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Deciphering context-specific gene programs from single-cell and spatial transcriptomics data with DeCEP

Lin Li
Xianbin Su
Ze-Guang Han

First Published August 21, 2025

Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships" > Binding profiles for 961 Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships

Michelle Kudron
Louis Gevirtzman
Alec Victorsen
Bridget C. Lear
Jiahao Gao
Jinrui Xu Swapna Samanta Emily Frink Adri Tran-Pearson Chau Huynh Dionne Vafeados Ann Hammonds William Fisher Martha Wall Greg Wesseling Vanessa Hernandez Zhichun Lin Mary Kasparian Kevin White Ravi Allada Mark Gerstein
... [+16 authors] ...,
LaDeana Hillier
Susan E. Celniker
Valerie Reinke
Robert H. Waterston

First Published October 22, 2024

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

A high-resolution gene expression atlas links dedicated meristem genes to key architectural traits

Steffen Knauer
Marie Javelle
Lin Li
Xianran Li
Xiaoli Ma
Kokulapalan Wimalanathan Sunita Kumari Robyn Johnston Samuel Leiboff Robert Meeley Patrick S. Schnable Doreen Ware Carolyn Lawrence-Dill
... [+8 authors] ...,
Jianming Yu
Gary J. Muehlbauer
Michael J. Scanlon
Marja C.P. Timmermans

First Published November 19, 2019

C. elegans embryonic transcriptome with tissue, time, and alternative splicing resolution" > The C. elegans embryonic transcriptome with tissue, time, and alternative splicing resolution

Adam D. Warner
Louis Gevirtzman
LaDeana W. Hillier
Brent Ewing
Robert H. Waterston

First Published May 23, 2019

John Sulston (1942–2018)

Robert H. Waterston

First Published June 1, 2018

C. elegans" > The time-resolved transcriptome of C. elegans

Max E. Boeck
Chau Huynh
Lou Gevirtzman
Owen A. Thompson
Guilin Wang
Dionna M. Kasper
Valerie Reinke
LaDeana W. Hillier
Robert H. Waterston

First Published August 16, 2016

Caenorhabditis elegans" > The million mutation project: A new approach to genetics in Caenorhabditis elegans

Owen Thompson
Mark Edgley
Pnina Strasbourger
Stephane Flibotte
Brent Ewing
Ryan Adair Vinci Au Iasha Chaudhry Lisa Fernando Harald Hutter Armelle Kieffer Joanne Lau Norris Lee Angela Miller Greta Raymant Bin Shen Jay Shendure Jon Taylor
... [+13 authors] ...,
Emily H. Turner
LaDeana W. Hillier
Donald G. Moerman
Robert H. Waterston

First Published June 25, 2013

Whole-genome sequencing identifies recurrent mutations in hepatocellular carcinoma

Zhengyan Kan
Hancheng Zheng
Xiao Liu
Shuyu Li
Thomas D. Barber
Zhuolin Gong Huan Gao Ke Hao Melinda D. Willard Jiangchun Xu Robert Hauptschein Paul A. Rejto Julio Fernandez Guan Wang Qinghui Zhang Bo Wang Ronghua Chen Jian Wang Nikki P. Lee Wei Zhou Zhao Lin Zhiyu Peng Kang Yi Shengpei Chen Lin Li Xiaomei Fan Jie Yang Rui Ye Jia Ju Kai Wang Heather Estrella Shibing Deng Ping Wei Ming Qiu Isabella H. Wulur Jiangang Liu Mariam E. Ehsani Chunsheng Zhang Andrey Loboda Wing Kin Sung Amit Aggarwal Ronnie T. Poon Sheung Tat Fan Jun Wang James Hardwick Christoph Reinhard
... [+41 authors] ...,
Hongyue Dai
Yingrui Li
John M. Luk
Mao Mao

First Published June 20, 2013

C. elegans embryo" > Multidimensional regulation of gene expression in the C. elegans embryo

John Isaac Murray
Thomas J. Boyle
Elicia Preston
Dionne Vafeados
Barbara Mericle
Peter Weisdepp
... [+1 authors] ...,
Zhongying Zhao
Zhirong Bao
Max Boeck
Robert H. Waterston

First Published April 16, 2012

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