Dr. Melissa Anne Haendel
725 Amelia Ave., Brownsville, OR, 97327
haendel@ohsu.edu
503-407-5970
http://orcid.org/0000-0001-9114-8737
http://scholar.google.com/citations?user=HtAV9dIAAAAJ
Twitter: @ontowonka
Education
Ph.D. Neuroscience, University of Wisconsin, 1999
B.A. Chemistry, Reed College, 1991
Positions
Associate Professor
2015-present
Director 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
2010-2014
Director 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
2009-2010
Director 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
2004-2009
University 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
2002-2004
Oregon 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
2000-2002
University of Oregon, Dr. Eisen and Dr. Darimont
Involvement of thyroid hormone during early neural development in the zebrafish.
Doctoral Research Assistant
1993-1999
University of Wisconsin, Dr. Gary Lyons
Identification and knock-out of a novel gene important for neural development in mice.
Laboratory Technician
Oregon State University, Dr. David Barnes
Maintenance of zebrafish stocks and cell culture lines.
1993
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-deepphenotyping-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 phenotypebased 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, 2013-2015
Co-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, 2010-2012
Mentored post-doctoral fellow to model reagents, cell lines, and observational clinical studies
with ontologies for the purposes of resource discovery, experimental inference, and
development of new data standards.
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.
Funding
Ongoing:
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 crossspecies 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
03/14-8/15
Project 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. 20112013. (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 earlydeveloping neurons in zebrafish.
5F31MH011560, Individual Pre-doctoral National Research Service Award, NIH, Role: Predoctoral 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, 2014present
International Rare Diseases Research Consortium (IRDiRC), Ontology working group, 2014present
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, 2013present
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)
Publications
See 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 CommunityBased 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 medicine
Molecular 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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Dr. Melissa Haendel
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 diseaseassociated 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, RobinsonRechavi 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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Dr. Melissa Haendel
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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Dr. Melissa Haendel
M., Van Auken K., Li Y., Chan J., Muller, H., Cui H., Balhoff J.P., Chi-Yang Wu J., Lu Z., Wei C.,
Tudor C.O., Raja K., Subramani S., Natarajan J., Cejuela J.M., Dubey P., Wu C. (2013) An overview
of the BioCreative 2012 Workshop Track III: interactive text mining task. Database, The Journal of
Biological Databases and Curation 01/2013; 2013:bas056.
Dahdul W.M., Balhoff J.P., Blackburn D.C., Diehl A.D., Haendel M.A., Hall B.K., Lapp H., Lundberg
J.G., Mungall C.J., Ringwald M., Segerdell E., Van Slyke C.E., Vickaryous M.K., Westerfield M.,
Mabee P.M. (2012) A unified anatomy ontology of the vertebrate skeletal system. PLoS One.
2012;7(12):e51070. doi: 10.1371/journal.pone.0051070. Epub 2012 Dec 10. PMID: 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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Dr. Melissa Haendel
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. 136:297307.
Hunter, P.J., Swanson, B.S., Haendel, M.A., Lyons, G.E., and Cross, J.C. (1999) Mrj encodes a DnaJrelated 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;21:935. 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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Dr. Melissa Haendel
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/B978-0-12388408-4.00001-0. 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-everyonehelps-solve-disease
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Dr. Melissa Haendel
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-givingcredit-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-genotypephenotypeplatform-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, “Crossspecies 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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Dr. Melissa Haendel
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/OntologySummit2013/2013-0307_OntologySummit2013_OntologyEvaluation-IntrinsicAspects-2/OntologySummit2013_biologistperspective-on-ontology-utility--MelissaHaendel_20130307.pdf
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Dr. Melissa Haendel
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. CTSAconnect
http://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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Dr. Melissa Haendel
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-12032.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-forinformation-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-ontology
Zebrafish anatomy http://purl.obolibrary.org/obo/zfa.owl
Biological spatial ontology http://purl.obolibrary.org/obo/bspo.owl
eagle-i resource ontology http://purl.obolibrary.org/obo/ero.owl
VIVO Integrated semantic framework https://code.google.com/p/connect-isf/
Uberon uberon.org
Human 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.owl
Common anatomy reference ontology http://purl.obolibrary.org/obo/caro.owl
Ontology for oral health and disease https://code.google.com/p/ohd-ontology/
Database development contributions:
Zebrafish information Network http://zfin.org
Neuroscience 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, mRNA
4,309 bp linear mRNA
NM_001159500.1 GI:226958366
2. Mus musculus estrogen related receptor, beta (Esrrb), transcript variant 1, mRNA
4,208 bp linear mRNA
NM_011934.4 GI:226958364
3. Mus musculus C-terminal binding protein 2 (Ctbp2), transcript variant 1, mRNA
4,170 bp linear mRNA
NM_001170744.1 GI:282721028
4. Mus musculus C-terminal binding protein 2 (Ctbp2), transcript variant 2, mRNA
3,047 bp linear mRNA
NM_009980.4 GI:144922610
5. Mus musculus glial cells missing homolog 1 (Drosophila) (Gcm1), mRNA
2,034 bp linear mRNA
NM_008103.3 GI:118130983
6. Mus musculus DnaJ (Hsp40) homolog, subfamily B, member 6 (Dnajb6), transcript variant 1, mRNA
2,708 bp linear mRNA
NM_001037940.4 GI:188219639
7. Mus musculus glial cells missing homolog 2 (Drosophila) (Gcm2), mRNA
2,879 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),
mRNA
3,484 bp linear mRNA
NM_022826.2 GI:53828927
9. Danio rerio family with sequence similarity 32, member A, like (fam32al), mRNA
780 bp linear mRNA
NM_001002203.1 GI:50345059
10. Danio rerio nuclear receptor coactivator 2 (ncoa2), mRNA
4,958 bp linear mRNA
NM_131777.1 GI:18859480
11. Mus musculus membrane-associated ring finger (C3HC4) 7 (March7), mRNA
2,719 bp linear mRNA
NM_020575.2 GI:118130502
12. Danio rerio thyroid hormone receptor beta (thrb), mRNA
2,198 bp linear mRNA
NM_131340.1 GI:18859510
13. Mus musculus ring finger protein 4 (Rnf4), mRNA
2,936 bp linear mRNA
NM_011278.4 GI:158508477
14. Mus musculus DnaJ (Hsp40) homolog, subfamily B, member 6 (Dnajb6), transcript variant 4, mRNA
1,642 bp linear mRNA
NM_001127367.1 GI:188219643
15. Mus musculus DnaJ (Hsp40) homolog, subfamily B, member 6 (Dnajb6), transcript variant 2, mRNA
1,120 bp linear mRNA
NM_001037941.3 GI:188219641
16. Mus musculus DnaJ (Hsp40) homolog, subfamily B, member 6 (Dnajb6), transcript variant 3, mRNA
1,645 bp linear mRNA
NM_011847.4 GI:188219640
17. Danio rerio thyroid hormone receptor alpha B (thraB) mRNA, partial cds
653 bp linear mRNA
DQ991962.1 GI:118162028
18. Danio rerio thyroid hormone receptor alpha A 1-2 (thraA) mRNA, partial cds
651 bp linear mRNA
DQ991961.1 GI:118162026
19. Mus musculus axotrophin mRNA, complete cds
2,720 bp linear mRNA
AF155739.1 GI:5052030
20. Homo sapiens CHD2-52 Down syndrome cell adhesion molecule (DSCAM) mRNA, complete cds
6,413 bp linear mRNA
AF023450.1 GI:3169767
21. Mus musculus MRJ (Mrj) mRNA, complete cds
1,546 bp linear mRNA
AF035962.1 GI:3142371
22
Dr. Melissa Haendel
22. Homo sapiens CHD2-42 Down syndrome cell adhesion molecule (DSCAM) mRNA, partial cds
6,110 bp linear mRNA
AF023449.1 GI:3169765
23