James A. Foster

Microbial diversity and ecology (Evolution and Ecosystems)

We develop algorithmic and statistical techniques and tools with which to infer the makeup of a microbial community from the total DNA in a sample. We are particularly interested in microbial communities in human milk, and in communities that may make some species of newts toxic. But our results generalize to any microbial ecosystem. Our goal is to understand why different ecosystems host the communities they do, and how those communities change as they and their ecosystems evolve.

Evolutionary computation and machine learning for bioinformatics (Theory and Algorithms)

We are applying evolutionary computation and other machine learning algorithms interpret large biological datasets. For example, we have developed and algorithms that use genetic programming and genetic algorithms for multiple (DNA or protein) sequence alignment, for phylogenetic reconstruction, and for disease-microbial ecology association studies.

Algorithmic efficiency for computational biology (Theory and Algorithms)

We help colleagues design efficient algorithms and implement them as effective programs. This uses our expertise in computational complexity theory, the theory and practice of algorithm analysis, and algorithmic design.

Refereed

1. J Madan, D Koestler, B Stanton, L Davidson, JH Moore, M Sogin, MR Karagas, H Morrison, T Hampton, P Palumbo, M Guill, JA Foster, PH Hibberd (never) Serial Analysis Of The Gut And Respiratory Microbiome in CF in Infancy: The Interaction Between Intestinal And Respiratory Tracts And The Impact Of Nutritional Exposures. eBio, 3(4). 10.1128/mBio.00251-12@
2. HK Allen, J Bunge, JA Foster, DO Bayles, TB Stanton (2013) estimation of viral species richness from shotgun metagenomes using a frequency count approach. Microbiome, 1(5) DOI: 10.1186/2049-2618-1-5
3. WK Copeland, V Krishnan, DL Beck, M Settles, JA Foster, K-C Cho, M Day, R Hickey, UME Sch@tte, X Zhou, CJ Williams, LJ Forney, Z Abdo (2012) mcaGUI: Microbial Community Analysis R-GUI. Bioinformatics, 2012 Aug 15;28(16):2198–9. doi: 10.1093/bioinformatics/bts338
4. J Bunge, L Woodard, D Bohning, HK Allen, JA Foster, S Conolly (2012) Estimating population diversity with CatchAll. Bioinformatics, Apr 1;28(7):1045-47. DOI: 10.1093/bioinformatics/bts075
5. JA Foster, J Bunge, J Gilbert, JH Moore (2012) Measuring the Microbiome: Perspectives on advances in DNA-based techniques for exploring microbial life. Briefings in Bioinformatics, 10.1093/bib/bbr080
6. JC Madan, R Cowper-Sallari, D Saxena, L Davidson, GA O\'Toole Jr, JH Moore, M Sogin, JA Foster, P Palumbo, PL Hibbard (2012) Gut microbial colonization in premature neonates predicts neonatal sepsis . Archives of Disease in Childhood, 10.1136/fetalneonatal-2011-301373
7. J Bunge, D Bohning, HK Allen, JA Foster (2012) Estimating population diversity with unreliable low frequency counts. Pacific Symposium on Biocomputing, 203-212
8. M Day, DL Beck, JA Foster (2011) Microbial Communities as Experimental Units. Bioscience, 61(5):398@406.
9. KM Hunt, JA Foster, LJ Forney, UME Sch@tte, 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.
10. V Norris, A Zemirline, P Amar, JN Audinot, P Ballet, B-E Jacob, G Bernot, G Beslon, A Cabin, E Fanshon, JL Giavitto, N Glade, P Greussay, Y Grondin, JA Foster, G Hutzler, J Jost, F K@p@s, O Michel, F Molina, J Signorini, P Stano, AR Thierry (2011) Computing with bacterial constituents, cells and populations: from bioputing to bactoputing. Theory Biosci, 130(3):211@228
11. DL Beck, M Settles, JA Foster (2011) OTUbase: an R infrastructure package for operational taxonomic unit data. Bioinformatics, 27(12):1700-1701. doi: 10.1093/bioinformatics/btr196
12. U Sch@tte, Z Abdo, JA Foster, LJ Forney (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.
13. JA Foster, SM Krone, LJ Forney (2009) Application of Ecological Network Theory to the Human Microbiome. Interdisciplinary Perspectives on Infection Diseases. 2009:6pp, doi:10.1155/2009/839501.
14. M Keitzer, JA Foster (2007) Crossover Bias in Genetic Programming. Proceedings of the 10th European Conference on Genetic Programming, LNCS 4445:33-44.
15. L Sheneman, 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.
16. LJ Forney, JA Foster, W Ledger (2006) The vaginal flora of healthy women is not always dominated by Lactobacillus sp Journal of Infectious Disease. Journal of Infectious Disease , 195:1468-1469
17. J Evans, L Sheneman, JA Foster (2006) Relaxed neighbor joining: a fast distance-based phylogenetic tree construction method. Journal of Molecular Evolution. 62(6):785-92, PMID: 16752216.
18. C Shyu, T Soule, SJ Bent, JA Foster, LJ Forney (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.
19. W Banzhaf, G Beslon, S Christensen, JA Foster, F K@p@s, V Lefort, JF Miller, M Radman, JJ Ramsden (2006) From artificial evolution to computational evolution: a research agenda. Nature Reviews Genetics, 7(9):729-735
20. C Shyu, JA Foster (2004) Evolving consensus sequence for multiple sequence alignment with a genetic algorithm. Proc Genetic and Evolutionary Computing Conference (GECCO),
21. C Shyu, L Sheneman, JA Foster (2004) Evolutionary computation for multiple sequence alignment. Genetic Programming and Evolvable Machines. Kluwer, 5(2) pp 121-144.
22. L Sheneman, JA 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.
23. M Harrison, JA Foster (2004) Co-evolving faults to improve the fault tolerance of sorting networks. Proc. European conference on genetic programming, Springer Verlag, Lecture Notes in Computer Science, M Keijzer, UM. O@Reilly, SM. Lucas, E Costa and T Soule, Eds, Volume 3003, pp 57-66.
24. M Harrison, JA Foster (2004) Improving the Survivability of a Simple Evolved Circuit through Co-evolution. Proc. NASA/DoD Conference on Evolvable Hardware, IEEE Press, R Zebulum , D Gwaltney, G Horbny, D Keymeulen, J Lohn, A Stoica, Eds, pp 123-129.
25. W Banzhaf, JA Foster (2004) Special Issue on Biological Applications of Genetic and Evolutionary Computation. Genetic Programming and Evolvable Machines. Kluwer, 5(2).
26. K Imamura, T Soule, RB Heckendorn, JA Foster (2003) Behavioral Diversity and a Probabilistically Optimal GP Ensemble. Genetic Programming and Evolvable Machines, Kluwer, 4:235-253.
27. R Shepherd, JA Foster (2003) Inherent fault tolerance in evolved sorting networks. Proc. Genetic and Evolutionary Computing Conference (GECCO). Springer-Verlag, p. 461, July
28. MM Meysenburg, D Hoelting, D McElvain, JA Foster (2002) How random generator quality impacts genetic algorithm performance. Proc. Int. Conf. On Genetic and Evol. Comp. (GECCO), Morgan Kaufmann, pp, 480-483.
29. K Imamura, JA Foster (2002) Abstention reduces errors@decision abstaining N-version genetic programming. Proc. Int. Conf. On Genetic and Evol. Comp. (GECCO), Morgan Kaufmann, 796-803.
30. K Imamura, RB Heckendorn, T Soule, JA Foster (2002) N-version genetic programming via fault masking, Genetic Programming: Proc. 5th European Conference, EuroGP 2002, Lecture Notes in Computer Science, 2278, Springer-Verlag, 172-181.
31. C Shyu, JA Foster, LJ Forney (2002) Electronic Polymerase Chain Reaction (EPCR) Search Algorithm. Proc. IEEE 1st Bioinformatics Conference. p, 338.
32. C Shyu, JA Foster, K Liao, SJ Bent, K Sale, LJ Forney, T Soule (2002) MiCA: Microbial Community Analysis. Proc. IEEE 1st Bioinformatics Conference. p, 341.
33. MM Meysenburg, D Hoelting, D McElvain, JA Foster (2002) A genetic algorithm-specific test of random generator quality. Proc. Int. Conf. On Genetic and Evol. Comp. (GECCO). Morgan Kaufmann, p 691.
34. JA Foster (2001) Discipulus: the first commercial genetic programming system, invited publication in J. Genetic Programming and Evolvable Hardware. 2:2, pp, 201@203.
35. J Determan, JA Foster (2001) A genetic algorithm for expert system rule generation. Proc. Int. Conf. On Genetic and Evol. Comp. (GECCO), Morgan Kaufmann, p 757.
36. K Imamura, JA Foster (2001) Fault-tolerant computing with N-version genetic programming. Proc. Int. Conf. On Genetic and Evol. Comp. (GECCO). Morgan Kaufmann, p 178.
37. K Imamura, JA Foster (2001) Fault-tolerant hardware through n-version genetic programming. Proc. 5th World Multiconference on Systemics, Cybernetics and Informatics (SCI 2001).
38. B Rylander, T Soule, JA Foster, J Alves-Foss (2001) Quantum evolutionary programming. Proc. Int. Conf. On Genetic and Evol. Comp. (GECCO). Morgan Kaufmann, pp. 1005-1011, Morgan Kaufmann.
39. JA Foster (2001) Evolutionary computation. Nature Genetics Reviews, 2:428-436.
40. B Rylander, JA Foster (2001) Genetic algorithms and hardness. Advances in Fuzzy Systems and Evolutionary Computation. Artificial Intelligence Series, E Nikos Mastorakis, ed., World Scientific and Engineering Society Press. pp, 323-329.
41. B Rylander, JA Foster (2001) Computational complexity and genetic algorithms. Advances in Fuzzy Systems and Evolutionary Computation. Artificial Intelligence Series, E Nikos Mastorakis, ed., World Scientific and Engineering Society Press, pp, 248-253.
42. B Rylander, T Soule, JA Foster (2001) Computational complexity, genetic programming and implications. Genetic Programming: Proc. 4th European Conference, EuroGP 2001, Lecture Notes in Computer Science, 2038, Springer-Verlag, 348-360.
43. B Rylander, T Soule, JA Foster (2000) Quantum evolutionary computation. Proc. Int. Conf. On Genetic and Evol. Comp. (GECCO). Morgan Kaufmann. p, 373.
44. B Rylander, JA Foster (2000) GA hard problems. Proc. Int. Conf. On Genetic and Evol. Comp. (GECCO). Morgan Kaufmann. p, 367.
45. J Dumoulin, S McGrew, J Frenzel, JA Foster (2000) Special purpose image convolution with evolvable hardware. Proc. Int. Workshop on Evolvable Image and Digital Signal Processing, Lecture notes in computer science no. 1803, Eds. Stefano Cagnoni, et al. Springer-Verlag, pp, 1@11.
46. GKM Goh, JA Foster (2000) Evolving Molecules for Drug Design Using Genetic Algorithms via Molecular Trees. Proc. Int. Conf. On Genetic and Evol. Comp. (GECCO), Morgan Kaufmann, pp, 27@33.
47. J Masner, J Cavalieri, J Frenzel, JA Foster (2000) Size versus robustness in evolved sorting networks: is bigger better? Proc. NASA/DoD Workshop on Evolvable Hardware (EH), IEEE Press, pp, 81@90.
48. K Imamura, JA Foster, A Krings (2000) The test vector problem and limitations to evolving digital circuits. Proc. NASA/DoD Workshop on Evolvable Hardware (EH), IEEE Press, pp, 75@80.
49. HS Snevily, JA Foster (2000) The 2-pebbling property and a conjecture of graham@s. Graphs and Combinatorics, 16, pp, 231@344.
50. B Harvey, D Frincke, JA Foster (1999) Toward byte code genetic programming. Proc. Int. Congress on Genetic and Evol. Comp. (CEC). p, 1234.
51. MM Meysenburg, JA Foster (1999) Random number generator and GP performance. Proc. Int. Conf. On Genetic and Evol. Comp. (GECCO), Morgan Kaufmann, pp, 1121@1126.
52. MM Meysenburg, JA Foster (1999) Random number generator and GA performance revisited. Proc. Int. Conf. On Genetic and Evol. Comp. (GECCO), Morgan Kaufmann, pp, 425@432.
53. J Determan, JA Foster (1999) Using chaos in genetic algorithms. Proc. Int. Congress on Evol. Comp. (CEC), IEEE press, pp, 2094@2101.
54. A Morris, JA Foster, FE Petry (1999) Providing support for multiple collection types in a fuzzy object oriented spatial data model. Proc. Int. Conf. North American Fuzzy Inf. Proc. Soc. (AFIPS), IEEE Press.
55. WB Langdon, T Soule, R Poli, JA Foster (1999) The evolution of size and shape. Advances in Genetic Programming (AIGP), Lee Spector, WB Langdon, Una-May O@Reilly and Peter J Angeline, eds. MIT Press, pp, 162@191.
56. J Masner, J Cavalieri, J Frenzel, JA Foster (1999) Representation and robustness for evolved sorting networks. Proc. NASA/DoD Workshop on Evolvable Hardware (EH), IEEE press, pp, 255@261.
57. T Soule, JA Foster (1998) Removal bias: a new cause of code growth in tree based evolutionary programming. Proc. Int. Conf. On Evolutionary Computing (ICEC), DB. Fogel and PJ. Angeline, eds., IEEE Press, pp, 781-786.
58. J Shoaf, JA Foster (1998) The efficient set GA for stock portfolios. Proc. Int. Conf. On Evolutionary Computing (ICEC), DB. Fogel and PJ. Angeline, eds., IEEE Press, pp, 354-359.
59. J Marconi, JA Foster (1998) Finding cliques in Keller graphs with genetic algorithms. Proc. Int. Conf. On Evolutionary Computing (ICEC), DB. Fogel and PJ. Angeline, eds., IEEE Press, pp, 650-655.
60. WF Danielson III, JA Foster, D Frincke (1998) GABSyS: Using genetic algorithms to breed a combustion engine. Proc. Int. Conf. On Evolutionary Computing (ICEC), DB. Fogel and PJ. Angeline, eds., IEEE Press, pp, 259-264.
61. T Soule, JA Foster (1998) Limiting code growth in genetic programming. J Evolutionary Computation, 6:4, 293@310.
62. T Soule, JA Foster (1997) Code size and depth flows in genetic programming. Proc. Int. Conf. On Genetic Programming (GP), Koza, Goldberg, Fogel and Riolo (eds), Morgan Kaufmann, pp, 313-320.
63. T Soule, JA Foster (1997) Genetic algorithm hardness measures applied to the maximum clique problem. Proc. Int. Conf. On Genetic Algorithms (ICGA), ed. B@ck, Morgan Kaufmann, pp, 81-88.
64. MM Meysenburg, JA Foster (1997) The effect of the quality of pseudo-random number generators on the performance of a simple genetic algorithm. Proc. Int. Conf. On Genetic Algorithms (ICGA), ed. B@ck, Morgan Kaufmann, pp, 276-282.
65. J Clough, JA Foster, M Barnett, HA Wichman (1996) Computer simulation of transposable element evolution: Random template and strict master models. J Mol. Evol., 42:52-58.
66. T Soule, JA Foster, J Dickinson (1996) Using genetic programming to approximate maximum cliques. Proc. Genetic Programming (GP), Koza, Goldberg, Fogel and Riolo ed.s, Morgan Kaufmann, pp, 400-405.
67. T Soule, JA Foster, J Dickinson (1996) Code growth in genetic programming. Proc. Genetic Programming (GP), Koza, Goldberg, Fogel and Riolo ed.s, Morgan Kaufmann, pp, 215-223.
68. JS Shoaf, JA Foster (1996) A Genetic algorithm solution to the efficient set problem: a technique for portfolio selection based on the Markowitz model. Proc. of the 1996 Annual Meeting, Decision Sciences Institute. Vol. II, pages 571-573.
69. JA Foster (1995) Exploring the polynomial hierarchy with generic sets. J Computing and Info., pages 166-183, July
70. JA Foster, PW Oman, K Van Houten, W Zhu (1995) Using self-delimiting strings to represent trees. Congressus Numerantium, 107:5-22, July
71. JA Foster, M Barnett, K Van Houten, L Sheneman (1995) (In-)Formal methods: Teaching program derivation via the Moore method. Computer Science Education, 6(1), pp. 67-91, July
72. PW Oman, K Van Houten, JA Foster (1993) Representing arbitrary trees as self-delimiting binary strings. Congressus Numerantium, 96:47-56, December
73. JA Foster (1993) The generic oracle hypothesis is false. Info. Proc. Letters, 45:59-62, 26 February
74. JA Foster, PW Oman, K Van Houten (1993) A highly compact representation of tree structures (abstract). Proceedings of the Data Compression Conference. p 453, March

Peer Reviewed

1. JA Foster (2012) tagged barcode analysis of microbial communities, in Encyclopedia of Metagenomics. Springer,
2. C Shyu, JA Foster (2004) Characterization of Microbial Diversity Based on T-RFLP Data with Nonparametric Statistics. Proc, American Society of Microbiologists (ASM).
3. C Shyu, JA Foster (2004) Performance Comparison of Multiple Sequence Alignment Programs Using Nonparametric Statistics. Research in Computational Biology (RECOMB),
4. C Shyu, JA Foster (2004) Nonparametric Statistical Approaches for Inferring Microbial Community Structures Based on Terminal Restriction Fragment Length Polymorphisms (T-RFLP). Pacific Symposium on Biocomputing,
5. L Sheneman, JA Foster (2004) Evolving Better Alignments. Pacific Symposium on Biocomputing,
6. C Shyu, JA Foster (2003) Inferring Microbial Community Structures with Dynamic Programming and Bayesian Statistics, Proc. American Society of Microbiologists (ASM), May 18-22,
7. C Shyu, JA Foster, K Liao, SJ Bent, K Sale, LJ Forney, T Soule (2002) Computational Methods for the Analysis of Microbial Community Structure and Composition. Proc. American Society of Microbiologists (ASM). p, 461.
8. C Shyu, JA Foster, K Liao, SJ Bent, K Sale, LJ Forney, T Soule (2002) Microbial Community Analysis (MiCA): Web-Based Computational Tools for the Analysis of Microbial Community Structure and Composition Based on Terminal Restriction Fragment Length Polymorphism (T-RFLP) of 16S rDNA genes. Proc. American Society of Microbiologists (ASM), p, 462.
9. B Harvey, JA Foster, D Frincke (1998) Byte code Genetic Programming. Late Breaking Papers at GP98, J. Koza, ed., pp 59-63.
10. LW Lass, DC Thill, B Shafii, W Price, JA Foster (1998) . Protected spatial data exchange from multiple data sources using the World Wide Web, Proceedings of the 1998 meeting of the Weed Sciences Society of America.
11. JA Foster (1992) The generic oracle hypothesis fails. In WW Koczkodaj, PE Lauer, and AA Toptsis, editors, International Conference on Computing and Information. pages 75-78. IEEE, May
12. JA Foster (1992) Structure in complexity theory. Bulletin of the European Association for Theoretical Computer Science. 46:239-47, February
13. JA Foster (1987) Differential geometry on fractal manifolds. The Journal of Chaos and Graphics, 2(30), August
14. JA Foster (1979) The greatness which was Greece. Inquiry, 1(1).
15. JA Foster (1978) The formal incomprehensibility of the creation stories in genesis. Illinois Libertarian,

Book Chapter

1. JA Foster (1979) Real security. Critical Inquiry, 1(1)
2. JA Foster, M Barnett (1996) Moore formal methods in the classroom: A how-to manual. In M.@Hinchey and N.@Dean, editors, Teaching and Learning Formal Methods. Academic Press. pp, 79-98.
3. JA Foster (1998) Evolutionary Computing. Encyclopedia of Distributed Computing,
4. JA Foster, E Lutton (2002) Introduction to European Conference on Genetic Programming. European Conference on Genetic Programming (EuroGP), Editor, Springer Verlag LNCS 2278, ISBN 3-540-43378-3
5. E Cantu-Paz, JA Foster (2003) Genetic and Evolutionary Computation. Genetic and Evolutionary Computation Conference (GECCO), Introduction, Springer Verlag LNCS 2723 and 2724
6. S Silva, JA Foster (2010) Introduction to the GPEM special issue on the best of EuroGP 2010. Genetic Programming and Evolvable Machines,
7. JA Foster, JH Moore (2011) Microbiome Studies: PSB 2011 special session introduction. Proc, Pacific Symposium in Biocomputing.
8. JA Foster, JH Moore (2011) Microbiome Studies: PSB 2011 special session introduction. Proc, Pacific Symposium in Biocomputing.

Book

1. E Cantu-Paz, JA Foster (2005) Special issue on best papers from GECCO. Genetic and Evolutionary Computation Conference, Guest editor, special issue of best papers
2. JA Foster, E Lutton, J Miller, C Ryan, AGB Tettamanzi (2002) European Conference on Genetic Programming. European Conference on Genetic Programming (EuroGP), Editor, Springer Verlag LNCS 2278, ISBN 3-540-43378-3
3. E Cantu-Paz, JA Foster (2003) Genetic and Evolutionary Computation. Genetic and Evolutionary Computation Conference (GECCO), proceedings, Springer Verlag LNCS 2723 and 2724
4. W Banzhaf, JA Foster (2004) GPEM Special issue on biological applications of genetic and evolutionary computation. Genetic and Evolutionary Computation Conference, Guest editor, special issue of biological applications
5. S Silva, JA Foster, M Nicolau, P Machado, M Giacobini (2011) European Conference on Genetic Programming. European Conference on Genetic Programming (EuroGP), Editor, Springer Verlag LNCS 6621, ISBN 978-3-642-20406-7
6. S Silva, JA Foster (2012) Special Best Papers Issue European Conference on Genetic Programming. Genetic Programming and Evolvable Machines,

Pending

1. (2013) SlopMap: a software application tool for quick and flexible identification of similar sequences using exact k-mer matching. . Journal of Data Mining in Genomics and Proteomics, special issue on Bioinformatics for High Throughput Sequencing
2. (2013) decisivatoR: an R infrastructure package that addresses the problem of phylogenetic decisiveness . ACM Conference on Bioinformatics and Computational Biology,

Short

Technical Reports

1. JA Foster (1986) Trip report for pubtech @86. Technical Report TR92-0004, International Business Machines, March
2. JA Foster (1986) Conferencing with confdisk. Technical Report TR92-0005, International Business Machines.
3. JA Foster (1987) Branch and bound versus backtracking. Technical Report TR92-0015, International Business Machines.
4. JA Foster (1987) The data mapping program: An early entity relationship database. Technical Report TR92-0011, International Business Machines.
5. JA Foster (1987) A prisoner@s dilemma with a divide and conquer solution. Technical Report TR92-0010, International Business Machines.
6. JA Foster (1987) Searching and sorting with a 3-way compare. Technical Report TR92-0009, International Business Machines.
7. JA Foster (1987) Tagproc: A grammar driven tag rewriter. Technical Report TR92-0012, International Business Machines.
8. JA Foster (1988) Computational complexity. Technical Report TR92-0013, International Business Machines.
9. JA Foster (1988) Context sensitive grammars are closed under complementation. Technical Report TR92-0014, International Business Machines.
10. JA Foster (1989) Introduction to predicate logic. Technical Report CS-JAF-89-1, Illinois Institute of Technology.
11. JA Foster (1989) Models of space-bounded relativization. Technical Report CS-JAF-89-2, Illinois Institute of Technology.
12. JA Foster (1989) My work at IIT. Technical Report CS-JAF-89-3, Illinois Institute of Technology.
13. JA Foster (1991) A note on relativized counting classes. Technical Report TR 91-10, University of Idaho, October
14. JA Foster (1991) Dense properties and generic witnesses for PH. Technical Report TR 91-09, University of Idaho, Department of Computer Science; Moscow, Id 83855, January
15. JA Foster, S Fenner (1995) NPCVt c NPSVt$ if disjoint pairs of Co-NP sets are P-separable. Technical Report LAL 95-01, University of Idaho, Moscow, ID 83844-1010, January
16. JA Foster (1995) Genetic algorithm hardness and approximation complexity: A research agenda. Technical Report TR-LAL-95-04, University of Idaho, Department of Computer Science, Moscow, ID 83844-1010, May
17. J Clough, RW Ireland, M Barnett, JA Foster (1995) Transposable element simulator: Technical documentation. Technical Report LAL 95-11, University of Idaho, Dept. of Computer Science, Moscow, ID 83844-1010, August
18. JA Foster, PW Oman, K Van Houten, W Zhu (1995) Using self delimiting strings to represent trees. Using self delimiting strings to represent trees. Technical report CS 92-06, U. of Idaho, October
19. JA Foster (1995) The generic oracle hypothesis is false. Technical Report TR 92-04, University of Idaho, Department of Computer Science; Moscow, Id 83855, January
20. JA Foster, M Barnett, K Van Houten, L Sheneman (1995) (In-)Formal methods: Teaching program derivation via the Moore method. Technical Report LAL 94-01, University of Idaho, Moscow, ID 83844-1010, September
21. H Snevily, JA Foster (1995) The 2-pebbling property and a conjecture of graham@s. Technical Report LAL 95-03, University of Idaho, Moscow, ID 83844-1010, September
22. JA Foster, T Soule (1995) Using genetic algorithms to find maximum cliques. Technical Report LAL 95-12, University of Idaho, Moscow, ID 83844-1010, August
23. T Soule, JA Foster, J Dickinson (1996) Using genetic programming to find maximum cliques. Technical Report LAL 96-3, University of Idaho, Moscow, ID 83844-1010, January
24. T Soule, JA Foster, J Dickinson (1996) Limiting program size in genetic programming. Technical Report LAL 96-2, University of Idaho, Moscow, ID 83844-1010, January

Miscellaneous

Research Presentations

• (2013) SlopMap: a software application tool for quick and flexible identification of similar sequences using exact k-mer matching. . Inland Northwest Genomics Syposium, Moscow, ID
• (2013) decisivatoR: an R package that addresses the problem of phylogenetic decisiveness. IBEST Science Update Series,
• (2013) BALMNet: Biologically Associated Text Miner and Network builder. Idaho Academy of Science, Pocatallo, ID
• I Zhbannikov, M Settles, S Hunter, JA Foster (2012) How many viruses are there in a pig?. NH INBRE visit to GBCC, Great Bend Community College, as part of visit to NH INBRE
• D Beck, JA Foster (2012) Using machine learning techniques to classify microbial communities. First annual IBEST research Symposium, University of Idaho, Moscow ID
• JA Foster, W Schroeder (2012) Extensive IBEST interactions transcend college and university boundaries. First annual IBEST research Symposium, University of Idaho, Moscow ID
• I Zhbannikov, M Settles, S Hunter, JA Foster (2012) SeqyClean as a novel approach in next generation sequencing cleaning. First annual IBEST research Symposium, University of Idaho, Moscow ID
• (2012) Vaginal microbiome biological network constructed by processing PubMed abstracts. BEACON NSF Site Visit poster session, MSU, East Lansing, MI
• HK Allen, J Bunge, JA Foster, TB Stanton (2012) Estimating richness from phage metagenomes. ASM General Meeting,
• D Tabis, M Raish, DL Beck, P Hohenlohe, JA Foster, MD Day (2012) Validation of the OpenPCR Using Multiplex PCR and Open Hardware. Biological Sciences Undergraduate Research Symposium, University of Idaho, Moscow ID
• D Tabis, M Raish, DL Beck, P Hohenlohe, JA Foster, MD Day (2012) Validation of the OpenPCR Using Multiplex PCR and Open-source Hardware. . UI Undergraduate Poster Competition, April 2012
• JC Madan, D Koestler, BA Stanton, L Davidson, JH Moore, M Sogin, H Morrison, T Hampton, PE Palumbo, M Guill, R Cowper Salari, MR Karagas, JA Foster, GA O\'Toole, PL Hibberd (2012) The impact of dietary and medical interventions on the developing lung and intestinal microbiota in infants with Cystic Fibrosis. Integrated Biology Symposium on the Microbiome, Dartmouth College, Hannover, NH
• JC Madan, D Koestler, BA Stanton, L Davidson, JH Moore, M Sogin, H Morrison, T Hampton, PE Palumbo, M Guill, R Cowper Salari, MR Karagas, JA Foster, GA O\'Toole, PL Hibberd (2012) The impact of dietary and medical interventions on the developing lung and intestinal microbiota in infants with Cystic Fibrosis. Pediatric Academic Society, Boston, MA
• JA Foster (2012) How many viruses are there in a pig: new inferential statistics for metagenomic data. CS Colloquiuum, University of Idaho, Moscow ID
• JC Madan, P Palumbra, GA O@Toole Jr, JA Foster, JH Moore (2011) The Premature Neonatal Microbiome in Sepsis and in Health. FASEB meeting on probiotics and the microbiome, Unknown
• JA Foster (2010) IBEST has had national impact. NIH, Bethesda MD
• JA Foster (2010) 17 years of sustained high performance interdisciplinarity (IBEST). Enhancing Communications in Cross Disciplinary Research, Coeur D\'Alene, ID
• JA Foster (2010) The human milk microbiome: Healthy breasts, mothers and babies. Dartmouth Medical School, Hanover, NH
• JA Foster (2010) the Milk Microbiome: healthy mothers, breasts and babies. Idaho INBRE, Moscow, ID
• JA Foster (2010) OTUbase: an R package for OTU data analysis. Idaho INBRE, Moscow, ID
• JA Foster (2010) Artificial Ecosystem Selection. Idaho INBRE, University of Idaho, Moscow ID
• JA Foster (2010) the core milk microbiome. Idaho INBRE, University of Idaho, Moscow ID
• JA Foster (2010) IBEST Bioinformatics and Sequencing Cores. Post Genomics Technology for biological Discovery, Santa Fe, NM
• JA Foster (2010) IBEST Bioinformatics and Sequencing Cores. Assoc for Biological Res Facilities, annual meeting, Sacramento, CA
• JA Foster (2005) Evolving multiple sequence alignments. Washington State University, Pullman WA
• JA Foster (2004) Evolving multiple sequence alignments with Evalyn. Idaho State University, Pocatallo, ID
• JA Foster (2004) Tutorial: Biological Applications of Genetic and Evolutionary Computation. Genetic and Evolutionary Computation Conference, Seattle
• JA Foster (2004) Evolving multiple sequence alignments with Evalyn. U. Wyoming, Laramie, WY
• JA Foster (2004) Evolving multiple sequence alignments with Evalyn. Limerick University, Ireland
• JA Foster (2004) Tutorial: Biological Applications of Genetic and Evolutionary Computation. Parallel Problem Solving from Nature (PPSN 8), Birmingham, UK
• JA Foster (2003) Evolutionary Computation for Multiple Sequence Alignment. U. Arkansas Little Rock. Little Rock, AR, Jan
• C Shyu, JA Foster (2003) Shyu, JA Foster. Evolving consensus sequences for multiple sequence alignment with a genetic algorithm, Idaho BRIN meeting
• JA Foster (2003) Life of an Eccentric: Truly interdisciplinary studies. Idaho Phi Beta Kappa society, Moscow, ID
• J Evans, JA Foster (2003) Tabu Search: A fast heuristic search algorithm for large data sets. Biology 545 poster session, Moscow, ID
• L Sheneman, JA Foster (2003) EVALYN: Evolving Guide Trees for Progressive Multiple Sequence Alignment. Biology 545 poster session, Moscow, ID
• C Shyu, JA Foster (2003) Shyu, JA Foster. Nonparametric Approaches for Inferring Microbial Community Structures based on Terminal Restriction Fragment Length Polymorphisms (T-RFLP), COBRE meeting, Moscow, ID
• J Evans, JA Foster (2003) Searching phylogenetic tree space efficiently. COBRE meeting, Moscow, ID
• L Sheneman, JA Foster (2003) Evolving Better Alignments. COBRE meeting, Moscow, ID
• L Sheneman, HA Wichman, J Sullivan, JA Foster (2003) Generating MSA Algorithm Test Cases by Manipulation of Real Mitochondrial DNA Sequences. COBRE meeting, Moscow, ID
• JA Foster (2002) IBEST: forming an interdisciplinary bioinformatics research group. National EPSCoR meeting, Anchorage, AK
• JA Foster (2001) Genetic programming: building programs without using programmers. Microsoft research, Seattle, WA
• JA Foster (2000) Experimental Evolution with x174 Bacteriophage. Dagstuhl workshop on Bioinformatics, Germany
• JA Foster (2000) Using Evolution in Computation. National Evolution Meetings. Indiana University, Bloomington, IN
• JA Foster (1999) Experimental Evolution with x174 Bacteriophage. Dagstuhl workshop on Evolutionary Computation Theory, Germany
• JA Foster (1998) Realism and Anti-Realism in Mathematics. Respondent at Inland Northwest Philosophy Conference on Realism and Anti-Realism, Moscow, ID
• JA Foster (1997) The C-Value Paradox and Implications for Evolutionary Computation. Int. Conf. On Genetic Algorithms, Workshop on Variable Length Encodings, Orlando, FL
• JA Foster, RW Ireland, M Barnett, HA Wichman, C Cassavant, J Clough (1996) Computer Aided Simulation of Transposable Element Evolution. Idaho Academy of Science, 38th Annual Meeting, Idaho
• JA Foster (1996) Stochastic Algorithms and Approximations: Implications for Genetic Algorithms. Idaho Academy of Science, 38th Annual Meeting, Idaho
• JA Foster, J Shoaf (1996) A Genetic Algorithm Solution to the Efficient Set Problem: A Technique for Portfolio Selection Based on the Markowitz Model. Idaho Academy of Science, 38th Annual Meeting, Idaho
• JA Foster (1996) Introduction to Genetic Algorithms and Genetic Programming. Idaho Academy of Science, 38th Annual Meeting, Idaho
• T Soule, JA Foster (1996) Using Genetic Algorithms to Solve Maximum Clique. Idaho Academy of Science, 38th Annual Meeting, Idaho
• T Soule, JA Foster (1996) Code Growth in Genetic Programming. Idaho Academy of Science, 38th Annual Meeting, Idaho
• JA Foster, PW Oman, K Van Houten, W Zhu (1995) Using self delimiting strings to represent trees. Southeastern International Conference on Graph Theory, Combinatorics and Computing, Boca Raton, FL
• JA Foster, M Barnett, C Cassavant, J Clough, RW Ireland, HA Wichman (1995) Computer aided simulation of Transposable element evolution. EVOL 95, Unknown
• JA Foster (1995) Exploring the polynomial hierarchy with generic sets. Int. Conf. On Computing and Information, Toronto, CA
• M Barnett, C Cassavant, J Clough, A Edwards, JA Foster, HA Wichman (1994) Transposable Element Computer Aided Simulation: a First Attempt. SINEs, LINEs and Retrotransposable Elements: Functional Implications, Taho, CA
• JA Foster, PW Oman, K Van Houten (1993) Representing tree structures as binary strings. Southeastern International Conference on Graph Theory, Combinatorics and Computing, Boca Raton, FL
• JA Foster (1993) Inductive inferencing: Models and results. Griffith University, Brisbane, Australia
• JA Foster (1991) Dense properties and generic witnesses. Illinois Institute of Technology, Chicago, IL
• JA Foster (1990) Forcing and genericity on the polynomial hierarchy. Washington, Ontario, British Columbia, Alberta Theory Seminar (WOBCATS), Banff, BC

I teach (or have taught) classes in bioethics, bioinformatics, computational biology, evolutionary computation, theory of computation, design and analysis of algorithms, computational complexity, and just about everything else.

I have taught most courses in the computer science curriculum, with a particular emphasis and depth in theoretical computer science (computability and complexity). I have also taught bioethics for freshmen as part of the UI core curricula for many years.

These are classes I have taught in the past. These links age, and some may not be reliable. Caveat emptor!

I have also taught various independent studies and seminars, which may not be listed here.

I am currently developing an undergraduate course on "Quantitative Thinking"

I have given several talks for the general public, and even more for scientific audiences. Here are slides from some of these talks.