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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

H3K36 dimethylation shapes the epigenetic interaction landscape by directing repressive chromatin modifications in embryonic stem cells

Haifen Chen
Bo Hu
Cynthia Horth
Eric Bareke
Phillip Rosenbaum
Sin Young Kwon Jacinthe Sirois Daniel N. Weinberg Faith M. Robison
... [+4 authors] ...,
Benjamin A. Garcia
Chao Lu
William A. Pastor
Jacek Majewski

First Published April 8, 2022

Deep profiling and custom databases improve detection of proteoforms generated by alternative splicing

Laura M. Agosto
Matthew R. Gazzara
Caleb M. Radens
Simone Sidoli
Josue Baeza
Benjamin A. Garcia
Kristen W. Lynch

First Published November 14, 2019

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

One minute analysis of 200 histone posttranslational modifications by direct injection mass spectrometry

Simone Sidoli
Yekaterina Kori
Mariana Lopes
Zuo-Fei Yuan
Hee Jong Kim
Katarzyna Kulej Kevin A. Janssen
... [+2 authors] ...,
Laura M. Agosto
Julia Pinheiro Chagas da Cunha
Andrew J. Andrews
Benjamin A. Garcia

First Published May 23, 2019

Loss of HP1 causes depletion of H3K27me3 from facultative heterochromatin and gain of H3K27me2 at constitutive heterochromatin

Kirsty Jamieson
Elizabeth T. Wiles
Kevin J. McNaught
Simone Sidoli
Neena Leggett
Yanchun Shao
Benjamin A. Garcia
Eric U. Selker

First Published November 4, 2015

C. elegans through genome-wide analysis of the heterochromatin protein 1 homolog HPL-2" > Defining heterochromatin in C. elegans through genome-wide analysis of the heterochromatin protein 1 homolog HPL-2

Jacob M. Garrigues
Simone Sidoli
Benjamin A. Garcia
Susan Strome

First Published December 2, 2014

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

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

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