Photo of Melissa A. Haendel, Ph.D.

Melissa A. Haendel Ph.D.

  •      (503) 407-5970
    • Associate Professor of Medical Informatics and Clinical Epidemiology School of Medicine
    • Co-Director, OHSU Library Library
    • Director of the Ontology Development Group Library
    • Biomedical Informatics Graduate Program School of Medicine

Melissa is co-director of the OHSU Library and the director of the Ontology Development Group and an Associate Professor in the Library and the Department of Medical Informatics and Clinical Epidemiology.

Major Responsibilities

Interim Co-Director of the Library Director of the Ontology Development Research Laboratory within the OHSU Library and Department of Medical Informatics and Epidemiology

Principal investigator of: 

The Monarch Initiative
The NCATS Data Translator
PCORI "Realization of a Standard of Care for Rare Diseases Using Patient-Engaged Phenotyping”

Development of ontologies and data standards

End-user requirements and user interface design and testing

Science of Science

Promotion of research reproducibility

Development of open science policies and practices

Areas of interest

  • When not working, Melissa is usually planting, harvesting, cooking, or eating food.

Education

  • B.A., Reed College, Portland Oregon United States 1991
  • Ph.D., University of Wisconsin, Madison Wisconsin United States 1999

Publications

Selected publications

  • Vasilevsky NA, Brush MH, Paddock H, Ponting L, Tripathy SJ, LaRocca GM, Haendel MA. (2013) On the reproducibility of science: unique identification of research resources in the biomedical literature.PeerJ 1:e148      

  • Meehan TF, Vasilevsky NA, Mungall CJ, Dougall DS, Haendel MA, Blake JA, Diehl AD. (2013) Ontology based molecular signatures for immune cell types via gene expression analysis. BMC Bioinformatics. 2013 Aug 30;14(1):263.

  • Haendel MA, Chesler EJ. Lost and found in behavioral informatics. (2012) Int Rev Neurobiol. 2012;103:1-18. doi:10.1016/B978-0-12-388408-4.00001-0.     

  • Nicole Vasilevsky, Tenille Johnson, Karen Corday, Carlo Torniai, Matthew Brush, Erik Segerdell, Melanie Wilson, Chris Shaffer, David Robinson and Melissa Haendel (2012) Research resources: curating the new eagle-i discovery system. Database Vol. 2012, bar067.            

  • Torniai, C., Brush, M., Vasilevsky, N., Segerdell, E., Wison, M., Johnson, T., Corday, K., Shaffer, C., and Haendel, M. (2011) Developing an application ontology for biomedical resource annotation and retrieval: Challenges and lessons learned. International Conference on Biomedical Ontology 2011; July 26–30, 2011; Buffalo, NY.   

  • Mungall CJ, Anderson D, Bandrowski A, Canada B, Chatyr-Aryamontri A, Cheng K, Conn PM, Dolinski K, Ellisman M, Eppig J, Grethe JS, Kemnitz J, Iadonato S, Larson SD, Magness C, Martone ME, Tyers M, Torniai C, Troyanskaya O, Turner J, Westerfield M, Haendel MA. (2011) An ontology-based approach to linking model organisms and resources to human diseases. Poster presentation at: International Conference on Biomedical Ontology 2011; July 26–30, 2011; Buffalo, NY.        

  • Mitchell S, Torniai C, Lowe, B, Corson-Rikert J, Wilson M, Ahmed M, Chen S, Ding Y, Rejack N, Haendel MA. (2011) Aligning research resource and researcher representation: the eagle-i and VIVO use case. Poster presentation at: International Conference on Biomedical Ontology 2011; July 26–30, 2011; Buffalo, NY.

  • Brush MH, Vasilevsky N, Torniai C, Johnson T, Shaffer C, Haendel MA. (2011) Developing a reagent application ontology within the OBO Foundry Framework. Poster presentation at: International Conference on Biomedical Ontology 2011; July 26–30, 2011; Buffalo, NY.

  • Mungall, C.J., Gkoutos, G.V., Smith, C.L., Haendel, M.A., Lewis, S.E., and Ashburner, M. (2010) Integrating Phenotype Ontologies across Multiple Species. Genome Biol. 2010 Jan 8;11(1):R2.        

  • Washington, N.L.*, Haendel, M.A.*, Mungall, C.J., Ashburner, M., Westerfield, M., and Lewis, S.L. (2009) Linking human disease to animal models using ontology-based phenotype annotation. PLoS Biol. 2009 Nov;7(11):e1000247. Epub 2009 Nov 24.                                                                     *These authors contributed equally to this manuscript.       

Publications

  • "Aligning research resource and researcher representation"   2011
  • "On the reproducibility of science" PeerJ  2013
  • "DSCAM" Human Molecular Genetics February 1998
  • "Developmental toxicity of the dithiocarbamate pesticide sodium metam in Zebrafish" Toxicological Sciences October 2004
  • "The zebrafish anatomy and stage ontologies" Journal of Biomedical Semantics February 25 2014
  • "Linking human diseases to animal models using ontology-based phenotype annotation" PLoS Biology November 2009
  • "Leukaemia inhibitory factor (LIF) is functionally linked to axotrophin and both LIF and axotrophin are linked to regulatory immune tolerance" FEBS Letters January 31 2005
  • "The Human Phenotype Ontology" American Journal of Human Genetics  2015
  • "Cytoskeletal changes during neurogenesis in cultures of avian neural crest cells" Journal of Neurocytology  1996
  • "A Unified Anatomy Ontology of the Vertebrate Skeletal System" PLoS One December 10 2012
  • "Dealing with data" PLoS Biology May 2012
  • "Uberon, an integrative multi-species anatomy ontology" Genome Biology January 31 2012
  • "An F-domain introduced by alternative splicing regulates activity of the zebrafish thyroid hormone receptor α" General and Comparative Endocrinology January 1 2008
  • "OBO-Edit - An ontology editor for biologists" Bioinformatics August 15 2007
  • "Lost and Found in Behavioral Informatics" International Review of Neurobiology  2012
  • "Ontology based molecular signatures for immune cell types via gene expression analysis" BMC Bioinformatics August 30 2013
  • "An overview of the BioCreative 2012 Workshop Track III" Database : the journal of biological databases and curation  2013
  • "Use of Model Organism and Disease Databases to Support Matchmaking for Human Disease Gene Discovery" Human Mutation October 1 2015
  • "PhenomeCentral" Human Mutation October 1 2015
  • "Improved exome prioritization of disease genes through cross-species phenotype comparison" PCR Methods and Applications February 2014
  • "Summarizing and visualizing structural changes during the evolution of biomedical ontologies using a Diff Abstraction Network" Journal of Biomedical Informatics August 1 2015
  • "Modularization for the cell ontology"   2011
  • "Gene trapping in embryonic stem cells in vitro to identify novel developmentally regulated genes in the mouse." Methods in molecular biology (Clifton, N.J.)  2000
  • "An ontology-based approach to linking model organisms and resources to human diseases"   2011
  • "Phenotype ontologies" Trends in Ecology and Evolution July 2007
  • "Use of animal models for exome prioritization of rare disease genes" Orphanet Journal of Rare Diseases November 11 2014
  • "The Resource Identification Initiative" F1000Research May 29 2015
  • "The Human Phenotype Ontology project" Nucleic Acids Research January 1 2014
  • "Nose to tail, roots to shoots" Journal of Biomedical Semantics August 11 2014
  • "Next-generation diagnostics and disease-gene discovery with the Exomiser" Nature Protocols December 1 2015

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