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Joint imputation and deconvolution of gene expression across spatial transcriptomics platforms

  • Hongyu Zheng
  • Hirak Sarkar
  • Benjamin J. Raphael
  • First Published November 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

Partial alignment of multislice spatially resolved transcriptomics data

  • Xinhao Liu
  • Ron Zeira
  • Benjamin J. Raphael
  • First Published August 8, 2023

Reconstruction of clone- and haplotype-specific cancer genome karyotypes from bulk tumor samples

  • Sergey Aganezov
  • Benjamin J. Raphael
  • First Published September 4, 2020

netNMF-sc: leveraging gene–gene interactions for imputation and dimensionality reduction in single-cell expression analysis

  • Rebecca Elyanow
  • Bianca Dumitrascu
  • Barbara E. Engelhardt
  • Benjamin J. Raphael
  • First Published January 28, 2020

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

Single-cell sequencing data reveal widespread recurrence and loss of mutational hits in the life histories of tumors

  • Jack Kuipers
  • Katharina Jahn
  • Benjamin J. Raphael
  • Niko Beerenwinkel
  • First Published October 13, 2017

GenomeVIP: a cloud platform for genomic variant discovery and interpretation

  • R. Jay Mashl
  • Adam D. Scott
  • Kuan-lin Huang
  • Matthew A. Wyczalkowski
  • Christopher J. Yoon
  • Beifang Niu Erin DeNardo Venkata D. Yellapantula Robert E. Handsaker Ken Chen Daniel C. Koboldt Kai Ye
  • ... [+7 authors] ...,
  • David Fenyö
  • Benjamin J. Raphael
  • Michael C. Wendl
  • Li Ding
  • First Published May 18, 2017

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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