Sean Whalen

Sean Whalen

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Sean Whalen

Sean Whalen

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15Publications

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Reply to 'Inflated performance measures in enhancer-promoter interaction-prediction methods'.

Authors:
Sean Whalen Katherine S Pollard

Nat Genet 2019 Aug;51(8):1198-1200

Gladstone Institutes, San Francisco, CA, USA.

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http://dx.doi.org/10.1038/s41588-019-0473-0DOI Listing
August 2019

AlleleAnalyzer: a tool for personalized and allele-specific sgRNA design.

Authors:
Kathleen C Keough Svetlana Lyalina Michael P Olvera Sean Whalen Bruce R Conklin Katherine S Pollard

Genome Biol 2019 08 15;20(1):167. Epub 2019 Aug 15.

Gladstone Institutes, San Francisco, CA, USA.

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http://dx.doi.org/10.1186/s13059-019-1783-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6694686PMC
August 2019

The glycan CA19-9 promotes pancreatitis and pancreatic cancer in mice.

Authors:
Dannielle D Engle Hervé Tiriac Keith D Rivera Arnaud Pommier Sean Whalen Tobiloba E Oni Brinda Alagesan Eun Jung Lee Melissa A Yao Matthew S Lucito Benjamin Spielman Brandon Da Silva Christina Schoepfer Kevin Wright Brianna Creighton Lauren Afinowicz Kenneth H Yu Robert Grützmann Daniela Aust Phyllis A Gimotty Katherine S Pollard Ralph H Hruban Michael G Goggins Christian Pilarsky Youngkyu Park Darryl J Pappin Michael A Hollingsworth David A Tuveson

Science 2019 06;364(6446):1156-1162

Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.

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http://dx.doi.org/10.1126/science.aaw3145DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6705393PMC
June 2019

Most chromatin interactions are not in linkage disequilibrium.

Authors:
Sean Whalen Katherine S Pollard

Genome Res 2019 03 7;29(3):334-343. Epub 2019 Jan 7.

Gladstone Institutes, San Francisco, California 94158, USA.

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http://genome.cshlp.org/lookup/doi/10.1101/gr.238022.118
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http://dx.doi.org/10.1101/gr.238022.118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6396425PMC
March 2019

The Epstein-Barr Virus Episome Maneuvers between Nuclear Chromatin Compartments during Reactivation.

Authors:
Stephanie A Moquin Sean Thomas Sean Whalen Alix Warburton Samantha G Fernandez Alison A McBride Katherine S Pollard Jj L Miranda

J Virol 2018 02 17;92(3). Epub 2018 Jan 17.

Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA

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http://dx.doi.org/10.1128/JVI.01413-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5774889PMC
February 2018

Genomic analyses identify hundreds of variants associated with age at menarche and support a role for puberty timing in cancer risk.

Authors:
Felix R Day Deborah J Thompson Hannes Helgason Daniel I Chasman Hilary Finucane Patrick Sulem Katherine S Ruth Sean Whalen Abhishek K Sarkar Eva Albrecht Elisabeth Altmaier Marzyeh Amini Caterina M Barbieri Thibaud Boutin Archie Campbell Ellen Demerath Ayush Giri Chunyan He Jouke J Hottenga Robert Karlsson Ivana Kolcic Po-Ru Loh Kathryn L Lunetta Massimo Mangino Brumat Marco George McMahon Sarah E Medland Ilja M Nolte Raymond Noordam Teresa Nutile Lavinia Paternoster Natalia Perjakova Eleonora Porcu Lynda M Rose Katharina E Schraut Ayellet V Segrè Albert V Smith Lisette Stolk Alexander Teumer Irene L Andrulis Stefania Bandinelli Matthias W Beckmann Javier Benitez Sven Bergmann Murielle Bochud Eric Boerwinkle Stig E Bojesen Manjeet K Bolla Judith S Brand Hiltrud Brauch Hermann Brenner Linda Broer Thomas Brüning Julie E Buring Harry Campbell Eulalia Catamo Stephen Chanock Georgia Chenevix-Trench Tanguy Corre Fergus J Couch Diana L Cousminer Angela Cox Laura Crisponi Kamila Czene George Davey Smith Eco J C N de Geus Renée de Mutsert Immaculata De Vivo Joe Dennis Peter Devilee Isabel Dos-Santos-Silva Alison M Dunning Johan G Eriksson Peter A Fasching Lindsay Fernández-Rhodes Luigi Ferrucci Dieter Flesch-Janys Lude Franke Marike Gabrielson Ilaria Gandin Graham G Giles Harald Grallert Daniel F Gudbjartsson Pascal Guénel Per Hall Emily Hallberg Ute Hamann Tamara B Harris Catharina A Hartman Gerardo Heiss Maartje J Hooning John L Hopper Frank Hu David J Hunter M Arfan Ikram Hae Kyung Im Marjo-Riitta Järvelin Peter K Joshi David Karasik Manolis Kellis Zoltan Kutalik Genevieve LaChance Diether Lambrechts Claudia Langenberg Lenore J Launer Joop S E Laven Stefania Lenarduzzi Jingmei Li Penelope A Lind Sara Lindstrom YongMei Liu Jian'an Luan Reedik Mägi Arto Mannermaa Hamdi Mbarek Mark I McCarthy Christa Meisinger Thomas Meitinger Cristina Menni Andres Metspalu Kyriaki Michailidou Lili Milani Roger L Milne Grant W Montgomery Anna M Mulligan Mike A Nalls Pau Navarro Heli Nevanlinna Dale R Nyholt Albertine J Oldehinkel Tracy A O'Mara Sandosh Padmanabhan Aarno Palotie Nancy Pedersen Annette Peters Julian Peto Paul D P Pharoah Anneli Pouta Paolo Radice Iffat Rahman Susan M Ring Antonietta Robino Frits R Rosendaal Igor Rudan Rico Rueedi Daniela Ruggiero Cinzia F Sala Marjanka K Schmidt Robert A Scott Mitul Shah Rossella Sorice Melissa C Southey Ulla Sovio Meir Stampfer Maristella Steri Konstantin Strauch Toshiko Tanaka Emmi Tikkanen Nicholas J Timpson Michela Traglia Thérèse Truong Jonathan P Tyrer André G Uitterlinden Digna R Velez Edwards Veronique Vitart Uwe Völker Peter Vollenweider Qin Wang Elisabeth Widen Ko Willems van Dijk Gonneke Willemsen Robert Winqvist Bruce H R Wolffenbuttel Jing Hua Zhao Magdalena Zoledziewska Marek Zygmunt Behrooz Z Alizadeh Dorret I Boomsma Marina Ciullo Francesco Cucca Tõnu Esko Nora Franceschini Christian Gieger Vilmundur Gudnason Caroline Hayward Peter Kraft Debbie A Lawlor Patrik K E Magnusson Nicholas G Martin Dennis O Mook-Kanamori Ellen A Nohr Ozren Polasek David Porteous Alkes L Price Paul M Ridker Harold Snieder Tim D Spector Doris Stöckl Daniela Toniolo Sheila Ulivi Jenny A Visser Henry Völzke Nicholas J Wareham James F Wilson Amanda B Spurdle Unnur Thorsteindottir Katherine S Pollard Douglas F Easton Joyce Y Tung Jenny Chang-Claude David Hinds Anna Murray Joanne M Murabito Kari Stefansson Ken K Ong John R B Perry

Nat Genet 2017 Jun 24;49(6):834-841. Epub 2017 Apr 24.

MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, UK.

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http://dx.doi.org/10.1038/ng.3841DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5841952PMC
June 2017

Analysis of Transcriptional Variability in a Large Human iPSC Library Reveals Genetic and Non-genetic Determinants of Heterogeneity.

Authors:
Ivan Carcamo-Orive Gabriel E Hoffman Paige Cundiff Noam D Beckmann Sunita L D'Souza Joshua W Knowles Achchhe Patel Dimitri Papatsenko Fahim Abbasi Gerald M Reaven Sean Whalen Philip Lee Mohammad Shahbazi Marc Y R Henrion Kuixi Zhu Sven Wang Panos Roussos Eric E Schadt Gaurav Pandey Rui Chang Thomas Quertermous Ihor Lemischka

Cell Stem Cell 2017 04 22;20(4):518-532.e9. Epub 2016 Dec 22.

Department of Developmental and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.

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http://dx.doi.org/10.1016/j.stem.2016.11.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5384872PMC
April 2017

Unboxing cluster heatmaps.

Authors:
Sophie Engle Sean Whalen Alark Joshi Katherine S Pollard

BMC Bioinformatics 2017 Feb 15;18(Suppl 2):63. Epub 2017 Feb 15.

Gladstone Institutes, San Francisco, 94158, CA, USA.

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http://dx.doi.org/10.1186/s12859-016-1442-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5333167PMC
February 2017

Enhancer-promoter interactions are encoded by complex genomic signatures on looping chromatin.

Authors:
Sean Whalen Rebecca M Truty Katherine S Pollard

Nat Genet 2016 05 4;48(5):488-96. Epub 2016 Apr 4.

Gladstone Institutes, San Francisco, California, USA.

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http://dx.doi.org/10.1038/ng.3539DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4910881PMC
May 2016

Predicting protein function and other biomedical characteristics with heterogeneous ensembles.

Authors:
Sean Whalen Om Prakash Pandey Gaurav Pandey

Methods 2016 Jan 2;93:92-102. Epub 2015 Sep 2.

Icahn Institute for Genomics and Multiscale Biology and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ymeth.2015.08.016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4718788PMC
January 2016

Enhancing the functional content of eukaryotic protein interaction networks.

Authors:
Gaurav Pandey Sonali Arora Sahil Manocha Sean Whalen

PLoS One 2014 2;9(10):e109130. Epub 2014 Oct 2.

Institute for Genomics and Multiscale Biology and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America; Gladstone Institutes, University of California San Francisco, San Francisco, CA, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0109130PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4183583PMC
December 2015

Structural drift: the population dynamics of sequential learning.

Authors:
James P Crutchfield Sean Whalen

PLoS Comput Biol 2012 7;8(6):e1002510. Epub 2012 Jun 7.

Complexity Sciences Center, Physics Department, University of California Davis, Davis, California, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1002510DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3369870PMC
October 2012

Abduction and external rotation in shoulder impingement: an open MR study on healthy volunteers initial experience.

Authors:
Garry E Gold George P Pappas Silvia S Blemker Sean T Whalen Gordon Campbell Timothy A McAdams Christopher F Beaulieu

Radiology 2007 Sep 9;244(3):815-22. Epub 2007 Aug 9.

Department of Radiology, Stanford University School of Medicine, CA 94305-5105, and Harvard Combined Orthopaedics Program, Department of Orthopaedic Surgery, Massachusetts General Hospital, Boston, MA, USA.

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http://dx.doi.org/10.1148/radiol.2443060998DOI Listing
September 2007

In vivo anatomy of the Neer and Hawkins sign positions for shoulder impingement.

Authors:
George P Pappas Silvia S Blemker Christopher F Beaulieu Timothy R McAdams Sean T Whalen Garry E Gold

J Shoulder Elbow Surg 2006 Jan-Feb;15(1):40-9

Medical Center, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1016/j.jse.2005.04.007DOI Listing
May 2006

Intrapulpal temperature increases with temporary crown and bridge materials.

Authors:
Sean Whalen Murray Bouschlicher

Gen Dent 2003 Nov-Dec;51(6):534-7

University of Iowa, Iowa City, USA.

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April 2004