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Research

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
Research

Whole-genome resequencing of temporally stratified samples reveals substantial loss of haplotype diversity in the highly inbred Scandinavian wolf population

  • Agnese Viluma
  • Øystein Flagstad
  • Mikael Åkesson
  • Camilla Wikenros
  • Håkan Sand
  • Petter Wabakken
  • Hans Ellegren
  • First Published February 8, 2022
Research

Ficedula flycatchers and their naturally occurring F1 hybrids" > Tissue-specific patterns of regulatory changes underlying gene expression differences among Ficedula flycatchers and their naturally occurring F1 hybrids

  • Carina F. Mugal
  • Mi Wang
  • Niclas Backström
  • David Wheatcroft
  • Murielle Ålund
  • Marie Sémon
  • ... [+1 authors] ...,
  • S. Eryn McFarlane
  • Ludovic Dutoit
  • Anna Qvarnström
  • Hans Ellegren
  • First Published November 3, 2020
Research

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
Research

Direct estimate of the rate of germline mutation in a bird

  • Linnéa Smeds
  • Anna Qvarnström
  • Hans Ellegren
  • First Published July 13, 2016
Research

Ficedula flycatchers" > Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum of Ficedula flycatchers

  • Reto Burri
  • Alexander Nater
  • Takeshi Kawakami
  • Carina F. Mugal
  • Pall I. Olason
  • Linnea Smeds Alexander Suh Ludovic Dutoit Stanislav Bureš Laszlo Z. Garamszegi Silje Hogner Juan Moreno Anna Qvarnström Milan Ružić
  • ... [+9 authors] ...,
  • Stein-Are Sæther
  • Glenn-Peter Sætre
  • Janos Török
  • Hans Ellegren
  • First Published September 9, 2015
Method

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
Method

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
Method

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
Method

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
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