Search | Genome Research

Resource

Inversion variants in human and primate genomes

Claudia Rita Catacchio
Flavia Angela Maria Maggiolini
Pietro D'Addabbo
Miriana Bitonto
Oronzo Capozzi
Martina Lepore Signorile Mattia Miroballo
... [+2 authors] ...,
Nicoletta Archidiacono
Evan E. Eichler
Mario Ventura
Francesca Antonacci

First Published May 18, 2018

Resource

Chlorocebus aethiops sabaeus)" > The genome of the vervet (Chlorocebus aethiops sabaeus)

Wesley C. Warren
Anna J. Jasinska
Raquel García-Pérez
Hannes Svardal
Chad Tomlinson
Mariano Rocchi Nicoletta Archidiacono Oronzo Capozzi Patrick Minx Michael J. Montague Kim Kyung LaDeana W. Hillier Milinn Kremitzki Tina Graves Colby Chiang Jennifer Hughes Nam Tran Yu Huang Vasily Ramensky Oi-wa Choi Yoon J. Jung Christopher A. Schmitt Nikoleta Juretic Jessica Wasserscheid Trudy R. Turner Roger W. Wiseman Jennifer J. Tuscher Julie A. Karl Jörn E. Schmitz Roland Zahn David H. O'Connor Eugene Redmond Alex Nisbett Béatrice Jacquelin Michaela C. Müller-Trutwin Jason M. Brenchley Michel Dione Martin Antonio Gary P. Schroth Jay R. Kaplan Matthew J. Jorgensen Gregg W.C. Thomas Matthew W. Hahn Brian J. Raney Bronwen Aken Rishi Nag Juergen Schmitz Gennady Churakov Angela Noll Roscoe Stanyon David Webb Francoise Thibaud-Nissen Magnus Nordborg Tomas Marques-Bonet
... [+49 authors] ...,
Ken Dewar
George M. Weinstock
Richard K. Wilson
Nelson B. Freimer

First Published September 16, 2015

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

Resource

A comprehensive molecular cytogenetic analysis of chromosome rearrangements in gibbons

Oronzo Capozzi
Lucia Carbone
Roscoe R. Stanyon
Annamaria Marra
Fengtang Yang
Christopher W. Whelan
Pieter J. de Jong
Mariano Rocchi
Nicoletta Archidiacono

First Published August 14, 2012

Research

Gorilla genome structural variation reveals evolutionary parallelisms with chimpanzee

Mario Ventura
Claudia R. Catacchio
Can Alkan
Tomas Marques-Bonet
Saba Sajjadian
Tina A. Graves Fereydoun Hormozdiari Arcadi Navarro Maika Malig Carl Baker Choli Lee Emily H. Turner Lin Chen Jeffrey M. Kidd
... [+9 authors] ...,
Nicoletta Archidiacono
Jay Shendure
Richard K. Wilson
Evan E. Eichler

First Published June 17, 2011

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

Letter

Evolutionary descent of a human chromosome 6 neocentromere: A jump back to 17 million years ago

Oronzo Capozzi
Stefania Purgato
Pietro D'Addabbo
Nicoletta Archidiacono
Paola Battaglia
Anna Baroncini
... [+1 authors] ...,
Antonella Capucci
Roscoe Stanyon
Giuliano Della Valle
Mariano Rocchi

First Published May 1, 2009

RESOURCE

Hylobates and Nomascus Gibbons by high-resolution synteny mapping" > Tracking the complex flow of chromosome rearrangements from the Hominoidea Ancestor to extant Hylobates and Nomascus Gibbons by high-resolution synteny mapping

Doriana Misceo
Oronzo Capozzi
Roberta Roberto
Maria P. Dell’Oglio
Mariano Rocchi
Roscoe Stanyon
Nicoletta Archidiacono

First Published June 13, 2008

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

RESOURCE

Molecular refinement of gibbon genome rearrangements

Roberta Roberto
Oronzo Capozzi
Richard K. Wilson
Elaine R. Mardis
Mariana Lomiento
Eray Tuzun Ze Cheng
... [+2 authors] ...,
Alan R. Mootnick
Nicoletta Archidiacono
Mariano Rocchi
Evan E. Eichler

First Published December 21, 2006

PERSPECTIVE

Ancestral genomes reconstruction: An integrated, multi-disciplinary approach is needed

Mariano Rocchi
Nicoletta Archidiacono
Roscoe Stanyon

First Published October 19, 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

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

LETTER

Recurrent Sites for New Centromere Seeding

Mario Ventura
Stefania Weigl
Lucia Carbone
Maria Francesca Cardone
Doriana Misceo
Mariagrazia Teti Pietro D'Addabbo Annelise Wandall Erik Björck Pieter J. de Jong
... [+5 authors] ...,
Xinwei She
Evan E. Eichler
Nicoletta Archidiacono
Mariano Rocchi