Search | Genome Research

ZFX acts as a transcriptional activator in multiple types of human tumors by binding downstream from transcription start sites at the majority of CpG island promoters

Suhn Kyong Rhie
Lijun Yao
Zhifei Luo
Heather Witt
Shannon Schreiner
Yu Guo
Andrew A. Perez
Peggy J. Farnham

First Published February 2, 2018

Great ape Y Chromosome and mitochondrial DNA phylogenies reflect subspecies structure and patterns of mating and dispersal

Pille Hallast
Pierpaolo Maisano Delser
Chiara Batini
Daniel Zadik
Mariano Rocchi
Werner Schempp
Chris Tyler-Smith
Mark A. Jobling

First Published February 16, 2016

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

The role of DNA methylation in directing the functional organization of the cancer epigenome

Fides D. Lay
Yaping Liu
Theresa K. Kelly
Heather Witt
Peggy J. Farnham
Peter A. Jones
Benjamin P. Berman

First Published March 6, 2015

Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm

Bo Zhang
Yan Zhou
Nan Lin
Rebecca F. Lowdon
Chibo Hong
Raman P. Nagarajan Jeffrey B. Cheng Daofeng Li Michael Stevens Hyung Joo Lee Xiaoyun Xing Jia Zhou Vasavi Sundaram GiNell Elliott Junchen Gu Taoping Shi Philippe Gascard Mahvash Sigaroudinia Thea D. Tlsty Theresa Kadlecek Arthur Weiss Henriette O’Geen Peggy J. Farnham Cécile L. Maire Keith L. Ligon Pamela A.F. Madden Angela Tam Richard Moore Martin Hirst
... [+24 authors] ...,
Marco A. Marra
Baoxue Zhang
Joseph F. Costello
Ting Wang

First Published June 26, 2013

Spark: A navigational paradigm for genomic data exploration

Cydney B. Nielsen
Hamid Younesy
Henriette O'Geen
Xiaoqin Xu
Andrew R. Jackson
Aleksandar Milosavljevic Ting Wang
... [+2 authors] ...,
Joseph F. Costello
Martin Hirst
Peggy J. Farnham
Steven J.M. Jones

First Published September 7, 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

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

Copy number variation analysis in the great apes reveals species-specific patterns of structural variation

Elodie Gazave
Fleur Darré
Carlos Morcillo-Suarez
Natalia Petit-Marty
Angel Carreño
Urko M. Marigorta Oliver A. Ryder Antoine Blancher Mariano Rocchi Elena Bosch
... [+5 authors] ...,
Carl Baker
Tomàs Marquès-Bonet
Evan E. Eichler
Arcadi Navarro

First Published August 8, 2011

Gene amplification as double minutes or homogeneously staining regions in solid tumors: Origin and structure

Clelia Tiziana Storlazzi
Angelo Lonoce
Maria C. Guastadisegni
Domenico Trombetta
Pietro D'Addabbo
Giulia Daniele Alberto L'Abbate Gemma Macchia Cecilia Surace Klaas Kok Reinhard Ullmann Stefania Purgato
... [+7 authors] ...,
Orazio Palumbo
Massimo Carella
Peter F. Ambros
Mariano Rocchi

First Published July 14, 2010

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

Sequencing human–gibbon breakpoints of synteny reveals mosaic new insertions at rearrangement sites

Santhosh Girirajan
Lin Chen
Tina Graves
Tomas Marques-Bonet
Mario Ventura
Catrina Fronick Lucinda Fulton Mariano Rocchi
... [+3 authors] ...,
Robert S. Fulton
Richard K. Wilson
Elaine R. Mardis
Evan E. Eichler

First Published November 24, 2008

E2F in vivo binding specificity: Comparison of consensus versus nonconsensus binding sites

Alina Rabinovich
Victor X. Jin
Roman Rabinovich
Xiaoqin Xu
Peggy J. Farnham

First Published October 3, 2008

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

Using ChIP-chip technology to reveal common principles of transcriptional repression in normal and cancer cells

Vitalina M. Komashko
Luis G. Acevedo
Sharon L. Squazzo
Sushma S. Iyengar
Alina Rabinovich
Henriette O’Geen
Roland Green
Peggy J. Farnham

First Published March 17, 2008

Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets

David S. Johnson
Wei Li
D. Benjamin Gordon
Arindam Bhattacharjee
Bo Curry
Jayati Ghosh Leonardo Brizuela Jason S. Carroll Myles Brown Paul Flicek Christoph M. Koch Ian Dunham Mark Bieda Xiaoqin Xu Peggy J. Farnham Philipp Kapranov David A. Nix Thomas R. Gingeras Xinmin Zhang Heather Holster Nan Jiang Roland D. Green Jun S. Song Scott A. McCuine Elizabeth Anton Loan Nguyen Nathan D. Trinklein Zhen Ye Keith Ching David Hawkins Bing Ren Peter C. Scacheri Joel Rozowsky Alexander Karpikov Ghia Euskirchen Sherman Weissman Mark Gerstein Michael Snyder Annie Yang Zarmik Moqtaderi Heather Hirsch Hennady P. Shulha Yutao Fu Zhiping Weng
... [+39 authors] ...,
Kevin Struhl
Richard M. Myers
Jason D. Lieb
X. Shirley Liu

First Published February 7, 2008

A comprehensive ChIP–chip analysis of E2F1, E2F4, and E2F6 in normal and tumor cells reveals interchangeable roles of E2F family members

Xiaoqin Xu
Mark Bieda
Victor X. Jin
Alina Rabinovich
Mathew J. Oberley
Roland Green
Peggy J. Farnham

First Published October 1, 2007

Identification of an OCT4 and SRY regulatory module using integrated computational and experimental genomics approaches

Victor X. Jin
Henriette O’Geen
Sushma Iyengar
Roland Green
Peggy J. Farnham

First Published June 13, 2007

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

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

Mariano Rocchi
Nicoletta Archidiacono
Roscoe Stanyon

First Published October 19, 2006

cis-regulatory modules from chromatin immunoprecipitation microarray data—A case study using E2F1" > A computational genomics approach to identify cis-regulatory modules from chromatin immunoprecipitation microarray data—A case study using E2F1

Victor X. Jin
Alina Rabinovich
Sharon L. Squazzo
Roland Green
Peggy J. Farnham

First Published October 19, 2006

Locating mammalian transcription factor binding sites: A survey of computational and experimental techniques

Laura Elnitski
Victor X. Jin
Peggy J. Farnham
Steven J.M. Jones

First Published October 19, 2006

Suz12 binds to silenced regions of the genome in a cell-type-specific manner

Sharon L. Squazzo
Henriette O’Geen
Vitalina M. Komashko
Sheryl R. Krig
Victor X. Jin
Sung-wook Jang
... [+1 authors] ...,
Raphael Margueron
Danny Reinberg
Roland Green
Peggy J. Farnham

First Published June 2, 2006

Unbiased location analysis of E2F1-binding sites suggests a widespread role for E2F1 in the human genome

Mark Bieda
Xiaoqin Xu
Michael A. Singer
Roland Green
Peggy J. Farnham

First Published April 10, 2006

A preliminary comparative analysis of primate segmental duplications shows elevated substitution rates and a great-ape expansion of intrachromosomal duplications

Xinwei She
Ge Liu
Mario Ventura
Shaying Zhao
Doriana Misceo
Roberta Roberto Maria Francesca Cardone
... [+2 authors] ...,
Mariano Rocchi
Eric D. Green
Nicoletta Archidiacano
Evan E. Eichler

First Published April 10, 2006

A genome-wide survey of structural variation between human and chimpanzee

Tera L. Newman
Eray Tuzun
V. Anne Morrison
Karen E. Hayden
Mario Ventura
Sean D. McGrath
Mariano Rocchi
Evan E. Eichler

First Published September 16, 2005

Punctuated duplication seeding events during the evolution of human chromosome 2p11

Julie E. Horvath
Cassandra L. Gulden
Rhea U. Vallente
Marla Y. Eichler
Mario Ventura
John D. McPherson Tina A. Graves
... [+2 authors] ...,
Richard K. Wilson
Stuart Schwartz
Mariano Rocchi
Evan E. Eichler

First Published June 17, 2005

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

First Published September 1, 2004

Insertion of Telomeric Repeats at Intrachromosomal Break Sites During Primate Evolution

Solomon G. Nergadze
Mariano Rocchi
Claus M. Azzalin
Chiara Mondello
Elena Giulotto

First Published August 12, 2004

Analysis of Segmental Duplications and Genome Assembly in the Mouse

Jeffrey A. Bailey
Deanna M. Church
Mario Ventura
Mariano Rocchi
Evan E. Eichler

First Published May 3, 2004

Complex Events in the Evolution of the Human Pseudoautosomal Region 2 (PAR2)

Fadi J. Charchar
Marta Svartman
Nisrine El-Mogharbel
Mario Ventura
Patrick Kirby
Maria R. Matarazzo
... [+1 authors] ...,
Alfredo Ciccodicola
Mariano Rocchi
Maurizio D'Esposito
Jennifer A. Marshall Graves

First Published January 14, 2003

Neocentromeres in 15q24-26 Map to Duplicons Which Flanked an Ancestral Centromere in 15q25

Mario Ventura
Jonathan M. Mudge
Valeria Palumbo
Sally Burn
Elisabeth Blennow
Mauro Pierluigi Roberto Giorda
... [+2 authors] ...,
Orsetta Zuffardi
Nicoletta Archidiacono
Michael S. Jackson
Mariano Rocchi

First Published January 1, 2003

KIAA0187 Were Created through Independent Pericentromeric-Directed and Chromosome-Specific Duplication Mechanisms" > Human Paralogs of KIAA0187 Were Created through Independent Pericentromeric-Directed and Chromosome-Specific Duplication Mechanisms

Moira Crosier
Luigi Viggiano
Jane Guy
Doriana Misceo
Robert Stones
Wenbin Wei Tom Hearn
... [+2 authors] ...,
Mario Ventura
Nicoletta Archidiacono
Mariano Rocchi
Michael S. Jackson

First Published January 1, 2002

Centromere Emergence in Evolution

Mario Ventura
Nicoletta Archidiacono
Mariano Rocchi

First Published April 1, 2001

Centromere Repositioning

Giuseppe Montefalcone
Sergio Tempesta
Mariano Rocchi
Nicoletta Archidiacono

First Published December 1, 1999

CAGGG Repeats and the Pericentromeric Duplication of the Hominoid Genome

Evan E. Eichler
Nicoletta Archidiacono
Mariano Rocchi

First Published November 1, 1999

Extreme Reduction of Chromosome-Specific α-Satellite Array Is Unusually Common in Human Chromosome 21

Anthony W.I. Lo
Gregory C.-C. Liao
Mariano Rocchi
K.H. Andy Choo

First Published October 1, 1999

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Your search for returned 37 results

ZFX acts as a transcriptional activator in multiple types of human tumors by binding downstream from transcription start sites at the majority of CpG island promoters

Great ape Y Chromosome and mitochondrial DNA phylogenies reflect subspecies structure and patterns of mating and dispersal

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

The role of DNA methylation in directing the functional organization of the cancer epigenome

Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm

Spark: A navigational paradigm for genomic data exploration

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

A comprehensive molecular cytogenetic analysis of chromosome rearrangements in gibbons

Copy number variation analysis in the great apes reveals species-specific patterns of structural variation

Gene amplification as double minutes or homogeneously staining regions in solid tumors: Origin and structure

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

Sequencing human–gibbon breakpoints of synteny reveals mosaic new insertions at rearrangement sites

E2F in vivo binding specificity: Comparison of consensus versus nonconsensus binding sites

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

Using ChIP-chip technology to reveal common principles of transcriptional repression in normal and cancer cells

Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets

A comprehensive ChIP–chip analysis of E2F1, E2F4, and E2F6 in normal and tumor cells reveals interchangeable roles of E2F family members

Identification of an OCT4 and SRY regulatory module using integrated computational and experimental genomics approaches

Molecular refinement of gibbon genome rearrangements

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

cis-regulatory modules from chromatin immunoprecipitation microarray data—A case study using E2F1" > A computational genomics approach to identify cis-regulatory modules from chromatin immunoprecipitation microarray data—A case study using E2F1

Locating mammalian transcription factor binding sites: A survey of computational and experimental techniques

Suz12 binds to silenced regions of the genome in a cell-type-specific manner

Unbiased location analysis of E2F1-binding sites suggests a widespread role for E2F1 in the human genome

A preliminary comparative analysis of primate segmental duplications shows elevated substitution rates and a great-ape expansion of intrachromosomal duplications

A genome-wide survey of structural variation between human and chimpanzee

Punctuated duplication seeding events during the evolution of human chromosome 2p11

Recurrent Sites for New Centromere Seeding

Insertion of Telomeric Repeats at Intrachromosomal Break Sites During Primate Evolution

Analysis of Segmental Duplications and Genome Assembly in the Mouse

Complex Events in the Evolution of the Human Pseudoautosomal Region 2 (PAR2)

Neocentromeres in 15q24-26 Map to Duplicons Which Flanked an Ancestral Centromere in 15q25

KIAA0187 Were Created through Independent Pericentromeric-Directed and Chromosome-Specific Duplication Mechanisms" > Human Paralogs of KIAA0187 Were Created through Independent Pericentromeric-Directed and Chromosome-Specific Duplication Mechanisms

Centromere Emergence in Evolution

Centromere Repositioning

CAGGG Repeats and the Pericentromeric Duplication of the Hominoid Genome

Extreme Reduction of Chromosome-Specific α-Satellite Array Is Unusually Common in Human Chromosome 21

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Your search for returned 37 results