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Current Opinion in Systems Biology|November 23, 2020
Data integration for inferring context-specific gene regulatory networksBrittany Baur, Junha Shin, Shilu Zhang, et al.Cancer Informatics|November 7, 2014
A pan-cancer modular regulatory network analysis to identify common and cancer-specific network componentsSara A Knaack, Alireza Fotuhi Siahpirani, Sushmita RoyMethods in Molecular Biology (Clifton, N.J.)|October 21, 2015
Reconstruction and Analysis of the Evolution of Modular Transcriptional Regulatory Programs Using ArboretumSara A Knaack, Dawn A Thompson, Sushmita RoyGenome Research|November 9, 2007
Reliable prediction of regulator targets using 12 Drosophila genomesPouya Kheradpour, Alexander Stark, Sushmita Roy, et al.Nature Communications|December 8, 2019
In silico prediction of high-resolution Hi-C interaction matricesShilu Zhang, Deborah Chasman, Sara Knaack, et al.Arxiv|July 10, 2026
MERLIN-SUITE: Probabilistic modular GRN inference from multi-omics data integrating regulatory priors and transcription factor activitySuvojit Hazra, Marina Kotvanova, Kirstan Gimse, et al.Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing|February 13, 2009
Inference of functional networks of condition-specific response--a case study of quiescence in yeastSushmita Roy, Terran Lane, Margaret Werner-Washburne, et al.Plant Physiology|February 5, 2017
Physiological Responses and Gene Co-Expression Network of Mycorrhizal Roots under K<sup>+</sup> DeprivationKevin Garcia, Deborah Chasman, Sushmita Roy, et al.Microbial Pathogenesis|August 6, 2025
Deciphering genetic overlaps between pulmonary tuberculosis and GERD for drug target discovery: A structural bioinformatics perspectiveSanjukta Dasgupta, Bishnupriya Saha, Sushmita Roy Chowdhury, et al.Scientific Reports|April 3, 2023
Rewiring of the 3D genome during acquisition of carboplatin resistance in a triple-negative breast cancer patient-derived xenograftMikhail G Dozmorov, Maggie A Marshall, Narmeen S Rashid, et al.Pageof 13