Literature DB >> 19483690

MoDIL: detecting small indels from clone-end sequencing with mixtures of distributions.

Seunghak Lee, Fereydoun Hormozdiari, Can Alkan, Michael Brudno.   

Abstract

Mesh:

Year:  2009        PMID: 19483690     DOI: 10.1038/nmeth.f.256

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


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  6 in total

1.  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

2.  An initial map of insertion and deletion (INDEL) variation in the human genome.

Authors:  Ryan E Mills; Christopher T Luttig; Christine E Larkins; Adam Beauchamp; Circe Tsui; W Stephen Pittard; Scott E Devine
Journal:  Genome Res       Date:  2006-08-10       Impact factor: 9.043

3.  A robust framework for detecting structural variations in a genome.

Authors:  Seunghak Lee; Elango Cheran; Michael Brudno
Journal:  Bioinformatics       Date:  2008-07-01       Impact factor: 6.937

4.  Mapping and sequencing of structural variation from eight human genomes.

Authors:  Jeffrey M Kidd; Gregory M Cooper; William F Donahue; Hillary S Hayden; Nick Sampas; Tina Graves; Nancy Hansen; Brian Teague; Can Alkan; Francesca Antonacci; Eric Haugen; Troy Zerr; N Alice Yamada; Peter Tsang; Tera L Newman; Eray Tüzün; Ze Cheng; Heather M Ebling; Nadeem Tusneem; Robert David; Will Gillett; Karen A Phelps; Molly Weaver; David Saranga; Adrianne Brand; Wei Tao; Erik Gustafson; Kevin McKernan; Lin Chen; Maika Malig; Joshua D Smith; Joshua M Korn; Steven A McCarroll; David A Altshuler; Daniel A Peiffer; Michael Dorschner; John Stamatoyannopoulos; David Schwartz; Deborah A Nickerson; James C Mullikin; Richard K Wilson; Laurakay Bruhn; Maynard V Olson; Rajinder Kaul; Douglas R Smith; Evan E Eichler
Journal:  Nature       Date:  2008-05-01       Impact factor: 49.962

5.  PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data.

Authors:  Jan O Korbel; Alexej Abyzov; Xinmeng Jasmine Mu; Nicholas Carriero; Philip Cayting; Zhengdong Zhang; Michael Snyder; Mark B Gerstein
Journal:  Genome Biol       Date:  2009-02-23       Impact factor: 13.583

6.  Accurate whole human genome sequencing using reversible terminator chemistry.

Authors:  David R Bentley; Shankar Balasubramanian; Harold P Swerdlow; Geoffrey P Smith; John Milton; Clive G Brown; Kevin P Hall; Dirk J Evers; Colin L Barnes; Helen R Bignell; Jonathan M Boutell; Jason Bryant; Richard J Carter; R Keira Cheetham; Anthony J Cox; Darren J Ellis; Michael R Flatbush; Niall A Gormley; Sean J Humphray; Leslie J Irving; Mirian S Karbelashvili; Scott M Kirk; Heng Li; Xiaohai Liu; Klaus S Maisinger; Lisa J Murray; Bojan Obradovic; Tobias Ost; Michael L Parkinson; Mark R Pratt; Isabelle M J Rasolonjatovo; Mark T Reed; Roberto Rigatti; Chiara Rodighiero; Mark T Ross; Andrea Sabot; Subramanian V Sankar; Aylwyn Scally; Gary P Schroth; Mark E Smith; Vincent P Smith; Anastassia Spiridou; Peta E Torrance; Svilen S Tzonev; Eric H Vermaas; Klaudia Walter; Xiaolin Wu; Lu Zhang; Mohammed D Alam; Carole Anastasi; Ify C Aniebo; David M D Bailey; Iain R Bancarz; Saibal Banerjee; Selena G Barbour; Primo A Baybayan; Vincent A Benoit; Kevin F Benson; Claire Bevis; Phillip J Black; Asha Boodhun; Joe S Brennan; John A Bridgham; Rob C Brown; Andrew A Brown; Dale H Buermann; Abass A Bundu; James C Burrows; Nigel P Carter; Nestor Castillo; Maria Chiara E Catenazzi; Simon Chang; R Neil Cooley; Natasha R Crake; Olubunmi O Dada; Konstantinos D Diakoumakos; Belen Dominguez-Fernandez; David J Earnshaw; Ugonna C Egbujor; David W Elmore; Sergey S Etchin; Mark R Ewan; Milan Fedurco; Louise J Fraser; Karin V Fuentes Fajardo; W Scott Furey; David George; Kimberley J Gietzen; Colin P Goddard; George S Golda; Philip A Granieri; David E Green; David L Gustafson; Nancy F Hansen; Kevin Harnish; Christian D Haudenschild; Narinder I Heyer; Matthew M Hims; Johnny T Ho; Adrian M Horgan; Katya Hoschler; Steve Hurwitz; Denis V Ivanov; Maria Q Johnson; Terena James; T A Huw Jones; Gyoung-Dong Kang; Tzvetana H Kerelska; Alan D Kersey; Irina Khrebtukova; Alex P Kindwall; Zoya Kingsbury; Paula I Kokko-Gonzales; Anil Kumar; Marc A Laurent; Cynthia T Lawley; Sarah E Lee; Xavier Lee; Arnold K Liao; Jennifer A Loch; Mitch Lok; Shujun Luo; Radhika M Mammen; John W Martin; Patrick G McCauley; Paul McNitt; Parul Mehta; Keith W Moon; Joe W Mullens; Taksina Newington; Zemin Ning; Bee Ling Ng; Sonia M Novo; Michael J O'Neill; Mark A Osborne; Andrew Osnowski; Omead Ostadan; Lambros L Paraschos; Lea Pickering; Andrew C Pike; Alger C Pike; D Chris Pinkard; Daniel P Pliskin; Joe Podhasky; Victor J Quijano; Come Raczy; Vicki H Rae; Stephen R Rawlings; Ana Chiva Rodriguez; Phyllida M Roe; John Rogers; Maria C Rogert Bacigalupo; Nikolai Romanov; Anthony Romieu; Rithy K Roth; Natalie J Rourke; Silke T Ruediger; Eli Rusman; Raquel M Sanches-Kuiper; Martin R Schenker; Josefina M Seoane; Richard J Shaw; Mitch K Shiver; Steven W Short; Ning L Sizto; Johannes P Sluis; Melanie A Smith; Jean Ernest Sohna Sohna; Eric J Spence; Kim Stevens; Neil Sutton; Lukasz Szajkowski; Carolyn L Tregidgo; Gerardo Turcatti; Stephanie Vandevondele; Yuli Verhovsky; Selene M Virk; Suzanne Wakelin; Gregory C Walcott; Jingwen Wang; Graham J Worsley; Juying Yan; Ling Yau; Mike Zuerlein; Jane Rogers; James C Mullikin; Matthew E Hurles; Nick J McCooke; John S West; Frank L Oaks; Peter L Lundberg; David Klenerman; Richard Durbin; Anthony J Smith
Journal:  Nature       Date:  2008-11-06       Impact factor: 49.962

  6 in total
  61 in total

1.  Simultaneous structural variation discovery among multiple paired-end sequenced genomes.

Authors:  Fereydoun Hormozdiari; Iman Hajirasouliha; Andrew McPherson; Evan E Eichler; S Cenk Sahinalp
Journal:  Genome Res       Date:  2011-11-02       Impact factor: 9.043

2.  Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome.

Authors:  Aaron R Quinlan; Royden A Clark; Svetlana Sokolova; Mitchell L Leibowitz; Yujun Zhang; Matthew E Hurles; Joshua C Mell; Ira M Hall
Journal:  Genome Res       Date:  2010-03-22       Impact factor: 9.043

3.  Savant: genome browser for high-throughput sequencing data.

Authors:  Marc Fiume; Vanessa Williams; Andrew Brook; Michael Brudno
Journal:  Bioinformatics       Date:  2010-06-20       Impact factor: 6.937

Review 4.  Annotating non-coding regions of the genome.

Authors:  Roger P Alexander; Gang Fang; Joel Rozowsky; Michael Snyder; Mark B Gerstein
Journal:  Nat Rev Genet       Date:  2010-07-13       Impact factor: 53.242

Review 5.  Detecting structural variations in the human genome using next generation sequencing.

Authors:  Ruibin Xi; Tae-Min Kim; Peter J Park
Journal:  Brief Funct Genomics       Date:  2011-01-06       Impact factor: 4.241

6.  Hybrid capture and next-generation sequencing identify viral integration sites from formalin-fixed, paraffin-embedded tissue.

Authors:  Eric J Duncavage; Vincent Magrini; Nils Becker; Jon R Armstrong; Ryan T Demeter; Todd Wylie; Haley J Abel; John D Pfeifer
Journal:  J Mol Diagn       Date:  2011-05       Impact factor: 5.568

7.  MATE-CLEVER: Mendelian-inheritance-aware discovery and genotyping of midsize and long indels.

Authors:  Tobias Marschall; Iman Hajirasouliha; Alexander Schönhuth
Journal:  Bioinformatics       Date:  2013-09-25       Impact factor: 6.937

Review 8.  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

9.  Metabolomics technology and bioinformatics for precision medicine.

Authors:  Rajeev K Azad; Vladimir Shulaev
Journal:  Brief Bioinform       Date:  2019-11-27       Impact factor: 11.622

10.  Detecting highly differentiated copy-number variants from pooled population sequencing.

Authors:  Daniel R Schrider; David J Begun; Matthew W Hahn
Journal:  Pac Symp Biocomput       Date:  2013
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