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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

Genome-wide cancer-specific chromatin accessibility patterns derived from archival processed xenograft tumors

Shelsa S. Marcel
Austin L. Quimby
Melodie P. Noel
Oscar C. Jaimes
Marjan Mehrab-Mohseni
Suud A. Ashur Brian Velasco James K. Tsuruta Sandeep K. Kasoji Charlene M. Santos
... [+5 authors] ...,
Paul A. Dayton
Joel S. Parker
Ian J. Davis
Samantha G. Pattenden

First Published November 23, 2021

An optogenetic switch for the Set2 methyltransferase provides evidence for transcription-dependent and -independent dynamics of H3K36 methylation

Andrew M. Lerner
Austin J. Hepperla
Gregory R. Keele
Hashem A. Meriesh
Hayretin Yumerefendi
David Restrepo Seth Zimmerman
... [+2 authors] ...,
James E. Bear
Brian Kuhlman
Ian J. Davis
Brian D. Strahl

First Published October 5, 2020

High-resolution structural genomics reveals new therapeutic vulnerabilities in glioblastoma

Michael J. Johnston
Ana Nikolic
Nicoletta Ninkovic
Paul Guilhamon
Florence M.G. Cavalli
Steven Seaman Franz J. Zemp John Lee Aly Abdelkareem Katrina Ellestad Alex Murison Michelle M. Kushida Fiona J. Coutinho Yussanne Ma Andrew J. Mungall Richard Moore Marco A. Marra Michael D. Taylor Peter B. Dirks Trevor J. Pugh Sorana Morrissy
... [+16 authors] ...,
Bradley St Croix
Douglas J. Mahoney
Mathieu Lupien
Marco Gallo

First Published June 27, 2019

TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data

Gavin Ha
Andrew Roth
Jaswinder Khattra
Julie Ho
Damian Yap
Leah M. Prentice Nataliya Melnyk Andrew McPherson Ali Bashashati Emma Laks Justina Biele Jiarui Ding Alan Le Jamie Rosner Karey Shumansky Marco A. Marra C. Blake Gilks
... [+12 authors] ...,
David G. Huntsman
Jessica N. McAlpine
Samuel Aparicio
Sohrab P. Shah

First Published July 24, 2014

Variation in chromatin accessibility in human kidney cancer links H3K36 methyltransferase loss with widespread RNA processing defects

Jeremy M. Simon
Kathryn E. Hacker
Darshan Singh
A. Rose Brannon
Joel S. Parker
Matthew Weiser Thai H. Ho Pei-Fen Kuan Eric Jonasch Terrence S. Furey
... [+5 authors] ...,
Jan F. Prins
Jason D. Lieb
W. Kimryn Rathmell
Ian J. Davis

First Published October 24, 2013

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

Estimating absolute methylation levels at single-CpG resolution from methylation enrichment and restriction enzyme sequencing methods

Michael Stevens
Jeffrey B. Cheng
Daofeng Li
Mingchao Xie
Chibo Hong
Cécile L. Maire Keith L. Ligon
... [+2 authors] ...,
Martin Hirst
Marco A. Marra
Joseph F. Costello
Ting Wang

First Published June 26, 2013

Integrative analysis of genome-wide loss of heterozygosity and monoallelic expression at nucleotide resolution reveals disrupted pathways in triple-negative breast cancer

Gavin Ha
Andrew Roth
Daniel Lai
Ali Bashashati
Jiarui Ding
Rodrigo Goya Ryan Giuliany Jamie Rosner Arusha Oloumi Karey Shumansky Suet-Feung Chin Gulisa Turashvili Martin Hirst
... [+8 authors] ...,
Carlos Caldas
Marco A. Marra
Samuel Aparicio
Sohrab P. Shah

First Published May 25, 2012

Tumor-specific retargeting of an oncogenic transcription factor chimera results in dysregulation of chromatin and transcription

Mukund Patel
Jeremy M. Simon
Michael D. Iglesia
Sam B. Wu
Andrew W. McFadden
Jason D. Lieb
Ian J. Davis

First Published November 15, 2011

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