James A. Foster

Dr. Foster’s current research is focused on characterizing evolutionarily permissible ecological structures in microbial ecosystems and on developing bioinformatics for very large sequence datasets. He continues to examine simulations of evolutionary processes to design complex artifacts and optimize functions. He works in close collaboration with biologists, statisticians, mathematicians, and computer scientists.

• Beck D, Settles M, Foster JA. OTUbase: an R infrastructure package for operational taxonomic unit data. Bioinformatics. 2011 Jun. 15;27(12):1700–1701.
• KM Hunt, JA Foster, LJ Forney, UME Shuette, DL Beck, Z Abdo, LK Fox, JE Williams, MK McGuire, MA McGuire (2011) Characterization of the Diversity and Temporal Stability of Bacterial Communities in Human Milk. PLOS One. 6(6) e21313. doi:10.1371/journal.pone.
• Norris V, Zemirline A, Amar P, Audinot JN, Ballet P, Ben-Jacob E, et al. Computing with bacterial constituents, cells and populations: from bioputing to bactoputing. Theory Biosci. 2011 Mar. 8;130(3):211–22
• Microbial Communities as Experimental Units. 2011 May;61(5):398–406. Schütte, U, Abdo Z, Foster JA, Forney LJ (2010) Bacterial diversity in a glacier foreland of the High Arctic, Molecular Ecology. 19(1):41-53. DOI 10.1111j. 1365-294X.2009.04483.x
• Foster, JA, Krone SM, Forney LJ (2009) Application of Ecological Network Theory to the Human Microbiome. Interdisciplinary Perspectives on Infection Diseases. 2009:6pp. doi:10.1155/2009/839501.
• Keitzer, M & Foster, JA (2007). Crossover Bias in Genetic Programming. Proceedings of the 10th European Conference on Genetic Programming, LNCS 4445:33-44.
• Sheneman, L, J. Evans, JA Foster (2006). Clearcut: the reference implementation for the relaxed neighbor joining phylogenetic tree construction method. Bioinformatics. 15(22):2823-4. PMID: 16982706
• Forney, L. J., Foster, J. A., & Ledger, W. (2006). The vaginal flora of healthy women is not always dominated by Lactobacillus sp. Journal of Infectious Disease. 194, 1468-1469.
• Banzhaf, W., Beslon, G., Christensen, S., Foster, J. A., Képès, F., Lefort, V., et al. (2006, in press). From artificial evolution to computational evolution: a research agenda. Nature Reviews Genetics. 7, 729-735.
• Evans, J., Sheneman, L., & Foster, J. A. (2006). Relaxed neighbor joining: a fast distance-based phylogenetic tree construction method. Journal of Molecular Evolution. 62(6):785-92. PMID: 16752216.
• Shyu, C., Soule, T., Bent, S., Foster, J. A., & Forney, L. J. (2006). MiCA: A Web-Based Tool for the Analysis of Microbial Communities Based on Terminal-Restriction Fragment Length Polymorphisms (T-RFLP). Journal of Microbial Ecology. 53(4):562-570. PMID 17406775.
• C. Shyu, Sheneman, L., and James A. Foster (2004) Evolutionary computation for multiple sequence alignment, Genetic Programming and Evolvable Machines, Kluwer, 5(2) pp 121-144.
• L. Sheneman and James A. Foster (2004) Evolving better multiple sequence alignments. Proc. Genetic and Evolutionary Computing Conference (GECCO), Springer Verlag, K. Deb et al., eds, Lecture Notes in Computer Science, Volume 3102, pp. 449-460.
• Harrison, M. and James A. Foster (2004) Co-evolving faults to improve the fault tolerance of sorting networks. Proc. European conference on genetic programming, Springer Verlag, Limerick University, Ireland.  September 2004.

• Characterizing evolutionary origins and dynamics of microbial ecosystems, especially using metagenomic data, with an emphasis on communities associated with the human microbiome.
• Exploring computational biology and Bioinformatics. In particular: simulations for transposable element evolution; phylogenetic inferencing algorithms; multiple sequence alignment algorithms.
• Exploring techniques for and inherent properties of biologically inspired computing. In particular: applications to Bioinformatics; applications to survivable hardware and software systems; use in self-repairing and fault tolerant hardware and software systems. Genetic programming, genetic algorithms, evolutionary computation, evolvable hardware.

• UI Teaching Excellence, 1999
• Founding member of IBEST
• Founder, first director of BCB program
• Founder, IBEST Computational Resources Core