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Method

Aggregation of recount3 RNA-seq data improves inference of consensus and tissue-specific gene coexpression networks

  • Prashanthi Ravichandran
  • Princy Parsana
  • Rebecca Keener
  • Kasper D. Hansen
  • Alexis Battle
  • First Published July 17, 2025
Method

Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease

  • Tanner D. Jensen
  • Bohan Ni
  • Chloe M. Reuter
  • John E. Gorzynski
  • Sarah Fazal
  • Devon Bonner Rachel A. Ungar Pagé C. Goddard Archana Raja Euan A. Ashley Jonathan A. Bernstein Stephan Zuchner Michael D. Greicius
  • ... [+8 authors] ...,
  • Stephen B. Montgomery
  • Michael C. Schatz
  • Matthew T. Wheeler
  • Alexis Battle
  • First Published March 20, 2025
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
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

Impact of the X Chromosome and sex on regulatory variation

  • Kimberly R. Kukurba
  • Princy Parsana
  • Brunilda Balliu
  • Kevin S. Smith
  • Zachary Zappala
  • David A. Knowles Marie-Julie Favé Joe R. Davis Xin Li Xiaowei Zhu James B. Potash Myrna M. Weissman Jianxin Shi Anshul Kundaje Douglas F. Levinson
  • ... [+10 authors] ...,
  • Philip Awadalla
  • Sara Mostafavi
  • Alexis Battle
  • Stephen B. Montgomery
  • First Published April 21, 2016
Research

Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals

  • Alexis Battle
  • Sara Mostafavi
  • Xiaowei Zhu
  • James B. Potash
  • Myrna M. Weissman
  • Courtney McCormick Christian D. Haudenschild Kenneth B. Beckman Jianxin Shi Rui Mei
  • ... [+5 authors] ...,
  • Alexander E. Urban
  • Stephen B. Montgomery
  • Douglas F. Levinson
  • Daphne Koller
  • First Published October 3, 2013
Research

Chimeras taking shape: Potential functions of proteins encoded by chimeric RNA transcripts

  • Milana Frenkel-Morgenstern
  • Vincent Lacroix
  • Iakes Ezkurdia
  • Yishai Levin
  • Alexandra Gabashvili
  • Jaime Prilusky Angela del Pozo
  • ... [+2 authors] ...,
  • Michael Tress
  • Rory Johnson
  • Roderic Guigo
  • Alfonso Valencia
  • First Published May 15, 2012
Research

Reshaping the gut microbiome with bacterial transplantation and antibiotic intake

  • Chaysavanh Manichanh
  • Jens Reeder
  • Prudence Gibert
  • Encarna Varela
  • Marta Llopis
  • Maria Antolin
  • Roderic Guigo
  • Rob Knight
  • Francisco Guarner
  • First Published August 24, 2010
RESOURCE

Islands of euchromatin-like sequence and expressed polymorphic sequences within the short arm of human chromosome 21

  • Robert Lyle
  • Paola Prandini
  • Kazutoyo Osoegawa
  • Boudewijn ten Hallers
  • Sean Humphray
  • Baoli Zhu Eduardo Eyras Robert Castelo Christine P. Bird Sarantos Gagos Carol Scott Antony Cox Samuel Deutsch Catherine Ucla Marc Cruts Sophie Dahoun Xinwei She Frederique Bena Sheng-Yue Wang Christine Van Broeckhoven Evan E. Eichler Roderic Guigo
  • ... [+17 authors] ...,
  • Jane Rogers
  • Pieter J. de Jong
  • Alexandre Reymond
  • Stylianos E. Antonarakis
  • First Published September 25, 2007
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