Search | Genome Research

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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

Parente2: a fast and accurate method for detecting identity by descent

Jesse M. Rodriguez
Sivan Bercovici
Lin Huang
Roy Frostig
Serafim Batzoglou

First Published October 1, 2014

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

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

Linking disease associations with regulatory information in the human genome

Marc A. Schaub
Alan P. Boyle
Anshul Kundaje
Serafim Batzoglou
Michael Snyder

First Published September 5, 2012

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

RECOMB Special/Methods

Effect of genetic divergence in identifying ancestral origin using HAPAA

Andreas Sundquist
Eugene Fratkin
Chuong B. Do
Serafim Batzoglou

First Published March 18, 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

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

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

Methods

Eukaryotic Regulatory Element Conservation Analysis and Identification Using Comparative Genomics

Yueyi Liu
X. Shirley Liu
Liping Wei
Russ B. Altman
Serafim Batzoglou

First Published March 1, 2004

Methods

Identification of Promoter Regions in the Human Genome by Using a Retroviral Plasmid Library-Based Functional Reporter Gene Assay

Shirin Khambata-Ford
Yueyi Liu
Christopher Gleason
Mark Dickson
Russ B. Altman
Serafim Batzoglou
Richard M. Myers

First Published June 12, 2003

ARTICLE

Targeting a Complex Transcriptome: The Construction of the Mouse Full-Length cDNA Encyclopedia

Piero Carninci
Kazunori Waki
Toshiyuki Shiraki
Hideaki Konno
Kazuhiro Shibata
Masayoshi Itoh Katsunori Aizawa Takahiro Arakawa Yoshiyuki Ishii Daisuke Sasaki Hidemasa Bono Shinji Kondo Yuichi Sugahara Rintaro Saito Naoki Osato Shiro Fukuda Kenjiro Sato Akira Watahiki Tomoko Hirozane-Kishikawa Mari Nakamura Yuko Shibata Ayako Yasunishi Noriko Kikuchi Atsushi Yoshiki Moriaki Kusakabe Stefano Gustincich Kirk Beisel William Pavan Vassilis Aidinis Akira Nakagawara William A. Held Hiroo Iwata Tomohiro Kono Hiromitsu Nakauchi Paul Lyons Christine Wells David A. Hume Michela Fagiolini Takao K. Hensch Michelle Brinkmeier Sally Camper Junji Hirota Peter Mombaerts
... [+38 authors] ...,
Masami Muramatsu
Yasushi Okazaki
Jun Kawai
Yoshihide Hayashizaki

First Published June 2, 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

METHODS

A Computer-Based Method of Selecting Clones for a Full-Length cDNA Project: Simultaneous Collection of Negligibly Redundant and Variant cDNAs

Naoki Osato
Masayoshi Itoh
Hideaki Konno
Shinji Kondo
Kazuhiro Shibata
Piero Carninci Toshiyuki Shiraki Akira Shinagawa Takahiro Arakawa
... [+4 authors] ...,
Shoshi Kikuchi
Kouji Sato
Jun Kawai
Yoshihide Hayashizaki

First Published June 18, 2002

METHODS

ARACHNE: A Whole-Genome Shotgun Assembler

Serafim Batzoglou
David B. Jaffe
Ken Stanley
Jonathan Butler
Sante Gnerre
Evan Mauceli
Bonnie Berger
Jill P. Mesirov
Eric S. Lander

First Published January 1, 2002

METHODS

Computer-Based Methods for the Mouse Full-Length cDNA Encyclopedia: Real-Time Sequence Clustering for Construction of a Nonredundant cDNA Library

Hideaki Konno
Yoshifumi Fukunishi
Kazuhiro Shibata
Masayoshi Itoh
Piero Carninci
Yuichi Sugahara
Yoshihide Hayashizaki

First Published January 18, 2001

LETTER

RIKEN Integrated Sequence Analysis (RISA) System—384-Format Sequencing Pipeline with 384 Multicapillary Sequencer

Kazuhiro Shibata
Masayoshi Itoh
Katsunori Aizawa
Sumiharu Nagaoka
Nobuya Sasaki
Piero Carninci Hideaki Konno Junichi Akiyama Katsuo Nishi Tokuji Kitsunai Hideo Tashiro Mari Itoh Noriko Sumi Yoshiyuki Ishii Shin Nakamura Makoto Hazama Tsutomu Nishine Akira Harada Rintaro Yamamoto Hiroyuki Matsumoto Sumito Sakaguchi Takashi Ikegami Katsuya Kashiwagi Syuji Fujiwake Kouji Inoue Yoshiyuki Togawa Masaki Izawa Eiji Ohara Masanori Watahiki Yuko Yoneda Tomokazu Ishikawa Kaori Ozawa Takumi Tanaka Shuji Matsuura Jun Kawai Yasushi Okazaki
... [+31 authors] ...,
Masami Muramatsu
Yorinao Inoue
Akira Kira
Yoshihide Hayashizaki

First Published November 1, 2000

METHODS

Normalization and Subtraction of Cap-Trapper-Selected cDNAs to Prepare Full-Length cDNA Libraries for Rapid Discovery of New Genes

Piero Carninci
Yuko Shibata
Norihito Hayatsu
Yuichi Sugahara
Kazuhiro Shibata
Masayoshi Itoh
... [+1 authors] ...,
Hideaki Konno
Yasushi Okazaki
Masami Muramatsu
Yoshihide Hayashizaki

First Published October 1, 2000

LETTER

Human and Mouse Gene Structure: Comparative Analysis and Application to Exon Prediction

Serafim Batzoglou
Lior Pachter
Jill P. Mesirov
Bonnie Berger
Eric S. Lander

First Published July 1, 2000

RESEARCH

Sequencing a Genome by Walking with Clone-End Sequences: A Mathematical Analysis

Serafim Batzoglou
Bonnie Berger
Jill Mesirov
Eric S. Lander

First Published December 1, 1999

LETTER

Automated Filtration-Based High-Throughput Plasmid Preparation System

Masayoshi Itoh
Tokuji Kitsunai
Junichi Akiyama
Kazuhiro Shibata
Masaki Izawa
Jun Kawai Yasuhiro Tomaru Piero Carninci Yuko Shibata
... [+4 authors] ...,
Yasuhiro Ozawa
Masami Muramatsu
Yasushi Okazaki
Yoshihide Hayashizaki

First Published May 1, 1999