Kiran Garimella

Kiran Garimella

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Kiran Garimella

Kiran Garimella

Publications by authors named "Kiran Garimella"

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15Publications

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Integrating long-range connectivity information into de Bruijn graphs.

Authors:
Isaac Turner Kiran V Garimella Zamin Iqbal Gil McVean

Bioinformatics 2018 08;34(15):2556-2565

Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.

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http://dx.doi.org/10.1093/bioinformatics/bty157DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6061703PMC
August 2018

A framework for the detection of de novo mutations in family-based sequencing data.

Authors:
Laurent C Francioli Mircea Cretu-Stancu Kiran V Garimella Menachem Fromer Wigard P Kloosterman Kaitlin E Samocha Benjamin M Neale Mark J Daly Eric Banks Mark A DePristo Paul Iw de Bakker

Eur J Hum Genet 2017 02 23;25(2):227-233. Epub 2016 Nov 23.

Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands.

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http://dx.doi.org/10.1038/ejhg.2016.147DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5255947PMC
February 2017

From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline.

Authors:
Geraldine A Van der Auwera Mauricio O Carneiro Chris Hartl Ryan Poplin Guillermo Del Angel Ami Levy-Moonshine Tadeusz Jordan Khalid Shakir David Roazen Joel Thibault Eric Banks Kiran V Garimella David Altshuler Stacey Gabriel Mark A DePristo

Curr Protoc Bioinformatics 2013 ;43:11.10.1-33

Broad Institute, Genome Sequencing and Analysis Group, 301 Binney Street, Cambridge MA 02142.

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http://dx.doi.org/10.1002/0471250953.bi1110s43DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4243306PMC
July 2016

A polygenic burden of rare disruptive mutations in schizophrenia.

Authors:
Shaun M Purcell Jennifer L Moran Menachem Fromer Douglas Ruderfer Nadia Solovieff Panos Roussos Colm O'Dushlaine Kimberly Chambert Sarah E Bergen Anna Kähler Laramie Duncan Eli Stahl Giulio Genovese Esperanza Fernández Mark O Collins Noboru H Komiyama Jyoti S Choudhary Patrik K E Magnusson Eric Banks Khalid Shakir Kiran Garimella Tim Fennell Mark DePristo Seth G N Grant Stephen J Haggarty Stacey Gabriel Edward M Scolnick Eric S Lander Christina M Hultman Patrick F Sullivan Steven A McCarroll Pamela Sklar

Nature 2014 Feb 22;506(7487):185-90. Epub 2014 Jan 22.

1] Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA [2] Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA [3] Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.

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http://dx.doi.org/10.1038/nature12975DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4136494PMC
February 2014

Analysis of rare, exonic variation amongst subjects with autism spectrum disorders and population controls.

Authors:
Li Liu Aniko Sabo Benjamin M Neale Uma Nagaswamy Christine Stevens Elaine Lim Corneliu A Bodea Donna Muzny Jeffrey G Reid Eric Banks Hillary Coon Mark Depristo Huyen Dinh Tim Fennel Jason Flannick Stacey Gabriel Kiran Garimella Shannon Gross Alicia Hawes Lora Lewis Vladimir Makarov Jared Maguire Irene Newsham Ryan Poplin Stephan Ripke Khalid Shakir Kaitlin E Samocha Yuanqing Wu Eric Boerwinkle Joseph D Buxbaum Edwin H Cook Bernie Devlin Gerard D Schellenberg James S Sutcliffe Mark J Daly Richard A Gibbs Kathryn Roeder

PLoS Genet 2013 Apr 11;9(4):e1003443. Epub 2013 Apr 11.

Department of Statistics, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1003443DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3623759PMC
April 2013

Exome sequencing can improve diagnosis and alter patient management.

Authors:
Tracy J Dixon-Salazar Jennifer L Silhavy Nitin Udpa Jana Schroth Stephanie Bielas Ashleigh E Schaffer Jesus Olvera Vineet Bafna Maha S Zaki Ghada H Abdel-Salam Lobna A Mansour Laila Selim Sawsan Abdel-Hadi Naima Marzouki Tawfeg Ben-Omran Nouriya A Al-Saana F Müjgan Sonmez Figen Celep Matloob Azam Kiley J Hill Adrienne Collazo Ali G Fenstermaker Gaia Novarino Naiara Akizu Kiran V Garimella Carrie Sougnez Carsten Russ Stacey B Gabriel Joseph G Gleeson

Sci Transl Med 2012 Jun;4(138):138ra78

Howard Hughes Medical Institute, Institute for Genomic Medicine, Rady Children's Hospital, University of California, San Diego, San Diego, CA 92093, USA.

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http://dx.doi.org/10.1126/scitranslmed.3003544DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4442637PMC
June 2012

Extremely low-coverage sequencing and imputation increases power for genome-wide association studies.

Authors:
Bogdan Pasaniuc Nadin Rohland Paul J McLaren Kiran Garimella Noah Zaitlen Heng Li Namrata Gupta Benjamin M Neale Mark J Daly Pamela Sklar Patrick F Sullivan Sarah Bergen Jennifer L Moran Christina M Hultman Paul Lichtenstein Patrik Magnusson Shaun M Purcell David W Haas Liming Liang Shamil Sunyaev Nick Patterson Paul I W de Bakker David Reich Alkes L Price

Nat Genet 2012 May 20;44(6):631-5. Epub 2012 May 20.

Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA.

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http://www.nature.com/articles/ng.2283
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http://dx.doi.org/10.1038/ng.2283DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3400344PMC
May 2012

Exome sequencing and the genetic basis of complex traits.

Authors:
Adam Kiezun Kiran Garimella Ron Do Nathan O Stitziel Benjamin M Neale Paul J McLaren Namrata Gupta Pamela Sklar Patrick F Sullivan Jennifer L Moran Christina M Hultman Paul Lichtenstein Patrik Magnusson Thomas Lehner Yin Yao Shugart Alkes L Price Paul I W de Bakker Shaun M Purcell Shamil R Sunyaev

Nat Genet 2012 May 29;44(6):623-30. Epub 2012 May 29.

Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.

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http://dx.doi.org/10.1038/ng.2303DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3727622PMC
May 2012

Patterns and rates of exonic de novo mutations in autism spectrum disorders.

Authors:
Benjamin M Neale Yan Kou Li Liu Avi Ma'ayan Kaitlin E Samocha Aniko Sabo Chiao-Feng Lin Christine Stevens Li-San Wang Vladimir Makarov Paz Polak Seungtai Yoon Jared Maguire Emily L Crawford Nicholas G Campbell Evan T Geller Otto Valladares Chad Schafer Han Liu Tuo Zhao Guiqing Cai Jayon Lihm Ruth Dannenfelser Omar Jabado Zuleyma Peralta Uma Nagaswamy Donna Muzny Jeffrey G Reid Irene Newsham Yuanqing Wu Lora Lewis Yi Han Benjamin F Voight Elaine Lim Elizabeth Rossin Andrew Kirby Jason Flannick Menachem Fromer Khalid Shakir Tim Fennell Kiran Garimella Eric Banks Ryan Poplin Stacey Gabriel Mark DePristo Jack R Wimbish Braden E Boone Shawn E Levy Catalina Betancur Shamil Sunyaev Eric Boerwinkle Joseph D Buxbaum Edwin H Cook Bernie Devlin Richard A Gibbs Kathryn Roeder Gerard D Schellenberg James S Sutcliffe Mark J Daly

Nature 2012 Apr 4;485(7397):242-5. Epub 2012 Apr 4.

Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA.

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http://www.nature.com/doifinder/10.1038/nature11011
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http://dx.doi.org/10.1038/nature11011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3613847PMC
April 2012

The functional spectrum of low-frequency coding variation.

Authors:
Gabor T Marth Fuli Yu Amit R Indap Kiran Garimella Simon Gravel Wen Fung Leong Chris Tyler-Smith Matthew Bainbridge Tom Blackwell Xiangqun Zheng-Bradley Yuan Chen Danny Challis Laura Clarke Edward V Ball Kristian Cibulskis David N Cooper Bob Fulton Chris Hartl Dan Koboldt Donna Muzny Richard Smith Carrie Sougnez Chip Stewart Alistair Ward Jin Yu Yali Xue David Altshuler Carlos D Bustamante Andrew G Clark Mark Daly Mark DePristo Paul Flicek Stacey Gabriel Elaine Mardis Aarno Palotie Richard Gibbs

Genome Biol 2011 Sep 14;12(9):R84. Epub 2011 Sep 14.

Department of Biology, Boston College, 140 Commonwealth Avenue, Chestnut Hill, MA 02467, USA.

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http://dx.doi.org/10.1186/gb-2011-12-9-r84DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3308047PMC
September 2011

Variation in genome-wide mutation rates within and between human families.

Authors:
Donald F Conrad Jonathan E M Keebler Mark A DePristo Sarah J Lindsay Yujun Zhang Ferran Casals Youssef Idaghdour Chris L Hartl Carlos Torroja Kiran V Garimella Martine Zilversmit Reed Cartwright Guy A Rouleau Mark Daly Eric A Stone Matthew E Hurles Philip Awadalla

Nat Genet 2011 Jun 12;43(7):712-4. Epub 2011 Jun 12.

Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.

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http://www.nature.com/ng/journal/v43/n7/pdf/ng.862.pdf%3FWT.
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http://www.nature.com/doifinder/10.1038/ng.862
Publisher Site
http://dx.doi.org/10.1038/ng.862DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3322360PMC
June 2011

A framework for variation discovery and genotyping using next-generation DNA sequencing data.

Authors:
Mark A DePristo Eric Banks Ryan Poplin Kiran V Garimella Jared R Maguire Christopher Hartl Anthony A Philippakis Guillermo del Angel Manuel A Rivas Matt Hanna Aaron McKenna Tim J Fennell Andrew M Kernytsky Andrey Y Sivachenko Kristian Cibulskis Stacey B Gabriel David Altshuler Mark J Daly

Nat Genet 2011 May 10;43(5):491-8. Epub 2011 Apr 10.

Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.

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http://dx.doi.org/10.1038/ng.806DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3083463PMC
May 2011

Exome sequencing reveals a novel mutation for autosomal recessive non-syndromic mental retardation in the TECR gene on chromosome 19p13.

Authors:
Minal Çalışkan Jessica X Chong Lawrence Uricchio Rebecca Anderson Peixian Chen Carrie Sougnez Kiran Garimella Stacey B Gabriel Mark A dePristo Khalid Shakir Dietrich Matern Soma Das Darrel Waggoner Dan L Nicolae Carole Ober

Hum Mol Genet 2011 Apr 6;20(7):1285-9. Epub 2011 Jan 6.

Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA.

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http://dx.doi.org/10.1093/hmg/ddq569DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3115579PMC
April 2011

Exome sequencing, ANGPTL3 mutations, and familial combined hypolipidemia.

Authors:
Kiran Musunuru James P Pirruccello Ron Do Gina M Peloso Candace Guiducci Carrie Sougnez Kiran V Garimella Sheila Fisher Justin Abreu Andrew J Barry Tim Fennell Eric Banks Lauren Ambrogio Kristian Cibulskis Andrew Kernytsky Elena Gonzalez Nicholas Rudzicz James C Engert Mark A DePristo Mark J Daly Jonathan C Cohen Helen H Hobbs David Altshuler Gustav Schonfeld Stacey B Gabriel Pin Yue Sekar Kathiresan

N Engl J Med 2010 Dec 13;363(23):2220-7. Epub 2010 Oct 13.

Cardiovascular Research Center, Massachusetts General Hospital, and Department of Medicine, Boston University School of Public Health, Boston, MA 02114, USA.

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http://dx.doi.org/10.1056/NEJMoa1002926DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3008575PMC
December 2010

The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.

Authors:
Aaron McKenna Matthew Hanna Eric Banks Andrey Sivachenko Kristian Cibulskis Andrew Kernytsky Kiran Garimella David Altshuler Stacey Gabriel Mark Daly Mark A DePristo

Genome Res 2010 Sep 19;20(9):1297-303. Epub 2010 Jul 19.

Program in Medical and Population Genetics, The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.

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http://dx.doi.org/10.1101/gr.107524.110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2928508PMC
September 2010