Search | Genome Research

Method

High-throughput characterization of genetic effects on DNA–protein binding and gene transcription

Cynthia A. Kalita
Christopher D. Brown
Andrew Freiman
Jenna Isherwood
Xiaoquan Wen
Roger Pique-Regi
Francesca Luca

First Published September 25, 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

Transposable elements are the primary source of novelty in primate gene regulation

Marco Trizzino
YoSon Park
Marcia Holsbach-Beltrame
Katherine Aracena
Katelyn Mika
Minal Caliskan
George H. Perry
Vincent J. Lynch
Christopher D. Brown

First Published August 30, 2017

Research

Drosophila" > Fragile regions and not functional constraints predominate in shaping gene organization in the genus Drosophila

Marcin von Grotthuss
Michael Ashburner
José M. Ranz

First Published July 2, 2010

PERSPECTIVE

Qualifying the relationship between sequence conservation and molecular function

Gregory M. Cooper
Christopher D. Brown

First Published February 1, 2008

LETTER

Ciona exhibit strong correspondence between evolutionary constraint and functional importance" > Noncoding regulatory sequences of Ciona exhibit strong correspondence between evolutionary constraint and functional importance

David S. Johnson
Brad Davidson
Christopher D. Brown
William C. Smith
Arend Sidow

First Published November 15, 2004

LETTER

Drosophila melanogaster" > Assessment of Genome-Wide Protein Function Classification for Drosophila melanogaster

Huaiyu Mi
Jody Vandergriff
Michael Campbell
Apurva Narechania
William Majoros
Suzanna Lewis
Paul D. Thomas
Michael Ashburner

First Published September 2, 2003

LETTER

X Chromosome of Drosophila melanogaster, a Comparison of Two Sequencing Strategies" > From First Base: The Sequence of the Tip of the X Chromosome of Drosophila melanogaster, a Comparison of Two Sequencing Strategies

Panayiotis V. Benos
Melanie K. Gatt
Lee Murphy
David Harris
Bart Barrell
Concepcion Ferraz Sophie Vidal Christine Brun Jacques Demaille Edouard Cadieu Stephane Dreano Stéphanie Gloux Valerie Lelaure Stephanie Mottier Francis Galibert Dana Borkova Belen Miñana Fotis C. Kafatos Slava Bolshakov Inga Sidén-Kiamos George Papagiannakis Lefteris Spanos Christos Louis Encarnación Madueño Beatriz de Pablos Juan Modolell Annette Peter Petra Schöttler Meike Werner Fotini Mourkioti Nicole Beinert Gordon Dowe Ulrich Schäfer Herbert Jäckle Alain Bucheton Debbie Callister Lorna Campbell Nadine S. Henderson Paul J. McMillan Cathy Salles Evelyn Tait Phillipe Valenti Robert D.C. Saunders
... [+38 authors] ...,
Alain Billaud
Lior Pachter
David M. Glover
Michael Ashburner

First Published May 1, 2001

INSIGHT/OUTLOOK

Drosophila Genome Annotation Assessment Project" > A Biologist's View of the Drosophila Genome Annotation Assessment Project

Michael Ashburner

First Published April 1, 2000

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Method

High-throughput characterization of genetic effects on DNA–protein binding and gene transcription

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

Method

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

Research

Transposable elements are the primary source of novelty in primate gene regulation

Research

Drosophila" > Fragile regions and not functional constraints predominate in shaping gene organization in the genus Drosophila

PERSPECTIVE

Qualifying the relationship between sequence conservation and molecular function

LETTER

Ciona exhibit strong correspondence between evolutionary constraint and functional importance" > Noncoding regulatory sequences of Ciona exhibit strong correspondence between evolutionary constraint and functional importance

LETTER

Drosophila melanogaster" > Assessment of Genome-Wide Protein Function Classification for Drosophila melanogaster

LETTER

X Chromosome of Drosophila melanogaster, a Comparison of Two Sequencing Strategies" > From First Base: The Sequence of the Tip of the X Chromosome of Drosophila melanogaster, a Comparison of Two Sequencing Strategies

INSIGHT/OUTLOOK

Drosophila Genome Annotation Assessment Project" > A Biologist's View of the Drosophila Genome Annotation Assessment Project

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