Literature DB >> 19844227

Next-generation gap.

John D McPherson1.   

Abstract

There is a growing gap between the generation of massively parallel sequencing output and the ability to process and analyze the resulting data. New users are left to navigate a bewildering maze of base calling, alignment, assembly and analysis tools with often incomplete documentation and no idea how to compare and validate their outputs. Bridging this gap is essential, or the coveted $1,000 genome will come with a $20,000 analysis price tag.

Mesh:

Year:  2009        PMID: 19844227     DOI: 10.1038/nmeth.f.268

Source DB:  PubMed          Journal:  Nat Methods        ISSN: 1548-7091            Impact factor:   28.547


  29 in total

1.  The human genome browser at UCSC.

Authors:  W James Kent; Charles W Sugnet; Terrence S Furey; Krishna M Roskin; Tom H Pringle; Alan M Zahler; David Haussler
Journal:  Genome Res       Date:  2002-06       Impact factor: 9.043

2.  A Sanger/pyrosequencing hybrid approach for the generation of high-quality draft assemblies of marine microbial genomes.

Authors:  Susanne M D Goldberg; Justin Johnson; Dana Busam; Tamara Feldblyum; Steve Ferriera; Robert Friedman; Aaron Halpern; Hoda Khouri; Saul A Kravitz; Federico M Lauro; Kelvin Li; Yu-Hui Rogers; Robert Strausberg; Granger Sutton; Luke Tallon; Torsten Thomas; Eli Venter; Marvin Frazier; J Craig Venter
Journal:  Proc Natl Acad Sci U S A       Date:  2006-07-13       Impact factor: 11.205

3.  Automating resequencing-based detection of insertion-deletion polymorphisms.

Authors:  Tushar R Bhangale; Matthew Stephens; Deborah A Nickerson
Journal:  Nat Genet       Date:  2006-11-19       Impact factor: 38.330

Review 4.  Next-generation DNA sequencing methods.

Authors:  Elaine R Mardis
Journal:  Annu Rev Genomics Hum Genet       Date:  2008       Impact factor: 8.929

5.  Mapping and quantifying mammalian transcriptomes by RNA-Seq.

Authors:  Ali Mortazavi; Brian A Williams; Kenneth McCue; Lorian Schaeffer; Barbara Wold
Journal:  Nat Methods       Date:  2008-05-30       Impact factor: 28.547

Review 6.  Sense from sequence reads: methods for alignment and assembly.

Authors:  Paul Flicek; Ewan Birney
Journal:  Nat Methods       Date:  2009-11       Impact factor: 28.547

Review 7.  Computational methods for discovering structural variation with next-generation sequencing.

Authors:  Paul Medvedev; Monica Stanciu; Michael Brudno
Journal:  Nat Methods       Date:  2009-11       Impact factor: 28.547

8.  A physical map of the human genome.

Authors:  J D McPherson; M Marra; L Hillier; R H Waterston; A Chinwalla; J Wallis; M Sekhon; K Wylie; E R Mardis; R K Wilson; R Fulton; T A Kucaba; C Wagner-McPherson; W B Barbazuk; S G Gregory; S J Humphray; L French; R S Evans; G Bethel; A Whittaker; J L Holden; O T McCann; A Dunham; C Soderlund; C E Scott; D R Bentley; G Schuler; H C Chen; W Jang; E D Green; J R Idol; V V Maduro; K T Montgomery; E Lee; A Miller; S Emerling; R Gibbs; S Scherer; J H Gorrell; E Sodergren; K Clerc-Blankenburg; P Tabor; S Naylor; D Garcia; P J de Jong; J J Catanese; N Nowak; K Osoegawa; S Qin; L Rowen; A Madan; M Dors; L Hood; B Trask; C Friedman; H Massa; V G Cheung; I R Kirsch; T Reid; R Yonescu; J Weissenbach; T Bruls; R Heilig; E Branscomb; A Olsen; N Doggett; J F Cheng; T Hawkins; R M Myers; J Shang; L Ramirez; J Schmutz; O Velasquez; K Dixon; N E Stone; D R Cox; D Haussler; W J Kent; T Furey; S Rogic; S Kennedy; S Jones; A Rosenthal; G Wen; M Schilhabel; G Gloeckner; G Nyakatura; R Siebert; B Schlegelberger; J Korenberg; X N Chen; A Fujiyama; M Hattori; A Toyoda; T Yada; H S Park; Y Sakaki; N Shimizu; S Asakawa; K Kawasaki; T Sasaki; A Shintani; A Shimizu; K Shibuya; J Kudoh; S Minoshima; J Ramser; P Seranski; C Hoff; A Poustka; R Reinhardt; H Lehrach
Journal:  Nature       Date:  2001-02-15       Impact factor: 49.962

9.  Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing.

Authors:  Gordon Robertson; Martin Hirst; Matthew Bainbridge; Misha Bilenky; Yongjun Zhao; Thomas Zeng; Ghia Euskirchen; Bridget Bernier; Richard Varhol; Allen Delaney; Nina Thiessen; Obi L Griffith; Ann He; Marco Marra; Michael Snyder; Steven Jones
Journal:  Nat Methods       Date:  2007-06-11       Impact factor: 28.547

10.  The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing.

Authors:  Jonas Binladen; M Thomas P Gilbert; Jonathan P Bollback; Frank Panitz; Christian Bendixen; Rasmus Nielsen; Eske Willerslev
Journal:  PLoS One       Date:  2007-02-14       Impact factor: 3.240

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  55 in total

Review 1.  RNA-Seq and human complex diseases: recent accomplishments and future perspectives.

Authors:  Valerio Costa; Marianna Aprile; Roberta Esposito; Alfredo Ciccodicola
Journal:  Eur J Hum Genet       Date:  2012-06-27       Impact factor: 4.246

Review 2.  Next-generation sequencing techniques for eukaryotic microorganisms: sequencing-based solutions to biological problems.

Authors:  Minou Nowrousian
Journal:  Eukaryot Cell       Date:  2010-07-02

3.  ParMap, an algorithm for the identification of small genomic insertions and deletions in nextgen sequencing data.

Authors:  Hossein Khiabanian; Pieter Van Vlierberghe; Teresa Palomero; Adolfo A Ferrando; Raul Rabadan
Journal:  BMC Res Notes       Date:  2010-05-27

4.  High-throughput molecular diagnosis of von Willebrand disease by next generation sequencing methods.

Authors:  Irene Corrales; Susana Catarino; Júlia Ayats; David Arteta; Carmen Altisent; Rafael Parra; Francisco Vidal
Journal:  Haematologica       Date:  2012-02-07       Impact factor: 9.941

Review 5.  Cardiovascular genomics: a biomarker identification pipeline.

Authors:  John H Phan; Chang F Quo; May Dongmei Wang
Journal:  IEEE Trans Inf Technol Biomed       Date:  2012-05-16

6.  Next generation sequencing in research and diagnostics of ocular birth defects.

Authors:  Gordana Raca; Craig Jackson; Berta Warman; Tom Bair; Lisa A Schimmenti
Journal:  Mol Genet Metab       Date:  2010-03-15       Impact factor: 4.797

Review 7.  Mechanisms of specificity in neuronal activity-regulated gene transcription.

Authors:  Michelle R Lyons; Anne E West
Journal:  Prog Neurobiol       Date:  2011-05-18       Impact factor: 11.685

Review 8.  Genome studies at the PAG 2011 conference.

Authors:  R Appels; D L Adelson; P Moolhuijzen; H Webster; R Barrero; M Bellgard
Journal:  Funct Integr Genomics       Date:  2011-03-01       Impact factor: 3.410

9.  Ray Meta: scalable de novo metagenome assembly and profiling.

Authors:  Sébastien Boisvert; Frédéric Raymond; Elénie Godzaridis; François Laviolette; Jacques Corbeil
Journal:  Genome Biol       Date:  2012-12-22       Impact factor: 13.583

Review 10.  Uncovering the complexity of transcriptomes with RNA-Seq.

Authors:  Valerio Costa; Claudia Angelini; Italia De Feis; Alfredo Ciccodicola
Journal:  J Biomed Biotechnol       Date:  2010-06-27
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