Project Manager, Biocurator and Ontologist
skype ID: nicolevasilevsky
Nicole assists with project management of the major projects and activities of the Ontology Development Group, as well as participating in biocuration and ontology development. Her major duties include:
• Development of ontologies and best practices for representation and query of biomedical resources, model organisms and clinical specimens
• Project management for the BD2K Open Educational Resources and Skills Courses
• Biocuration for the Monarch Initiative and Colorado Richly Annotated Full Text (CRAFT) Corpus
PhD, Cell biology (2009) Oregon Health & Science University, Portland, OR
BA, Biology (2000) Reed College, Portland, OR
• Post-doctoral research fellow (2009-2010) Dr. Kate Morris, Cancer Research, Legacy Health Research, Portland, OR
• Graduate Research Assistant, (2003 – 2009) Dr. Andrew Weinberg, Earle A. Chiles Research Institute, Providence Portland Medical Center, Portland, OR
• Research Assistant (2001-2002) Dr. Mark Garzotto, VA Medical Center, Portland, OR
• Graduate Research Assistant (2001) Dr. Jan Gorter, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
• Undergraduate Research Assistant (1999-2000) Dr. Glen Kisby, Center for Research on Occupational and Environmental Toxicology, Oregon Health and Science University, Portland, OR
• Adjunct faculty (2011 – Present) Master of Science in Integrative Medicine Research program, National College of Natural Medicine, Portland, OR
• Part-time faculty (2009-2010) Bioscience Technology, Portland Community College, Portland, OR
Select Publications and Presentations
- Bone WP, Washington NL, Buske OJ, Adams DR, Davis J, Draper D, Flynn ED, Girdea M, Godfrey R, Golas G, Groden C, Jacobsen J, Köhler S, Lee EM, Links AE, Markello TC, Mungall CJ, Nehrebecky M, Robinson PN, Sincan M, Soldatos AG, Tifft CJ, Toro C, Trang H, Valkanas E, Vasilevsky N, Wahl C, Wolfe LA, Boerkoel CF, Brudno M, Haendel MA, Gahl WA, Smedley D. Computational evaluation of exome sequence data using human and model organism phenotypes improves diagnostic efficiency. Genetics in medicine : official journal of the American College of Medical Genetics, 2015 Nov 12. doi: 10.1038/gim.2015.137.
- Tudor Groza, Sebastian Köhler, Dawid Moldenhauer, Nicole Vasilevsky, Gareth Baynam, Tomasz Zemojtel, Lynn Marie Schriml, Warren Alden Kibbe, Paul Schofield, Tim Beck, Drashtti Vasant, Anthony J Brookes, Andreas Zankl, Nicole L Washington, Christopher J Mungall, Suzanna E Lewis, Melissa Haendel, Helen Parkinson, Peter N Robinson. The Human Phenotype Ontology: Semantic unification of common and rare disease. The American Journal of Human Genetics (2015), http://dx.doi.org/10.1016/j.ajhg.2015.05.020.
- Haendel MA, Vasilevsky N, Brush M, Hochheiser HS, Jacobsen J, Oellrich A, Mungall CJ, Washington N, Köhler S, Lewis SE, Robinson PN, Smedley D. Disease insights through cross-species phenotype comparisons. Mamm Genome. 2015 Jun 20. PMID: 26092691.
- Bandrowski A, Brush M, Grethe JS, Haendel MA, Kennedy DN, Hill S, Hof PR, Martone ME, Pols M, Tan S, Washington N, Zudilova-Seinstra E, Vasilevsky N. The Resource Identification Initiative: A cultural shift in publishing [version 2;referees: 2 approved] F1000Research 2015, 4:134 (doi: 10.12688/f1000research.6555.2) http://f1000research.com/articles/4-134/v2
- Lions, Tigers, and Gummi Bears: Springing Towards Effective Engagement with Research Data Management. Vasilevsky N, Wirz J, Champieux R, Hannon T, Laraway B, Banerjee K, Shaffer C and Haendel M. (2014).Scholar Archive. Paper 3571.
- The Role of Libraries in Data Management and Curation. Vasilevsky N. American Library Association, Las Vegas, NV, June 2014.
- 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 http://dx.doi.org/10.7717/peerj.148
- 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.
- Vasilevsky N, Wirz J and Haendel M. Data Management. SPARC, Portland, OR. May 2013.
- Nicole Vasilevsky, Carlo Torniai, Melissa Haendel and Chris Shaffer (2012) The semantic web is changing research and library science. Presentation at the Oregon Library Association Meeting. April 27, 2012; Bend, OR.
- 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.
- Brush M, Vasilevsky N, Torniai C, Johnson T, Shaffer C, and Haendel M. (2011) Developing a Reagent Application Ontology within the OBO Foundry Framework. International Conference on Biomedical Ontology 2011; July 26–30, 2011; Buffalo, NY.
- Frost HR, Hadden L, Bourges-Waldegg D, MacFadden D, Haendel M, Torniai C, Vasilevsky N, Thompson P. (2011) Discovering biomedical research resources in text: an ontology-driven approach using curated data for incremental retraining. AMIA Summit on Translational Bioinformatics, San Francisco, CA.
- Vasilevsky NA, Ruby CE, Hurlin PJ, Weinberg AD. OX40 engagement stabilizes Mxd4 and Mnt protein levels in antigen-stimulated T cells leading to an increase in cell survival. Eur J Immunol. 2011 Apr; 41(4):1024-34. Eur J Immunol. 2011 Apr;41(4):1024-34.
• International Conference on Biomedical Ontology fellowship 2011
• International Society for Biocuration 2011-present
• Association of Biomolecular Resource Facilities 2011
• Portland Community College Bioscience Technology Advisory Board 2009-present
• Member, Oregon Bioscience Association 2008-present
• American Association of Cancer Research 2010