Search | Genome Research

Research

Rapid evolution of piRNA clusters in the Drosophila melanogaster ovary

Satyam P. Srivastav
Cédric Feschotte
Andrew G. Clark

First Published May 15, 2024

Method

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

Evidence for the fixation of gene duplications by positive selection in Drosophila

Margarida Cardoso-Moreira
J. Roman Arguello
Srikanth Gottipati
L.G. Harshman
Jennifer K. Grenier
Andrew G. Clark

First Published April 12, 2016

Research

Indigenous Arabs are descendants of the earliest split from ancient Eurasian populations

Juan L. Rodriguez-Flores
Khalid Fakhro
Francisco Agosto-Perez
Monica D. Ramstetter
Leonardo Arbiza
Thomas L. Vincent Amal Robay Joel A. Malek Karsten Suhre Lotfi Chouchane Ramin Badii Ajayeb Al-Nabet Al-Marri Charbel Abi Khalil Mahmoud Zirie Amin Jayyousi Jacqueline Salit
... [+11 authors] ...,
Alon Keinan
Andrew G. Clark
Ronald G. Crystal
Jason G. Mezey

First Published January 4, 2016

Method

Centromere reference models for human chromosomes X and Y satellite arrays

Karen H. Miga
Yulia Newton
Miten Jain
Nicolas Altemose
Huntington F. Willard
W. James Kent

First Published February 5, 2014

Research

Chromosome-wide profiling of X-chromosome inactivation and epigenetic states in fetal brain and placenta of the opossum, Monodelphis domestica

Xu Wang
Kory C. Douglas
John L. VandeBerg
Andrew G. Clark
Paul B. Samollow

First Published September 24, 2013

Research

Random X inactivation in the mule and horse placenta

Xu Wang
Donald C. Miller
Andrew G. Clark
Douglas F. Antczak

First Published May 29, 2012

Research

Genome sequencing reveals complex speciation in the Drosophila simulans clade

Daniel Garrigan
Sarah B. Kingan
Anthony J. Geneva
Peter Andolfatto
Andrew G. Clark
Kevin R. Thornton
Daven C. Presgraves

First Published April 13, 2012

Research

Disentangling the relationship between sex-biased gene expression and X-linkage

Richard P. Meisel
John H. Malone
Andrew G. Clark

First Published April 12, 2012

Research

Impact of microRNA regulation on variation in human gene expression

Jian Lu
Andrew G. Clark

First Published March 28, 2012

Letter

Population dynamics of PIWI-interacting RNAs (piRNAs) and their targets in Drosophila

Jian Lu
Andrew G. Clark

First Published November 30, 2009

Letter

Darwinian and demographic forces affecting human protein coding genes

Rasmus Nielsen
Melissa J. Hubisz
Ines Hellmann
Dara Torgerson
Aida M. Andrés
Anders Albrechtsen Ryan Gutenkunst Mark D. Adams Michele Cargill
... [+4 authors] ...,
Adam Boyko
Amit Indap
Carlos D. Bustamante
Andrew G. Clark

First Published March 11, 2009

LETTER

Population genetic analysis of shotgun assemblies of genomic sequences from multiple individuals

Ines Hellmann
Yuan Mang
Zhiping Gu
Peter Li
Francisco M. de la Vega
Andrew G. Clark
Rasmus Nielsen

First Published April 14, 2008

RESOURCE

28-Way vertebrate alignment and conservation track in the UCSC Genome Browser

Webb Miller
Kate Rosenbloom
Ross C. Hardison
Minmei Hou
James Taylor
Brian Raney Richard Burhans David C. King Robert Baertsch Daniel Blankenberg Sergei L. Kosakovsky Pond Anton Nekrutenko Belinda Giardine Robert S. Harris Svitlana Tyekucheva Mark Diekhans Thomas H. Pringle William J. Murphy Arthur Lesk George M. Weinstock Kerstin Lindblad-Toh Richard A. Gibbs
... [+17 authors] ...,
Eric S. Lander
Adam Siepel
David Haussler
W. James Kent

First Published November 5, 2007

ARTICLE

Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome

Elliott H. Margulies
Gregory M. Cooper
George Asimenos
Daryl J. Thomas
Colin N. Dewey
Adam Siepel Ewan Birney Damian Keefe Ariel S. Schwartz Minmei Hou James Taylor Sergey Nikolaev Juan I. Montoya-Burgos Ari Löytynoja Simon Whelan Fabio Pardi Tim Massingham James B. Brown Peter Bickel Ian Holmes James C. Mullikin Abel Ureta-Vidal Benedict Paten Eric A. Stone Kate R. Rosenbloom W. James Kent Gerard G. Bouffard Xiaobin Guan Nancy F. Hansen Jacquelyn R. Idol Valerie V.B. Maduro Baishali Maskeri Jennifer C. McDowell Morgan Park Pamela J. Thomas Alice C. Young Robert W. Blakesley Donna M. Muzny Erica Sodergren David A. Wheeler Kim C. Worley Huaiyang Jiang George M. Weinstock Richard A. Gibbs Tina Graves Robert Fulton Elaine R. Mardis Richard K. Wilson Michele Clamp James Cuff Sante Gnerre David B. Jaffe Jean L. Chang Kerstin Lindblad-Toh Eric S. Lander Angie Hinrichs Heather Trumbower Hiram Clawson Ann Zweig Robert M. Kuhn Galt Barber Rachel Harte Donna Karolchik Matthew A. Field Richard A. Moore Carrie A. Matthewson Jacqueline E. Schein Marco A. Marra Stylianos E. Antonarakis Serafim Batzoglou Nick Goldman Ross Hardison David Haussler
... [+68 authors] ...,
Webb Miller
Lior Pachter
Eric D. Green
Arend Sidow

First Published June 13, 2007

Methods

Reconstructing contiguous regions of an ancestral genome

Jian Ma
Louxin Zhang
Bernard B. Suh
Brian J. Raney
Richard C. Burhans
W. James Kent
Mathieu Blanchette
David Haussler
Webb Miller

First Published September 18, 2006

LETTER

Identification by full-coverage array CGH of human DNA copy number increases relative to chimpanzee and gorilla

Gary M. Wilson
Stephane Flibotte
Perseus I. Missirlis
Marco A. Marra
Steven Jones
Kevin Thornton
Andrew G. Clark
Robert A. Holt

First Published December 19, 2005

Methods

Genomic scans for selective sweeps using SNP data

Rasmus Nielsen
Scott Williamson
Yuseob Kim
Melissa J. Hubisz
Andrew G. Clark
Carlos Bustamante

First Published October 26, 2005

PERSPECTIVE

Determinants of the success of whole-genome association testing

Andrew G. Clark
Eric Boerwinkle
James Hixson
Charles F. Sing

First Published October 26, 2005

LETTER

Ascertainment bias in studies of human genome-wide polymorphism

Andrew G. Clark
Melissa J. Hubisz
Carlos D. Bustamante
Scott H. Williamson
Rasmus Nielsen

First Published October 26, 2005

RESOURCE

Galaxy: A platform for interactive large-scale genome analysis

Belinda Giardine
Cathy Riemer
Ross C. Hardison
Richard Burhans
Laura Elnitski
Prachi Shah Yi Zhang Daniel Blankenberg Istvan Albert
... [+4 authors] ...,
James Taylor
Webb Miller
W. James Kent
Anton Nekrutenko

First Published September 16, 2005

ARTICLE

Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes

Adam Siepel
Gill Bejerano
Jakob S. Pedersen
Angie S. Hinrichs
Minmei Hou
Kate Rosenbloom Hiram Clawson John Spieth LaDeana W. Hillier Stephen Richards George M. Weinstock Richard K. Wilson
... [+7 authors] ...,
Richard A. Gibbs
W. James Kent
Webb Miller
David Haussler

First Published July 15, 2005

ARTICLE

The linkage disequilibrium maps of three human chromosomes across four populations reflect their demographic history and a common underlying recombination pattern

Francisco M. De La Vega
Hadar Isaac
Andrew Collins
Charles R. Scafe
Bjarni V. Halldórsson
Xiaoping Su Ross A. Lippert Yu Wang Marion Laig-Webster Ryan T. Koehler Janet S. Ziegle Lewis T. Wogan Junko F. Stevens Kyle M. Leinen Sheri J. Olson Karl J. Guegler Xiaoqing You Lily H. Xu Heinz G. Hemken Francis Kalush Mitsuo Itakura Yi Zheng Guy de Thé Stephen J. O'Brien Andrew G. Clark
... [+20 authors] ...,
Sorin Istrail
Michael W. Hunkapiller
Eugene G. Spier
Dennis A. Gilbert

First Published March 21, 2005

Article

Comparative genome sequencing of Drosophila pseudoobscura: Chromosomal, gene, and cis-element evolution

Stephen Richards
Yue Liu
Brian R. Bettencourt
Pavel Hradecky
Stan Letovsky
Rasmus Nielsen Kevin Thornton Melissa J. Hubisz Rui Chen Richard P. Meisel Olivier Couronne Sujun Hua Mark A. Smith Peili Zhang Jing Liu Harmen J. Bussemaker Marinus F. van Batenburg Sally L. Howells Steven E. Scherer Erica Sodergren Beverly B. Matthews Madeline A. Crosby Andrew J. Schroeder Daniel Ortiz-Barrientos Catharine M. Rives Michael L. Metzker Donna M. Muzny Graham Scott David Steffen David A. Wheeler Kim C. Worley Paul Havlak K. James Durbin Rain Simons Rachel Gill Jennifer Hume Margaret B. Morgan George Miner Cerissa Hamilton Yanmei Huang Lenée Waldron Daniel Verduzco Kerstin P. Clerc-Blankenburg Inna Dubchak Mohamed A.F. Noor Wyatt Anderson Kevin P. White Andrew G. Clark
... [+43 authors] ...,
Stephen W. Schaeffer
William Gelbart
George M. Weinstock
Richard A. Gibbs

First Published January 3, 2005

Methods

Optimal Haplotype Block-Free Selection of Tagging SNPs for Genome-Wide Association Studies

Bjarni V. Halldórsson
Vineet Bafna
Ross Lippert
Russell Schwartz
Francisco M. De La Vega
Andrew G. Clark
Sorin Istrail

First Published August 2, 2004

RESOURCE

Aligning Multiple Genomic Sequences With the Threaded Blockset Aligner

Mathieu Blanchette
W. James Kent
Cathy Riemer
Laura Elnitski
Arian F.A. Smit
Krishna M. Roskin Robert Baertsch Kate Rosenbloom
... [+3 authors] ...,
Hiram Clawson
Eric D. Green
David Haussler
Webb Miller

First Published April 1, 2004

ARTICLE

Covariation in Frequencies of Substitution, Deletion, Transposition, and Recombination During Eutherian Evolution

Ross C. Hardison
Krishna M. Roskin
Shan Yang
Mark Diekhans
W. James Kent
Ryan Weber Laura Elnitski Jia Li Michael O'Connor Diana Kolbe Scott Schwartz Terrence S. Furey Simon Whelan Nick Goldman
... [+9 authors] ...,
Arian Smit
Webb Miller
Francesca Chiaromonte
David Haussler