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Method

Kernel-bounded clustering for spatial transcriptomics enables scalable discovery of complex spatial domains

Hang Zhang
Yi Zhang
Kai Ming Ting
Jie Zhang
Qiuran Zhao

First Published February 5, 2025

Resource

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

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

Resource

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

In memoriam

John Sulston (1942–2018)

Robert H. Waterston

First Published June 1, 2018

Resource

Annotation and cluster analysis of spatiotemporal- and sex-related lncRNA expression in rhesus macaque brain

Siling Liu
Zhengbo Wang
Dong Chen
Bowen Zhang
Ren-Rong Tian
Jing Wu Ying Zhang Kaiyu Xu Liu-Meng Yang Chao Cheng Jian Ma Longbao Lv Yong-Tang Zheng
... [+8 authors] ...,
Xintian Hu
Yi Zhang
Xiangting Wang
Jiali Li

First Published July 7, 2017

Resource

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

Resource

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

Research

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

Research

C. elegans trans-splicing" > A global analysis of C. elegans trans-splicing

Mary Ann Allen
LaDeana W. Hillier
Robert H. Waterston
Thomas Blumenthal

First Published December 22, 2010

Research

C. elegans" > Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans

Wei Niu
Zhi John Lu
Mei Zhong
Mihail Sarov
John I. Murray
Cathleen M. Brdlik Judith Janette Chao Chen Pedro Alves Elicia Preston Cindie Slightham Lixia Jiang Anthony A. Hyman Stuart K. Kim
... [+9 authors] ...,
Robert H. Waterston
Mark Gerstein
Michael Snyder
Valerie Reinke

First Published December 22, 2010

Method

C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data" > Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data

Zhi John Lu
Kevin Y. Yip
Guilin Wang
Chong Shou
LaDeana W. Hillier
Ekta Khurana Ashish Agarwal Raymond Auerbach Joel Rozowsky Chao Cheng Masaomi Kato David M. Miller Frank Slack
... [+8 authors] ...,
Michael Snyder
Robert H. Waterston
Valerie Reinke
Mark B. Gerstein

First Published December 22, 2010

Methods

MS-qFRET: A quantum dot-based method for analysis of DNA methylation

Vasudev J. Bailey
Hariharan Easwaran
Yi Zhang
Elizabeth Griffiths
Steven A. Belinsky
James G. Herman
Stephen B. Baylin
Hetty E. Carraway
Tza-Huei Wang

First Published May 14, 2009

Resource

C. elegans" > Massively parallel sequencing of the polyadenylated transcriptome of C. elegans

LaDeana W. Hillier
Valerie Reinke
Philip Green
Martin Hirst
Marco A. Marra
Robert H. Waterston

First Published January 30, 2009

RESOURCE

A framework for collaborative analysis of ENCODE data: Making large-scale analyses biologist-friendly

Daniel Blankenberg
James Taylor
Ian Schenck
Jianbin He
Yi Zhang
Matthew Ghent Narayanan Veeraraghavan Istvan Albert
... [+3 authors] ...,
Webb Miller
Kateryna D. Makova
Ross C. Hardison
Anton Nekrutenko

First Published June 13, 2007

PERSPECTIVE

C. elegans: So many genes, such a little worm" > Genomics in C. elegans: So many genes, such a little worm

LaDeana W. Hillier
Alan Coulson
John I. Murray
Zhirong Bao
John E. Sulston
Robert H. Waterston

First Published December 8, 2005

RESOURCE

Galaxy: A platform for interactive large-scale genome analysis

Belinda Giardine
Cathy Riemer
Ross C. Hardison
Richard Burhans
Laura Elnitski
Prachi Shah Yi Zhang Daniel Blankenberg Istvan Albert
... [+4 authors] ...,
James Taylor
Webb Miller
W. James Kent
Anton Nekrutenko

First Published September 16, 2005

ARTICLE

Interchromosomal segmental duplications of the pericentromeric region on the human Y chromosome

Stefan Kirsch
Birgit Weiß
Tracie L. Miner
Robert H. Waterston
Royden A. Clark
Evan E. Eichler
Claudia Münch
Werner Schempp
Gudrun Rappold

First Published January 14, 2005

LETTER

Caenorhabditis elegans muscle genes" > Novel transcription regulatory elements in Caenorhabditis elegans muscle genes

Debraj GuhaThakurta
Lawrence A. Schriefer
Robert H. Waterston
Gary D. Stormo

First Published December 1, 2004

ARTICLE

Strongyloides stercoralis and Caenorhabditis elegans" > Comparative Genomics of Gene Expression in the Parasitic and Free-Living Nematodes Strongyloides stercoralis and Caenorhabditis elegans

Makedonka Mitreva
James P. McCarter
John Martin
Mike Dante
Todd Wylie
Brandi Chiapelli
... [+1 authors] ...,
Deana Pape
Sandra W. Clifton
Thomas B. Nutman
Robert H. Waterston

First Published February 2, 2004

METHODS

Software for Automated Analysis of DNA Fingerprinting Gels

Daniel R. Fuhrmann
Martin I. Krzywinski
Readman Chiu
Parvaneh Saeedi
Jacqueline E. Schein
Ian E. Bosdet Asif Chinwalla LaDeana W. Hillier
... [+3 authors] ...,
Robert H. Waterston
John D. McPherson
Steven J.M. Jones
Marco A. Marra

First Published May 1, 2003

LETTER

Gene Discovery in the Apicomplexa as Revealed by EST Sequencing and Assembly of a Comparative Gene Database

Li Li
Brian P. Brunk
Jessica C. Kissinger
Deana Pape
Keliang Tang
Robert H. Cole John Martin Todd Wylie Mike Dante Steven J. Fogarty Daniel K. Howe Paul Liberator Carmen Diaz Jennifer Anderson Michael White Maria E. Jerome Emily A. Johnson Jay A. Radke Christian J. Stoeckert
... [+14 authors] ...,
Robert H. Waterston
Sandra W. Clifton
David S. Roos
L. David Sibley

First Published March 1, 2003

METHODS

Generalized Gap Model for Bacterial Artificial Chromosome Clone Fingerprint Mapping and Shotgun Sequencing

Michael C. Wendl
Robert H. Waterston

First Published December 1, 2002

ARTICLE

Saccharomyces Genomes to Identify Functional Elements by Comparative DNA Sequence Analysis" > Surveying Saccharomyces Genomes to Identify Functional Elements by Comparative DNA Sequence Analysis

Paul F. Cliften
LaDeana W. Hillier
Lucinda Fulton
Tina Graves
Tracie Miner
Warren R. Gish
Robert H. Waterston
Mark Johnston

First Published July 1, 2001

METHODS

Theories and Applications for Sequencing Randomly Selected Clones

Michael C. Wendl
Marco A. Marra
LaDeana W. Hillier
Asif T. Chinwalla
Richard K. Wilson
Robert H. Waterston

First Published January 18, 2001

LETTER

A High-Resolution Physical Map of Human Chromosome 21p Using Yeast Artificial Chromosomes

Sheng-Yue Wang
Marc Cruts
Jurgen Del-Favero
Yi Zhang
Fadel Tissir
Marie-Claude Potier David Patterson Dean Nizetic Assumpció Bosch Haiming Chen Lynda Bennett
... [+6 authors] ...,
Xavier Estivill
Anna Kessling
Stylianos E. Antonarakis
Christine van Broeckhoven

First Published November 1, 1999

LETTER

High Throughput Fingerprint Analysis of Large-Insert Clones

Marco A. Marra
Tamara A. Kucaba
Nicole L. Dietrich
Eric D. Green
Buddy Brownstein
Richard K. Wilson
... [+1 authors] ...,
Ken M. McDonald
LaDeana W. Hillier
John D. McPherson
Robert H. Waterston

First Published November 1, 1997