Literature DB >> 23138308

The expanding scope of DNA sequencing.

Jay Shendure1, Erez Lieberman Aiden.   

Abstract

In just seven years, next-generation technologies have reduced the cost and increased the speed of DNA sequencing by four orders of magnitude, and experiments requiring many millions of sequencing reads are now routine. In research, sequencing is being applied not only to assemble genomes and to investigate the genetic basis of human disease, but also to explore myriad phenomena in organismic and cellular biology. In the clinic, the utility of sequence data is being intensively evaluated in diverse contexts, including reproductive medicine, oncology and infectious disease. A recurrent theme in the development of new sequencing applications is the creative 'recombination' of existing experimental building blocks. However, there remain many potentially high-impact applications of next-generation DNA sequencing that are not yet fully realized.

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Year:  2012        PMID: 23138308      PMCID: PMC4149750          DOI: 10.1038/nbt.2421

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


  139 in total

1.  Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming.

Authors:  Jie Deng; Robert Shoemaker; Bin Xie; Athurva Gore; Emily M LeProust; Jessica Antosiewicz-Bourget; Dieter Egli; Nimet Maherali; In-Hyun Park; Junying Yu; George Q Daley; Kevin Eggan; Konrad Hochedlinger; James Thomson; Wei Wang; Yuan Gao; Kun Zhang
Journal:  Nat Biotechnol       Date:  2009-03-29       Impact factor: 54.908

2.  Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts.

Authors:  Jeremy R Sanford; Xin Wang; Matthew Mort; Natalia Vanduyn; David N Cooper; Sean D Mooney; Howard J Edenberg; Yunlong Liu
Journal:  Genome Res       Date:  2008-12-30       Impact factor: 9.043

3.  Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling.

Authors:  Nicholas T Ingolia; Sina Ghaemmaghami; John R S Newman; Jonathan S Weissman
Journal:  Science       Date:  2009-02-12       Impact factor: 47.728

4.  Comprehensive polymorphism survey elucidates population structure of Saccharomyces cerevisiae.

Authors:  Joseph Schacherer; Joshua A Shapiro; Douglas M Ruderfer; Leonid Kruglyak
Journal:  Nature       Date:  2009-02-11       Impact factor: 49.962

5.  Public clonotype usage identifies protective Gag-specific CD8+ T cell responses in SIV infection.

Authors:  David A Price; Tedi E Asher; Nancy A Wilson; Martha C Nason; Jason M Brenchley; Ian S Metzler; Vanessa Venturi; Emma Gostick; Pratip K Chattopadhyay; Mario Roederer; Miles P Davenport; David I Watkins; Daniel C Douek
Journal:  J Exp Med       Date:  2009-04-06       Impact factor: 14.307

6.  Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing.

Authors:  Andreas Gnirke; Alexandre Melnikov; Jared Maguire; Peter Rogov; Emily M LeProust; William Brockman; Timothy Fennell; Georgia Giannoukos; Sheila Fisher; Carsten Russ; Stacey Gabriel; David B Jaffe; Eric S Lander; Chad Nusbaum
Journal:  Nat Biotechnol       Date:  2009-02-01       Impact factor: 54.908

7.  A core gut microbiome in obese and lean twins.

Authors:  Peter J Turnbaugh; Micah Hamady; Tanya Yatsunenko; Brandi L Cantarel; Alexis Duncan; Ruth E Ley; Mitchell L Sogin; William J Jones; Bruce A Roe; Jason P Affourtit; Michael Egholm; Bernard Henrissat; Andrew C Heath; Rob Knight; Jeffrey I Gordon
Journal:  Nature       Date:  2008-11-30       Impact factor: 49.962

8.  Virus-free induction of pluripotency and subsequent excision of reprogramming factors.

Authors:  Keisuke Kaji; Katherine Norrby; Agnieszka Paca; Maria Mileikovsky; Paria Mohseni; Knut Woltjen
Journal:  Nature       Date:  2009-03-01       Impact factor: 49.962

9.  Analysis of combinatorial cis-regulation in synthetic and genomic promoters.

Authors:  Jason Gertz; Eric D Siggia; Barak A Cohen
Journal:  Nature       Date:  2008-11-23       Impact factor: 49.962

10.  Global mapping of protein-DNA interactions in vivo by digital genomic footprinting.

Authors:  Jay R Hesselberth; Xiaoyu Chen; Zhihong Zhang; Peter J Sabo; Richard Sandstrom; Alex P Reynolds; Robert E Thurman; Shane Neph; Michael S Kuehn; William S Noble; Stanley Fields; John A Stamatoyannopoulos
Journal:  Nat Methods       Date:  2009-03-22       Impact factor: 28.547

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  106 in total

1.  RAD Capture (Rapture): Flexible and Efficient Sequence-Based Genotyping.

Authors:  Omar A Ali; Sean M O'Rourke; Stephen J Amish; Mariah H Meek; Gordon Luikart; Carson Jeffres; Michael R Miller
Journal:  Genetics       Date:  2015-12-29       Impact factor: 4.562

Review 2.  Applications of high-throughput DNA sequencing to benign hematology.

Authors:  Vijay G Sankaran; Patrick G Gallagher
Journal:  Blood       Date:  2013-09-10       Impact factor: 22.113

Review 3.  Massively parallel sequencing: the new frontier of hematologic genomics.

Authors:  Jill M Johnsen; Deborah A Nickerson; Alex P Reiner
Journal:  Blood       Date:  2013-09-10       Impact factor: 22.113

4.  Mechanisms of bacterial morphogenesis: evolutionary cell biology approaches provide new insights.

Authors:  Chao Jiang; Paul D Caccamo; Yves V Brun
Journal:  Bioessays       Date:  2015-02-09       Impact factor: 4.345

5.  The Global Invertebrate Genomics Alliance (GIGA): developing community resources to study diverse invertebrate genomes.

Authors:  Heather Bracken-Grissom; Allen G Collins; Timothy Collins; Keith Crandall; Daniel Distel; Casey Dunn; Gonzalo Giribet; Steven Haddock; Nancy Knowlton; Mark Martindale; Mónica Medina; Charles Messing; Stephen J O'Brien; Gustav Paulay; Nicolas Putnam; Timothy Ravasi; Greg W Rouse; Joseph F Ryan; Anja Schulze; Gert Wörheide; Maja Adamska; Xavier Bailly; Jesse Breinholt; William E Browne; M Christina Diaz; Nathaniel Evans; Jean-François Flot; Nicole Fogarty; Matthew Johnston; Bishoy Kamel; Akito Y Kawahara; Tammy Laberge; Dennis Lavrov; François Michonneau; Leonid L Moroz; Todd Oakley; Karen Osborne; Shirley A Pomponi; Adelaide Rhodes; Scott R Santos; Nori Satoh; Robert W Thacker; Yves Van de Peer; Christian R Voolstra; David Mark Welch; Judith Winston; Xin Zhou
Journal:  J Hered       Date:  2014 Jan-Feb       Impact factor: 2.645

Review 6.  Emerging tools for synthetic genome design.

Authors:  Bo-Rahm Lee; Suhyung Cho; Yoseb Song; Sun Chang Kim; Byung-Kwan Cho
Journal:  Mol Cells       Date:  2013-05-02       Impact factor: 5.034

7.  Next-generation sequencing: The genome jigsaw.

Authors:  Vivien Marx
Journal:  Nature       Date:  2013-09-12       Impact factor: 49.962

8.  Systematic investigation of cancer-associated somatic point mutations in SNP databases.

Authors:  HyunChul Jung; Thomas Bleazard; Jongkeun Lee; Dongwan Hong
Journal:  Nat Biotechnol       Date:  2013-09       Impact factor: 54.908

9.  Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions.

Authors:  Joshua N Burton; Andrew Adey; Rupali P Patwardhan; Ruolan Qiu; Jacob O Kitzman; Jay Shendure
Journal:  Nat Biotechnol       Date:  2013-11-03       Impact factor: 54.908

Review 10.  Haplotype-resolved genome sequencing: experimental methods and applications.

Authors:  Matthew W Snyder; Andrew Adey; Jacob O Kitzman; Jay Shendure
Journal:  Nat Rev Genet       Date:  2015-05-07       Impact factor: 53.242

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