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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

Long genes linked to autism spectrum disorders harbor broad enhancer-like chromatin domains

Ying-Tao Zhao
Deborah Y. Kwon
Brian S. Johnson
Maria Fasolino
Janine M. Lamonica
Yoon Jung Kim Boxuan Simen Zhao
... [+2 authors] ...,
Chuan He
Golnaz Vahedi
Tae Hoon Kim
Zhaolan Zhou

First Published May 30, 2018

Mapping and characterizing N6-methyladenine in eukaryotic genomes using single-molecule real-time sequencing

Shijia Zhu
John Beaulaurier
Gintaras Deikus
Tao P. Wu
Maya Strahl
Ziyang Hao Guanzheng Luo James A. Gregory Andrew Chess Chuan He
... [+5 authors] ...,
Andrew Xiao
Robert Sebra
Eric E. Schadt
Gang Fang

First Published May 15, 2018

N⁶-methyladenosine in primates" > Evolution of transcript modification by N⁶-methyladenosine in primates

Lijia Ma
Boxuan Zhao
Kai Chen
Amber Thomas
Jigyasa H. Tuteja
Xin He
Chuan He
Kevin P. White

First Published January 4, 2017

Bacterial infection remodels the DNA methylation landscape of human dendritic cells

Alain Pacis
Ludovic Tailleux
Alexander M. Morin
John Lambourne
Julia L. MacIsaac
Vania Yotova Anne Dumaine Anne Danckaert Francesca Luca Jean-Christophe Grenier Kasper D. Hansen Brigitte Gicquel Miao Yu Athma Pai Chuan He Jenny Tung Tomi Pastinen
... [+12 authors] ...,
Michael S. Kobor
Roger Pique-Regi
Yoav Gilad
Luis B. Barreiro

First Published September 21, 2015

The dynamics of DNA methylation fidelity during mouse embryonic stem cell self-renewal and differentiation

Lei Zhao
Ming-an Sun
Zejuan Li
Xue Bai
Miao Yu
Min Wang Liji Liang Xiaojian Shao Stephen Arnovitz Qianfei Wang
... [+5 authors] ...,
Chuan He
Xuemei Lu
Jianjun Chen
Hehuang Xie

First Published May 16, 2014

Spatiotemporal clustering of the epigenome reveals rules of dynamic gene regulation

Pengfei Yu
Shu Xiao
Xiaoyun Xin
Chun-Xiao Song
Wei Huang
Darina McDee
... [+1 authors] ...,
Tetsuya Tanaka
Ting Wang
Chuan He
Sheng Zhong

First Published October 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

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

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