B.S.E. ​Duke University, 1999​M.S. University of California, San Diego, 2001Ph.D. ​University of California, San Diego, 2006

"My teaching is focused on providing students with the practical experience needed to engage in research and design that spans the breadth of BME."

Timothy E. Allen, Professor

Timothy E. Allen teaches and mentors students in the areas of computational modeling of complex biological systems, molecular and cell biology assays, and medical device design. He is a Professor in the Department of Biomedical Engineering at the University of Virginia. He received a B.S.E. in Biomedical Engineering at Duke University and M.S. and Ph.D. degrees in Bioengineering at the University of California, San Diego.

Dr. Allen's teaching activities include coordinating the undergraduate teaching labs and the Capstone Design sequence in the BME department at the University of Virginia, and his research interests are in the fields of computational biology and bioinformatics. He is also interested in evaluating the pedagogical approaches optimal for teaching lab concepts and skills, computational modeling approaches, and professionalism within design classes. He is active within the Biomedical Engineering Division of the American Society for Engineering Education and previously served on the executive committee of this division (Program Chair 2011, Division Chair 2012, & Nominating Committee Chair 2013). Dr. Allen serves on the BMES Education Committee. He is also the PI on a newly renewed NSF REU site focused on multi-scale systems bioengineering and biomedical data sciences, a collaboration involving faculty in SEAS, SOM, SDS, and CLAS at U.Va., as well as six partner institutions in the mid-Atlantic and Southeast.


  • All-University Teaching Award 2017
  • Faculty Banner Carrier for SEAS Class of 2017 at Final Exercises 2017
  • The Society of P.R.I. Recognition for Commitment to Students 2016
  • Jefferson Scholars Foundation Faculty Fellow 2014-present
  • Hartfield-Jefferson Teaching Prize 2014
  • Most Dedicated BME Professor Award 2011
  • Award for Excellence in Biomedical Engineering Undergraduate Education 2008, 2010, & 2011
  • Seven Society 20th Annual Monticello Dinner Series 2010
  • Thomas E. Hutchinson Faculty Award for Dedication and Excellence in Teaching 2009

Research Interests

  • Human Factors
  • Biomedical Data Sciences
  • Computational Systems Biology
  • Quantitative Biosciences

In the News

Selected Publications

  • BME Labs in the Era of COVID-19: Transitioning a Hands-on Integrative Lab Experience to Remote Instruction Using Gamified Lab Simulations. 2020. Biomedical Engineering Education ABS Allen, T.E. and Barker, S.D.
  • Retrospective Multi-year Analysis of Team Composition Dynamics and Performance within a Yearlong Integrative BME Laboratory Sequence. 2019. Proceedings for the 2019 ASEE Annual Conference and Exposition ABS Allen, T.E.
  • Patient Centered Design in Undergraduate Biomedical Engineering. 2018. Proceedings for the 2018 ASEE Annual Conference and Exposition ABS Allen, T.E. and Chen, D.
  • Development and assessment of a novel systems bioengineering course integrating modeling and experimentation. 2009. Proc. for the 2009 ASEE Ann. Conference & Expo. ABS Allen, T.E., Saucerman, J.J., Papin, J.A., and Peirce, S.M.
  • Career development and professionalism within a biomedical engineering capstone course. 2008. Proceedings for the 2008 ASEE Annual Conference and Exposition. ABS Allen, T.E. and Peirce, S.M.
  • Integrative Design and Experimental Analysis: A Yearlong Laboratory Course in Biomedical Engineering. 2007. Proceedings for the 2007 ASEE Annual Conference and Exposition. ABS Allen, T.E. and Blackman, B.R.
  • Long-range patterns in prokaryotic genome sequences indicate significant chromosomal organization. 2006. PLoS Computational Biology, 2(1):e2. (Featured on the cover of the January 2006 issue) ABS Allen, T.E., Price, N.D., Joyce, A.R., and Palsson, B.O.
  • Genome-scale analysis of the uses of the Escherichia coli genome: a model-driven analysis of heterogeneous datasets. 2003. Journal of Bacteriology, 185(21):6392-6399. Allen, T.E., Herrgard, M.J., Mingzhu, L., Qiu, Y., Glasner, J.D., Blattner, F.R., and Palsson, B.O.

Courses Taught

  • BME 3030: Design & Innovation in Medicine (co-instructor)
  • BME 3080/3090: BME IDEAS Lab I & II
  • BME 4550: Systems Bioengineering Modeling and Experimentation (co-instructor)
  • BME 4063/4064: BME Capstone Design I & II
  • BME 6102: Engineering Physiology II

Featured Grants & Projects

  • NSF Research Experiences for Undergraduates Site: Multi-Scale Systems Bioengineering and Biomedical Data Sciences (Role: PI).

    Advances in the biomedical sciences and medicine will increasingly depend upon the application of rigorous and quantitative engineering-based approaches to characterize and interrogate biological systems. This REU Site in Multi-Scale Systems Bioengineering and Biomedical Data Sciences at the University of Virginia will train ten undergraduate participants per summer in state-of-the-art systems bioengineering and data science research. While open to a broad national pool of top students in STEM, the REU Site will specifically target talented UGs majoring in STEM fields at institutions with limited research opportunities in the field of systems bioengineering and biomedical data science, with an emphasis on recruiting students from underrepresented groups. The research experience and mentorship these REU students will prepare them for work in this fast-growing and pioneering field that would otherwise be unavailable to them at their home institutions. Faculty mentors will maintain continuing relationships with the participants after completing the program, helping to improve the likelihood that the students will remain in STEM.