Scalable molecular dynamics with NAMD. - James C. Phillips; Rosemary Braun; Wei Wang 342; James C. Gumbart; Emad Tajkhorshid; Elizabeth Villa; Christophe Chipot; Robert D. Skeel; Laxmikant V. Kalé; Klaus Schulten (J. Comput. Chem., 2005)

Identifying differential correlation in gene/pathway combinations. - Rosemary Braun; Leslie Cope; Giovanni Parmigiani (BMC Bioinform., 2008)

Partition decoupling for multi-gene analysis of gene expression profiling data. - Rosemary Braun; Gregory Leibon; Scott D. Pauls; Daniel N. Rockmore (BMC Bioinform., 2011)

Semi-supervised network inference using simulated gene expression dynamics. - Phan Nguyen; Rosemary Braun (Bioinform., 2018)

Time-lagged Ordered Lasso for network inference. - Phan Nguyen; Rosemary Braun (BMC Bioinform., 2018)

GeneSurrounder: network-based identification of disease genes in expression data. - Sahil D. Shah; Rosemary Braun (BMC Bioinform., 2019)

Mutation, drift and selection in single-driver hematologic malignancy: Example of secondary myelodysplastic syndrome following treatment of inherited neutropenia. - Tomasz Wojdyla; Hrishikesh Mehta; Taly Glaubach; Roberto Bertolusso; Marta Iwanaszko; Rosemary Braun; Seth J. Corey; Marek Kimmel (PLoS Comput. Biol., 2019)

TimeCycle: topology inspired method for the detection of cycling transcripts in circadian time-series data. - Elan Ness-Cohn; Rosemary Braun (Bioinform., 2021)

fasano.franceschini.test: An Implementation of a Multivariate KS Test in R. - Connor Puritz; Elan Ness-Cohn; Rosemary Braun (R J., 2023)

Temperature-driven coordination of circadian transcriptional regulation. - Bingxian Xu; Dae-Sung Hwangbo; Sumit Saurabh; Clark Rosensweig; Ravi Allada; William L. Kath; Rosemary Braun (PLoS Comput. Biol., 2024)