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Research

CRX classifies clinical variants and reveals biochemical properties of the transcriptional effector domain" > Mutational scanning of CRX classifies clinical variants and reveals biochemical properties of the transcriptional effector domain

  • James L. Shepherdson
  • David M. Granas
  • Jie Li
  • Zara Shariff
  • Stephen P. Plassmeyer
  • Alex S. Holehouse
  • Michael A. White
  • Barak A. Cohen
  • First Published September 25, 2024
Research

Drosophila melanogaster ovary" > Rapid evolution of piRNA clusters in the Drosophila melanogaster ovary

  • Satyam P. Srivastav
  • Cédric Feschotte
  • Andrew G. Clark
  • First Published May 15, 2024
Research

CRX have distinct cis-regulatory effects on enhancers and silencers in photoreceptors" > Pathogenic variants in CRX have distinct cis-regulatory effects on enhancers and silencers in photoreceptors

  • James L. Shepherdson
  • Ryan Z. Friedman
  • Yiqiao Zheng
  • Chi Sun
  • Inez Y. Oh
  • David M. Granas
  • Barak A. Cohen
  • Shiming Chen
  • Michael A. White
  • First Published February 14, 2024
Research

Functional characterization of enhancer activity during a long terminal repeat's evolution

  • Alan Y. Du
  • Xiaoyu Zhuo
  • Vasavi Sundaram
  • Nicholas O. Jensen
  • Hemangi G. Chaudhari
  • Nancy L. Saccone
  • Barak A. Cohen
  • Ting Wang
  • First Published October 3, 2022
Research

Genomic environments scale the activities of diverse core promoters

  • Clarice K.Y. Hong
  • Barak A. Cohen
  • First Published December 27, 2021
Research

cis-regulatory activity" > Local sequence features that influence AP-1 cis-regulatory activity

  • Hemangi G. Chaudhari
  • Barak A. Cohen
  • First Published January 5, 2018
Research

cis-regulation in embryonic stem cells" > Interactions between pluripotency factors specify cis-regulation in embryonic stem cells

  • Chris Fiore
  • Barak A. Cohen
  • First Published April 15, 2016
Research

Drosophila" > 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

Promoter-distal RNA polymerase II binding discriminates active from inactive CCAAT/ enhancer-binding protein beta binding sites

  • Daniel Savic
  • Brian S. Roberts
  • Julia B. Carleton
  • E. Christopher Partridge
  • Michael A. White
  • Barak A. Cohen
  • Gregory M. Cooper
  • Jason Gertz
  • Richard M. Myers
  • First Published October 20, 2015
Research

High-throughput functional testing of ENCODE segmentation predictions

  • Jamie C. Kwasnieski
  • Christopher Fiore
  • Hemangi G. Chaudhari
  • Barak A. Cohen
  • First Published July 17, 2014
Research

Monodelphis domestica" > 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
Method

Massively parallel synthetic promoter assays reveal the in vivo effects of binding site variants

  • Ilaria Mogno
  • Jamie C. Kwasnieski
  • Barak A. Cohen
  • First Published August 6, 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

Drosophila simulans clade" > 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

TATA is a modular component of synthetic promoters

  • Ilaria Mogno
  • Francesco Vallania
  • Robi D. Mitra
  • Barak A. Cohen
  • First Published July 13, 2010
Letter

Drosophila" > 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
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
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
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
Methods

Discovery, validation, and genetic dissection of transcription factor binding sites by comparative and functional genomics

  • Jason Gertz
  • Linda Riles
  • Peter Turnbaugh
  • Su-Wen Ho
  • Barak A. Cohen
  • First Published August 2, 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

Drosophila pseudoobscura: Chromosomal, gene, and cis-element evolution" > 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 Amy Egan 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
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