Search | Genome Research

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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

Modeling cis-regulation with a compendium of genome-wide histone H3K27ac profiles

Su Wang
Chongzhi Zang
Tengfei Xiao
Jingyu Fan
Shenglin Mei
Qian Qin Qiu Wu Xujuan Li Kexin Xu
... [+4 authors] ...,
Housheng Hansen He
Myles Brown
Clifford A. Meyer
X. Shirley Liu

First Published July 27, 2016

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

Research

Sequence determinants of improved CRISPR sgRNA design

Han Xu
Tengfei Xiao
Chen-Hao Chen
Wei Li
Clifford A. Meyer
Qiu Wu Di Wu Le Cong
... [+3 authors] ...,
Feng Zhang
Jun S. Liu
Myles Brown
X. Shirley Liu

First Published June 10, 2015

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

Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics

Housheng Hansen He
Clifford A. Meyer
Mei Wei Chen
V. Craig Jordan
Myles Brown
X. Shirley Liu

First Published April 16, 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

Research

Epigenetic switch involved in activation of pioneer factor FOXA1-dependent enhancers

Aurélien A. Sérandour
Stéphane Avner
Frédéric Percevault
Florence Demay
Maud Bizot
Céline Lucchetti-Miganeh Frédérique Barloy-Hubler Myles Brown
... [+3 authors] ...,
Mathieu Lupien
Raphaël Métivier
Gilles Salbert
Jérôme Eeckhoute

First Published January 13, 2011

Letter

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

Jian Lu
Andrew G. Clark

First Published November 30, 2009

Letter

Elucidation of the ELK1 target gene network reveals a role in the coordinate regulation of core components of the gene regulation machinery

Joanna Boros
Ian J. Donaldson
Amanda O'Donnell
Zaneta A. Odrowaz
Leo Zeef
Mathieu Lupien
... [+1 authors] ...,
Clifford A. Meyer
X. Shirley Liu
Myles Brown
Andrew D. Sharrocks

First Published August 17, 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

Cell-type selective chromatin remodeling defines the active subset of FOXA1-bound enhancers

Jérôme Eeckhoute
Mathieu Lupien
Clifford A. Meyer
Michael P. Verzi
Ramesh A. Shivdasani
X. Shirley Liu
Myles Brown

First Published January 7, 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

LETTER

Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets

David S. Johnson
Wei Li
D. Benjamin Gordon
Arindam Bhattacharjee
Bo Curry
Jayati Ghosh Leonardo Brizuela Jason S. Carroll Myles Brown Paul Flicek Christoph M. Koch Ian Dunham Mark Bieda Xiaoqin Xu Peggy J. Farnham Philipp Kapranov David A. Nix Thomas R. Gingeras Xinmin Zhang Heather Holster Nan Jiang Roland D. Green Jun S. Song Scott A. McCuine Elizabeth Anton Loan Nguyen Nathan D. Trinklein Zhen Ye Keith Ching David Hawkins Bing Ren Peter C. Scacheri Joel Rozowsky Alexander Karpikov Ghia Euskirchen Sherman Weissman Mark Gerstein Michael Snyder Annie Yang Zarmik Moqtaderi Heather Hirsch Hennady P. Shulha Yutao Fu Zhiping Weng
... [+39 authors] ...,
Kevin Struhl
Richard M. Myers
Jason D. Lieb
X. Shirley Liu

First Published February 7, 2008

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

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

INSIGHT/OUTLOOK

The Search for Meaning in Noncoding DNA

Andrew G. Clark

First Published August 1, 2001

LETTER

Sequence Diversity and Large-Scale Typing of SNPs in the Human Apolipoprotein E Gene

Deborah A. Nickerson
Scott L. Taylor
Stephanie M. Fullerton
Kenneth M. Weiss
Andrew G. Clark
Jari H. Stengård
Veikko Salomaa
Eric Boerwinkle
Charles F. Sing

First Published October 1, 2000