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Research

Locus-resolution analysis of L1 regulation and retrotransposition potential in mouse embryonic development

  • Patricia Gerdes
  • Dorothy Chan
  • Mischa Lundberg
  • Francisco J. Sanchez-Luque
  • Gabriela O. Bodea
  • Adam D. Ewing
  • Geoffrey J. Faulkner
  • Sandra R. Richardson
  • First Published October 5, 2023
Research

Somatic retrotransposition in the developing rhesus macaque brain

  • Victor Billon
  • Francisco J. Sanchez-Luque
  • Jay Rasmussen
  • Gabriela O. Bodea
  • Daniel J. Gerhardt
  • Patricia Gerdes Seth W. Cheetham Stephanie N. Schauer Prabha Ajjikuttira Thomas J. Meyer Cora E. Layman Kimberly A. Nevonen Natasha Jansz Jose L. Garcia-Perez
  • ... [+9 authors] ...,
  • Sandra R. Richardson
  • Adam D. Ewing
  • Lucia Carbone
  • Geoffrey J. Faulkner
  • First Published June 21, 2022
Research

A hidden layer of structural variation in transposable elements reveals potential genetic modifiers in human disease-risk loci

  • Elisabeth J. van Bree
  • Rita L.F.P. Guimarães
  • Mischa Lundberg
  • Elena R. Blujdea
  • Jimi L. Rosenkrantz
  • Fred T.G. White Josse Poppinga Paula Ferrer-Raventós Anne-Fleur E. Schneider Isabella Clayton David Haussler Marcel J.T. Reinders
  • ... [+7 authors] ...,
  • Henne Holstege
  • Adam D. Ewing
  • Colette Moses
  • Frank M.J. Jacobs
  • First Published March 24, 2022
Research

The genomic basis of evolutionary differentiation among honey bees

  • Bertrand Fouks
  • Philipp Brand
  • Hung N. Nguyen
  • Jacob Herman
  • Francisco Camara
  • Daniel Ence Darren E. Hagen Katharina J. Hoff Stefanie Nachweide Lars Romoth Kimberly K.O. Walden Roderic Guigo Mario Stanke Giuseppe Narzisi Mark Yandell Hugh M. Robertson Nikolaus Koeniger Panuwan Chantawannakul Michael C. Schatz
  • ... [+14 authors] ...,
  • Kim C. Worley
  • Gene E. Robinson
  • Christine G. Elsik
  • Olav Rueppell
  • First Published May 4, 2021
Research

L1 retrotransposition is a common feature of mammalian hepatocarcinogenesis

  • Stephanie N. Schauer
  • Patricia E. Carreira
  • Ruchi Shukla
  • Daniel J. Gerhardt
  • Patricia Gerdes
  • Francisco J. Sanchez-Luque Paola Nicoli Michaela Kindlova Serena Ghisletti Alexandre Dos Santos Delphine Rapoud Didier Samuel
  • ... [+7 authors] ...,
  • Jamila Faivre
  • Adam D. Ewing
  • Sandra R. Richardson
  • Geoffrey J. Faulkner
  • First Published April 11, 2018
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

Heritable L1 retrotransposition in the mouse primordial germline and early embryo

  • Sandra R. Richardson
  • Patricia Gerdes
  • Daniel J. Gerhardt
  • Francisco J. Sanchez-Luque
  • Gabriela-Oana Bodea
  • Martin Muñoz-Lopez J. Samuel Jesuadian Marie-Jeanne H.C. Kempen Patricia E. Carreira Jeffrey A. Jeddeloh
  • ... [+5 authors] ...,
  • Jose L. Garcia-Perez
  • Haig H. Kazazian
  • Adam D. Ewing
  • Geoffrey J. Faulkner
  • First Published May 8, 2017
Research

Widespread somatic L1 retrotransposition occurs early during gastrointestinal cancer evolution

  • Adam D. Ewing
  • Anthony Gacita
  • Laura D. Wood
  • Florence Ma
  • Dongmei Xing
  • Min-Sik Kim Srikanth S. Manda Gabriela Abril Gavin Pereira Alvin Makohon-Moore Leendert H.J. Looijenga Ad J.M. Gillis Ralph H. Hruban Robert A. Anders Katharine E. Romans Akhilesh Pandey Christine A. Iacobuzio-Donahue
  • ... [+12 authors] ...,
  • Bert Vogelstein
  • Kenneth W. Kinzler
  • Haig H. Kazazian
  • Szilvia Solyom
  • First Published August 10, 2015
Research

Extensive somatic L1 retrotransposition in colorectal tumors

  • Szilvia Solyom
  • Adam D. Ewing
  • Eric P. Rahrmann
  • Tara Doucet
  • Heather H. Nelson
  • Michael B. Burns Reuben S. Harris David F. Sigmon Alex Casella Bracha Erlanger Sarah Wheelan Kyle R. Upton
  • ... [+7 authors] ...,
  • Ruchi Shukla
  • Geoffrey J. Faulkner
  • David A. Largaespada
  • Haig H. Kazazian
  • First Published September 11, 2012
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