Nicole A. Vasilevsky bio photo

Nicole A. Vasilevsky

Research Assistant Professor, Oregon Health & Science University

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Publications

Semantic Phenotyping of Diseases

  • Sebastian Köhler, Michael Gargano, Nicolas Matentzoglu, Leigh C Carmody, David Lewis-Smith, Nicole A Vasilevsky, Daniel Danis, Ganna Balagura, Gareth Baynam, Amy M Brower, Tiffany J Callahan, Christopher G Chute, Johanna L Est, Peter D Galer, Shiva Ganesan, Matthias Griese, Matthias Haimel, Julia Pazmandi, Marc Hanauer, Nomi L Harris, Michael J Hartnett, Maximilian Hastreiter, Fabian Hauck, Yongqun He, Tim Jeske, Hugh Kearney, Gerhard Kindle, Christoph Klein, Katrin Knoflach, Roland Krause, David Lagorce, Julie A McMurry, Jillian A Miller, Monica C Munoz-Torres, Rebecca L Peters, Christina K Rapp, Ana M Rath, Shahmir A Rind, Avi Z Rosenberg, Michael M Segal, Markus G Seidel, Damian Smedley, Tomer Talmy, Yarlalu Thomas, Samuel A Wiafe, Julie Xian, Zafer Yüksel, Ingo Helbig, Christopher J Mungall, Melissa A Haendel, Peter N Robinson (2020) The Human Phenotype Ontology in 2021 Nucleic Acids Research, gkaa1043, https://doi.org/10.1093/nar/gkaa1043 Link here
  • Thessen, Anne E, Grondin, Cynthia J, Kulkarni, Resham D, Brander, Susanne, Truong, Lisa, Vasilevsky, Nicole A, … Haendel, Melissa A. (2020). Computable Exposures Workshop Report (Version 1). http://doi.org/10.5281/zenodo.3697113. Link here
  • Leigh C. Carmody, Hannah Blau, Daniel Danis, Xingman A. Zhang, Jean-Philippe Gourdine, Nicole Vasilevsky, Peter Krawitz, Miles D. Thompson, Peter N. Robinson. Significantly different clinical phenotypes associated with mutations in synthesis and transamidase+remodeling glycosylphosphatidylinositol (GPI)-anchor biosynthesis genes. Orphanet J Rare Dis (2020) 15: 40. https://doi.org/10.1186/s13023-020-1313-0 Link here
  • 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 Link here
  • Jean-Philippe F Gourdine, Matthew H Brush, Nicole A Vasilevsky, Kent Shefchek, Sebastian Köhler, Nicolas Matentzoglu, Monica C Munoz-Torres, Julie A McMurry, Xingmin Aaron Zhang, Peter N Robinson, Melissa A Haendel. Representing glycophenotypes: semantic unification of glycobiology resources for disease discovery Database, Volume 2019, 2019, baz114, https://doi.org/10.1093/database/baz114. Link here
  • 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. Link here
  • Sebastian Köhler, N. Christine Øien, Orion J. Buske, Tudor Groza, Julius O. B. Jacobsen, Craig McNamara, Nicole Vasilevsky, Leigh C. Carmody, J. P. Gourdine, Michael Gargano, Julie A. McMurry, Daniel Danis Christopher J. Mungall, Damian Smedley, Melissa Haendel, Peter N. Robinson. Encoding Clinical Data with the Human Phenotype Ontology for Computational Differential Diagnostics. Current Protocols in Human Genetics.Volume103, Issue1 September 2019, e92, https://doi.org/10.1002/cphg.92. Link here
  • 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 Medicinevolume 2, Article number: 32 (2019) Preprint here, Link here
  • Sebastian Köhler, Leigh Carmody, Nicole Vasilevsky, et al. Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources. 22 November 2018. Nucleic Acids Research, gky1105, https://doi.org/10.1093/nar/gky1105 Link here
  • 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) Link here
  • Vasilevsky N, Engelstad M, Foster E, Mungall C, Robinson P, Köhler S, Haendel M. 2016. IT402: Enhancing the Human Phenotype Ontology for Use by the Layperson. International Conference on Biomedical Ontology and BioCreative (Conference paper, ICBO BioCreative 2016). Link here
  • Christopher J. Mungall, …, Nicole Vasilevsky, Zhou Yuan, Nicole Washington, Harry Hochheiser, Tudor Groza, Damian Smedley, Peter N. Robinson, and Melissa A. Haendel. (2017) The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species. Nucleic Acids Res. 2017 Jan 4;45(D1):D712-D722. doi: 10.1093/nar/gkw1128 Link here
  • Sebastian Köhler, Nicole A. Vasilevsky, …, and Peter N. Robinson. The Human Phenotype Ontology in 2017. Nucl. Acids Res. first published online November 28, 2016 doi:10.1093/nar/gkw1039 Link here
  • Julie A. McMurry, …, Nicole A. Vasilevsky, Zhou Yuan, Suzanna E. Lewis, Harry Hochheiser, Tudor Groza, Damian Smedley, Peter N. Robinson, Christopher J. Mungall, Melissa A. Haendel. Navigating the Phenotype Frontier: The Monarch Initiative. GENETICS August 1, 2016 vol. 203 no. 4 1491-1495; DOI: 10.1534/genetics.116.188870 Link here
  • Bone WP, …, 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. Link here
  • Tudor Groza, …, Nicole Vasilevsky, et al. The Human Phenotype Ontology: Semantic unification of common and rare disease. The American Journal of Human Genetics (2015). [Link here](http://dx.doi.org/10.1016/j.ajhg
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  • 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. Link here

Biomedical Ontologies and Bioinformatics

  • Lauren Chan, Nicole Vasilevsky, Anne Thessen, Julie McMurry, Melissa Haendel, The landscape of nutri-informatics: a review of current resources and challenges for integrative nutrition research, Database, Volume 2021, 2021, baab003, https://doi.org/10.1093/database/baab00
  • Anne E. Thessen, Cynthia J. Grondin, Resham D. Kulkarni, Susanne Brander, Lisa Truong, Nicole A. Vasilevsky, Tiffany J. Callahan, Lauren E. Chan, Brian Westra, Mary Willis, Sarah E. Rothenberg, Annie M. Jarabek, Lyle Burgoon, Susan A. Korrick, and Melissa A. Haendel. Community Approaches for Integrating Environmental Exposures into Human Models of Disease. Environmental Health Perspectives. Vol. 128, No. 12. December 2020. Link here
  • Hotchkiss, J.; Manyisa, N.; Adadey, S.M.; Oluwole, O.G.; Wonkam, E.; Mnika, K.; Yalcouye, A.; Nembaware, V.; Haendel, M.; Vasilevsky, N.; Mulder, N.J.; Jupp, S.; Wonkam, A.; Mazandu, G.K. The Hearing Impairment Ontology: A Tool for Unifying Hearing Impairment Knowledge to Enhance Collaborative Research. Genes 2019, 10, 960 Link here
  • Matentzoglu, Nicolas;… Vasilevsky, Nicole; Zhang, Xingmin A.; Haendel, Melissa A. Phenotype Ontologies Traversing All The Organisms (POTATO) workshop aims to reconcile logical definitions across species. Zenodo. http://doi.org/10.5281/zenodo.2382757
  • 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.
  • Terry Meehan, Nicole A. Vasilevsky, Christopher J. Mungall, Melissa A. Haendel, Judith A. Blake, Alexander D. Diehl (2013) Ontology based molecular signatures for immune cell types via gene expression analysis. BMC Bioinformatics 14:263. *These authors contributed equally to the work.

Biocuration

  • International Society for Biocuration (2018) Biocuration: Distilling data into knowledge. PLoS Biol 16(4): e2002846. https://doi.org/10.1371/journal.pbio.2002846. Link here
  • 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. Link here
  • Wang Q, …,Vasilevsky N, Wang X, Chatr-Aryamontri A, Laulederkind SJ, Matis-Mitchell S, McEntyre J, Orchard S, Pundir S, Rodriguez-Esteban R, Van Auken K, Lu Z, Schaeffer M, Wu CH, Hirschman L, Arighi CN. Overview of the interactive task in BioCreative V. Database (Oxford). 2016 Sep 1;2016. pii: baw119. Print 2016. Link here

Attribution and Representing Researcher Expertise

  • Nicole A. Vasilevsky, Mohammad Hosseini, Samantha Teplitzky, Violeta Ilik, Ehsan Mohammadi, Juliane Schneider, Barbara Kern, Julien Colomb, Scott C. Edmunds, Karen Gutzman, Daniel S. Himmelstein, Marijane White, Britton Smith, Lisa O’Keefe, Melissa Haendel, Kristi L. Holmes. Is authorship sufficient for today’s collaborative research? A call for contributor roles. Accountability in Research: Policies and Quality Assurance. DOI: 10.1080/08989621.2020.1779591. Link here. Preprint here.
  • Craig D. Newgard, MD… Nicole Vasilevsky, PhD; Marijane White, MSLIS; Adrienne Zell, PhD. The First National Institutes of Health Institutional Training Program in Emergency Care Research: Productivity and Outcomes. Ann Emerg Med. 2018 Aug 2. pii: S0196-0644(18)30549-3. doi: 10.1016/j.annemergmed.2018.06.018. Link here
  • Haendel MA, Torniai C, Vasilevsky N, Hoffmann S, Bourges-Waldegg D. eagle-i: ontology-driven federated search and data entry tools for discovering biomedical research resources. (2013) International Conference on Biomedical Ontology; July 7-13, 2013; Montreal, Canada. Link here
  • Vasilevsky NA, Johnson T, Corday K, Torniai C, Brush M, Segerdell E, Wilson M, Shaffer C and Haendel M. (2012) Research Resources: Curating the new eagle-i discovery system. Database, Vol. 2012, Article ID bar067. Link here
  • 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. Link here

Education and Training

  • Ted Laderas, Nicole Vasilevsky, Bjorn Pederson, Melissa Haendel, Shannon McWeeney, David Dorr (2017): Teaching data science fundamentals through realistic synthetic clinical cardiovascular data. BioRxiv preprint: doi: https://doi.org/10.1101/232611
  • Nicole Vasilevsky, Morgan Schafer, Deanne Tibbitts, Kirsten Wright and Heather Zwickey. Curriculum Development of a Research Laboratory Methodology Course for Complementary and Integrative Medicine Students. (2015) Medical Science Educator. DOI:10.1007/s40670-015-0113-y

Data Management, Data Standards and Altmetrics

  • Anja Füllgrabe, Nancy George, Matthew Green, Parisa Nejad, Bruce Aronow, Silvie Korena Fexova, Clay Fischer, Mallory Ann Freeberg, Laura Huerta, Norman Morrison, Richard H. Scheuermann, Deanne Taylor, Nicole Vasilevsky, Laura Clarke, Nils Gehlenborg, Jim Kent, John Marioni, Sarah Teichmann, Alvis Brazma, Irene Papatheodorou. Guidelines for reporting single-cell RNA-seq experiments. Nat Biotechnol (2020). https://doi.org/10.1038/s41587-020-00744-z. Link here.
  • Nicole Vasilevsky, Jackie Wirz, Robin Champieux, Todd Hannon, Bryan Laraway, Kyle Banerjee, Chris Shaffer, Melissa Haendel. Lions, Tigers, and Gummi Bears: Springing Towards Effective Engagement with Research Data Management, (2014). Scholar Archive. Paper 3571. http://digitalcommons.ohsu.edu/etd/3571
  • Haendel MA, Vasilevsky NA, and Wirz JA. (2012) Dealing with Data: A case study on information and data management literacy. PLoS Biol 10(5): e1001339. doi:10.1371/journal.pbio.1001339.

Open Science and Scientific Reproducibility

  • David B Resnik, Melissa Morales, Rachel Landrum, Min Shi, Jessica Minnier, Nicole A. Vasilevsky & Robin E. Champieux (2019) Effect of Impact Factor and Discipline on Journal Data Sharing Policies, Accountability in Research, DOI: 10.1080/08989621.2019.1591277. Link here
  • 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)
  • Nicole A. Vasilevsky, Matthew H. Brusfh, 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/
  • 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
  • Babette Haven, Elysia Heilig, Cristine Donham, Michael Settles, Nicole Vasilevsky, Katherine Owen, Reproducibility Project: Cancer Biology. Registered report: A chromatin-mediated reversible drug-tolerant state in cancer cell subpopulations (2016) eLife 2016;5:e09462
  • Vita R, Vasilevsky N, Bandrowski A, Haendel M, Sette A, Peters B. (2016) Reproducibility and Conflicts in Immune Epitope Data. Immunology. 2016 Mar;147(3):349-54. doi: 10.1111/imm.12566.

Cancer immunology

  • 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.