Mark B Gerstein

Affiliations

Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA. mark@gersteinlab.org.
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA. mark@gersteinlab.org.
Department of Statistics and Data Science, Yale University, New Haven, CT, USA. mark@gersteinlab.org.
Department of Computer Science, Yale University, New Haven, CT, USA. mark@gersteinlab.org.

ORCID: http://orcid.org/0000-0002-9746-3719

Publications (13)

Using sigLASSO to optimize cancer mutation signatures jointly with sampling likelihood.

Nature communications

Avec: Shantao Li , Forrest W Crawford , Mark B Gerstein

A Single-Cell Transcriptomic Atlas of Human Neocortical Development during Mid-gestation.

Neuron

Avec: Damon Polioudakis , Luis de la Torre-Ubieta , Justin Langerman , Andrew G Elkins , Xu Shi , Jason L Stein , Celine K Vuong , Susanne Nichterwitz , Melinda Gevorgian , Carli K Opland , Daning Lu , William Connell , Elizabeth K Ruzzo , Jennifer K Lowe , Tarik Hadzic , Flora I Hinz , Shan Sabri , William E Lowry , Mark B Gerstein , Kathrin Plath , Daniel H Geschwind

Cross-platform transcriptomic profiling of the response to recombinant human erythropoietin.

Scientific reports

Avec: Guan Wang , Traci Kitaoka , Ali Crawford , Qian Mao , Andrew Hesketh , Fergus M Guppy , Garrett I Ash , Jason Liu , Mark B Gerstein , Yannis P Pitsiladis

Author Correction: Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples.

Nature communications

Avec: Matthew H Bailey , William U Meyerson , Lewis Jonathan Dursi , Liang-Bo Wang , Guanlan Dong , Wen-Wei Liang , Amila Weerasinghe , Shantao Li , Yize Li , Sean Kelso , Auteur inconnu , Auteur inconnu , Gordon Saksena , Kyle Ellrott , Michael C Wendl , David A Wheeler , Gad Getz , Jared T Simpson , Mark B Gerstein , Li Ding , Auteur inconnu

Expectations and blind spots for structural variation detection from long-read assemblies and short-read genome sequencing technologies.

American journal of human genetics

Avec: Xuefang Zhao , Ryan L Collins , Wan-Ping Lee , Alexandra M Weber , Yukyung Jun , Qihui Zhu , Ben Weisburd , Yongqing Huang , Peter A Audano , Harold Wang , Mark Walker , Chelsea Lowther , Jack Fu , Auteur inconnu , Mark B Gerstein , Scott E Devine , Tobias Marschall , Jan O Korbel , Evan E Eichler , Mark J P Chaisson , Charles Lee , Ryan E Mills , Harrison Brand , Michael E Talkowski

Nodal modulator (NOMO) is required to sustain endoplasmic reticulum morphology.

The Journal of biological chemistry

Avec: Catherine Amaya , Christopher J F Cameron , Swapnil C Devarkar , Sebastian J H Seager , Mark B Gerstein , Yong Xiong , Christian Schlieker

The ENCODE4 long-read RNA-seq collection reveals distinct classes of transcript structure diversity.

bioRxiv : the preprint server for biology

Avec: Fairlie Reese , Brian Williams , Gabriela Balderrama-Gutierrez , Dana Wyman , Muhammed Hasan Çelik , Elisabeth Rebboah , Narges Rezaie , Diane Trout , Milad Razavi-Mohseni , Yunzhe Jiang , Beatrice Borsari , Samuel Morabito , Heidi Yahan Liang , Cassandra J McGill , Sorena Rahmanian , Jasmine Sakr , Shan Jiang , Weihua Zeng , Klebea Carvalho , Annika K Weimer , Louise A Dionne , Ariel McShane , Karan Bedi , Shaimae I Elhajjajy , Sean Upchurch , Jennifer Jou , Ingrid Youngworth , Idan Gabdank , Paul Sud , Otto Jolanki , J Seth Strattan , Meenakshi S Kagda , Michael P Snyder , Ben C Hitz , Jill E Moore , Zhiping Weng , David Bennett , Laura Reinholdt , Mats Ljungman , Michael A Beer , Mark B Gerstein , Lior Pachter , Roderic Guigó , Barbara J Wold , Ali Mortazavi

exRNA Atlas Analysis Reveals Distinct Extracellular RNA Cargo Types and Their Carriers Present across Human Biofluids.

Cell

Avec: Oscar D Murillo , William Thistlethwaite , Joel Rozowsky , Sai Lakshmi Subramanian , Rocco Lucero , Neethu Shah , Andrew R Jackson , Srimeenakshi Srinivasan , Allen Chung , Clara D Laurent , Robert R Kitchen , Timur Galeev , Jonathan Warrell , James A Diao , Joshua A Welsh , Kristina Hanspers , Anders Riutta , Sebastian Burgstaller-Muehlbacher , Ravi V Shah , Ashish Yeri , Lisa M Jenkins , Mehmet E Ahsen , Carlos Cordon-Cardo , Navneet Dogra , Stacey M Gifford , Joshua T Smith , Gustavo Stolovitzky , Ashutosh K Tewari , Benjamin H Wunsch , Kamlesh K Yadav , Kirsty M Danielson , Justyna Filant , Courtney Moeller , Parham Nejad , Anu Paul , Bridget Simonson , David K Wong , Xuan Zhang , Leonora Balaj , Roopali Gandhi , Anil K Sood , Roger P Alexander , Liang Wang , Chunlei Wu , David T W Wong , David J Galas , Kendall Van Keuren-Jensen , Tushar Patel , Jennifer C Jones , Saumya Das , Kei-Hoi Cheung , Alexander R Pico , Andrew I Su , Robert L Raffai , Louise C Laurent , Matthew E Roth , Mark B Gerstein , Aleksandar Milosavljevic

Passenger Mutations in More Than 2,500 Cancer Genomes: Overall Molecular Functional Impact and Consequences.

Cell

Avec: Sushant Kumar , Jonathan Warrell , Shantao Li , Patrick D McGillivray , William Meyerson , Leonidas Salichos , Arif Harmanci , Alexander Martinez-Fundichely , Calvin W Y Chan , Morten Muhlig Nielsen , Lucas Lochovsky , Yan Zhang , Xiaotong Li , Shaoke Lou , Jakob Skou Pedersen , Carl Herrmann , Gad Getz , Ekta Khurana , Mark B Gerstein

Haplotype-resolved diverse human genomes and integrated analysis of structural variation.

Science (New York, N.Y.)

Avec: Peter Ebert , Peter A Audano , Qihui Zhu , Bernardo Rodriguez-Martin , David Porubsky , Marc Jan Bonder , Arvis Sulovari , Jana Ebler , Weichen Zhou , Rebecca Serra Mari , Feyza Yilmaz , Xuefang Zhao , PingHsun Hsieh , Joyce Lee , Sushant Kumar , Jiadong Lin , Tobias Rausch , Yu Chen , Jingwen Ren , Martin Santamarina , Wolfram Höps , Hufsah Ashraf , Nelson T Chuang , Xiaofei Yang , Katherine M Munson , Alexandra P Lewis , Susan Fairley , Luke J Tallon , Wayne E Clarke , Anna O Basile , Marta Byrska-Bishop , André Corvelo , Uday S Evani , Tsung-Yu Lu , Mark J P Chaisson , Junjie Chen , Chong Li , Harrison Brand , Aaron M Wenger , Maryam Ghareghani , William T Harvey , Benjamin Raeder , Patrick Hasenfeld , Allison A Regier , Haley J Abel , Ira M Hall , Paul Flicek , Oliver Stegle , Mark B Gerstein , Jose M C Tubio , Zepeng Mu , Yang I Li , Xinghua Shi , Alex R Hastie , Kai Ye , Zechen Chong , Ashley D Sanders , Michael C Zody , Michael E Talkowski , Ryan E Mills , Scott E Devine , Charles Lee , Jan O Korbel , Tobias Marschall , Evan E Eichler

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples.

Nature communications

Avec: Matthew H Bailey , William U Meyerson , Lewis Jonathan Dursi , Liang-Bo Wang , Guanlan Dong , Wen-Wei Liang , Amila Weerasinghe , Shantao Li , Yize Li , Sean Kelso , Auteur inconnu , Auteur inconnu , Gordon Saksena , Kyle Ellrott , Michael C Wendl , David A Wheeler , Gad Getz , Jared T Simpson , Mark B Gerstein , Li Ding , Auteur inconnu

Establishing a Global Standard for Wearable Devices in Sport and Exercise Medicine: Perspectives from Academic and Industry Stakeholders.

Sports medicine (Auckland, N.Z.)

Avec: Garrett I Ash , Matthew Stults-Kolehmainen , Michael A Busa , Allison E Gaffey , Konstantinos Angeloudis , Borja Muniz-Pardos , Robert Gregory , Robert A Huggins , Nancy S Redeker , Stuart A Weinzimer , Lauren A Grieco , Kate Lyden , Esmeralda Megally , Ioannis Vogiatzis , LaurieAnn Scher , Xinxin Zhu , Julien S Baker , Cynthia Brandt , Michael S Businelle , Lisa M Fucito , Stephanie Griggs , Robert Jarrin , Bobak J Mortazavi , Temiloluwa Prioleau , Walter Roberts , Elias K Spanakis , Laura M Nally , Andre Debruyne , Norbert Bachl , Fabio Pigozzi , Farzin Halabchi , Dimakatso A Ramagole , Dina C Janse van Rensburg , Bernd Wolfarth , Chiara Fossati , Sandra Rozenstoka , Kumpei Tanisawa , Mats Börjesson , José Antonio Casajus , Alex Gonzalez-Aguero , Irina Zelenkova , Jeroen Swart , Gamze Gursoy , William Meyerson , Jason Liu , Dov Greenbaum , Yannis P Pitsiladis , Mark B Gerstein

Insights from incorporating quantum computing into drug design workflows.

Bioinformatics (Oxford, England)

Avec: Bayo Lau , Prashant S Emani , Jackson Chapman , Lijing Yao , Tarsus Lam , Paul Merrill , Jonathan Warrell , Mark B Gerstein , Hugo Y K Lam

Réseau de co-auteurs

None None 7 collaborations

Shantao Li 4 collaborations

Gad Getz 3 collaborations

Jonathan Warrell 3 collaborations

Garrett I Ash 2 collaborations

Jason Liu 2 collaborations

Yannis P Pitsiladis 2 collaborations

Matthew H Bailey 2 collaborations

William U Meyerson 2 collaborations

Lewis Jonathan Dursi 2 collaborations

Liang-Bo Wang 2 collaborations

Guanlan Dong 2 collaborations

Wen-Wei Liang 2 collaborations

Amila Weerasinghe 2 collaborations

Yize Li 2 collaborations

Sean Kelso 2 collaborations

Gordon Saksena 2 collaborations

Kyle Ellrott 2 collaborations

Michael C Wendl 2 collaborations

David A Wheeler 2 collaborations

Jared T Simpson 2 collaborations

Li Ding 2 collaborations

Xuefang Zhao 2 collaborations

Qihui Zhu 2 collaborations

Peter A Audano 2 collaborations

Scott E Devine 2 collaborations

Tobias Marschall 2 collaborations

Jan O Korbel 2 collaborations

Evan E Eichler 2 collaborations

Mark J P Chaisson 2 collaborations

Charles Lee 2 collaborations

Ryan E Mills 2 collaborations

Harrison Brand 2 collaborations

Michael E Talkowski 2 collaborations

Sushant Kumar 2 collaborations

William Meyerson 2 collaborations

Forrest W Crawford 1 collaboration

Damon Polioudakis 1 collaboration

Luis de la Torre-Ubieta 1 collaboration

Justin Langerman 1 collaboration

Andrew G Elkins 1 collaboration

Xu Shi 1 collaboration

Jason L Stein 1 collaboration

Celine K Vuong 1 collaboration

Susanne Nichterwitz 1 collaboration

Melinda Gevorgian 1 collaboration

Carli K Opland 1 collaboration

Daning Lu 1 collaboration

William Connell 1 collaboration

Elizabeth K Ruzzo 1 collaboration

Jennifer K Lowe 1 collaboration

Tarik Hadzic 1 collaboration

Flora I Hinz 1 collaboration

Shan Sabri 1 collaboration

William E Lowry 1 collaboration

Kathrin Plath 1 collaboration

Daniel H Geschwind 1 collaboration

Guan Wang 1 collaboration

Traci Kitaoka 1 collaboration

Ali Crawford 1 collaboration

Qian Mao 1 collaboration

Andrew Hesketh 1 collaboration

Fergus M Guppy 1 collaboration

Ryan L Collins 1 collaboration

Wan-Ping Lee 1 collaboration

Alexandra M Weber 1 collaboration

Yukyung Jun 1 collaboration

Ben Weisburd 1 collaboration

Yongqing Huang 1 collaboration

Harold Wang 1 collaboration

Mark Walker 1 collaboration

Chelsea Lowther 1 collaboration

Jack Fu 1 collaboration

Catherine Amaya 1 collaboration

Christopher J F Cameron 1 collaboration

Swapnil C Devarkar 1 collaboration

Sebastian J H Seager 1 collaboration

Yong Xiong 1 collaboration

Christian Schlieker 1 collaboration

Fairlie Reese 1 collaboration

Brian Williams 1 collaboration

Gabriela Balderrama-Gutierrez 1 collaboration

Dana Wyman 1 collaboration

Muhammed Hasan Çelik 1 collaboration

Elisabeth Rebboah 1 collaboration

Narges Rezaie 1 collaboration

Diane Trout 1 collaboration

Milad Razavi-Mohseni 1 collaboration

Yunzhe Jiang 1 collaboration

Beatrice Borsari 1 collaboration

Samuel Morabito 1 collaboration

Heidi Yahan Liang 1 collaboration

Cassandra J McGill 1 collaboration

Sorena Rahmanian 1 collaboration

Jasmine Sakr 1 collaboration

Shan Jiang 1 collaboration

Weihua Zeng 1 collaboration

Klebea Carvalho 1 collaboration

Annika K Weimer 1 collaboration

Louise A Dionne 1 collaboration

Ariel McShane 1 collaboration

Karan Bedi 1 collaboration

Shaimae I Elhajjajy 1 collaboration

Sean Upchurch 1 collaboration

Jennifer Jou 1 collaboration

Ingrid Youngworth 1 collaboration

Idan Gabdank 1 collaboration

Paul Sud 1 collaboration

Otto Jolanki 1 collaboration

J Seth Strattan 1 collaboration

Meenakshi S Kagda 1 collaboration

Michael P Snyder 1 collaboration

Ben C Hitz 1 collaboration

Jill E Moore 1 collaboration

Zhiping Weng 1 collaboration

David Bennett 1 collaboration

Laura Reinholdt 1 collaboration

Mats Ljungman 1 collaboration

Michael A Beer 1 collaboration

Lior Pachter 1 collaboration

Roderic Guigó 1 collaboration

Barbara J Wold 1 collaboration

Ali Mortazavi 1 collaboration

Oscar D Murillo 1 collaboration

William Thistlethwaite 1 collaboration

Joel Rozowsky 1 collaboration

Sai Lakshmi Subramanian 1 collaboration

Rocco Lucero 1 collaboration

Neethu Shah 1 collaboration

Andrew R Jackson 1 collaboration

Srimeenakshi Srinivasan 1 collaboration

Allen Chung 1 collaboration

Clara D Laurent 1 collaboration

Robert R Kitchen 1 collaboration

Timur Galeev 1 collaboration

James A Diao 1 collaboration

Joshua A Welsh 1 collaboration

Kristina Hanspers 1 collaboration

Anders Riutta 1 collaboration

Sebastian Burgstaller-Muehlbacher 1 collaboration

Ravi V Shah 1 collaboration

Ashish Yeri 1 collaboration

Lisa M Jenkins 1 collaboration

Mehmet E Ahsen 1 collaboration

Carlos Cordon-Cardo 1 collaboration

Navneet Dogra 1 collaboration

Stacey M Gifford 1 collaboration

Joshua T Smith 1 collaboration

Gustavo Stolovitzky 1 collaboration

Ashutosh K Tewari 1 collaboration

Benjamin H Wunsch 1 collaboration

Kamlesh K Yadav 1 collaboration

Kirsty M Danielson 1 collaboration

Justyna Filant 1 collaboration

Courtney Moeller 1 collaboration

Parham Nejad 1 collaboration

Anu Paul 1 collaboration

Bridget Simonson 1 collaboration

David K Wong 1 collaboration

Xuan Zhang 1 collaboration

Leonora Balaj 1 collaboration

Roopali Gandhi 1 collaboration

Anil K Sood 1 collaboration

Roger P Alexander 1 collaboration

Liang Wang 1 collaboration

Chunlei Wu 1 collaboration

David T W Wong 1 collaboration

David J Galas 1 collaboration

Kendall Van Keuren-Jensen 1 collaboration

Tushar Patel 1 collaboration

Jennifer C Jones 1 collaboration

Saumya Das 1 collaboration

Kei-Hoi Cheung 1 collaboration

Alexander R Pico 1 collaboration

Andrew I Su 1 collaboration

Robert L Raffai 1 collaboration

Louise C Laurent 1 collaboration

Matthew E Roth 1 collaboration

Aleksandar Milosavljevic 1 collaboration

Patrick D McGillivray 1 collaboration

Leonidas Salichos 1 collaboration

Arif Harmanci 1 collaboration

Alexander Martinez-Fundichely 1 collaboration

Calvin W Y Chan 1 collaboration

Morten Muhlig Nielsen 1 collaboration

Lucas Lochovsky 1 collaboration

Yan Zhang 1 collaboration

Xiaotong Li 1 collaboration

Shaoke Lou 1 collaboration

Jakob Skou Pedersen 1 collaboration

Carl Herrmann 1 collaboration

Ekta Khurana 1 collaboration

Peter Ebert 1 collaboration

Bernardo Rodriguez-Martin 1 collaboration

David Porubsky 1 collaboration

Marc Jan Bonder 1 collaboration

Arvis Sulovari 1 collaboration

Jana Ebler 1 collaboration

Weichen Zhou 1 collaboration

Rebecca Serra Mari 1 collaboration

Feyza Yilmaz 1 collaboration

PingHsun Hsieh 1 collaboration

Joyce Lee 1 collaboration

Jiadong Lin 1 collaboration

Tobias Rausch 1 collaboration

Yu Chen 1 collaboration

Jingwen Ren 1 collaboration

Martin Santamarina 1 collaboration

Wolfram Höps 1 collaboration

Hufsah Ashraf 1 collaboration

Nelson T Chuang 1 collaboration

Xiaofei Yang 1 collaboration

Katherine M Munson 1 collaboration

Alexandra P Lewis 1 collaboration

Susan Fairley 1 collaboration

Luke J Tallon 1 collaboration

Wayne E Clarke 1 collaboration

Anna O Basile 1 collaboration

Marta Byrska-Bishop 1 collaboration

André Corvelo 1 collaboration

Uday S Evani 1 collaboration

Tsung-Yu Lu 1 collaboration

Junjie Chen 1 collaboration

Chong Li 1 collaboration

Aaron M Wenger 1 collaboration

Maryam Ghareghani 1 collaboration

William T Harvey 1 collaboration

Benjamin Raeder 1 collaboration

Patrick Hasenfeld 1 collaboration

Allison A Regier 1 collaboration

Haley J Abel 1 collaboration

Ira M Hall 1 collaboration

Paul Flicek 1 collaboration

Oliver Stegle 1 collaboration

Jose M C Tubio 1 collaboration

Zepeng Mu 1 collaboration

Yang I Li 1 collaboration

Xinghua Shi 1 collaboration

Alex R Hastie 1 collaboration

Kai Ye 1 collaboration

Zechen Chong 1 collaboration

Ashley D Sanders 1 collaboration

Michael C Zody 1 collaboration

Matthew Stults-Kolehmainen 1 collaboration

Michael A Busa 1 collaboration

Allison E Gaffey 1 collaboration

Konstantinos Angeloudis 1 collaboration

Borja Muniz-Pardos 1 collaboration

Robert Gregory 1 collaboration

Robert A Huggins 1 collaboration

Nancy S Redeker 1 collaboration

Stuart A Weinzimer 1 collaboration

Lauren A Grieco 1 collaboration

Kate Lyden 1 collaboration

Esmeralda Megally 1 collaboration

Ioannis Vogiatzis 1 collaboration

LaurieAnn Scher 1 collaboration

Xinxin Zhu 1 collaboration

Julien S Baker 1 collaboration

Cynthia Brandt 1 collaboration

Michael S Businelle 1 collaboration

Lisa M Fucito 1 collaboration

Stephanie Griggs 1 collaboration

Robert Jarrin 1 collaboration

Bobak J Mortazavi 1 collaboration

Temiloluwa Prioleau 1 collaboration

Walter Roberts 1 collaboration

Elias K Spanakis 1 collaboration

Laura M Nally 1 collaboration

Andre Debruyne 1 collaboration

Norbert Bachl 1 collaboration

Fabio Pigozzi 1 collaboration

Farzin Halabchi 1 collaboration

Dimakatso A Ramagole 1 collaboration

Dina C Janse van Rensburg 1 collaboration

Bernd Wolfarth 1 collaboration

Chiara Fossati 1 collaboration

Sandra Rozenstoka 1 collaboration

Kumpei Tanisawa 1 collaboration

Mats Börjesson 1 collaboration

José Antonio Casajus 1 collaboration

Alex Gonzalez-Aguero 1 collaboration

Irina Zelenkova 1 collaboration

Jeroen Swart 1 collaboration

Gamze Gursoy 1 collaboration

Dov Greenbaum 1 collaboration

Bayo Lau 1 collaboration

Prashant S Emani 1 collaboration

Jackson Chapman 1 collaboration

Lijing Yao 1 collaboration

Tarsus Lam 1 collaboration

Paul Merrill 1 collaboration

Hugo Y K Lam 1 collaboration