Joe Allen

Research Associate
Campus Engagement Office

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

Allen, W.J.; Gabr, R.E.; Tefera, G.B.; Pednekar, A.S.; Vaughn, M.W.; Narayana, P.A. "Platform for Automated Real-Time High Performance Analytics on Medical Image Data." J. Biomed. Health Inform. 2018, 22, 318-324.

Gabr, R.E.; Tefera, G.B.; Allen, W.J.; Pednekar, A.S.; Narayana, P.A. "GRAPE: A Graphical Pipeline Environment for Image Analysis in Adaptive Magnetic Resonance Imaging." Int. J. Comput. Assist. Radiol. Surg. 2017, 12, 449-457.

Allen, W.J.; Yi, H.A.; Gochin, M.; Jacobs, A.; Rizzo, R.C. "Small Molecule Inhibitors of HIVgp41 N-heptad Repeat Trimer Formation." Bioorg. Med. Chem. Lett. 2015, 25, 2853-2859.

Allen, W.J.; Balius, T.E.; Mukherjee, S.; Brozell, S.R.; Moustakas, D.T.; Lang, P.T.; Case, D.A.; Kuntz, I.D.; Rizzo, R.C. "DOCK 6: Impact of New Features and Current Docking Performance." J. Comput. Chem. 2015, 36, 1132-1156.

Allen, W.J.; Rizzo, R.C. "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, W.J.; Rizzo, R.C. "Computer-Aided Approaches for Targeting HIVgp41." Biology 2012, 1, 311-338.

Allen, W.J.; Bevan, D.R. "Steered Molecular Dynamics Simulations Reveal Important Mechanisms in Reversible Monoamine Oxidase B Inhibition." Biochemistry 2011, 50, 6441-6454.

Allen, W.J.; Lemkul, J.A.; Bevan, D.R. "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

• 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

Memberships

• American Chemical Society
• Ken Kennedy Institute