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Nucleic Acids Research|October 31, 2016
A prior-based integrative framework for functional transcriptional regulatory network inferenceAlireza F Siahpirani, Sushmita RoyFEMS Yeast Research|October 10, 2015
Evolution of regulatory networks in Candida glabrata: learning to live with the human hostSushmita Roy, Dawn ThompsonGenome Research|April 21, 2017
Chromatin module inference on cellular trajectories identifies key transition points and poised epigenetic states in diverse developmental processesSushmita Roy, Rupa SridharanCell Reports Methods|September 26, 2023
Predicting patient-specific enhancer-promoter interactionsBrittany Baur, Sushmita RoyCurrent Opinion in Systems Biology|October 31, 2017
Inference of cell type specific regulatory networks on mammalian lineagesDeborah Chasman, Sushmita RoyGenome Biology|May 26, 2021
GRiNCH: simultaneous smoothing and detection of topological units of genome organization from sparse chromatin contact count matrices with matrix factorizationDa-Inn Lee, Sushmita RoyGenome Research|March 20, 2025
Examining the dynamics of three-dimensional genome organization with multitask matrix factorizationDa-Inn Lee, Sushmita RoyMethods in Molecular Biology (Clifton, N.J.)|May 6, 2022
Enabling Studies of Genome-Scale Regulatory Network Evolution in Large Phylogenies with MRTLEShilu Zhang, Sara Knaack, Sushmita RoyAnnual Review of Cell and Developmental Biology|September 11, 2015
Comparative analysis of gene regulatory networks: from network reconstruction to evolutionDawn Thompson, Aviv Regev, Sushmita RoyArxiv|July 10, 2026
scMTNI: Leveraging cellular trajectory and context to infer dynamic GRNs from single-cell multi-omics dataSuvojit Hazra, Chandrani Kumari, Sushmita RoyPageof 13