Dr. Melissa Anne Haendel725 Amelia Ave., Brownsville, OR, 97327

haendel@ohsu.eduhttp://www.ohsu.edu/library/ontology

503-407-5970http://orcid.org/0000-0001-9114-8737

http://scholar.google.com/citations?user=HtAV9dIAAAAJTwitter: @ontowonka

Education

Ph.D. Neuroscience, University of Wisconsin, 1999B.A. Chemistry, Reed College, 1991

Positions

Interim Co-Director, OHSU Library 2017-presentDirector of Data Science, Oregon Health and Science University, Library

Interim Library leadership, including managerial and fiscal oversight, change management, and strategic visioning, with a particular focus on integration of data science research and service at OHSU.

Associate Professor 2015-presentDirector of the Ontology Development Group, Oregon Health and Science University, Library and Department of Medical Informatics and Clinical Epidemiology

Development of data standards and semantic technologies for disease research and scholarly communication, research data and ethics education, educational program development, community data sharing coordination, reproducibility and attribution informatics, strategic/organizational planning, programmatics and project management, Leadership in international and national consortia, Library leadership.

Assistant Professor 2010-2014Director of the Ontology Development Group, Oregon Health and Science University, Library and Department of Medical Informatics and Clinical Epidemiology

Development of data standards and outreach; end-user requirements and user interface design and testing; data services development; management of data curation team; data stewardship training; educational program development.

Senior Research Associate, Lead Ontologist 2009-2010Director of the Ontology Development Group, Oregon Health and 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. Lead the ontology effort for the eagle-i consortium.

Ontologist, Scientific Ontologist, Genetics Nomenclature Lead 2004-2009University of Oregon, Dr. Westerfield

Development of anatomical ontologies and syntax for phenotype ontologies; community genetic nomenclature coordinator; curation of genomic, gene expression and phenotype data from the zebrafish literature; and development of data standards.

Post-doctoral Fellow 2002-2004Oregon State University, Dr. Bailey and Dr. Tanguay

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Dr. Melissa Haendel

Effects of biocides and carcinogens on zebrafish and trout development and microarray analysis. Set up a new laboratory.

Post-doctoral Fellow 2000-2002University of Oregon, Dr. Eisen and Dr. Darimont

Involvement of thyroid hormone during early neural development in the zebrafish.

Doctoral Research Assistant 1993-1999University of Wisconsin, Dr. Gary Lyons

Identification and knock-out of a novel gene important for neural development in mice. Neural crest cell differentiation in chick.

Laboratory Technician 1993Oregon State University, Dr. David Barnes

Maintenance of zebrafish stocks and cell culture lines.

Teaching

Areas of focus: Ontology design and knowledge engineering, 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.

Co-Instructor: Data Standards for Translational Research, 2017. Length: 1 term.Overview of data types and standards needed to integrate clinical and biological data in translational research. Focuses on 1) reference genome annotation standards, 2) semantic integration of genotype and phenotype data, 3) EHR standards, data types and usage for phenotyping, and 4) clinical trials. This is a new course under development and will be taught in 2017.

Co-Instructor: Ethical, Legal and Social Issues in Biomedical Informatics, 2014, 2105, 2016, 2017. Length: 1 term.Development of an updated, group participation based syllabus for cross-disciplinary bioethical issues in informatics and data science.

ACMG Short Course: Tools and Approaches to Assess the Genetic Basis of Disease. Length: 5 hrs. Continuing education for clinical geneticists. Co-taught the use of semantically encoded phenotype data for use in variant prioritization for genetic diagnosis. http://www.slideshare.net/mhaendel/the-monarch-initiative-leveraging-crossspecies-deep-phenotyping-for-variant-prioritization

Co-Instructor: Big Data To Knowledge Short Course “Data after Dark”, Jan 2016. Length: 2 days. An short course designed for beginning students and faculty to learn basic principles of data science for inclusion in their research and education.

Co-Instructor: Big Data To Knowledge Short Course, July 2015. Length: 1 week.Development of a data science curriculum for undergraduates and pre-graduate students focused on defining scientific problems, data integration, data visualization, and data analytics.

Mentor: DMICE summer intern, 2015. Length: 12 weeks.Hosted undergraduate summer student to perform software development for a phenotype-based genome browser.

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Instructor: Foundations of Interprofessional Practice and Research I: Patient Safety, 2014, 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.

Instructor: II INTERNATIONAL SUMMER SCHOOL “Rare disease and orphan drug registries.” Length: 1 week. September 2014. Rome, Istituto Superiore di Sanità. Instruction in the application of the Human Phenotype Ontology.

Co-Chair: NIEHS BD2K workshop “Developing an environmental health language standard”, 2014. Length: 2 days.Organized workshop, invited participants and speakers, developed goals and outcomes, and collaborated with NIEHS on strategic directions.

Instructor: Genetics of Addiction, 2014, 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.

Mentor: DMICE summer intern, 2014. Length: 12 weeks.Hosted minority undergraduate summer student to perform curation and analysis of mouse background phenotypes.

Instructor: Ontologies 101, International Neuroscience Coordinating Facility annual meeting, Stockholm, Sweden, August, 2013. Length: 1 day.Taught neuroimaging, physiology, and data sharing task force members how to use and develop ontologies.

Guest Lecturer: BMI 552 Research Methods, May, 2013. Length: 1 class.Guest lectured on problem analysis and use of public data for an upper-level informatics course.

Workshop coordinator: International Conference on Biomedical Ontology, 2013. Length: 1 day.Co-organized a tutorial to introduce best practices in ontology development and semantic engineering.

Workshop coordinator: Data Management Workshop, Symposium for Portland Area Research on Complementary & Alternative Medicine (SPARC), 2013. 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.

Workshop coordinator: Inter-model organism workshop, Stanford University, 2013. Length: 1 day.Organized workshop on unification of data models for representation of model organism data.

Workshop coordinator: Neural crest workshop, National Evolutionary Synthesis Center, 2012. Length: 1 day.Organized workshop on representation of anatomical structures pertaining to neural crest development for evolutionary and biomedical purposes

Course instructor, Ontologies for Evolutionary computation, National Evolutionary Synthesis Center, 2012 and 2013. Length: 1 week (taught twice). Course on semantic technology development best practices for a multi-disciplinary groups at different career stages.

Workshop coordinator: Skeletal ontology workshop, 2011. Length: 2 days.Organized workshop on representation of skeletal structures for evolutionary and biomedical purposes.

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Mentor: Informatics Fellows mentor, Oregon Health and Science University, 2013-2015Co-mentored post-doctoral fellow on ontologies for craniofacial findings and surgical interventions, human phenotypes, and Truamatic Brain Injury.

Mentor: Informatics Fellows mentor, Oregon Health and Science University, 2010-2012Mentored 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.

Workshop coordinator: International Conference on Biomedical Ontology, 2011, Length: 1 day.Co-organized a workshop to disseminate best practices in anatomy ontology development.

Workshop co-instructor: Working with Zebrafish Genome Resources, 2009, Sanger Institute. Length: 1 day. At the 6th European Meeting on Zebrafish Genetics and Development, Rome, Italy.

Mentor: Undergraduate student mentor, University of Oregon, 2008, Length: 3 months.Mentored student project to model the zebrafish brain with ontologies.

Meeting facilitator: National Evolutionary Synthesis Center, 2008, Length: 2 days.Taught principles of ontology construction and interoperability to evolutionary biologists.

Meeting facilitator: National Center for Biomedical Ontology, 2006, Length: 2 days.Lead group of anatomists in developing good ontology principles for representing anatomy and homology.

Instructor: Biochemistry: Writing in the discipline, University of Oregon, 2002, Length: 1 semester.Formulated and taught a writing course for undergraduates in the biological sciences, utilizing peer review and editorial skills.

Guest Lecturer: Developmental neurobiology, 2001-2002, Length: 2 lectures.Guest lectured on neurogenesis and fate specification for an upper-level neuroscience course.

Mentor: Molecular biology rotation student mentor, University of Oregon, 2001, Length: 3 months.Taught the student basic molecular and embryological techniques, bioinformatics analysis, and presentation skills.

Instructor: Center for Talented Youth, Johns Hopkins University, 1999 and 2000, length: 3 weeks (taught 3 times).

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.

Mentor: Summer Research Program in Biology mentor, University of Wisconsin, 1998-1999, Length (3 months, taught twice).

Taught students molecular and histological techniques, bioinformatics analysis, experimental design, literature analysis, and presentation skills.

Teaching Assistant: Cell and Molecular Biology, Biocore program, University of Wisconsin, 1998, Length: 1 semester.

Led discussion sections, graded and wrote homework and exams.

Volunteer: OMSI science museum, Neuroscience exhibit, 2001, Length: 1 day.

Volunteer: Participation in Brain Awareness Week at local high schools, 1993-1999, Length: annually, for a few hours.

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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.

Funding15.2M total since 2013 to OHSU

Ongoing

PCORI Contract. Role co-PD. 8/1/17-7/31/19. $367,135/yr.Realization of a Standard of Care for Rare Diseases Using Patient-Engaged Phenotyping.

NCI/Leidos Contract. Role PI. 6/1/17-9/30/17. $225,000 Development of evidence models and semantic interoperability capabilities for cancer data analysis.

NIH NCATS Biomedical Data Translator Technical Feasibility Assessment and Architecture Design. Role: co-PD. 1OT3TR002019-01 10/1/2016 – 9/30/2018. $2,000,000/yr (Note that as an OT3, funding will be allocated incrementally and this is only an estimate).

NIH NCATS Undiagnosed Diseases Network Metabolomics Core, 5 U01 TR001395. Role: Co-I. (MPI: Metz/Koeller) 9/20/15-07/31/18. The goal of this project is to provide clinical expertise in the interpretation of the metabolomic data generated by the scientists at PNNL.

NIH NIAID BioCADDIE: Biomedical and healthCAre Data Discovery and Indexing Engine center. 3U24AI117966-03S1 (Ohno-Machado PI/Haendel supplement co-PD). 09/15/16-08/31/17. $70,000. 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.

NIH BD2K Intelligent Concept Agent for Assisting with the Application of Metadata. 1 U01 HG009453-01 (Mungall PI, Role: co-PI). 07/01/16-06/30/19. An Intelligent Concept Agent to assist in creation, extension, application, and maintenance of metadata describing experiments and datasets derived from experiments.

Office of the Director, NIH, 2R24OD011883, Role: PI. 2016-2020 (4yrs). $1,290,295/year. Monarch Initiative. Program to develop software and standardize data to enable cross-species genotype to phenotype analysis and promote publication of data standards. http://www.monarchinitiative.org

NIH BD2K 1R25GM114820. Role Co-PD. 12/1/14-11/30/17. $199,354.Adding Big Data Open Educational Resources to the ONC Health IT Curriculum. The goal is to develop and make available online big data curricular materials.

NIH BD2K 1R25EB020379. Role Co-PD.12/1/14-11/30/17. $150,000.OHSU Informatics Analytics BD2K Skill Course The goal is to teach an online course in big data stewardship and analytics.

Completed:

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NIH BD2K Standards Coordinating Center. HHSN316201200001W Role: subcontract to ESAC/Basu. 5/17/16 – 9/30/16. $107,815/6.

NIH BD2K PA-15-144-U01 Role subcontract to Kesselman (PI), Semantic integration of craniofacial phenotyping across species. 9/2015 - 8/2016, $119,697.Goal is to achieve bidirectional FaceBase-Monarch integration.

NIH Undiagnosed Disease Program, HHSN268201300036C, Role: PI, contract. 2015-2016 (1yr). $84,000. The goal is to represent patient families in the Monarch Initiative website, and perform patient clustering.

NCI/Leidos Contract. Role PI. 7/1/15-6/30/16. $248,799 Development of use cases for cancer data analysis using semantic technologies.

NIH U54HG007990-S2. Role subcontract to Haussler (PI)/USC Center for Big Data in Translational Genomics. 2016, $94,368. Goal was to develop GA4GH genotype-to-phenotype schemas and evidence models for the BRCA Exchange.

National Cancer Institute R25 GM114820 02S1, Role: PI. 2016. $54,000. Supplement to evaluate use of Open Educational Resources for data science at a Force2016 event.

Office of the Director, NIH, 1R24OD011883, Role: PI. 2010-2016 (4yrs). $1,290,295/year. Monarch Initiative. Program to develop software and standardize data to enable cross-species genotype to phenotype analysis and promote publication of data standards. http://www.monarchinitiative.org

Office of the Director, NIH, Supplement 4 R24 OD011883 04S1 Role: PI. 09/18/2015 - 07/31/2016. $132,400. Goal was to migrate infrastructure for the Monarch application to OHSU and implement advanced systems.

DARPA-BAA-14-14 Big Mechanism. Role co-PI. 7/1/14-12/31/15. $75,000.The goal of this subcontract was to provide expert annotation using ontologies to specific text spans in the CRAFT Corpus and additional documents.

NIH Undiagnosed Disease Program, HHSN268201400093P, Role: PI, contract. 2014-2015 (1yr). $175,000. The goal was to extend visualization tools for phenotype comparison and to better represent glycomics phenotype data.

Office of the Director, NIH, Supplement 3 R24 OD011883 03S1 Role:PI 09/18/2014 - 07/31/2015. $452,622 Goals were to develop an online model organism phenotyping tool in support of functional validation studies in a variety of organisms according to community data standards.

Elsevier, 2014, Role: PI. 10/14-12/14 (3 mo). $30,000. Semantic representation for Mendeley publication of research protocols, contract. The goal was to create an open, semantic framework for representation of research workflows.

Beyond the PDF 2 1K challenge award, Role: Awardee, 2013. $1,000. Titled “Starting at Ground Zero,” the goal of this award was to promote development of library capabilities to support research data management and publication. http://www.force11.org/1Kchallenge#1k2

NIH Undiagnosed Disease Program, HHSN268201300036C, Role: PI, contract. 2013-2014 (1yr). $200,000. The goal was to develop phenotype comparison algorithms and support for undiagnosed disease phenotyping, quality assurance mechanisms for phenotype data, and perform usability testing for NIH software tools.

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NIH contract HHSN 30220140 Haendel Role: PI, contract 03/14-8/15Project name: Improvements to the PhenoGrid Viewer. Goal is to improve display of phenotype comparison tool within the Monarch interface and in third party applications.

NIH NCATs CTSA 10-001: 100928SB23. PROJECT #: 00921-0001, Role: PI, contract. 2011-2013. (1.5 yrs) $1,457,362 total. CTSAconnect. Development and integration of data standards for research profiling, including the integration of VIVO, eagle-i, and clinical vocabularies for translational research.

Medical Research Foundation of Oregon New Investigator Award, Role: PI. 2011-2012 (1yr). $40,000. “Indexing and retrieval of biospecimen Information within the Oregon Health & Science University Biolibrary.”

RJ Reynolds Post-doctoral Research award, Role: Post-doctoral awardee. 2002-2004 (2 yrs).The goal was to investigate the effects of biocides on early zebrafish development.

NIH 5F32NS011170, Individual Post-doctoral National Research Service Award, NIH, Role: Post-doctoral awardee. 2000-2003 (3 yrs) “Differentiation factor receptors and neural cell fate.” Goal was to investigate the role of thyroid hormone in maintenance of early-developing neurons in zebrafish.

5F31MH011560, Individual Pre-doctoral National Research Service Award, NIH, Role: Pre-doctoral awardee. 1997-1999 (3 yrs) “Trapping novel genes involved in neural development.” Goal was to identify novel genes in mouse that played a role in neuronal development using gene trap knockout and in vitro preselection techniques.

Professional honors and memberships

Awards/Nominations

Association of Academic Health Sciences Libraries Scholarship awardee, 2017

Harvard School of Education Academic Leadership Institute, 2017

Bioinformatics Benjamin Franklin Award for Open Access in the Life Sciences finalist, 2017

OHSU 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, 2014

Medical Research Foundation of Oregon Richard T. Jones New Investigator Award nomination,2013 and 2014

American Association of Cancer Research Pathobiology Workshop Fellowship Awardee, 2003

Commended for Excellence in Scholarship, Reed College, 1991

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Dr. Melissa Haendel

International/national committees and memberships

National Library of Medicine Literature Selection Technical Review Committee, 2017-present

Swiss Institute of Bioinformatics Advisory Board, 2017-present

Vice President Joe Biden Cancer Moonshot Blue Ribbon panel on Open Data sharing, 2016

National Cancer Institute Genomic Data Commons Advisory board, 2016-present

PloS Data Guidelines Board (2015-present)

NIH BD2K Standards Coordinating Center Advisory Committee, 2015-2016

Reactome Advisory Board, 2015-present

Sickle Cell Disease Ontology Project, independent review board (IRB) member, 2015-present

Global Alliance for Genomics and Health (GA4GH), Data and Clinical working groups, 2014-present

International Rare Diseases Research Consortium (IRDiRC), Ontology working group, 2014-present

CASRAI Working Group on contribution roles 2014-2015

Research Data Alliance Working Group co-chair: The BioSharing Registry: connecting data policies, standards & databases in life sciences 2014-2016

NIDCR FaceBase2 Scientific Leadership Group 2014-2015, 2017

Galaxy, reproducible workflows, Advisory Board 2014-present

Force11 Advisory Board 2014- present

Force11 Executive Board, 2015-present

Force11 member, 2012-present

Resource Identification Initiative Co-Director 2013-2016

NIH BD2K Software Discovery Workshop committee member-2014

NIH BD2K Data Integration Workshop participant-2014

International Society for Biocuration Executive Board 2013-present

International Biocuration Society member, 2006-present

VIVO Ontology Working Group Lead, 2013 – 2016

VIVO steering committee, 2014-2016

Reproducibility Initiative Advisory Board, 2013-2015

American Society of Human Genetics member 2013-present

One Mind Data Standards working group member, 2013-2015

CTSA IKFC Informatics Ontology Interest Group, 2012-2014

American Medical Informatics Association, member 2011-present

Open Biomedical Ontology, Coordinating Executive member 2009-present

Phenotype Resource Coordination Network Vertebrate Working Group Lead 2010-2016

Society for Developmental Biology member 1996-99

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Institutional committees

OHSU Research Computing Advisory group, 2017- present

Dept. of Medical Informatics & Epidemiology Graduate Committee, Jason Li, 2016- present

Dept. of Medical Informatics & Epidemiology Graduate Committee, Jeffrey Hunter, 2016-2017

OHSU Data Science Advisory Board, 2015-2016

OHSU Provost’s AML Big Challenge, 2015

OHSU Bioimaging Data Publication taskforce, 2014-2015

Dept. of Medical Informatics & Epidemiology Graduate Committee, Bryan Laraway, 2014-2015

Dept. of Medical Informatics & Epidemiology Graduate Committee, Bryan Gamble, 2013-2016

OHSU Library Data Stewardship Taskforce, chair, 2013-2014

Dept. of Medical Informatics & Epidemiology Graduate Committee, Maryan Zirkle, 2011-2013

Dept. of Medical Informatics & Epidemiology Graduate Committee, Kyle Ambert, 2011-2013

Dept. of Medical Informatics & Epidemiology Fellows Committee, Shahim Essaid, 2011-2012

OHSU School of Medicine Research Roadmap committee and IT subgroup, 2012-present

OHSU Cloud computing taskforce, 2013-2015

OHSU Office of Research Data stewardship taskforce, 2011-2012

University of Oregon Post-doctoral committee, 2000-2002

University of Wisconsin Medical School Graduate Representative, 1998-1999

Program committees

American Medical Informatics Association, Summit on Translational Bioinformatics (TBI), co-chair, 2018

FORCE17 conference, Program committee, 2017

Pacific Biocomputing Session Chair, 2016

NIH BD2K Workshop on Community-Based Data and Metadata Standards, co-chair, 2015

SWAT4LS Program committee, 2015, 2016

ISWC 2015 Data Sets & Ontology Track, 2015

PhenoDay, ISMB, program committee 2014, 2015, 2016

International Society for Biocuration Program Committee, 2013, 2014, 2015, 2016, 2017

FORCE16 conference, Chair, Research communication and e-scholarship, 2016

FORCE15 conference, Program Chair, Research communication and e-scholarship, 2015

VIVO Annual Conference, Program Chair, 2015

VIVO Annual Conference Program committee, 2012, 2013, 2014

International Conference of Biomedical Ontologies Scientific Program Committee, Workshop and Tutorials chair, 2014

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Dr. Melissa Haendel

Conference on Semantics in Healthcare and Life Sciences Scientific Program Committee 2014

International Society for Computational Biology Conference, Ontology Special Interest Group Program Committee, 2014

Discovery Informatics: Scientific Discoveries Enabled by AI Scientific Program Committee, 2014

International Conference of Biomedical Ontologies Scientific Program Committee, Early Career Chair, 2013

American Medical Informatics Association Scientific Program Committee of the 2013 Annual meeting

American Medical Informatics Association Scientific Program Committee of the 2013, 2016, 2017 Summit on Translational Bioinformatics (TBI)

International Conference of Biomedical Ontologies Scientific Program Committee, 2011, 2014, 2015

Reviewer/Editor for Journals:

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)

Review Editor, Scholarly Metrics and Analytics, Frontiers in Library and Information Science (2015-present)

Science Translational Medicine (2015-present)

BMJ Open, Reviewer (2015-present)

Journal of Biomedical Semantics, Guest Editor (2013 - present) and Reviewer (2011-present)

Database, Editorial Board (2014 - present) and Reviewer (2009-present)

Journal of Biomedical Informatics, Reviewer (2009-present)

PloS Biology, Reviewer (2013-present)

Nucleic Acids Research, Reviewer (2010-present)

Bioinformatics, Reviewer (2012-present)

Journal of Web Semantics, Reviewer (2014-present)

Pacific Biocomputing, Reviewer (2014-present)

Nature Data, Reviewer (2014-present)

Reviewer for Grants

National Cancer Institute ITCR (2017)

Helmsley Charitable Trust (2015)

National Institutes of Health, Big Data to Knowledge Program (2015-present)

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Dr. Melissa Haendel

National Institutes of Health, Office of Director and Common Fund (2015- present)

UK Medical Research Council (2014, 2015, 2016)

Genome Canada (2013-present)

PublicationsSee Google Scholar profile here: https://scholar.google.com/citations?user=HtAV9dIAAAAJ&hl=en3722 citations to 123 peer reviewed, conference papers, and gray literature manuscripts.

Refereed manuscripts:

McMurry JA, Juty N, Blomberg N, Burdett T, Conlin T, Conte N, Courtot M, Deck J, Dumontier M, Fellows DK, Gonzalez-Beltran A, Gormanns P, Grethe J, Hastings J, Hériché JK, Hermjakob H, Ison JC, Jimenez RC, Jupp S, Kunze J, Laibe C, Le Novère N, Malone J, Martin MJ, McEntyre JR, Morris C, Muilu J, Müller W, Rocca-Serra P, Sansone SA, Sariyar M, Snoep JL, Soiland-Reyes S, Stanford NJ, Swainston N, Washington N, Williams AR, Wimalaratne SM, Winfree LM, Wolstencroft K, Goble C, Mungall CJ, Haendel MA, Parkinson H. (2017) Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data. PLoS Biol. 2017 Jun 29;15(6):e2001414. doi: 10.1371/journal.pbio.2001414. eCollection 2017 Jun.

Meehan TF, Conte N, West DB, Jacobsen JO, Mason J, Warren J, Chen CK, Tudose I, Relac M, Matthews P, Karp N, Santos L, Fiegel T, Ring N, Westerberg H, Greenaway S, Sneddon D, Morgan H, Codner GF, Stewart ME, Brown J, Horner N; International Mouse Phenotyping Consortium, Haendel M, Washington N, Mungall CJ, Reynolds CL, Gallegos J, Gailus-Durner V, Sorg T, Pavlovic G, Bower LR, Moore M, Morse I, Gao X, Tocchini-Valentini GP, Obata Y, Cho SY, Seong JK, Seavitt J, Beaudet AL, Dickinson ME, Herault Y, Wurst W, de Angelis MH, Lloyd KCK, Flenniken AM, Nutter LMJ, Newbigging S, McKerlie C, Justice MJ, Murray SA, Svenson KL, Braun RE, White JK, Bradley A, Flicek P, Wells S, Skarnes WC, Adams DJ, Parkinson H, Mallon AM, Brown SDM, Smedley D. (2017). Disease model discovery from 3,328 gene knockouts by The International Mouse Phenotyping Consortium. Nat Genet. 2017 Jun 26. doi: 10.1038/ng.3901.

Gall T, Valkanas E, Bello C, Markello T, Adams C, Bone WP, Brandt AJ, Brazill JM, Carmichael L, Davids M, Davis J, Diaz-Perez Z, Draper D, Elson J, Flynn ED, Godfrey R, Groden C, Hsieh CK, Fischer R, Golas GA, Guzman J, Huang Y, Kane MS, Lee E, Li C, Links AE, Maduro V, Malicdan MCV, Malik FS, Nehrebecky M, Park J, Pemberton P, Schaffer K, Simeonov D, Sincan M, Smedley D, Valivullah Z, Wahl C, Washington N, Wolfe LA, Xu K, Zhu Y, Gahl WA, Tifft CJ, Toro C, Adams DR, He M, Robinson PN, Haendel MA, Zhai RG, Boerkoel CF. (2017) Defining Disease, Diagnosis, and Translational Medicine within a Homeostatic Perturbation Paradigm: The National Institutes of Health Undiagnosed Diseases Program Experience. (2017) Front Med (Lausanne). 2017 May 26;4:62. doi: 10.3389/fmed.2017.00062. eCollection 2017.

M Lawler, D Haussler, LL Siu, MA Haendel, JA McMurry, BM Knoppers, SJ Chanock, FCalvo, BT Guneet Walia, IBanks, PP Yu, LM Staudt, CL Sawyers, The Clinical Cancer Genome Task Team of the Global Alliance for Genomics and Health. (2017) Sharing Clinical and Genomic Data on Cancer — The Need for Global Solutions. N Engl J Med 2017; 376:2006-2009. DOI: 10.1056/NEJMp1612254.

NA Vasilevsky, J Minnier, MA Haendel, RE Champieux (2017). Reproducible and reusable research: Are journal data sharing policies meeting the mark? PeerJ 5, e3208. 10.7717/peerj.3208.

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Manolio TA, Fowler DM, Starita LM, Haendel MA, MacArthur DG, Biesecker LG, Worthey E, Chisholm RL, Green ED, Jacob HJ, McLeod HL, Roden D, Rodriguez LL, Williams MS, Cooper GM, Cox NJ, Herman GE, Kingsmore S, Lo C, Lutz C, MacRae CA, Nussbaum RL, Ordovas JM, Ramos EM, Robinson PN, Rubinstein WS, Seidman C, Stranger BE, Wang H, Westerfield M, Bult C. (2017). Bedside Back to Bench: Building Bridges between Basic and Clinical Genomic Research. Cell. 2017 Mar 23;169(1):6-12. doi: 10.1016/j.cell.2017.03.005.

Chao HT, Davids M, Burke E, Pappas JG, Rosenfeld JA, McCarty AJ, Davis T, Wolfe L, Toro C, Tifft C, Xia F, Stong N, Johnson TK, Warr CG; *Undiagnosed Diseases Network., Yamamoto S, Adams DR, Markello TC, Gahl WA, Bellen HJ, Wangler MF, Malicdan MC. Am J Hum Genet. A Syndromic Neurodevelopmental Disorder Caused by De Novo Variants in EBF3. Jan 5;100(1):128-137. doi: 10.1016/j.ajhg.2016.11.018. *Collaborator

Mungall CJ, McMurry JA, Kohler S, Balhoff JP, Borromeo C, Brush M, Carbon S, Conlin T, Dunn N, Engelstad M, Foster E, Gourdine JP, Jacobsen JOB, Keith D, Laraway B, Lewis SE, Xuan JN, Shefchek K, Vasilevsky N, Yuan Z, Washington N, Hochheiser H, Groza T, Smedley D, Robinson PN, and Haendel MA. (2016) The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species. Nucleic Acids Research, 2016 1 doi: 10.1093/nar/gkw1128

Kohler S, Vasilevsky NA, Engelstad M, Foster E, McMurry J, Ayme S, Baynam G, Bello S, Boerkoel C, Boycott K, Brudno M, Buske OJ, Chinnery PF, Cipriani V, Connell LE, Dawkins H, DeMare LE, Devereau A, deVries B, Firth HV, Freson K, Greene D, Hamosh A, Helbig I, Hum C, Jahn JA, James R, Krause R, Laulederkind SJF, Lochmuller H, Lyon GJ, Ogishima S, Olry A, Ouwehand WH, Pontikos N, Rath A, Schaefer F, Scott R, Segal M, Sergouniotis P, Sever R, Smith C, Straub V, Thompson R, Turner C, Turro E, Veltman M, Vulliamy T, Yu J, von Ziegenweidt J, Zankl A, Zuchner S, Jacobsen JOB, Groza T, Smedley D, Mungall CJ, Haendel MA, and Robinson PN. (2016) The human phenotype ontology in 2017. Nucleic Acids Research, 2016 1-12 doi: 10.1093/nar/gkw1039

Links AE, Draper D, Lee E, Guzman J, Valivullah Z, Maduro V, Lebedev V, Didenko M, Tomlin G, Brudno M, Girdea M, Dumitriu S, Haendel MA, Mungall CJ, Smedley D, Hochheiser H, Arnold AM, Coessens B, Verhoeven S, Bone W, Adams D, Boerkoel CF, Gahl WA, Sincan M. Distributed Cognition and Process Management Enabling Individualized Translational Research: The NIH Undiagnosed Diseases Program Experience. Front Med. 2016 Oct 12;3:39. eCollection 2016.

Smedley D, Schubach M, Jacobsen J, Köhler S, Zemojtel T, Spielmann M, Jäger M, Hochheiser H, Washington NL, McMurry JA, Haendel MA, Mungall CJ, Lewis SE, Groza T, Valentini G, Robinson PN. (2016) A Whole-Genome Analysis Framework for Effective Identification of Pathogenic Regulatory Variants in Mendelian Disease. Am J Human Genetics. http://dx.doi.org/10.1016/j.ajhg.2016.07.005

Diehl AD, Meehan TF, Bradford YM, Brush MH, Dahdul WM, Dougall DS, He Y, Osumi-Sutherland D,

Ruttenberg A, Sarntivijai S, Van Slyke CE, Vasilevsky NA, Haendel MA, Blake JA, Mungall CJ. (2016) The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability. J Biomed Semantics. 2016 Jul 4;7(1):44. doi: 10.1186/s13326-016-0088-7.

Mulder N, Nembaware V, Adekile A, Anie KA, Inusa B, Brown B, Campbell A, Chinenere F, Chunda-Liyoka C, Derebail VK, Geard A, Ghedira K, Hamilton CM, Hanchard NA, Haendel M, Huggins W, Ibrahim M, Jupp S, Kamga KK, Knight-Madden J, Lopez-Sall P, Mbiyavanga M, Munube D, Nirenberg D, Nnodu O, Ofori-Acquah SF, Ohene-Frempong K, Opap KB, Panji S, Park M, Pule G, Royal C, Sangeda R, Tayo B, Treadwell M, Tshilolo L, Wonkam A. (2016) Proceedings of a Sickle Cell Disease Ontology workshop - Towards the first comprehensive ontology for Sickle Cell Disease. Appl Transl Genom. Mar 15;9:23-9. doi: 10.1016/j.atg.2016.03.005. eCollection 2016 Jun.

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Pederson, B., Vasilevsky, N., Hersh, W., McWeeney, S., Haendel, M. & Wirz, J. (2016). Big Data to Knowledge Open Educational Resources: Development and Dissemination Considerations. In Proceedings of EdMedia: World Conference on Educational Media and Technology 2016 (pp. 1723-1727). Association for the Advancement of Computing in Education (AACE).

Bandrowski A, Brinkman R, Brochhausen M, Brush MH, Bug B, Chibucos MC, Clancy K, Courtot M, Derom D, Dumontier M, Fan L, Fostel J, Fragoso G, Gibson F, Gonzalez-Beltran A, Haendel MA, He Y, Heiskanen M, Hernandez-Boussard T, Jensen M, Lin Y, Lister AL, Lord P, Malone J, Manduchi E, McGee M, Morrison N, Overton JA, Parkinson H, Peters B, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Schober D, Smith B, Soldatova LN, Stoeckert CJ Jr, Taylor CF, Torniai C, Turner JA, Vita R, Whetzel PL, Zheng J. (2016) The Ontology for Biomedical Investigations. PLoS One. Apr 29;11(4):e0154556. doi: 10.1371/journal.pone.0154556. eCollection 2016.

Mattingly CJ, Boyles R, Lawler CP, Haugen AC, Deary A, Haendel M. (2016) Laying a Community-Based Foundation for Data-Driven Semantic Standards in Environmental Health Sciences. Environ Health Perspect. Feb 12. Review. PMID: 26871594

Druzinsky RE, Balhoff JP, Crompton AW, Done J, German RZ, Haendel MA, Herrel A, Herring SW, Lapp H, Mabee PM, Muller HM, Mungall CJ, Sternberg PW, Van Auken K, Vinyard CJ, Williams SH, Wall CE. (2016) Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of the Literature on the Feeding Muscles of Mammals. PLoS One. 2016 Feb 12;11(2):e0149102. doi: 10.1371/journal.pone.0149102. eCollection 2016. PMID: 26870952

Bandrowski A, Brush M, Grethe JS, Haendel MA, Kennedy DN, Hill S, Hof PR, Martone ME, Pols M, Tan SC, Washington N, Zudilova-Seinstra E, Vasilevsky N. (2016) The Resource Identification Initiative: A Cultural Shift in Publishing. J Comp Neurol. 2016 Jan 1;524(1):8-22. doi: 10.1002/cne.23913.

Vita R, Vasilevsky N, Bandrowski A, Haendel M, Sette A, Peters B. (2015) Reproducibility and Conflicts in Immune Epitope Data. Immunology. Dec 17. doi: 10.1111/imm.12566. PMID: 26678806

Smedley D, Jacobsen JO, Jäger M, Köhler S, Holtgrewe M, Schubach M, Siragusa E, Zemojtel T, Buske OJ, Washington NL, Bone WP, Haendel MA, Robinson PN. (2015) Next-generation diagnostics and disease-gene discovery with the Exomiser. Nat Protoc. Dec;10(12):2004-15. doi: 10.1038/nprot.2015.124. Epub 2015 Nov 12. PMID: 26562621

Bone WP, Washington NL, Buske OJ, Adams DR, Davis J, Draper D, Flynn ED, Girdea M, Godfrey R, Golas G, Groden C, Jacobsen J, Köhler S, Lee EM, Links AE, Markello TC, Mungall CJ, Nehrebecky M, Robinson PN, Sincan M, Soldatos AG, Tifft CJ, Toro C, Trang H, Valkanas E, Vasilevsky N, Wahl C, Wolfe LA, Boerkoel CF, Brudno M, Haendel MA, Gahl WA, Smedley D. (2015) Computational evaluation of exome sequence data using human and model organism phenotypes improves diagnostic efficiency. Genet Med. 2015 Nov 12. doi: 10.1038/gim.2015.137. PMID: 26562225

Philippakis AA, Azzariti DR, Beltran S, Brookes AJ, Brownstein CA, Brudno M, Brunner HG, Buske OJ, Carey K, Doll C, Dumitriu S, Dyke SO, den Dunnen JT, Firth HV, Gibbs RA, Girdea M, Gonzalez M, Haendel MA, Hamosh A, Holm IA, Huang L, Hurles ME, Hutton B, Krier JB, Misyura A, Mungall CJ, Paschall J, Paten B, Robinson PN, Schiettecatte F, Sobreira NL, Swaminathan GJ, Taschner PE, Terry SF, Washington NL, Züchner S, Boycott KM, Rehm HL. (2015) The Matchmaker Exchange: a platform for rare disease gene discovery. Hum Mutat. 2015 Oct;36(10):915-21. doi: 10.1002/humu.22858. PMID: 26295439

Bandrowski A, Brush M, Grethe JS, Haendel MA, Kennedy DN, Hill S, Hof PR, Martone ME, Pols M, Tan S, Washington N, Zudilova-Seinstra E, Vasilevsky N, Resource Identification Initiative Consortium. (2015) The

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Dr. Melissa Haendel

Resource Identification Initiative: A cultural shift in publishing. Version 2. F1000Res. 4:134. doi: 10.12688/f1000research.6555.2. eCollection 2015. PMID: 26594330

Mungall CJ, Washington NL, Nguyen-Xuan J, Condit C, Smedley D, Köhler S, Groza T, Shefchek K, Hochheiser H, Robinson PN, Lewis SE, Haendel MA. (2015) Use of Model Organism and Disease Databases to Support Matchmaking for Human Disease Gene Discovery. Hum Mutat. 2015 Aug 13. doi: 10.1002/humu.22857. PMID:26269093

Buske OJ, Girdea M, Dumitriu S, Gallinger B, Hartley T, Trang H, Misyura A, Friedman T, Beaulieu C, Bone WP, Links AE, Washington NL, Haendel MA, Robinson PN, Boerkoel CF, Adams D, Gahl WA, Boycott KM, Brudno M. (2015) PhenomeCentral: A Portal for Phenotypic and Genotypic Matchmaking of Patients with Rare Genetic Diseases. Hum Mutat. 2015 Aug 7. doi: 10.1002/humu.22851. PMID: 26251998

Groza T, Köhler S, Moldenhauer D, Vasilevsky N, Baynam G, Zemojtel T, Schriml LM, Kibbe WA, Schofield PN, Beck T, Vasant D, Brookes AJ, Zankl A, Washington NL, Mungall CJ, Lewis SE, Haendel MA, Parkinson H, Robinson PN. (2015) The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease. Am J Hum Genet. 2015 Jul 2;97(1):111-24. doi: 10.1016/j.ajhg.2015.05.020. Epub 2015 Jun 25.

Haendel MA, Vasilevsky N, Brush M, Hochheiser HS, Jacobsen J, Oellrich A, Mungall CJ, Washington N, Köhler S, Lewis SE, Robinson PN, Smedley D. (2015) Disease insights through cross-species phenotype comparisons. Mamm Genome. 2015 Jun 20.

Ochs C, Perl Y, Geller J, Haendel M, Brush M, Arabandi S, Tu S. (2015) Summarizing and visualizing structural changes during the evolution of biomedical ontologies using a Diff Abstraction Network. J Biomed Inform. Jun 3. pii: S1532-0464(15)00106-9. doi: 10.1016/j.jbi.2015.05.018. [Epub ahead of print] PMID:26048076

Starr J, Castro E, Crosas M, Dumontier M, Downs RR, Duerr R, Haak LL, Haendel M, Herman I, Hodson S, Hourclé J, Kratz JE, Lin J, Nielsen LH, Nurnberger A, Proell S, Rauber A, Sacchi S, Smith A, Taylor M, Clark T. (2015) Achieving human and machine accessibility of cited data in scholarly publications.PeerJ Computer Science 1:e1 https://dx.doi.org/10.7717/peerj-cs.1

Deans AR, Lewis SE, Huala E, Anzaldo SS, Ashburner M, Balhoff JP, Blackburn DC, Blake JA, Burleigh JG, Chanet B, Cooper LD, Courtot M, Csösz S, Cui H, Dahdul W, Das S, Dececchi TA, Dettai A, Diogo R, Druzinsky RE, Dumontier M, Franz NM, Friedrich F, Gkoutos GV, Haendel M, Harmon LJ, Hayamizu TF, He Y, Hines HM, Ibrahim N, Jackson LM, Jaiswal P, James-Zorn C, Köhler S, Lecointre G, Lapp H, Lawrence CJ, Le Novère N, Lundberg JG, Macklin J, Mast AR, Midford PE, Mikó I, Mungall CJ, Oellrich A, Osumi-Sutherland D, Parkinson H, Ramírez MJ, Richter S, Robinson PN, Ruttenberg A, Schulz KS, Segerdell E, Seltmann KC, Sharkey MJ, Smith AD, Smith B, Specht CD, Squires RB, Thacker RW, Thessen A, Fernandez-Triana J, Vihinen M, Vize PD, Vogt L, Wall CE, Walls RL, Westerfeld M, Wharton RA, Wirkner CS, Woolley JB, Yoder MJ, Zorn AM, Mabee P. (2015). Finding Our Way through Phenotypes. PLoS Biol. Jan 6;13(1):e1002033. doi: 10.1371/journal.pbio.1002033. eCollection

Iorns E, Gunn W, Erath J, Rodriguez A, Zhou J, Benzinou M; *Reproducibility Initiative. (2014) Replication attempt: "Effect of BMAP-28 antimicrobial peptides on Leishmania major promastigote and amastigote growth: role of leishmanolysin in parasite survival". PLoS One. 2014 Dec 17;9(12):e114614. doi: 10.1371/journal.pone.0114614. eCollection 2014. PMID:25517992

*Haendel M, member of Advisory Committee and contribution to this manuscript

Smedley, D, Kohler, S, Bone, W, Oellrich, A, Jacobsen, J, Wang, K, Mungall, C, Washington, N, Bauer, S, Seelow, D, Krawitz, P, Boerkel, C, Gilissen, C, Haendel, M, Lewis, SE, Robinson, PN. (2014). Use of animal models for exome prioritization of rare disease genes. Orphanet Journal of Rare Diseases 9:Suppl 1

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Sirarat Sarntivijai, Yu Lin, Zuoshuang Xiang, Terrence F Meehan, Alexander D Diehl, Uma D Vempati, Stephan C Schürer, Chao Pang, James Malone, Helen Parkinson, Yue Liu, Terue Takatsuki, Kaoru Saijo, Hiroshi Masuya, Yukio Nakamura, Matthew H Brush, Melissa A Haendel, Jie Zheng, Christian J Stoeckert, Bjoern Peters, Christopher J Mungall, Thomas E Carey, Brian D Athey, Yongqun He. (2014). CLO: The Cell Line Ontology. Journal of Biomedical Semantics 5 (1), 37

Robinson PN, Köhler S, Oellrich A; Sanger Mouse Genetics Project, Wang K, Mungall CJ, Lewis SE, Washington N, Bauer S, Seelow D, Krawitz P, Gilissen C, Haendel M, Smedley D. (2014) Improved exome prioritization of disease genes through cross-species phenotype comparison. Genome Res. 2014 Jan 2. PMID:24162188

Köhler S, Schoeneberg U, Czeschik JC, Doelken SC, Hehir-Kwa JY, Ibn-Salem J, Mungall CJ, Smedley D, Haendel MA, Robinson PN. (2014) Clinical interpretation of CNVs with cross-species phenotype data. J Med Genet. 2014 Oct 3. pii: jmedgenet-2014-102633. doi: 10.1136/jmedgenet-2014-102633.

Ibn-Salem J, Köhler S, Love MI, Chung HR, Huang N, Hurles ME, Haendel M, Washington NL, Smedley D, Mungall CJ, Lewis SE, Ott CE, Bauer S, Schofield PN, Mundlos S, Spielmann M, Robinson PN (2014). Deletions of chromosomal regulatory boundaries are associated with congenital disease. Genome Biology 2014, 15:423 (4 September 2014)

Thacker RW, Díaz MC, Kerner A, Vignes-Lebbe R, Segerdell E, Haendel MA, Mungall CJ. (2014) The Porifera Ontology (PORO): enhancing sponge systematics with an anatomy ontology. J Biomed Semantics. 2014 Sep 8;5(1):39. doi: 10.1186/2041-1480-5-39. eCollection 2014.

Zemojtel T, Köhler S, Mackenroth L, Jäger M, Hecht J, Krawitz P, Graul-Neumann L, Doelken S, Ehmke N, Spielmann M, Øien NC, Schweiger MR, Krüger U, Frommer G, Fischer B, Kornak U, Flöttmann R, Ardeshirdavani A, Moreau Y, Lewis SE, Haendel M, Smedley D, Horn D, Mundlos S, Robinson PN. (2014) Effective diagnosis of genetic disease by computational phenotype analysis of the disease-associated genome. Science Translational Medicine. 3 September 2014 Vol 6 Issue 252 252ra124

Dahdul WM, Cui H, Mabee PM, Mungall CJ, Osumi-Sutherland D, Walls RL, Haendel MA. (2014) Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology. J Biomed Semantics. Aug 11;5:34. doi: 10.1186/2041-1480-5-34.

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-S4

Tenenbaum 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.

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Köhler 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, Jähn 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:24217912

Torniai 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

Schleyer 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:24303273

Druzinsky 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

Meehan 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

Arighi 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.

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.

Arighi 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.

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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: 23251424

Haendel, 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

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.

Mungall, 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. http://genomebiology.com/2012/13/1/R5

Torniai, C., Brush, M., Vasilevsky, N., Segerdell, E., Wison, M., Johnson, T., Corday, K., Shaffer, C., and Haendel, M. (2011) Developing an application ontology for biomedical resource annotation and retrieval: Challenges and lessons learned. International Conference on Biomedical Ontology 2011; July 26–30, 2011; Buffalo, NY.

Mungall 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.

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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., Melançon, E., and Eisen, J.S. (2004) Slow degeneration of zebrafish Rohon-Beard neurons during programmed cell death. Dev. Dyn. 229(1):30-41.

Haendel, M.A., (1999) In vitro preselection and characterization of the novel gene, axotrophin, University of Wisconsin Ph.D. Thesis.

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.

Non-refereed manuscripts:

Vasilevsky N, Minnier J, Haendel MA, Champieux RE. (2016) Reproducible and reusable research: Are journal data sharing policies meeting the mark? PeerJ preprint 10.7287/peerj.preprints.2588v1

McMurry JA, Köhler S, Washington NL, Balhoff JP, Borromeo C, Brush M, Carbon S, Conlin T, Dunn N, Engelstad M, Foster E, Gourdine JP, Jacobsen JO, Keith D, Laraway B, Xuan JN, Shefchek K, Vasilevsky NA, Yuan Z, Lewis SE, Hochheiser H, Groza T, Smedley D, Robinson PN, Mungall CJ, Haendel MA. Navigating the Phenotype Frontier: The Monarch Initiative. Genetics. 2016 Aug;203(4):1491-5. doi: 10.1534/genetics.116.188870.

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Mungall 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: http://dx.doi.org/10.1101/048843

Dumontier 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 https://doi.org/10.7287/peerj.preprints.1982v1

McMurry 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. https://doi.org/10.5281/zenodo.163459

Haendel 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), 25

Vasilevsky, 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. http://digitalcommons.ohsu.edu/etd/3571 DOI:10.6083/M4QC0273

Hoehndorf 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. - 28.03.2008

Thesis and Dissertation

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Dr. Melissa Haendel

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.

Edited volumes

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.

Oral presentations(posters not shown)

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.

Haendel, 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, MA. (2017) OHSU Data Jamboree Open Data Day, Portland, OR. Science in the open, what does it take? 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) 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. (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.

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Haendel, M.A. (2016) Open Access Scholarly Publishers Association (OASPA), Washington DC. “Credit where Credit is Due: Acknowledging all Types of Contributions”. Invited speaker. http://oaspa.org/wp-content/uploads/2016/10/haendel_COASP_2016_final.pdf

Haendel, 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. http://www.slideshare.net/mhaendel/deep-phenotyping-for-everyone

Haendel, 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) Force2016. Haendel, Melissa (2016): Phenopackets: Making phenotype profiles FAIR++ for disease diagnosis and discovery. https://dx.doi.org/10.6084/m9.figshare.3180898.v1 Invited speaker.

Haendel, M.A. (2016) International Society for Biocuration Conference 2016, Geneva, Switzerland. Keynote. (April) http://www.slideshare.net/mhaendel/why-the-world-needs-phenopacketeers-and-how-to-be-one

Haendel, 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. (2015) Semantic Web Applications and Tools for Life Sciences (SWAT4LS) 2015, Cambridge, UK. Keynote. http://www.slideshare.net/mhaendel/envisioning-a-world-where-everyone-helps-solve-disease

Haendel, M.A. (2015) NISO webinar for Research Data Metrics from the Altmetrics working group on output types and identifiers. Invited Speaker. http://www.slideshare.net/mhaendel/getting-and-giving-credit-for-all-that-we-do

Haendel, M.A. (2015) American Society for Human Genetics, Baltimore, MD. Platform talk. http://www.slideshare.net/mhaendel/the-monarch-initiative-an-integrated-genotypephenotype-platform-for-disease-discovery

Haendel, M.A. (2015) Linking Disease Model Phenotypes to Human Conditions Symposium, Co-chair and invited talk. Office of Director. http://www.scgcorp.com/linkingdisease2015/

Haendel, M.A. (2015) “A semantic approach to disease discovery” Invitae, San Francisco. Private corporation invited seminar.

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Dr. Melissa Haendel

Haendel, M.A. (2015) ClinGen-Decipher joint meeting, Washington DC. Invited Speaker. http://www.slideshare.net/mhaendel/haendel-clin-genfinal

Melissa Haendel, Stacy Konkiel, Karen Guzman, Kristi Holmes (2015). Measuring Success Through Improved Attribution. VIVO 2015 conference, Boston. Panelist. http://www.slideshare.net/kristiholmes/measuring-success-through-improved-attribution?related=1

Haendel, 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. http://www.slideshare.net/mhaendel/haendelnisoforce112015

Haendel, 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. http://www.slideshare.net/mhaendel/nci-cbiit-haendel12115

Haendel, 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. http://www.slideshare.net/mhaendel/haendel-force15hclsdataset

Haendel, M.A. (2014) Project CredIT workshop, “On the nature of credit” Invited speaker. http://www.slideshare.net/mhaendel/contribution-roles

Haendel, 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.” http://www.slideshare.net/mhaendel/standardizing-scholarly-output-with-the-vivo-ontology

Haendel, M.A., Lowe, B., and Ilik, V. (2014) VIVO 2014 Conference, Austin, TX. “The Case for Stable VIVO URIs.” http://www.slideshare.net/violetaili/vivo-bib-final

Haendel, M.A. (2014) Bio-ontologies SIG at ISMB in Boston, MA, keynote, “From baleen to cleft palate: an ontological exploration of evolution and disease.” http://www.slideshare.net/mhaendel/haendelismbsig20142

Haendel, M.A. (2014) Harvard Center for Bioinformatics, Boston, MA, invited speaker, “Use of semantic phenotyping to aid disease diagnosis.” http://www.slideshare.net/mhaendel/ud-npresentation

Whitmire, 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” http://www.slideshare.net/amandawhitmire/20140618-rml-rendezvousfinal

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Washington 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). OHSU Clinical Genetics Grand Rounds, June 5th, Portland, OR, invited speaker, “Expanding the Clinical Phenotype Space Using Model Systems Data.”

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.” http://www.slideshare.net/mhaendel/haendel-clingenetics31414

Haendel, 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?” http://www.slideshare.net/mhaendel/biocuration-2014-the-resource-identification-initiative

Haendel, 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.” http://www.slideshare.net/mhaendel/reproducibility-ofscience-final

E 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." http://www.slideshare.net/mhaendel/isf-vivo2013

Haendel, M.A. (2013) OHSU PCMB Retreat, May, invited speaker, “Creating presentations that don’t suck.” http://www.slideshare.net/mhaendel/creating-presentations-that-dont-suck

Haendel, M.A. (2013) National Center for Biomedical Ontology Seminar series, invited speaker, “Removing Roadblocks: Leveraging ontologies for data aggregation and computation.” http://www.slideshare.net/mhaendel/ncb-ohaendel2013

Haendel, M.A. (2013) Ontolog Ontology Evaluation Forum, invited speaker, “Intrinsic ontology evaluation from a biologist’s perspective.” http://ontolog.cim3.net/file/work/OntologySummit2013/2013-03-07_OntologySummit2013_OntologyEvaluation-IntrinsicAspects-2/OntologySummit2013_biologist-perspective-on-ontology-utility--MelissaHaendel_20130307.pdf

Haendel, 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.” http://www.vivoweb.com/files/Schedule%20At%20A%20Glance%2020120730%20v5.pdf

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Haendel, M.A. (2013) International Society for Biocuration Conference. “A merger of multi-species anatomy ontologies.” http://www.slideshare.net/mhaendel/haendelbiocurator2013-uberonv2

Haendel, 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.” http://nnlm.gov/2013escience/

Haendel, M.A. (2012) CTSA tool shop Webinar series, invited speaker, CTSAconnect presentation. https://www.ctsacentral.org/sites/default/files/documents/CTSAconnect_FactSheet_MH.pdf

Haendel 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.” http://ctsaconnect.org/system/files/presenationsandpapers/Haendel_WACD_2012.pdf

Melissa 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.http://ctsaconnect.org/system/files/presenationsandpapers/ctsaconnectVIVOconf.pdf

Melissa Haendel et al. (2012) NCBO conference. Baltimore, MD. CTSAconnecthttp://ctsaconnect.org/system/files/presenationsandpapers/ctsaconnect.ncbo_.final_.pdf

CJ 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.”

Haendel, 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”

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Other scholarly products

Letters

Haendel, M.A. et al.. Letter to the NIH Scientific Data Council and Francis Collins. “Request for Community partnership in data resource licensing planning” (2017).

Blogs

McMurry, J., Winfree, L., Haendel, M.A. “Bad Identifiers are the Potholes of the Information Superhighway: Take-Home Lessons for Researchers” (2017) http://blogs.plos.org/biologue/2017/07/06/bad-identifiers-potholes-of-information-superhighway/

Haendel, M.A. Force11. “Musings about the Open Science Prize.” (2016) https://www.force11.org/node/7716/

Haendel, M.A. and Vasilevsky N. PloS. “Data sharing in a modern world, well, maybe not so modern.” (2016) http://blogs.plos.org/collections/data-sharing-in-a-modern-world-well-maybe-not-so-modern/

Haendel, M.A. Force11. “I AM W7MAH” (2016) https://www.force11.org/blog/i-am-w7mah

Vasilevsky, N, Engelstad, M; Foster, E.; McMurry, J.; Mungall, C.; Robinson, P.; Köhler, S.; Haendel, M. Monarch Initiative. (2016) “Finally, a medical terminology that patients, doctors, and machines can all understand.” http://monarch-initiative.blogspot.com/2016/03/finally-medical-terminology-that.html

Haendel, M.A. Force11. “MAY THE FORCE11 BE WITH THE RESEARCH PARASITES” (2016) https://www.force11.org/blog/may-force11-be-research-parasites

Haendel, M.A. Force11. “NEW BONDS: FORCE11 AND THE DIGITAL LIBRARY FEDERATION (2015)https://www.force11.org/blog/new-bonds-force11-and-digital-library-federation

Haendel, M.A. Force11. “THE SECRET VIVO OF ATTRIBUTION” (2015) https://www.force11.org/blog/secret-vivo-attribution

Haendel, M.A. Force11. “CHANGING THE SCIENTIFIC VALUE SYSTEM, ONE CV AT A TIME” (2015)https://www.force11.org/blog/changing-scientific-value-system-one-cv-time

Haendel, M.A. Force11. “STUDY SHOWS SCIENTIFIC REPRODUCIBILITY IS HAMPERED BY LACK OF SPECIFICITY OF RESOURCES” (2013) https://www.force11.org/node/4478

Responses to Requests for Information (lead by M Haendel):

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NIH: Request for Information (RFI): Metrics to Assess Value of Biomedical Digital Repositories (2016) http://grants.nih.gov/grants/guide/notice-files/NOT-OD-16-133.html ; https://zenodo.org/record/203295#.WFL_faIrJp8

NIH: Request for Information (RFI): Undiagnosed Diseases Research (2015) https://grants.nih.gov/grants/guide/notice-files/NOT-RM-16-001.html

NIH: Soliciting Input into the Deliberations of the Advisory Committee to the NIH Director (ACD) Working Group on the National Library of Medicine (NLM)

https://grants.nih.gov/grants/guide/notice-files/NOT-OD-15-067.html

NIH: Input on Information Resources for Data-Related Standards Widely Used in Biomedical Science (2014) http://grants.nih.gov/grants/guide/notice-files/NOT-CA-14-054.html

NIEHS: Input on Development of a Language Standard for Environmental Health Sciences (2014) http://grants.nih.gov/grants/guide/notice-files/NOT-ES-14-004.html

NIH: Input on Development of a NIH Data Catalog (2013) http://grants.nih.gov/grants/guide/notice-files/NOT-HG-13-011.html

NIH: Training Needs in Response to Big Data to Knowledge Initiative (2013) http://grants.nih.gov/grants/guide/notice-files/NOT-HG-13-003.html

NIH: Input into the Deliberations of the Advisory Committee to the NIH Director Working Group on Data and Informatics (2012) http://grants.nih.gov/grants/guide/notice-files/NOT-OD-12-032.html.

NIH: Input on Proposed Modifications of the Biographical Sketch Used in NIH Grant (2012) http://grants.nih.gov/grants/guide/notice-files/NOT-OD-12-115.html

NIH: Enhancing the Clinical and Translational Science Awards (CTSA) Program (2012) http://grants.nih.gov/grants/guide/notice-files/NOT-TR-12-003.html

OSTP: Public Access to Digital Data Resulting From Federally Funded Scientific Research (2011) https://www.federalregister.gov/articles/2011/11/04/2011-28621/request-for-information-public-access-to-digital-data-resulting-from-federally-funded-scientific

Ontologies:

Disease ontology https://github.com/monarch-initiative/monarch-disease-ontologyHuman Phenotype Ontology http://www.human-phenotype-ontology.org/Genotype ontology https://github.com/monarch-initiative/GENO-ontologyZebrafish anatomy http://purl.obolibrary.org/obo/zfa.owlBiological spatial ontology http://purl.obolibrary.org/obo/bspo.owleagle-i resource ontology http://purl.obolibrary.org/obo/ero.owlVIVO Integrated semantic framework https://code.google.com/p/connect-isf/Uberon uberon.orgOntology of biomedical investigations http://obi-ontology.org/Reagent ontology https://code.google.com/p/reagent-ontology/Cell ontology http://purl.obolibrary.org/obo/cl.owl

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Common anatomy reference ontology http://purl.obolibrary.org/obo/caro.owlOntology for oral health and disease https://code.google.com/p/ohd-ontology/

Major database development contributions:

Monarch Initiative http://monarchinitiative.org Zebrafish information Network http://zfin.orgNeuroscience Information Framework http://neuinfo.org eagle-i http://eagle-i.net

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