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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

SvABA: genome-wide detection of structural variants and indels by local assembly

Jeremiah A. Wala
Pratiti Bandopadhayay
Noah F. Greenwald
Ryan O'Rourke
Ted Sharpe
Chip Stewart Steve Schumacher Yilong Li Joachim Weischenfeldt Xiaotong Yao Chad Nusbaum Peter Campbell Gad Getz
... [+8 authors] ...,
Matthew Meyerson
Cheng-Zhong Zhang
Marcin Imielinski
Rameen Beroukhim

First Published March 13, 2018

Whole-genome and multisector exome sequencing of primary and post-treatment glioblastoma reveals patterns of tumor evolution

Hoon Kim
Siyuan Zheng
Seyed S. Amini
Selene M. Virk
Tom Mikkelsen
Daniel J. Brat Jonna Grimsby Carrie Sougnez Florian Muller Jian Hu Andrew E. Sloan Mark L. Cohen Erwin G. Van Meir Lisa Scarpace Peter W. Laird John N. Weinstein Eric S. Lander Stacey Gabriel Gad Getz
... [+14 authors] ...,
Matthew Meyerson
Lynda Chin
Jill S. Barnholtz-Sloan
Roel G.W. Verhaak

First Published February 3, 2015

Somatic retrotransposition in human cancer revealed by whole-genome and exome sequencing

Elena Helman
Michael S. Lawrence
Chip Stewart
Carrie Sougnez
Gad Getz
Matthew Meyerson

First Published May 13, 2014

Somatic rearrangements across cancer reveal classes of samples with distinct patterns of DNA breakage and rearrangement-induced hypermutability

Yotam Drier
Michael S. Lawrence
Scott L. Carter
Chip Stewart
Stacey B. Gabriel
Eric S. Lander
Matthew Meyerson
Rameen Beroukhim
Gad Getz

First Published November 2, 2012

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

Fusobacterium with colorectal carcinoma" > Genomic analysis identifies association of Fusobacterium with colorectal carcinoma

Aleksandar D. Kostic
Dirk Gevers
Chandra Sekhar Pedamallu
Monia Michaud
Fujiko Duke
Ashlee M. Earl Akinyemi I. Ojesina Joonil Jung Adam J. Bass Josep Tabernero José Baselga Chen Liu Ramesh A. Shivdasani Shuji Ogino
... [+9 authors] ...,
Bruce W. Birren
Curtis Huttenhower
Wendy S. Garrett
Matthew Meyerson

First Published October 18, 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

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