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

haendel@ohsu.edu503-407-5970

http://orcid.org/0000-0001-9114-8737http://scholar.google.com/citations?user=HtAV9dIAAAAJ

Twitter: @ontowonka

Education

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

Positions

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

Development of data standards and semantic technologies, research data and ethics education, educational program development, community data sharing coordination, reproducibility and attribution informatics, strategic/organizational planning, Library leadership.

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

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

Senior Research Associate, Lead Ontologist 2009-2010Director of the Ontology Development Group, Oregon Health and Science University, Library and Department of Medical Informatics and 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 Curator, Nomenclature Lead 2004-2009University of Oregon, Dr. Westerfield

Development of anatomical ontologies and syntax for phenotype ontologies; 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

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

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Dr. Melissa Haendel

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.

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.

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.

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

Instructor: Foundations of Interprofessional Practice and Research I: Patient Safety, 2014, OHSU. Length: 4 hour session.Co-facilitated beginning professional group of students beginning diverse clinical professions in developing clinical care team strategies surrounding patient safety.

Instructor: II INTERNATIONAL SUMMER SCHOOL “Rare disease and orphan drug registries.” Length: 1 week. September 2014. Rome, Istituto Superiore di Sanità.

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Dr. Melissa Haendel

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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Dr. Melissa Haendel

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.

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Dr. Melissa Haendel

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.

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.

FundingOngoing:

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

NIH U54HG007990-S2. Role subcontract to Haussler (PI)/USC Center for Big Data in Translational Genomics. 9/2014 - 8/2018, $94,368. Goal is to develop GA4GH genotype-to-phenotype schemas and evidence models for the BRCA Exchange.

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.

Office of the Director, NIH, Supplement 4 R24 OD011883 04S1 Role: PI. 09/18/2015 - 07/31/2016. $100,000. Goal is to migrate infrastructure for the Monarch application to OHSU.

NIH Undiagnosed Disease Program, HHSN268201300036C, Role: PI, contract. 2015-2015 (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 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.

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Dr. Melissa Haendel

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:

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 Melissa Haendel (PI)09/18/2014 - 07/31/2015. 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.

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. http://www.ctsaconnect.org

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.

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Dr. Melissa Haendel

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

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

Commended for Excellence in Scholarship, Reed College, 1991

International/national committees and memberships

NIH BD2K Standards Coordinating Center Advisory Committee, 2015- present

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

ResearchObject.org publishing digital objects Advisory Board 2014 - present

CASRAI Working Group on contribution roles 2014- present

Research Data Alliance Working Group co-chair: The BioSharing Registry: connecting data

policies, standards & databases in life sciences 2014 - present

NIDCR FaceBase2 Scientific Leadership Group 2014-present

Galaxy, reproducible workflows, Advisory Board 2014 -present

Force11 Advisory Board 2014 – present; Force11 Executive committee, 2015- present

Resource Identification Initiative Co-Director 2013 - present

NIH BD2K Software Discovery Workshop committee member – 2014

NIH BD2K Data Integration Workshop participant - 2014

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Dr. Melissa Haendel

International Society for Biocuration Executive Board 2013 - present

VIVO Ontology Working Group Lead, 2013 – present; VIVO steering committee, 2014-present

Reproducibility Initiative Advisory Board, 2013 - present

American Society of Human Genetics member 2013- present

One Mind Data Standards working group member, 2013 - present

Force11 member, 2012 – present

CTSA IKFC Informatics Ontology Interest Group, 2012 - present

American Medical Informatics Association, member 2011-2013 (need to renew for 2014)

Open Biomedical Ontology, Coordinating Board 2010-present

Phenotype Resource Coordination Network Vertebrate Working Group Lead 2010-present

International Biocuration Society member, 2006 - present

American Association of Cancer Research Pathobiology Workshop participant, 2003

Society for Developmental Biology member 1996-99

Institutional committees

OHSU Data Science Advisory Board, 2015- present

OHSU Provost’s AML Big Challenge, 2015 (merged with above)

OHSU Bioimaging Data Publication taskforce, 2014-present

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

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

present

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 - present (quiescent)

OHSU Office of Research Data stewardship taskforce, 2011-present (quiescent)

University of Oregon Post-doctoral committee, 2000-2002

University of Wisconsin Medical School Graduate Representative, 1998-1999

Program committees

Pacific Biocomputing Session Chair, 2016

SWAT4LS 2015 Program committee, 2015

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Dr. Melissa Haendel

ISWC 2015 Data Sets & Ontology Track, 2015

PhenoDay, ISMB, 2014, 2015, 2016

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

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

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 Summit on Translational Bioinformatics (TBI)

International Conference of Biomedical Ontologies Scientific Program Committee, Program committee, 2011

Reviewer/Editor for Journals:

PloS Data Guidelines Board (2015- 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)

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Dr. Melissa Haendel

Pacific Biocomputing, Reviewer (2014 - present)

Nature Data, Reviewer (2014 - present)

Reviewer for Grants

Helmsley Charitable Trust (2015)

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

National Institutes of Health, Office of Director (2015)

UK Medical Research Council (2014, 2015, 2016)

Genome Canada (2013-present)

PublicationsSee Google Scholar profile here: https://scholar.google.com/citations?user=HtAV9dIAAAAJ&hl=en

Refereed manuscripts:

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

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

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.

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

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Dr. Melissa Haendel

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

Robinson PN, Mungall CJ, Haendel M (2015) Capturing phenotypes for precision medicineMolecular Case Studies 1 (1), a000372

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

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

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,

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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

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

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

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.

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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.

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

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

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

On the reproducibility of science: unique identification of research resources in the biomedical literature. Vasilevsky NA, Brush MH, Paddock H, Ponting L, Tripathy SJ, Larocca GM, Haendel MA. PeerJ. 2013 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

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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: 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.

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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., 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:

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

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

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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

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 Chesler, E.J. Editors. Elsevier.

Oral presentations(posters not shown)

Haendel, M.A. (2016) International Society for Biocuration Conference 2016, Geneva, Switzerland. Keynote. (April)

Haendel, M.A. (2016) Phenotype RCN, Biosphere, AZ. Invited speaker.

Haendel, M.A. (2016) TorBUG. Seminar Series Invited speaker. 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

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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. 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) 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, invited speaker, “Cross-Species Phenotype Comparisons for disease diagnostics.”

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

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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

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

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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

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.”

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Haendel, M.A. (2005) Neuroscience Training Program Career Development Seminar series, Madison, WI, Invited speaker. “Scientific Curation: At the crossroads of bioinformatics”

Other scholarly products

Requests for Information (lead by M Haendel):

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 Available at: http://www.ctsaconnect.org/system/files/Response_Input%20on%20Development%20of%20a%20NIH%20Data%20Catalog.docx

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. Available at: http://www.ctsaconnect.org/system/files/NIH_Data_RFI_response_0.docx

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 Available at: http://ctsaconnect.org/system/files/ResponsetoRFI_NOT-OD-12-115.doc

NIH: Enhancing the Clinical and Translational Science Awards (CTSA) Program (2012) http://grants.nih.gov/grants/guide/notice-files/NOT-TR-12-003.html Available at: http://ctsaconnect.org/system/files/CTSAconnectResponsetoCTSARFI_0.doc

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

Major Ontologies:

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Dr. Melissa Haendel

Disease ontology https://github.com/monarch-initiative/monarch-disease-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.orgHuman Phenotype Ontology http://www.human-phenotype-ontology.org/Ontology of biomedical investigations http://obi-ontology.org/Reagent ontology https://code.google.com/p/reagent-ontology/Genotype ontology https://code.google.com/p/monarch-ontology/Cell ontology http://purl.obolibrary.org/obo/cl.owlCommon anatomy reference ontology http://purl.obolibrary.org/obo/caro.owlOntology for oral health and disease https://code.google.com/p/ohd-ontology/

Database development contributions:

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

Genbank submissions: 1. Mus musculus estrogen related receptor, beta (Esrrb), transcript variant 2, mRNA4,309 bp linear mRNA NM_001159500.1 GI:226958366

2. Mus musculus estrogen related receptor, beta (Esrrb), transcript variant 1, mRNA4,208 bp linear mRNA NM_011934.4 GI:226958364

3. Mus musculus C-terminal binding protein 2 (Ctbp2), transcript variant 1, mRNA4,170 bp linear mRNA NM_001170744.1 GI:282721028

4. Mus musculus C-terminal binding protein 2 (Ctbp2), transcript variant 2, mRNA3,047 bp linear mRNA NM_009980.4 GI:144922610

5. Mus musculus glial cells missing homolog 1 (Drosophila) (Gcm1), mRNA2,034 bp linear mRNA NM_008103.3 GI:118130983

6. Mus musculus DnaJ (Hsp40) homolog, subfamily B, member 6 (Dnajb6), transcript variant 1, mRNA2,708 bp linear mRNA NM_001037940.4 GI:188219639

7. Mus musculus glial cells missing homolog 2 (Drosophila) (Gcm2), mRNA2,879 bp linear mRNA NM_008104.2 GI:113680508

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Dr. Melissa Haendel

8. Homo sapiens membrane-associated ring finger (C3HC4) 7, E3 ubiquitin protein ligase (MARCH7), mRNA3,484 bp linear mRNA NM_022826.2 GI:53828927

9. Danio rerio family with sequence similarity 32, member A, like (fam32al), mRNA780 bp linear mRNA NM_001002203.1 GI:50345059

10. Danio rerio nuclear receptor coactivator 2 (ncoa2), mRNA4,958 bp linear mRNA NM_131777.1 GI:18859480

11. Mus musculus membrane-associated ring finger (C3HC4) 7 (March7), mRNA2,719 bp linear mRNA NM_020575.2 GI:118130502

12. Danio rerio thyroid hormone receptor beta (thrb), mRNA2,198 bp linear mRNA NM_131340.1 GI:18859510

13. Mus musculus ring finger protein 4 (Rnf4), mRNA2,936 bp linear mRNA NM_011278.4 GI:158508477

14. Mus musculus DnaJ (Hsp40) homolog, subfamily B, member 6 (Dnajb6), transcript variant 4, mRNA1,642 bp linear mRNA NM_001127367.1 GI:188219643

15. Mus musculus DnaJ (Hsp40) homolog, subfamily B, member 6 (Dnajb6), transcript variant 2, mRNA1,120 bp linear mRNA NM_001037941.3 GI:188219641

16. Mus musculus DnaJ (Hsp40) homolog, subfamily B, member 6 (Dnajb6), transcript variant 3, mRNA1,645 bp linear mRNA NM_011847.4 GI:188219640

17. Danio rerio thyroid hormone receptor alpha B (thraB) mRNA, partial cds653 bp linear mRNA DQ991962.1 GI:118162028

18. Danio rerio thyroid hormone receptor alpha A 1-2 (thraA) mRNA, partial cds651 bp linear mRNA DQ991961.1 GI:118162026

19. Mus musculus axotrophin mRNA, complete cds2,720 bp linear mRNA AF155739.1 GI:5052030

20. Homo sapiens CHD2-52 Down syndrome cell adhesion molecule (DSCAM) mRNA, complete cds6,413 bp linear mRNA AF023450.1 GI:3169767

21. Mus musculus MRJ (Mrj) mRNA, complete cds1,546 bp linear mRNA AF035962.1 GI:3142371

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Dr. Melissa Haendel

22. Homo sapiens CHD2-42 Down syndrome cell adhesion molecule (DSCAM) mRNA, partial cds6,110 bp linear mRNA AF023449.1 GI:3169765

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