Search | Genome Research

Targeted single-cell RNA sequencing of transcription factors enhances the identification of cell types and trajectories

Alexandra Pokhilko
Adam E. Handel
Fabiola Curion
Viola Volpato
Emma S. Whiteley
Sunniva Bøstrand Sarah E. Newey Colin J. Akerman
... [+3 authors] ...,
Caleb Webber
Michael B. Clark
Rory Bowden
M. Zameel Cader

First Published May 19, 2021

Corrigendum: Extensive microRNA-mediated crosstalk between lncRNAs and mRNAs in mouse embryonic stem cells

Jennifer Y. Tan
Tamara Sirey
Frantisek Honti
Bryony Graham
Allison Piovesan
Matthias Merkenschlager
Caleb Webber
Chris P. Ponting
Ana C. Marques

First Published September 1, 2015

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

The clustering of functionally related genes contributes to CNV-mediated disease

Tallulah Andrews
Frantisek Honti
Rolph Pfundt
Nicole de Leeuw
Jayne Hehir-Kwa
Anneke Vulto-van Silfhout
Bert de Vries
Caleb Webber

First Published April 17, 2015

Extensive microRNA-mediated crosstalk between lncRNAs and mRNAs in mouse embryonic stem cells

Jennifer Y. Tan
Tamara Sirey
Frantisek Honti
Bryony Graham
Allison Piovesan
Matthias Merkenschlager
Caleb Webber
Chris P. Ponting
Ana C. Marques

First Published March 19, 2015

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

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

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

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

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

Natural genetic variation caused by small insertions and deletions in the human genome

Ryan E. Mills
W. Stephen Pittard
Julienne M. Mullaney
Umar Farooq
Todd H. Creasy
Anup A. Mahurkar David M. Kemeza
... [+2 authors] ...,
Daniel S. Strassler
Chris P. Ponting
Caleb Webber
Scott E. Devine

First Published April 1, 2011

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

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

Reduced purifying selection prevails over positive selection in human copy number variant evolution

Duc-Quang Nguyen
Caleb Webber
Jayne Hehir-Kwa
Rolph Pfundt
Joris Veltman
Chris P. Ponting

First Published August 7, 2008

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

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

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

Monodelphis domestica: Evolution of lineage-specific genes and giant chromosomes" > An analysis of the gene complement of a marsupial, Monodelphis domestica: Evolution of lineage-specific genes and giant chromosomes

Leo Goodstadt
Andreas Heger
Caleb Webber
Chris P. Ponting

First Published May 10, 2007

Hotspots of mutation and breakage in dog and human chromosomes

Caleb Webber
Chris P. Ponting

First Published December 8, 2005

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

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

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

Eric A. Stone
Arend Sidow

First Published June 17, 2005

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

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

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

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

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

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

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Your search for returned 28 results

Targeted single-cell RNA sequencing of transcription factors enhances the identification of cell types and trajectories

Corrigendum: Extensive microRNA-mediated crosstalk between lncRNAs and mRNAs in mouse embryonic stem cells

Read clouds uncover variation in complex regions of the human genome

The clustering of functionally related genes contributes to CNV-mediated disease

Extensive microRNA-mediated crosstalk between lncRNAs and mRNAs in mouse embryonic stem cells

Discovery of recurrent structural variants in nasopharyngeal carcinoma

Genome evolution during progression to breast cancer

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

Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements

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

Natural genetic variation caused by small insertions and deletions in the human genome

Evolutionary constraint facilitates interpretation of genetic variation in resequenced human genomes

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

Reduced purifying selection prevails over positive selection in human copy number variant evolution

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

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

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

Monodelphis domestica: Evolution of lineage-specific genes and giant chromosomes" > An analysis of the gene complement of a marsupial, Monodelphis domestica: Evolution of lineage-specific genes and giant chromosomes

Hotspots of mutation and breakage in dog and human chromosomes

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

Distribution and intensity of constraint in mammalian genomic sequence

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

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

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

Characterization of Evolutionary Rates and Constraints in Three Mammalian Genomes

Quantitative Estimates of Sequence Divergence for Comparative Analyses of Mammalian Genomes

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

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

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Your search for returned 28 results