M
Mark Gerstein
Researcher at Yale University
Publications - 802
Citations - 172183
Mark Gerstein is an academic researcher from Yale University. The author has contributed to research in topics: Genome & Gene. The author has an hindex of 168, co-authored 751 publications receiving 149578 citations. Previous affiliations of Mark Gerstein include Rutgers University & Structural Genomics Consortium.
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Assessing the limits of genomic data integration for predicting protein networks
TL;DR: By integrating a few good features, this work approaches the maximal predictive power of current genomic data integration; moreover, this limitation does not reflect (potentially removable) inter-relationships between the features.
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Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition.
Bernardo Rodriguez-Martin,Bernardo Rodriguez-Martin,Eva G. Alvarez,Eva G. Alvarez,Adrian Baez-Ortega,Jorge Zamora,Fran Supek,Jonas Demeulemeester,Jonas Demeulemeester,Martin Santamarina,Martin Santamarina,Young Seok Ju,Young Seok Ju,Javier Temes,Daniel García-Souto,Harald Detering,Yang Li,Jorge Rodríguez-Castro,Ana Dueso-Barroso,Ana Dueso-Barroso,Alicia L. Bruzos,Alicia L. Bruzos,Stefan C. Dentro,Stefan C. Dentro,Stefan C. Dentro,Miguel G. Blanco,Gianmarco Contino,Daniel Ardeljan,Marta Tojo,Nicola D. Roberts,Sonia Zumalave,Paul A.W. Edwards,Joachim Weischenfeldt,Joachim Weischenfeldt,Joachim Weischenfeldt,Montserrat Puiggròs,Zechen Chong,Zechen Chong,Ken Chen,Eunjung Lee,Eunjung Lee,Jeremiah Wala,Jeremiah Wala,Keiran Raine,Adam Butler,Sebastian M. Waszak,Fabio C. P. Navarro,Steven E. Schumacher,Steven E. Schumacher,Jean Monlong,Francesco Maura,Francesco Maura,Niccolo Bolli,Guillaume Bourque,Mark Gerstein,Peter J. Park,David C. Wedge,David C. Wedge,Rameen Beroukhim,Rameen Beroukhim,David Torrents,David Torrents,Jan O. Korbel,Inigo Martincorena,Rebecca C. Fitzgerald,Peter Van Loo,Peter Van Loo,Haig H. Kazazian,Kathleen H. Burns,Peter J. Campbell,Peter J. Campbell,Jose M. C. Tubio +71 more
TL;DR: Long interspersed nuclear element (LINE-1; L1 hereafter) insertions emerged as the first most frequent type of somatic structural variation in esophageal adenocarcinoma, and the second most frequent in head-and-neck and colorectal cancers.
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Mapping accessible chromatin regions using Sono-Seq
Raymond K. Auerbach,Ghia Euskirchen,Joel Rozowsky,Nathan Lamarre-Vincent,Zarmik Moqtaderi,Philippe Lefrançois,Kevin Struhl,Mark Gerstein,Michael Snyder +8 more
TL;DR: The results demonstrate that Sono-Seq can be a useful and simple method by which to map many local alterations in chromatin structure and provide insights into the mapping of binding sites by using ChIP–Seq experiments and the value of reference samples that should be used in such experiments.
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The origin, evolution, and functional impact of short insertion–deletion variants identified in 179 human genomes
Stephen B. Montgomery,Stephen B. Montgomery,David L Goode,Erika Kvikstad,Erika Kvikstad,Cornelis A. Albers,Cornelis A. Albers,Zhengdong D. Zhang,Xinmeng Jasmine Mu,Guruprasad Ananda,Bryan Howie,Konrad J. Karczewski,Kevin S. Smith,Vanessa Anaya,Rhea Richardson,Joseph S. Davis,Daniel G. MacArthur,Daniel G. MacArthur,Arend Sidow,Laurent Duret,Mark Gerstein,Kateryna D. Makova,Jonathan Marchini,Gil McVean,Gil McVean,Gerton Lunter +25 more
TL;DR: It is found that indel length modulates selection strength, and that indels affecting multiple functionally constrained nucleotides undergo stronger purifying selection than SNPs, and the causal variant underlying some of these associations may be indels.
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A question of size: the eukaryotic proteome and the problems in defining it
TL;DR: The problems in defining the extent of the proteomes for completely sequenced eukaryotic organisms, focusing on yeast, worm, fly and human, are discussed, and the current estimates for the numbers of human genes are surveyed and a range for the size of the human proteome is estimated.