Ph.D. in Civil & Environmental Engineering
Dissertation: "Efficient Data Inversion for Large Multi-Dimensional Problems Using an Approximate Extended Kalman Filter with Data Driven Zonation"

Advisor: Dr. David E. Dougherty

University of Vermont, 1997.

Continuing Education

· New England Complex Systems Institute Summer School (5-day): Complex Physical, Biological and Social Systems, MIT, Cambridge, MA, June 2005.

· New England Complex Systems Institute Summer School (5-day): Modeling, Networks and Evolution of Complex Systems, MIT, Cambridge, MA, June 2005.

· New Directions in Bioinformatics and Biotechnology Workshop, Chautauqua Short Course #65 (3-day), RPI, July 2002.

· NPACI Parallel Computing Workshop (1-day), San Diego Supercomputer Center, San Diego, CA. January, 2002

· Inter-Institute Workshop on In Vivo Optical Imaging at NIH (2-day), October, 1999.

· Parallel Virtual Machine Workshop (1-day) at the 6^th SIAM Conference on Parallel Processing for Scientific Computing, Norfolk, VA, March, 1993.

· Follow-up Parallel Processing Workshop (4-day), Colgate University, Hamilton, NY. 1992.

· Parallel Processing for Undergraduate Educators (2-week), Colgate University, Hamilton, NY. 1991.

· Workshop for the Foundations of Artificial Intelligence (2-day), New Mexico State University, Las Cruces, NM. 1986.

Awards and Honors

· Best Student Paper Award (my graduate student is 1^st author, I am 2^nd author), IEEE Symposium on Artificial Life, 2007.

· The American Association of Physicists in Medicine Sylvia Sorkin Greenfield Award for the best paper (other than radiation dosimetry) published in Medical Physics in 2004.

· Outstanding Student Paper Award, American Geophysical Union, Fall 1996.

· American Association of University Women Career Development Award, 1993.

· Finalist for the U.V.M. Kroepsch-Maurice Teaching Award, 1992.

· U.V.M. graduate student travel mini-grants, 1982 and 1994.

· National Science Foundation 3-year graduate fellowship, 1980-1983.

· Initiated as Member, Upsilon Pi Epsilon, Computer Science Honor Society, 1983.

· Member, Michigan State University Honor’s College, 1974-1979

· Initiated as Member Phi Kappa Phi Honor Society, 1978.

Professional Positions

(in reverse chronological order)

· 2002-present Assistant Professor (Primary Appointment), Department of Computer Science, University of Vermont, Burlington, Vermont.

· 2006-present founding co-Director, Complex Systems Center at the University of Vermont. College of Engineering and Mathematical Sciences, University of Vermont, Burlington, Vermont.

· 2006-present Adjunct Member, Computational Genetics Laboratory, Dartmouth College, Lebanon, NH.

· 2005-present Assistant Professor (Secondary Appointment), Department of Biology, University of Vermont, Burlington, VT.

· 2001-2003 Adjunct Assistant Professor, Department of Chemical Engineering, Texas A&M University, College Station, TX.

· 2001-present Member, Vermont Cancer Center.

· 1997-2002 Research Assistant Professor (Primary Appointment 1998-2002), Department of Computer Science, University of Vermont, Burlington, VT.

· 1998-2003 Research Assistant Professor (Secondary Appointment), Department of Civil & Environmental Engineering, University of Vermont, Burlington, VT.

· 1983-2001 Lecturer (Primary Appointment 1983-1998), Department of Computer Science, University of Vermont, Burlington, VT.

· 1993-1997 Graduate Research Assistant, Department of Civil & Environmental Engineering, University of Vermont, Burlington, VT.

· 1990 Consultant, Digital Equipment Corporation, S. Burlington, VT.

· 1987-1988 Bioinformatics Software Engineer, International Biotechnologies, Inc., New Haven, CT (tele-commuted from VT).

· 1986 System Graphics Software Engineer, Vermont Microsystems, Inc., Winooski, VT.

· 1986 Consultant, Computing Research Laboratory, New Mexico State University, Las Cruces, NM.

· 1982 Graduate Teaching Assistant, Department of Computer Science, University of Vermont, Burlington, VT.

· 1982 Programmer, Academic Computing Center, University of Vermont, Burlington, VT.

· 1981-1982 Graduate Teaching Assistant, Department of Zoology, University of Vermont, Burlington, VT.

· 1979-1980 Research Associate, Department of Zoology, Michigan State University, E. Lansing, MI.

· 1977 Undergraduate Teaching Assistant, Department of Mathematics, Michigan State University, E. Lansing, MI.

· 1975-1979 Archaeologist for various institutions, including the Department of Anthropology at Michigan State University, the Tennessee Valley Authority, the State of Tennessee, and the U.S. Army Corps of Engineers.

Research

Research Interests

In keeping with my interdisciplinary educational background in biology, computer science, and environmental engineering, my research interests involve computational forward and inverse modeling and analysis of biological and environmental problems. Most of my research has focused on developing novel computational methods for large-scale, nonlinear, multi-scale tomographic inverse image reconstruction problems in subsurface hydrology, geophysics, and deep-tissue near-infrared fluorescence imaging. However, in the past couple of years I have shifted my research towards modeling and analysis of complex adaptive systems in a variety of biological and environmental systems. Current projects include developing, studying, and using novel evolutionary and agent-based computational approaches for a wide range of important problems, including plant species’ invasiveness in ecological communities, biological speciation, the impact of spatial topologies on information flow through complex interaction networks, identifying nonlinear interactions between single nucleotide polymorphisms that predispose for complex disease traits, and agent-based integrated assessment modeling of transportation energy alternatives.

Publications

Refereed Journal Publications

In review:

1. Payne, J.L. and Eppstein, M.J. “Modeling Takeover Dynamics with Pair Approximations in Regular Population Structures”, Evolutionary Computation (in review).

Published or accepted:

1. Eppstein, M.J., Payne, J.L., White, B.C., and Moore. J.H. "Genomic mining for complex disease traits with 'Random Chemistry'", Genetic Programming and Evolvable Machines (special issue on Medical Applications), 8:395-411, 2007. (DOI 10.1007/s10710-007-9039-5) pdf

2. Zhu, B., Eppstein, M.J., Sevick-Muraca, E.M., and Godavarty, A. "Noise pre-filtering techniques in fluorescence-enhanced optical tomography", Optics Express, 15(18):11285-11300, 2007. pdf

3. Eppstein, M.J. and Molofsky, J. "Invasiveness in plant communities with feedbacks". Ecology Letters, 10:253-263, 2007. pdf

4. Eppstein, M.J., Bever, J.D., and Molofsky, J., "Spatio-temporal community dynamics induced by frequency dependent interactions", Ecological Modelling, 197:133-147, 2006. pdf

5. Fedele, F., Eppstein, M.J., Laible, J.P., Godavarty, A., and Sevick-Muraca, E.M., “Fluorescence Photon Migration by the Boundary Element Method”, J. Computational Physics, 210(1):109-132, 2005. pdf

6. Godavarty, A., Sevick-Muraca, E.M., and Eppstein, M.J. "Three-dimensional fluorescence lifetime tomography", Medical Physics, 32(4): 992-1000, 2005. pdf

7. Godavarty, A., Eppstein, M.J., Zhang, C., and Sevick-Muraca, E.M., "Detection of single and multiple targets in tissue phantoms using fluorescence-enhanced optical imaging", Radiology, 235: 148-154, 2005. pdf

8. Godavarty, A., Thompson, A.B., Roy, R., Gurfinkel, M., Eppstein, M.J., Zhang, C., and Sevick-Muraca, E.M., “Diagnostic imaging of breast cancer using fluorescence-enhanced optical tomography: phantom studies,” J. Biomed. Opics.: Special edition on Biomedical Optics and Women’s Health 9:488-496, 2004. pdf

9. Godavarty, A., Zhang, C., Eppstein, M.J., and Sevick-Muraca, E.M., "Fluorescence-enhanced optical imaging of large phantoms using single and simultaneous dual point illumination geometries", Medical Physics 31(2):183-190, 2004. (Awarded the American Association of Physicists in Medicine Sylvia Sorkin Greenfield Award for the best paper published in Medical Physics in 2004) pdf

10. Eppstein, M.J., Fedele, F., Laible, J.P., Zhang, C., Godavarty, A., and Sevick-Muraca, E.M., "A comparison of exact and approximate adjoint sensitivities in fluorescence tomography", IEEE Transactions on Medical Imaging, 22(10):1215-1223, 2003. pdf

11. Godavarty, A., Eppstein, M.J., Zhang, C., Thompson, A.B., Gurfinkel, M., Theru, S., and Sevick-Muraca, E.M., "Fluorescence-enhanced optical imaging in large tissue volumes using a gain modulated ICCD camera, Physics in Medicine and Biology, 48:1701-1720, 2003. pdf

12. Fedele, F. Laible, J. P., and Eppstein, M.J., "Coupled complex adjoint sensitivities for frequency-domain fluorescence tomography: theory and vectorized implementation", J Computational Physics, 187(2):597-619, 2003. pdf

13. Godavarty, A., Hawrysz, D.J., Roy, R., Sevick-Muraca, E.M., and Eppstein, M.J., "The influence of the refractive index-mismatch at the boundaries measured in fluorescence-enhanced frequency-domain photon migration imaging", Optics Express, 10(15):653:662, 2002. pdf

14. Eppstein, M.J., Hawrysz, D.J., Godavarty, A., and Sevick-Muraca, E.M., "Three-dimensional, Bayesian image reconstruction from sparse and noisy data sets: Near-infrared fluorescence tomography", Proc. Natl. Acad. Sci. USA, 99(15):9619-9624, 2002. pdf

15. Hawrysz, D.J., Eppstein, M.J., Lee, J., and Sevick-Muraca, E.M., "Error Consideration in Contrast-Enhanced Three Dimensional Optical Tomography", Optics Letters, 26(10):704-706, 2001. pdf

16. Eppstein, M.J., Dougherty, D.E., Hawrysz, D.J., Sevick-Muraca, E.M., "3-D Bayesian optical image reconstruction with domain decomposition", IEEE Transactions on Medical Imaging, 20(3):147-163, 2001. pdf

17. Eppstein, M.J., Dougherty, D.E., Troy, T.L, and Sevick-Muraca, E.M., "Biomedical optical tomography using dynamic parameterization and Bayesian conditioning on photon migration measurements", Applied Optics, 38:2138-2150, 1999 (cover article). pdf

18. Eppstein, M.J. and Dougherty, D.E., "Efficient 3-D data inversion: Soil characterization and moisture monitoring from crosswell GPR at a Vermont test site", Water Resources Research, 34(8):1889-1900, 1998. pdf

19. Eppstein, M.J. and Dougherty, D.E., "Optimal 3-D traveltime tomography", Geophysics, 63(3):1053-1061, 1998. pdf

20. Eppstein, M.J. and Dougherty, D.E., "Simultaneous estimation of transmissivity values and zonation", Water Resources Research, 32(11):3321-3336, 1996. pdf

21. Eppstein, M.J. and Dougherty, D.E., "A comparative study of PVM workstation cluster implementations of a two-phase subsurface flow model", Adv. In Water Resources, 17:181-195, 1994. abstract

22. Heinrich, B. and Heinrich (née Eppstein), M.J.E., "The pit-trapping foraging strategy of the ant lion, Myrmeleon immaculatus", Behav. Ecol. and Sociobiol., 14:151-160, 1984. pdf

23. Heinrich, B. and Heinrich (née Eppstein), M.J.E., "Size and caste in temperature regulation by bumblebees", Phys. Zool., 56:552-562, 1983. link

24. Heinrich, B. and Heinrich (née Eppstein), M.J.E., "Heterothermia in foraging workers and drones of the bumblebee Bombus terricola", Phys. Zool., 56: 563-567, 1983. link

Published Refereed Conference Proceedings

1. Payne, J.L, and Eppstein, M.J. "Using Pair Approximations to Predict Takeover Dynamics in Spatially Structured Populations", Genetic and Evolutionary Computation Conference (GECCO), late-breaking papers pp. 2557-2563, 2007. pdf

2. Payne, J.L. and Eppstein, M.J., “Takeover Times on Scale-Free Topologies”, Genetic and Evolutionary Computation Conference (GECCO), pp. 308-315, 2007.pdf

3. Payne, J.L., Eppstein, M.J., and Goodnight, C.J. “Sensitivity of Self-Organized Speciation to Long Distance Dispersal”, Proceedings of the 2007 IEEE Symposium on Artificial Life (Alife’07), pp. 1-7, 2007 (best student paper award). pdf

4. Eppstein, M.J., Payne, J.L., White, B.C., and Moore. J.H., "Hill-climbing through ‘random chemistry’ for detecting epistasis", Genetic and Evolutionary Computation Conference (GECCO), late-breaking papers, 2006. pdf

5. Eppstein, M.J., Payne, J.L, and Goodnight, C.J. "Speciation by Self-Organizing Barriers to Gene Flow in Simulated Populations with Localized Mating", Workshop Proceedings for Genetic and Evolutionary Computation Conference (GECCO), 2006. pdf

6. J.L. Payne and M.J. Eppstein, "Emergent Mating Topologies in Spatially Structured Genetic Algorithms", Proceedings of Genetic and Evolutionary Computation Conference (GECCO) 2006, pp. 207-214. pdf

7. J.L. Payne and M.J. Eppstein, “A Hybrid Genetic Algorithm with Pattern Search for finding Heavy Atoms in Protein Crystals”, Genetic and Evolutionary Computation Conference (GECCO) 2005, Part 1, Eds. H-G Bayer et al., pp. 377-384, 2005. (nominated for a best-paper award). pdf

8. Godavarty, A., Eppstein, M.J., Zhang, C., and Sevick-Muraca, E.M., "Fluorescence-enhanced optical tomography on large phantoms using dual point illumination geometry", OSA Biomedical Topical Meetings, OSA Technical Digest, Optical Society of America, Washington, DC, April, 2004.

9. Godavarty, A., Eppstein, M.J., and Sevick-Muraca, E.M., "Fluorescence-enhanced optical tomography: Absorption and lifetime contrast studies", OSA Biomedical Topical Meetings, OSA Technical Digest, Optical Society of America, Washington, DC, April, 2004.

10. Fedele, F., Laible, J.P., and Eppstein, M.J., "Boundary Element Solution of the Coupled Fluorescence Diffusion Equations", OSA Biomedical Topical Meetings, OSA Technical Digest, Optical Society of America, Washington, DC, April, 2004.

11. Gilbert, J., and Eppstein, M.J., "Codons in Evolutionary Computation", Genetic and Evolutionary Computation Conference (GECCO) 2003, Part 1, Eds. E. Cantu-Paz et al., Lecture Notes in Computer Science, 2723:967-978, 2003. pdf

12. Eppstein, M.J., Zhang, C., Godavarty, A., and Sevick-Muraca, E.M.,"Advances in 3-D frequency domain fluorescence tomography", Proc SPIE 4955:211-218, 2003.

13. Zhang, C., Eppstein, M.J., Godavarty, A., and Sevick-Muraca, E.M., "A hybrid approach to Bayesian image reconstruction", SPIE 2003 ProcSPIE 4955:591-599, 2003.

14. Eppstein, M.J., and Laible, J.P., "The benefits of vectorization in optical tomography", Proc SPIE 4955:59-69, 2003.

15. Godavarty, A., Sevick-Muraca, E.M., Eppstein, M.J., Zhang, C., "Fluorescence-enhanced tomographic imaging in large phantoms using gain-modulated ICCD camera", SPIE 4949:433-443, 2003.

16. Eppstein, M.J., Hawrysz, D.J., Godavarty, A., and Sevick-Muraca, E.M., “Experimental Frequency Domain Fluorescence Tomography”, OSA Biomedical Topical Meetings, OSA Technical Digest, Optical Society of America, Washington, DC, pp. 510-512, April, 2002.

17. Godavarty, A.., Sevick-Muraca, E.M., and Eppstein, M.J., “Minimizing mismatch of forward model and experimental measurements for fluorescence-enhanced optical imaging”, OSA Biomedical Topical Meetings, OSA Technical Digest, Optical Society of America, Washington, DC, pp. 516-518, April, 2002.

18. Joshi, A.., Sevick-Muraca, E.M., and Eppstein, M.J., “A Method to Determine the Optimal Number of Measurements for Three-Dimensional Optical Tomography for a Physiologically Realistic Geometry”, OSA Biomedical Topical Meetings, OSA Technical Digest, Optical Society of America, Washington, DC, pp. 128-130, April, 2002.

19. Fedele, F., Laible, J.P., and Eppstein, M.J., “Generalized Adjoint Sensitivities of the Coupled Frequency Domain Fluorescence Diffusion Equations”, OSA Biomedical Topical Meetings, OSA Technical Digest, Optical Society of America, Washington, DC, pp. 371-373, April, 2002.

20. Hawrysz, D.J., Eppstein, M.J., and E.M. Sevick-Muraca, "Measurement and Model Error Assessment of a Single Pixel, Frequency Domain Photon Migration Apparatus and Diffusion Model for Imaging Applications." European Biomedical Optics and Spectroscopy Conference, Amsterdam, 2000.

21. Eppstein, M.J. and Rizzo, D.M., "Rapid 3-D Bayesian site characterization: A tandem strategy", Proceedings of the XIII International Conference on Computational Methods in Water Resources, L.R. Bentley, J.F. Sykes, C.A. Brebbia, W.G. Gray, and G.F. Pinder, eds., Vol 1: Computational Methods for Subsurface Flow and Transport, Balkema, Rotterdam, The Netherlands, pp. 491-494, 2000.

22. Eppstein, M.J., "Three-dimensional fluorescence absorption imaging with domain decomposition", in Biomedical Topical Meetings, OSA Technical Digest, Optical Society of America, Washington, DC, pp. 173-176, 2000.

23. Eppstein, M.J., Dougherty, D.E., Hawrysz, D.J., and Sevick-Muraca, E.M., "Three-dimensional optical tomography", Optical Tomography and Spectroscopy of Tissue III,Chance, B., Alfano, R.R., and Tromberg, B.J., eds., SPIE Proceedings, 3597:97-105, 1999.

24. Eppstein, M.J., Dougherty, D.E., Troy, T.L., and Sevick-Muraca, E.M., "Stochastic optical tomography using beta-distributed parameters to model absorption, lifetime, and quantum efficiency", Biomedical Imaging: Reporters, Dyes, and Instrumentation, Bornhop, D.J., Contag, C.H., and E.M. Sevick-Muraca, SPIE Proceedings, 3600:230-236, 1999.

25. Eppstein, M.J. and Dougherty, D.E., "3-D computed subsurface tomography", Proceedings of the XII International Conference on Computational Methods in Water Resources", Vol. 2, pp. 329-336, 1998.

26. Eppstein, M.J. and Dougherty, D.E., "Optimal 3-D geophysical tomography", Proceedings of the Symposium on the Application of Geophysics to Environmental and Engineering Problems (SAGEEP), pp. 249-256, 1998.

27. Eppstein, M.J. and Laible, J.P., "A practical parallel retrofit of a 3-Dimensional surface water model", Proceedings of the 2^nd International Conference on Computer Modeling of Seas and Coastal Regions: COASTAL 95, Cancun, Mexico, September, 1995.

28. Eppstein, M.J. and Dougherty, D.E., "Parameter estimation with data-driven zonation", Proc. of the 10^th International Conference on Computational Methods in Water Resources, Vol. 1, pp. 727-734, Heidelberg, Germany, June, 1994.

29. Eppstein, M.J., Guarnaccia, J.F., and Dougherty, D.E., "Parallel groundwater computations using PVM", Proc. of the 9^th International Conference on Computational Methods in Water Resources, Vol. 1, pp. 713-720, Denver, CO, 1992.

Patents

1. Eppstein, M.J. and Dougherty, D.E., "Three-dimensional stochastic tomography with upscaling", U.S. Patent #6,067,340, 2000.

Invited Talks

1. "Predicting naturalization vs. invasion in plant communities using stochastic cellular automata models", NKS 2007 Wolfram Science Conference, Burlington, VT, July 14, 2007.

2. "Genomic mining for complex disease traits with 'Random Chemistry'", Computational Genetics Laboratory, Dartmouth College, Hanover, NH, Dec 1, 2006.

3. "A 'Random Chemistry' algorithm for detecting epistatic genetic interactions", Department of Computer Science, Middlebury College, Middlebury, VT, April 7, 2006.

4. "Molecularly-targeted imaging with diffuse fluorescence tomography for biomedical diagnostics", Vermont Lung Center, University of Vermont College of Medicine, Burlington, VT, Sept. 30, 2003.

5. "The benefits of vectorization in Matlab: obtaining speedups without parallelism", Department of Computer Science, Rochester Institute of Technology, Rochester, NY, May 6, 2003.

6. "Algorithm Development for Biomedical Fluorescence Tomography", Department of Imaging Science, Rochester Institute of Technology, Rochester, NY, May 5, 2003.

7. "Fluorescence Tomography for Biomedical Diagnostics: Mathematical and Computational Challenges", Departments of Mathematics, Rensselaer Polytechnic Institute, Troy, NY, March, 31, 2003.

8. "3-D Bayesian fluorescence tomography from sparse and noisy frequency domain photon migration data sets", Harvard Medical School, Photon Migration Seminar Series, Massachusetts General Hospital Imaging Center, Boston, MA, September, 2001.

9. "Recursive, Minimum-Variance Optical Imaging with Domain Decomposition",Optical Society of America spring meeting "Advances in Optical Imaging and Photon Migration 2000", Miami, Florida, April, 2000.

10. "Rapid Bayesian 3-D Biomedical Optical Imaging", Biomedical Computation Group, Thayer School of Engineering, Dartmouth College, Hanover, NH, November, 1999.

11. "3-D Site Characterization Using APPRIZE", Center for Geophysical Investigations of the Shallow Subsurface, Distinguished Lecture Series, Boise State University, May, 1999.

12. "Using PVM to Implement Grand-Challenge Problems in Environmental Engineering: a Case Study of a Finite-Element Groundwater Model", Workshop in Parallel Processing for Undergraduate Educators, Colgate University, Hamilton, NY, January, 1993.

Funding: (Total Funding Awarded $1,668,667)

Research Grants: ($1,537,705 total)

1. P.I. for "Recursive Bayesian Optical Tomography for Imaging Tissues", DBI/CBA 987-0779, National Science Foundation, Division of Biological Infrastructure/Computational Biology Activities, $290,043, 09/15/98-8/31/01. Supplemented with an additional $27,000, 10/1/00-4/31/01.

2. P.I. for "3-D Frequency-Domain NIR Diagnostic Breast Imaging with APPRIZE", R01 EB 002763 (formerly R01 CA 88082), National Institutes of Health, National Institute for Biomedical Imaging and Bioengineering and National Cancer Institute, Bioengineering Research Grants, $805,662, 4/3/01-3/31/04 (no-cost extension to 3/31/05).

3. P.I. (with J. Molofsky) for "Disentangling the mechanisms of species diversity in landscapes", DOE EPSCoR Computational Biology pilot project (funded out of DE-FG02-00ER45828, P.I.: S. Wallace), $35,000 direct, 7/1/02-6/31/04 (no-cost extension to 6/30/07).

4. P.I. (originally, with M. Rould, who later left the project) for "A Bayesian Genetic Algorithm Approach to Crystallographic Phasing"; later generalized to “Evolutionary Computational Approaches to Complex Biological Problems”, DOE EPSCoR Computational Biology pilot project (funded out of DE-FG02-00ER45828, P.I.: S. Wallace), $40,000 direct, 9/1/03-8/31/05 (no-cost extension to 6/30/07).

5. P.I. (with co-P.I.s J. Marshall and D. Rizzo and subcontract P.I. M. Dworkin) for “Regulatory Control Prediction for Transportation Alternative Energy Usage via a Multiscale Agent-Based Model”, University of Vermont Transportation Center, $335,000 direct, 7/1/2008-6/30/2010.

Research Infrastructure Grants: ($6,692,531 total; see below)

1. P.I. is EPSCoR director J. VanHouten. “Complex Systems Thinking and Modeling for Ecosystem Analysis”, National Science Foundation EPSCoR Research Infrastructure Improvement (RII) Grant, $6,692,531 from 8/15/07-6/30/10. Note: this amount is not included in my funding total since I am not a listed P.I. However, I am a funded core faculty and made significant contributions to writing the science portions of this grant related to complex systems analysis and modeling.

Equipment Grants: ($20,000 total)

1. Co-P.I. (with G.Pinder, T.Keller, F. Sansoz, D. Rizzo) for "Enabling Technology for High Speed Computing", UVM Faculty Equipment Acquisition funded by NSF EPSCoR, $20,000 direct, awarded 3/31/04.

Grants Specifically To Fund Graduate Students: ($66,892 total)

1. Supervisor (with R. Costanza and B. Bowden) for " Methods for Parameterization and Parameter Estimation of a Complex Systems Model of the Winooski Watershed ", NSF EPSCoR graduate research fellowship to fund Karim Chichakly, $30,000, 1/1/08-6/30/08.

2. Supervisor for "Computational Modeling in Ecology and Evolution", DOE EPSCoR Computational Biology graduate research fellowship to fund Ph.D. student Joshua Payne, (funded out of DE-FG02-00ER45828, P.I.: S. Wallace), $20,000, 7/1/05-6/30/06. Renewed for $20,722, 7/1/06-6/30/07.

2. P.I. for "Biomedical Fluorescence Tomography using the Boundary Element Method", Vermont Genetics Network graduate research assistantship to fund Ph.D. student Francesco Fedele, (funded out of NIH grant NCRR, 1 P20 RR16462, P.I.: C. Allen), $22,000, 6/1/03-5/31/04.

3. P.I. for "Application of Proper Orthogonal Decomposition to Biomedical Fluorescence Tomography", DOE EPSCoR Computational Biology summer graduate research fellowship to fund M.S. student Scott Wakefield, (funded out of DE-FG02-00ER45828, P.I.: S. Wallace), $4170, 6/15/03-8/15/03.

Grants to Support Teaching: ($8,165 total)

1. P.I. (with J. Hoffmann) for "Developing Cross-Disciplinary Learning Experiences in Evolutionary Computation", University of Vermont Center for Teaching and Learning, $3,165 direct, 7/1/04-6/31/05.

2. P.I. for "A novel computational science course for life science majors", University of Vermont Center for Teaching and Learning, $5000 direct, 7/1/07-6/30/08.

Planning Grants: ($5,000 total)

1. P.I. (with D. Rizzo, L. Stevens, C. Goodnight, J. Molofsky, and J. Hoffmann) for "Proposed VACC focal research area in Biocomplexity", Vermont Advanced Computing Center; $5,000 direct, 9/1/05-5/31/06 (no cost extension through 5/31/07).

Contracts: ($96,839 total)

1. P.I. for contract "Tools for Inversion and Imaging", from Subterranean Research, Inc., as subaward of a U.S. Department of Energy SBIR Phase II (P.I. D.M. Rizzo); contract amount $51,839, 01/01/99-08/31/99; renewal amount $30,000, 01/01/00-05/31/00.

2. P.I. for contract "Professional Development Course on Inversion and APPRIZE", Subterranean Research, Inc., contract amount $15,000, 01/01/00-06/30/00.

Teaching and Advising

Courses Taught

I have independently developed and taught the following courses at UVM.

Level	Course	Semester	Title
literacy	CS 2	S '89	Microcomputer Applications Software
literacy	CS 3	F'83, S'84, F'87, S'88	Computer Literacy
programming	CS 11	F '91(×3), S'92 (×2), F'92, S'93	Computer Programming I
	CS 12	S'85, S'86, F'86, Sum'87,F'88, S'89, F'89, F'90, S'91	Computer Programming II
	CS 16	F'94, S'95, F'95, S'96, F'96, S'97, S'04	Programming in MATLAB for Engineers and Scientists
	CS 95	F'88	C Programming for Pascal Programmers
	CS 27	F'96, S'97	C++ for C Programmers
Sophomore/junior	CS 195	F'07	Data Analysis, Modeling, & Visualization for Life Scientists
	CS 100	F'97, F'00, S'01	Object-Oriented Programming
	CS 103	F'83, F'84, F'90, S'92	Programming Languages
	CS 104	S'85, S'86, S'87, S'90, S'91, F'92, S'93, S'05, F'05, S'06, F'06	Data Structures
	CS 105	S'96	Software Engineering
Senior/graduate	CS 260	S'03, S'05	Parallel Algorithms and Prog. Techniques
	CS 381	S'04	Graduate Seminar in Evolutionary Computation
	CS 295/Bot 295, CS 395 /Biol 395.	F'04, F'06	Evolutionary Computation
	CS 295	S'06	Intro to Scientific Computing: Modeling Complex Nonlinear Dynamic Systems

Graduate Student Thesis/Dissertation Supervision

Ongoing:

1. Supervisor of Ph.D. student, Joshua L. Payne, "Interaction topologies and the flow of information in complex adaptive systems", Department of Computer Science, UVM, 2004-present.

2. Supervisor of M.S. student, Paul Haake, "Detecting Large Supersets of SNPs that contain small epistatically interacting subsets", Department of Computer Science, UVM, 2006-present.

3. Supervisor of Ph.D. student, Jeff Sprenger, “Rapid sound recognition and recall using spiking neural networks grown from a single neurode using a multi-objective evolutionary algorithm”, Department of Computer Science, 2007-present.

4. Supervisor (with co-supervisor R. Costanza) of Ph.D. student, Karim Chichakly, "Methods for Parameterization and Parameter Estimation of
a Complex Systems Model of the Winooski Watershed", Department of Computer Science, 2007-present.

Completed:

1. Supervisor of M.S. student, Peter Duval, "Canonical Disjunctive Normal Form Genetic Programming for nonlinear-SNP Association Studies". Department of Computer Science, 2006-2008. M.S. granted 2008.

2. Supervisor of M.S. student, Joshua Gilbert, “Bayesian evolutionary algorithms for locating heavy atoms in protein crystals”, Department of Computer Science, UVM, 2003-2005. No degree granted.

3. Co-supervisor (with primary advisor J. Laible) of Francesco Fedele, "Novel Numerical Techniques for Problems in Engineering Science", Department of Civil & Environmental Engineering, UVM, 2001-2004. Ph.D. granted 2004. Post-doctoral associate in the Global Modeling and Assimilation Office, NASA Goddard Space Flight Center, Greenbelt, Md, 2004-2006. Currently, assistant professor, Dept. of Civil & Environmental Engineering, Georgia Institute of Technology, Savannah.

4. Co-supervisor (with primary advisor E.M. Sevick-Muraca) Anuradha Godavarty, "Fluorescence enhanced optical tomography in breast phantoms with measurements using a gain modulated intensified CCD imaging system", Department of Chemical Engineering, Texas A&M Univ, 2001-2003. Ph.D. granted 2003. Currently, assistant professor in Biomedical Engineering at Florida International University.

Post-Doctoral Supervision

1. Funded and supervised Dr. Anuradha Godavarty as a postdoctoral research associate in computer science, UVM, 2003-2004. Currently, assistant professor in Biomedical Engineering at Florida International University.

2. Funded and supervised Dr. Chaoyang Zhang as a research assistant professor in computer science, UVM, 2001-2003. Currently, assistant professor in the School of Computing at University of Southern Mississippi.

Other Student Research Supervision

1. Chair, Undergraduate Honor's Thesis Committee, Kyle John Palmer, Thesis on aggressive behavior in individual workers of 6 different species of harvester ant whose colony-level aggressive behaviors differ dramatically, Environmental Science, CAS, UVM, spring 2007.

2. Supervised M.S. student, Scott Wakefield, research in biomedical fluorescence tomography, funded through DOE EPSCoR summer research grant, Department of Computer Science, UVM, summer 2003.

3. Supervised undergraduate Joshua Gilbert (Computer Science Major, University of Vermont) through the SURE program (funded by the UVM Dept of Biochemistry and NIH) for research in evolutionary algorithms in structural biology, summer 2003.

4. Co-supervised (with J. Molofsky), undergraduate Chris Pyman (Mathematics major, Computer Science minor) for research in computational modeling of plant species interactions (funded by DOE EPSCoR pilot project), summer 2003.

5. Supervised M.S. student, Tyler Carr, research in phylogenetic tree algorithms, Department of Computer Science, UVM, spring 2003.

6. Supervised undergraduate Scott Wakefield (Computer Science Major, University of Vermont), funded through my discretionary funds, for exploratory research in DNA folding algorithms and their application to mutation spectra analysis, spring 2003.

7. Supervised undergraduate Joshua Gilbert (Computer Science Major, University of Vermont) through the HELIX program (funded by DOE EPSCoR summer internship) for research on use of codons for genetic representation in genetic algorithms, summer 2002

8. Supervised M.S. student, Zheng Zheng Wei, independent study in mutation spectra analysis, Department of Computer Science, UVM, spring 2002.

9. Funded and unofficially helped to co-supervise (with E.M. Sevick-Muraca) Daniel J. Hawrysz, "Bayesian approach to the inverse problem in contrast-enhanced, three-dimensional, biomedical optical imaging using frequency domain photon migration", Department of Chemical Engineering, Purdue Univ., 1998-2001. Ph.D. granted 2001. Currently, research scientist at Exxon Mobil.

Graduate Student Committees

1. Karim Chichakly, Member Ph.D. Studies Committee, Department of Computer Science, UVM, 2007-present.

2. Jeffrey Sprenger, Member Ph.D. Studies Committee, Department of Computer Science, UVM, 2007-present.

3. Casey Greene, Ph.D. Dissertation Committee, Genetics, Molecular, and Cellular Biology Graduate Program, Dartmouth Medical School, Hanover, NH, 2007-present.

4. Ryan Urbanowicz, Ph.D. Dissertation Committee, Genetics, Molecular, and Cellular Biology Graduate Program, Dartmouth Medical School, Hanover, NH, 2007-present.

5. Casey Korecki, Member Ph.D. Dissertation committee, Mechanical Engineering, School of Engineering, UVM, 2007-present.

6. Brittny Starford, Member Ph.D. Studies committee, Department of Biology, UVM, 2006- present.

7. Zhiqaing, Li, Chair Ph.D. Dissertation Defense Committee, Civil & Environmental Engineering Program, UVM, Defended, Dec. 2006.

8. Robin Collins, Member Ph.D. Studies committee and Comprehensive Examination Committee, Department of Plant Biology, UVM, 2005- present.

9. Thomas Weicht, Member Ph.D. Studies committee, Department of Biology, Univ. of Toledo, 2005- present.

10. Joshua Gilbert, Chair M.S. Project committee, Department of Computer Science, UVM, 2005- present.

11. Joshua Payne, Member Ph. D. Studies committee, Comprehensive Examination Committee, Department of Computer Science, UVM, 2004- present.

12. Nagi Basha, Member Ph. D. Studies committee, Comprehensive Examination Committee, Department of Computer Science, UVM, 2004- present.

13. Tri Tran, Member Ph. D. Studies committee, Department of Computer Science, UVM, 2004- present.

14. Thomas Tucker, Member, M.S. Comprehensive Examination Committee, Department of Biology, UVM, January, 2004.

15. Francesco Fedele: Member, Ph.D Dissertation Defense Committee, Dept. of Civil & Environmental Engineering, defended Dec 2004.

16. Charles Mark: Chair, MS Thesis Defense Committee, Department of Civil & Environmental Engineering, defended October, 2004.

17. Linda Mayer: Chair, MS Thesis Defense Committee, Department of Electrical & Computer Engineering, defended July 2004.

18. Norman Kennedy: Chair, Ph.D. Dissertation Defense Committee, Department of Cellular and Molecular Biology, UVM, November, 1999.

19. Mengchun Yu: Member, Ph.D. Dissertation Defense Committee, Department of Civil & Environmental Engineering, UVM, September, 1998.

20. Henry Tufo: Member, M.S. Thesis Defense Committee, Department of Computer Science, UVM, June 1995.

Service

National Service

Federal Agency Reviews

· Panel Member, Biomedical Imaging Technology Study Section (BMIT), National Institutes of Health, 2005.

· Panel Member, Physical Imaging 2 Review Panel of the U.S. Army Breast Cancer Research Program, 2004.

· Panel Member, National Science Foundation Review Panel for Information Technology Bioinformatics, 2001.

· Panel Member, National Science Foundation Review Panel for Computational Biological Activities, 1999.

· Mail Reviewer for several National Science Foundation Grant Proposals, 1997-present.

Conference Service (Program Committees, Conference Peer Reviewing, and Session Chairing)

· Conference Organizing Committee, Complex Systems in Transportation Conference, 2007-2008.

· Member, Standing Program Committee, OSA Biomedical Topical Meetings, Advances in Optical Imaging and Photon Migration, 2003-2008.

· Program Committee Member for the 6th European Conference on Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics (EvoBIO), 2008.

· Program Committee Member for the 3rd International IEEE Workshop on Software Evolvability at the IEEE International Conference on Software Maintenance (ICMS), 2007.

· Program Committee Member for the Biological Applications Track, Genetic and Evolutionary Computation Conference, 2007.

· Reviewer for 2nd IAPR Workshop on Pattern Recognition in Bioinformatics (PRIB), 2007.

· Reviewer for IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, 2005 and 2006.

· Session chair, Optical Tomography and Spectroscopy of Tissue IV at Photonics West (International Society for Optical Engineering), San Jose, CA, January 2000.

· Session chair, XII International Conference on Computational Methods in Water Resources, Crete, Greece, 1998.

Editorial Boards

· Editorial Board Member for BioData Mining, published by BioMed Central, 2007-present

External Peer Reviewer for Grants, Journals, Book Chapters

· External peer reviewer for book chapter in Stochastic Methods in Subsurface Contaminant Hydrology, 1999.

· External peer reviewer for the following journals, 1997-present.

o Water Resources Research

o Geophysics

o Advances in Water Resources

o Optics Letters

o Optics Express

o Optics Communications

o Medical Physics

o Journal of the Optical Society of America A

o Journal of Biomedical Optics

o Physics in Medicine and Biology

o IEEE Transactions in Medical Imaging

o Journal of Soft Computing

o Ecological Modelling

o Evolutionary Computation

o American Journal of Human Genetics

o Inverse Problems

o Engineering in Biology and Medicine Magazine

University Level Service

· Member, Vermont Advanced Computing Center Director Search Committee (2007-08).

· · Member of the DEPSCoR Pre-proposal review committee, (2007).

· Biosciences PhD Umbrella Steering Committee (2007-present).

· Aiken Lecture ‘08-‘09 Planning Committee (2007-present).

· University Diversity Curriculum Committee (2005).

· Member of the VT EPSCoR SBIR Phase 0 proposal review committee, (2005).

· Member of the DEPSCoR Pre-proposal review committee, (2003).

College Level Service (CEMS is College of Engineering and Mathematical Sciences)

· CEMS Curriculum Committee member (1994-present) and Chair (1994-1996, 2000-present).

· Founding co-Director, Complex Systems Center (2006-present).

· Dean’s Faculty Advisory Committee, (2006-present).

· Bioengineering Faculty Search Committee (2007-08).

· Bioengineering & Computational Biology PhD Track Director (2007-present).

· CEMS Bioengineering Advisory Committee (2005).

· Electrical and Computer Engineering Chair Search Committee (2003-04).

· CEMS Studies Committee (1986-1994).

Department Level Service (CS is Department of Computer Science)

· CS Curriculum Committee member (1983-present) and Chair (1997-2005).

· CS Faculty Search Committee (2005-06).

· UPE (CS Honor Society) Faculty Advisor (1983-2006).

· CS Computational Biology Faculty Search Committee (2001-02).

· CS certificate coordinator (1983-2001).

· CS Interim Chair Search Committee (1999)

· CS Co-op advisor (1983-1990).

· CS Open Houses/Visitation Days: I regularly participate in approximately 2 sessions per year.