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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

Hydra genome reveals conserved regulators of cell state" > A chromosome-scale epigenetic map of the Hydra genome reveals conserved regulators of cell state

  • Jack F. Cazet
  • Stefan Siebert
  • Hannah Morris Little
  • Philip Bertemes
  • Abby S. Primack
  • Peter Ladurner Matthias Achrainer Mark T. Fredriksen R. Travis Moreland Sumeeta Singh Suiyuan Zhang Tyra G. Wolfsberg Christine E. Schnitzler
  • ... [+8 authors] ...,
  • Andreas D. Baxevanis
  • Oleg Simakov
  • Bert Hobmayer
  • Celina E. Juliano
  • First Published January 13, 2023

Profiling the quantitative occupancy of myriad transcription factors across conditions by modeling chromatin accessibility data

  • Kaixuan Luo
  • Jianling Zhong
  • Alexias Safi
  • Linda K. Hong
  • Alok K. Tewari
  • Lingyun Song
  • ... [+1 authors] ...,
  • Timothy E. Reddy
  • Li Ma
  • Gregory E. Crawford
  • Alexander J. Hartemink
  • First Published May 24, 2022

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

cis-regulatory elements, their cognate transcription factors, and regulatory DNA sequence variants" > Human cardiac cis-regulatory elements, their cognate transcription factors, and regulatory DNA sequence variants

  • Dongwon Lee
  • Ashish Kapoor
  • Alexias Safi
  • Lingyun Song
  • Marc K. Halushka
  • Gregory E. Crawford
  • Aravinda Chakravarti
  • First Published August 23, 2018

Glucocorticoid receptor recruits to enhancers and drives activation by motif-directed binding

  • Ian C. McDowell
  • Alejandro Barrera
  • Anthony M. D'Ippolito
  • Christopher M. Vockley
  • Linda K. Hong
  • Sarah M. Leichter Luke C. Bartelt William H. Majoros Lingyun Song Alexias Safi D. Dewran Koçak Charles A. Gersbach
  • ... [+7 authors] ...,
  • Alexander J. Hartemink
  • Gregory E. Crawford
  • Barbara E. Engelhardt
  • Timothy E. Reddy
  • First Published August 10, 2018

Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha

  • James M. Davison
  • Colin R. Lickwar
  • Lingyun Song
  • Ghislain Breton
  • Gregory E. Crawford
  • John F. Rawls
  • First Published April 6, 2017

Genome-wide specificity of DNA binding, gene regulation, and chromatin remodeling by TALE- and CRISPR/Cas9-based transcriptional activators

  • Lauren R. Polstein
  • Pablo Perez-Pinera
  • D. Dewran Kocak
  • Christopher M. Vockley
  • Peggy Bledsoe
  • Lingyun Song
  • ... [+1 authors] ...,
  • Alexias Safi
  • Gregory E. Crawford
  • Timothy E. Reddy
  • Charles A. Gersbach
  • First Published May 29, 2015

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
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