Literature DB >> 19287448

Application of 'next-generation' sequencing technologies to microbial genetics.

Daniel MacLean1, Jonathan D G Jones, David J Studholme.   

Abstract

New sequencing methods generate data that can allow the assembly of microbial genome sequences in days. With such revolutionary advances in technology come new challenges in methodologies and informatics. In this article, we review the capabilities of high-throughput sequencing technologies and discuss the many options for getting useful information from the data.

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Year:  2009        PMID： 19287448     DOI： 10.1038/nrmicro2122

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


  74 in total

1.  Genome-wide location and function of DNA binding proteins.

Authors:  B Ren; F Robert; J J Wyrick; O Aparicio; E G Jennings; I Simon; J Zeitlinger; J Schreiber; N Hannett; E Kanin; T L Volkert; C J Wilson; S P Bell; R A Young
Journal:  Science       Date:  2000-12-22       Impact factor: 47.728

2.  The generic genome browser: a building block for a model organism system database.

Authors:  Lincoln D Stein; Christopher Mungall; ShengQiang Shu; Michael Caudy; Marco Mangone; Allen Day; Elizabeth Nickerson; Jason E Stajich; Todd W Harris; Adrian Arva; Suzanna Lewis
Journal:  Genome Res       Date:  2002-10       Impact factor: 9.043

3.  Short read fragment assembly of bacterial genomes.

Authors:  Mark J Chaisson; Pavel A Pevzner
Journal:  Genome Res       Date:  2007-12-14       Impact factor: 9.043

4.  De novo assembly of the Pseudomonas syringae pv. syringae B728a genome using Illumina/Solexa short sequence reads.

Authors:  Rhys A Farrer; Eric Kemen; Jonathan D G Jones; David J Studholme
Journal:  FEMS Microbiol Lett       Date:  2008-12-09       Impact factor: 2.742

5.  Mapping short DNA sequencing reads and calling variants using mapping quality scores.

Authors:  Heng Li; Jue Ruan; Richard Durbin
Journal:  Genome Res       Date:  2008-08-19       Impact factor: 9.043

Review 6.  Microbiology in the post-genomic era.

Authors:  Duccio Medini; Davide Serruto; Julian Parkhill; David A Relman; Claudio Donati; Richard Moxon; Stanley Falkow; Rino Rappuoli
Journal:  Nat Rev Microbiol       Date:  2008-05-13       Impact factor: 60.633

7.  High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi.

Authors:  Kathryn E Holt; Julian Parkhill; Camila J Mazzoni; Philippe Roumagnac; François-Xavier Weill; Ian Goodhead; Richard Rance; Stephen Baker; Duncan J Maskell; John Wain; Christiane Dolecek; Mark Achtman; Gordon Dougan
Journal:  Nat Genet       Date:  2008-07-27       Impact factor: 38.330

8.  ALLPATHS: de novo assembly of whole-genome shotgun microreads.

Authors:  Jonathan Butler; Iain MacCallum; Michael Kleber; Ilya A Shlyakhter; Matthew K Belmonte; Eric S Lander; Chad Nusbaum; David B Jaffe
Journal:  Genome Res       Date:  2008-03-13       Impact factor: 9.043

9.  Genome-wide mapping of in vivo protein-DNA interactions.

Authors:  David S Johnson; Ali Mortazavi; Richard M Myers; Barbara Wold
Journal:  Science       Date:  2007-05-31       Impact factor: 47.728

10.  PatMaN: rapid alignment of short sequences to large databases.

Authors:  Kay Prüfer; Udo Stenzel; Michael Dannemann; Richard E Green; Michael Lachmann; Janet Kelso
Journal:  Bioinformatics       Date:  2008-05-08       Impact factor: 6.937
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  120 in total

1.  Comparison of large-insert, small-insert and pyrosequencing libraries for metagenomic analysis.

Authors:  Thomas Danhorn; Curtis R Young; Edward F DeLong
Journal:  ISME J       Date:  2012-04-26       Impact factor: 10.302

2.  Normal and compound poisson approximations for pattern occurrences in NGS reads.

Authors:  Zhiyuan Zhai; Gesine Reinert; Kai Song; Michael S Waterman; Yihui Luan; Fengzhu Sun
Journal:  J Comput Biol       Date:  2012-06       Impact factor: 1.479

Review 3.  Advantages and limitations of current network inference methods.

Authors:  Riet De Smet; Kathleen Marchal
Journal:  Nat Rev Microbiol       Date:  2010-08-31       Impact factor: 60.633

Review 4.  Engineering ecosystems and synthetic ecologies.

Authors:  Michael T Mee; Harris H Wang
Journal:  Mol Biosyst       Date:  2012-10

Review 5.  Mass spectrometry tools for the classification and identification of bacteria.

Authors:  Sascha Sauer; Magdalena Kliem
Journal:  Nat Rev Microbiol       Date:  2010-01       Impact factor: 60.633

6.  Quantitative phenotyping via deep barcode sequencing.

Authors:  Andrew M Smith; Lawrence E Heisler; Joseph Mellor; Fiona Kaper; Michael J Thompson; Mark Chee; Frederick P Roth; Guri Giaever; Corey Nislow
Journal:  Genome Res       Date:  2009-07-21       Impact factor: 9.043

7.  Effect of the Organic Loading Rate Increase and the Presence of Zeolite on Microbial Community Composition and Process Stability During Anaerobic Digestion of Chicken Wastes.

Authors:  Elvira E Ziganshina; Dmitry E Belostotskiy; Olga N Ilinskaya; Eugenia A Boulygina; Tatiana V Grigoryeva; Ayrat M Ziganshin
Journal:  Microb Ecol       Date:  2015-06-05       Impact factor: 4.552

8.  Complete genome sequence of Bacillus amyloliquefaciens TA208, a strain for industrial production of guanosine and ribavirin.

Authors:  Guoqiang Zhang; Aihua Deng; Qingyang Xu; Yong Liang; Ning Chen; Tingyi Wen
Journal:  J Bacteriol       Date:  2011-04-22       Impact factor: 3.490

9.  Molecular complexity of successive bacterial epidemics deconvoluted by comparative pathogenomics.

Authors:  Stephen B Beres; Ronan K Carroll; Patrick R Shea; Izabela Sitkiewicz; Juan Carlos Martinez-Gutierrez; Donald E Low; Allison McGeer; Barbara M Willey; Karen Green; Gregory J Tyrrell; Thomas D Goldman; Michael Feldgarden; Bruce W Birren; Yuriy Fofanov; John Boos; William D Wheaton; Christiane Honisch; James M Musser
Journal:  Proc Natl Acad Sci U S A       Date:  2010-02-08       Impact factor: 11.205

10.  Titanium Ions Inhibit the Bacteria in Vase Solutions of Freshly Cut Gerbera jamesonii and Extend the Flower Longevity.

Authors:  Cai-Xia Li; Yan-Fen Fan; Wei Luan; Ya Dai; Ming-Xiu Wang; Chun-Mei Wei; Yan Wang; Xiang Tao; Ping Mao; Xin-Rong Ma
Journal:  Microb Ecol       Date:  2018-10-24       Impact factor: 4.552
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