Search | Genome Research

CL_GR_GenSeq_728x90

Your search for returned 7 results

Method

Examining the dynamics of three-dimensional genome organization with multitask matrix factorization

Da-Inn Lee
Sushmita Roy

First Published March 20, 2025

Method

Dynamic regulatory module networks for inference of cell type–specific transcriptional networks

Alireza Fotuhi Siahpirani
Sara Knaack
Deborah Chasman
Morten Seirup
Rupa Sridharan
Ron Stewart
James Thomson
Sushmita Roy

First Published June 15, 2022

Method

Enzymatic methyl sequencing detects DNA methylation at single-base resolution from picograms of DNA

Romualdas Vaisvila
V.K. Chaithanya Ponnaluri
Zhiyi Sun
Bradley W. Langhorst
Lana Saleh
Shengxi Guan Nan Dai Matthew A. Campbell Brittany S. Sexton Katherine Marks Mala Samaranayake James C. Samuelson Heidi E. Church Esta Tamanaha Ivan R. Corrêa Sriharsa Pradhan
... [+11 authors] ...,
Eileen T. Dimalanta
Thomas C. Evans
Louise Williams
Theodore B. Davis

First Published June 17, 2021

Method

Nondestructive enzymatic deamination enables single-molecule long-read amplicon sequencing for the determination of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution

Zhiyi Sun
Romualdas Vaisvila
Laura-Madison Hussong
Bo Yan
Chloé Baum
Lana Saleh Mala Samaranayake Shengxi Guan Nan Dai Ivan R. Corrêa
... [+5 authors] ...,
Sriharsa Pradhan
Theodore B. Davis
Thomas C. Evans
Laurence M. Ettwiller

First Published January 19, 2021

Method

Chromatin module inference on cellular trajectories identifies key transition points and poised epigenetic states in diverse developmental processes

Sushmita Roy
Rupa Sridharan

First Published April 19, 2017

Method

Arboretum: Reconstruction and analysis of the evolutionary history of condition-specific transcriptional modules

Sushmita Roy
Ilan Wapinski
Jenna Pfiffner
Courtney French
Amanda Socha
Jay Konieczka
... [+1 authors] ...,
Naomi Habib
Manolis Kellis
Dawn Thompson
Aviv Regev

First Published May 2, 2013

Method

Drosophila melanogaster by integrative inference of transcriptional networks" > Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks

Daniel Marbach
Sushmita Roy
Ferhat Ay
Patrick E. Meyer
Rogerio Candeias
Tamer Kahveci
Christopher A. Bristow
Manolis Kellis

First Published March 28, 2012