Modeling 5' regions of histone genes using Bayesian networks. - Rajesh Chowdhary; R. Ayesha Ali; Vladimir B. Bajic (APBC, 2005)

Promoter modeling: the case study of mammalian histone promoters. - Rajesh Chowdhary; R. Ayesha Ali; Werner Albig; Detlef Doenecke; Vladimir B. Bajic (Bioinform., 2005)

Dragon Promoter Mapper (DPM): a Bayesian framework for modelling promoter structures. - Rajesh Chowdhary; Sin Lam Tan; R. Ayesha Ali; Brent Boerlage; Limsoon Wong; Vladimir B. Bajic (Bioinform., 2006)

A simple approach to analyzing clustered longitudinal data. - Matthew Stephenson; R. Ayesha Ali; Gerarda A. Darlington (Commun. Stat. Simul. Comput., 2017)

DSRIG: Incorporating graphical structure in the regularized modeling of SNP data. - Matthew Stephenson; Gerarda A. Darlington; Flavio S. Schenkel; E. James Squires; R. Ayesha Ali (J. Bioinform. Comput. Biol., 2019)

DSLRIG: Leveraging predictor structure in logistic regression. - Matthew Stephenson; R. Ayesha Ali; Gerarda A. Darlington; Flavio S. Schenkel; E. James Squires (Commun. Stat. Simul. Comput., 2021)

Comparative transcriptomics analysis pipeline for the meta-analysis of phylogenetically divergent datasets (CoRMAP). - Yiru Sheng; R. Ayesha Ali; Andreas Heyland (BMC Bioinform., 2022)

Interpreting capsule networks for image classification by routing path visualization. - Amanjot Bhullar; Michael Czomko; R. Ayesha Ali; Douglas L. Welch (Artif. Intell., 2025)