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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

A deconvolution framework that uses single-cell sequencing plus a small benchmark data set for accurate analysis of cell type ratios in complex tissue samples

Shuai Guo
Xiaoqian Liu
Xuesen Cheng
Yujie Jiang
Shuangxi Ji
Qingnan Liang Andrew Koval Yumei Li Leah A. Owen Ivana K. Kim Ana Aparicio Sanghoon Lee Anil K. Sood Scott Kopetz John Paul Shen
... [+10 authors] ...,
John N. Weinstein
Margaret M. DeAngelis
Rui Chen
Wenyi Wang

First Published November 25, 2024

Accelerated somatic mutation calling for whole-genome and whole-exome sequencing data from heterogenous tumor samples

Shuangxi Ji
Tong Zhu
Ankit Sethia
Wenyi Wang

First Published April 8, 2024

Deep sequencing of short capped RNAs reveals novel families of noncoding RNAs

Michiel de Hoon
Alessandro Bonetti
Charles Plessy
Yoshinari Ando
Chung-Chau Hon
Yuri Ishizu Masayoshi Itoh Sachi Kato Dongyan Lin Sho Maekawa Mitsuyoshi Murata Hiromi Nishiyori Jay W. Shin Jens Stolte Ana Maria Suzuki Michihira Tagami Hazuki Takahashi Supat Thongjuea
... [+13 authors] ...,
Alistair R.R. Forrest
Yoshihide Hayashizaki
Juha Kere
Piero Carninci

First Published August 12, 2022

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

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

Comparative transcriptomics of primary cells in vertebrates

Tanvir Alam
Saumya Agrawal
Jessica Severin
Robert S. Young
Robin Andersson
Erik Arner Akira Hasegawa Marina Lizio Jordan A. Ramilowski Imad Abugessaisa Yuri Ishizu Shohei Noma Hiroshi Tarui Martin S. Taylor Timo Lassmann Masayoshi Itoh Takeya Kasukawa Hideya Kawaji Luigi Marchionni Guojun Sheng Alistair R.R. Forrest
... [+16 authors] ...,
Levon M. Khachigian
Yoshihide Hayashizaki
Piero Carninci
Michiel J.L. de Hoon

First Published July 27, 2020

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

Corrigendum: 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 May 1, 2018

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

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