Shamil R Sunyaev

Shamil R Sunyaev

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Shamil R Sunyaev

Shamil R Sunyaev

Publications by authors named "Shamil R Sunyaev"

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69Publications

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PINES: phenotype-informed tissue weighting improves prediction of pathogenic noncoding variants.

Genome Biol 2018 10 25;19(1):173. Epub 2018 Oct 25.

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

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https://genomebiology.biomedcentral.com/articles/10.1186/s13
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http://dx.doi.org/10.1186/s13059-018-1546-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6203199PMC
October 2018

Excess of Deleterious Mutations around HLA Genes Reveals Evolutionary Cost of Balancing Selection.

Mol Biol Evol 2016 10 28;33(10):2555-64. Epub 2016 Jun 28.

Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School Program in Medical and Population Genetics, The Broad Institute, Cambridge, MA

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http://dx.doi.org/10.1093/molbev/msw127DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5026253PMC
October 2016

Leveraging Distant Relatedness to Quantify Human Mutation and Gene-Conversion Rates.

Am J Hum Genet 2015 Dec 12;97(6):775-89. Epub 2015 Nov 12.

Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA.

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http://dx.doi.org/10.1016/j.ajhg.2015.10.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4678427PMC
December 2015

Dominance of Deleterious Alleles Controls the Response to a Population Bottleneck.

PLoS Genet 2015 Aug 28;11(8):e1005436. Epub 2015 Aug 28.

Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts, United States of America; Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America; Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1005436DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4552954PMC
August 2015

Exome sequencing identifies rare LDLR and APOA5 alleles conferring risk for myocardial infarction.

Nature 2015 Feb 10;518(7537):102-6. Epub 2014 Dec 10.

1] Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts 02114, USA. [2] Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts 02114, USA. [3] Department of Medicine, Harvard Medical School, Boston, Massachusetts 02114, USA. [4] Program in Medical and Population Genetics, Broad Institute, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA.

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http://kooperberg.fhcrc.org/papers/2015do.pdf
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http://www.nature.com/doifinder/10.1038/nature13917
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http://dx.doi.org/10.1038/nature13917DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4319990PMC
February 2015

Cell-of-origin chromatin organization shapes the mutational landscape of cancer.

Nature 2015 Feb;518(7539):360-364

Division of Genetics, Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA, 02115.

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http://dx.doi.org/10.1038/nature14221DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4405175PMC
February 2015

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

Reduced local mutation density in regulatory DNA of cancer genomes is linked to DNA repair.

Nat Biotechnol 2014 Jan 15;32(1):71-5. Epub 2013 Dec 15.

1] Division of Genetics, Department of Medicine, Brigham & Women's Hospital, Boston, Massachusetts, USA. [2] Harvard Medical School, Boston, Massachusetts, USA. [3] The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.

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http://dx.doi.org/10.1038/nbt.2778DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4116484PMC
January 2014

Systems biology and the analysis of genetic variation.

Curr Opin Genet Dev 2013 Dec 28;23(6):599-601. Epub 2013 Nov 28.

Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA. Electronic address:

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http://dx.doi.org/10.1016/j.gde.2013.11.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4116483PMC
December 2013

Impact of deleterious passenger mutations on cancer progression.

Proc Natl Acad Sci U S A 2013 Feb 6;110(8):2910-5. Epub 2013 Feb 6.

Graduate Program in Biophysics, Harvard University, Boston, MA 02115, USA.

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http://dx.doi.org/10.1073/pnas.1213968110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3581883PMC
February 2013

Predicting functional effect of human missense mutations using PolyPhen-2.

Curr Protoc Hum Genet 2013 Jan;Chapter 7:Unit7.20

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

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http://dx.doi.org/10.1002/0471142905.hg0720s76DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4480630PMC
January 2013

Network-based inference from complex proteomic mixtures using SNIPE.

Bioinformatics 2012 Dec 11;28(23):3115-22. Epub 2012 Oct 11.

Division of Genetics, Brigham and Women's Hospital, Boston, MA 02115, USA.

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http://dx.doi.org/10.1093/bioinformatics/bts594DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3509492PMC
December 2012

Inferring causality and functional significance of human coding DNA variants.

Authors:
Shamil R Sunyaev

Hum Mol Genet 2012 Oct 17;21(R1):R10-7. Epub 2012 Sep 17.

Genetics Division, Brigham and Women's Hospital, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.

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http://dx.doi.org/10.1093/hmg/dds385DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3459643PMC
October 2012

The mystery of missing heritability: Genetic interactions create phantom heritability.

Proc Natl Acad Sci U S A 2012 Jan 5;109(4):1193-8. Epub 2012 Jan 5.

Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.

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http://dx.doi.org/10.1073/pnas.1119675109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3268279PMC
January 2012

Human allelic variation: perspective from protein function, structure, and evolution.

Curr Opin Struct Biol 2010 Jun;20(3):342-50

Division of Genetics, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, USA.

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http://dx.doi.org/10.1016/j.sbi.2010.03.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2921592PMC
June 2010

Pooled association tests for rare variants in exon-resequencing studies.

Am J Hum Genet 2010 Jun 13;86(6):832-8. Epub 2010 May 13.

Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA.

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http://dx.doi.org/10.1016/j.ajhg.2010.04.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3032073PMC
June 2010

Human mutation rate associated with DNA replication timing.

Nat Genet 2009 Apr 15;41(4):393-5. Epub 2009 Mar 15.

Department of Genome Sciences and Medicine, University of Washington, Seattle, WA, USA.

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http://dx.doi.org/10.1038/ng.363DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2914101PMC
April 2009

Power of deep, all-exon resequencing for discovery of human trait genes.

Proc Natl Acad Sci U S A 2009 Mar 6;106(10):3871-6. Epub 2009 Feb 6.

Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.

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http://dx.doi.org/10.1073/pnas.0812824106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2656172PMC
March 2009

Adaptive mutations in the JC virus protein capsid are associated with progressive multifocal leukoencephalopathy (PML).

PLoS Genet 2009 Feb 6;5(2):e1000368. Epub 2009 Feb 6.

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

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http://dx.doi.org/10.1371/journal.pgen.1000368DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2629573PMC
February 2009

Large-scale identification and evolution indexing of tyrosine phosphorylation sites from murine brain.

J Proteome Res 2008 Jan 23;7(1):311-8. Epub 2007 Nov 23.

Department of Biology, University of Vermont, Burlington, Vermont 05405, USA.

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http://dx.doi.org/10.1021/pr0701254DOI Listing
January 2008

Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms.

Am J Hum Genet 2008 Jan;82(1):100-12

Department of Epidemiology, The University of Texas M. D. Anderson Cancer Center, Houston, TX 77030, USA.

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http://dx.doi.org/10.1016/j.ajhg.2007.09.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2253956PMC
January 2008

Toxicity of influenza A virus matrix protein 2 for mammalian cells is associated with its intrinsic proton-channeling activity.

Cell Cycle 2007 Aug 12;6(16):2043-7. Epub 2007 Jun 12.

Cure Lab, Inc., Canton, Massachusetts 02021, USA.

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http://dx.doi.org/10.4161/cc.6.16.4564DOI Listing
August 2007

Most rare missense alleles are deleterious in humans: implications for complex disease and association studies.

Am J Hum Genet 2007 Apr 8;80(4):727-39. Epub 2007 Mar 8.

Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02125, USA.

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http://linkinghub.elsevier.com/retrieve/pii/S000292970761104
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http://dx.doi.org/10.1086/513473DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852724PMC
April 2007

From analysis of protein structural alignments toward a novel approach to align protein sequences.

Proteins 2004 Feb;54(3):569-82

Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.

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http://dx.doi.org/10.1002/prot.10503DOI Listing
February 2004