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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

Locus-resolution analysis of L1 regulation and retrotransposition potential in mouse embryonic development

Patricia Gerdes
Dorothy Chan
Mischa Lundberg
Francisco J. Sanchez-Luque
Gabriela O. Bodea
Adam D. Ewing
Geoffrey J. Faulkner
Sandra R. Richardson

First Published October 5, 2023

Research

Somatic retrotransposition in the developing rhesus macaque brain

Victor Billon
Francisco J. Sanchez-Luque
Jay Rasmussen
Gabriela O. Bodea
Daniel J. Gerhardt
Patricia Gerdes Seth W. Cheetham Stephanie N. Schauer Prabha Ajjikuttira Thomas J. Meyer Cora E. Layman Kimberly A. Nevonen Natasha Jansz Jose L. Garcia-Perez
... [+9 authors] ...,
Sandra R. Richardson
Adam D. Ewing
Lucia Carbone
Geoffrey J. Faulkner

First Published June 21, 2022

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

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

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

Research

Glucocorticoid receptor recruits to enhancers and drives activation by motif-directed binding

Ian C. McDowell
Alejandro Barrera
Anthony M. D'Ippolito
Christopher M. Vockley
Linda K. Hong
Sarah M. Leichter Luke C. Bartelt William H. Majoros Lingyun Song Alexias Safi D. Dewran Koçak Charles A. Gersbach
... [+7 authors] ...,
Alexander J. Hartemink
Gregory E. Crawford
Barbara E. Engelhardt
Timothy E. Reddy

First Published August 10, 2018

Research

L1 retrotransposition is a common feature of mammalian hepatocarcinogenesis

Stephanie N. Schauer
Patricia E. Carreira
Ruchi Shukla
Daniel J. Gerhardt
Patricia Gerdes
Francisco J. Sanchez-Luque Paola Nicoli Michaela Kindlova Serena Ghisletti Alexandre Dos Santos Delphine Rapoud Didier Samuel
... [+7 authors] ...,
Jamila Faivre
Adam D. Ewing
Sandra R. Richardson
Geoffrey J. Faulkner

First Published April 11, 2018

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