Ictr.johnshopkins.edu

 CURRICULUM VITAEMELISSA ANNE HAENDEL, PhDOctober 29th, 2020Melissa@ ? 503-407-5970 ? ? Linus Pauling Institute, Corvallis, 0000-0001-9114-8737 ? scholar.citations?user=HtAV9dIAAAAJ ? @ontowonkaVISIONI aim to utilize my art as a data translator to weave together healthcare systems, basic science research, and patients. I accomplish this by leading the development of data integration technologies, innovative communication strategies, and collaborative education and outreach. My demonstrated success in leadership of cross-disciplinary international teams, development of applications used for rare disease diagnostics, implementation of platforms and tools for translational research, commitment to diversity and inclusion, and open and reproducible science to effect real change.EDUCATIONPost-doctoral Fellow2002-2004Oregon State University, Dr. Bailey and Dr. TanguayMicroarray-based research of biocides and carcinogens on development of zebrafish and trout. Post-doctoral Fellow2000-2002University of Oregon, Dr. Eisen and Dr. DarimontStudy of the involvement of thyroid hormone during early neural development in the zebrafish. Ph.D. Neuroscience, Doctoral Research Assistant 1993-1999University of Wisconsin, Dr. Gary LyonsIdentification and knock-out of a novel gene important for neural development in mice. Research on neural crest cell differentiation in chick.B.A. Chemistry (Biochemistry focus) 1991Reed College, Portland, Dr. Alan ShustermanDrug-activity modeling of dopamine receptors. Leadership developmentHedwig van Ameringen Executive Leadership in Academic Medicine (ELAM) Program for Women 2020-21 (1 year)Drexel University, Philadelphia, PA This is a unique year-long part-time fellowship for women faculty in schools of medicine, dentistry, public health and pharmacy. The program is dedicated to developing the professional and personal skills required to lead and manage in today's complex health care environment, with special attention to the unique challenges facing women in leadership positions. Harvard School of Education Academic Leadership Institute 2017 (1 week)Harvard University, Cambridge MA This is a unique program that focuses on learning to guide constituents to understand the fast-changing information landscape, deepen management skills, and to become more effective leaders in a time of institutional change. The program focuses on three areas of leadership — planning, organizational strategy and change, and transformational learning — with an overarching goal of increasing leadership and management capacity.Professional Executive coaching2016-2018 (~16 months) OHSU, Portland, OR OHSU hired an external expert executive coach to support my leadership advancement. Training focused on (1) management strategies at different organizational levels – managing supervisors, managing peers, managing subordinates, and managing subordinates via different reporting lines; (2) Development of professional goals and strategic planning; (3) Development of organizational partnerships; and (4) Change management.II. PROFESSIONAL EXPERIENCEAcademic positionsProfessor 2020-presentOregon Health & Science University, Department of Medical Informatics and Clinical Epidemiology Director of the Translational and Integrative Sciences LaboratoryDirector of the Center for Data to HealthLeadership of informatics consortia dedicated to data sharing, semantic engineering, data standards development; community development; ontological research and semantic technologies for disease research.Associate professor2018-presentOregon State UniversityDirector of the Translational and Integrative Sciences LaboratoryAssociate Professor, Dept. of Environmental and Molecular ToxicologyAssociate Professor, School of Biological & Population Health SciencesIntegrative research in environmental health science, public health, and bioinformatics.Associate Professor 2015-2019Oregon Health & Science University, Department of Medical Informatics and Clinical EpidemiologyDirector of the Translational and Integrative Sciences LaboratoryBiomedical informatics focused on disease research and scholarly communication; research data and ethics education; educational program development; community data sharing coordination; reproducibility and attribution informatics development. Assistant Professor 2010-2014Director of the Ontology Development Group, Oregon Health & Science University, Library and Department of Medical Informatics and Clinical EpidemiologyDevelopment of new semantic methods and standards and their use in application development.Administrative positionsDirector of the Center for Data to Health2017-presentOregon Health & Science UniversityOregon Clinical and Translational Science Research Institute Leadership of a collaboration network of nine institutions to innovate and implement clinical and translational informatics and open science practice across a ~60 clinical institutions in the United States. Director of Translational Data Science2018-presentOregon State UniversityCenter for Genome Research and BiocomputingLinus Pauling InstituteStrategic vision for the university and the region, focusing on integration across basic research, environmental science, public health, and clinical domains. Interim Director, OHSU Library2017- 2018Oregon Health & Science University, Library Managerial oversight of ~40 employees; fiscal oversight change management and strategic visioning for the Library, with a particular focus on integration of data science research, education, and services at OHSU.Other positionsSenior Research Associate, Lead Ontologist2009-2010Director of the Ontology Development Group, Oregon Health & Science University, Library and Department of Medical Informatics and Clinical Epidemiology Development of community ontologies and best practices for representation and query of biomedical data. Leadership of the ontology effort for the eagle-i consortium.Scientific Ontologist & Genetics Nomenclature Lead2004-2009University of Oregon, Dr. WesterfieldDevelopment of anatomical ontologies and syntax for phenotype ontologies; community genetic nomenclature coordinator.Laboratory Technician1993Oregon State University, Dr. David BarnesMaintenance of zebrafish stocks and cell culture lines, evaluation of techniques for making zebrafish stem cell lines.III. SCHOLARSHIP HONORS AND AWARDS FOR SCHOLARSHIP AND SERVICENominated for Donald A.B. Lindberg Award for Innovation in Informatics, 2020, pendingFellow of the American Medical Informatics Association (FACMI), 2020OHSU Women in Academic Health and Medicine Emerging Leader award, finalist, 2019Association of Academic Health Sciences Libraries Scholarship awardee, 2017 Bioinformatics Benjamin Franklin Award for Open Access in the Life Sciences finalist, 2017 and 2018OHSU Women in Academic Medicine Emerging Leader Award nomination, 2016.NIH/Wellcome Trust/HHMI Open Science Competition finalist runner up for “Phenopackets: Encapsulating and contextualizing phenotypic data in an open science ecosystem” 2016 OHSU Faculty Senate Collaboration Award nomination and runner-up award, 2014Medical Research Foundation of Oregon Richard T. Jones New Investigator Award nomination,2013 and 2014 American Association of Cancer Research Pathobiology Workshop Fellowship Awardee, 2003Commended for Excellence in Scholarship, Reed College, 1991FEDERAL GRANTS AND CONTRACTSOngoingSummary: Ten current programs totalling 9.9M/year, seven as PI and three as co-I/PI. Title: Data Management and Portal for the INCLUDE (DAPI)Award: OD 1U2CHL156291Role: co-PI Dates: 09/01/2020 – 08/31/2025Amount: (annual, OSU+OHSU) $228,631; (annual, total) $4,002,500Goal: Community aggregation and analytics for Downs Syndrome genotypic and phenotypic data. Title: Bill and Melinda Gates FoundationAward: COVID-19: Cohort Collaborative for Disease ModelingRole: co-PI, subcontract from Sage BionetworksDates: 7/10/20-7/31/22Amount: $31, 513 (to OHSU); ($100,000 to OCHIN)Goal: Onboard OCHIN to support diversity and inclusion in the National COVID Cohort CollaborativeTitle: A phenomics-first resource for interpretation of variants.Award: NHGRI RM1; Center of Excellence in Genome Science Role: contact PI, multi-PI w Mungall Dates: 07/01/20 – 06/30/25Amount: $2,042,061 (annual)Goal: Community coordination of disease-phenotype knowledge for precision medicine.Title: Biomedical Data Translator Translator Standards and Reference Implementations Component (SRI)Award: NCATS OT2Role: Co-PD w Mungall and BizonDates: 2020-2025Amount: $750,000 (annual) *Note that as an OT3, funding will be allocated incrementally, this is an estimate shared amongst team membersGoal: Develop standards, services, and a reference graph database implementation for the Translator reasoners, knowledge sources, and workflows. Title: Center for Cancer Data Harmonization (CCDH)Award: NCI S19-077 Leidos Biomedical Research, Inc, ContractDates: 09/01/19 – 12/31/22Amount: $8,650,00 (total)Role: contact PI, multi-PI w Volchenboum, ChuteGoal: Create a harmonized data model, terminology services, and tools for cancer across the Cancer Research Data CommonsTitle: A National Center for Digital Health Informatics InnovationAward: NIH NCATS U24TR002306Role: contact PI (multi-PI w Chute, Eichmann, Guinney, Wilcox)Dates: 11/01/17 – 10/31/22Amount: $5,014,915 (annual)Goal: Coordinate informatics across 60 clinical and translational science award sites; support data interoperability and sharing; and create collaborative frameworks.Title: GA4GH-HL7Award: NLM Contract: Dates: 09/30/19 – 09/29/21$700,000 (total)Role: multiPIDevelop interoperability between FHIR and Phenopackets, a new standard developed within the GA4GH Clinical and Phenotypic Exchange workstream, co-led by Haendel.Title: Gabriella Miller Kids First Pediatric Data Resource CenterAward: NIH 5U2CHL138346, Office of Director Role: site PIDates: 06/01/18 – 22/05/22Amount: $294,663 (annual)Goal: Innovation through collaboration at the intersection of childhood development and cancer: a platform for the Gabriella Miller Kids First Pediatric Data Resource CenterTitle: Forums for Integrative InformaticsAward: NIH BD2K U13 | CA221044Role: contact PI, multi-PI w RobinsonDates: 8/1/17-7/31/21Amount: $74,995 (annual)Goal: Host community events to advance phenotype data representation and standardization.Title: Monarch InitiativeAward: NIH Office of the Director 2R24OD011883; Second four-year funding period. (note pending renewal, below)Role: Co-PD w Mungall and RobinsonDates: 2016-2021Amount: $1,290,295 (annual)Goal: Develop software and standardize data to enable cross-species genotype to phenotype analysis and promote the publication of data standards. Pending Title: Monarch InitiativeAward: NIH Office of the Director 3R24OD011883; Third four-year funding period. Role: Co-PD w Mungall and RobinsonDates: 2020-2024Amount; $1,290,000 (annual)Goal: Develop software and standardize data to enable cross-species genotype to phenotype analysis and promote the publication of data standards. Title: The Human Phenotype Ontology: Accelerating Computational Integration of Clinical Data for Genomics Award: NHGRI U24Role: Co-PI w RobinsonDates: 2020-2025Amount; $500,000 (annual)Goal: Community development of the Human Phenotype Ontology, Medical Actions Ontology, and disease models for diagnostic use. CompletedTitle: NHLBI Data STAGEAward: NIH 1 OT3 HL142479-01Role: co-PIDates: 10/1/17 - 3/29/20Amount: $1,224,574 (total) *Note that as an OT3, funding will be allocated incrementally.Title: Biomedical Data Translator Technical Feasibility Assessment and Architecture Design.Award: NIH NCATS 1OT3TR002019-01Role: co-PD w Mungall and ChuteDates: 10/1/2016 – 9/30/2018Amount: $2,000,000 (total)Goal: Develop a large scale suite of data integration technologies for mechanism discovery and drug repurposing. Title: Realization of a Standard of Care for Rare Diseases Using Patient-Engaged PhenotypingAward: PCORI ContractRole: co-PDDates: 8/1/17-7/31/19Amount: $367,135 (annual)Goal: Develop methods for using the layperson translation of the Human Phenotype Ontology in cohorts of rare disease patients to aid diagnosis.Title: INCA: Intelligent Concept Agent for Assisting with the Application of MetadataAward: NIH BD2K 1 U01 HG009453-01 Role: co-PIDates: 07/01/16-06/30/19Amount: $60,232 (annual)Goal: Assist in creation, extension, application, and maintenance of metadata describing experiments and datasets derived from experiments.Title: Implementation of zebrafish ontologies for toxicology screening Award: NIEHS ContractRole: contactPIDates: 07/31/18 – 10/31/19Amount: $50,745 (annual)Goal: Map zebrafish data to ontologies for data querying and integration.Title: NIH Data Commons Pilot Phase (DCPPC)NIH OT3 RM-17-026Role: co-PIDates: 10/1/17 - 3/29/18Dates: $1,224,574 (annual)Goal: Pilot identifier management and provisioning system and develop model for making data FAIR.*Note that as an OT3, funding will be allocated incrementally, this is shared amongst team membersTitle: Adding Big Data Open Educational Resources to the ONC Health IT Curriculum.NIH BD2K 1R25GM114820Role: Co-PDDates: 12/1/14-11/30/17Amount: $199,354 (annual)Goal: The goal is to develop and make available online big data curricular materials.Title: OHSU Informatics Analytics BD2K Skill Course NIH BD2K 1R25EB020379Role: Co-PDDates: 12/1/14-11/30/17Amount: $150,000 (annual)Goal: The goal is to teach online courses in big data stewardship and analytics.Title: NCI/Leidos ContractRole: PIDates: 6/1/17-9/30/17Amount: $225,000 (total)Goal: Development of evidence models and semantic interoperability capabilities for cancer data analysis.Title: BioCaddie: Biomedical and healthCAre Data Discovery and Indexing Engine center. Award: NIH NIAID 3U24AI117966-03S1Role: supplement co-PDDates: 09/15/16-08/31/17Amount: $70,000 (total)Goal: Develop a framework to provide authoritative and integration-ready prefixed identifiers, to capture and consolidate prefixes used across the biomedical data spectrum, and build links across key resource registries.Title: BD2K Standards Coordinating CenterAward: NIH BD2K HHSN316201200001WRole: Subcontract PIDates: 5/17/16 – 9/30/16Amount: $107,815 (total)Goal: Develop portal for standards for the translational science community.Title: FACEBASE Supplement: Semantic integration of craniofacial phenotyping across speciesAward: NIH BD2K PA-15-144-U01Role: Subcontract PIDates: 9/2015 - 8/2016Amount: $119,697 (total)Goal: Achieve bidirectional FaceBase-Monarch integration.Title: NIH Undiagnosed Disease Program contractAward: HHSN268201300036CRole: Subcontract PIDates: 2015-2016Amount: $84,000 (total)Goal: represent patient families in the Monarch Initiative website, and perform patient clustering.Title: NCI/Leidos ContractRole: PIDates: 7/1/15-6/30/16Amount: $248,799 (total)Goal: Development of use cases for cancer data analysis using semantic technologies. Title: USC Center for Big Data in Translational Genomics. NIH U54HG007990-S2Subcontract PIDates: 2016Amount: $94,368. (total)Goal: Develop GA4GH genotype-to-phenotype schemas and evidence models for the BRCA Exchange.Title: Force11 Open Educational Resources supplementAward: National Cancer Institute R25 GM114820 02S1Role: PIDates: 2016Amount: $54,000 (total)Goal: Evaluate use of Open Educational Resources for data science at a Force2016 event.Title: Monarch InitiativeOffice of the Director, NIH 1R24OD011883Role: PIDates: 2010-2016Amount: $1,290,295 (annual)Goal: Program to develop software and standardize data to enable cross-species genotype to phenotype analysis and promote the publication of data standards. Title: Monarch InfrastructureOffice of the Director, NIH Suppl 4 R24 OD011883 04S1Role: PIDates: 09/18/2015 - 07/31/2016Amount: $132,400 (total)Goal: To migrate infrastructure for the Monarch application to OHSU and implement advanced systems.Title: DARPA Big MechanismAward DARPA-BAA-14-14 Role: co-PIDates: 7/1/14-12/31/15Amount: $75,000 (total)Goal: Provide expert annotation using ontologies to specific text spans in the CRAFT Corpus and additional documents.Title: NIH Undiagnosed Disease Program contractAward: HHSN268201400093PRole: Contract PIDates: 2014-2015Amount: $175,000 (total)Goal: Extend visualization tools for phenotype comparison and to better represent glycomics phenotype data.Title: Online model organism phenotyping tool Office of the Director, NIH, Supplement 3 R24 OD011883 03S1Role: PIDates: 09/18/2014 - 07/31/2015Amount: $452,622 (total)Goal: Develop an online model organism phenotyping tool in support of functional validation studies in a variety of organisms according to community data standards.Title: Semantic representation for Mendeley publication of research protocols,Elsevier, 2014 ContractRole: PIDates: 10/14-12/14Amount: $30,000 (total)Goal: Create an open, semantic framework for representation of research workflows.Title: Force11Role: AwardeeDates: 2013Amount: $1,000 (total)Goal: Beyond the PDF 2 1K challenge award. “Starting at Ground Zero,” the goal of this award was to promote development of library capabilities to support research data management and publication. 1Kchallenge#1k2Title: phenotype comparison algorithms and support for undiagnosed disease phenotypingNIH Undiagnosed Disease Program HHSN268201300036CRole: Contract PIDates: 2013-2014Amount: $200,000 (total)Goal: Develop phenotype comparison algorithms and support for undiagnosed disease phenotyping, quality assurance mechanisms for phenotype data, and perform usability testing for NIH software tools.Title: Improvements to the PhenoGrid Viewer. Award: NIH Undiagnosed Disease Program, NIH contract HHSN 30220140Role: Contract PIDates: 03/14-8/15Goal: Improve display of phenotype comparison tool within the Monarch interface and in third party applications.Title: CTSAconnect. NIH NCATs CTSA 10-001: 100928SB23. PROJECT #: 00921-0001 Role: PIDates: 2011-2013. (1.5 yrs)Amount: $1,457,362Goal: Development and integration of data standards for research profiling, including the integration of VIVO, eagle-i, and clinical vocabularies for translational research.Title: Medical Research Foundation of Oregon New Investigator Award Role PIDates: 2011-2012 (1yr)Amount: $40,000 (total)Goal: Indexing and retrieval of biospecimen Information within the Oregon Health & Science University Biolibrary.Title: RJ Reynolds Post-doctoral Research award Role: Post-doctoral awardee. Dates: 2002-2004Goal: To investigate the effects of biocides on early zebrafish development.Title: Differentiation factor receptors and neural cell fate. Award: NIH 5F32NS011170, NIH Individual Post-doctoral National Research Service Award, Role Post-doctoral awardeeDates: 2000-2003 (3 yrs)Goal: Investigate the role of thyroid hormone in maintenance of early-developing neurons in zebrafish.Title: Trapping novel genes involved in neural developmentAward: 5F31MH011560, Individual Pre-doctoral National Research Service Award, NIH, Role Pre-doctoral awardeeDates: 1997-1999 (3 yrs)Goal: Identify novel genes in mouse that played a role in neuronal development using gene trap knockout and in vitro preselection techniques.PUBLICATIONS AND CREATIVE WORKS8943 citations to 220 peer reviewed, conference papers, and gray literature manuscripts. h-index 48.See Google Scholar profile here: MANUSCRIPTS:Haendel MA, Chute C, ...<182 authors>…. Austin C, Gersing K. (2020) The National COVID Cohort Collaborative (N3C): Rationale, Design, Infrastructure, and Deployment. (2020). Journal of the Medical Informatics Association. Accepted. Preprint at: Rubinstein YR, Robinson PN, Gahl BA, Avillach P, Baynam G, Cederroth H, Goodwin RM, Groft SC, Hansson MG, Harris NL, Huser V, Mascalzoni D, McMurry JA, Might M, Nellaker C, Mons B, Paltoo DN, Pevsner J, Posada M, Rockett-Frase AP, Roos M, Rubinstein TB, Taruscio D, van Enckevort E, Haendel MA, The case for open science: rare diseases, JAMIA Open, ooaa030, WD, Thyvalikakath T, Haendel M, Torniai C, Hernandez P, Song M, Acharya A, Caplan DJ, Schleyer T, Ruttenberg A. (2020) Structuring, reuse and analysis of electronic dental data using the Oral Health and Disease Ontology. Journal of Biomedical Semantics 11 (1), 1-19Robinson PN, Haendel MA. Ontologies, Knowledge Representation, and Machine Learning for Translational Research: Recent Contributions. Yearb Med Inform. 2020;29(1):159-162. doi:10.1055/s-0040-1701991*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, Kristi L Holmes (2020). Is authorship sufficient for today’s collaborative research? A call for contributor roles. Accountability in Research. doi: 10.1080/08989621.2020.1779591 *menteeWagner AH, Walsh B, Mayfield G, Tamborero D, Sonkin D, Krysiak K, Deu-Pons J, Duren RP, Gao J, McMurry J, Patterson S, Del Vecchio Fitz C, Pitel BA, Sezerman OU, Ellrott K, Warner JL, Rieke DT, Aittokallio T, Cerami E, Ritter DI, Schriml LM, Freimuth RR, Haendel M, Raca G, Madhavan S, Baudis M, Beckmann JS, Dienstmann R, Chakravarty D, Li XS, Mockus S, Elemento O, Schultz N, Lopez-Bigas N, Lawler M, Goecks J, Griffith M, Griffith OL, Margolin AA; Variant Interpretation for Cancer Consortium. A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer. (2020) Nat Genet. Apr;52(4):448-457. doi: 10.1038/s41588-020-0603-8. Epub 2020 Apr 3. Shefchek KA, Harris NL, Gargano M, Matentzoglu N, Unni D, *Brush M, Keith D, Conlin T, *Vasilevsky N, Zhang XA, Balhoff JP, Babb L, Bello SM, Blau H, Bradford Y, Carbon S, Carmody L, Chan LE, Cipriani V, Cuzick A, Rocca MD, Dunn N, *Essaid S, Fey P, Grove C, *Gourdine JP, Hamosh A, Harris M, Helbig I, Hoatlin M, Joachimiak M, Jupp S, Lett KB, Lewis SE, McNamara C, Pendlington ZM, Pilgrim C, Putman T, Ravanmehr V, Reese J, Riggs E, Robb S, Roncaglia P, Seager J, *Segerdell E, Similuk M, Storm AL, Thaxon C, Thessen A, Jacobsen JOB, McMurry JA, Groza T, K?hler S, Smedley D, Robinson PN, Mungall CJ,?Haendel?MA, Munoz-Torres MC, Osumi-Sutherland D. (2019) The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species. Nucleic Acids Res. 2019 Nov 8. pii: gkz997. doi: 10.1093/nar/gkz997. *menteeHaendel MA, *Vasilevsky N, Unni D, Bologa C, Harris N, Rehm H, Hamosh A, Baynam G, Groza T, McMurry J, Dawkins H, Rath A, Thaxon C, Bocci G, Joachimiak MP, K?hler S, Robinson PN, Mungall C, and Oprea TI. (2019) How many rare diseases are there? Nature Reviews Drug Discovery, November 5, doi: 10.1038/d41573-019-00180-y *menteeMishra R, Burke A, Gitman B, Verma P, Engelstad M, Haendel MA, Alevizos I, Gahl BA, Collins MT, Lee JS, Sincan M. (2019) Data-driven method to enhance craniofacial and oral phenotype vocabularies. The Journal of the American Dental Association. Volume 150, Issue 11, November 2019, Pages 933-939.e2Clarke DJB, Wang L, Jones A, Wojciechowicz ML, Torre D, Jagodnik KM, Jenkins SL, McQuilton P, Flamholz Z, Silverstein MC, Schilder BM, Robasky K, Castillo C, Idaszak R, Ahalt SC, Williams J, Schurer S, Cooper DJ, de Miranda Azevedo R, Klenk JA, Haendel MA, Nedzel J, Avillach P, Shimoyama ME, Harris RM, Gamble M, Poten R, Charbonneau AL, Larkin J, Brown CT, Bonazzi VR, Dumontier MJ, Sansone SA, Ma'ayan A. (2019) FAIRshake: Toolkit to Evaluate the FAIRness of Research Digital Resources Cell Syst. 2019 Oct 10. pii: S2405-4712(19)30345-X. doi: 10.1016/j.cels.2019.09.011. Boyles RR, Thessen AE, Waldrop A, and Haendel MA. (2019) Ontology-based data integration for advancing toxicological knowledge. Vol 19:67-74. Fukushima M, Austin C, Sato N, Maruyama T, Navarro E, Rocca M, Demotes J, Haendel M, Volchenboum SL, Cowperthwaite M, Silverstein JC, Webb C, Sim I, Chase M, Speakman J, Augustine E, Ford DE, Kush R. (2019) The Global academic research organization network: Data sharing to cure diseases and enable learning health systems. Learn Health Syst. 2018 Dec 3;3(1):e10073. doi: 10.1002/lrh2.10073. eCollection 2019 Jan.K?hler S, NC ?ien, OJ Buske, T Groza, JOB Jacobsen, C McNamara, *N Vasilevsky, LC Carmody, *JP Gourdine, M Garano JA McMurry, D Danis, CJ Mungall, D Smedley, M Haendel, PN Robinson. (2019) Encoding Clinical Data with the Human Phenotype Ontology for Computational Differential Diagnostics. Current Protocols in Human Genetics 103 (1), e92 *menteeCacheiro, P., Haendel, M.A., Smedley, D. the International Mouse Phenotyping Consortium and the Monarch Initiative. (2019) New models for human disease from the International Mouse Phenotyping Consortium. Mamm Genome. YA, Pichler K, Füllgrabe A, Lomax J, Malone J, Munoz-Torres MC, Vasant DV, Williams E,?Haendel M. (2019) PLoS Comput Biol. Ten quick tips for biocuration. May 2;15(5):e1006906. doi: 10.1371/journal.pcbi.1006906. eCollection 2019 May. Xingmin Aaron Zhang, Amy Yates, *Nicole Vasilevsky, *J. P. Gourdine, Tiffany J. Callahan, Leigh C. Carmody, Daniel Danis, Marcin P. Joachimiak, Vida Ravanmehr, Emily R. Pfaff, James Champion, Kimberly Robasky, Hao Xu, Karamarie Fecho, Nephi A. Walton, Richard L. Zhu, Justin Ramsdill, Christopher J. Mungall, Sebastian K?hler, Melissa A. Haendel, Clement J. McDonald, Daniel J. Vreeman, David B. Peden, Tellen D. Bennett, James A. Feinstein, Blake Martin, Adrianne L. Stefanski, Lawrence E. Hunter, Christopher G. Chute & Peter N. Robinson. (2019) Semantic integration of clinical laboratory tests from electronic health records for deep phenotyping and biomarker discovery. npj Digital Medicine. volume 2, Article number: 32 *menteeCarbon S, *Champieux R, McMurry JA, *Winfree L, Wyatt LR, Haendel MA. (2019) An analysis and metric of reusable data licensing practices for biomedical resources. PLoS One. Mar 27;14(3):e0213090. doi: 10.1371/journal.pone.0213090. eCollection 2019. *menteeTaylor DM, Aronow BJ, Tan K, Bernt K, Salomonis N, Greene CS, Frolova A, Henrickson SE, Wells A, Pei L, Jaiswal JK, Whitsett J, Hamilton KE, MacParland SA, Kelsen J, Heuckeroth RO, Potter SS, Vella LA, Terry NA, Ghanem LR, Kennedy BC, Helbig I, Sullivan KE, Castelo-Soccio L, Kreigstein A, Herse F, Nawijn MC, Koppelman GH,?Haendel M, Harris NL, Rokita JL, Zhang Y, Regev A, Rozenblatt-Rosen O, Rood JE, Tickle TL, Vento-Tormo R, Alimohamed S, Lek M, Mar JC, Loomes KM, Barrett DM, Uapinyoying P, Beggs AH, Agrawal PB, Chen YW, Muir AB, Garmire LX, Snapper SB, Nazarian J, Seeholzer SH, Fazelinia H, Singh LN, Faryabi RB, Raman P, Dawany N, Xie HM, Devkota B, Diskin SJ, Anderson SA, Rappaport EF, Peranteau W, Wikenheiser-Brokamp KA, Teichmann S, Wallace D, Peng T, Ding YY, Kim MS, Xing Y, Kong SW, B?nnemann CG, Mandl KD, White PS. Dev Cell. (2019) The Pediatric Cell Atlas: defining the growth phase of human development at single-cell resolution. Apr 8;49(1):10-29. doi: 10.1016/j.devcel.2019.03.001.?Sebastian Kohler?,?Leigh Carmody?,?Nicole Vasilevsky?,?Julius O B Jacobsen?,?Daniel Danis?,?Jean-Philippe Gourdine?,?Michael Gargano?,?…. ,?Tudor Groza?,?Damian Smedley?,?Melissa A Haendel?, Chris Mungall?,?Peter N Robinson. (2018) Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources. Nucleic acids research Nov 22, 2018 doi: 10.1093/nar/gky1105 L Dolman, A Page, L Babb, RR Freimuth, H Arachchi, C Bizon, M Brush, ?Marc Fiume, Melissa Haendel, David P Hansen, Aleksandar Milosavljevic, Ronak Y Patel, Piotr Pawliczek, Andrew D Yates, Heidi L Rehm (2018) ClinGen advancing genomic data‐sharing standards as a GA4GH driver project. Human Mutation 39 (11), 1686-1689Haendel M, Chute C, Robinson PN. (2018) Enabling Precision Medicine -- Classification, Ontology, and Computational Reasoning. New England Journal of Medicine. 379 (15), 1452-1462Harindra Arachchi, Monica H Wojcik, Benjamin Weisburd, Julius OB Jacobsen, Elise Valkanas, Samantha Baxter, Alicia B Byrne, Anne H O'Donnell‐Luria, Melissa Haendel, Damian Smedley, Daniel G MacArthur, Anthony A Philippakis, Heidi L Rehm (2018) matchbox: An open‐source tool for patient matching via the Matchmaker Exchange. Hum Mutat.?2018 Sep 21. doi: 10.1002/humu.23655Tan et. al. (2018) Further evidence for the involvement of EFL1 in a Shwachman–Diamond-like syndrome and expansion of the phenotypic features. Molecular case studies. 4 (5), a003046 (middle author of >50 authors)Pena et al. (2018) Looking beyond the exome: a phenotype-first approach to molecular diagnostic resolution in rare and undiagnosed diseases. Genetics in Medicine 20 (4), 464 (middle author of >50 authors)Marcogliese PC, Shashi V, …..Haendel M, …Pena LM. (2018) IRF2BPL?Is Associated with Neurological Phenotypes. American Journal of Human Genetics. Volume 103, Issue 2,?2 August 2018, Pages 245-260Pena LM, Jiang YH, ….Haendel M, ……Vandana Shashi (2018) Looking beyond the exome: a phenotype-first approach to molecular diagnostic resolution in rare and undiagnosed diseases. Genetics in Medicine volume 20, pages 464–469Baynam G, Bowman F, Lister K, Walker CE, Pachter N, Goldblatt J, Boycott KM, Gahl WA, Kosaki K, Adachi T, Ishii K, Mahede T, McKenzie F, Townshend S, Slee J, Kiraly-Borri C, Vasudevan A, Hawkins A, Broley S, Schofield L, Verhoef H, Groza T, Zankl A, Robinson PN,?Haendel?M, Brudno M, Mattick JS, Dinger ME, Roscioli T, Cowley MJ, Olry A, Hanauer M, Alkuraya FS, Taruscio D, Posada de la Paz M, Lochmüller H, Bushby K, Thompson R, Hedley V, Lasko P, Mina K, Beilby J, Tifft C, Davis M, Laing NG, Julkowska D, Le Cam Y, Terry SF, Kaufmann P, Eerola I, Norstedt I, Rath A, Suematsu M, Groft SC, Austin CP, Draghia-Akli R, Weeramanthri TS, Molster C, Dawkins HJS. 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Haendel MA, Balhoff JP, Bastian FB, Blackburn DC, Blake JA, Bradford Y, Comte A, Dahdul WM, Dececchi TA, Druzinsky RE, Hayamizu TF, Ibrahim N, Lewis SE, Mabee PM, Niknejad A, Robinson-Rechavi M, Sereno PC, Mungall CJ. (2014) Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon. J Biomed Semantics. May 19;5:21. doi: 10.1186/2041-1480-5-21.Oellrich A, Koehler S, Washington N, Lewis S Mungall C, Haendel M, Robinson PN, Smedley D. (2014) The influence of disease categories on gene candidate predictions from model organism phenotypes. J Biomed Semantics. 2014 Jun 3;5(Suppl 1 Proceedings of the Bio-Ontologies Spec Interest G):S4. doi: 10.1186/2041-1480-5-S1-S4Tenenbaum JD, Sansone SA, Haendel M. (2014) A sea of standards for omics data: sink or swim? J Am Med Inform Assoc. Mar 1;21(2):200-3. doi: 10.1136/amiajnl-2013-002066. PMCID:PMC3932466.Van Slyke CE1, Bradford YM, Westerfield M, Haendel MA. (2014) The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio. J Biomed Semantics. 2014 Feb 25;5(1):12.K?hler S, Doelken SC, Mungall CJ, Bauer S, Firth HV, Bailleul-Forestier I, Black GC, Brown DL, Brudno M, Campbell J, Fitzpatrick DR, Eppig JT, Jackson AP, Freson K, Girdea M, Helbig I, Hurst JA, J?hn J, Jackson LG, Kelly AM, Ledbetter DH, Mansour S, Martin CL, Moss C, Mumford A, Ouwehand WH, Park SM, Riggs ER, Scott RH, Sisodiya S, Vooren SV, Wapner RJ, Wilkie AO, Wright CF, Vulto-van Silfhout AT, Leeuw Nd, de Vries BB, Washingthon NL, Smith CL, Westerfield M, Schofield P, Ruef BJ, Gkoutos GV,?Haendel?M, Smedley D, Lewis SE, Robinson PN. (2013) The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. Nucleic Acids Res. 2014 Jan 1;42(1):D966-74. doi: 10.1093/nar/gkt1026. Epub 2013 Nov 11. PMID:24217912Torniai C, *Essaid S, Barnes C, Conlon M, Williams S, Hajagos JG, Bremer E, Corson-Rikert J, Haendel?M. (2013) From EHRs to Linked Data: representing and mining encounter data for clinical expertise evaluation. AMIA Summits Transl Sci Proc. 2013 Mar 18;2013:165. PMID:24303330 *menteeSchleyer TK, Ruttenberg A, Duncan W,?Haendel?M, Torniai C, Acharya A, Song M, Thyvalikakath TP, Liu K, Hernandez P. (2013) An ontology-based method for secondary use of electronic dental record data. AMIA Summits Transl Sci Proc. Mar 18;2013:234-8. PMID:24303273Druzinsky R, Mungall C,?Haendel?M, Lapp H, Mabee P. What is an anatomy ontology? (2013) Anat Rec (Hoboken). 2013 Dec;296(12):1797-9. doi: 10.1002/ar.22805. Epub 2013 Oct 11. No abstract available. PMID:24127438*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. Sep 5;1:e148. doi: 10.7717/peerj.148. PMID:24032093 *menteeMeehan 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;14:263. doi: 10.1186/1471-2105-14-263. PMID:24004649 *menteeArighi CN, Carterette B, Cohen KB, Krallinger M, Wilbur WJ, Fey P, Dodson R, Cooper L, Van Slyke CE, Dahdul W, Mabee P, Li D, Harris B, Gillespie M, Jimenez S, Roberts P, Matthews L, Becker K, Drabkin H, Bello S, Licata L, Chatr-aryamontri A, Schaeffer ML, Park J, Haendel?M, Van Auken K, Li Y, Chan J, Muller HM, Cui H, Balhoff JP, Chi-Yang Wu J, Lu Z, Wei CH, Tudor CO, Raja K, Subramani S, Natarajan J, Cejuela JM, Dubey P, Wu C. An overview of the BioCreative 2012 Workshop Track III: interactive text mining task. (2013) Database (Oxford). 2013 Jan 17;2013:bas056. doi: 10.1093/database/bas056. Print 2013. PMID:23327936*Brush M., Mungall C.J., Washington N., and Haendel M. (2013) What’s in a Genotype?: An Ontological Characterization for Integration of Genetic Variation Data. International Conference on Biomedical Ontology proceedings. July 7-9; Montreal. *mentee*Essaid E., Torniai C., and Haendel, M. (2013) Enabling semantic search in a bio-specimen repository. International Conference on Biomedical Ontology proceedings. July 7-9; Montreal. *menteeArighi C.N., Carterette B., Cohen K.B., Krallinger M., Wilbur W.J., Fey P., Dodson R., Cooper L., Van Slyke C.E., Dahdul W., Mabee P., Li D., Harris B., Gillespe M., Jimenez S., Roberts P., Mathews L., Becker, K., Drabkin, H., Bellow S., Licata L., Chatr-Aryamontri A., Schaeffer M.L., Park, J., Haendel M., Van Auken K., Li Y., Chan J., Muller, H., Cui H., Balhoff J.P., Chi-Yang Wu J., Lu Z., Wei C., Tudor C.O., Raja K., Subramani S., Natarajan J., Cejuela J.M., Dubey P., Wu C. (2013) An overview of the BioCreative 2012 Workshop Track III: interactive text mining task. Database, The Journal of Biological Databases and Curation 01/2013; 2013:bas056.Dahdul W.M., Balhoff J.P., Blackburn D.C., Diehl A.D., Haendel M.A., Hall B.K., Lapp H., Lundberg J.G., Mungall C.J., Ringwald M., Segerdell E., Van Slyke C.E., Vickaryous M.K., Westerfield M., Mabee P.M. (2012) A unified anatomy ontology of the vertebrate skeletal system. PLoS One. 2012;7(12):e51070. doi: 10.1371/journal.pone.0051070. Epub 2012 Dec 10. PMID: 23251424Haendel, M.A., *Vasilevsky N.A. and *Wirz, J.A. (2012) Dealing with Data: A Case Study on Information and Data Management Literacy. Plos Biology 10(5): e1001339. doi:10.1371/journal.pbio.1001339 *mentee*Vasilevsky N., Johnson T., Corday K, Torniai C., *Brush M. *Segerdell E. *Wilson M., Shaffer C., Robinson D., Haendel M. (2012) Research resources: curating the new eagle-i discovery system. Database?Vol.?2012?published online?March 20, 2012,?doi:10.1093/database/bar067. *menteeMungall, C.J., Torniai, C., Gkoutos, G.V., Lewis, S.E., and Haendel, M.A. (2012)?Uberon, an integrative multi-species anatomy ontology”,?Genome Biology 13, R5.?, 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. *menteeMungall CJ, Haendel MA, Ireland A, Manzoor S, Meehan T, Osumi-Sutherland D, Torniai C, and Diehl A. (2011) Modularization for the Cell Ontology. International Conference on Biomedical Ontology; July 26–30; Buffalo, NY.Mungall, C.J., Gkoutos, G.V., Smith, C.L., Haendel, M.A., Lewis, S.E., and Ashburner, M. (2010) Integrating Phenotype Ontologies across Multiple Species. Genome Biol. 2010 Jan 8;11(1):R2.Washington, N.L.*, Haendel, M.A.*, Mungall, C.J., Ashburner, M., Westerfield, M., and Lewis, S.L. (2009) Linking human disease to animal models using ontology-based phenotype annotation. PLoS Biol. 2009 Nov;7(11):e1000247. Epub 2009 Nov 24. *These authors contributed equally to this manuscript.Dahdul, W.M., Mabee, P.M., Lundberg, J.G., Midford, P.E., Balhoff, J.P., Lapp, H., Vision, T.J., Haendel, M.A., Westerfield, M. (2009) The Teleost Anatomy Ontology: Anatomical Representation for the Genomics Age. Systematic Biology, 59(4):369-383.Sprague, J., Bayraktaroglu, L.,Bradford, Y., Conlin, T., Dunn, N., Fashena, D., Frazer, K., Haendel, M., Howe, D., Mani, P., Moxon, S., Pich, C., Ramachandran, S., Schaper, K., Shao, X., Singer, A., Song, P., Sprunger, B., Van Slyke, C., Westerfield, M. (2008) The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes. Nucleic Acids Research. Jan;36(Database issue):D768-72.Takayama, S., Hostick, U., Haendel, M., Eisen, J., and Darimont, B. (2008) An F-domain introduced by alternative splicing regulates activity of the zebrafish thyroid hormone receptor alpha. Gen. Comp. Endocrinol. Jan 1;155(1):176-89.Day-Richter, J., Harris, M.A., Haendel, M.A., The Gene Ontology OBO-Edit Working Group and Lewis, S. (2007). OBO-Edit - An Ontology Editor for Biologists. Bioinformatics. 23(16):2198-2200.Mabee, P.M., Arratia, G., Coburn, M., Haendel, M., Hilton, E.J., Lundberg, J.G., Mayden, R.L., Rios, N., and Westerfield, M. (2007) Connecting evolutionary morphology to genomics using ontologies: a case study from Cypriniformes including zebrafish. J. Exp. Zoolog. B Mol. Dev. Evol. 308B(5):655-668.Mabee, P.M., Ashburner, M., Cronk, Q., Gkoutos, G.V., Haendel, M., Segerdell, E., Mungall, C., and Westerfield, M. (2007) Phenotype ontologies: the bridge between genomics and evolution. Trends Ecol. Evol. 22(7):345-350.Sprague, J., Bayraktaroglu, L., Clements, D., Conlin, T., Fashena, D., Frazer, K., Haendel, M., Howe, D.G., Mani, P., Ramachandran, S., Schaper, K., Segerdell, E., Song, P., Sprunger, B., Taylor, S., Van Slyke, C.E., and Westerfield, M. (2006) The Zebrafish Information Network: the zebrafish model organism database. Nucleic Acids Res. 34:D581-585.Metcalfe S.M., Muthukumarana P.A., Thompson H.L., Haendel M.A., Lyons G.E. (2005) Leukaemia inhibitory factor (LIF) is functionally linked to axotrophin and both LIF and axotrophin are linked to regulatory immune tolerance. FEBS Lett. 579(3):609-14.Haendel, M.A., Tilton, F., Bailey, G.S., and Tanguay, R.L. (2004) Developmental Toxicity of the Dithiocarbamate Pesticide Sodium Metam in Zebrafish. Toxicol. Sci. 81(2):390-400.Reyes, R., Haendel, M., Grant, D., Melan?on, E., and Eisen, J.S. (2004) Slow degeneration of zebrafish Rohon-Beard neurons during programmed cell death. Dev. Dyn. 229(1):30-41.Lyons, G.E., Swanson, B.J., Haendel, M.A., and Daniels, J. (2000) Gene trapping in embryonic stem cells in vitro to identify novel developmentally regulated genes in the mouse. Methods Mol Biol. 136:297-307.Hunter, P.J., Swanson, B.S., Haendel, M.A., Lyons, G.E., and Cross, J.C. (1999) Mrj encodes a DnaJ-related chaperone that is essential for murine placental development. Development. 126:1247-1258.Yamakawa, K., Huo, Y.K. Haendel, M. A., Huber., R., Cehn, X.N., Lyons, G.E., and Korenburg, J. R. (1998) DS-CAM: A novel member of the immunoglobulin superfamily maps in a Down Syndrome region and is involved in the development of the nervous system. Hum Mol Genet. 7(2):227-37.Baker*, R.K., Haendel*, M.A., Swanson*, B.J., Shcambaugh, J.C., Micales, B.K., and Lyons, G.E. (1997) In vitro preselection of gene-trapped embryonic stem cell clones for characterizing novel developmentally regulated genes in the mouse. Dev Biol. 185(2):201-214.*These authors contributed equally to this manuscript.Haendel, M.A., Bollinger, K.E., and Baas, P.W. (1996) Cytoskeletal changes during neurogenesis in cultures of avian neural crest cells. J Neurocytol. 25:289-301.EDITORIALS, REVIEWS, BOOK CHAPTERS, AND PREPRINTS:Nicole Vasilevsky, Julien Colomb, Scott Edmunds, Karen Gutzman, Melissa Haendel, Daniel Himmelstein, Mohammad Hosseini, Violeta Ilik, Barbara Kern, Ehsan Mohammadi, Lisa O'Keefe, Juliane Schneider, Britton Smith, Samantha Teplitzky, Marijane White, Kristi Holmes. (2020) Major challenges on authorship and concept of authorship-why is something more needed on contributorship? Manubot N Robinson, Vida Ravanmehr, Julius OB Jacobsen, Daniel Danis, Xingmin Aaron Zhang, Leigh Carmody, Michael Gargano, Courtney Thaxton, Justin Reese, Manuel Holtgrewe, Sebastian Koehler, Julie A McMurry, Melissa A Haendel, Damian Smedley. (2020) Interpretable Clinical Genomics with a Likelihood Ratio Paradigm. MedArxiv. Haendel;?Julie McMurry;?Anne Thessen;?Chris Bizon;?Nomi Harris;?Chris Mungall. (2019, November 18). A Common Dialect for Infrastructure and Services in Translator. Zenodo. Aaron Zhang, Amy Yates, Nicole Vasilevsky, JP Gourdine, Leigh C Carmody, Daniel Danis, Marcin P Joachimiak, Vida Ravanmehr, Emily R Pfaff, James Champion, Kimberly Robasky, Hao Xu, Karamarie Fecho, Nephi A Walton, Richard Zhu, Justin Ramsdill, Chris Mungall, Sebastian Kohler, Melissa A Haendel, Clem McDonald, Daniel J Vreeman, David B Peden, Christopher G Chute, Peter N Robinson. (2019) Semantic Integration of Clinical Laboratory Tests from Electronic Health Records for Deep Phenotyping and Biomarker Discovery. , Nicolas, Balhoff, James P., Bello, Susan M., Boerkoel, Cornelius F., Bradford, Yvonne M., Carmody, Leigh C., … Haendel, Melissa A. (2018, December 20). Phenotype Ontologies Traversing All The Organisms (POTATO) workshop aims to reconcile logical definitions across species. Zenodo. G , Veiga DF , Deslattes Mays A , Kesarwani AK , Danis D , Kararigas G , Zhang XA , George J , Ananda G , Steinhaus R , Hansen P , Seelow D , Bizon C , Boyles R , Ball C , McMurry JA , Haendel MA , Yang J , Oprea T , Mukerji M , Anczukow O , Banchereau J , Robinson PN (2018) The impact of sex on alternative splicing. bioRxiv 490904; Laderas, N Vasilevsky, B Pederson, M Haendel, S McWeeney, D Dorr (2018). Teaching data science fundamentals through realistic synthetic clinical cardiovascular data. bioRxiv, 232611 Pons,?Ryan?Duren,?Jianjiong?Gao,?Julie?McMurry,?Sara?Patterson,?Catherine?Del Vecchio Fitz,?Ozman Ugur?Sezerman,?Jeremy?Warner,?Damian T?Rieke,?Tero?Aittokallio,?Ethan?Cerami,?Deborah?Ritter,?Lynn M?Schriml,?Melissa?Haendel,?Gordana?Raca,?Subha?Madhavan,?Michael?Baudis,?Jacques S?Beckmann,?Rodrigo?Dienstmann,?Debyani?Chakravarty,?Xuan Shirley?Li,?Susan M?Mockus,?OlivierElemento,?Nikolaus?Schultz,?Nuria?LopezBigas,?Mark?Lawler,?Jeremy?Goecks,?MalachiGriffith,?Obi L?Griffith,?Adam?Margolin. (2018). A harmonized meta-knowledgebase of clinical interpretations of cancer genomic variants. bioRxiv?366856;? R?Wyatt,?Melissa Haendel (2018). A Measure of Open Data: A Metric and Analysis of Reusable Data Practices in Biomedical Data Resources. bioRxiv?282830;?doi:? Ilik, M Conlon, G Triggs, M Haendel, KL Holmes (2017) OpenVIVO: Transparency in Scholarship. Open Science Framework. 10.17605/OSF.IO/5N2TQMungall CJ, Koehler S, Robinson P, Holmes I, Haendel M. (2016) k-BOOM: A Bayesian approach to ontology structure inference, with applications in disease ontology construction. bioRxiv 048843; doi: M, Gray AJG, Marshall MS, Alexiev V, Ansell P, Bader G, Baran J, Bolleman JT, Callahan A, Cruz-Toledo J, Gaudet P, Gombocz EA, Gonzalez Beltran AN, Groth P, Haendel M, Ito M, Jupp S, Juty N, Katayama T, Kobayashi N, Krishnaswami K, Laibe C, Le Novère N, Lin S, Malone J, Miller M, Mungall CJ, Rietveld L, Wimalaratne SM, Yamaguchi A.?(2016)?The health care and life sciences community profile for dataset descriptions.?PeerJ Preprints?4:e1982v1? J, Blomberg N, Burdett T, Conte N, Dumontier M, Fellows DK, Gonzalez-Beltran A, Gormanns P, Hastings J, Haendel MA, Hermjakob H, Hériché JK, Ison JC, Jimenez RC, Jupp S, Juty N, LaibeC, Le Novère N, Malone J, Martin MJ, McEntyre JR, Morris C, Muilu J, Müller W, Mungall CJ, Rocca-Serra P, Sansone S, Sariyar M, Snoep JL, Stanford NJ, Swainston N, Washington NL, Williams AR, Wolstencroft K, Goble C, Parkinson H. (2015) Identifiers for the 21st century: How to design, provision, and reuse identifiers to maximize data utility and impact Zenodo. MA, Kann MG, Washington NL. (2016) Innovative approaches to combining genotype, phenotype, epigenetic, and exposure data for precision diagnostics. Pac Symp Biocomput. 2016;21:93-5. PMID: 26776176 Robinson PN, Mungall CJ, Haendel M. (2015) Capturing phenotypes for precision medicine. Cold Spring Harb Mol Case Stud. 2015 Oct;1(1):a000372. doi: 10.1101/mcs.a000372.Deck J, Guralnick R, Walls R, Blum S, Haendel M, Matsunaga A, Wieczorek J. (2015) Meeting report: Identifying practical applications of ontologies for biodiversity informatics. Standards in Genomic Sciences 10 (1), 25Vasilevsky, N, Wirz, J, Champieux, R, Hannon, T, Laraway, B, Banerjee, K, Shaffer, C, and Haendel, M. (2014). Lions, Tigers, and Gummi Bears: Springing Towards Effective Engagement with Research Data Management. Scholar Archive. Paper 3571. DOI:10.6083/M4QC0273Hoehndorf R, Haendel M, Stevens R, Rebholz-Schuhmann D. (2014) Thematic series on biomedical ontologies in JBMS: challenges and new directions. J Biomed Semantics. 2014 Mar 6;5:15. doi: 10.1186/2041-1480-5-15. Review.Haendel M.A. and Chesler E.J. (2012) Lost and found in behavioral informatics, in Int Rev Neurobiol. 103:1-18. doi: 10.1016/B978-0-12-388408-4.00001-0.Haendel, M.A., F. Neuhaus, D.S. Osumi-Sutherland, P.M. Mabee, J.L.V. Mejino, C.J. Mungall and B. Smith. (2008) CARO - The Common Anatomy Reference Ontology. In: Anatomy Ontologies for Bioinformatics: Principles and Practice, A. Burger, D. Davidson and R. Baldock (eds).N. Washington, M. Gibson, Mungall C., Ashburner M., Gkoutos G.V., Westerfield M., Haendel M., Lewis S.E. (2008) NLP and Phenotypes: using Ontologies to link Human Diseases to Animal Models. In proceeding of: Ontologies and Text Mining for Life Sciences: Current Status and Future Perspectives, 24.03. - 28.03.2008THESES & EDITED VOLUMES:Haendel, M.A. (1999) Identification and characterization of the novel gene, axotrophin, using an in vitro gene trap preselection method. Presented to the University of Wisconsin Neuroscience Training Program in partial fulfillment of a Ph.D. degree. OCLC:?ocm50951661.Haendel, M.A. (1991) Designing Drugs: A New Method Using MEPs in Constructing QSARs. Presented to the Reed College Chemistry Department in partial fulfillment of a B.A. degree.Bioinformatics of Behavior. Int Rev Neurobiol. (2012) Vol 103 and Vol 104. doi: 10.1016/B978-0-12-388408-4.00001-0. Haendel, M.A. and Chessler, E.J. Editors. Elsevier.NATIONAL AND INTERNATIONAL INVITED PRESENTATIONS:15 International presentations since 2017, 10 Keynotes total Haendel, MA. [2020] Advance-CTR, Dakota Cancer Collaborative on Translational Activity, Great Plains IDeA-CTR, Mississippi Center for Clinical and Translational Research, and Oklahoma Clinical and Translational Science Institute, Featured Speaker, October 28th, 2020. Slides: in mp4 format: Haendel, MA. [2020] Inaugural Precision Medicine Leaders’ Summit – Research Triangle Park, North Carolina. October 20, 2020. Invited Panelist, Using Data to Enable Precision Health Programs. , MA. [2020] Artificial Intelligence for Data Discovery and Reuse (AIDR) Symposium 2020, invited speaker. bit.ly/aidr-2020Haendel, MA. NIH Jumpstart Clinical Data Access to COVID-19 Research Workshop, Featured Speaker, Weds, July 29th, 2020. “National COVID Cohort Collaborative (N3C)” bit.ly/n3c-jumpHaendel, MA. 2nd COV-IRT Symposium Friday, July 17th, 2020 Featured Speaker. bit.ly/n3c-cov-irtHaendel MA, Gersing K, Chute C, and Robinson P. [2020] NIH National Institute of Allergy and Infectious Diseases (NIAID) System Biology Working Group webinar, Invited panel, May 15, 2020. “National COVID Cohort Collaborative (N3C)” bit.ly/n3c-sysbioHaendel, MA [2020] NIH National Institute of Allergy and Infectious Diseases (NIAID) Data Science webinar, Invited speaker, May 15, 2020. “Realizing the National COVID CohortCollaborative (N3C)” bit.ly/n3c-webinar-3Haendel, MA, Chute, C; Rocca, M., and Gersing, K. American Medical Informatics Association webinar series. Invited panelist. April 13, 2020. “Building a Nationwide COVID-19 Cohort Through Informatics: A New Initiative From CD2H & NCATS.” bit.ly/n3c-amiaHaendel, MA (2020) NIH Biomedical Information Science and Technology Initiative (BISTI), Invited Speaker, April 2, 2020. “Phenopackets on FHIR: the wide world of phenotype exchange” bit.ly/mh-bisti-20200402 Haendel, MA (2020) Space Science Week: Life and physical sciences in space; Preparing for the future of space exploration. National Academy of Sciences, Invited Speaker, March 31, 2020, “Bringing Phenotype to the Genotype: Semantics for Maximizing Disease Discovery.” bit.ly/semantics-space Haendel, MA (2019) International Society for Computational Biology, Keynote, November 13, 2019, Kumasi, Ghana, Africa. “Born Reusable: data in harmony to realize the dream of AI.” bit.ly/melissa-iscbafrica?Haendel, MA (2019) SINAinnovations Invited speaker. October 15th, Mt Sinai, New York, NY. 2019. “Using Reason(ers): Classification of Patients for Diagnosis, Care Management, and Translational Research.” bit.ly/ai-haendelHaendel, MA (2019) National Cancer Institute, “Born Reusable: Best Practices for Data Providers”. Oct 10, 2019. Webinar. , MA (2019) University of Michigan, Special Joint Lecture (MICHR and DCMB), Oct 2, 2019, Ann Arbor, MI, Invited Speaker.?"Semantic integration across species for rare disease diagnostics" , MA (2019) National Library of Medicine, Sept 25th, 2019, Washington, DC. Invited speaker. bit.ly/bornreusable19Haendel, MA (2019) NHGRI, USDA, & NSF Interagency Symposium on Perspectives in Comparative Genomics & Evolution, Aug 15, 2019, Washington, DC, Invited Speaker. bit.ly/compgen19Haendel, MA (2019) PID workshop, Portland, OR, Invited Speaker. Haendel, MA. (2019) Manton Center for Rare Diseases. “Mama, dogs are a lot like people.” Encapsulating a comparative phenomics odyssey. Boston, MA. Invited speaker. Haendel, M.A. (2018) The 7th Annual Big Data in Bioscience Symposium hosted by the Georgetown University Innovation?Center for Biomedical Informatics. Washington, DC. Keynote.Haendel M.A. (2018) Fanconi Anemia Research Foundation Symposium, Newport Beach, CA. From butterflies to patient-engaged phenotyping to advance clinical care and rare disease science. bit.y/lay-FARF. Invited speaker.Haendel M.A. (2018) Vancouver Bioinformatics Symposium, Vancouver BC. Power to the patient: an ontological approach for patient-clinician collaboration on rare disease diagnosis. Invited seminar.Haendel M.A. (2018) Kidney Precision Medicine Initiative, Seattle, WA. Deep phenotyping for diagnostics using the Human Phenotype Ontology. Invited speaker. Haendel M.A. (2018) Society for Developmental Biology, Portland, OR. Cross-species phenomics for interpretation of disease variants. Invited speaker.Haendel M.A. (2018) Frontiers in Pediatric Genomic Medicine Conference. Rady Children’s Institute, La Jolla, CA. Collaborative phenotyping with your patient using the HPO. Invited speaker.Haendel M.A. (2018) U.S. Semantic Technologies Symposium. Semantics for rare disease phenotyping, diagnostics, and discovery. Invited speaker.Association of University Technology Managers (AUTM) Annual Conference 2018?Moderator: Arvin Paranjpe, Oregon Health & Science University?Speakers: Frank Curci, Ater Wynne LLP?Melissa Haendel, Oregon Health & Science University?Charles Williams, University of Oregon?mhaendel/the-software-and-data-licensing-solution-not-your-dads-ubmtaInvited speaker.Haendel M.A. (2018) PIDapalooza Keynote, Jan 24th Girona, Spain. Equivalency is in the (ID) of the beholder. mhaendel/equivalence-is-in-the-id-of-the-beholderHaendel M.A. (2017) NIH Data Commons Pilot Phase Consortium (DCPPC) meeting, Dec 6, Washington, DC. Building (and traveling) the data-brick road: A report from the front lines of data integration mhaendel/building-and-traveling-the-databrick-road-a-report-from-the-front-lines-of-data-integration Invited speaker.Haendel, M.A. (2017) Japan Global Academic Research Organization Council, workshop on A New Paradigm for Medical Science based upon Data Sharing. Standards for phenotype representation, exchange, and diagnostics. November 17th, Austin, Texas. Invited speaker.Haendel, M.A. (2017) NCATS CTSA PI Annual symposium, October 26, Washington, DC. mhaendel/the-ctsa-program-center-for-data-to-health-cd2hHaendel, M.A. (2017) Global Alliance for Genomics and Health. October 15. Orlando, Florida. Phenotype Ontologies. , M.A. (2017) Global Alliance for Genomics and Health. October 15. Orlando, Florida. Monarch Initiative Driver project. , M.A. (2017) Fanconi Anemia Research Fund Annual Symposium. Sept 17. Data Translator: an Open Science Data Platform for Mechanistic Disease Discovery.Haendel, M.A. (2017) Research Data Alliance. Sept 20th. Montreal, Canada. Reusable data for biomedicine: A Data Licensing Odyssey. , M.A. (2017) ILAR Roundtable, National Academy of Sciences. Making connections between human and animal phenotypes. Oct. 6th. Invited speaker.Haendel, M.A. (2017) Kids First. Deep Phenotyping for Improved Diagnostics and Analysis. Sept 7th.Haendel, M.A. (2017) University of Pennsylvania, Institute of Bioinformatics. August 8, Philadelphia, PA. Crossing the semantic chasm of despair: semantics for translational research. Invited speaker.Haendel, M.A. (2017) H3ABioNet 2nd Sickle Cell Disease Ontology Workshop. June 6th, Capetown, South Africa. Using Ontologies for disease research. Invited speaker.Haendel, MA. (2017). NIH Data Standards for Registries Meeting, Office of Rare Disease Research. June 28, Washington, DC. Identifiers, metadata, ontologies, oh my! Working towards a translational data ecosystem. Invited speaker.Haendel, M.A. and Koehler, S. (2017) RD-Action European Reference Network workshop. April 26-27, Brussels, Belgium. Global phenotypic data sharing standards to maximize diagnostic discovery. Invited speaker.Haendel, M.A. (2017) International Rare Diseases Research Consortium (IRDiRC), Paris, France. Global Phenotypic Data Sharing Standards to Maximize Diagnostics and Mechanism Discovery. Invited speaker.Haendel, M.A. (2016) Sanford Healthcare Imagenetics program. Sioux Falls, SD. “Human Model data integration for diagnosis”. Invited speaker and continuing medical education seminar.Haendel, M.A. and Mungall, CJ. (2016) Global Alliance for Genomics and Health. Vancouver, BC. “What is a phenopacket, anyway?” Invited speaker.Haendel, M.A. and Mungall, CJ. (2016) Global Alliance for Genomics and Health. Vancouver, BC. “Patient phenotyping” Invited speaker.Haendel, M.A. (2016) NHGRI Workshop on Computational Genomics and Data Science. Washington, DC. “Interoperability of organism data (technical, semantic, legal)”. Invited speaker.Haendel, M.A. (2016) University of British Columbia Centre for Molecular Medicine and Therapeutics. “Data integration across the translational divide for mechanistic discovery”. Invited speaker. Haendel, M.A. (2016) Open Access Scholarly Publishers Association (OASPA), Washington DC. “Credit where Credit is Due: Acknowledging all Types of Contributions”. Invited speaker. , M.A. (2016) FDA. Washington, DC. Workshop to Build Systems Pharmacology Model for Adverse Events. “An Introduction to ontology-based cross-species data integration in the Monarch Initiative”. Invited speaker.Haendel, M.A. (2016) ISMB, Orlando, FL. PhenoDay. “Deep phenotyping for everyone”. Keynote. , M.A. (2016) Regeneron. Tarrytown, NY. “Translating Human to Models and Back Again: Deep Phenotyping for Disease Discovery”. Private corporation invited seminar. Haendel, M.A. (2016) eMERGE consortium. Washington, DC. “Phenotype Ontologies for Data Integration and Discovery”. Keynote. Haendel, M.A. (2016) NHGRI Genomic Medicine IX: NHGRI’s Genomic Medicine Portfolio – Bedside to Bench. April 19-20, Silver Spring, MD. Invited speaker. Haendel, M.A. (2016) International Society for Biocuration Conference 2016, Geneva, Switzerland. Keynote. (April) , M.A. (2016) Phenotype RCN, Biosphere, AZ. “Use of ontologies for genotype-phenotype data integration”. Invited speaker. Haendel, M.A. (2016) TorBUG. Seminar Series Invited speaker. University of Toronto, Canada. “The Monarch Initiative: An integrated genotype-phenotype platform for disease discovery.”Haendel, M.A. (2016) National Institute of Environmental Health Sciences (NIEHS) Predictive Toxicology and Disease Seminar Series. Invited speaker. “A semantic approach to cross-species phenomics for disease discovery.”Haendel, M.A. (2016) Force2016. Haendel, Melissa (2016): Phenopackets: Making phenotype profiles FAIR++ for disease diagnosis and discovery. Invited speaker. Haendel, M.A. (2015) Semantic Web Applications and Tools for Life Sciences (SWAT4LS) 2015, Cambridge, UK. Keynote. , M.A. (2015) NISO webinar for Research Data Metrics from the Altmetrics working group on output types and identifiers. Invited Speaker. Haendel, M.A. (2015) Linking Disease Model Phenotypes to Human Conditions Symposium, Co-chair and invited talk. Office of Director. , M.A. (2015) “A semantic approach to disease discovery” Invitae, San Francisco. Private corporation invited seminar.Haendel, M.A. (2015) ClinGen-Decipher joint meeting, Washington DC. Invited Speaker. , M.A. (2015) Undiagnosed Disease Steering Committee Meeting, Stanford. “Patient Matchmaking.” Invited speaker.Haendel, M.A. (2015) NISO Virtual Conference: Scientific Data Management: Caring for Your Institution and its Intellectual Wealth. Invited Speaker. , M.A. (2015) NCI Center for Biomedical Informatics and Information Technology (CBIIT) Speaker Series. “The Monarch Initiative: Semantic Phenotyping for Disease Diagnosis and Discovery.” Invited speaker. , M.A. and Dumontier, M. (2015). BioCaddie Workshop, Do we know how to cite data? If so, let's go.... “Describing Datasets with the W3C HCLS standard” Invited speaker. , M.A. (2014) Project CredIT workshop, “On the nature of credit” Invited speaker. , M.A. (2014) University of Maryland, Institute for Genome Sciences Seminar Series, “Cross-species phenotyping for disease discovery.” Invited speaker.Haendel, M.A. (2014) NIH BD2K Data Standards Working group, guest lecture. “Envisioning a semantically linked scientific landscape.” Invited speaker.Haendel, M.A. (2014) NIEHS/Environmental Protection Agency, Data Science Symposium, “Cross-Species Phenotype Comparisons for disease diagnostics.” Invited speaker.Haendel, M.A. (2014) NIH ORIP Tenth Comparative Medicine Resource Directors Meeting, Bethesda, MD, invited speaker, “Reproducibility in Translational Science.”Haendel, M.A. (2014) VIVO 2014 Conference, Austin, TX, invited speaker, “Standardizing scholarly output.” , M.A. (2014) Bio-ontologies SIG at ISMB in Boston, MA, keynote, “From baleen to cleft palate: an ontological exploration of evolution and disease.” , M.A. (2014) Harvard Center for Bioinformatics, Boston, MA, invited speaker, “Use of semantic phenotyping to aid disease diagnosis.” , A and Haendel, M. (2014) National Network of Libraries of Medicine Pacific Northwest Region PNR Rendezvous June 18th, invited speaker, “Developing data services: a tale from two Oregon universities” N. and Haendel, M.A. (2014) NIH Undiagnosed Disease Program Translational Seminar Series, June 18th, invited speaker, “What’s in a model? ”Haendel, M.A. (2014) NIH Undiagnosed Disease Program Translational Seminar Series, Jan 20th, invited speaker, “The integrated cross-species phenome as a tool for understanding disease.”Haendel, M.A. (2014). Updates in Clinical Genetics 2014 Conference. University of British Columbia, invited speaker, “Expanding the clinical phenotype space with semantics and model systems.” , M.A. (2014) Research Profiles Conference at the University of Melbourne, invited speaker, “Reproducibility: What does it mean and how can libraries help achieve it?”Haendel, M.A. (2014) International Society for Biocuration Conference, invited speaker, “The Resource Identification Initiative: What are we curating anyway?” , M.A. (2013) ISCB Rocky Bioinformatics, December, keynote, “Tales from the Crypt: Do You Know Where Your Data Has Been?”Haendel M. (2013) Intrafrontier IMPC-IKMC, Rome, Italy, December, invited speaker, “The integrated cross-species phenome as a tool for understanding disease.” Haendel, M.A. (2013). Beyond the PDF2, March 19-20th, Amsterdam, Netherlands, invited speaker, “On the reproducibility of science.” , M.A. (2013) National Center for Biomedical Ontology Seminar series, invited speaker, “Removing Roadblocks: Leveraging ontologies for data aggregation and computation.” , M.A. (2013) Ontolog Ontology Evaluation Forum, invited speaker, “Intrinsic ontology evaluation from a biologist’s perspective.” , M.A. (2012) VIVO Annual Conference. Miami, FL, invited speaker, “CTSAconnect: A Linked Open Data approach to represent clinical and research expertise, activities, and resources” and “Panel – Building better teams: innovative approaches to the design and deployment of researcher recommendation systems.” , M.A. (2013) Science Beyond the Ivory Tower Seminar Series, Information Careers in the Biosciences, City of Hope, invited speaker, “Biocurator: Add equal parts biologist, librarian, philosopher, and engineer.” Haendel, M.A., (2013) eScience Workshop: The Research Lifecycle: Partnering for Success, University of Utah, UT, invited speaker, “The eagle-i Network: enabling research resource discovery.” , M.A. (2012) CTSA tool shop Webinar series, invited speaker, CTSAconnect presentation. MA. (2012) Western Association of Core Directors meeting in Portland, OR. November, invited speaker, “Connecting researchers and research resources using eagle-i and other networking tools.” , M.A. (2010). Open Biomedical Ontologies Conference, Cambridge, UK, invited speaker, “An introduction to the eagle-i consortium.”Haendel, MA, Mungall, C, and Gkoutos G. (2010). Cell Ontology Workshop. Jackson Lab, ME, invited speaker, “The “über-ontology” (Uberon).”Haendel, M.A. (2009) The 6th European Meeting on Zebrafish Genetics and Development, Rome, Italy, Invited speaker. “Amplify the Impact of your Research: Ensure that your data can be integrated into the electronic data stream.”Haendel, M.A. (2008) Society for the Study of Evolution Annual Conference. Minneapolis, MN, invited speaker. “The Common Anatomy Reference Ontology (CARO) and queries across species”Haendel, M.A. (2006) Western Oregon University, Monmouth, OR, invited speaker. “Zebrafish: a model for development and disease.”Haendel, M.A. (2005) Neuroscience Training Program Career Development Seminar series, Madison, WI, Invited speaker. “Scientific Curation: At the crossroads of bioinformatics”LOCAL AND INSTITUTIONAL INVITED PRESENTATIONS: School of Psychological Sciences Colloquium Series Talk (2019) Oregon State University, Team Science for the Win: Collaborative Grant Writing”Center for Genome Research and Biocomputing, Corvallis, OR, Seminar series invited speaker, April 17, 2019, “The yellow brick road of open science” State University Dept. of Applied Economics. “The yellow brick road of Open Science: Barriers to bringing data to its highest valued use.” bit.ly/aec-melissaOHSU DMICE Informatics Conference Series, January 31, 2019, Portland, OR, "Barriers in Data Integration and Open Science"OHSU Molecular and Medical Genetics Grand Rounds, February 1st, 2018, Portland, OR, invited speaker, “An open science approach for rare disease patients”Oregon State University, Center for Genomics and Biocomputing annual genomics symposium. Sept. 8th, 2017, Keynote.OHSU Data Jamboree Open Data Day, 2017, Portland, OR. Science in the open, what does it take? Invited speaker. HYPERLINK "; OHSU Molecular and Medical Genetics Grand Rounds, June 5th, 2014, Portland, OR, invited speaker, “Expanding the Clinical Phenotype Space Using Model Systems Data.”OHSU Research week, Oral presentation, May 20, 2013. OHSU PCMB Retreat, May 2013, “Creating presentations that don’t suck.” REVIEWED ABSTRACT PRESENTATIONS: Haendel M.A. (2018) International Conference on Biomedical Ontologies, Corvallis, OR. The many faces of ontological data? and An (ontological) patient perspectiveHaendel M.A. (2018) American Medical Informatics Association Informatics Summit. San Francisco. HYPERLINK "; Patient-led deep phenotyping using a lay-friendly version of the Human Phenotype OntologyHaendel M.A. (2018) American Medical Informatics Association Informatics Summit. San Francisco. Panel on: The CTSA Program Center for Data to Health. Melissa Haendel, Oregon Health Sciences University; Kristi Holmes, Northwestern University; Sean Mooney, University of Washington; Christopher Chute, Johns Hopkins University; Justin Guinney, Sage Bionetworks.Haendel M.A. (2018) American Medical Informatics Association Informatics Summit. Open science integration for mechanistic disease discovery in Fanconi AnemiaHaendel, M.A. (2017) International Society of Biocuration annual conference. How open is open? An evaluation rubric for public knowledgebases Accepted abstract talk.Smedley, D, Schubach, M, Jacobsen J, Valentini, G, Mungall, C, Kohler, S, Lewis, S, Haendel, M, Robinson, PN. (2017) AMIA. Deep phenotyping to aid coding and non-coding rare disease variant prioritization. Deep phenotyping to aid identification of coding & non-coding rare disease variants. Accepted abstract talk (presented by Haendel).Haendel, M.A. (2016) Big Data to Knowledge All Hands Meeting, Washington DC. “Making Phenotypic Data FAIR++ for Disease Diagnosis and Discovery (Phenotype Exchange Format)”. Accepted abstract talk.Haendel, M.A. (2015) American Society for Human Genetics, Baltimore, MD. Platform talk. Haendel, Stacy Konkiel, Karen Guzman, Kristi Holmes (2015). Measuring Success Through Improved Attribution. VIVO 2015 conference, Boston. Panelist. , M.A., Lowe, B., and Ilik, V. (2014) VIVO 2014 Conference, Austin, TX. “The Case for Stable VIVO URIs.” Bremer, J Corson-Rikert, M Haendel, J Hajagos, B Lowe. (2013) VIVO conference St Louis, MO. August 2013. “Integrated Semantic Framework: launching the next generation VIVO ontology." , M.A. (2013) International Society for Biocuration Conference. “A merger of multi-species anatomy ontologies.” Haendel, Chris Kelleher, Stephen Williams, Janos Hajagos, Erich Bremer.?VIVO conference. VIVO conference, Miami, FL. 2012. CTSAconnect: A Linked Open Data approach to represent clinical and research expertise, activities, and resources. Haendel et al. (2012) NCBO conference. Baltimore, MD. CTSAconnect Mungall, M Haendel, A Ireland, S Manzoor, T Meehan, D Osumi-Sutherland, C Torniai, A Diehl. ICBO, Buffalo, NY. (2011). Modularization for the Cell Ontology.Carlo Torniai, Matt Brush, Nicole Vasilevsky, Erik Segerdell, Melanie Wilson, Tenille Johnson, Karen Corday, Chris Shaffer, Melissa Haendel. ICBO, Buffalo, NY. (2011). “Developing an Application Ontology for Biomedical Resource Annotation and Retrieval: Challenges and Lessons Learned.”NEWS MEDIA COVERAGEThe Verge. Story about the history of the National COVID Cohort Collaborative. THE AMBITIOUS EFFORT TO PIECE TOGETHER AMERICA’S FRAGMENTED HEALTH DATA. Scientist. Interviewed for a national news story on the National Covid Cohort Collaborative and the role of data sharing and collaboration in fighting COVID-19.. Interviewed for a news story about the rise of COVID-19 incidence in Oregon. . Press release on the National COVID Cohort Collaborative (N3C). KATU Portland. Interviewed for a news story about comparing COVID death and infection rates. Portland. Interviewed for a news story on covid changes in population movement. Reporter. Interviewed for a news story on covid relating to incidence rates. Gazette-times. Interviewed for a news story on covid related to social distancing. of GA4GH. Interviewed for comments on genomic healthcare. Genes RARE CAST. Podcast interview “Developing a Common Language for Rare Diseases” KEZI ABC news Local news interview regarding the new Center for Cancer Data Harmonization. State University related press release: NewsWise. Mount Sinai Innovation Festival Explores Artificial Intelligence. Leading Scientist and Practitioners Discuss Innovation, Trends and What’s Next in AI Hackathon Challenge Kicks-Off Two Day Festival Event. Science Daily, Pediatric cell atlas will map single-cell changes for a deeper view of child health and disease, March 28, Oregon State University Newsroom, OSU advancing disease understanding, diagnosis through use of big data, October 10. Portland Business Journal, #4 on top 15 NIH grant winners at OHSU, April.2017 OHSU News, OHSU to pioneer digital health innovation for the benefit of patients nationwide. October 3. Science Daily, 'Bench to bedside to bench': Scientists call for closer basic-clinical collaborations, March 24, OHSU Research News, Making all the data count for disease diagnosis and discovery, February 3, Portland Business Journal, OHSU team receives $1.8M grant to support mystery diseases research, Oct 14. Nature, Digital badges aim to clear up politics of authorship, Sept 28, Nature, Irreproducible biology research costs put at $28 billion per year, June 9, Economist, Trouble at the lab: Scientists like to think of science as self-correcting, to an alarming degree, it is not. October 8. SCHOLARLY PRODUCTSLettersHaendel, M.A. et al. Letter to the NIH Scientific Data Council and Francis Collins. “Request for Community partnership in data resource licensing planning” (2017). BlogsHaendel, M. A. et al. covidaware.me: There is strength in numbers (2020). , M.A. “Rare Diseases: A Call to Arms for Coordinated, Global Research” (2019) , M.A. et al. “GA4GH Approves Phenopackets Data-Exchange Standard” (2019). , M.A. “Socio-legal barriers to data reuse”. (2019) NLM Musings from the Mezzanine guest blog. J, Brush M, de Coronado S, Fragoso G, Haendel M, Mungall M, Vasilevsky V. ? Oregon.Wright L. “Tailoring the NCI Thesaurus for semantic interoperability” (2018) , J., Winfree, L., Haendel, M.A. “Bad Identifiers are the Potholes of the Information Superhighway: Take-Home Lessons for Researchers” (2017) , M.A. Force11. “Musings about the Open Science Prize.” (2016) , M.A. and Vasilevsky N. PloS. “Data sharing in a modern world, well, maybe not so modern.” (2016) , M.A. Force11. “I AM W7MAH” (2016) , N, Engelstad, M; Foster, E.; McMurry, J.; Mungall, C.; Robinson, P.; K?hler, S.; Haendel, M. Monarch Initiative. (2016) “Finally, a medical terminology that patients, doctors, and machines can all understand.” , M.A. Force11. “MAY THE FORCE11 BE WITH THE RESEARCH PARASITES” (2016) , M.A. Force11. “NEW BONDS: FORCE11 AND THE DIGITAL LIBRARY FEDERATION (2015), M.A. Force11. “THE SECRET VIVO OF ATTRIBUTION” (2015) , M.A. Force11. “CHANGING THE SCIENTIFIC VALUE SYSTEM, ONE CV AT A TIME” (2015), M.A. Force11. “STUDY SHOWS SCIENTIFIC REPRODUCIBILITY IS HAMPERED BY LACK OF SPECIFICITY OF RESOURCES” (2013) also: to Requests for Information (lead by M Haendel):Requests for information are when the government asks the community for their opinion on specific topics. The feedback they get is often used to design new NIH programs or funding mechanisms. I have regularly led community-level responses; where relevant we have made these responses publicly available.NIH: Request for Information (RFI): NIH Policy for Data Management and Sharing and Supplemental DRAFT Guidance (2020). : Request for Information (RFI): Enhancing the Clinical and Translational Science Awards (CTSA) Program (2019). : Request for Information (RFI): Inviting comments and suggestions on the development of a prize competition for Gender Diversity in the Biomedical Research Workforce (2019) : Request for Information (RFI): Request for Information on Proposed Provisions for a Draft Data Management and Sharing Policy for NIH Funded or Supported Research (2018) : Request for Information (RFI): Soliciting Input for the National Institutes of Health (NIH) Strategic Plan for Data Science (2018) : Request for Information (RFI): Metrics to Assess Value of Biomedical Digital Repositories (2016) ; : Request for Information (RFI): Undiagnosed Diseases Research (2015) : Soliciting Input into the Deliberations of the Advisory Committee to the NIH Director (ACD) Working Group on the National Library of Medicine (NLM) : Input on Information Resources for Data-Related Standards Widely Used in Biomedical Science (2014) : Input on Development of a Language Standard for Environmental Health Sciences (2014) NIH: Input on Development of a NIH Data Catalog (2013) NIH: Training Needs in Response to Big Data to Knowledge Initiative (2013) : Input into the Deliberations of the Advisory Committee to the NIH Director Working Group on Data and Informatics (2012) . NIH: Input on Proposed Modifications of the Biographical Sketch Used in NIH Grant (2012) NIH: Enhancing the Clinical and Translational Science Awards (CTSA) Program (2012) OSTP: Public Access to Digital Data Resulting From Federally Funded Scientific Research (2011) Ontology contributionsOntologies are knowledge artifacts used to standardize data across sources, disciplines, and applications. They are especially useful for data integration and algorithmic and analytical applications. My contributions to the following ontologies have been to define their scope, to design the patterns for their implementation, to iteratively add content, and to guide the community in their contributions and development.Monarch Disease ontology Phenotype Ontology Ontology Ontology Ontology ontology anatomy spatial ontology resource ontology Integrated semantic framework Ontology of biomedical investigations ontology ontology anatomy reference ontology for oral health and disease database development contributions:I have played a major role in leading or contributing significantly to the data modeling and content development for the following well-renowned public databases: National COVID Cohort Collaborative covid.NHLBI Data STAGE Data Translator Initiative Zebrafish information Network Information Framework eagle-i . SERVICESOCIETY MEMBERSHIPSInternational Biocuration Society member, 2006-presentAmerican Society of Human Genetics member 2013-presentAmerican Medical Informatics Association, member 2011-presentOpen Biomedical Ontology, Coordinating Executive member 2009-presentSociety for Developmental Biology member 1996-99REVIEWER FOR GRANTSKing Abdullah University of Science and Technology Research (2020)National Human Genome Institute U24 Resource Awards (2019)NCATS CTSA Collaborative Innovation Award?(2018)NIH Common Fund Undiagnosed Disease Research Network Clinical Sites (2018)ELIXIR Core Data Resources (2018)NIH Small Business Innovation Research (SBIR) Program (2017)National Cancer Institute ITCR (2017 - present)Helmsley Charitable Trust (2015)National Institutes of Health, Big Data to Knowledge Program (2015-2018)National Institutes of Health, Office of Director and Common Fund (2015 - present)UK Medical Research Council (2014, 2015, 2016)Genome Canada (2013-present)EDITOR FOR JOURNALS Mammalian Genome Editorial Board (2019 - present) Review Editor, Scholarly Metrics and Analytics, Frontiers in Library and Information Science (2015-present)Database, Editorial Board (2014 - present)Journal of Biomedical Semantics, Guest Editor (2013 - 2014)REVIEWER FOR JOURNALSNew England Journal of Medicine (2019 - present)American Journal of Human Genetics (2019-present)PloS ONE (2016-present)European Journal of Human Genetics (2016-present)Journal of Neuromuscular Diseases (2018 - present)Data Science Journal (2018 present)Genetics in Medicine (2018 - present)Circulation: Cardiovascular Genetics (2017- present)Molecular Genetics & Genomic Medicine (2017-present)Frontiers in Medicine Translational Medicine Review Editor (2016-present)European Journal of Human Genetics (2016-present)Genetics (2016-present)PloS Computational Biology (2016-present)Science Translational Medicine (2015-present)BMJ Open, Reviewer (2015-present)Journal of Biomedical Semantics (2011-present)Database Reviewer (2009-present)Journal of Biomedical Informatics (2009-present)PloS Biology, Reviewer (2013-present)Nucleic Acids Research (2010-present)Bioinformatics, Reviewer (2012-present)Journal of Web Semantics (2014-present)Pacific Biocomputing (2014-present)Scientific Data (2014-present)INTERNATIONAL/NATIONAL COMMITTEES COV-IRT Board of Directors, 2020-present KBase External Advisory Board, 2020-presentiTHRIV CTSA External Advisory Board, University of Virginia, 2019-presentU2C Metabolomics Governing Board, 2019-presentResearch Oversight Committee, Silent Genomes project, GenomeCanada, 2018-presentInterdisciplinary?Scientific?Committee, International Rare Disease Research Consortium, 2018-presentElixir European Scientific Advisory Board, 2018- presentNational Library of Medicine Literature Selection Technical Review Committee, 2017-presentSwiss Institute of Bioinformatics Advisory Board, 2017-presentGlobal Alliance for Genomics and Health (GA4GH), Phenotype and Clinical Data Capture Workstream lead, 2017-presentGlobal Alliance for Genomics and Health (GA4GH), Data and Clinical working groups, 2014-2016Vice President Joe Biden Cancer Moonshot Blue Ribbon panel on Open Data sharing, 2016 National Cancer Institute Genomic Data Commons Advisory board, 2016-presentPloS Data Guidelines Board (2015-present)NIH BD2K Standards Coordinating Center Advisory Committee, 2015-2016Reactome Advisory Board, 2015-presentSickle Cell Disease Ontology Project, independent review board (IRB) member, 2015-presentInternational Rare Diseases Research Consortium (IRDiRC), Ontology working group, 2014-presentCASRAI Working Group on contribution roles 2014-2015Research Data Alliance Working Group co-chair: The BioSharing Registry: connecting data policies, standards & databases in life sciences 2014-2016NIDCR FaceBase2 Scientific Leadership Group 2014-2015, 2017Galaxy, reproducible workflows, Advisory Board 2014-presentForce11 Advisory Board 2014-2017Force11 Executive Board, 2015-2017Force11 member, 2012-presentResource Identification Initiative Co-Director 2013-2016NIH BD2K Software Discovery Workshop committee member-2014NIH BD2K Data Integration Workshop participant-2014International Society for Biocuration Executive Board 2013-2017VIVO Ontology Working Group Lead, 2013 – 2016VIVO steering committee, 2014-2016Reproducibility Initiative Advisory Board, 2013-2015One Mind Data Standards working group member, 2013-2015CTSA IKFC Informatics Ontology Interest Group, 2012-2014Phenotype Resource Coordination Network Vertebrate Working Group Lead 2010-2016INSTITUTIONAL COMMITTEESOSU Open and Sustainable Scholarly Communication Advisory Group, 2020 - presentOSU Center for Genome Research and Biocomputing Strategic planning committee, 2019-2020OSU President and Provost’s Leadership Council for Equity, Inclusion and Social Justice, 2019-presentOHSU Research Computing Advisory group, 2017- 2018OHSU Data Science Advisory Board, 2015-2016OHSU Provost’s AML Big Challenge, 2015OHSU Bioimaging Data Publication taskforce, 2014-2015OHSU School of Medicine Research Roadmap committee and IT subgroup, 2012-presentOHSU Cloud computing taskforce, 2013-2015OHSU Office of Research Data stewardship taskforce, 2011-2012University of Oregon Post-doctoral committee, 2000-2002University of Wisconsin Medical School Graduate Representative, 1998-1999DEPARTMENTAL/STUDENT COMMITTEESOSU Nutrition Graduate Program, primary Graduate Mentor, Lauren Chan, 2019-presentOSU Environmental and Occupational Health, Biological Data Science Graduate Mentor, Mary Willis 2018-presentOSU EMT Curriculum committee, 2018Dept. of Medical Informatics & Epidemiology Graduate Committee, Jason Li, 2016- 2017Dept. of Medical Informatics & Epidemiology Graduate Committee, Jeffrey Hunter, 2016-2017Dept. of Medical Informatics & Epidemiology Graduate Committee, Bryan Laraway, 2014-2015Dept. of Medical Informatics & Epidemiology Graduate Committee, Bryan Gamble, 2013-2016OHSU Library Data Stewardship Taskforce, chair, 2013-2014Dept. of Medical Informatics & Epidemiology Graduate Committee, Maryan Zirkle, 2011-2013Dept. of Medical Informatics & Epidemiology Graduate Committee, Kyle Ambert, 2011-2013Dept. of Medical Informatics & Epidemiology Fellows Committee, Shahim Essaid, 2011-2012PROGRAM COMMITTEESNCI Semantics for Cancer Research Data Commons workshop co-chair, 2018Galaxy and Bioinformatics Open Source Conference organizing committee and host, 2018American Medical Informatics Association, Summit on Translational Bioinformatics (TBI), co-chair, 2018FORCE17 conference, Program committee, 2017Pacific Biocomputing Session Chair, 2016NIH BD2K Workshop on Community-Based Data and Metadata Standards, co-chair, 2015SWAT4LS Program committee, 2015, 2016, 2017ISWC 2015 Data Sets & Ontology Track, 2015PhenoDay, ISMB, program committee 2014, 2015, 2016 International Society for Biocuration Program Committee, 2013, 2014, 2015, 2016, 2017FORCE16 conference, Chair, Research communication and e-scholarship, 2016FORCE15 conference, Program Chair, Research communication and e-scholarship, 2015VIVO Annual Conference, Program Chair, 2015VIVO Annual Conference Program committee, 2012, 2013, 2014International Conference of Biomedical Ontologies Scientific Program Committee, Workshop and Tutorials chair, 2014Conference on Semantics in Healthcare and Life Sciences Scientific Program Committee 2014International Society for Computational Biology Conference, Ontology Special Interest Group Program Committee, 2014Discovery Informatics: Scientific Discoveries Enabled by AI Scientific Program Committee, 2014International Conference of Biomedical Ontologies Scientific Program Committee, Early Career Chair, 2013American Medical Informatics Association Scientific Program Committee of the 2013 Annual meetingAmerican Medical Informatics Association Scientific Program Committee of the 2013, 2016, 2017 Summit on Translational Bioinformatics (TBI)International Conference of Biomedical Ontologies Program Committee, 2011, 2014, 2015, 2016, 2018V. TEACHING Areas of focus: Knowledge engineering and ontology design, information management, data standards and management, biomedical writing and presentations, scientific reproducibility, biomedical ethics, developmental biology, anatomy and physiology, genetics and molecular biology, neuroscience, introductory biology. Development of open science educational materials and courses in data science. I have a strong commitment to diversity and inclusion and try to include this in all teaching contexts. 2020 Faculty instructor, Oregon State University, TOX 599/699 Special Topics: Evidence, reproducibility, and justifying policy in environmental health; aims to teach students about reproducibility and evidence-based policy in environmental science. 1 credit, co-taught with Dr. Jenkins. 2019 Faculty instructor, Oregon State University, TOX 599/699 Special Topics: Integrated Environmental and Molecular Toxicology, Pay it forward: collaborative data-driven and deep-thinking based decision making; aims to teach students collaboration and open science skills. 1 credit, co-taught with Dr. Curtis. 2018-2019 Faculty Mentor, Oregon State University Pilot Faculty Student Mentor ProgramYear-long program that aims to increase student retention of first-year students and their success at OSU.2018 Co-Instructor, Interpreting Genomes for Rare Disease: Variant and Gene Interpretation, Broad Institute, June, Length: 1day Continuing education credit for MDs in Clinical Genetics and other clinical fields. Seminar and hands-on training focused on deep phenotyping and exome analysis to support diagnosis of rare disease, and standards for phenotypic and genomic data sharing. 2018 Lecturer, Clinical Genetics Grand Rounds Continuing Education Program, January, Length: 1hr Provided continuing education credit for MDs in Clinical Genetics. Seminar focused on deep phenotyping to support diagnosis of rare disease, use of improved evidence structuring for pathogenicity of variant determination, patient centered phenotyping, and standards for phenotypic data sharing. 2014 – 2018 Co-Instructor: Ethical, Legal and Social Issues in Biomedical Informatics. Length: 1 term, 3 credits, annually.In this course, I teach cross-disciplinary bioethical issues in informatics and data science, including ethical analysis frameworks, secondary findings, genomic data privacy, authorship, p-value hacking, and reproducibility. 2016 ACMG Short Course: Tools and Approaches to Assess the Genetic Basis of Disease. Length: 5 hrs. Provided continuing education for clinical geneticists. Co-taught the use of semantically encoded phenotype data for use in variant prioritization for genetic diagnosis. Co-Instructor: Big Data To Knowledge Short Course “Data after Dark”. Length: 2 days. A repeating short course designed for beginning students and faculty to learn basic principles of data science for inclusion in their research and education.2015 Co-Instructor: Big Data To Knowledge Short Course, July. Length: 1 week.Developed a data science curriculum for undergraduates and pre-graduate students focused on defining scientific problems, data integration, data visualization, and data analytics.2015 Mentor: DMICE summer intern. Length: 12 weeks.Hosted undergraduate summer student to perform software development for a phenotype-based genome browser.e2014 Instructor: Foundations of Interprofessional Practice and Research I: Patient Safety, OHSU. Length: 4 hour session.Instructed professional group of students beginning diverse clinical professions in developing clinical care team strategies across disciplines and expertise using patient safety as the organizing principle for information and knowledge transfer and teamwork. 2014 Instructor: II INTERNATIONAL SUMMER SCHOOL “Rare disease and orphan drug registries.” Length: 1 week. September. Rome, Istituto Superiore di Sanità. Instruction in the application of the Human Phenotype Ontology.2014 Co-Chair: NIEHS BD2K workshop “Developing an environmental health language standard”. Length: 2 anized workshop, invited participants and speakers, developed goals and outcomes, and collaborated with NIEHS on strategic directions.2014 Instructor: Genetics of Addiction, Jackson Laboratory. Length: 1 week.Participated in group-taught course on various aspects of managing biomedical data to support analysis of a diversity of addiction data. 2014 Mentor: DMICE summer intern. Length: 12 weeks.Hosted minority undergraduate summer student to perform curation and analysis of mouse background phenotypes.2013 Instructor: Ontologies 101, International Neuroscience Coordinating Facility annual meeting, Stockholm, Sweden, August. Length: 1 day.Taught neuroimaging, physiology, and data sharing task force members how to use and develop ontologies.2013 Guest Lecturer: BMI 552 Research Methods, May. Length: 1 class.Guest lectured on problem analysis and use of public data for an upper-level informatics course.2013 Workshop coordinator: International Conference on Biomedical Ontology. Length: 1 day.Co-organized a tutorial to introduce best practices in ontology development and semantic engineering.2013 Workshop coordinator: Data Management Workshop, Symposium for Portland Area Research on Complementary & Alternative Medicine (SPARC). Length: 1 day.Co-organized and taught a workshop on information management to graduate students in naturopathic medicine at the National College of Natural Medicine.2013 Workshop coordinator: Inter-model organism workshop, Stanford University. Length: 1 anized workshop on unification of data models for representation of model organism data.2012 Workshop coordinator: Neural crest workshop, National Evolutionary Synthesis Center. Length: 1 anized workshop on representation of anatomical structures pertaining to neural crest development for evolutionary and biomedical purposes2012-2013 Course instructor, Ontologies for Evolutionary computation, National Evolutionary Synthesis Center, Length: 1 week (taught twice). Course on semantic technology development best practices for a multi-disciplinary groups at different career stages.2011 Workshop coordinator: Skeletal ontology workshop. Length: 2 anized workshop on representation of skeletal structures for evolutionary and biomedical purposes.2013-2015 Mentor: Informatics Fellows mentor, Oregon Health and Science University. Co-mentored post-doctoral fellow on ontologies for craniofacial findings and surgical interventions, human phenotypes, and Truamatic Brain Injury.2010-2012 Mentor: Informatics Fellows mentor, Oregon Health and Science University. Mentored post-doctoral fellow to model reagents, cell lines, and observational clinical studies with ontologies for the purposes of resource discovery, experimental inference, and development of new data standards. 2011 Workshop coordinator: International Conference on Biomedical Ontology, Length: 1 day.Co-organized a workshop to disseminate best practices in anatomy ontology development.2009 Workshop co-instructor: Working with Zebrafish Genome Resources, Sanger Institute. Length: 1 day. At the 6th European Meeting on Zebrafish Genetics and Development, Rome, Italy.2008 Mentor: Undergraduate student mentor, University of Oregon, Length: 3 months.Mentored student project to model the zebrafish brain with ontologies. 2008 Meeting facilitator: National Evolutionary Synthesis Center, Length: 2 days.Taught principles of ontology construction and interoperability to evolutionary biologists.2006 Meeting facilitator: National Center for Biomedical Ontology, Length: 2 days.Lead group of anatomists in developing good ontology principles for representing anatomy and homology.2002 Instructor: Biochemistry: Writing in the discipline, University of Oregon, Length: 1 semester.Formulated and taught a course for undergraduates in biological sciences, utilizing peer review and editorial skills. 2001-2002 Guest Lecturer: Developmental neurobiology, Length: 2 lectures.Guest lectured on neurogenesis and fate specification for an upper-level neuroscience course. 2001 Mentor: Molecular biology rotation student mentor, University of Oregon, Length: 3 months.Taught the student basic molecular and embryological techniques, bioinformatics analysis, and presentation skills.1999-2000 Instructor: Center for Talented Youth, Johns Hopkins University, length: 3 weeks (taught 3 times, over 2 years).Designed and taught an accelerated introductory course in neuroscience for high school students. This included teaching the students how to find, read, interpret and write scientific literature.1998-1999 Mentor: Summer Research Program in Biology mentor, University of Wisconsin, Length (3 months, taught twice).Taught students molecular and histological techniques, bioinformatics analysis, experimental design, literature analysis, and presentation skills.1998 Teaching Assistant: Cell and Molecular Biology, Biocore program, University of Wisconsin, Length: 1 semester.Led discussion sections, graded and wrote homework and exams.OtherBD2K Educational resources: : OMSI science museum, Neuroscience exhibit, 2001, Length: 1 day. Volunteer: Brain Awareness Week at local high schools, 1993-1999, Length: annually, for a few hours.Trainee: Course in Teaching College Biology, 1999, Length: 1 semester (collaborative learning/teaching).Mentor: High School Honors in Science Program, Madison, WI, 1994, Length: two semesters. Teaching Assistant: Organic Chemistry Laboratory, Reed College, 1989, Length: two semesters. ................
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