Peter E. Midford
Address:
Department of Ecology and Evolutionary Biology
University of Kansas
2041 Haworth Hall
1200 Sunnyside Avenue
Lawrence, KS 66045
Telephone: 785-864-1768
Email: peteremidford@yahoo.com
Education
PhD Zoology, 1999
University of Wisconsin, Madison, WI
Advisor: Jack P. Hailman
MS Computer Science, 1987
Yale University, New Haven, CT
Advisor: Roger C. Schank
BS Mathematics, 1983
Harvey Mudd College, Claremont, CA
Professional
and Research Experience
2007-present: Adjunct
Research Associate University of Kansas.
Conducting research in phylogenetics and ontology construction.
2007-present: Ontology
curator, Phenoscape project
Construct, extend and maintain ontologies of teleost taxonomy and specimen
collections.
2006-2007: Research
Associate University of British Columbia.
Conducted research in phylogenetics.
2005: Contract
Bioinformatics Programmer.
Designed and implemented enhancements for the Mesquite Phylogeny package.
2004-2005: Short-term
Bioinformatics Programmer, University of Michigan Zoology Museum.
Designed and implemented web-interfaces to two biological specimen databases
and several utility programs for molecular evolution at the University of
Michigan.
2003: Staff
Programmer Cycorp, Austin TX.
Developed prototype of a trainable natural language parser and contributed to
construction of the Cyc knowledge base.
2001-2002: NSF
Bioinformatics Postdoctoral Fellow, University of Arizona.
Developed ontologies for behavior and phylogenetic comparative methods using
Mesquite.
2000: Post
doctoral position, Ruhr UniversitŠt Bochum.
Conducted experiments, and developed software related to pigeon courtship and
perception of biological motion.
1993-1999: Graduate
student programmer, University of Wisconsin - Madison.
Designed, implemented and extended "Phenotypic Diversity Analysis
Programs" for phylogenetic comparative methods along with several data
acquisition and editing programs.
1990-1999: Doctoral
student, University of Wisconsin Ð Madison.
Conducted dissertation research on social learning in Florida scrub jays at the
Archbold Biological Station, Lake Placid FL. Funded by fellowship, teaching assistantship, and research
assistantship.
1986-1990: Software
Engineer, Hughes Simulation Systems, West Covina CA.
Implemented and lead enhancement effort on graphical front end for an automated
computer software generation tool.
1984-1985: Graduate
student, Yale University.
Contributed to group research projects in models of human learning and
automatic generation of explanations by computer.
1983: Undergraduate
senior research, Harvey Mudd College.
Built simulation model of early visual processing.
1982-1983: Undergraduate
research assistant in linguistics, Pitzer College.
Assisted in data analysis and. development of a model of human understanding of
linguistic understanding of terms for social roles.
Publications
Maddison, W. P., Midford, P. E., and Otto, S. P. 2007.
Estimating a binary character's effect on speciation and extinction. Systematic
Biology 56:701-710.
Ramirez, M. J., Coddington, J. A., Maddison, W. P.,
Midford P. E., Prendini, L., Miller, J., Griswold, C. E., Hormiga, G.,
Sierwald, P., Scharff, N., Benjamin, S. P., and Wheeler, W. C. 2007. Linking of
digital images to phylogenetic data matrices using a morphological ontology. Systematic
Biology 56:283-294.
Ives, A. R., Midford P. E., and Garland, T., Jr. 2007.
Within-species variation and measurement error in phylogenetic comparative
methods. Systematic Biology
56:252-270.
Midford, P. E., 2004.
Ontologies for Behavior. Bioinformatics 20:3700-3701.
Midford, P. E., 2002.
Robots aren't the only physical models. Behavioral and Brain Sciences 24:1069-1070.
Midford, P. E., Hailman,
J. P., and Woolfenden, G. E. 2000. Social learning of a novel foraging patch in
families of free-living Florida scrub-jays. Animal Behaviour 59:1199-1027.
Garland, T., Jr,
Midford, P. E., and Ives, A. R., 1999. An introduction to phylogenetically
based statistical methods, with a new method for confidence intervals on
ancestral values. American Zoologist 39:374-388.
Midford, P. E., 1998.
HighÐLevel social learning in apes: imitation or observationÐassisted planning?
Behavioral
and Brain Sciences
21:698-699.
Midford, P. E., 1993.
Cultural transmission is more than cultural learning. Behavioral and Brain Sciences 16:529-530.
Publications
in Preparation
Midford, P. E., Balhoff, J. and Vision, T. in prep. TTO: An ontology for teleost taxonomy.
Midford, P. E., and Hailman, J. P., in prep. Juvenile Florida Scrub-jays fail to retain.
Midford, P. E., Maddison, W. P., and Otto, S. P. in prep. Detecting and distinguishing biases in character change, speciation and extinction using the BiSSE method.
Software
Publications
"PDAP:PDTREE"
package for Mesquite, Version 1.15 November 2008. P. E. Midford, T. Garland, Jr.
and W. Maddison. Available at: http://mesquiteproject.org/pdap_mesquite/
This package has been cited over 130 times in publications listed in Web of
Scicnce
ÒOwlWatcherÓ
0.036, May 2008. P. E. Midford.
ÒDiverseÓ module for Mesquite, September
2007. P. E. Midford, and W
Maddison.
ÒCorrelÓ module for Mesquite, May 2006.
Included in Mesquite 1.1 and later versions. This package has been cited in a
publication listed in Web of Science
ÒEKBÓ demonstration ontology for
behavior. Available at
http://mesquiteproject.org/ontology/
"Phenotypic
Diversity Analysis ProgramsÓ (PDAP) Distributed privately and Version 6.0
Copyright 25 September 2001 by T.
Garland, Jr., J. A. Jones, A. W. Dickerman, P. E. Midford, and R. D’az-Uriarte.
Available from T. Garland (tgarland@ucr.edu).
Garland, T., Ives, A. R., Midford, P. E. 2004. Within-species variation and measurement error in phylogenetic comparative methods. Integrative and Comparative Biology, 44:556.
Midford, P. E. 2002.
Ontology as ethogram: Knowledge representation for behavior. Measuring
Behavior 2002 (Amsterdam, The Netherlands), p.176. Poster Abstract.
Jokisch, D., Midford, P.
E., & Troje, N. F. 2001. Biological motion as a cue for the perception of
absolute size. Journal of Vision, 1(3), 357a.
Invited talks
2008: ÒOntologies
and the Rebirth of the EthogramÓ Department of Biology, University of South
Dakota
2008: ÒNames,
Ranks, Clades, and Taxonomy OntologiesÓ Workshop on Ontologies in Evolutionary
Biology, Evolution 2008, Minneapolis MN
2007: ÒThe
two trees: Phylogeny meets ontologyÓ Department of Zoology, Southern Illinois
University, Carbondale IL
2003: ÒRepresenting
and analyzing behavior using ontologiesÓ Rat Genome Database project, Medical
College of Wisconsin, Milwaukee WI
2009: ÒDo
optimization issues limit the power of BiSSE analyses: A preliminary
comparisonÓ Evolution 2009 Moscow ID
2008: ÒTaxonomic
ontologies: Bridging phylogenetic and taxonomic historyÓ TDWG 2008, Fremantle,
Western Australia
2007: ÒUsing
ontologies to answer comparative behavior questions: Three approachesÓ Animal
Behavior Society, Burlington, VT
2004: ÒOntologies
and the comparative methodÓ Evolution 2004, Fort Collins, CO
2002: ÒOntology
as an ethogram: A case study using jumping spider courtshipÓ Animal Behavior
Society, Bloomington, IN
2002: ÒRepresenting
behavior: A case study using Habronattus courtshipÓ American Arachnology Society,
Riverside, CA
2002: ÒThe
ethogram as an ontologyÓ Gene Ontology Users Group, Tucson, AZ
1998: ÒTraining
and retention of a simple foraging task by the Florida scrub-jayÓ Animal
Behavior Society, Carbondale, IL
1998: ÒTraining
and retention of a simple foraging task by the Florida scrub-jayÓ North American
Ornithological Conference, St. Louis, MO
1996: ÒSocial
learning and tradition in the Florida scrub-jayÓ American Ornithological Union
114th stated meeting, Boise, ID
1996: ÒSocial
learning and tradition in the Florida scrub-jayÓ Animal Behavior Society,
Flagstaff, AZ
1994: ÒTradition
and social learning in the Florida scrub-jayÓ Midwest Animal Behavior
Conference, Carbondale, IL
Conference Posters
2008: ÒOntology
patterns for behavior: From counting to annotatingÓ Congress of the
International Society for Behavioral Ecology 2008, Ithaca, NY.
2008: ÒLinking
evolutionary morphology to genomics using ontologiesÓ Evolution 2008,
Minneapolis, MN (with multiple co-authors)
2008: ÒUsing
context dependent methods and ontologies to address comparative questions in
Animal BehaviorÓ Evolution 2008, Minneapolis, MN
2007: ÒLinking
evolution to genomics using phenotype ontologiesÓ Biocurator meeting 2007, San
Jose CA (with multiple co-authors)
2006: ÒOwlwatcher:
An ontology-based tool for collecting behavior dataÓ Animal Behavior
Society, Snowbird UT
2001: ÒOntologies
for the study of behaviorÓ Animal Behavior Society, Corvalis OR
2001: ÒThe
development of an ontology for behavior and its application to comparative
studiesÓ Evolution 2001, Knoxville, TN
1998: ÒSocial learning the Florida scrub-jay: A field studyÓ Napoli Social Learning Conference, Naples Italy
1996: ÒDo
Florida scrub-jays learn the concept center-ofÓ Symposium on animal
cognition preceding the Animal Behavior Society meeting, Flagstaff, AZ
2008: OBO (Open Biomedical Ontologies) relations meeting, Denver CO.
2007: Evoinformatics working group, NESCent, Durham NC.
2006: Second Fish Evolution Database Workgroup meeting, NESCent, Durham NC.
2005: Behavior
MetaData II, Ithaca, NY
2004: Behavior
MetaData I, Ithaca, NY
2002: Ethoinformatics,
Bloomington, IN
2001: Evolution
Synthesis Center I, Arlington, VA (rapporteur)
2004: Designed
and taught computer literacy courses (e.g., Introduction to the Internet, Power
Point) to adult students in Austin TX.
2001-2002: Tutored
and taught adult students in GED math course in Tucson AZ.
1991-1999: As
graduate student served as teaching assistant and guest lecturer in courses
including Evolution (3x), Animal Behavior, Animal Behavior Lab, Ornithology
Lab, Non-majors Ecology, Introductory Zoology, Introductory Zoology Lab (3x).
2009: Google
summer of code Ð Mentored Kasia Hayden in development and initial release of a
Mesquite-based viewer for ontology-based annotations of cells in character
matrices
2008: Google
summer of code Ð Mentored Mathew Ackermann in development and initial release
of PDSIM, an implementation of PDSIMUL (part of PDAP) for Mesquite
Evolution (2009,2008x2,2007,2002,2001)
Integrative and Comparative Biology (2008)
Journal of Theoretical Biology (2008)
Systematic Biology (2009x2,2007)
IEEE-BIBE (International Conference on BioInformatics and BioEngineering) (2007)
American Naturalist (2007)
Evolution and Development (2007)
Journal of Comparative Psychology (1999,1998,1996)
Awards
and Fellowships
2001-2002: National
Science Foundation Bioinformatics Postdoctoral Fellowship
1996: John
Emlen Memorial Award, Department of Zoology, University of Wisconsin Ð Madison
1993: John
Jefferson Davis summer fellowship, Department of Zoology, University of
Wisconsin Ð Madison
1990-1991: University
Fellowship, University of Wisconsin Ð Madison
1990: Hughes
Simulation Systems Technical Excellence award for ÒModel Builder DebuggerÓ
software project
1983-1985: Departmental
Fellowship, Department of Computer Science, Yale University
Sigma Xi, Animal Behavior Society, Society for
Integrative and Comparative Biology, TDWG, American Association for Artificial
Intelligence
Other
Service
2008-2009: Ethosource
advisory board