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Research

Genetic effects on chromatin accessibility uncover mechanisms of liver gene regulation and quantitative traits

  • Kevin W. Currin
  • Hannah J. Perrin
  • Gautam K. Pandey
  • Abdalla A. Alkhawaja
  • Swarooparani Vadlamudi
  • Annie E. Musser Amy S. Etheridge K. Alaine Broadaway Jonathan D. Rosen Arushi Varshney Amarjit S. Chaudhry Paul J. Gallins Fred A. Wright Yi-hui Zhou Stephen C.J. Parker
  • ... [+10 authors] ...,
  • Laura M. Raffield
  • Erin G. Schuetz
  • Federico Innocenti
  • Karen L. Mohlke
  • First Published May 20, 2025
Resource

An integrative TAD catalog in lymphoblastoid cell lines discloses the functional impact of deletions and insertions in human genomes

  • Chong Li
  • Marc Jan Bonder
  • Sabriya Syed
  • Matthew Jensen
  • Mark B. Gerstein
  • Michael C. Zody Mark J.P. Chaisson Michael E. Talkowski Tobias Marschall
  • ... [+4 authors] ...,
  • Jan O. Korbel
  • Evan E. Eichler
  • Charles Lee
  • Xinghua Shi
  • First Published December 5, 2024
Method

Assessing and mitigating privacy risks of sparse, noisy genotypes by local alignment to haplotype databases

  • Prashant S. Emani
  • Maya N. Geradi
  • Gamze Gürsoy
  • Monica R. Grasty
  • Andrew Miranker
  • Mark B. Gerstein
  • First Published December 14, 2023
Method

cis-mediators for trans-eQTLs across many human tissues using genomic mediation analysis" > Identifying cis-mediators for trans-eQTLs across many human tissues using genomic mediation analysis

  • Fan Yang
  • Jiebiao Wang
  • Brandon L. Pierce
  • Lin S. Chen
  • François Aguet
  • Kristin G. Ardlie Beryl B. Cummings Ellen T. Gelfand Gad Getz Kane Hadley Robert E. Handsaker Katherine H. Huang Seva Kashin Konrad J. Karczewski Monkol Lek Xiao Li Daniel G. MacArthur Jared L. Nedzel Duyen T. Nguyen Michael S. Noble Ayellet V. Segrè Casandra A. Trowbridge Taru Tukiainen Nathan S. Abell Brunilda Balliu Ruth Barshir Omer Basha Alexis Battle Gireesh K. Bogu Andrew Brown Christopher D. Brown Stephane E. Castel Lin S. Chen Colby Chiang Donald F. Conrad Nancy J. Cox Farhan N. Damani Joe R. Davis Olivier Delaneau Emmanouil T. Dermitzakis Barbara E. Engelhardt Eleazar Eskin Pedro G. Ferreira Laure Frésard Eric R. Gamazon Diego Garrido-Martín Ariel D.H. Gewirtz Genna Gliner Michael J. Gloudemans Roderic Guigo Ira M. Hall Buhm Han Yuan He Farhad Hormozdiari Cedric Howald Hae Kyung Im Brian Jo Eun Yong Kang Yungil Kim Sarah Kim-Hellmuth Tuuli Lappalainen Gen Li Xin Li Boxiang Liu Serghei Mangul Mark I. McCarthy Ian C. McDowell Pejman Mohammadi Jean Monlong Stephen B. Montgomery Manuel Muñoz-Aguirre Anne W. Ndungu Dan L. Nicolae Andrew B. Nobel Meritxell Oliva Halit Ongen John J. Palowitch Nikolaos Panousis Panagiotis Papasaikas YoSon Park Princy Parsana Anthony J. Payne Christine B. Peterson Jie Quan Ferran Reverter Chiara Sabatti Ashis Saha Michael Sammeth Alexandra J. Scott Andrey A. Shabalin Reza Sodaei Matthew Stephens Barbara E. Stranger Benjamin J. Strober Jae Hoon Sul Emily K. Tsang Sarah Urbut Martijn van de Bunt Gao Wang Xiaoquan Wen Fred A. Wright Hualin S. Xi Esti Yeger-Lotem Zachary Zappala Judith B. Zaugg Yi-Hui Zhou Joshua M. Akey Daniel Bates Joanne Chan Lin S. Chen Melina Claussnitzer Kathryn Demanelis Morgan Diegel Jennifer A. Doherty Andrew P. Feinberg Marian S. Fernando Jessica Halow Kasper D. Hansen Eric Haugen Peter F. Hickey Lei Hou Farzana Jasmine Ruiqi Jian Lihua Jiang Audra Johnson Rajinder Kaul Manolis Kellis Muhammad G. Kibriya Kristen Lee Jin Billy Li Qin Li Xiao Li Jessica Lin Shin Lin Sandra Linder Caroline Linke Yaping Liu Matthew T. Maurano Benoit Molinie Stephen B. Montgomery Jemma Nelson Fidencio J. Neri Meritxell Oliva Yongjin Park Brandon L. Pierce Nicola J. Rinaldi Lindsay F. Rizzardi Richard Sandstrom Andrew Skol Kevin S. Smith Michael P. Snyder John Stamatoyannopoulos Barbara E. Stranger Hua Tang Emily K. Tsang Li Wang Meng Wang Nicholas Van Wittenberghe Fan Wu Rui Zhang Concepcion R. Nierras Philip A. Branton Latarsha J. Carithers Ping Guan Helen M. Moore Abhi Rao Jimmie B. Vaught Sarah E. Gould Nicole C. Lockart Casey Martin Jeffery P. Struewing Simona Volpi Anjene M. Addington Susan E. Koester A. Roger Little Lori E. Brigham Richard Hasz Marcus Hunter Christopher Johns Mark Johnson Gene Kopen William F. Leinweber John T. Lonsdale Alisa McDonald Bernadette Mestichelli Kevin Myer Brian Roe Michael Salvatore Saboor Shad Jeffrey A. Thomas Gary Walters Michael Washington Joseph Wheeler Jason Bridge Barbara A. Foster Bryan M. Gillard Ellen Karasik Rachna Kumar Mark Miklos Michael T. Moser Scott D. Jewell Robert G. Montroy Daniel C. Rohrer Dana R. Valley David A. Davis Deborah C. Mash Anita H. Undale Anna M. Smith David E. Tabor Nancy V. Roche Jeffrey A. McLean Negin Vatanian Karna L. Robinson Leslie Sobin Mary E. Barcus Kimberly M. Valentino Liqun Qi Steven Hunter Pushpa Hariharan Shilpi Singh Ki Sung Um Takunda Matose Maria M. Tomaszewski Laura K. Barker Maghboeba Mosavel Laura A. Siminoff Heather M. Traino Paul Flicek Thomas Juettemann Magali Ruffier Dan Sheppard Kieron Taylor Stephen J. Trevanion Daniel R. Zerbino Brian Craft Mary Goldman Maximilian Haeussler W. James Kent Christopher M. Lee
  • ... [+234 authors] ...,
  • Benedict Paten
  • Kate R. Rosenbloom
  • John Vivian
  • Jingchun Zhu
  • First Published October 11, 2017
Method

Co-expression networks reveal the tissue-specific regulation of transcription and splicing

  • Ashis Saha
  • Yungil Kim
  • Ariel D.H. Gewirtz
  • Brian Jo
  • Chuan Gao
  • Ian C. McDowell Barbara E. Engelhardt Alexis Battle François Aguet Kristin G. Ardlie Beryl B. Cummings Ellen T. Gelfand Gad Getz Kane Hadley Robert E. Handsaker Katherine H. Huang Seva Kashin Konrad J. Karczewski Monkol Lek Xiao Li Daniel G. MacArthur Jared L. Nedzel Duyen T. Nguyen Michael S. Noble Ayellet V. Segrè Casandra A. Trowbridge Taru Tukiainen Nathan S. Abell Brunilda Balliu Ruth Barshir Omer Basha Alexis Battle Gireesh K. Bogu Andrew Brown Christopher D. Brown Stephane E. Castel Lin S. Chen Colby Chiang Donald F. Conrad Nancy J. Cox Farhan N. Damani Joe R. Davis Olivier Delaneau Emmanouil T. Dermitzakis Barbara E. Engelhardt Eleazar Eskin Pedro G. Ferreira Laure Frésard Eric R. Gamazon Diego Garrido-Martín Ariel D.H. Gewirtz Genna Gliner Michael J. Gloudemans Roderic Guigo Ira M. Hall Buhm Han Yuan He Farhad Hormozdiari Cedric Howald Hae Kyung Im Brian Jo Eun Yong Kang Yungil Kim Sarah Kim-Hellmuth Tuuli Lappalainen Gen Li Xin Li Boxiang Liu Serghei Mangul Mark I. McCarthy Ian C. McDowell Pejman Mohammadi Jean Monlong Stephen B. Montgomery Manuel Muñoz-Aguirre Anne W. Ndungu Dan L. Nicolae Andrew B. Nobel Meritxell Oliva Halit Ongen John J. Palowitch Nikolaos Panousis Panagiotis Papasaikas YoSon Park Princy Parsana Anthony J. Payne Christine B. Peterson Jie Quan Ferran Reverter Chiara Sabatti Ashis Saha Michael Sammeth Alexandra J. Scott Andrey A. Shabalin Reza Sodaei Matthew Stephens Barbara E. Stranger Benjamin J. Strober Jae Hoon Sul Emily K. Tsang Sarah Urbut Martijn van de Bunt Gao Wang Xiaoquan Wen Fred A. Wright Hualin S. Xi Esti Yeger-Lotem Zachary Zappala Judith B. Zaugg Yi-Hui Zhou Joshua M. Akey Daniel Bates Joanne Chan Lin S. Chen Melina Claussnitzer Kathryn Demanelis Morgan Diegel Jennifer A. Doherty Andrew P. Feinberg Marian S. Fernando Jessica Halow Kasper D. Hansen Eric Haugen Peter F. Hickey Lei Hou Farzana Jasmine Ruiqi Jian Lihua Jiang Audra Johnson Rajinder Kaul Manolis Kellis Muhammad G. Kibriya Kristen Lee Jin Billy Li Qin Li Xiao Li Jessica Lin Shin Lin Sandra Linder Caroline Linke Yaping Liu Matthew T. Maurano Benoit Molinie Stephen B. Montgomery Jemma Nelson Fidencio J. Neri Meritxell Oliva Yongjin Park Brandon L. Pierce Nicola J. Rinaldi Lindsay F. Rizzardi Richard Sandstrom Andrew Skol Kevin S. Smith Michael P. Snyder John Stamatoyannopoulos Barbara E. Stranger Hua Tang Emily K. Tsang Li Wang Meng Wang Nicholas Van Wittenberghe Fan Wu Rui Zhang Concepcion R. Nierras Philip A. Branton Latarsha J. Carithers Ping Guan Helen M. Moore Abhi Rao Jimmie B. Vaught Sarah E. Gould Nicole C. Lockart Casey Martin Jeffery P. Struewing Simona Volpi Anjene M. Addington Susan E. Koester A. Roger Little Lori E. Brigham Richard Hasz Marcus Hunter Christopher Johns Mark Johnson Gene Kopen William F. Leinweber John T. Lonsdale Alisa McDonald Bernadette Mestichelli Kevin Myer Brian Roe Michael Salvatore Saboor Shad Jeffrey A. Thomas Gary Walters Michael Washington Joseph Wheeler Jason Bridge Barbara A. Foster Bryan M. Gillard Ellen Karasik Rachna Kumar Mark Miklos Michael T. Moser Scott D. Jewell Robert G. Montroy Daniel C. Rohrer Dana R. Valley David A. Davis Deborah C. Mash Anita H. Undale Anna M. Smith David E. Tabor Nancy V. Roche Jeffrey A. McLean Negin Vatanian Karna L. Robinson Leslie Sobin Mary E. Barcus Kimberly M. Valentino Liqun Qi Steven Hunter Pushpa Hariharan Shilpi Singh Ki Sung Um Takunda Matose Maria M. Tomaszewski Laura K. Barker Maghboeba Mosavel Laura A. Siminoff Heather M. Traino Paul Flicek Thomas Juettemann Magali Ruffier Dan Sheppard Kieron Taylor Stephen J. Trevanion Daniel R. Zerbino Brian Craft Mary Goldman Maximilian Haeussler W. James Kent Christopher M. Lee
  • ... [+238 authors] ...,
  • Benedict Paten
  • Kate R. Rosenbloom
  • John Vivian
  • Jingchun Zhu
  • First Published October 11, 2017
Research

Dynamic RNA–protein interactions underlie the zebrafish maternal-to-zygotic transition

  • Vladimir Despic
  • Mario Dejung
  • Mengting Gu
  • Jayanth Krishnan
  • Jing Zhang
  • Lydia Herzel
  • ... [+1 authors] ...,
  • Korinna Straube
  • Mark B. Gerstein
  • Falk Butter
  • Karla M. Neugebauer
  • First Published April 5, 2017
Research

Pangolin genomes and the evolution of mammalian scales and immunity

  • Siew Woh Choo
  • Mike Rayko
  • Tze King Tan
  • Ranjeev Hari
  • Aleksey Komissarov
  • Wei Yee Wee Andrey A. Yurchenko Sergey Kliver Gaik Tamazian Agostinho Antunes Richard K. Wilson Wesley C. Warren Klaus-Peter Koepfli Patrick Minx Ksenia Krasheninnikova Antoinette Kotze Desire L. Dalton Elaine Vermaak Ian C. Paterson Pavel Dobrynin Frankie Thomas Sitam Jeffrine J. Rovie-Ryan Warren E. Johnson Aini Mohamed Yusoff Shu-Jin Luo Kayal Vizi Karuppannan Gang Fang Deyou Zheng
  • ... [+23 authors] ...,
  • Mark B. Gerstein
  • Leonard Lipovich
  • Stephen J. O'Brien
  • Guat Jah Wong
  • First Published August 10, 2016
Research

Great ape Y Chromosome and mitochondrial DNA phylogenies reflect subspecies structure and patterns of mating and dispersal

  • Pille Hallast
  • Pierpaolo Maisano Delser
  • Chiara Batini
  • Daniel Zadik
  • Mariano Rocchi
  • Werner Schempp
  • Chris Tyler-Smith
  • Mark A. Jobling
  • First Published February 16, 2016
Resource

Chlorocebus aethiops sabaeus)" > The genome of the vervet (Chlorocebus aethiops sabaeus)

  • Wesley C. Warren
  • Anna J. Jasinska
  • Raquel García-Pérez
  • Hannes Svardal
  • Chad Tomlinson
  • Mariano Rocchi Nicoletta Archidiacono Oronzo Capozzi Patrick Minx Michael J. Montague Kim Kyung LaDeana W. Hillier Milinn Kremitzki Tina Graves Colby Chiang Jennifer Hughes Nam Tran Yu Huang Vasily Ramensky Oi-wa Choi Yoon J. Jung Christopher A. Schmitt Nikoleta Juretic Jessica Wasserscheid Trudy R. Turner Roger W. Wiseman Jennifer J. Tuscher Julie A. Karl Jörn E. Schmitz Roland Zahn David H. O'Connor Eugene Redmond Alex Nisbett Béatrice Jacquelin Michaela C. Müller-Trutwin Jason M. Brenchley Michel Dione Martin Antonio Gary P. Schroth Jay R. Kaplan Matthew J. Jorgensen Gregg W.C. Thomas Matthew W. Hahn Brian J. Raney Bronwen Aken Rishi Nag Juergen Schmitz Gennady Churakov Angela Noll Roscoe Stanyon David Webb Francoise Thibaud-Nissen Magnus Nordborg Tomas Marques-Bonet
  • ... [+49 authors] ...,
  • Ken Dewar
  • George M. Weinstock
  • Richard K. Wilson
  • Nelson B. Freimer
  • First Published September 16, 2015
Resource

A comprehensive molecular cytogenetic analysis of chromosome rearrangements in gibbons

  • Oronzo Capozzi
  • Lucia Carbone
  • Roscoe R. Stanyon
  • Annamaria Marra
  • Fengtang Yang
  • Christopher W. Whelan
  • Pieter J. de Jong
  • Mariano Rocchi
  • Nicoletta Archidiacono
  • First Published August 14, 2012
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