Nils Homer

Nils Homer

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Nils Homer

Nils Homer

Publications by authors named "Nils Homer"

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An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge.

Authors:
Catherine A Brownstein Alan H Beggs Nils Homer Barry Merriman Timothy W Yu Katherine C Flannery Elizabeth T DeChene Meghan C Towne Sarah K Savage Emily N Price Ingrid A Holm Lovelace J Luquette Elaine Lyon Joseph Majzoub Peter Neupert David McCallie Peter Szolovits Huntington F Willard Nancy J Mendelsohn Renee Temme Richard S Finkel Sabrina W Yum Livija Medne Shamil R Sunyaev Ivan Adzhubey Christopher A Cassa Paul I W de Bakker Hatice Duzkale Piotr Dworzyński William Fairbrother Laurent Francioli Birgit H Funke Monica A Giovanni Robert E Handsaker Kasper Lage Matthew S Lebo Monkol Lek Ignaty Leshchiner Daniel G MacArthur Heather M McLaughlin Michael F Murray Tune H Pers Paz P Polak Soumya Raychaudhuri Heidi L Rehm Rachel Soemedi Nathan O Stitziel Sara Vestecka Jochen Supper Claudia Gugenmus Bernward Klocke Alexander Hahn Max Schubach Mortiz Menzel Saskia Biskup Peter Freisinger Mario Deng Martin Braun Sven Perner Richard J H Smith Janeen L Andorf Jian Huang Kelli Ryckman Val C Sheffield Edwin M Stone Thomas Bair E Ann Black-Ziegelbein Terry A Braun Benjamin Darbro Adam P DeLuca Diana L Kolbe Todd E Scheetz Aiden E Shearer Rama Sompallae Kai Wang Alexander G Bassuk Erik Edens Katherine Mathews Steven A Moore Oleg A Shchelochkov Pamela Trapane Aaron Bossler Colleen A Campbell Jonathan W Heusel Anne Kwitek Tara Maga Karin Panzer Thomas Wassink Douglas Van Daele Hela Azaiez Kevin Booth Nic Meyer Michael M Segal Marc S Williams Gerard Tromp Peter White Donald Corsmeier Sara Fitzgerald-Butt Gail Herman Devon Lamb-Thrush Kim L McBride David Newsom Christopher R Pierson Alexander T Rakowsky Aleš Maver Luca Lovrečić Anja Palandačić Borut Peterlin Ali Torkamani Anna Wedell Mikael Huss Andrey Alexeyenko Jessica M Lindvall Måns Magnusson Daniel Nilsson Henrik Stranneheim Fulya Taylan Christian Gilissen Alexander Hoischen Bregje van Bon Helger Yntema Marcel Nelen Weidong Zhang Jason Sager Lu Zhang Kathryn Blair Deniz Kural Michael Cariaso Greg G Lennon Asif Javed Saloni Agrawal Pauline C Ng Komal S Sandhu Shuba Krishna Vamsi Veeramachaneni Ofer Isakov Eran Halperin Eitan Friedman Noam Shomron Gustavo Glusman Jared C Roach Juan Caballero Hannah C Cox Denise Mauldin Seth A Ament Lee Rowen Daniel R Richards F Anthony San Lucas Manuel L Gonzalez-Garay C Thomas Caskey Yu Bai Ying Huang Fang Fang Yan Zhang Zhengyuan Wang Jorge Barrera Juan M Garcia-Lobo Domingo González-Lamuño Javier Llorca Maria C Rodriguez Ignacio Varela Martin G Reese Francisco M De La Vega Edward Kiruluta Michele Cargill Reece K Hart Jon M Sorenson Gholson J Lyon David A Stevenson Bruce E Bray Barry M Moore Karen Eilbeck Mark Yandell Hongyu Zhao Lin Hou Xiaowei Chen Xiting Yan Mengjie Chen Cong Li Can Yang Murat Gunel Peining Li Yong Kong Austin C Alexander Zayed I Albertyn Kym M Boycott Dennis E Bulman Paul M K Gordon A Micheil Innes Bartha M Knoppers Jacek Majewski Christian R Marshall Jillian S Parboosingh Sarah L Sawyer Mark E Samuels Jeremy Schwartzentruber Isaac S Kohane David M Margulies

Genome Biol 2014 Mar 25;15(3):R53. Epub 2014 Mar 25.

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http://dx.doi.org/10.1186/gb-2014-15-3-r53DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073084PMC
March 2014

Improved variant discovery through local re-alignment of short-read next-generation sequencing data using SRMA.

Genome Biol 2010 8;11(10):R99. Epub 2010 Oct 8.

Department of Computer Science, University of California, Los Angeles, Boelter Hall, Los Angeles, CA 90095, USA.

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http://genomebiology.biomedcentral.com/articles/10.1186/gb-2
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http://dx.doi.org/10.1186/gb-2010-11-10-r99DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3218665PMC
June 2011

A survey of sequence alignment algorithms for next-generation sequencing.

Authors:
Heng Li Nils Homer

Brief Bioinform 2010 Sep 11;11(5):473-83. Epub 2010 May 11.

Broad Institute, Cambridge, MA 02142, USA.

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http://dx.doi.org/10.1093/bib/bbq015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2943993PMC
September 2010

Local alignment of generalized k-base encoded DNA sequence.

BMC Bioinformatics 2010 Jun 24;11:347. Epub 2010 Jun 24.

Department of Computer Science, University of California Los Angeles, Los Angeles, California 90095, USA.

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http://dx.doi.org/10.1186/1471-2105-11-347DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2911458PMC
June 2010

U87MG decoded: the genomic sequence of a cytogenetically aberrant human cancer cell line.

PLoS Genet 2010 Jan 29;6(1):e1000832. Epub 2010 Jan 29.

Department of Human Genetics, University of California Los Angeles, Los Angeles, California, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1000832DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2813426PMC
January 2010

BFAST: an alignment tool for large scale genome resequencing.

PLoS One 2009 Nov 11;4(11):e7767. Epub 2009 Nov 11.

Department of Computer Science, University of California Los Angeles, Los Angeles, CA, USA.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0007767PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2770639PMC
November 2009

The Sequence Alignment/Map format and SAMtools.

Bioinformatics 2009 Aug 8;25(16):2078-9. Epub 2009 Jun 8.

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK, Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA.

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http://dx.doi.org/10.1093/bioinformatics/btp352DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723002PMC
August 2009

Local alignment of two-base encoded DNA sequence.

BMC Bioinformatics 2009 Jun 9;10:175. Epub 2009 Jun 9.

Department of Computer Science, University of California Los Angeles, Los Angeles, California 90095, USA.

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http://www.biomedcentral.com/1471-2105/10/175
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http://dx.doi.org/10.1186/1471-2105-10-175DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2709925PMC
June 2009