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Allen Holder

Professor of Mathematics

Dr. Allen Holder's areas of expertise and research are in optimization and mathematical programming and their applications in medicine, medical physics, biology, and economics. He has research affiliations with the Indiana University School of Medicine, the Cancer Therapy Research Center in San Antonio, and the Huntsman Cancer Center in Salt Lake City. Dr. Holder is involved in cross-disciplinary research with biology and chemistry faculty, and helped establish a new major in biomathematics. He also worked with fellow math professor Dr. Yosi Shibberu to develop the fastest algorithm at the time for protein analysis, enabling researchers to do in minutes what had previously taken days. Dr. Holder has directed nearly 50 undergraduate research projects, is the editor of several publications, and has received the Board of Trustees Outstanding Scholar Award.

Teaching Interests

  • Calculus
  • Differential equations
  • Linear algebra
  • Operations research
  • Optimization
  • Mathematical modeling
  • Computational biology
  • Computational science
  • Bioinformatics
  • Systems biology

Research Interests

  • Mathematical programming and applications in medicine and biology
  • Optimal radiotherapy design
  • Protein structure alignment
  • Metabolic network analysis
  • Foundry scheduling
  • Research affiliations with Indiana School of Medicine (Indianapolis), the Cancer Therapy Research Center (San Antonio, Texas), and the Huntsman Cancer Center (Salt Lake City, Utah)

Select Publications & Presentations

  • Goulet, D. and Holder A., “Computational Biology and Bioinformatics: Applications in Operations Research,” Wiley Encyclopedia of Operations Research and Management Science, John Wiley & Sons, 2015
  • Ebrahim, A., Almaas, E., Bauer, E.,  Bordbar, A., Burgard, A., Chang, R., Drager, A., Famili, I., Feist, A., Fleming, R., Fong, S., Hatzimanikatis, V., Herrgard, M., Holder, A., Hucka, M., Hyduke, D., Jamshidi, N., Lee, S., Novere18, N., Lerman, J., Lewis, N., Ma, D., Mahadevan, R., Maranas, C., Nagarajan, H., Navid, A., Nielsen, J., Nielsen, L., Nogales, J., Noronha, A., Pal, C., Palsson, B., Papin, J., Patil, K., Price, N., Reed, J., Saunders, M., Senger, R., Sonnenschein, N., Sun33, Y., and Thiele, I., “Do Genome-scale Models Need Exact Solvers or Clearer Standards?,” Molecular Systems Biology, 11, 2015
  • Austgen, B., Hofheins, D., Holder, A., and Upadhyay, P., “Scheduling Foundry Production without Mold Inventory,” Operations Research and Computing: Algorithms and Software for Analytics (Proceedings of 2015 INFORMS ICS Conference), INFORMS, 1-14, 2014
  • Ehrgott, M. and Holder, A., “Operations Research Methods for Optimization in Radiation Oncology,” 2014, Journal of Radiation Oncology Informatics, 6, 1, 1-41, 2014
  • Shibberu, Y. and Holder, A., “A Spectral Approach to Protein Structure Alignment,”  IEEE/ACM Transactions on Computational Biology and Bioinformatics, 8, 4, 867-875, 2011

Awards & Honors

  • Board of Trustees Outstanding Scholar, Rose-Hulman Institute of Technology, 2015
  • Blue Key Honor Society͛s Favorite Professor, Rose-Hulman Institute of Technology, 2006, 2005, 2003, and 2001
  • Moving Spirit Award, INFORMS, 2003.
  • Alpha Lambda Delta͛s Professor of the Month, 2003 and 2000

Academic Degrees

  • PhD, University of Colorado-Denver, 1998
  • MS, University of Southern Mississippi, 1993
  • BS, University of Southern Mississippi, 1990