College of Arts & Sciences Biology

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Paula Mabee

Paula Mabee
Professor
Biology, College of Arts & Sciences
UCL Churchill-Haines Labs 169B
Phone: 605-677-6171
Education:
  • Ph D, Zoology, Duke University, 1987
  • BA, Biology, Religion, St. Olaf College, 1981
Grants:
  • Supplement: NSF 1062542 (NSF - ABI "Ontology-enabled reasoning across phenotypes from evolution and model organisms", National Science Foundation
  • RCN: Phenotype Ontology Research Coordination Network , National Science Foundation (NSF-DEB-0956049), (2010 - 2015)
  • National Science Foundation: Ontology-enabled reasoning across phenotypes from evolution and model organisms, National Science Foundation DBI-1062542, (2011 - 2015)
  • Linking evolution to genomics using phenotype ontologies, National Science Foundation (NSF- DBI 0641025), (2007 - 2011)
  • Collaborative Research: Systematics of Cypriniformes, Earth’s Most Diverse Clade of Freshwater Fishes, National Science Foundation (NSF- EF-0431326), (2004 - 2010)
Publications:
  • Haendel, M. A., Balhoff, J. P., Bastian, F. B., Blackburn, D. C., Blake, J. A., Bradford, Y., Comte, A., Dahdul, W., Druzinsky, R., Hayamizu, T., Ibrahim, N., Lewis, S., Mabee, P., Niknejad, A., Robinson-Rechavi, M., Sereno, P., Mungall, C., , , , Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon, Journal of Biomedical Semantics.
  • Druzinsky, R. E., Mungall, C., Haendel, M., Lapp, H., Mabee, P., (2013), What is an anatomy ontology? , The Anatomical Record, vol. 296, iss. 12, pp. 1797-1799.
  • Arighi, C. N., et, a., Mabee, P., , (2013), An overview of the BioCreative 2012 Workshop Track III: Interactive Text Mining Task, Database , vol. 2013.
  • Midford, P. E., Dececchi, T. A., Balhoff, J. P., Dahdul, W. M., Ibrahim, N., Lapp, H., Lundberg, J. G., Mabee, P., Sereno, P., Westerfield, M., Vision, T. J., , , (2013), The Vertebrate Taxonomy Ontology: A framework for reasoning across model organism and species phenotypes. , Journal of Biomedical Semantics, vol. 4, iss. 1, p. 34.
  • Dahdul, W. M., Cui, H., Mabee, P., Mungall, C. J., Osumi-Sutherland, D., Walls, R., Haendel, M. A., Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology, Journal of Biological Semantics, p. 23.
  • Mabee, P., Deans, A., Huala, E., Lewis, S., (2012), Phenotype Ontology Research Coordination Network meeting report: creating a community network for comparing and leveraging phenotype-genotype knowledge across species, Standards in Genomic Sciences , vol. 6, pp. 440-443.
  • Mabee, P., Balhoff, J. P., Dahdul, W. M., Lapp, H., Midford, P., Vision, T., Westerfield, M., (2012), 500,000 fish phenotypes: The new informatics landscape of evolutionary and developmental skeletal biology, Journal of Applied Icthyology, vol. 28, iss. 3, pp. 300-305.
  • Grey, E. A., Mabee, P., (2012), Description of the gill-arch musculature of the quillback Carpoides cyprinus (Cypriniformes: Catostomidae) with a comparison to cyprinids, Journal of Morphology, vol. 273, pp. 909-918.
  • Engeman, J., Mabee, P., (2012), Segmentation and fusion on the midline: Basibranchial homologies in cypriniform fishes, Journal of Morphology, vol. 273, pp. 725-736.
  • Block, A. J., Mabee, P., , (2012), Development of the mandibular, hyoid, and gill arch skeleton in the Chinese barb Puntius semifasciolatus: comparisons of ossification sequences among Cypriniformes, Journal of Fish Biology, vol. 81, pp. 54-80.
  • Dahdul, W., Balhoff, J. P., Blackburn, D., Diehl, A., Melissa, H., Brian, H., Hilmar, L., John, L., Chris, M., Martin, R., Erik, S., Ceri, V., Matthew, V., Monte, W., Mabee, P., , (2012), A unified anatomy ontology of the vertebrate skeletal system, PLoS ONE, vol. 7, iss. 12, p. e51070 (10 pages).
  • Mabee, P., Grey, E., Arratia, G., Bogutskaya, N. G., Boron, A., Coburn, M. M., Conway, K. W., He, S., Naseka, A., Rios, N., Simons, A. M., Szlachciak, J., Wang, J., (2011), Gill arch and hyoid arch diversity and cypriniform phylogeny: Distributed integration of morphology and Web-based tools, Zootaxa, vol. 2877, pp. 1-40.
  • Mungall, C. J., Kothari, C. R., Balhoff, J. P., Dahdul, W. M., Lewis, S., Mabee, P., Midford, P. E., Vision, T. J., Westerfield, M., Lapp, H., The Ontology-Based Database: A knowledge management system for descriptive biological data , Database.
  • Mabee, P., (2011), Book Review: Development of Non-Teleost Fishes," edited by Yvette W. Kunz et al., Quarterly Review of Biology, vol. 86, iss. 1, p. 61.
  • Mabee, P., (2010), Vertebrate Anatomy Ontology, www.obofoundry.org/cgi-bin/detail.cgi?id=vertebrate_anatomy.
  • Mabee, P., (2010), A multifaceted view of evo-devo, Bioscience, vol. 60, iss. 7, pp. 555-556.
  • Dahdul, W. M., Balhoff, J. P., Engeman, J., Grande, T., Hilton, E. J., Kothari, C. R., Lapp, H., Lundberg, J. G., Midford, P. E., Vision, T. J., Westerfield, M., Mabee, P., (2010), Evolutionary characters, phenotypes and ontologies: curating data from the systematic biology literature, PLoS ONE, vol. 5, iss. 5, p. e10708.
  • Dahdul, W. M., Balhoff, J. P., Kothari, C. R., Lapp, H., Lundberg, J. G., Mabee, P., Midford, P. E., Westerfield, M., Vision, T. J., (2010), Phenex: Ontological annotation of phenotypic diversity, PLoS ONE, vol. 5, iss. 5, p. e10500.
  • Haendel, M. A., Neuhaus, F., Osumi-Sutherland, D. S., Mabee, P., Mejino, J. L., Mungall, C., Smith, B., (2009), CARO - The Common Anatomy Reference Ontology.
  • Engeman, J., Aspinwall, N., Mabee, P., (2009), Development of the pharyngeal arch skeleton in Catostomus commersoni (Teleostei: Cypriniformes, Journal of Morphology, iss. 270, pp. 291-305.
  • Dahdul, W. M., Lundberg, J. G., Midford, P. E., Balhoff, J. P., Lapp, H., Vision, T. J., Haendel, M. A., Westerfield, M., Mabee, P., (2009), The Teleost Anatomy Ontology: Anatomical representation for the genomics age., Systematic Biology, iss. 59, pp. 369-383.
Awards and Honors:
  • President's Award for Research Excellence , USD, 2009
  • AAAS Fellow for “Fundamental studies on the development and evolution of fishes” , AAAS, 2004
  • President’s Award for Innovation and Entrepreneurship, University of South Dakota, 2003
  • Belbas Larson teaching award nominee, University of South Dakota, 2002
  • Sally Richardson Award, Best Paper, ELHS/AFS, 1993
  • Environmental Biology Postdoctoral Fellowship , NSF, 1989
  • Research and Development Grant, Dalhousie University , 1989
  • Sally Richardson Award, Best Paper, ELHS/AFS, 1988
  • Honorable mention, Stoye Award; General Ichthyology, ASIH, 1987
  • Distinguished Undergraduate Teaching Award , Duke University, 1985
  • Doctoral Dissertation Improvement Grant , NSF, 1985
  • Honorable mention, Stoye Award: Genetics, Development, & Morphology, ASIH, 1985
  • Theodore Roosevelt Memorial Fund Grant, AMNH, 1985
  • Sigma Xi Grant-in-Aid of Research , Sigma Xi, 1984
  • Departmental Distinction in Biology , St. Olaf College , 1981
  • National Merit Scholar , 1977
  • Phi Beta Kappa, St. Olaf College, 1977
Presentations:
  • Lewis, S., Deans, A., Huala, E., Mabee, P. (2013, November). An in silico strategy for integration of big (phenotype) data. Presented at the Annual conference of the Taxonomic Database Working Group, Florence, Italy.
  • Balhoff, J. P., Dececchi, T. A., Mabee, P., Lapp, H. (2013, November). Semantic tools for aggregation of morphological characters across studies. Presented at the Annual conference of the Taxonomic Database Working Group, Florence, Italy.
  • Mabee, P., Dececchi, T. A., Ibrahim, N., Sereno, P., Balhoff, J. P. (2013, October). Aggregation of morphological characters across studies using an ontology-based phenotype approach. Presented at the Society of Vertebrate Paleontology, Annual Meeting, San Diego, CA .
  • Mabee, P. (2013, October). Phylogenetic mapping of morphology from multiple studies using ontologies: Insights, prospects, and challenges. .
  • Mabee, P. (2013, July). Comparative morphology is integrated with genetics and development in the Phenoscape Knowledgebase. Presented at the International Congress of Vertebrate Morphology (ICVM), Barcelona, Spain .
  • Catlett, J., Mabee, P., (2013, April). Your Inner Fin: Studying Zebrafish Pectoral Fin Development to Understand Human Forelimb Mutations. Presented at the Ideafest, Vermillion, SD.
  • Hanscom, J., Catlett, J., Mabee, P. (2013, April). Morphological Trends in Fin Reduction and Loss in Fishes. Presented at the Ideafest , Vermillion, SD.
  • Mabee, P. (2013, February). Introduction to phenotype ontologies. Presented at the The third annual summit of the Phenotype Ontology RCN, Durham, NC.
  • Dececchi, T. A., Mabee, P., , e., , Mabee, P., , , (2012, October). Phenoscape: Bridging the gap between fossils and genes. Presented at the Society of Vertebrate Paleontology, Annual Meeting, Raleigh, NC.
  • Mabee, P. (2012, August). Synthesis of evolutionary and developmental data for fishes using new informatics tools. Presented at the World Congress of Herpetology, Vancouver, BC, Canada.
  • Balhoff, J., Dahdul, W., Lapp, H., Mabee, P., Midford, P., Vision, T., Westerfield, M. (2012, June). The Phenoscape Knowledgebase: Integrating phenotypic data across taxonomy, from biodiversity to developmental genetics. Presented at the Data Integration in the Life Sciences, College Park, MD.
  • Cui, H., Mabee, P. (2012, April). Integration of Charaparser in the Phenoscape workflow. Presented at the BioCreative-2012 Workshop; Fifth International Biocuration Conference, Georgetown (Washington, D.C.).
  • Dahdul, W., Mabee, P., (2012, April). VAO: A backbone for the ontological representation of vertebrate musculoskeletal anatomy. Presented at the Fifth International Biocuration Conference, Georgetown (Washington, D.C.).
  • Mabee, P. (2011, December). An informatics basis for comparative anatomy at museums.
  • Mabee, P. (2011, November). Comparative anatomy for the genomics age: Informatics to reason across vertebrate evolutionary and developmental biology.
  • Mabee, P. (2011, April). 500,000 fish phenotypes: the new informatics landscape of evolutionary and developmental skeletal biology (Keynote talk). Presented at the Interdisciplinary Approaches in Fish Skeletal Biology, Tavira, Portugal.
  • Mabee, P. (2010, December). Presented at the NOTE: At least a dozen presentations were made in the past year where Mabee was a co-author with others in her research team. Only those presentations where Mabee conceived, wrote and delivered the presentation are listed below. .
  • Mabee, P. (2010, December). Newly Funded! Phenotype RCN (poster). Presented at the NSF Research Coordination Network Principle Investigator meeting, Arlington, VA.
  • Mabee, P. (2010, October). Phenoscape: Integration with ontologies. Presented at the Encyclopedia of Life/Hymenoptera Anatomy Ontology meeting , Raleigh, NC.
  • Mabee, P., Dahdul, W. M. (2010, July). New Tools for Study of Development and Evolution of the Fish Skeleton. Presented at the Joint Meeting of Ichthyologists and Herpetologists, Providence, RI.
  • Mabee, P. (2010, May). Linking phenotypes of species, mutants, and human diseases to genetics and evolution. Presented at the Sanford Health USD Biomedical Research Symposium, Vermillion, SD.
  • Engeman, J., Mabee, P. (2010, April). Homology of the posterior median skeletal elements of the gill arches in cypriniform fishes. Presented at the IdeaFest, Vermillion, SD.
  • Grey, E., Mabee, P. (2010, April). Cypriniform Gill Arches: Determining the homology of bone morphology using myology. Presented at the IdeaFest, Vermillion, SD.
  • Mabee, P., Zalud, A., Block, A. (2010, April). Development of the pharyngeal arch structures in Cypriniformes. Presented at the IdeaFest, Vermillion, SD.
  • Mabee, P. (2010, March). Phenoscape integration. Presented at the Collections Web Workshop II: New research opportunities emerging from integrating data across different taxonomic colletions, New Orleans, LA.
  • Mabee, P. (2010, March). Presented at the Informatics tools for integrating morphological data, Field Museum of Natural History, Chicago, IL.
  • Mabee, P. (2010, February). Phenoscape and use of the PATO ontology. Presented at the Phenotype and Trait Ontology Workshop, Rome, Italy.
  • Mabee, P. (2010, February). Phenoscape: species phenotypes, genes, development...and environment. Presented at the Locating Biology: The Development and Application of an Environment Ontology, Schloss Dagstuhl - Leibniz Center for Informatics, Germany.