William (Joe) Allen

William (Joe) Allen

Research Associate

Life Sciences Computing Group

512-475-9448
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).


Areas of Research and Interest

  • 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

Current Projects

  • UTRC – UT System Research Cyberinfrastructure
  • DARPA-SD2E – Synergistic Discovery and Design
  • CyVerse – cyberinfrastructure for data management and analysis
  • RT-MRI – automated real-time quantitative MRI
  • DrugDiscovery@TACC – web portal for virtual screening

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 list of publications, please see: Google Scholar.


Education

Ph.D., Biochemistry,
Virginia Tech

B.S., Chemistry,
University of Jamestown

Memberships and Affiliations

  • American Chemical Society
  • Ken Kennedy Institute