Quantifying reproducibility for differential proteomics: noise analysis for protein liquid chromatography-mass spectrometry of human serum. - Markus Anderle II; Sushmita Roy; Hua Lin; Christopher Becker; Keith Joho (Bioinform., 2004)

A datamining approach to cell population deconvolution from gene expressions using particle filters. - Sushmita Roy; Terran Lane; Margaret Werner-Washburne (BIOKDD, 2005)

Multivariate curve resolution of time course microarray data. - Peter D. Wentzell; Tobias K. Karakach; Sushmita Roy; M. Juanita Martinez; Christopher P. Allen; Margaret Werner-Washburne (BMC Bioinform., 2006)

A Hidden-State Markov Model for Cell Population Deconvolution. - Sushmita Roy; Terran Lane; Christopher P. Allen; Anthony D. Aragon; Margaret Werner-Washburne (J. Comput. Biol., 2006)

Integrative Construction and Analysis of Condition-specific Biological Networks. - Sushmita Roy; Terran Lane; Margaret Werner-Washburne (AAAI, 2008)

A system for generating transcription regulatory networks with combinatorial control of transcription. - Sushmita Roy; Margaret Werner-Washburne; Terran Lane (Bioinform., 2008)

Learning structurally consistent undirected probabilistic graphical models. - Sushmita Roy; Terran Lane; Margaret Werner-Washburne (ICML, 2009)

Inference of Functional Networks of Condition-Specific Response–A Case Study Of Quiescence In Yeast. - Sushmita Roy; Terran Lane; Margaret Werner-Washburne; Diego Martínez (Pacific Symposium on Biocomputing, 2009)

Information-Theoretic Inference of Gene Networks Using Backward Elimination. - Patrick Meyer; Daniel Marbach; Sushmita Roy; Manolis Kellis (BIOCOMP, 2010)

A multiple network learning approach to capture system-wide condition-specific responses. - Sushmita Roy; Margaret Werner-Washburne; Terran Lane (Bioinform., 2011)

Integrated Module and Gene-Specific Regulatory Inference Implicates Upstream Signaling Networks. - Sushmita Roy; Stephen Lagree; Zhonggang Hou; James A. Thomson; Ron M. Stewart; Audrey P. Gasch (PLoS Comput. Biol., 2013)

High-order interactions observed in multi-task intrinsic networks are dominant indicators of aberrant brain function in schizophrenia. - Sergey M. Plis; Jing Sui; Terran Lane; Sushmita Roy; Vincent P. Clark; Vamsi K. Potluru; René J. Huster; Andrew Michael; Scott R. Sponheim; Michael P. Weisend; Vince D. Calhoun (NeuroImage, 2014)

Multi-task consensus clustering of genome-wide transcriptomes from related biological conditions. - Zhen Niu; Deborah Chasman; Amie J. Eisfeld; Yoshihiro Kawaoka; Sushmita Roy (Bioinform., 2016)

Integrating Transcriptomic and Proteomic Data Using Predictive Regulatory Network Models of Host Response to Pathogens. - Deborah Chasman; Kevin B. Walters; Tiago J. S. Lopes; Amie J. Eisfeld; Yoshihiro Kawaoka; Sushmita Roy (PLoS Comput. Biol., 2016)

Comparison of deep and shallow graph representation learning algorithms for detecting modules in molecular networks. - Zhiwei Song; Brittany A. Baur; Sushmita Roy (BIBM, 2022)

ISMB 2022 proceedings. - Christophe Dessimoz; Sushmita Roy (Bioinform., 2022)

ISMB/ECCB 2023 proceedings. - Yann Ponty; Sushmita Roy (Bioinform., 2023)

Leveraging epigenomes and three-dimensional genome organization for interpreting regulatory variation. - Brittany Baur; Junha Shin; Jacob Schreiber; Shilu Zhang; Yi Zhang 055; Mohith Manjunath; Jun S. Song; William Stafford Noble; Sushmita Roy (PLoS Comput. Biol., 2023)