Bogdan Pasaniuc

Bogdan Pasaniuc

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Bogdan Pasaniuc

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Integrative analysis of Dupuytren's disease identifies novel risk locus and reveals a shared genetic etiology with BMI.

Genet Epidemiol 2019 Sep 13;43(6):629-645. Epub 2019 May 13.

Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, California.

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http://dx.doi.org/10.1002/gepi.22209DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6699495PMC
September 2019

Accurate estimation of SNP-heritability from biobank-scale data irrespective of genetic architecture.

Nat Genet 2019 Aug 29;51(8):1244-1251. Epub 2019 Jul 29.

Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.

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http://dx.doi.org/10.1038/s41588-019-0465-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6686906PMC
August 2019

RAISS: Robust and Accurate imputation from Summary Statistics.

Bioinformatics 2019 Jun 7. Epub 2019 Jun 7.

Groupe de Génétique Statistique, Département de Génomes and Génétique, C3BI, Institut Pasteur, Paris, France.

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http://dx.doi.org/10.1093/bioinformatics/btz466DOI Listing
June 2019

Probabilistic fine-mapping of transcriptome-wide association studies.

Nat Genet 2019 04 29;51(4):675-682. Epub 2019 Mar 29.

Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.

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http://dx.doi.org/10.1038/s41588-019-0367-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6619422PMC
April 2019

Leveraging Polygenic Functional Enrichment to Improve GWAS Power.

Am J Hum Genet 2019 Jan 27;104(1):65-75. Epub 2018 Dec 27.

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

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http://dx.doi.org/10.1016/j.ajhg.2018.11.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323418PMC
January 2019

Author Correction: Large-scale transcriptome-wide association study identifies new prostate cancer risk regions.

Nat Commun 2019 01 8;10(1):171. Epub 2019 Jan 8.

Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, 90095, CA, USA.

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http://www.nature.com/articles/s41467-018-08108-7
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http://dx.doi.org/10.1038/s41467-018-08108-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6325152PMC
January 2019

Shared heritability and functional enrichment across six solid cancers.

Authors:
Xia Jiang Hilary K Finucane Fredrick R Schumacher Stephanie L Schmit Jonathan P Tyrer Younghun Han Kyriaki Michailidou Corina Lesseur Karoline B Kuchenbaecker Joe Dennis David V Conti Graham Casey Mia M Gaudet Jeroen R Huyghe Demetrius Albanes Melinda C Aldrich Angeline S Andrew Irene L Andrulis Hoda Anton-Culver Antonis C Antoniou Natalia N Antonenkova Susanne M Arnold Kristan J Aronson Banu K Arun Elisa V Bandera Rosa B Barkardottir Daniel R Barnes Jyotsna Batra Matthias W Beckmann Javier Benitez Sara Benlloch Andrew Berchuck Sonja I Berndt Heike Bickeböller Stephanie A Bien Carl Blomqvist Stefania Boccia Natalia V Bogdanova Stig E Bojesen Manjeet K Bolla Hiltrud Brauch Hermann Brenner James D Brenton Mark N Brook Joan Brunet Hans Brunnström Daniel D Buchanan Barbara Burwinkel Ralf Butzow Gabriella Cadoni Trinidad Caldés Maria A Caligo Ian Campbell Peter T Campbell Géraldine Cancel-Tassin Lisa Cannon-Albright Daniele Campa Neil Caporaso André L Carvalho Andrew T Chan Jenny Chang-Claude Stephen J Chanock Chu Chen David C Christiani Kathleen B M Claes Frank Claessens Judith Clements J Margriet Collée Marcia Cruz Correa Fergus J Couch Angela Cox Julie M Cunningham Cezary Cybulski Kamila Czene Mary B Daly Anna deFazio Peter Devilee Orland Diez Manuela Gago-Dominguez Jenny L Donovan Thilo Dörk Eric J Duell Alison M Dunning Miriam Dwek Diana M Eccles Christopher K Edlund Digna R Velez Edwards Carolina Ellberg D Gareth Evans Peter A Fasching Robert L Ferris Triantafillos Liloglou Jane C Figueiredo Olivia Fletcher Renée T Fortner Florentia Fostira Silvia Franceschi Eitan Friedman Steven J Gallinger Patricia A Ganz Judy Garber José A García-Sáenz Simon A Gayther Graham G Giles Andrew K Godwin Mark S Goldberg David E Goldgar Ellen L Goode Marc T Goodman Gary Goodman Kjell Grankvist Mark H Greene Henrik Gronberg Jacek Gronwald Pascal Guénel Niclas Håkansson Per Hall Ute Hamann Freddie C Hamdy Robert J Hamilton Jochen Hampe Aage Haugen Florian Heitz Rolando Herrero Peter Hillemanns Michael Hoffmeister Estrid Høgdall Yun-Chul Hong John L Hopper Richard Houlston Peter J Hulick David J Hunter David G Huntsman Gregory Idos Evgeny N Imyanitov Sue Ann Ingles Claudine Isaacs Anna Jakubowska Paul James Mark A Jenkins Mattias Johansson Mikael Johansson Esther M John Amit D Joshi Radka Kaneva Beth Y Karlan Linda E Kelemen Tabea Kühl Kay-Tee Khaw Elza Khusnutdinova Adam S Kibel Lambertus A Kiemeney Jeri Kim Susanne K Kjaer Julia A Knight Manolis Kogevinas Zsofia Kote-Jarai Stella Koutros Vessela N Kristensen Jolanta Kupryjanczyk Martin Lacko Stephan Lam Diether Lambrechts Maria Teresa Landi Philip Lazarus Nhu D Le Eunjung Lee Flavio Lejbkowicz Heinz-Josef Lenz Goska Leslie Davor Lessel Jenny Lester Douglas A Levine Li Li Christopher I Li Annika Lindblom Noralane M Lindor Geoffrey Liu Fotios Loupakis Jan Lubiński Lovise Maehle Christiane Maier Arto Mannermaa Loic Le Marchand Sara Margolin Taymaa May Lesley McGuffog Alfons Meindl Pooja Middha Austin Miller Roger L Milne Robert J MacInnis Francesmary Modugno Marco Montagna Victor Moreno Kirsten B Moysich Lorelei Mucci Kenneth Muir Anna Marie Mulligan Katherine L Nathanson David E Neal Andrew R Ness Susan L Neuhausen Heli Nevanlinna Polly A Newcomb Lisa F Newcomb Finn Cilius Nielsen Liene Nikitina-Zake Børge G Nordestgaard Robert L Nussbaum Kenneth Offit Edith Olah Ali Amin Al Olama Olufunmilayo I Olopade Andrew F Olshan Håkan Olsson Ana Osorio Hardev Pandha Jong Y Park Nora Pashayan Michael T Parsons Tanja Pejovic Kathryn L Penney Wilbert H M Peters Catherine M Phelan Amanda I Phipps Dijana Plaseska-Karanfilska Miranda Pring Darya Prokofyeva Paolo Radice Kari Stefansson Susan J Ramus Leon Raskin Gad Rennert Hedy S Rennert Elizabeth J van Rensburg Marjorie J Riggan Harvey A Risch Angela Risch Monique J Roobol Barry S Rosenstein Mary Anne Rossing Kim De Ruyck Emmanouil Saloustros Dale P Sandler Elinor J Sawyer Matthew B Schabath Johanna Schleutker Marjanka K Schmidt V Wendy Setiawan Hongbing Shen Erin M Siegel Weiva Sieh Christian F Singer Martha L Slattery Karina Dalsgaard Sorensen Melissa C Southey Amanda B Spurdle Janet L Stanford Victoria L Stevens Sebastian Stintzing Jennifer Stone Karin Sundfeldt Rebecca Sutphen Anthony J Swerdlow Eloiza H Tajara Catherine M Tangen Adonina Tardon Jack A Taylor M Dawn Teare Manuel R Teixeira Mary Beth Terry Kathryn L Terry Stephen N Thibodeau Mads Thomassen Line Bjørge Marc Tischkowitz Amanda E Toland Diana Torres Paul A Townsend Ruth C Travis Nadine Tung Shelley S Tworoger Cornelia M Ulrich Nawaid Usmani Celine M Vachon Els Van Nieuwenhuysen Ana Vega Miguel Elías Aguado-Barrera Qin Wang Penelope M Webb Clarice R Weinberg Stephanie Weinstein Mark C Weissler Jeffrey N Weitzel Catharine M L West Emily White Alice S Whittemore H-Erich Wichmann Fredrik Wiklund Robert Winqvist Alicja Wolk Penella Woll Michael Woods Anna H Wu Xifeng Wu Drakoulis Yannoukakos Wei Zheng Shanbeh Zienolddiny Argyrios Ziogas Kristin K Zorn Jacqueline M Lane Richa Saxena Duncan Thomas Rayjean J Hung Brenda Diergaarde James McKay Ulrike Peters Li Hsu Montserrat García-Closas Rosalind A Eeles Georgia Chenevix-Trench Paul J Brennan Christopher A Haiman Jacques Simard Douglas F Easton Stephen B Gruber Paul D P Pharoah Alkes L Price Bogdan Pasaniuc Christopher I Amos Peter Kraft Sara Lindström

Nat Commun 2019 01 25;10(1):431. Epub 2019 Jan 25.

Public Health Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA, 98109-1024, USA.

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http://dx.doi.org/10.1038/s41467-018-08054-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6347624PMC
January 2019

GWAS and colocalization analyses implicate carotid intima-media thickness and carotid plaque loci in cardiovascular outcomes.

Authors:
Nora Franceschini Claudia Giambartolomei Paul S de Vries Chris Finan Joshua C Bis Rachael P Huntley Ruth C Lovering Salman M Tajuddin Thomas W Winkler Misa Graff Maryam Kavousi Caroline Dale Albert V Smith Edith Hofer Elisabeth M van Leeuwen Ilja M Nolte Lingyi Lu Markus Scholz Muralidharan Sargurupremraj Niina Pitkänen Oscar Franzén Peter K Joshi Raymond Noordam Riccardo E Marioni Shih-Jen Hwang Solomon K Musani Ulf Schminke Walter Palmas Aaron Isaacs Adolfo Correa Alan B Zonderman Albert Hofman Alexander Teumer Amanda J Cox André G Uitterlinden Andrew Wong Andries J Smit Anne B Newman Annie Britton Arno Ruusalepp Bengt Sennblad Bo Hedblad Bogdan Pasaniuc Brenda W Penninx Carl D Langefeld Christina L Wassel Christophe Tzourio Cristiano Fava Damiano Baldassarre Daniel H O'Leary Daniel Teupser Diana Kuh Elena Tremoli Elmo Mannarino Enzo Grossi Eric Boerwinkle Eric E Schadt Erik Ingelsson Fabrizio Veglia Fernando Rivadeneira Frank Beutner Ganesh Chauhan Gerardo Heiss Harold Snieder Harry Campbell Henry Völzke Hugh S Markus Ian J Deary J Wouter Jukema Jacqueline de Graaf Jacqueline Price Janne Pott Jemma C Hopewell Jingjing Liang Joachim Thiery Jorgen Engmann Karl Gertow Kenneth Rice Kent D Taylor Klodian Dhana Lambertus A L M Kiemeney Lars Lind Laura M Raffield Lenore J Launer Lesca M Holdt Marcus Dörr Martin Dichgans Matthew Traylor Matthias Sitzer Meena Kumari Mika Kivimaki Mike A Nalls Olle Melander Olli Raitakari Oscar H Franco Oscar L Rueda-Ochoa Panos Roussos Peter H Whincup Philippe Amouyel Philippe Giral Pramod Anugu Quenna Wong Rainer Malik Rainer Rauramaa Ralph Burkhardt Rebecca Hardy Reinhold Schmidt Renée de Mutsert Richard W Morris Rona J Strawbridge S Goya Wannamethee Sara Hägg Sonia Shah Stela McLachlan Stella Trompet Sudha Seshadri Sudhir Kurl Susan R Heckbert Susan Ring Tamara B Harris Terho Lehtimäki Tessel E Galesloot Tina Shah Ulf de Faire Vincent Plagnol Wayne D Rosamond Wendy Post Xiaofeng Zhu Xiaoling Zhang Xiuqing Guo Yasaman Saba Abbas Dehghan Adrie Seldenrijk Alanna C Morrison Anders Hamsten Bruce M Psaty Cornelia M van Duijn Deborah A Lawlor Dennis O Mook-Kanamori Donald W Bowden Helena Schmidt James F Wilson James G Wilson Jerome I Rotter Joanna M Wardlaw John Deanfield Julian Halcox Leo-Pekka Lyytikäinen Markus Loeffler Michele K Evans Stéphanie Debette Steve E Humphries Uwe Völker Vilmundur Gudnason Aroon D Hingorani Johan L M Björkegren Juan P Casas Christopher J O'Donnell

Nat Commun 2018 12 3;9(1):5141. Epub 2018 Dec 3.

Intramural Administration Management Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, 20892, USA.

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http://dx.doi.org/10.1038/s41467-018-07340-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6277418PMC
December 2018

Large-scale transcriptome-wide association study identifies new prostate cancer risk regions.

Nat Commun 2018 10 4;9(1):4079. Epub 2018 Oct 4.

Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, 90095, CA, USA.

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http://www.nature.com/articles/s41467-018-06302-1
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http://dx.doi.org/10.1038/s41467-018-06302-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6172280PMC
October 2018

Phenotype-Specific Enrichment of Mendelian Disorder Genes near GWAS Regions across 62 Complex Traits.

Am J Hum Genet 2018 10;103(4):535-552

Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00029297183028
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http://dx.doi.org/10.1016/j.ajhg.2018.08.017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6174356PMC
October 2018

A Bayesian framework for multiple trait colocalization from summary association statistics.

Bioinformatics 2018 08;34(15):2538-2545

Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.

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http://dx.doi.org/10.1093/bioinformatics/bty147DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6061859PMC
August 2018

Transcriptome-wide association studies accounting for colocalization using Egger regression.

Genet Epidemiol 2018 07 29;42(5):418-433. Epub 2018 May 29.

Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts.

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http://dx.doi.org/10.1002/gepi.22131DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6342197PMC
July 2018

A unifying framework for joint trait analysis under a non-infinitesimal model.

Bioinformatics 2018 07;34(13):i195-i201

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

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http://dx.doi.org/10.1093/bioinformatics/bty254DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6022541PMC
July 2018

Methods for fine-mapping with chromatin and expression data.

PLoS Genet 2018 02 26;14(2):e1007240. Epub 2018 Feb 26.

Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, California, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1007240DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5843356PMC
February 2018

Local Genetic Correlation Gives Insights into the Shared Genetic Architecture of Complex Traits.

Am J Hum Genet 2017 Nov;101(5):737-751

Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90024, USA; Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90024, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90024, USA.

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http://dx.doi.org/10.1016/j.ajhg.2017.09.022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5673668PMC
November 2017

Enhanced methods to detect haplotypic effects on gene expression.

Bioinformatics 2017 Aug;33(15):2307-2313

Bioinformatics IDP, University of California Los Angeles, Los Angeles, CA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btx142DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5860109PMC
August 2017

A Genetic Population Isolate in The Netherlands Showing Extensive Haplotype Sharing and Long Regions of Homozygosity.

Genes (Basel) 2017 May 4;8(5). Epub 2017 May 4.

Brain Center Rudolf Magnus, Department of Psychiatry, University Medical Center Utrecht, Utrecht 3584 CX, The Netherlands.

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http://dx.doi.org/10.3390/genes8050133DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5448007PMC
May 2017

Widespread Allelic Heterogeneity in Complex Traits.

Am J Hum Genet 2017 May;100(5):789-802

Department of Computer Science, University of California, Los Angeles, CA 90095, USA; Department of Human Genetics, University of California, Los Angeles, CA 90095, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2017.04.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5420356PMC
May 2017

Integrating Gene Expression with Summary Association Statistics to Identify Genes Associated with 30 Complex Traits.

Am J Hum Genet 2017 Mar 23;100(3):473-487. Epub 2017 Feb 23.

Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90024, USA; Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90024, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90024, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2017.01.031DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5339290PMC
March 2017

Dissecting the genetics of complex traits using summary association statistics.

Nat Rev Genet 2017 02 14;18(2):117-127. Epub 2016 Nov 14.

Departments of Epidemiology and Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA.

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http://dx.doi.org/10.1038/nrg.2016.142DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5449190PMC
February 2017

Colocalization of GWAS and eQTL Signals Detects Target Genes.

Am J Hum Genet 2016 Dec 17;99(6):1245-1260. Epub 2016 Nov 17.

Department of Computer Science, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA. Electronic address:

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http://www.cell.com/ajhg/pdf/S0002-9297(16)30439-6.pdf
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http://biorxiv.org/content/biorxiv/early/2016/08/29/065037.f
Web Search
http://dx.doi.org/10.1016/j.ajhg.2016.10.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5142122PMC
December 2016

Prostate Cancer Susceptibility in Men of African Ancestry at 8q24.

J Natl Cancer Inst 2016 Jul 27;108(7). Epub 2016 Jan 27.

Affiliations of authors: Department of Preventive Medicine (YH, KAR, DJH, SAI, FRS, GC, LCP, XS, GAC, DOS, DVC, BEH, CAH) and Department of Urology (GAC), Keck School of Medicine, and Norris Comprehensive Cancer Center (SAI, FRS, GC, GAC, DOS, DVC, BEH, CAH), University of Southern California , Los Angeles, CA ; University of Arizona College of Medicine and University of Arizona Cancer Center , Tucson, AZ (RAK); Department of Epidemiology (SSS) and Department of Urology (CAP), University of Texas M. D. Anderson Cancer Center , Houston, TX ; Department of Public Health Sciences (BAR) and Department of Public Health Sciences (CND), Henry Ford Hospital , Detroit, MI ; Department of Preventive Medicine, Stony Brook University , Stony Brook, NY (BN, MCL, SYW, AJMH); James Buchanan Brady Urological Institute, Johns Hopkins Hospital and Medical Institution , Baltimore, MD (WBI); Division of Public Health Sciences (JLS, SK) and SWOG Statistical Center (PJG), Fred Hutchinson Cancer Research Center , Seattle, WA ; Department of Epidemiology, School of Public Health, University of Washington , Seattle, WA (JLS); Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine , Nashville, TN (WZ, WJB); Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health , Bethesda, MD (SIB, ZW, MBC, SJC); Cancer Genomics Research Laboratory, NCI-DCEG, SAIC-Frederick Inc. , Frederick, MD (ZW); Program for Personalized Cancer Care and Department of Surgery, NorthShore University HealthSystem , Evanston, IL (JX); Department of Genetics (NR, DR, AT, AA, DQ, SM) and Howard Hughes Medical Institute (DR, SM), Harvard Medical School, Harvard University , Boston, MA ; Broad Institute of MIT and Harvard , Cambridge, MA (NR, DR, AT, AA, DQ, SM); Department of Pathology and Laboratory Medicine and Department of Human Genetics, David Geffen School of Medicine, University of California , Los Angeles, Los Angeles, CA (BP); Howard Hughes Medical Institute, Department of Medicine, School of Medicine, University of California , San Diego, San Diego, CA (DN, MGR, RSJ); Epidemiology Research Program, American Cancer Society , Atlanta, GA (SMG, VLS); Korle Bu Teaching Hospital , Accra , Ghana (EDY, YT, RBB, AAA, ET); University of Ghana Medical School , Accra , Ghana (EDY, YT, RBB, AAA, ET); Westat , Rockville, MD (AT, SN); School of Public Health, University of California , Berkeley, Berkeley, CA (APC); Cancer Prevention Institute of California , Fremont, CA (EMJ, AWH, LC); Stanford University School of Medicine and Stanford Cancer Institute , Palo Alto, CA (EMJ, AWH, LC); Department of Urology, Northwestern University , Chicago, IL (ABM); Department of Epidemiology, Harvard School of Public Health , Boston, MA (LBS, WJB); The Translational Genomics Research Institute , Phoenix, AZ (JC); Chronic Disease Research Centre and Faculty of Medical Sciences, University of the West Indies , Bridgetown, Barbados (AJMH); Glickman Urological & Kidney Institute, Cleveland Clinic , Cleveland, OH (EAK); Center for Cancer Genomics, Wake Forest School of Medicine , Winston-Salem, NC (SLZ); Department of Epidemiology and Biostatistics and Institute for Human Genetics, University of California , San Francisco, San Francisco, CA (JSW); School of Public Health, Makerere University College of Health Sciences , Kampala, Uganda (AL, SW); Uro Care , Kampala , Uganda (SW).

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http://dx.doi.org/10.1093/jnci/djv431DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4948565PMC
July 2016

Contrasting the Genetic Architecture of 30 Complex Traits from Summary Association Data.

Am J Hum Genet 2016 07 23;99(1):139-53. Epub 2016 Jun 23.

Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90024, USA; Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90024, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90024, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2016.05.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5005444PMC
July 2016

Atlas of prostate cancer heritability in European and African-American men pinpoints tissue-specific regulation.

Authors:
Alexander Gusev Huwenbo Shi Gleb Kichaev Mark Pomerantz Fugen Li Henry W Long Sue A Ingles Rick A Kittles Sara S Strom Benjamin A Rybicki Barbara Nemesure William B Isaacs Wei Zheng Curtis A Pettaway Edward D Yeboah Yao Tettey Richard B Biritwum Andrew A Adjei Evelyn Tay Ann Truelove Shelley Niwa Anand P Chokkalingam Esther M John Adam B Murphy Lisa B Signorello John Carpten M Cristina Leske Suh-Yuh Wu Anslem J M Hennis Christine Neslund-Dudas Ann W Hsing Lisa Chu Phyllis J Goodman Eric A Klein John S Witte Graham Casey Sam Kaggwa Michael B Cook Daniel O Stram William J Blot Rosalind A Eeles Douglas Easton Zsofia Kote-Jarai Ali Amin Al Olama Sara Benlloch Kenneth Muir Graham G Giles Melissa C Southey Liesel M Fitzgerald Henrik Gronberg Fredrik Wiklund Markus Aly Brian E Henderson Johanna Schleutker Tiina Wahlfors Teuvo L J Tammela Børge G Nordestgaard Tim J Key Ruth C Travis David E Neal Jenny L Donovan Freddie C Hamdy Paul Pharoah Nora Pashayan Kay-Tee Khaw Janet L Stanford Stephen N Thibodeau Shannon K McDonnell Daniel J Schaid Christiane Maier Walther Vogel Manuel Luedeke Kathleen Herkommer Adam S Kibel Cezary Cybulski Dominika Wokolorczyk Wojciech Kluzniak Lisa Cannon-Albright Craig Teerlink Hermann Brenner Aida K Dieffenbach Volker Arndt Jong Y Park Thomas A Sellers Hui-Yi Lin Chavdar Slavov Radka Kaneva Vanio Mitev Jyotsna Batra Amanda Spurdle Judith A Clements Manuel R Teixeira Hardev Pandha Agnieszka Michael Paula Paulo Sofia Maia Andrzej Kierzek David V Conti Demetrius Albanes Christine Berg Sonja I Berndt Daniele Campa E David Crawford W Ryan Diver Susan M Gapstur J Michael Gaziano Edward Giovannucci Robert Hoover David J Hunter Mattias Johansson Peter Kraft Loic Le Marchand Sara Lindström Carmen Navarro Kim Overvad Elio Riboli Afshan Siddiq Victoria L Stevens Dimitrios Trichopoulos Paolo Vineis Meredith Yeager Gosia Trynka Soumya Raychaudhuri Frederick R Schumacher Alkes L Price Matthew L Freedman Christopher A Haiman Bogdan Pasaniuc

Nat Commun 2016 Apr 7;7:10979. Epub 2016 Apr 7.

Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, California 90095, USA.

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http://dx.doi.org/10.1038/ncomms10979DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4829663PMC
April 2016

Leveraging ancestry to improve causal variant identification in exome sequencing for monogenic disorders.

Eur J Hum Genet 2016 Jan 22;24(1):113-9. Epub 2015 Apr 22.

Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA, USA.

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http://dx.doi.org/10.1038/ejhg.2015.68DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4795218PMC
January 2016

Whole-exome sequencing of over 4100 men of African ancestry and prostate cancer risk.

Hum Mol Genet 2016 Jan 24;25(2):371-81. Epub 2015 Nov 24.

Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA,

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http://dx.doi.org/10.1093/hmg/ddv462DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4865031PMC
January 2016

A multivariate Bernoulli model to predict DNaseI hypersensitivity status from haplotype data.

Bioinformatics 2015 Nov 2;31(21):3514-21. Epub 2015 Jul 2.

Bioinformatics Interdepartmental Program, University of California, Los Angeles, Department of Human Genetics and Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90024, USA.

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http://dx.doi.org/10.1093/bioinformatics/btv397DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4836401PMC
November 2015

Modeling Linkage Disequilibrium Increases Accuracy of Polygenic Risk Scores.

Am J Hum Genet 2015 Oct;97(4):576-92

Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Program in Genetic Epidemiology and Statistical Genetics, 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. Electronic address:

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http://biorxiv.org/content/biorxiv/early/2015/03/01/015859.f
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http://dx.doi.org/10.1016/j.ajhg.2015.09.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4596916PMC
October 2015

Leveraging local ancestry to detect gene-gene interactions in genome-wide data.

BMC Genet 2015 Oct 24;16:124. Epub 2015 Oct 24.

Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4619349PMC
October 2015

Leveraging Functional-Annotation Data in Trans-ethnic Fine-Mapping Studies.

Am J Hum Genet 2015 Aug 16;97(2):260-71. Epub 2015 Jul 16.

Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2015.06.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4573268PMC
August 2015

Identification of causal genes for complex traits.

Bioinformatics 2015 Jun;31(12):i206-13

Department of Computer Science, Inter-Departmental Program in Bioinformatics, Department of Human Genetics and Department of Pathology and Laboratory Medicine, University of California, Los Angeles, CA 90095, USA Department of Computer Science, Inter-Departmental Program in Bioinformatics, Department of Human Genetics and Department of Pathology and Laboratory Medicine, University of California, Los Angeles, CA 90095, USA.

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http://dx.doi.org/10.1093/bioinformatics/btv240DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542778PMC
June 2015

A spatial haplotype copying model with applications to genotype imputation.

J Comput Biol 2015 May 19;22(5):451-62. Epub 2014 Dec 19.

1 Department of Computer Science, University of California , Los Angeles, California.

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http://dx.doi.org/10.1089/cmb.2014.0151DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4425418PMC
May 2015

Spatial localization of recent ancestors for admixed individuals.

G3 (Bethesda) 2014 Nov 3;4(12):2505-18. Epub 2014 Nov 3.

Interdepartmental Program in Bioinformatics, University of California, Los Angeles, California 90095 Department of Human Genetics, University of California, Los Angeles, California 90095 Department of Pathology and Laboratory Medicine, Geffen School of Medicine at University of California, Los Angeles, California 90095

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http://dx.doi.org/10.1534/g3.114.014274DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4267945PMC
November 2014

Fast and accurate imputation of summary statistics enhances evidence of functional enrichment.

Bioinformatics 2014 Oct 1;30(20):2906-14. Epub 2014 Jul 1.

Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, 90024, Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, 90024, Department of Medicine, Lung Biology Center, University of California San Francisco, San Francisco, 94143, Program in Genetic Epidemiology and Statistical Genetics, Harvard School of Public Health, Boston, 02115, Departments of Epidemiology and Biostatistics, Harvard School of Public Health, Boston, MA, 02115, Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, 02142, Department of Genetics Harvard Medical School, Boston, MA, 02115 and Division of Population Health Sciences and Education, St George's, University of London, UK Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, 90024, Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, 90024, Department of Medicine, Lung Biology Center, University of California San Francisco, San Francisco, 94143, Program in Genetic Epidemiology and Statistical Genetics, Harvard School of Public Health, Boston, 02115, Departments of Epidemiology and Biostatistics, Harvard School of Public Health, Boston, MA, 02115, Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, 02142, Department of Genetics Harvard Medical School, Boston, MA, 02115 and Division of Population Health Sciences and Education, St George's, University of London, UK Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, 90024, Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, 90024, Department of Medicine, Lung Biology Center, University of California San Francisco, San Francisco, 94143, Program in Genetic Epidemiology and Statistical Genetics, Har

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http://dx.doi.org/10.1093/bioinformatics/btu416DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4184260PMC
October 2014

Identifying causal variants at loci with multiple signals of association.

Genetics 2014 Oct 7;198(2):497-508. Epub 2014 Aug 7.

Department of Computer Science, University of California, Los Angeles, California 90095 Department of Human Genetics, University of California, Los Angeles, California 90095

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http://dx.doi.org/10.1534/genetics.114.167908DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4196608PMC
October 2014

Integrating functional data to prioritize causal variants in statistical fine-mapping studies.

PLoS Genet 2014 Oct 30;10(10):e1004722. Epub 2014 Oct 30.

Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, California, United States of America; Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America; Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1004722DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4214605PMC
October 2014

Quantifying missing heritability at known GWAS loci.

PLoS Genet 2013 26;9(12):e1003993. Epub 2013 Dec 26.

Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America ; Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America ; Medical and Population Genetics Program, Broad Institute, Cambridge, Massachusetts, United States of America.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3873246PMC
August 2014

IBD genetics: focus on (dys) regulation in immune cells and the epithelium.

Gastroenterology 2014 Apr 22;146(4):896-9. Epub 2014 Feb 22.

Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California. Electronic address:

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http://dx.doi.org/10.1053/j.gastro.2014.02.023DOI Listing
April 2014

Enhanced methods for local ancestry assignment in sequenced admixed individuals.

PLoS Comput Biol 2014 Apr 17;10(4):e1003555. Epub 2014 Apr 17.

Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, California, United States of America; Department of Pathology and Laboratory Medicine, Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America; Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, California, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1003555DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3990492PMC
April 2014

Leveraging reads that span multiple single nucleotide polymorphisms for haplotype inference from sequencing data.

Bioinformatics 2013 Sep 3;29(18):2245-52. Epub 2013 Jul 3.

Department of Computer Science and Inter-Departmental Program in Bioinformatics, University of California, Los Angeles, CA 90095, USA.

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http://dx.doi.org/10.1093/bioinformatics/btt386DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3753566PMC
September 2013

Enhanced localization of genetic samples through linkage-disequilibrium correction.

Am J Hum Genet 2013 Jun 30;92(6):882-94. Epub 2013 May 30.

The Blavatnik School of Computer Science, Tel-Aviv University, Tel-Aviv, 69978, Israel.

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http://dx.doi.org/10.1016/j.ajhg.2013.04.023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3675263PMC
June 2013

Using extended genealogy to estimate components of heritability for 23 quantitative and dichotomous traits.

PLoS Genet 2013 May 30;9(5):e1003520. Epub 2013 May 30.

Department of Medicine, Lung Biology Center, University of California San Francisco, San Francisco, CA, USA.

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http://dx.doi.org/10.1371/journal.pgen.1003520DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3667752PMC
May 2013

Genotyping common and rare variation using overlapping pool sequencing.

BMC Bioinformatics 2011 28;12 Suppl 6:S2. Epub 2011 Jul 28.

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

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http://dx.doi.org/10.1186/1471-2105-12-S6-S2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3194190PMC
December 2011

Combining effects from rare and common genetic variants in an exome-wide association study of sequence data.

BMC Proc 2011 Nov 29;5 Suppl 9:S44. Epub 2011 Nov 29.

1Department of Epidemiology, Harvard School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA.

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http://dx.doi.org/10.1186/1753-6561-5-S9-S44DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3287881PMC
November 2011

New approaches to disease mapping in admixed populations.

Nat Rev Genet 2011 Jun 28;12(8):523-8. Epub 2011 Jun 28.

Department of Biochemistry and Molecular Medicine, University of California Davis, Davis, California, USA.

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http://dx.doi.org/10.1038/nrg3002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3142784PMC
June 2011

Accurate estimation of expression levels of homologous genes in RNA-seq experiments.

J Comput Biol 2011 Mar;18(3):459-68

Departments of Epidemiology and Biostatistics, Harvard School of Public Health, Boston, Massachusetts, USA.

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http://www.liebertpub.com/doi/10.1089/cmb.2010.0259
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March 2011

A generic coalescent-based framework for the selection of a reference panel for imputation.

Genet Epidemiol 2010 Dec;34(8):773-82

International Computer Science Institute, Berkeley, California 94704, USA.

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http://dx.doi.org/10.1002/gepi.20505DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3876740PMC
December 2010

Inference of locus-specific ancestry in closely related populations.

Bioinformatics 2009 Jun;25(12):i213-21

International Computer Science Institute, Computer Science Division, University of California, Berkeley, CA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btp197DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2687951PMC
June 2009

Genotype error detection using Hidden Markov Models of haplotype diversity.

J Comput Biol 2008 Nov;15(9):1155-71

Computer Science and Engineering Department, University of Connecticut, Storrs, Connecticut 06269-2155, USA.

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http://dx.doi.org/10.1089/cmb.2007.0133DOI Listing
November 2008

Highly scalable genotype phasing by entropy minimization.

IEEE/ACM Trans Comput Biol Bioinform 2008 Apr-Jun;5(2):252-61

Computer Science Department, Columbia University, New York, NY 10027, USA.

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http://dx.doi.org/10.1109/TCBB.2007.70223DOI Listing
July 2008

Highly scalable genotype phasing by entropy minimization.

Conf Proc IEEE Eng Med Biol Soc 2006 ;1:3482-6

Dept. of Comput. Sci. & Eng., Connecticut Univ., Storrs, CT 06269-2155, USA.

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http://dx.doi.org/10.1109/IEMBS.2006.259355DOI Listing
March 2008