11.205

4. A metagenome-wide association study of gut microbiota in type 2 diabetes.

Authors: Junjie Qin; Yingrui Li; Zhiming Cai; Shenghui Li; Jianfeng Zhu; Fan Zhang; Suisha Liang; Wenwei Zhang; Yuanlin Guan; Dongqian Shen; Yangqing Peng; Dongya Zhang; Zhuye Jie; Wenxian Wu; Youwen Qin; Wenbin Xue; Junhua Li; Lingchuan Han; Donghui Lu; Peixian Wu; Yali Dai; Xiaojuan Sun; Zesong Li; Aifa Tang; Shilong Zhong; Xiaoping Li; Weineng Chen; Ran Xu; Mingbang Wang; Qiang Feng; Meihua Gong; Jing Yu; Yanyan Zhang; Ming Zhang; Torben Hansen; Gaston Sanchez; Jeroen Raes; Gwen Falony; Shujiro Okuda; Mathieu Almeida; Emmanuelle LeChatelier; Pierre Renault; Nicolas Pons; Jean-Michel Batto; Zhaoxi Zhang; Hua Chen; Ruifu Yang; Weimou Zheng; Songgang Li; Huanming Yang; Jian Wang; S Dusko Ehrlich; Rasmus Nielsen; Oluf Pedersen; Karsten Kristiansen; Jun Wang
Journal: Nature Date: 2012-09-26 Impact factor: 49.962

5. Comparative genome sequencing for discovery of novel polymorphisms in Bacillus anthracis.

Authors: Timothy D Read; Steven L Salzberg; Mihai Pop; Martin Shumway; Lowell Umayam; Lingxia Jiang; Erik Holtzapple; Joseph D Busch; Kimothy L Smith; James M Schupp; Daniel Solomon; Paul Keim; Claire M Fraser
Journal: Science Date: 2002-05-09 Impact factor: 47.728

6. The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria.

Authors: Timothy D Read; Scott N Peterson; Nicolas Tourasse; Les W Baillie; Ian T Paulsen; Karen E Nelson; Hervé Tettelin; Derrick E Fouts; Jonathan A Eisen; Steven R Gill; Erik K Holtzapple; Ole Andreas Okstad; Erlendur Helgason; Jennifer Rilstone; Martin Wu; James F Kolonay; Maureen J Beanan; Robert J Dodson; Lauren M Brinkac; Michelle Gwinn; Robert T DeBoy; Ramana Madpu; Sean C Daugherty; A Scott Durkin; Daniel H Haft; William C Nelson; Jeremy D Peterson; Mihai Pop; Hoda M Khouri; Diana Radune; Jonathan L Benton; Yasmin Mahamoud; Lingxia Jiang; Ioana R Hance; Janice F Weidman; Kristi J Berry; Roger D Plaut; Alex M Wolf; Kisha L Watkins; William C Nierman; Alyson Hazen; Robin Cline; Caroline Redmond; Joanne E Thwaite; Owen White; Steven L Salzberg; Brendan Thomason; Arthur M Friedlander; Theresa M Koehler; Philip C Hanna; Anne-Brit Kolstø; Claire M Fraser
Journal: Nature Date: 2003-05-01 Impact factor: 49.962

7. Complete genome sequence of the oral pathogenic Bacterium porphyromonas gingivalis strain W83.

Authors: Karen E Nelson; Robert D Fleischmann; Robert T DeBoy; Ian T Paulsen; Derrick E Fouts; Jonathan A Eisen; Sean C Daugherty; Robert J Dodson; A Scott Durkin; Michelle Gwinn; Daniel H Haft; James F Kolonay; William C Nelson; Tanya Mason; Luke Tallon; Jessica Gray; David Granger; Hervé Tettelin; Hong Dong; Jamie L Galvin; Margaret J Duncan; Floyd E Dewhirst; Claire M Fraser
Journal: J Bacteriol Date: 2003-09 Impact factor: 3.490

8. Genome of the pathogen Porphyromonas gingivalis recovered from a biofilm in a hospital sink using a high-throughput single-cell genomics platform.

Authors: Jeffrey S McLean; Mary-Jane Lombardo; Michael G Ziegler; Mark Novotny; Joyclyn Yee-Greenbaum; Jonathan H Badger; Glenn Tesler; Sergey Nurk; Valery Lesin; Daniel Brami; Adam P Hall; Anna Edlund; Lisa Z Allen; Scott Durkin; Sharon Reed; Francesca Torriani; Kenneth H Nealson; Pavel A Pevzner; Robert Friedman; J Craig Venter; Roger S Lasken
Journal: Genome Res Date: 2013-04-05 Impact factor: 9.043

9. 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

10. Emergence and global spread of epidemic healthcare-associated Clostridium difficile.

Authors: Miao He; Fabio Miyajima; Paul Roberts; Louise Ellison; Derek J Pickard; Melissa J Martin; Thomas R Connor; Simon R Harris; Derek Fairley; Kathleen B Bamford; Stephanie D'Arc; Jon Brazier; Derek Brown; John E Coia; Gill Douce; Dale Gerding; Hee Jung Kim; Tse Hsien Koh; Haru Kato; Mitsutoshi Senoh; Tom Louie; Stephen Michell; Emma Butt; Sharon J Peacock; Nick M Brown; Tom Riley; Glen Songer; Mark Wilcox; Munir Pirmohamed; Ed Kuijper; Peter Hawkey; Brendan W Wren; Gordon Dougan; Julian Parkhill; Trevor D Lawley
Journal: Nat Genet Date: 2012-12-09 Impact factor: 38.330

10 in total

7 in total

What has high-throughput sequencing ever done for us?

1. Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica.

2. Community structure and metabolism through reconstruction of microbial genomes from the environment.

3. Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli.

4. A metagenome-wide association study of gut microbiota in type 2 diabetes.

5. Comparative genome sequencing for discovery of novel polymorphisms in Bacillus anthracis.

6. The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria.

7. Complete genome sequence of the oral pathogenic Bacterium porphyromonas gingivalis strain W83.

8. Genome of the pathogen Porphyromonas gingivalis recovered from a biofilm in a hospital sink using a high-throughput single-cell genomics platform.

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

10. Emergence and global spread of epidemic healthcare-associated Clostridium difficile.

Review 1. From local structure to a global framework: recognition of protein folds.

Review 2. The gut microbiome, diet, and links to cardiometabolic and chronic disorders.

Review 3. Twenty years of bacterial genome sequencing.

Review 4. Proteomic tools to decipher microbial community structure and functioning.

5. Metagenomic analyses of bacteria on human hairs: a qualitative assessment for applications in forensic science.

6. BMX: a tool for computing bacterial phyletic composition from orthologous maps.

Review 7. A Robust Framework for Microbial Archaeology.