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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
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
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

Resolving the full spectrum of human genome variation using Linked-Reads

  • Patrick Marks
  • Sarah Garcia
  • Alvaro Martinez Barrio
  • Kamila Belhocine
  • Jorge Bernate
  • Rajiv Bharadwaj Keith Bjornson Claudia Catalanotti Josh Delaney Adrian Fehr Ian T. Fiddes Brendan Galvin Haynes Heaton Jill Herschleb Christopher Hindson Esty Holt Cassandra B. Jabara Susanna Jett Nikka Keivanfar Sofia Kyriazopoulou-Panagiotopoulou Monkol Lek Bill Lin Adam Lowe Shazia Mahamdallie Shamoni Maheshwari Tony Makarewicz Jamie Marshall Francesca Meschi Christopher J. O'Keefe Heather Ordonez Pranav Patel Andrew Price Ariel Royall Elise Ruark Sheila Seal Michael Schnall-Levin Preyas Shah David Stafford Stephen Williams Indira Wu
  • ... [+35 authors] ...,
  • Andrew Wei Xu
  • Nazneen Rahman
  • Daniel MacArthur
  • Deanna M. Church
  • First Published March 20, 2019
Corrigendum

Corrigendum: Direct determination of diploid genome sequences

  • Neil I. Weisenfeld
  • Vijay Kumar
  • Preyas Shah
  • Deanna M. Church
  • David B. Jaffe
  • First Published April 2, 2018
Resource

Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly

  • Valerie A. Schneider
  • Tina Graves-Lindsay
  • Kerstin Howe
  • Nathan Bouk
  • Hsiu-Chuan Chen
  • Paul A. Kitts Terence D. Murphy Kim D. Pruitt Françoise Thibaud-Nissen Derek Albracht Robert S. Fulton Milinn Kremitzki Vincent Magrini Chris Markovic Sean McGrath Karyn Meltz Steinberg Kate Auger William Chow Joanna Collins Glenn Harden Timothy Hubbard Sarah Pelan Jared T. Simpson Glen Threadgold James Torrance Jonathan M. Wood Laura Clarke Sergey Koren Matthew Boitano Paul Peluso Heng Li Chen-Shan Chin Adam M. Phillippy Richard Durbin
  • ... [+29 authors] ...,
  • Richard K. Wilson
  • Paul Flicek
  • Evan E. Eichler
  • Deanna M. Church
  • First Published April 10, 2017
Method

Direct determination of diploid genome sequences

  • Neil I. Weisenfeld
  • Vijay Kumar
  • Preyas Shah
  • Deanna M. Church
  • David B. Jaffe
  • First Published April 5, 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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