Search | Genome Research

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Mini-Review

Toward telomere-to-telomere cat genomes for precision medicine and conservation biology

William J. Murphy
Andrew J. Harris

First Published June 7, 2024

Research

Genomic architecture constrained placental mammal X Chromosome evolution

Wesley A. Brashear
Kevin R. Bredemeyer
William J. Murphy

First Published July 22, 2021

Research

Bos taurus reveals pervasiveness of X–Y arms races in mammalian lineages" > Sequence analysis in Bos taurus reveals pervasiveness of X–Y arms races in mammalian lineages

Jennifer F. Hughes
Helen Skaletsky
Tatyana Pyntikova
Natalia Koutseva
Terje Raudsepp
Laura G. Brown Daniel W. Bellott Ting-Jan Cho Shannon Dugan-Rocha Ziad Khan Colin Kremitzki Catrina Fronick Tina A. Graves-Lindsay Lucinda Fulton Wesley C. Warren Richard K. Wilson Elaine Owens James E. Womack William J. Murphy Donna M. Muzny
... [+15 authors] ...,
Kim C. Worley
Bhanu P. Chowdhary
Richard A. Gibbs
David C. Page

First Published November 18, 2020

Research

Evolutionary conservation of Y Chromosome ampliconic gene families despite extensive structural variation

Wesley A. Brashear
Terje Raudsepp
William J. Murphy

First Published October 31, 2018

Research

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

Research

Phylogenomic evidence for ancient hybridization in the genomes of living cats (Felidae)

Gang Li
Brian W. Davis
Eduardo Eizirik
William J. Murphy

First Published October 30, 2015

Research

Comparative analysis of mammalian Y chromosomes illuminates ancestral structure and lineage-specific evolution

Gang Li
Brian W. Davis
Terje Raudsepp
Alison J. Pearks Wilkerson
Victor C. Mason
Malcolm Ferguson-Smith
Patricia C. O'Brien
Paul D. Waters
William J. Murphy

First Published June 20, 2013

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

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

Research

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

Letter

Ecological adaptation determines functional mammalian olfactory subgenomes

Sara Hayden
Michaël Bekaert
Tess A. Crider
Stefano Mariani
William J. Murphy
Emma C. Teeling

First Published December 1, 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

LETTER

Thylacinus cynocephalus)" > The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus)

Webb Miller
Daniela I. Drautz
Jan E. Janecka
Arthur M. Lesk
Aakrosh Ratan
Lynn P. Tomsho Mike Packard Yeting Zhang Lindsay R. McClellan Ji Qi Fangqing Zhao M. Thomas P. Gilbert Love Dalén Juan Luis Arsuaga Per G.P. Ericson Daniel H. Huson
... [+11 authors] ...,
Kristofer M. Helgen
William J. Murphy
Anders Götherström
Stephan C. Schuster

First Published January 12, 2009

LETTER

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

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

28-Way vertebrate alignment and conservation track in the UCSC Genome Browser

Webb Miller
Kate Rosenbloom
Ross C. Hardison
Minmei Hou
James Taylor
Brian Raney Richard Burhans David C. King Robert Baertsch Daniel Blankenberg Sergei L. Kosakovsky Pond Anton Nekrutenko Belinda Giardine Robert S. Harris Svitlana Tyekucheva Mark Diekhans Thomas H. Pringle William J. Murphy Arthur Lesk George M. Weinstock Kerstin Lindblad-Toh Richard A. Gibbs
... [+17 authors] ...,
Eric S. Lander
Adam Siepel
David Haussler
W. James Kent

First Published November 5, 2007

RESOURCE

Initial sequence and comparative analysis of the cat genome

Joan U. Pontius
James C. Mullikin
Douglas R. Smith
Kerstin Lindblad-Toh
Sante Gnerre
Michele Clamp Jean Chang Robert Stephens Beena Neelam Natalia Volfovsky Alejandro A. Schäffer Richa Agarwala Kristina Narfström William J. Murphy Urs Giger Alfred L. Roca Agostinho Antunes Marilyn Menotti-Raymond Naoya Yuhki Jill Pecon-Slattery
... [+15 authors] ...,
Warren E. Johnson
Guillaume Bourque
Glenn Tesler
Stephen J. O’Brien

First Published November 1, 2007

LETTER

Using genomic data to unravel the root of the placental mammal phylogeny

William J. Murphy
Thomas H. Pringle
Tess A. Crider
Mark S. Springer
Webb Miller

First Published February 23, 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

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

LETTER

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

LETTER

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

LETTER

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

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

First Published September 1, 2004

LETTER

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

ARTICLE

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

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

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

LETTER

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

LETTER

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

LETTER

Centromere Emergence in Evolution

Mario Ventura
Nicoletta Archidiacono
Mariano Rocchi

First Published April 1, 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

LETTER

Centromere Repositioning

Giuseppe Montefalcone
Sergio Tempesta
Mariano Rocchi
Nicoletta Archidiacono

First Published December 1, 1999

ARTICLE

CAGGG Repeats and the Pericentromeric Duplication of the Hominoid Genome

Evan E. Eichler
Nicoletta Archidiacono
Mariano Rocchi

First Published November 1, 1999

ARTICLE

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