Biocurator and Ontologist
Research Assistant Professor
skype ID: nicolevasilevsky
Major Responsibilities• Development of ontologies and best practices for representation and query of biomedical resources, model organisms and clinical specimens
• Curriculum development and instruction for the BD2K Open Educational Resources and Skills Courses and the OHSU Library Data Science Institute
• 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
- Biocurator and Ontologist (2010-prsent) Melissa Haendel, Oregon Health &Science University, Portland, OR
- Post-doctoral research fellow (2009-2010) Kate Morris, Cancer Research, Legacy Health Research, Portland, OR
- Graduate Research Assistant (2003 –2009) Andrew Weinberg, Earle A. Chiles Research Institute, Providence Portland Medical Center, Portland, OR
- Research Assistant (2001-2002) Mark Garzotto, VA Medical Center, Portland, OR
- Graduate Research Assistant (2001) Jan Gorter, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
- Undergraduate Research Assistant (1999-2000) 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 University of Natural Medicine, Portland, OR
- Part-time faculty (2009-2010) Bioscience Technology, Portland Community College, Portland, OR
A full list of publications is available here.
- NA Vasilevsky, J Minnier, MA Haendel, RE Champieux. Reproducible and Reusable Research: Are Journal Data Sharing Policies Meeting the Mark? PeerJ. PubMed:28462024
- Sebastian Kohler, Nicole A. Vasilevsky, ..., Peter Robinson. The Human Phenotype Ontology in 2017. Nucleic Acids Research, Volume 45, Issue D1, 04 January 2017, Pages D865-D876.
- McMurry JA, Köhler S, Washington NL, Balhoff JP, Borromeo C, Brush M, Carbon S, Conlin T, Dunn N, Engelstad M, Foster E, Gourdine JP, Jacobsen JO, Keith D, Laraway B, Xuan JN, Shefchek K, Vasilevsky NA, Yuan Z, Lewis SE, Hochheiser H, Groza T, Smedley D, Robinson PN, Mungall CJ, Haendel MA. Navigating the Phenotype Frontier: The Monarch Initiative. Genetics. 2016 Aug;203(4):1491-5. doi: 10.1534/genetics.116.188870.
- Diehl AD, Meehan TF, Bradford YM, Brush MH, Dahdul WM, Dougall DS, He Y, Osumi-Sutherland D, Ruttenberg A, Sarntivijai S, Van Slyke CE, Vasilevsky NA, Haendel MA, Blake JA, Mungall CJ. The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability. J Biomed Semantics. 2016 Jul 4;7(1):44. doi: 10.1186/s13326-016-0088-7.
- 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
- 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
- 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.
Professional honors and appointments
- Secretary of the International Society for Biocuration Executive Committee, 2017-2018
- Co-Chair, Galaxy Community Conference/Bioinformatics Open Source Conference 2018
- Outreach Co-Chair, Force2017 Conference, 2017
- Program Co-Chair, Force2016 Conference, 2016
- Member, International Society for Biocuration 2011-present
- International Conference on Biomedical Ontology fellowship 2011
- 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