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Method

Multicondition and multimodal temporal profile inference during mouse embryonic development

  • Ran Zhang
  • Chengxiang Qiu
  • Galina N. Filippova
  • Gang Li
  • Jay Shendure
  • Jean-Philippe Vert
  • Xinxian Deng
  • William Stafford Noble
  • Christine M. Disteche
  • First Published August 14, 2025
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
Resource

The western redcedar genome reveals low genetic diversity in a self-compatible conifer

  • Tal J. Shalev
  • Omnia Gamal El-Dien
  • Macaire M.S. Yuen
  • Shu Shengqiang
  • Shaun D. Jackman
  • René L. Warren Lauren Coombe Lise van der Merwe Ada Stewart Lori B. Boston Christopher Plott Jerry Jenkins Guifen He Juying Yan Mi Yan Jie Guo Jesse W. Breinholt Leandro G. Neves Jane Grimwood Loren H. Rieseberg Jeremy Schmutz Inanc Birol Matias Kirst
  • ... [+18 authors] ...,
  • Alvin D. Yanchuk
  • Carol Ritland
  • John H. Russell
  • Joerg Bohlmann
  • First Published September 15, 2022
Resource

Caenorhabditis elegans nematodes" > Comprehensive characterization of tissue-specific chromatin accessibility in L2 Caenorhabditis elegans nematodes

  • Timothy J. Durham
  • Riza M. Daza
  • Louis Gevirtzman
  • Darren A. Cusanovich
  • Olubusayo Bolonduro
  • William Stafford Noble
  • Jay Shendure
  • Robert H. Waterston
  • First Published April 22, 2021
Research

Genome-wide strand asymmetry in massively parallel reporter activity favors genic strands

  • Brian S. Roberts
  • E. Christopher Partridge
  • Bryan A. Moyers
  • Vikram Agarwal
  • Kimberly M. Newberry
  • Beth K. Martin
  • Jay Shendure
  • Richard M. Myers
  • Gregory M. Cooper
  • First Published April 20, 2021
Method

RNA-Bloom enables reference-free and reference-guided sequence assembly for single-cell transcriptomes

  • Ka Ming Nip
  • Readman Chiu
  • Chen Yang
  • Justin Chu
  • Hamid Mohamadi
  • René L. Warren
  • Inanc Birol
  • First Published August 17, 2020
Research

Mecp2-null mice implicate the DNA damage response in Rett syndrome pathology" > Suppressor mutations in Mecp2-null mice implicate the DNA damage response in Rett syndrome pathology

  • Adebola Enikanolaiye
  • Julie Ruston
  • Rong Zeng
  • Christine Taylor
  • Marijke Schrock
  • Christie M. Buchovecky
  • Jay Shendure
  • Elif Acar
  • Monica J. Justice
  • First Published April 21, 2020
Method

ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter

  • Shaun D. Jackman
  • Benjamin P. Vandervalk
  • Hamid Mohamadi
  • Justin Chu
  • Sarah Yeo
  • S. Austin Hammond Golnaz Jahesh
  • ... [+2 authors] ...,
  • Hamza Khan
  • Lauren Coombe
  • Rene L. Warren
  • Inanc Birol
  • First Published February 23, 2017
Research

A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity

  • Fumitaka Inoue
  • Martin Kircher
  • Beth Martin
  • Gregory M. Cooper
  • Daniela M. Witten
  • Michael T. McManus
  • Nadav Ahituv
  • Jay Shendure
  • First Published November 9, 2016
Corrigendum

Corrigendum: MIPSTR: a method for multiplex genotyping of germline and somatic STR variation across many individuals

  • Keisha D. Carlson
  • Peter H. Sudmant
  • Maximilian O. Press
  • Evan E. Eichler
  • Jay Shendure
  • Christine Queitsch
  • First Published August 3, 2015
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