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Closing the gaps, and improving somatic structural variant analysis and benchmarking using CHM13-T2T

  • Luis F. Paulin
  • Jeremy Fan
  • Kieran O'Neill
  • Erin Pleasance
  • Vanessa L. Porter
  • Steven J.M. Jones
  • Fritz J. Sedlazeck
  • First Published March 17, 2025

Rearrangements of viral and human genomes at human papillomavirus integration events and their allele-specific impacts on cancer genome regulation

  • Vanessa L. Porter
  • Michelle Ng
  • Kieran O'Neill
  • Signe MacLennan
  • Richard D. Corbett
  • Luka Culibrk Zeid Hamadeh Marissa Iden Rachel Schmidt Shirng-Wern Tsaih Carolyn Nakisige Martin Origa Jackson Orem Glenn Chang Jeremy Fan Ka Ming Nip Vahid Akbari Simon K. Chan James Hopkins Richard A. Moore Eric Chuah Karen L. Mungall Andrew J. Mungall
  • ... [+18 authors] ...,
  • Inanc Birol
  • Steven J.M. Jones
  • Janet S. Rader
  • Marco A. Marra
  • First Published December 5, 2024

Corrigendum: H3K4me1 marks DNA regions hypomethylated during aging in human stem and differentiated cells

  • Agustín F. Fernández
  • Gustavo F. Bayón
  • Rocío G. Urdinguio
  • Estela G. Toraño
  • María G. García
  • Antonella Carella Sandra Petrus-Reurer Cecilia Ferrero Pablo Martinez-Camblor Isabel Cubillo Javier García-Castro Jesús Delgado-Calle Flor M. Pérez-Campo José A. Riancho Clara Bueno Pablo Menéndez Anouk Mentink Katia Mareschi Fabian Claire Corrado Fagnani Emanuela Medda Virgilia Toccaceli Sonia Brescianini Sebastián Moran Manel Esteller Alexandra Stolzing
  • ... [+21 authors] ...,
  • Jan de Boer
  • Lorenza Nisticò
  • Maria A. Stazi
  • Mario F. Fraga
  • First Published April 1, 2019

H3K4me1 marks DNA regions hypomethylated during aging in human stem and differentiated cells

  • Agustín F. Fernández
  • Gustavo F. Bayón
  • Rocío G. Urdinguio
  • Estela G. Toraño
  • María G. García
  • Antonella Carella Sandra Petrus-Reurer Cecilia Ferrero Pablo Martinez-Camblor Isabel Cubillo Javier García-Castro Jesús Delgado-Calle Flor M. Pérez-Campo José A. Riancho Clara Bueno Pablo Menéndez Anouk Mentink Katia Mareschi Fabian Claire Corrado Fagnani Emanuela Medda Virgilia Toccaceli Sonia Brescianini Sebastián Moran Manel Esteller Alexandra Stolzing
  • ... [+21 authors] ...,
  • Jan de Boer
  • Lorenza Nisticò
  • Maria A. Stazi
  • Mario F. Fraga
  • First Published September 30, 2014

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

A DNA methylation fingerprint of 1628 human samples

  • Agustin F. Fernandez
  • Yassen Assenov
  • Jose Ignacio Martin-Subero
  • Balazs Balint
  • Reiner Siebert
  • Hiroaki Taniguchi Hiroyuki Yamamoto Manuel Hidalgo Aik-Choon Tan Oliver Galm Isidre Ferrer Montse Sanchez-Cespedes Alberto Villanueva Javier Carmona Jose V. Sanchez-Mut Maria Berdasco Victor Moreno Gabriel Capella David Monk Esteban Ballestar Santiago Ropero Ramon Martinez Marta Sanchez-Carbayo Felipe Prosper Xabier Agirre Mario F. Fraga Osvaldo Graña Luis Perez-Jurado Jaume Mora Susana Puig Jaime Prat Lina Badimon Annibale A. Puca Stephen J. Meltzer
  • ... [+29 authors] ...,
  • Thomas Lengauer
  • John Bridgewater
  • Christoph Bock
  • Manel Esteller
  • First Published May 25, 2011

Locus co-occupancy, nucleosome positioning, and H3K4me1 regulate the functionality of FOXA2-, HNF4A-, and PDX1-bound loci in islets and liver

  • Brad G. Hoffman
  • Gordon Robertson
  • Bogard Zavaglia
  • Mike Beach
  • Rebecca Cullum
  • Sam Lee Galina Soukhatcheva Leping Li Elizabeth D. Wederell Nina Thiessen Mikhail Bilenky Timothee Cezard Angela Tam Baljit Kamoh Inanc Birol Derek Dai YongJun Zhao Martin Hirst C. Bruce Verchere
  • ... [+14 authors] ...,
  • Cheryl D. Helgason
  • Marco A. Marra
  • Steven J.M. Jones
  • Pamela A. Hoodless
  • First Published June 15, 2010

The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance

  • Santosh S. Atanur
  • İnanç Birol
  • Victor Guryev
  • Martin Hirst
  • Oliver Hummel
  • Catherine Morrissey Jacques Behmoaras Xose M. Fernandez-Suarez Michelle D. Johnson William M. McLaren Giannino Patone Enrico Petretto Charles Plessy Kathleen S. Rockland Charles Rockland Kathrin Saar Yongjun Zhao Piero Carninci Paul Flicek Ted Kurtz Edwin Cuppen Michal Pravenec
  • ... [+17 authors] ...,
  • Norbert Hubner
  • Steven J.M. Jones
  • Ewan Birney
  • Timothy J. Aitman
  • First Published April 29, 2010

Changes in the pattern of DNA methylation associate with twin discordance in systemic lupus erythematosus

  • Biola M. Javierre
  • Agustin F. Fernandez
  • Julia Richter
  • Fatima Al-Shahrour
  • J. Ignacio Martin-Subero
  • Javier Rodriguez-Ubreva Maria Berdasco Mario F. Fraga Terrance P. O'Hanlon Lisa G. Rider Filipe V. Jacinto F. Javier Lopez-Longo Joaquin Dopazo Marta Forn Miguel A. Peinado Luis Carreño Amr H. Sawalha John B. Harley
  • ... [+13 authors] ...,
  • Reiner Siebert
  • Manel Esteller
  • Frederick W. Miller
  • Esteban Ballestar
  • First Published December 22, 2009

The completion of the Mammalian Gene Collection (MGC)

  • Gary Temple
  • Daniela S. Gerhard
  • Rebekah Rasooly
  • Elise A. Feingold
  • Peter J. Good
  • Cristen Robinson Allison Mandich Jeffrey G. Derge Jeanne Lewis Debonny Shoaf Francis S. Collins Wonhee Jang Lukas Wagner Carolyn M. Shenmen Leonie Misquitta Carl F. Schaefer Kenneth H. Buetow Tom I. Bonner Linda Yankie Ming Ward Lon Phan Alex Astashyn Garth Brown Catherine Farrell Jennifer Hart Melissa Landrum Bonnie L. Maidak Michael Murphy Terence Murphy Bhanu Rajput Lillian Riddick David Webb Janet Weber Wendy Wu Kim D. Pruitt Donna Maglott Adam Siepel Brona Brejova Mark Diekhans Rachel Harte Robert Baertsch Jim Kent David Haussler Michael Brent Laura Langton Charles L.G. Comstock Michael Stevens Chaochun Wei Marijke J. van Baren Kourosh Salehi-Ashtiani Ryan R. Murray Lila Ghamsari Elizabeth Mello Chenwei Lin Christa Pennacchio Kirsten Schreiber Nicole Shapiro Amber Marsh Elizabeth Pardes Troy Moore Anita Lebeau Mike Muratet Blake Simmons David Kloske Stephanie Sieja James Hudson Praveen Sethupathy Michael Brownstein Narayan Bhat Joseph Lazar Howard Jacob Chris E. Gruber Mark R. Smith John McPherson Angela M. Garcia Preethi H. Gunaratne Jiaqian Wu Donna Muzny Richard A. Gibbs Alice C. Young Gerard G. Bouffard Robert W. Blakesley Jim Mullikin Eric D. Green Mark C. Dickson Alex C. Rodriguez Jane Grimwood Jeremy Schmutz Richard M. Myers Martin Hirst Thomas Zeng Kane Tse Michelle Moksa Merinda Deng Kevin Ma Diana Mah Johnson Pang Greg Taylor Eric Chuah Athena Deng Keith Fichter Anne Go Stephanie Lee Jing Wang Malachi Griffith Ryan Morin Richard A. Moore Michael Mayo Sarah Munro Susan Wagner Steven J.M. Jones Robert A. Holt Marco A. Marra Sun Lu Shuwei Yang James Hartigan Marcus Graf Ralf Wagner Stanley Letovksy Jacqueline C. Pulido Keith Robison Dominic Esposito James Hartley
  • ... [+118 authors] ...,
  • Vanessa E. Wall
  • Ralph F. Hopkins
  • Osamu Ohara
  • Stefan Wiemann
  • First Published September 18, 2009
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