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Currently

Associate Director of Data Science, Critical Path Institute

Mondo Disease Ontology Lead Curator, Translational and Integrative Sciences Lab

Based in Portland, Oregon

Education

1996 - 2000 Reed College, Portland, OR, USA BA, Biology

2002 - 2009 Oregon Health & Science University, Portland, OR, USA PhD, Cell Biology

Professional Experience

Current Associate Director of Data Science, Critical Path Institute

2021-2023 Visiting Associate Research Professor, University of Colorado Anschutz Medical Campus

  • Lead Biocurator

2016-2021 Research Assistant Professor, Oregon Health & Science University

  • Lead Biocurator

2015-2016 Senior Research Associate, Oregon Health & Science University

  • Biocurator
  • Biomedical ontologist

2010-2015 Research Associate, Oregon Health & Science University

  • Biocurator
  • Biomedical ontologist

2011-2020
Assistant Professor, National University of Natural Medicine

  • Adunjct faculty, Master of Science in Integrative Medicine Research
  • Adunjct faculty, Undergratuate program
  • Member, Institional Review Board

2009-2010 Post-doctoral Research Fellow, Legacy Health Research

  • Research on angiogenesis in murine cancer model
  • Investigation of novel biomarkers in human breast cancer specimens

2009-2010 Part-time Faculty, Portland Community College, Bioscience Technology

  • Instructor, Introduction to Bioscience Technology (BIT 101)

Project Webpages

2023 - Present Rare Disease Cures Accelerator - Data and Analytics Platform (RDCA-DAP) | https://c-path.org/programs/rdca-dap/

2021 - 2023 Human Phenotype Ontology | hpo.jax.org/app

2020 – 2022 Center for Cancer Data Harmonization | ccdh.cancer.gov

2019 - 2022 Kids First Data Resource Portal | kidsfirstdrc.org

2016 - Present Mondo Disease Ontology | mondo.monarchinitiative.org

2015 - 2022 CRAFT Corpus | bionlp-corpora.sourceforge.net/CRAFT

2015 - 2022 Force11 Attribution Working Group | force11.org/groups/attribution-working-group

2014 - 2017 Big Data to Knowledge (BD2K) | dmice.ohsu.edu/bd2k

2012 – Present Monarch Initiative | monarchinitiative.org

2010 - 2012 eagle-i Network | www.eagle-i.net

2010 – Present Translational and Integrative Sciences Laboratory | tislab.org

Website development

Select Publications

For a complete list, see Publications tab

  1. Sebastian Köhler, Michael Gargano, Nicolas Matentzoglu, Leigh C Carmody, David Lewis-Smith, Nicole A Vasilevsky, et al., (2020) "The Human Phenotype Ontology in 2021." Nucleic Acids Research, gkaa1043, https://doi.org/10.1093/nar/gkaa1043
  2. Deer RR, Rock MA, Vasilevsky N, et al., "Characterizing Long COVID: Deep Phenotype of a Complex Condition." EBioMedicine. 2021 Nov 25;74:103722. doi: 10.1016/j.ebiom.2021.103722. Epub ahead of print. PMID: 34839263; PMCID: PMC8613500. Preprint: https://www.medrxiv.org/content/10.1101/2021.06.23.21259416v1
  3. Vasilevsky NA, Hosseini M, Teplitzky S, Ilik V, Mohammadi E, Schneider J, Kern B, Colomb J, Edmunds SC, Gutzman K, Himmelstein DS, White M, Smith B, O'Keefe L, Haendel M, Holmes KL. "Is authorship sufficient for today's collaborative research? A call for contributor roles." Account Res. 2021 Jan;28(1):23-43. Preprint: https://data2health.github.io/contributorship/v/bec492d69007e9fc79a1f0b0585c1593b4368a14/
  4. Kent A Shefchek, Nomi L Harris, Michael Gargano, Nicolas Matentzoglu, Deepak Unni, Matthew Brush, Daniel Keith, Tom Conlin, Nicole Vasilevsky, et al. "The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species." Nucleic Acids Research, gkz997, https://doi.org/10.1093/nar/gkz997
  5. Xingmin Aaron Zhang, Amy Yates, Nicole Vasilevsky, et al., "Semantic Integration of Clinical Laboratory Tests from Electronic Health Records for Deep Phenotyping and Biomarker Discovery." npj Digital Medicine volume 2, Article number: 32 (2019), https://www.nature.com/articles/s41746-019-0110-4. Preprint here: bioRxiv 519231; doi: https://doi.org/10.1101/519231
  6. Melissa Haendel, Nicole Vasilevsky, Deepak Unni, Cristian Bologa, Nomi Harris, Heidi Rehm, Ada Hamosh, Gareth Baynam, Tudor Groza, Julie McMurry, Hugh Dawkins, Ana Rath, Courtney Thaxon, Giovanni Bocci, Marcin P. Joachimiak, Sebastian Köhler, Peter N. Robinson, Chris Mungall & Tudor I. Oprea. How many rare diseases are there? Nature Reviews Drug Discovery 05 November 2019 https://www.nature.com/articles/d41573-019-00180-y
  7. Nicole A. Vasilevsky, et al., Plain-language medical vocabulary for precision diagnosis. Nature Genetics 50, 474--476 (2018). (Preprint available at: http://doi.org/10.5281/zenodo.1168737)
  8. Michael Bada, Nicole Vasilevsky, William A Baumgartner, Jr, Melissa Haendel, Lawrence E Hunter. "Gold-standard ontology-based anatomical annotation in the CRAFT Corpus." Database, Volume 2017, 1 January 2017, bax087, https://academic.oup.com/database/article/doi/10.1093/database/bax087/4780291
  9. Vasilevsky NA, Minnier J, Haendel MA, Champieux RE. (2017) "Reproducible and reusable research: Are journal data sharing policies meeting the mark?" PeerJ 5:e3208; DOI 10.7717/peerj.3208 (Preprint available at: https://doi.org/10.7287/peerj.preprints.2588v1)
  10. 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
  11. Nicole A. Vasilevsky​, Matthew H. Brush, Holly Paddock, Laura Ponting, Shreejoy J. Tripathy, Gregory M. LaRocca, Melissa A. Haendel (2013) "On the reproducibility of science: Unique Identification of Research Resources in the Biomedical Literature". PeerJ. https://peerj.com/articles/148/

Select Presentations

For a complete list, see Presentations tab

  • LOINC2HPO: Improving Translational Informatics by Standardizing EHR Phenotypic Data Using the Human Phenotype Ontology. Keynote address at Rocky Bioinformatics 2018, Snowmass, CO, December 07, 2018.
  • The Human Phenotype Ontology. Invited talk at the Sickle Cell Disease Ontology Workshop, Cape Town, South Africa, June 04, 2018.
  • A comprehensive disease ontology for human disease curation. Presentation at Biocuration 2018 conference, Shanghai, China, April 10, 2018.

Teaching

See Teaching tab

Service

Professional Societies:

2017-2023 International Society for Biocuration
2008-2021 Oregon Bioscience Association
2011 Association of Biomolecular Resource Facilities
2010 American Association of Cancer Research

Ad hoc Reviewer:

2020
Accountability in Research
2020-2021
Advances in Medical Education and Practice
2014
Alternative Therapies in Health and Medicine
2020
Applied Sciences
2018
Biodiversity
2017
BMC Medical Informatics and Decision Making 
2015
BMJ
2016-2024
Database
2018
Diagnostics
2016
eLife
2020-2021
F1000
2021
Human Mutation
2018
International Journal of Molecular Sciences
2017
Journal of Clinical Epidemiology
2020
Journal of Diabetes Research
2015
Mammalian Genome
2018
Methods of Information in Medicine
2018-2019
Nutrients 
2016-2020
PeerJ
2018
PLoS One Computational Biology
2017
PLoS One
2014-2019
Science and Engineering Ethics
2021
Scientific Data
2019-2020
Abstract review for AMIA conference

Committees:

International/National

2023-present
GA4GH Rare Disease Community Working Group, Co-Lead
2020-present
International Society for Biocuration, Executive Committee (Six year-elected position) 2019- 2020 Scientific Committee, Biocuration 2020 conference
2018-2019 Semantic Architecture Advisory Committee, National Cancer Institute
2019-2021 International Society for Biocuration, Executive Committee Chair
2017-2019 International Society for Biocuration, Executive Committee Secretary
2017-present International Society for Biocuration Awards Committee, Chair
2018 Co-Chair, Galaxy Community Conference
2017 Planning committee, Galaxy Community Conference
2016-2018 Program committee, International Conference on Biomedical Ontology
2017 Outreach Committee Co-chair, Force2017
2017-2018 Force11 Scholarly Communications Institute, Committee
2015-2016 Program Co-Chair, Force2016 Conference
2015-2016 NISO Bibliographic Roadmap
2014-2015 Logistics Committee, Force2015 Conference

Regional

2017-2020 Institutional Review Board Committee, National University of Natural Medicine

Departmental

2016-2018 Staff Development Committee, Oregon Health & Science University Library
2015-2016 Web Redesign Committee, Oregon Health & Science University Library
2014 Discovery Team, Oregon Health & Science University Library
2013-2014 Research Data Stewardship Committee, Oregon Health & Science University Library
2012-2013 Library Communications Committee, Oregon Health & Science University Library

Community Service:

2020-2021 Member, Oregon Health & Science University, Department of Medical Informatics and Clinical Epidemiology Diversity Committee
2018-present Member, Women in Science, Communications Committee
2013-2014 Chair, Overlook Neighborhood Association Board
2011- 2012 Volunteer, Event planning committee, Open Meadow
2009-2011 Board member, Portland Community College Bioscience Technology Advisory Board
2008-2010 Volunteer, Oregon Bioscience Association