James A. Foster

James A. Foster

I have the best job in the world: Professor. I am a Computer Scientist with a liberal arts degree in classical philosophy who works in a great biology department with inspiring colleagues. I live in beautiful northern Idaho, where the fishing is fantastic and the wilderness is just up ahead. I have a talented and interesting family and good friends.

Here is my full curriculum vitae.

Research
  • Projects
  • People
  • Products
  • Presentations

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.

Agent based modeling of signaling systems

Signaling systems are agent based models of signaling whereby one agent perceives the world but cannot act, and the other can act but not perceive the world, and the fitness of the dyad depends on whether an action is appropriate for a given world state. We use agent based simulations to form and test hypotheses about the type of signals that arrive via evolutionary processes under this model, and to test the limits under which effective communication is possible when perceptions are unreliable or actions non-deterministic.

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.

Name Position Research interests
Faculty, Staff, Collaborators
James A. Foster Prof. Bio. Sci. Everything, but especially evolutionary processes
Larry Forney Prof. Bio. Sci. Microbial ecology and spatial biology
Holly Wichman Prof., Bio. Sci. Genomic organization, experimental evolution
Robert Heckendorn Assoc. Prof., Comp Sci theory of evolutionary computation, epistasis, modeling
Jack Sullivan Prof. Bio Sci Phylogenetic inferencing
Larry Forney Prof., Biological Sciences Microbial ecology
Terence Soule Assoc. Prof. Comp. Sci. Mechanisms of evolution
Trent Lyon System Administrator Cool machines
Rob Lyons System Administrator Cool clusters
Celeste Brown Bioinformatics Coordinator All things bioinformatical
Current Students
NONE
Former Students
Daniel Beck Ph.D., BCB Machine learning approaches to interpreting the human microbiome and disease
Ilya Zhbannikov Ph.D., BCB Algorithms and tools for very large genomic and post-genomic data
Luke Sheneman Ph.D., BCB Multiple sequence alignment algorithms
Conrad Shyu Ph.D., BCB 2006 Limits to tRFLP analysis
Gerard Goh M.S., CS Protein flexibility
John Brunsfeld B.S., CS 2006 Transposable element evolution: the simulator
Mike Harrison M.S., CS 2004 Robustness of evolved systems
John Harrison B.S., CS Cloner: utility for using Beowulf clusters
Mark Meysenburg Ph.D., CS, 2003 Pseudorandomness and Evolutionary Computation
Kosuke Imamura Ph.D., CS 2003 Fault tolerance in Genetic Programming
Robert Shepherd M.S., CS, 2003 Robustness of large evolved sorting networks
Bart Rylander Ph.D., CS, 2001 Complexity of Evolutionary Computation
Jason Masner M.S., CS 2000 Evaluating the Cost of Evolved Hardware
Brad Harvey M.S., CS 1999 Byte Code Genetic Programming and Its Application to Data Mining
John Determan M.S., CS 2000 Automatic Expert System Rule Generation On Nondestructive Waste Assay Data
Chad Creighton B.S., Biology 2000 Bioinformatics: databases and simulations
John Cavalieri B.S., CS 2002 Sorting Networks
Jamie Marconi B.S., CS 1998 Complexity and Evolutionary Computation
Mark Pokorny M.S., CS 1998 Evolutionary Computation and Neural Nets
Jaqueline Shoaf M.S., CS, 1997 Evolutionary Computation in Stock Portfolio Selection
Terence Soule Ph.D., CS 1998 Code Bloat and Genetic Programming
Industrial Affiliates
Frank Francone President AIM learning
Steve McGrew President New Light Industries
Search PubMed:   

Here are my publications I have an open-source policy for software from my lab. Therefore, software that we have released is available on github. Currently available software:
  • MetAmp. Normalize distances between 16S amplicon reads using known full length sequences as guides. Corrects for bias in phylogenetic signal, and allows one to combine multiple 16S markers into a single OTU analysis. Please cite: IY Zhbannikov, JA Foster (2015) MetAmp: Analysis high-throughput microbial amplicon sequence data with multiple markers. Bioinformatics, 10.1093/bioinformatics/btv049
  • SEED. Interactive tool for exploring microbial ecology data, including visualization and multivariate statistics. Please cite: DL Beck, C Daniels, JA Foster (2014) Seed: A microbial community visualization tool. Bioinformatics, pii: btu693
  • Clearcut. Fast relaxed neighbor joining algorithm for very large datasets, especially next generation sequencing data. Also available as part of the Mothur suite. Please cite: LJ 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
  • SlopMap. Map next generation sequencing reads onto genomes, including those for non-model organisms. Please cite: IY Zhbannikov, M Settles, SS Hunter, JA Foster (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, 4(3):1-6. doi: 10.4172/2153-0602.1000133
  • Evalyn. Genetic algorithm approach to multiple sequence alignment.

Research

  • JA Foster (Nov 2015) Combining bacterial fingerprints: A new algorithm. College of Idaho, Caldwell, ID
  • JA Foster (Nov 2015) Combining bacterial fingerprints: A new algorithm. Northwest Nazarene University, Nampa, ID
  • JA Foster (Nov 2015) Combining bacterial fingerprints: A new algorithm. Boise State University, Boise, ID
  • B Baumgaertner, JA Foster (Oct 2015) Imperfect Observations Produce Asymmetric Signaling Roles. Northwest Philosophy Conference, Coeur Coeur D\'Alene, ID
  • P Fetros, C Britson, B Baumgaertner, JA Foster (Oct 2015) How to Tell When Ambiguous Signalling is Better than Guessing. IBEST Undergraduate Research, Moscow, ID
  • SL Brooker, JE Williams, K Davenport, L Bode, JA Foster, MA McGuire, MK McGuire, BM Murdoch (Aug 2015) Has evolution of human milk sugars responded to a biocultural sweet tooth?. BEACON Congress, East Lansing, MI
  • SL Brooker, JE Williams, K Davenport, L Bode, JA Foster, MA McGuire, MK McGuire, BM Murdoch (Aug 2015) Has evolution of human milk sugars responded to a biocultural sweet tooth?. FASEB Origins and Benefits of Biologically-Active Components of Human Milk, BIG Big Sky, MT
  • JA Foster (Jul 2015) Combining bacterial fingerprints: A new algorithm. FASEB, Big Sky, MT
  • JA Foster (Jul 2015) Combining bacterial fingerprints: A new algorithm. National meeting of the American Chemical Society, Pocatallo, ID
  • JA Foster (Jun 2014) Research cores as businesses. NIH NISBRE, Washington DC
  • IY Zhbannikov, JE Williams, JA Foster (May 2014) MetAmp: a novel approach to clustering analysis of microbial community structures using multiple genomic fingerprints. Inland Northwest Genomics Symposium, University of Idaho, Moscow ID
  • JA Foster (May 2014) Combining bacterial fingerprints: A new algorithm. UI CS Seminar, University of Idaho, Moscow ID
  • DL Beck, JA Foster (Oct 2013) Machine learning techniques accurately classify microbial communities by bacterial vaginosis characteristics. IBEST Research Symposium, UI, Moscow, ID
  • IY Zhbannikov, SS Hunter, H Mendes-Soares, R Hickey, JA Foster, M Settles (Sep 2013) BALMNet: Biologically associated text miner and network builder. ACM International Conference on Bioinformatics, Computational Biology, and Biomedical Informatics (ACM BCB 2013), Washington, DC. 22-25 September 2013
  • P Vasili, JA Foster, K Theis, H Eisthen, JE Williams (Aug 2013) Isolation and characterization of bacteria associated with the neurotoxic rough-skinned newt, Taricha grandulosa. BEACON Congress, MSU, East Lansing, MI
  • IY Zhbannikov, M Settles, SS Hunter, JA Foster (May 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
  • IY Zhbannikov, D Tank, JW Brown, JA Foster (Apr 2013) decisivatoR: an R package that addresses the problem of phylogenetic decisiveness. IBEST Science Update Series, Moscow, ID
  • IY Zhbannikov, SS Hunter, H Mendes-Soares, JA Foster, M Settles (Mar 2013) BALMNet: Biologically associated text miner and network builder. Idaho Academy of Science, Pocatallo, ID
  • IY Zhbannikov, M Settles, SS Hunter, JA Foster (Nov 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
  • DL Beck, JA Foster (Oct 2012) Using machine learning techniques to classify microbial communities. First annual IBEST research Symposium, University of Idaho, Moscow ID
  • JA Foster, W Schroeder (Oct 2012) Extensive IBEST interactions transcend college and university boundaries. First annual IBEST research Symposium, University of Idaho, Moscow ID
  • IY Zhbannikov, M Settles, SS Hunter, JA Foster (Oct 2012) SeqyClean as a novel approach in next generation sequencing cleaning. First annual IBEST research Symposium, University of Idaho, Moscow ID
  • IY Zhbannikov, JA Foster, M Settles (Aug 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, BA Stanton (Jun 2012) Estimating richness from phage metagenomes. ASM General Meeting, San Francisco, CA
  • D Tabish, M Raish, DL Beck, P Hohenlohe, JA Foster, MD Day (May 2012) Validation of the OpenPCR using multiplex PCR and open hardware. Biological Sciences Undergraduate Research Symposium, University of Idaho, Moscow ID
  • D Tabish, M Raish, DL Beck, P Hohenlohe, JA Foster, MD Day (May 2012) Validation of the OpenPCR using multiplex PCR and open 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, RC Salari, MR Karagas, JA Foster, GA O\'Toole Jr., PL Hibberd (Apr 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, RC Salari, MR Karagas, JA Foster, GA O\'Toole Jr, PL Hibberd (Apr 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 (Apr 2012) How many viruses are there in a pig: new inferential statistics for metagenomic data. CS Colloquiuum, University of Idaho, Moscow ID
  • JC Madan, PE Palumbo, GA O\'Toole Jr, JA Foster, JH Moore (Jun 2011) The premature neonatal microbiome in sepsis and in health. FASEB meeting on probiotics and the microbiome, Washington DC
  • JA Foster (Nov 2010) IBEST has had national impact. NIH NISBRE, Bethesda MD
  • JA Foster (Oct 2010) 17 years of sustained high performance interdisciplinarity (IBEST). Enhancing Communications in Cross Disciplinary Research, Coeur D\'Alene, ID
  • JA Foster (Sep 2010) The human milk microbiome: Healthy breasts, mothers and babies. Geisel School of Medicine, Dartmouth College, Hanover, NH
  • JA Foster (Aug 2010) The Milk Microbiome: healthy mothers, breasts and babies. Idaho INBRE annual meeting, Moscow, ID
  • DL Beck, JA Foster (Aug 2010) OTUbase: an R package for OTU data analysis. Idaho INBRE annual meeting, Moscow, ID
  • MD Day, JA Foster (Aug 2010) Artificial ecosystem selection. Idaho INBRE annual meeting, University of Idaho, Moscow ID
  • KM Hunt, MK McGuire, JA Foster (Aug 2010) The core milk microbiome. Idaho INBRE annual meeting, University of Idaho, Moscow ID
  • JA Foster (Mar 2010) IBEST Bioinformatics and Sequencing Cores. Post Genomics Technology for Biological Discovery, Santa Fe, NM
  • JA Foster, M Settles, R Lyon (Mar 2010) IBEST Bioinformatics and Sequencing Cores. Association for Biological Research Facilities, Sacramento, CA
  • JA Foster (Jun 2005) Evolving multiple sequence alignments. Washington State University, Pullman WA
  • JA Foster (Nov 2004) Evolving multiple sequence alignments with Evalyn. Idaho State University, Pocatallo, ID
  • JA Foster (Jun 2004) Tutorial: Biological applications of genetic and evolutionary computation. Genetic and Evolutionary Computation Conference, Seattle
  • JA Foster (Jun 2004) Evolving multiple sequence alignments with Evalyn. U. Wyoming, Laramie, WY
  • JA Foster (Jun 2004) Evolving multiple sequence alignments with Evalyn. Limerick University, Ireland
  • JA Foster (Jun 2004) Tutorial: Biological applications of genetic and evolutionary computation. Parallel Problem Solving from Nature (PPSN 8), Birmingham, UK
  • J Evans, JA Foster (Jun 2003) Tabu Search: A fast heuristic search algorithm for large data sets. Biology 545 poster session, Moscow, ID
  • LJ Sheneman, JA Foster (Jun 2003) EVALYN: Evolving guide trees for progressive multiple sequence alignment. Biology 545 poster session, Moscow, ID
  • C Shyu, JA Foster (Jun 2003) Nonparametric approaches for inferring microbial community structures based on terminal restriction fragment length polymorphisms (T-RFLP). Idaho COBRE, Moscow, ID
  • J Evans, JA Foster (Jun 2003) Searching phylogenetic tree space efficiently. COBRE meeting, Moscow, ID
  • LJ Sheneman, HA Wichman, J Sullivan, JA Foster (Jun 2003) Generating MSA algorithm test cases by manipulation of real mitochondrial DNA sequences. COBRE meeting, Moscow, ID
  • LJ Sheneman, JA Foster (Jun 2003) Evolving better alignments. COBRE meeting, Moscow, ID
  • C Shyu, JA Foster (Jun 2003) Evolving consensus sequences for multiple sequence alignment with a genetic algorithm. Idaho BRIN meeting, Moscow, ID
  • JA Foster (Jun 2003) Evolutionary computation for multiple sequence alignment. U. Arkansas Little Rock. Little Rock, AR, Jan
  • JA Foster (Jun 2003) Life of an Eccentric: Truly interdisciplinary studies. Idaho Phi Beta Kappa society, Moscow, ID
  • JA Foster (Jun 2002) IBEST: forming an interdisciplinary bioinformatics research group. National EPSCoR meeting, Anchorage, AK
  • JA Foster (Jun 2001) Genetic programming: building programs without using programmers. Microsoft research, Seattle, WA
  • JA Foster (Jun 2000) Experimental evolution with x174 bacteriophage. Dagstuhl workshop on Bioinformatics, Germany
  • JA Foster (Jun 2000) Using evolution in computation. Evolution meetings, Bloomington, IN
  • JA Foster (Jun 1999) Experimental evolution with x174 bacteriophage. Dagstuhl workshop on Evolutionary Computation Theory, Germany
  • JA Foster (Jun 1998) Realism and anti-realism in mathematics. Inland Northwest Philosophy Conference on Realism and Anti-Realism, Moscow, ID
  • JA Foster (Jun 1997) The C-value paradox and implications for evolutionary computation. International Conference On Genetic Algorithms, Workshop on Variable Length Encodings, Orlando, FL
  • JA Foster, RW Ireland, M Barnett, HA Wichman, C Cassavant, J Clough (Jun 1996) Computer aided simulation of transposable element evolution. Idaho Academy of Science, 38th Annual Meeting, Idaho
  • JA Foster (Jun 1996) Stochastic algorithms and approximations: Implications for genetic algorithms. Idaho Academy of Science, 38th Annual Meeting, Idaho
  • JA Foster (Jun 1996) Introduction to genetic algorithms and genetic programming. Idaho Academy of Science, 38th Annual Meeting, Idaho
  • T Soule, JA Foster (Jun 1996) Using genetic algorithms to solve maximum clique. Idaho Academy of Science, 38th Annual Meeting, Idaho
  • JA Foster, JS Shoaf (Jun 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
  • T Soule, JA Foster (Jun 1996) Code growth in genetic programming. Idaho Academy of Science, 38th Annual Meeting, Idaho
  • JA Foster, PW Oman, K Van Houten, W Zhu (Jun 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 (Jun 1995) Computer aided simulation of transposable element evolution. EVOL 95,
  • JA Foster (Jun 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 (Jun 1994) Transposable element computer aided simulation: a first attempt. SINEs, LINEs and Retrotransposable Elements: Functional Implications, Taho, CA
  • JA Foster (Jun 1993) Inductive inferencing: Models and results. Griffith University, Brisbane, Australia
  • JA Foster, PW Oman, K Van Houten (Jun 1993) Representing tree structures as binary strings. Southeastern International Conference on Graph Theory, Combinatorics and Computing, Boca Raton, FL
  • JA Foster (Jun 1991) Dense properties and generic witnesses. Illinois Institute of Technology, Chicago, IL
  • JA Foster (Jun 1990) Forcing and genericity on the polynomial hierarchy. Washington, Ontario, British Columbia, Alberta Theory Seminar (WOBCATS), Banff, BC
Teaching and Outreach (classes and talks)
  • Current
  • Past
  • Future
  • Public Talks

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.

Number (sec) CRN Cr Title
Fall Semesters
Bio 456 (even numbered years only)   3 Computation Skills for Biologists (office hours by appointment)
BCB 504   3 Computational skills for biologists (taught from MSU, proctored at UI)
BCB 500 sec 30   arr MS thesis
BCB 600 sec 30   arr PhD thesis
Spring Semesters
Biol 553   1 Ethics for Biologists
BCB 504   3 Evolutionary Biology for Non-Biolgists (taught from MSU, proctored at UI)
BCB 504   3 Interdisciplinary Research in Evolution Studies (taught from MSU, proctored at UI)
BCB 500 sec 30 arr MS thesis
BCB 600 sec 30 arr PhD thesis
Summer Semesters
BCB 500 sec 30   arr MS thesis
BCB 600 sec 30   arr PhD thesis

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.

Course Course Title or Topic Term Taught
Bioethics
Core 118/168 Bioethics FS05-06, FS06-07
Theoretical Computer Science
CS 4/504 Computational Complexity S91, F97
CS 490/Ma 495 Theory of Computation F90, F92, F94, F96, F00
CS 495/Ma 475 Analysis of Algorithms S92, S94, S96, S98, S05
CS 590 Computation and complexity S93, S94, S95, S96, S97, S99, S03, S04
CS 596 Computational Complexity Theory F94, F97
Bioinformatics & Computational Biology (Evolution Studies)
CS 4/504 Computational Biology F01
CS 4/504 Genetic Algorithms F95
CS 4/504 Bioinformatics and Evolutionary Studies F00
CS 4/504 Perl for Bioinformatics S02
Misc. Computer science
CS 4/572 Evolutionary Computation S98, F98
CS 101 Introduction to Computer Science F96
CS 360 Files and Databases S92
Programming and Software Engineering
CS 113 Program Design and Algorithms S91,F92, F97
CS 204 Programming Practice S92, F92, S93
CS 213 Data Structures F90
CS 386 Derivational Programming S97
CS 4/504 The Future of Programming F93, S95
Seminars and reading courses
CS 401 CS Undergraduate Seminar S03
CS 501 CS Graduate Seminar S96, F96, S03
CS 501 IBEST Seminar S01, S02, S03
CS 499/CS 502 Reading: Machine Learning S99

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.

Title Audience Length Description
Combining Bacterial Fingerprints: A New Algorithm (keynote, pdf) Computational and Micro- biologists, bioinformaticists 50 minutes Presents our new algorithm for using multiple 16S gene fingerprints to decipher amplicon-based microbiome data. Or: a better way to tell which bacteria are "there", even when you can't see or grow them.
The human milk microbiome (keynote) Computational and Micro- biologists, bioinformaticists 50 minutes Shows that there is a core set of bacteria present in the breast milk of healthy mothers. Presented at Michigan State University, ICER
The human milk microbiome (keynote) Health care professionals and microbiologists 50 minutes Shows that there is a core set of bacteria present in the breast milk of healthy mothers. Presented at Dartmouth Medical School
17 years of highly successful interdisciplinary research (IBEST) (keynote) Anyone interested in interdiscplinary research and education 50 minutes A case study in how we built a highly successful interdiscpilinary research and education group, and kept it going for almost two decades (so far). History of the Initiative for Bioinformatics and Evolutionary STudies (IBEST)
The data flood: we need a bigger boat (keynote, pdf) biologically literate general public 30 minutes next generation sequencing gives us much more data than we know how to handle. To avoid drowning, we need new techniques.
Bugs in the Arctic: how do soil bacterial communites change as glaciers retreat? microbial ecologists, bioinformaticists, students, general public 50 minutes techniques for data reduction of 454/FLX metagenomic study of microbial populations from soil in a transect below a receding glacier in Spitsbergen
Guide trees and alignment quality for multiple sequence alignment (in power point) bioinformaticists, students 20 minutes Guide trees for progressive multiple sequence alignments are correlated with alignment quality, but have only minor effect
Power versus efficiency in microbial communities (in keynote) microbial ecologists 20 minutes Summarizes research project testing the ability of bacterial species to coexist as a function of their protein translation strategy.
Microbial Diversity at the Marine Biology Lab (in keynote) General public 45 minutes - 1 hour My summer school at the Marine Biology Lab in Woods Hole. Has lots of pretty pictures of bacterial colonies.
Philosophy meets Biology General public 50 minutes New biological problems that strain current philosophical assumptions.

Ethics, public policy, politics, etc

Ethical analysis of US care (ppt, pdf) general public 10 minutes Presents a formal analysis of the ethics of the current and proposed US health care systems. The analysis method is broadly useful for public policy analysis. (full analysis here)
Evolutionary Computation
Evolutionary computation (keynote) evolutionary biologists, general public 30 minutes reviews how evolution is a process, and EC can be used to answer ill formed questions with lots of data. Presented at Evolution 2009, 6/14/09.
Introduction to evolutionary computation computer science students 50 minutes Using simulated evolution to solve problems computationally (GA, GP, etc.)
Using evolution to build computing software and hardware Biologists, computer scientists, or general public 15, 30 or 50 minutes Evolutionary computation (EC) techniques, including genetic algorithms (GA) and genetic programming (GP), for building computer programs and computing circuits
EC hardness EC researchers 50 minutes thoughts on how to measure problem hardness in EC.
Robustness of evolved circuits EC researchers 15 minutes Evolved sorting networks are fail less catastrophically than hand-designed ones when subjected to point circuit failures.
Using GAs for building stock market portfolios computer scientists 50 minutes Solving multi-objective functions (e.g. risk, return) with subtractive constraints (e.g. long and short positions), stock market portfolio example

Other Computer Science Stuff

What machines can never learn general public 50 minutes inductive inferencing: computational limits to what machines can learn
Pseudo randomness computer science students 50 minutes Different techniques for generating pseudorandom number sequences, measuring their quality
DNA computing general public 50 minutes Computing with DNA
Quantum computing general public 50 minutes how to use quantum mechanics to speed up computations

Other Stuff

Doing proofs computer science students 50 minutes Strategies for doing mathematical proofs
Bringing home the BEACON (keynote) members of IBEST 30 minutes The relationships between the BEACON STC on "evolution in action" and IBEST

University and Professional service

University Service

  • University Commencement Committee (1991 to 1994)
  • Faculty Affairs Committee (1994 to 1997)
  • Critical Thinking Advisory Council (2000 to 2005)
  • Graduate Council (2001 to 2006)
  • Director, IBEST Bioinformatics core (2001 to 2011)
  • Director, UI graduate degree program in Bioinformatics and Computational Biology (2003 to 2006)
  • University Wide Programs, Interdisciplinary Council (2003 to 2006)
  • Vision Resources Task Force, University of Idaho (2005 to 2005)
  • UI BCB Governing board (2006 to 2008)
  • Panelist on facilities that support data intensive research, University of Idaho (2012 to 2012)
  • Evaluation committee for Outstanding Graduate Research and Creativity Activity Award, University of Idaho (2013 to now)

College Service

  • Library Committee, Northeastern Illinois University (1988 to 1990)
  • Curriculum Committee, Northeastern Illinois University (1988 to 1990)
  • Faculty advisor for the student chapter of the ACM (1990 to 1993)
  • Faculty advisor for the student chapter of the ACM (1995 to 1998)
  • Tenure and Promotions, College of Engineering (1997 to 1998)
  • Faculty Morale Committee, College of Engineering, Chair (1997 to 1998)
  • Committee on Student Professional Fees, College of Engineering (1998)
  • Tenure and Promotions, College of Engineering (2002 to 2003)
  • CS chair search committee, College of Engineering (2002)
  • Faculty advisor, Bioinformatics Journal Club (2003 to 2006)
  • Tenure and Promotions, College of Engineering (2006)
  • CS Chair evaluation committee, College of Engineering (2006)
  • Core director search committee, IBEST (2007)

Department Service

  • Scott Nuismer Promotion Committee, University of Idaho (2010)
  • PostDoc Search committtee, Forney 2012, University of Idaho (2012)
  • Vandal Friday advisor for incoming freshmen, Biology Department (2012)
  • Curriculum Committee, Biological Sciences (2012 to now)
  • Strategic planning committee, Biological Sciences (2011)
  • Seminar Committee, Biological Sciences (2011)
  • BCB Governing Board, University of Idaho (2006 to 2009)
  • Search committee for IBEST system administrator, IBEST, Chair (2002 to now)
  • Space Committee, Computer Science (2002)
  • Computational Genomics Search Committee, Biological Sciences, Chair (2001)
  • Koza Fellowship Search Committee, Computer Science, Chair (2001)
  • Department Chair Search Committee, Computer Science (2001)
  • Faculty Search Committee, Computer Science (2000)
  • CS Alumni Committee, Computer Science, Chair (1998 to 1999)
  • Asst. Chair of Graduate Studies and Research, Computer Science (1998 to 1999)
  • Faculty Search Committee, Computer Science (1998)
  • Ad hoc committee on faculty evaluations, Computer Science (1998)
  • Strategic planning, Computer Science (1998 to 1999)
  • Faculty Search Committee, Computer Science (1995)
  • Ad hoc committee on service courses, Computer Science, Chair (1992)
  • Graduate Program Committee, Computer Science, Chair (1991 to 1995)
  • Faculty Search Committee, Computer Science (1991)
  • Graduate Program Committee, Computer Science (1990)
  • Coach of the Student Programming Team (1990 to 1998)

Professional Service

Reviewer/Referee for conferences and journals

  • American Naturalist
  • Journal of Parallel and Distributed Computing
  • NASA/JPL Evolvable Hardware conference (EH), NASA/JPL Evolvable Hardware conference (EH)
  • Journal of Artificial Intelligence Research
  • Int. Congress of Evolutionary Computation (ISGEC), Int. Congress of Evolutionary Computation (ISGEC)
  • Natural Sciences and Engineering Research Council of Canada
  • Int. Conf. on Genetic Programming (ICGP), Int. Conf. on Genetic Programming (ICGP)
  • Workshop on Foundations of Genetic Algorithms (FOGA), Workshop on Foundations of Genetic Algorithms (FOGA)
  • Information Processing Letters
  • Int. Conf. on Computing and Information (ICCI), Int. Conf. on Computing and Information (ICCI)
  • Int. Conf. on Genetic Algorithms (ICGA), Int. Conf. on Genetic Algorithms (ICGA)
  • Journal of Discrete Mathematics
  • Idaho BRIN Bioinformatics workshops, Moscow Moscow, ID
  • Idaho BRIN Bioinformatics workshops, Boise Boise, ID
  • Briefings in Bioinformatics
  • Journal of Evolutionary Comp (2012 to now)
  • Journal of Genetic Programming and Evolvable Hardware (2012 to now)
  • Program committee for GP track at GECCO 2013 (1996 to now)
  • Program Committee of ALEA-2011, the 5th Workshop on Artificial Life and Evolutionary Algorithms, Portugal (ALEA) (2011 to now)
  • Program Committee of ALEA-2013, the 6th Workshop on Artificial Life and Evolutionary Algorithms, Portugal (ALEA) (2013 to now)
  • Euro. GP (EUROGP), an international conference on Genetic Programming (2001 to now)
  • Int. Conf. on Genetic and Evolutionary Computation (GECCO) (2012 to now)
  • IEEE Trans. on Evolutionary Comp, IEEE Trans. on Evolutionary Comp (2012 to now)
  • Referee for CIBCB (2012 to now)
  • NASA/JPL Evolvable Hardware Workshop, NASA/JPL Evolvable Hardware Workshop (2000)
  • NASA/JPL Evolvable Hardware Workshop, NASA/JPL Evolvable Hardware Workshop (1999)
  • Int. Congress on Evolutionary Computation (1998)
  • Genetic and Evolutionary Computation Conference (GECCO), Genetic and Evolutionary Computation Conference (GECCO) (1998 to 2007)
  • Inland Northwest Philosophy Conference, a national meeting (1998)
  • Int. Conf. on Computing and Information, Int. Conf. on Computing and Information (1994)

Funding agencies

  • NSF IUCRC CISE FRP & CORBI Panel, NSF/CISE (2013)
  • Chair of EVOStar EVOBIO Steering CommitteeVOStar/EVOBio (2013 to now)
  • French National Research Academy (NAR) (2013)
  • Science Foundation Ireland (2005, 2012)
  • NSF, OSX III (2006)
  • NIH, Biomedical Data Management and Analysis, permanent member, NIH (2004 to 2008) Biomedical Data Management and Analysis, permanent member
  • U.K. Engineering and Physical Sciences Research Council, U.K. Engineering and Physical Sciences Research Council (2003)
  • NSF, Information Technology Research (ITR), NSF (2002) Information Technology Research (ITR)
  • NSF, Biological Databases and Informatics (BDI), NSF (2002)
  • NSF, Research Infrastructure (RI), NSF (2001) Research Infrastructure (RI)
  • NSF, Integrated Graduate Research, Education, Training (IGERT) (2001)

Editorial

  • Thematic Editor for Life Sciences, GPEM (2012 to now)
  • Genetic Programming and Evolvable Machines, Guest editor Special issue on best of GECCO (2005 to now)
  • Journal of Genetic Programming and Evolvable Machines, associate editor (2003 to now)
  • IEEE Transactions on Evolutionary Computation, Associate editor (2003 to 2006)
  • J. Evol. Comp, associate editor, J. Evol. Comp (2003 to now)
  • Journal of Genetic Programming and Evolvable Machines, editorial board (2000 to 2003)

Conference organization

  • European Conference on Genetic Programming (EuroGP), Program co-Chair (with Sara Silva) (2011)
  • European Evolutionary Computation Meetings (EuroStar), Executive committee (2009 to now)
  • Genetic and Evolutionary Computation Conference (GECCO), Chair miniconference on Biological Applications (2005)
  • Genetic Programming and Evolvable Machines, Guest editor, Special issue of on evolutionary computation in bioinformatics, Genetic Programming and Evolvable Machines (2004 to now)
  • Genetic and Evolutionary Computation Conference (GECCO), Chair miniconference on Biological Applications, Genetic and Evolutionary Computation Conference (GECCO) (2004)
  • Genetic and Evolutionary Computation Conference (GECCO), Program Chair, Genetic and Evolutionary Computation Conference (GECCO) (2003)
  • International Society on Genetic and Evolutionary Computing (ISGEC), chair of Council on Conferences (2003)
  • Genetic and Evolutionary Computation Conference (GECCO), co-chair Workshop on Biological applications (BioGEC, with Wolfgang Banzhaf) (2003)
  • Genetic and Evolutionary Computation Conference (GECCO), co-chair Workshop on Biological applications (BioGEC, with Wolfgang Banzhaf) (2002)
  • European Conference on Genetic Programming (EuroGP), Program co-Chair (with Evalyn Lutz) (2002)
  • European Conference on Genetic Programming (EuroGP), Executive committee (2002 to 2009)
  • GECCO Graduate Student Workshop (2000 to 2004)
  • GECCO Graduate Student Workshop (1999)

Other professional service

  • University of Idaho, NIH COBRE Research Advisory Board (2007 to now)
  • University of Alaska, NIH INBRE external advisory board (2006)
  • University of Nevada Reno, NIH INBRE external advisory board (2006)
  • University of Idaho, NIH INBRE Internal advisory board (2002 to now)
  • Director, NSF STC, BEACON: Evolution in Action, University of Idaho (2010 to now)
My Education and Training
Institution Degree Year Field of Study
University of Chicago A.B. 1977 Philosophy (classical)
Illinois Institute of Technology M.S. 1987 Computer Science (machine learning)
  Ph.D. 1990 Computer Science (computational complexity theory)
University of Idaho Sabbatical 1999 Molecular biology (experimental evolution)
Marine Biology Lab Sabbatical 2008 Microbial Diversity
Academic Appointments
Institution Department Rank Dates
University of Idaho Biological Sciences Professor 2005 to now
    Adjunct Professor 1995 to 2005
  Initiative for Bioinformatics and Evolutionary STudies (IBEST) Director, IBEST Bioinformatics Core 1999 to now
  Idaho INBRE Director, Bioinformatics Network 1999 to now
  Bioinformatics and Computational Biology (BCB) Professor 2003 to now
    Director 2003 to 2005
  Computer Science Adjunct Professor 2005 to now
    Professor 2001 to 2005
    Associate Professor 1996 to 2001
    Assistant Professor 1990 to 1996
  Philosophy Adjunct Professor 1998 to now
University of Washington Biomedical Informatics Adjunct Professor 2003 to now
Idaho State University Biology Adjunct Professor 2003 to now
Northeastern Illinois University Computer Science Assistant Professor 1989 to 1990
    Lecturer 1988 to 1999
News, Announcements, Positions

News and Announcements

News

I've been cutting back on travel, so far these are the upcoming meetings. Maybe I'll see you at one!

  • PSB January 2017
  • EvoSTAR April 2017

Press Releases

None currently

Recent Publications

  • CS Greene, JA Foster, BA Stanton, DA Hogan, Y Bromberg (2016) Computational approaches to study microbes and microbiomes. Pacific Pacific Symposium on Biocomputing, 21:557-567
  • DL Beck, JA Foster (2015) Machine learning classifiers provide insight into the relationship between microbial communities and bacterial vaginosis. Biomedical Data Mining and Analysis, 8:23, DOI 10.1186/s13040-015-0055-3
  • S Ma, JA Foster, LJ Forney (2015) Network analysis reveals a potentially \"evil\" alliance of opportunistic pathogens inhibited by a cooperative network. Nature Scientific Reports, 5, 8275–6
  • IY Zhbannikov, JA Foster (2015) MetaAmp: Analysis high-throughput microbial amplicon sequence data with multiple markers. Bioinformatics, 31(11), 1830–1832. http://doi.org/10.1093/bioinformatics/btv049
  • DL Beck, C Daniels, JA Foster (2014) Seed: A microbial community visualization tool. Bioinformatics, pii: btu693
  • J Carter, DL Beck, H Williams, G Dozier, JA Foster (2014) GA-Based Selection of Vaginal Microbiome Features Associated with Bacterial Vaginosis. Genetic and Evolutionary Computation Conference (GECCO), 2014, Vancouver, BC Canada
  • YS Baker, R Agrawal, JA Foster, DL Beck, G Dozier (2014) Detecting Bacterial Vaginosis Using Machine Learning. ACM Southeast Conference, Springer
  • JA Foster (2014) Microbial diversity, bar-coding approaches. Encyclopedia of Metagenomics, Springer
  • YS Baker, R Agrawal, JA Foster, DL Beck, G Dozier (2014) Applying Machine Learning Techniques in Detecting Bacterial Vaginosis. International Conference on Machine Learning and Cybernetics (ICMLC), Lanzhou, China
  • DL Beck, JA Foster (2014) Machine learning techniques accurately classify microbial communities by bacterial vaginosis characteristics. PLOS One, 9(2):e87830
  • KA Pattin, AC Greene, RB Altman, LE Hunter, DA Ross, JA Foster, JH Moore (2014) Building the next generation of quantitative biologists. Pacific Symposium in Biocomputing, 2014
  • IY Zhbannikov, M Settles, SS Hunter, JA Foster (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, 4(3):1-6. doi: 10.4172/2153-0602.1000133
  • HK Allen, J Bunge, JA Foster, DO Bayles, BA 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