Peter T. Hraber

P.O. Box 193
Santa Fe, NM 87504

Click here for the (slightly outdated) postscript version of this CV
or click here for the (slightly outdated) pdf version.

RESEARCH INTERESTS

Computational molecular biology, biostatistics, theoretical ecology, complex adaptive systems, coevolutionary dynamics, synthetic biology, and molecular evolution.

EDUCATION AND HONORS

2002. Granted ESF travel award to participate in "From Genome To Life" International Summer School in Functional Genomics, Cargese, Corsica.
2001. Granted NSF travel award to attend "Artificial Intelligence and Heuristic Methods in Bioinformatics" Advanced Study Institute, San Miniato, Italy.
2001. PhD, Department of Biology, University of New Mexico.
Dissertation entitled "Discovering Molecular Mechanisms of Mutualism with Computational Approaches to Endosymbiosis". Coadvisors: Jennifer W. Weller, George Mason University, and Mary Anne Nelson, University of New Mexico.
2000. Graduate Fellow, Santa Fe Institute.
1999. Participated in Lipari School for Computer Science Researchers, Lipari, Italy.
1999. Completed ``From the Laboratory to Leadership'' program, Santa Fe, NM.
1997. Graduate Fellow, NSF RTG in Ecological Complexity (UNM/SFI).
1996. MS, University of New Mexico, Albuquerque, NM.
1996. Graduate Fellow, Santa Fe Institute.
1991. MA, Saint John's College, Santa Fe, NM.
1989. BFA cum laude, Rochester Institute of Technology, Rochester, NY.
1988. Attended Salzburg College, Salzburg, Austria.

PUBLICATIONS

E. Trachtenberg, B. Korber, C. Sollars, T.B. Kepler, P.T. Hraber, E. Hayes, R. Funkhouser, M. Fugate, J. Theiler, Y.S. Hsu, K. Kunstman, S. Wu, J. Phair, H. Erlich, S. Wolinsky. 2003. Advantage of rare HLA supertype in HIV disease progression. Nature Medicine 9(7):928-35.
P.T. Hraber and J.W. Weller. 2001. On the species of origin: Diagnosing the source of symbiotic transcripts. Genome Biology 2(9):research0037.1-0037.14. (Full text available online here).
D. Qutob, P.T. Hraber, B.W.S. Sobral, and M. Gijzen. 2000. Comparative analysis of expressed sequences in Phytophthora sojae. Plant Physiology 123:243-254.
M. Waugh, P.T. Hraber, J.W. Weller, Y. Wu, G. Chen, J. Inman, D. Kiphart, and B.W.S. Sobral. 2000. The Phytophthora Genome Initiative Database: informatics and analysis for distributed pathogenomic research. Nucleic Acids Research 28(1):87-90.
S. Kamoun, P.T. Hraber, B.W.S. Sobral, D. Nuss, and F. Govers. 1999. Initial assessment of gene diversity for the oomycete pathogen Phytophthora infestans based on expressed sequences. Fungal Genetics and Biology 28:94-106.
E. Schultes, P.T. Hraber, and T.H. LaBean. 1999. Estimating the contributions of selection and self-organization in RNA secondary structure. Journal of Molecular Evolution 49(1):76-83.
E. Schultes, P.T. Hraber, and T.H. LaBean. 1999. A parameterization of RNA sequence space. Complexity 4:61-71.
C. Harger, M. Skupski, J. Bingham, A. Farmer, S. Hoisie, P. Hraber, D. Kiphart, L. Krakowski, M. MacLeod, J. Schwertfeger, G. Seluja. A. Siepel, G. Singh, D. Stamper, P. Steadman, N. Thayer, R. Thompson, P. Wargo, M. Waugh, J.J. Zhuang, and P.A. Schad. 1998. The Genome Sequence DataBase (GSDB): Improving data quality and data access. Nucleic Acids Research 26(1):21-26.
E. Schultes, P.T. Hraber and T.H. LaBean. 1997. Global similarities in nucleotide base composition among disparate functional classes of single-stranded RNA imply adaptive evolutionary convergence. RNA 3:808-822.
P.T. Hraber and B.T. Milne. 1997. Community assembly in a model ecosystem. Ecological Modelling 103:267-285.
P.T. Hraber, T. Jones, and S. Forrest. 1997. The ecology of Echo. Artificial Life 3(3):165-190.
B.T. Milne, A.R. Johnson, T.H. Keitt, C.A. Hatfield, J. David, and P.T. Hraber. 1996. Detection of critical densities associated with Pinyon-Juniper woodland ecotones. Ecology 77(3):805-821.
M. Mitchell, J.P. Crutchfield, and P.T. Hraber. 1994. Evolving cellular automata to perform computations: Mechanisms and impediments. Physica D 75:361-391.
M. Mitchell, J.P. Crutchfield, and P.T. Hraber. 1994. Dynamics, computation, and the ``Edge of chaos'': A re-examination. in G. Cowan, D. Pines, and D. Meltzer, eds. Complexity: Metaphors, Models, and Reality. Addison-Wesley, Reading MA.
M. Mitchell, P.T. Hraber, and J.P. Crutchfield. 1993. Revisiting the edge of chaos: Evolving cellular automata to perform computations. Complex Systems 7:89-130.

PRESENTED PAPERS

P.T. Hraber. 2002. Information-based models of complex ecological processes. Invited Keynote Lecture at the Third Meeting of the International Society for Ecological Informatics, Rome, Italy.
P.T. Hraber. 2002. Symbiosis and Macroevolution. International Workshop on Evolutionary Innovation. Prague, Czech Republic
P.T. Hraber and B.W. Sobral. 1999. The Phytophthora Genome Initiative: A database and analysis system for collaborative pathgenomic research. Presented at Plant and Animal Genome Conference VII (San Diego, CA).
P.T. Hraber and B.W. Sobral. 1998. The PGI Database: Informatics and Analysis. Poster, Advances in Phytophthora Molecular Genetics Symposium (Edinburgh, Scotland).
F. Arredondo, W.X. Shan, A. Chan, P.T. Hraber, M. Waugh, B.W. Sobral, and B.M. Tyler. 1998. Construction and DNA sequencing of a BAC contig spanning the Phytophthora sojae genome. International Congress of Plant Pathology (Edinburgh, Scotland).
E.H. Decker, P.T. Hraber, A.J. Kerkhoff and B.T. Milne. 1997. Direct probability mapping by stochastically induced percolation. Poster, US IALE conference (Durham, NC).
P.T. Hraber, E. Schultes and T.H. LaBean. 1997. RNA sequence composition and the dynamics of self-assembly. Poster, RECOMB97-Computational Molecular Biology (Santa Fe, NM).
E. Schultes, P.T. Hraber and T.H. LaBean. 1995. Predicting the evolutionary utility of nucleotide compositions using a statistical mechanics approach to RNA evolution. Poster, Exploring Sequence Space Conference (Bloomington, IN).
Click here for the abstract.
P.T. Hraber. 1995. An agent-based model of ecological disturbance. Poster, US IALE conference (Minneapolis, MN).
Click here for the abstract.
P.T. Hraber. 1995. Species-area relations in Echo. Oral presentation, Santa Fe Institute (Santa Fe, NM).
Click here for the abstract.
B.T. Milne, A.R. Johnson, T.H. Keitt, J. David, and P.T. Hraber. 1994. Indicators of spatial phase transitions and critical densities in woodland landscapes. Poster, US IALE conference (Tucson, AZ).

RECENT EMPLOYMENT

Postdoctoral Fellow, Spring 2001-Autumn 2002. Santa Fe Institute, Santa Fe, NM.

Developing methods to analyze data from sequencing and expression experiments in a plant-nematode system. Mentor: Tom Kepler.
Computational Biologist, Spring 1999-Autumn 2000. National Center for Genome Resources, Santa Fe, NM.

Collaborated to develop information and analysis systems to support functional genomics investigations and EST sequencing in Medicago truncatula and the genus Phytophthora. Participated in the design and implementation of a database to store and analyze data from gene expression experiments. Designed and implemented an object-relational database to store and analyze structural nucleotide motifs. Communicated progress of these projects to a variety of audiences. Participated in grant writing and project planning.
Software Developer, Autumn 1997-Spring 1999. National Center for Genome Resources, Santa Fe, NM.

Designed and implemented analysis algorithms and database applications using object-oriented development techniques to provide bioinformatics services via the internet. Coordinated group activities for several projects, such as an analysis system to facilitate EST sequencing. Presented analysis applications and results at conferences, in publications, and in technical documents.
Research Assistant, 1994-1997. Department of Biology, University of New Mexico, Albuquerque, NM.

Developed and tested simulation algorithms. Documented research results in technical reports and presented reports at national and international scientific meetings. Thesis project investigated the influence of ecological and evolutionary dynamics on simple model ecosystems. Other research activities included molecular evolution, RNA structure/function relations, species abundance distributions, spatial data analysis, multivariate analysis, and statistical inference.
Research Assistant, 1992-1996. Santa Fe Institute, Santa Fe, NM.

Developed and tested simulation algorithms. Designed and conducted simulation experiments. Analyzed, summarized, and archived experimental data. Project involved implementing a genetic algorithm and alternative search strategies to evolve (or discover) cellular automata rules to perform simple computational tasks.

TEACHING AND RELATED EXPERIENCE

Autumn 2000. Guest lecturer in Biology 544 - Genomes and Genome Analysis on "Sequence similarity searching: why and how" and "Putting it together with fragment assembly".
Summer 2000. Mentored and collaborated with Allison Styer, undergraduate student of biology and computer science at Carnegie-Mellon University, during her internship at the National Center for Genome Resources. Her research topic was "Screening ESTs for secreted peptides with PexFinder."
Autumn 1997. Guest-lectured in Biology 522, Ecological Complexity Seminar, taught by Professor J.H. Brown, on the subject "What is Complexity?".
Autumn 1996. Coordinated and taught the lab section of Biology 310 - Principles of Ecology. Also guest lectured in this class on "The World Wide Web as an Ecological Resource".
Summer 1991 through Autumn 1992. Worked as assistant to Program Coordinator at the Santa Fe Institute. Helped organize conferences and workshops, including Complex Systems Summer Schools 1991 and 1992, Artificial Life III, and the Integrative Themes Workshop

PROFESSIONAL SERVICE

Member, International Society for Computational Biology, International Society for Molecular Plant-Microbe Interactions, American Association for the Advancement of Science, and the Santa Fe Institute Library Committee.
Reviewer for Complex Systems, Complexity, Evolutionary Computation, and Advances in Complex Systems.

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Peter T. Hraber

P.O. Box 193 Santa Fe, NM 87504

RESEARCH INTERESTS

EDUCATION AND HONORS

PUBLICATIONS

PRESENTED PAPERS

RECENT EMPLOYMENT

Postdoctoral Fellow, Spring 2001-Autumn 2002. Santa Fe Institute, Santa Fe, NM.

Computational Biologist, Spring 1999-Autumn 2000. National Center for Genome Resources, Santa Fe, NM.

Software Developer, Autumn 1997-Spring 1999. National Center for Genome Resources, Santa Fe, NM.

Research Assistant, 1994-1997. Department of Biology, University of New Mexico, Albuquerque, NM.

Research Assistant, 1992-1996. Santa Fe Institute, Santa Fe, NM.

TEACHING AND RELATED EXPERIENCE

PROFESSIONAL SERVICE

P.O. Box 193
Santa Fe, NM 87504