Paula Mabee

Paula Mabee

Professor

BIOLOGY

Churchill-Haines Labs 169B

Phone: (605) 677-6171

Email: Paula.Mabee@usd.edu

Education:

  • Ph D, Zoology, Duke University, 1987
  • BA, Biology, Religion, St. Olaf College, 1981

Grants:

  • National Science Foundation: Ontology-enabled reasoning across phenotypes from evolution and model organisms, National Science Foundation DBI-1062542. Grant Role: Supporting. (2011 - 2016)
  • RCN: Phenotype Ontology Research Coordination Network, National Science Foundation (NSF-DEB-0956049). Grant Role: Supporting. (2010 - 2016)
  • Linking evolution to genomics using phenotype ontologies, National Science Foundation (NSF- DBI 0641025). Grant Role: Principal. (2007 - 2011)
  • Collaborative Research: Systematics of Cypriniformes, Earth's Most Diverse Clade of Freshwater Fishes, National Science Foundation (NSF- EF-0431326). Grant Role: Principal. (2004 - 2010)

Publications:

Citations listed below are presented in a standardized, modified format for display purposes only. They do not necessarily reflect the preferred style and conventions of the faculty member or discipline.

  • Dececchi, Thomas A., Mabee, Paula, and , David. Comparing the phenomic content of monographs and evolutionary matrices, e0155680. Vol. 11, Iss. 5. PLOS One, 2016. (DOI: 10.1371/journal.pone.0155680)
  • Druzinsky, Robert E., Balhoff, James P., Crompton, Alfred W., Done, James, German, Rebecca, Haendel, Melissa A., Herrel, Anthony, Herring, Susan W., Lapp, Hilmar, Mabee, Paula M., Muller, Hans-Michael, Mungall, Christopher J., Sternberg, Paul W., Van Auken, Kimberly, Vinyard, Christopher J., Williams, Susan H., Wall, Christine E., , , and . Muscle logic: New knowledge resource for anatomy enables comprehensive searches of the literature on the feeding muscles of mammals, e0149102. Vol. 11, Iss. 2. Plos One, 2016. (DOI: 10.1371/journal.pone.0149102)
  • Thessen, Anne E., Bunker, Daniel E., Buttigieg, Pier L., Cooper, Laurel D., Dahdul, Wasila M., Domisch, Sami, Franz, Nico M., Jaiswal, Pankaj, Lawrence-Dill, Carolyn J., Midford, Peter E., Mungall, Christopher J., Ramírez, Martin J., Specht, Chelsea D., Vogt, Lars, Vos, Rutger A., Walls, Ramona L., White, Jeffrey W., Zhang, Guanyang, Deans, Andrew R., Huala, Eva, Lewis, Suzanna E., and Mabee, Paula M.. Emerging semantics to link phenotype and environment. Vol. 3:e1470. PeerJ, 2015. (DOI: https://doi.org/10.7717/peerj.1470)
  • Cui, Hong, Dahdul, Wasila, Dececchi, Thomas A., Ibrahim, Nizar, Mabee, Paula, Balhoff, James P., and Gopalakrishnan, H. CharaParser+EQ: Performance Evaluation without Gold Standard. Vol. 51. Proceedings of the 78th Annual Meeting of the Association for Information Science and Technology Annual (ASIS&T), 2015.
  • Edmunds, Richard C., Su, Baofeng, Balhoff, James P., Eames, B F., Dahdul, Wasila M., Lapp, Hilmar, Lundberg, John G., Vision, Todd J., Dunham, Rex A., Mabee, Paula, and Westerfield, Monte. Phenoscape: Identifying candidate genes for evolutionary phenotypes, 13-24. Vol. 33, Iss. 1. Molecular Biology and Evolution, 2015. (DOI: doi: 10.1093/molbev/msv223)
  • Manda, Prashanti, Balhoff, James P., Lapp, Hilmar, Mabee, Paula, and Vision, Todd J.. Using the Phenoscape Knowledgebase to relate genetic perturbations to phenotypic evolution, 561-571. Vol. 53, Iss. 8. Genesis, 2015. (DOI: http://dx.doi.org/10.1002/dvg.22878)
  • Balhoff, James P., Manda, Prashanti, Lapp, Hilmar, Mabee, Paula, and Vision, Todd J.. Connecting genes with evolutionary knowledge using semantic similarity and ancestral profiles of variation, 1. Bio-ontologies SIG at Intelligent Systems for Molecular Biology (ISMB) 2015, 2015.
  • Dahdul, Wasila, Dececchi, Thomas A., Ibrahim, Nizar, Lapp, Hilmar, and Mabee, Paula. Moving the mountain: Analysis of the effort required to transform comparative anatomy into computable anatomy, bav040. Iss. 2015. Database, 2015. (DOI: 10.1093/database/bav040)
  • Dececchi, Thomas A., Balhoff, James, Lapp, Hilmar, and Mabee, Paula. Toward Synthesizing Our Knowledge of Morphology: Using Ontologies and Machine Reasoning to Extract Presence/Absence Evolutionary Phenotypes across Studies, 936-952. Vol. 64, Iss. 6. Systematic Biology, 2015. (DOI: doi:10.1093/sysbio/syv031)
  • Deans, Andrew, RCN Consortium members, and Mabee, Paula M.. Finding our way through phenotypes. PLOS Biology, 2015. (DOI: 10.1371/journal.pbio.1002033)
  • Dahdul, Wasila M., Cui, Hong, Mabee, Paula, Mungall, Chris J., Osumi-Sutherland, David, Walls, Ramona, and Haendel, Melissa. Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology, 21. Vol. 5. Journal of Biological Semantics , 2014. (DOI: 10.1186/2041-1480-5-34)
  • Haendel, Melissa A., Balhoff, James P., Bastian, Frederic B., Blackburn, David C., Blake, Judith A., Comte, A, Dahdul, Wasila, Hayamizu, Terry, Ibrahim, Nizar, and Mabee, Paula. Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon, 21. Vol. 5. Journal of Biomedical Semantics, 2014. (DOI: 10.1186/2041-1480-5-21)
  • Dahdul, Wasila, Balhoff, James, Dececchi, Thomas A., Lapp, Hilmar, Mabee, Paula, and Vision, T J.. Annotation of phenotypic diversity: decoupling data curation and ontology curation using Phenex, 45. Vol. 5. Journal of Biomedical Semantics, 2014. (DOI: 10.1186/2041-1480-5-45)
  • Mabee, Paula, Balhoff, James, Dececchi, Thomas A., and Lapp, Hilmar. Presence-absence reasoning for evolutionary phenotypes. International Society for Computational Biology (ISMB), 2014.
  • Druzinsky, Robert E., Mungall, Chris, Haendel, Melissa, Lapp, Hilmar, and Mabee, Paula. What is an anatomy ontology?, 1797-1799. Vol. 296, Iss. 12. The Anatomical Record, 2013. (DOI: doi/10.1002/ar.22805/)
  • Midford, Peter E., Dececchi, Thomas A., Balhoff, James P., Dahdul, Wasila M., Ibrahim, Nizar, Lapp, Hilmar, Lundberg, John G., Mabee, Paula, Sereno, Paul, Westerfield, Monte, Vision, Todd J., , and . The Vertebrate Taxonomy Ontology: A framework for reasoning across model organism and species phenotypes., 34. Vol. 4, Iss. 1. Journal of Biomedical Semantics, 2013. (DOI: doi:10.1186/2041-1480-4-34)
  • Arighi, C N., et, al, Mabee, Paula, and . An overview of the BioCreative 2012 Workshop Track III: Interactive Text Mining Task. Vol. 2013. Database , 2013. (DOI: 10.1093/database/bas056)
  • Dahdul, Wasila, Balhoff, James P., Blackburn, David, Diehl, Alex, Melissa, Haendel, Brian, Hall, Hilmar, Lapp, John, Lundberg, Chris, Mungall, Martin, Ringwald, Erik, Segerdell, Ceri, Van Slyke, Matthew, Vickaryous, Monte, Westerfield, Mabee, Paula, and . A unified anatomy ontology of the vertebrate skeletal system, e51070 (10 pages). Vol. 7, Iss. 12. PLoS ONE, 2012. (DOI: 10.1371/journal.pone.0051070 )
  • Mabee, Paula, Deans, Andy, Huala, Eva, and Lewis, Suzanna. Phenotype Ontology Research Coordination Network meeting report: creating a community network for comparing and leveraging phenotype-genotype knowledge across species, 440-443. Vol. 6. Standards in Genomic Sciences , 2012.
  • Mabee, Paula, Balhoff, James P., Dahdul, Wasila M., Lapp, Hilmar, Midford, Peter, Vision, Todd, and Westerfield, Monte. 500,000 fish phenotypes: The new informatics landscape of evolutionary and developmental skeletal biology, 300-305. Vol. 28, Iss. 3. Journal of Applied Icthyology, 2012.
  • Grey, Ericka A., and Mabee, Paula. Description of the gill-arch musculature of the quillback Carpoides cyprinus (Cypriniformes: Catostomidae) with a comparison to cyprinids, 909-918. Vol. 273. Journal of Morphology, 2012.
  • Engeman, Jeffrey, and Mabee, Paula. Segmentation and fusion on the midline: Basibranchial homologies in cypriniform fishes, 725-736. Vol. 273. Journal of Morphology, 2012.
  • Block, Alyssa J., Mabee, Paula, and . Development of the mandibular, hyoid, and gill arch skeleton in the Chinese barb Puntius semifasciolatus: comparisons of ossification sequences among Cypriniformes, 54-80. Vol. 81. Journal of Fish Biology, 2012.
  • Mabee, Paula, 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, and Wang, J. Gill arch and hyoid arch diversity and cypriniform phylogeny: Distributed integration of morphology and Web-based tools, 1-40. Vol. 2877. Zootaxa, 2011.
  • Mabee, Paula. Book Review: Development of Non-Teleost Fishes," edited by Yvette W. Kunz et al., 61. Vol. 86, Iss. 1. Quarterly Review of Biology, 2011. (DOI: 10.1086/658455)
  • Mabee, Paula. Vertebrate Anatomy Ontology. www.obofoundry.org/cgi-bin/detail.cgi?id=vertebrate_anatomy, 2010.
  • Mabee, Paula. A multifaceted view of evo-devo, 555-556. Vol. 60, Iss. 7. Bioscience, 2010. (DOI: doi:10.1525/bio.2010.60.7.13 )
  • 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, and Mabee, Paula. Evolutionary characters, phenotypes and ontologies: curating data from the systematic biology literature, e10708. Vol. 5, Iss. 5. PLoS ONE, 2010. (DOI: doi:10.1371/journal.pone.0010708 )
  • Dahdul, W M., Balhoff, J P., Kothari, C R., Lapp, H, Lundberg, J G., Mabee, Paula, Midford, P E., Westerfield, M, and Vision, T J.. Phenex: Ontological annotation of phenotypic diversity, e10500. Vol. 5, Iss. 5. PLoS ONE, 2010. (DOI: doi:10.1371/journal.pone.0010500)
  • Haendel, M A., Neuhaus, F, Osumi-Sutherland, D S., Mabee, Paula, Mejino, J L., Mungall, C, and Smith, B. CARO - The Common Anatomy Reference Ontology. In Anatomy Ontologies for Bioinformatics: Principles and Practice, edited by Albert Burger, Duncan Davidson and Richard Baldock..
  • Engeman, J, Aspinwall, N, and Mabee, Paula. Development of the pharyngeal arch skeleton in Catostomus commersoni (Teleostei: Cypriniformes, 291-305. Iss. 270. Journal of Morphology, 2009. (DOI: doi:10.1002/jmor.10688)
  • Dahdul, W M., Lundberg, J G., Midford, P E., Balhoff, J P., Lapp, H, Vision, T J., Haendel, M A., Westerfield, M, and Mabee, Paula. The Teleost Anatomy Ontology: Anatomical representation for the genomics age., 369-383. Iss. 59. Systematic Biology, 2009. (DOI: doi:10.1093/sysbio/syq013)
  • Dahdul, Wasila M., Cui, Hong, Mabee, Paula, Mungall, Christopher J., Osumi-Sutherland, David, Walls, Ramona, and Haendel, Melissa A.. Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology, 23. Journal of Biological Semantics.
  • Mungall, Chris J., Kothari, Carik R., Balhoff, James P., Dahdul, Wasila M., Lewis, Suzanna, Mabee, Paula, Midford, Peter E., Vision, Todd J., Westerfield, Monte, and Lapp, Hilmar. The Ontology-Based Database: A knowledge management system for descriptive biological data. Database.

Awards and Honors:

  • Richard and Sharon Cutler Faculty Award in Liberal Arts, 2014
  • 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:

  • Fernando, Pasan, Jackson, Laura, Zeng, Erliang, Mabee, Paula. A generic bioinformatics pipeline to integrate large-scale trait data with large phylogenies. Presented at the 2017 Great Lakes Bioinformatics Conference, Chicago, IL. (May 17, 2017)
  • Mabee, Paula, Dececchi, Thomas A., Lapp, Hilmar, Balhoff, James. Inference Expands Morphological Data: Filling in the "Unknown Knowns". Presented at the Evolution meetings, Austin, TX. (June 19, 2016)
  • Dahdul, Wasila, Mabee, Paula. How to Accelerate the Transformation of Comparative Anatomy into Computable Anatomy?. Presented at the Joint Meeting of Ichthyologists & Herpetologists, Reno, NV. (July 18, 2015)
  • Mabee, Paula. Progress in Comparative Morphology can be accelerated through Semantic Annotation. Presented at the Joint Meeting of Ichthyologists & Herpetologists, Reno, NV. (July 18, 2015)
  • Jackson, Laura M., Mabee, Paula. Automated Integration of Phenomics Data To Investigate Paired Fin Loss Across Teleost Fishes. Presented at the Joint Meeting of Ichthyologists & Herpetologists, Reno, NV. (July 17, 2015)
  • Balhoff, James P., Manda, Prashanti, Lapp, Hilmar, Mabee, Paula, Vision, Todd J.. Connecting genes with evolutionary knowledge using semantic similarity and ancestral profiles of variation. Presented at the Bio-ontologies SIG Phenotype Day at ISMB 2015, Dublin, Ireland. (July 11, 2015)
  • Mabee, Paula. Identification of Candidate Genes Involved in Fin/Limb Development and Evolution using Bioinformatic Methods.
  • Mabee, Paula, Dececchi, Thomas A., Blackburn, David. Matrix versus monograph: Comparison of phenotypic richness across data sources. Presented at the Society of Vertebrate Paleontology, Annual Meeting, Berlin, Germany. (November 8, 2014)
  • Mabee, Paula. Connecting evolutionary morphology and model organism genetics. Presented at the EuroEvoDevo conference, Vienna, Austria. (July 24, 2014)
  • Dahdul, Wasila M., Dececchi, Thomas A., Ibrahim, Nizar, Lapp, Hilmar, Mabee, Paula. Moving the mountain: How to transform comparative anatomy into computable anatomy?. Presented at the Evolution meetings, Raleigh, NC. (June 23, 2014)
  • Balhoff, James P., Dececchi, Thomas A., Lapp, Hilmar, Mabee, Paula. Synthetic morphological supermatrices: revealing unknown knowns and reducing missing data. Presented at the Evolution meetings, Raleigh, NC. (June 23, 2014)
  • Mabee, Paula. Big Anatomy: The new views from integrated anatomy, development, and genes. Presented at the Symposium: Anatomy ontologies: Bioinformatics in the anatomical sciences; American Association of Anatomists, Experimental Biology, San Diego, CA. (April 29, 2014)
  • Dececchi, Thomas A., Mabee, Paula, Balhoff, James P.. The modern character synthesis: Using semantic tools to aggregate morphological characters across studies. Presented at the Symposium: Anatomy ontologies: Bioinformatics in the anatomical sciences; American Association of Anatomists, Experimental Biology, San Diego, CA. (April 29, 2014)
  • Mabee, Paula. Introduction to phenotype and environment ontologies. Presented at the The fourth annual summit of the Phenotype Ontology RCN, Biosphere 2, Oracle, AZ. (February 21, 2014)
  • Lewis, Suzanna, Deans, Andrew, Huala, Eva, Mabee, Paula. An in silico strategy for integration of big (phenotype) data. Presented at the Annual conference of the Taxonomic Database Working Group, Florence, Italy. (November 1, 2013)
  • Balhoff, James P., Dececchi, T A., Mabee, Paula, Lapp, Hilmar. Semantic tools for aggregation of morphological characters across studies. Presented at the Annual conference of the Taxonomic Database Working Group, Florence, Italy. (November 1, 2013)
  • Mabee, Paula, Dececchi, T A., Ibrahim, Nizar, Sereno, Paul, Balhoff, James P.. Aggregation of morphological characters across studies using an ontology-based phenotype approach. Presented at the Society of Vertebrate Paleontology, Annual Meeting, San Diego, CA. (October 31, 2013)
  • Mabee, Paula. Phylogenetic mapping of morphology from multiple studies using ontologies: Insights, prospects, and challenges..
  • Mabee, Paula. Comparative morphology is integrated with genetics and development in the Phenoscape Knowledgebase. Presented at the International Congress of Vertebrate Morphology (ICVM), Barcelona, Spain. (July 11, 2013)
  • Mabee, Paula. Introduction to phenotype ontologies. Presented at the The third annual summit of the Phenotype Ontology RCN, Durham, NC. (February 25, 2013)
  • Dececchi, Thomas A., Mabee, Paula, , et al., , Mabee, Paula, , , . Phenoscape: Bridging the gap between fossils and genes. Presented at the Society of Vertebrate Paleontology, Annual Meeting, Raleigh, NC. (October 18, 2012)
  • Mabee, Paula. Synthesis of evolutionary and developmental data for fishes using new informatics tools. Presented at the World Congress of Herpetology, Vancouver, BC, Canada. (August 10, 2012)
  • Balhoff, James, Dahdul, Wasila, Lapp, Hilmar, Mabee, Paula, Midford, Peter, Vision, Todd, Westerfield, Monte. 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. (June 28, 2012)
  • Cui, Hong, Mabee, Paula. Integration of Charaparser in the Phenoscape workflow. Presented at the BioCreative-2012 Workshop; Fifth International Biocuration Conference, Georgetown (Washington, D.C.). (April 4, 2012)
  • Dahdul, Wasila, Mabee, Paula, . VAO: A backbone for the ontological representation of vertebrate musculoskeletal anatomy. Presented at the Fifth International Biocuration Conference, Georgetown (Washington, D.C.). (April 3, 2012)
  • Mabee, Paula. An informatics basis for comparative anatomy at museums.
  • Mabee, Paula. Comparative anatomy for the genomics age: Informatics to reason across vertebrate evolutionary and developmental biology.
  • Mabee, Paula. 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. (April 26, 2011)
  • Mabee, Paula. 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. . (December 31, 2010)
  • Mabee, Paula. Newly Funded! Phenotype RCN (poster). Presented at the NSF Research Coordination Network Principle Investigator meeting, Arlington, VA. (December 3, 2010)
  • Mabee, Paula. Phenoscape: Integration with ontologies. Presented at the Encyclopedia of Life/Hymenoptera Anatomy Ontology meeting , Raleigh, NC. (October 16, 2010)
  • Mabee, Paula, Dahdul, Wasila M.. New Tools for Study of Development and Evolution of the Fish Skeleton. Presented at the Joint Meeting of Ichthyologists and Herpetologists, Providence, RI. (July 11, 2010)
  • Mabee, Paula. Phenoscape integration. Presented at the Collections Web Workshop II: New research opportunities emerging from integrating data across different taxonomic colletions, New Orleans, LA. (March 26, 2010)
  • Mabee, Paula. Presented at the Informatics tools for integrating morphological data, Field Museum of Natural History, Chicago, IL. (March 19, 2010)
  • Mabee, Paula. Phenoscape and use of the PATO ontology. Presented at the Phenotype and Trait Ontology Workshop, Rome, Italy. (February 27, 2010)
  • Mabee, Paula. 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. (February 22, 2010)