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

Schimunek, J et al. "A Community Effort in SARS‐CoV‐2 Drug Discovery." Mol Inform 2024, 43, e202300262.

Huff, T; Darrow, A; Medina, J; Ferlanti, E; Carson, J; Fonner, J; Tijerina, S; Watowich, SJ; Allen, WJ. "Scalable and Reproducible Virtual Screening through an API-integrated Workflow." PEARC 2023, 196-199.

Sanchez, JE; Kc, GB; Franco, J; Allen, WJ; Garcia, JD; Sirimulla, S. "BiasNet: A Model to Predict Ligand Bias Toward GPCR Signaling." J Chem Inf Model 2021, 61, 4190-4199.

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

Fuentes, D; Muñoz, NM; Guo, C; Polak, U; Minhaj, AA; Allen, WJ; Gustin, MC; Cressman, ENK. "A Molecular Dynamics Approach Towards Evaluating Osmotic and Thermal Stress in the Extracellular Environment." Int J Hyperthermia 2019, 35, 559-567.

Allen, WJ; Gabr, RE; Tefera, GB; Pednekar, AS; Vaughn, MW; Narayana, PA. "Platform for Automated Real-Time High Performance Analytics on Medical Image Data." J Biomed Health Inform 2018, 22, 318-324.

Gabr, RE; Tefera, GB; Allen, WJ; Pednekar, AS; Narayana, PA. "GRAPE: A Graphical Pipeline Environment for Image Analysis in Adaptive Magnetic Resonance Imaging." Int J Comput Assist Radiol Surg 2017, 12, 449-457.

Allen, WJ; Balius, TE; Mukherjee, S; Brozell, SR; Moustakas, DT; Lang, PT; Case, DA; Kuntz, ID; Rizzo, RC. "DOCK 6: Impact of New Features and Current Docking Performance." J Comput Chem 2015, 36, 1132-1156.

Allen, WJ; Rizzo, RC. "Implementation of the Hungarian Algorithm to Account for Ligand Symmetry and Similarity in Structure-Based Design." J Chem Inf Model 2014, 54, 518-529.

Allen, WJ; Lemkul, JA; Bevan, DR. "GridMAT-MD: A Grid-Based Membrane Analysis Tool for Use with Molecular Dynamics." J Comput Chem 2009, 30, 1952-1958.

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