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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
Method

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
Method

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
Method

Mapping nucleosome positions using DNase-seq

  • Jianling Zhong
  • Kaixuan Luo
  • Peter S. Winter
  • Gregory E. Crawford
  • Edwin S. Iversen
  • Alexander J. Hartemink
  • First Published January 15, 2016
Method

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 February 6, 2015
Method

In vitro, long-range sequence information for de novo genome assembly via transposase contiguity

  • Andrew Adey
  • Jacob O. Kitzman
  • Joshua N. Burton
  • Riza Daza
  • Akash Kumar
  • Lena Christiansen Mostafa Ronaghi
  • ... [+2 authors] ...,
  • Sasan Amini
  • Kevin L. Gunderson
  • Frank J. Steemers
  • Jay Shendure
  • First Published October 19, 2014
Method

Single molecule molecular inversion probes for targeted, high-accuracy detection of low-frequency variation

  • Joseph B. Hiatt
  • Colin C. Pritchard
  • Stephen J. Salipante
  • Brian J. O'Roak
  • Jay Shendure
  • First Published February 4, 2013
Method

Predicting cell-type–specific gene expression from regions of open chromatin

  • Anirudh Natarajan
  • Galip Gürkan Yardımcı
  • Nathan C. Sheffield
  • Gregory E. Crawford
  • Uwe Ohler
  • First Published September 5, 2012
Method

Ultra-low-input, tagmentation-based whole-genome bisulfite sequencing

  • Andrew Adey
  • Jay Shendure
  • First Published March 30, 2012
Method

Trans genomic capture and sequencing of primate exomes reveals new targets of positive selection" > Trans genomic capture and sequencing of primate exomes reveals new targets of positive selection

  • Renee D. George
  • Graham McVicker
  • Rachel Diederich
  • Sarah B. Ng
  • Alexandra P. MacKenzie
  • Willie J. Swanson
  • Jay Shendure
  • James H. Thomas
  • First Published July 27, 2011
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