Joe Allen

Research Associate
Life Sciences Computing
Office of Campus Engagement, Lead

Phone: 512-475-9448 | Email: wallen@tacc.utexas.edu

Joe Allen joined the TACC Life Sciences Computing Group in 2015 where he works to advance computational biology and bioinformatics research at UT system academic and health institutions. His research experience spans a range of disciplines from computer-aided drug design to wet lab biochemistry. He is also interested in exploring new ways high performance computing resources can be used to answer challenging biological questions. Before joining TACC, Joe earned a B.S. in Chemistry from the University of Jamestown (2006), and a Ph.D. in Biochemistry from Virginia Tech (2011).

Selected Publications

"A High-Performance Computing Portal Applied to 3D Electron Microscopy," JP Carson, et al. SN Computer Science, 7 (5), 518, (2026).

"Predicted Protein 3D Structures Provide Essential Insights into the Genetic Architecture Underlying Phenotypic Diversity in Maize," S Wang, M Khaipho-Burch, LC Johnson, ZR Miller, PJ Bradbury, D Speed, WJ Allen, MC Romay, J Xue, ES Buckler, GP Ramstein, BSong. Genome Research, 36 (1), 214-225, (2026).

"A Community Effort in SARS‐CoV‐2 Drug Discovery," J Schimunek, et al. Molecular Informatics, 43 (1), e202300262, (2024).

"Scalable and Reproducible Virtual Screening through an API-integrated Workflow," T Huff, A Darrow, J Medina, E Ferlanti, J Carson, J Fonner, S Tijerina, SJ Watowich, WJ Allen. Practice & Experience in Advanced Research Computing, 196-199, (2023).

"BiasNet: A Model to Predict Ligand Bias toward GPCR Signaling," JE Sanchez, BKC Govinda, J Franco, WJ Allen, JD Garcia, S Sirimulla. Journal of Chemical Information and Modeling, 61 (9), 4190, (2021).

"Role of Alkylated Residues in the Tetrapeptide Self‐assembly—A Molecular Dynamics Study," R Muthusivarajan, WJ Allen, AD Pehere, KV Sokolov, D Fuentes. Journal of Computational Chemistry, 41 (31), 2634-2640, (2020).

"Brain and Lesion Segmentation in Multiple Sclerosis using Fully Convolutional Neural Networks: A Large-scale Study," RE Gabr, I Coronado, M Robinson, SJ Sujit, S Datta, X Sun, WJ Allen, FD Lublin, JS Wolinsky, PA Narayana. Multiple Sclerosis Journal, 26 (10), 1217-1226, (2020).

"Platform for Automated Real-Time High Performance Analytics on Medical Image Data," WJ Allen, RE Gabr, GB Tefera, AS Pednekar, MW Vaughn, PA Narayana. IEEE Journal of Biomedical and Health Informatics, 22 (2), 318-324, (2018).

"DOCK 6: Impact of New Features and Current Docking Performance," WJ Allen, TE Balius, S Mukherjee, SR Brozell, DT Moustakas, PT Lang, DA Case, ID Kuntz, RC Rizzo. Journal of Computational Chemistry, 36 (15), 1132-1156, (2015).

"Implementation of the Hungarian Algorithm to Account for Ligand Symmetry and Similarity in Structure-based Design," WJ Allen, RC Rizzo. Journal of Chemical Information and Modeling, 54 (2), 518-529, (2014).

"GridMAT‐MD: A Grid‐based Membrane Analysis Tool for Use with Molecular Dynamics," WJ Allen, JA Lemkul, DR Bevan. Journal of Computational Chemistry, 30 (12), 1952-1958, (2009).

For a full list of publications, please see: Google Scholar.

Current Projects

• epiENGAGE – pandemic scenario modeling
• Jetstream2 – distributed cloud infrastructure
• UTRC – UT System Research Cyberinfrastructure
• BrainMap – Portal for human brain mapping
• DrugDiscovery@TACC – web portal for virtual screening

Areas of Research

• Developing cyberinfrastructure for exploration, analysis, and visualization of biomedical data
• Drug discovery methods, algorithms, and applications; Protein structure-function
• Engaging and enabling researchers in life sciences computing