N
Nicole Vasilevsky
Researcher at Oregon Health & Science University
Publications - 85
Citations - 4080
Nicole Vasilevsky is an academic researcher from Oregon Health & Science University. The author has contributed to research in topics: Ontology (information science) & Computer science. The author has an hindex of 20, co-authored 66 publications receiving 2680 citations. Previous affiliations of Nicole Vasilevsky include Translational Research Institute & University of Colorado Denver.
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Journal ArticleDOI
The Human Phenotype Ontology in 2017
Sebastian Köhler,Nicole Vasilevsky,Mark Engelstad,Erin D. Foster,Julie A. McMurry,Ségolène Aymé,Gareth Baynam,Gareth Baynam,Susan M. Bello,Cornelius F. Boerkoel,Kym M. Boycott,Michael Brudno,Orion J. Buske,Patrick F. Chinnery,Valentina Cipriani,Laureen E. Connell,Hugh Dawkins,Laura E. DeMare,Andrew D. Devereau,Bert B.A. de Vries,Helen V. Firth,Kathleen Freson,Daniel Greene,Ada Hamosh,Ingo Helbig,Ingo Helbig,Courtney Hum,Johanna A. Jähn,Roger James,Roland Krause,Stanley J. F. Laulederkind,Hanns Lochmüller,Gholson J. Lyon,Soichi Ogishima,Annie Olry,Willem H. Ouwehand,Nikolas Pontikos,Ana Rath,Franz Schaefer,Richard H. Scott,Michael M. Segal,Panagiotis I. Sergouniotis,Richard Sever,Cynthia L. Smith,Volker Straub,Rachel Thompson,C. Turner,Ernest Turro,Marijcke W. M. Veltman,Tom Vulliamy,Jing Yu,Julie von Ziegenweidt,Andreas Zankl,Stephan Züchner,Tomasz Zemojtel,Julius O.B. Jacobsen,Tudor Groza,Damian Smedley,Christopher J. Mungall,Melissa A. Haendel,Peter N. Robinson +60 more
TL;DR: The progress of the HPO project is reviewed, including specific areas of expansion such as common (complex) disease, new algorithms for phenotype driven genomic discovery and diagnostics, integration of cross-species mapping efforts with the Mammalian Phenotype Ontology, an improved quality control pipeline, and the addition of patient-friendly terminology.
Journal ArticleDOI
Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources
Sebastian Köhler,Leigh C. Carmody,Nicole Vasilevsky,Julius O.B. Jacobsen,Daniel Danis,Jean-Philippe F. Gourdine,Michael A. Gargano,Nomi L. Harris,Nicolas Matentzoglu,Julie A. McMurry,David Osumi-Sutherland,Valentina Cipriani,James P. Balhoff,Tom Conlin,Hannah Blau,Gareth Baynam,Richard Palmer,Dylan Gratian,Hugh Dawkins,Michael M. Segal,Anna Jansen,Ahmed Muaz,Willie H. Chang,Jenna R.E. Bergerson,Stanley J. F. Laulederkind,Zafer Yüksel,Sergi Beltran,Alexandra F. Freeman,Panagiotis I. Sergouniotis,Daniel Durkin,Andrea L. Storm,Marc Hanauer,Michael Brudno,Susan M. Bello,Murat Sincan,Kayli Rageth,Matthew T. Wheeler,Renske Oegema,Halima Lourghi,Maria G. Della Rocca,Rachel Thompson,Francisco Castellanos,James R. Priest,Charlotte Cunningham-Rundles,Ayushi Hegde,Ruth C. Lovering,Catherine Hajek,Annie Olry,Luigi D. Notarangelo,Morgan Similuk,Xingmin Aaron Zhang,David Gómez-Andrés,Hanns Lochmüller,Hélène Dollfus,Sergio Rosenzweig,Shruti Marwaha,Ana Rath,Kathleen E. Sullivan,Cynthia L. Smith,Joshua D. Milner,Dorothée Leroux,Cornelius F. Boerkoel,Amy D. Klion,Melody C. Carter,Tudor Groza,Damian Smedley,Melissa A. Haendel,Melissa A. Haendel,Christopher J. Mungall,Peter N. Robinson +69 more
TL;DR: The HPO’s interoperability with other ontologies has enabled it to be used to improve diagnostic accuracy by incorporating model organism data and plays a key role in the popular Exomiser tool, which identifies potential disease-causing variants from whole-exome or whole-genome sequencing data.
Journal ArticleDOI
The Human Phenotype Ontology in 2021
Sebastian Köhler,Michael A. Gargano,Nicolas Matentzoglu,Leigh C. Carmody,David Lewis-Smith,David Lewis-Smith,Nicole Vasilevsky,Daniel Danis,Daniel Danis,Ganna Balagura,Gareth Baynam,Gareth Baynam,Amy Brower,Tiffany J. Callahan,Christopher G. Chute,Johanna L. Est,Peter D. Galer,Shiva Ganesan,Matthias Griese,Matthias Haimel,Julia Pazmandi,Julia Pazmandi,Marc Hanauer,Nomi L. Harris,Michael 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 Munoz-Torres,Rebecca L. Peters,Christina K Rapp,Ana 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,Ingo Helbig,Christopher J. Mungall,Melissa A. Haendel,Melissa A. Haendel,Peter N. Robinson +56 more
TL;DR: Recent major extensions of the Human Phenotype Ontology for neurology, nephrology, immunology, pulmonology, newborn screening, and other areas are presented and new efforts to harmonize computational definitions of phenotypic abnormalities across the HPO and multiple phenotype ontologies used for animal models of disease are presented.
Journal ArticleDOI
The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species.
Christopher J. Mungall,Julie A. McMurry,Sebastian Köhler,James P. Balhoff,Charles D. Borromeo,Matthew H. Brush,Seth Carbon,Tom Conlin,Nathan Dunn,Mark Engelstad,Erin D. Foster,Jean-Philippe F. Gourdine,Julius O.B. Jacobsen,Daniel Keith,Bryan Laraway,Suzanna E. Lewis,Jeremy Nguyen-Xuan,Kent Shefchek,Nicole Vasilevsky,Zhou Yuan,Nicole L. Washington,Harry Hochheiser,Tudor Groza,Damian Smedley,Peter N. Robinson,Melissa A. Haendel +25 more
TL;DR: The Monarch Initiative as discussed by the authors integrates information on genes, variants, genotypes, phenotypes and diseases in a variety of species, and allows powerful ontology-based search, and develops many widely adopted ontologies that together enable sophisticated computational analysis, mechanistic discovery and diagnostics of Mendelian diseases.
Journal ArticleDOI
On the reproducibility of science: unique identification of research resources in the biomedical literature
Nicole Vasilevsky,Matthew H. Brush,Holly Paddock,Laura Ponting,Shreejoy J. Tripathy,Gregory M. LaRocca,Melissa A. Haendel +6 more
TL;DR: An experiment to ascertain the “identifiability” of research resources in the biomedical literature and provides recommendations to authors, reviewers, journal editors, vendors, and publishers show that identifiability is a serious problem for reproducibility.