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Research

Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks

Marta Farré
Jaebum Kim
Anastasia A. Proskuryakova
Yang Zhang
Anastasia I. Kulemzina
Qiye Li Yang Zhou Yingqi Xiong Jennifer L. Johnson Polina L. Perelman Warren E. Johnson Wesley C. Warren Anna V. Kukekova Guojie Zhang Stephen J. O'Brien Oliver A. Ryder
... [+11 authors] ...,
Alexander S. Graphodatsky
Jian Ma
Harris A. Lewin
Denis M. Larkin

First Published February 13, 2019

Research

Pangolin genomes and the evolution of mammalian scales and immunity

Siew Woh Choo
Mike Rayko
Tze King Tan
Ranjeev Hari
Aleksey Komissarov
Wei Yee Wee Andrey A. Yurchenko Sergey Kliver Gaik Tamazian Agostinho Antunes Richard K. Wilson Wesley C. Warren Klaus-Peter Koepfli Patrick Minx Ksenia Krasheninnikova Antoinette Kotze Desire L. Dalton Elaine Vermaak Ian C. Paterson Pavel Dobrynin Frankie Thomas Sitam Jeffrine J. Rovie-Ryan Warren E. Johnson Aini Mohamed Yusoff Shu-Jin Luo Kayal Vizi Karuppannan Gang Fang Deyou Zheng
... [+23 authors] ...,
Mark B. Gerstein
Leonard Lipovich
Stephen J. O'Brien
Guat Jah Wong

First Published August 10, 2016

Method

Read clouds uncover variation in complex regions of the human genome

Alex Bishara
Yuling Liu
Ziming Weng
Dorna Kashef-Haghighi
Daniel E. Newburger
Robert West
Arend Sidow
Serafim Batzoglou

First Published August 18, 2015

Method

Discovery of recurrent structural variants in nasopharyngeal carcinoma

Anton Valouev
Ziming Weng
Robert T. Sweeney
Sushama Varma
Quynh-Thu Le
Christina Kong
Arend Sidow
Robert B. West

First Published November 8, 2013

Research

Genome evolution during progression to breast cancer

Daniel E. Newburger
Dorna Kashef-Haghighi
Ziming Weng
Raheleh Salari
Robert T. Sweeney
Alayne L. Brunner Shirley X. Zhu Xiangqian Guo Sushama Varma
... [+4 authors] ...,
Megan L. Troxell
Robert B. West
Serafim Batzoglou
Arend Sidow

First Published April 8, 2013

Research

The origin, evolution, and functional impact of short insertion–deletion variants identified in 179 human genomes

Stephen B. Montgomery
David L. Goode
Erika Kvikstad
Cornelis A. Albers
Zhengdong D. Zhang
Xinmeng Jasmine Mu Guruprasad Ananda Bryan Howie Konrad J. Karczewski Kevin S. Smith Vanessa Anaya Rhea Richardson Joe Davis Daniel G. MacArthur Arend Sidow Laurent Duret Mark Gerstein
... [+12 authors] ...,
Kateryna D. Makova
Jonathan Marchini
Gil McVean
Gerton Lunter

First Published March 11, 2013

Method

Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements

Anshul Kundaje
Sofia Kyriazopoulou-Panagiotopoulou
Max Libbrecht
Cheryl L. Smith
Debasish Raha
Elliott E. Winters
... [+1 authors] ...,
Steven M. Johnson
Michael Snyder
Serafim Batzoglou
Arend Sidow

First Published September 5, 2012

Resource

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

Stephen G. Landt
Georgi K. Marinov
Anshul Kundaje
Pouya Kheradpour
Florencia Pauli
Serafim Batzoglou Bradley E. Bernstein Peter Bickel James B. Brown Philip Cayting Yiwen Chen Gilberto DeSalvo Charles Epstein Katherine I. Fisher-Aylor Ghia Euskirchen Mark Gerstein Jason Gertz Alexander J. Hartemink Michael M. Hoffman Vishwanath R. Iyer Youngsook L. Jung Subhradip Karmakar Manolis Kellis Peter V. Kharchenko Qunhua Li Tao Liu X. Shirley Liu Lijia Ma Aleksandar Milosavljevic Richard M. Myers Peter J. Park Michael J. Pazin Marc D. Perry Debasish Raha Timothy E. Reddy Joel Rozowsky Noam Shoresh Arend Sidow Matthew Slattery John A. Stamatoyannopoulos Michael Y. Tolstorukov Kevin P. White Simon Xi
... [+38 authors] ...,
Peggy J. Farnham
Jason D. Lieb
Barbara J. Wold
Michael Snyder

First Published September 5, 2012

Method

Genome-wide characterization of centromeric satellites from multiple mammalian genomes

Can Alkan
Maria Francesca Cardone
Claudia Rita Catacchio
Francesca Antonacci
Stephen J. O'Brien
Oliver A. Ryder Stefania Purgato
... [+2 authors] ...,
Monica Zoli
Giuliano Della Valle
Evan E. Eichler
Mario Ventura

First Published November 16, 2010

Letter

Evolutionary constraint facilitates interpretation of genetic variation in resequenced human genomes

David L. Goode
Gregory M. Cooper
Jeremy Schmutz
Mark Dickson
Eidelyn Gonzales
Ming Tsai Kalpana Karra
... [+2 authors] ...,
Eugene Davydov
Serafim Batzoglou
Richard M. Myers
Arend Sidow

First Published January 12, 2010

Resource

ProPhylER: A curated online resource for protein function and structure based on evolutionary constraint analyses

Jonathan Binkley
Kalpana Karra
Andrew Kirby
Midori Hosobuchi
Eric A. Stone
Arend Sidow

First Published October 21, 2009

Commentary

Every genome sequence needs a good map

Harris A. Lewin
Denis M. Larkin
Joan Pontius
Stephen J. O'Brien

First Published July 13, 2009

RESOURCE

C. savignyi genetic map and its integration with the reference sequence facilitates insights into chordate genome evolution" > The C. savignyi genetic map and its integration with the reference sequence facilitates insights into chordate genome evolution

Matthew M. Hill
Karl W. Broman
Elia Stupka
William C. Smith
Di Jiang
Arend Sidow

First Published June 2, 2008

LETTER

C. elegans reveals a lack of universal sequence-dictated positioning" > A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning

Anton Valouev
Jeffrey Ichikawa
Thaisan Tonthat
Jeremy Stuart
Swati Ranade
Heather Peckham Kathy Zeng Joel A. Malek Gina Costa
... [+4 authors] ...,
Kevin McKernan
Arend Sidow
Andrew Fire
Steven M. Johnson

First Published May 13, 2008

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

LETTER

LIX1 function for motor neuron survival" > An ~140-kb deletion associated with feline spinal muscular atrophy implies an essential LIX1 function for motor neuron survival

John C. Fyfe
Marilyn Menotti-Raymond
Victor A. David
Lars Brichta
Alejandro A. Schäffer
Richa Agarwala William J. Murphy William J. Wedemeyer Brittany L. Gregory
... [+4 authors] ...,
Bethany G. Buzzell
Meghan C. Drummond
Brunhilde Wirth
Stephen J. O'Brien

First Published August 9, 2006

ARTICLE

De novo discovery of a tissue-specific gene regulatory module in a chordate

David S. Johnson
Qing Zhou
Kasumi Yagi
Nori Satoh
Wing Wong
Arend Sidow

First Published September 16, 2005

ARTICLE

Distribution and intensity of constraint in mammalian genomic sequence

Gregory M. Cooper
Eric A. Stone
George Asimenos
Eric D. Green
Serafim Batzoglou
Arend Sidow

First Published June 17, 2005

Methods

Physicochemical constraint violation by missense substitutions mediates impairment of protein function and disease severity

Eric A. Stone
Arend Sidow

First Published June 17, 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

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

Methods

Automated Whole-Genome Multiple Alignment of Rat, Mouse, and Human

Michael Brudno
Alexander Poliakov
Asaf Salamov
Gregory M. Cooper
Arend Sidow
Edward M. Rubin
Victor Solovyev
Serafim Batzoglou
Inna Dubchak

First Published April 1, 2004

LETTER

Characterization of Evolutionary Rates and Constraints in Three Mammalian Genomes

Gregory M. Cooper
Michael Brudno
Eric A. Stone
Inna Dubchak
Serafim Batzoglou
Arend Sidow

First Published April 1, 2004

LETTER

The Origin of Human Chromosome 1 and Its Homologs in Placental Mammals

William J. Murphy
Lutz Frönicke
Stephen J. O'Brien
Roscoe Stanyon

First Published July 17, 2003

LETTER

Comparative Genome Organization of Human, Murine, and Feline MHC Class II Region

Naoya Yuhki
Thomas Beck
Robert M. Stephens
Yoko Nishigaki
Kymberly Newmann
Stephen J. O'Brien

First Published May 12, 2003

LETTER

Quantitative Estimates of Sequence Divergence for Comparative Analyses of Mammalian Genomes

Gregory M. Cooper
Michael Brudno
NISC Comparative Sequencing Program
Eric D. Green
Serafim Batzoglou
Arend Sidow

First Published May 1, 2003

METHODS

LAGAN and Multi-LAGAN: Efficient Tools for Large-Scale Multiple Alignment of Genomic DNA

Michael Brudno
Chuong B. Do
Gregory M. Cooper
Michael F. Kim
Eugene Davydov
NISC Comparative Sequencing Program
Eric D. Green
Arend Sidow
Serafim Batzoglou

First Published March 12, 2003

LETTER

Genomic Microsatellites as Evolutionary Chronometers: A Test in Wild Cats

Carlos A. Driscoll
Marilyn Menotti-Raymond
George Nelson
David Goldstein
Stephen J. O'Brien

First Published March 1, 2002

LETTER

Partitioning of Tissue Expression Accompanies Multiple Duplications of the Na+/K+ ATPase α Subunit Gene

Fabrizio C. Serluca
Arend Sidow
John D. Mably
Mark C. Fishman

First Published September 20, 2001

LETTER

A Radiation Hybrid Map of the Cat Genome: Implications for Comparative Mapping

William J. Murphy
Shan Sun
Zhang-qun Chen
Naoya Yuhki
Deborah Hirschmann
Marilyn Menotti-Raymond
Stephen J. O'Brien

First Published May 1, 2000

LETTER

Extensive Conservation of Sex Chromosome Organization Between Cat and Human Revealed by Parallel Radiation Hybrid Mapping

William J. Murphy
Shan Sun
Zhang-Qun Chen
Jill Pecon-Slattery
Stephen J. O'Brien

First Published December 1, 1999