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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

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

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

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

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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