Human Immunodeficiency Virus: Quasi-Species and Drug Resistance. - John M. Murray; Alan S. Perelson (Multiscale Model. Simul., 2005)

Simultaneous classification and feature selection via convex quadratic programming with application to HIV-associated neurocognitive disorder assessment. - Michelle Dunbar; John M. Murray; Lucette A. Cysique; Bruce J. Brew; Vaithilingam Jeyakumar (Eur. J. Oper. Res., 2010)

Explaining the Determinants of First Phase HIV Decay Dynamics through the Effects of Stage-dependent Drug Action. - James B. Gilmore; Anthony D. Kelleher; David A. Cooper; John M. Murray (PLoS Comput. Biol., 2013)

A Quantitative Comparison of Anti-HIV Gene Therapy Delivered to Hematopoietic Stem Cells versus CD4+ T Cells. - Borislav Savkovic; James A. Nichols; Donald Birkett; Tanya Applegate; Scott Ledger; Geoff Symonds; John M. Murray (PLoS Comput. Biol., 2014)

The unrooted set covering connected subgraph problem differentiating between HIV envelope sequences. - Stephen J. Maher; John M. Murray (Eur. J. Oper. Res., 2016)

Fractional Order Compartment Models. - Christopher N. Angstmann; Austen M. Erickson; Bruce Ian Henry; Anna V. McGann; John M. Murray; James A. Nichols (SIAM J. Appl. Math., 2017)

NGlyAlign: an automated library building tool to align highly divergent HIV envelope sequences. - Elma Akand; John M. Murray (BMC Bioinform., 2021)

A General Framework for Fractional Order Compartment Models. - Christopher N. Angstmann; Austen M. Erickson; Bruce Ian Henry; Anna V. McGann; John M. Murray; James A. Nichols (SIAM Rev., 2021)

ENTRAIN: integrating trajectory inference and gene regulatory networks with spatial data to co-localize the receptor-ligand interactions that specify cell fate. - Wunna Kyaw; Ryan C. Chai; Weng Hua Khoo; Leonard D. Goldstein; Peter I Croucher; John M. Murray; Tri Giang Phan (Bioinform., 2023)