Michael Watkins

Education

PhD, Biomedical Informatics, University of Utah

2017–2021

Dissertation: Addressing Barriers to the Practical Utility of Genomic Data in the Clinical Setting
Concentrations: clinical genomics, variant representation, interoperable EHR app development
Dissertation Advisors: Karen Eilbeck (Chair), PhD; Guilherme Del Fiol, MD, PhD; Scott Narus, PhD, MS; Rong Mao, MD, FACMG; Wendy Kohlmann, MS

BS, Bioinformatics, Brigham Young University

2011–2017* Two year deferral (2012–2014), full-time volunteer mission for The Church of Jesus Christ of Latter-day Saints

Positions

Manager of Data Standards and Modeling, D4CG, Biological Sciences Division, University of Chicago

2021–present

The mission of Data for the Common Good (D4CG) is to connect and share useful, high-quality data between institutions, groups, and countries. The Pediatric Cancer Data Commons—our flagship project—is the largest collection of harmonized international pediatric cancer data in the world. As the head of data modeling, I lead a team that works with a variety of international clinical professionals (oncologists, pathologists, surgeons, statisticians, terminologists, etc.) with the goal of a consensus data model that appropriately represents and harmonizes both trial registry and EHR data from all contributors.
Highlighted experiences include:

• Leading various EHR and clinical registry data harmonization initiatives.
• Helping secure funding through several notable mechanisms and partners, such as: LLS, NCI, St. Baldrick's, Rally Foundation, Team Bright Side, US Department of the Interior, and others.
• Contracted federal work to develop a core model for pediatric cancer to be used by the NCI's Childhood Cancer Data Initiative (CCDI) and the Biden Cancer Moonshot Initiative.
• Working closely with the NCI EVS on pediatric cancer CDEs in the cancer data standards registry (caDSR).
• Managing a team of clinical data analysts and creating a version-controlled metadata change management pipeline.

Principal, STANDARDWISE LLC

2023–present

Consulting services primarily include strategy, review, and curation for a variety of clinical informatics solutions and clientele.

Technical Developer, STRATAMETRICS LLC

2018–present

Develop and administer technical workshops for academic and industry groups.
To-date, this includes the following:

• Topics: HL7® FHIR® 101 for Developers​, SMART on FHIR and CDS Hooks, Introduction to CQL
• Workshop participants: ~150
• Workshop hours: ~50

NLM Trainee, Department of Biomedical Informatics, University of Utah

2018–2021

The department supports seven pre-doctoral researchers through a training grant from the National Library of Medicine. With my appointment, I expanded my research efforts to include SMART on FHIR, CDS Hooks, CQL, HL7 Infobutton, Social Determinants of Health, and HL7 FHIR Genomics Reporting.

Research Assistant, Department of Biomedical Informatics, University of Utah

2017–2018

I spent this time supported by Dr. Karen Eilbeck, PhD, assisting in the maintenance of the Sequence Ontology, and developing tools to support our joint efforts on the GA4GH Variant Representation working group.

Research Assistant, Department of Computer Science, Brigham Young University

2016–2017

I spent this time supported by Dr. Mark Clement, PhD, using multi-GPU computing libraries to optimize machine learning algorithms designed to synthesize novel protein structures.

Funding

(a) Past
NLM/T15LM007124	07/13/18–07/01/21
National Library of Medicine Training Program	$100,000
Role: Trainee
Department of the Interior	01/01/20–06/30/22
Pediatric Cancer Data Harmonization	$1,160,124
Role: Other Personnel
(b) Current
St. Baldrick’s Foundation	07/01/19–06/30/24
Pediatric Cancer Data Commons	$2,700,000
Role: Other Personnel
NCI Leidos	04/25/22–09/30/24
Childhood Cancer Clinical Data Commons	$1,863,270
Role: Other Personnel
Gray Foundation	05/01/22–06/30/24
PREDICT—Monogenic Diabetes Data Commons	$89,500
Role: Key Personnel
Leukemia & Lymphoma Society	11/01/23–10/31/27
Dare to Dream	$2,997,218
Role: Key Personnel
MIB Agents	07/01/23–06/30/24
Data Commons Supported Precision Medicine	$100,000
Role: Key Personnel
(c) Pending
NIH/U24	06/02/24–06/01/29
RFA-CA-22-023	$3,850,020
Realizing a Unified Oncology Knowledge Graph
Role: Key Personnel

Techincal Skills

Back-End Programming

Python, JavaScript, C++, Java, SQL/SQLite

Front-End Programming

HTML/CSS, D3

Application Architecture

ExpressJS, Flask

Clinical Interoperability

HL7 FHIR, USCDI, HL7 V2, mCODE, OMOP, CDISC (SDTM), PCORnet, Sentinel, i2b2

Ontologies and Terminologies

SNOMED-CT, RxNorm, LOINC, ICD-9/ICD-10/ICD-O, CPT, MONDO, UBERON, UCUM, Sequence Ontology

Clinical Decision Support

HL7 Infobutton, CDS Hooks, SMART on FHIR, CQL, bulkFHIR

Semantic Engineering

LinkML, SSSOM, OWL, RDF, GraphQL

Genomics

FHIR Genomics Reporting IG, HGVS, GA4GH VRS, VCF, GFF3, ClinVar, PharmGKB

Analytics

RStudio, TensorFlow, Pandas, NumPy, SciPy

Honors

2020	Recipient, "John D. Morgan Award", University of Utah, Department of Biomedical Informatics

Committees and Leadership

External
2017–2020	Global Alliance for Genomic Health (GA4GH), Variant Representation Working Group
2018–Present	Health Level Seven International, Clinical Genomics Working Group (Co-Chair)
2018–2020	Electronic Medical Records and Genomics (eMERGE) EHR Integration (EHRI) Work Group (Lead Investigator)
2019–2021	American Medical Informatics Association, Genomics and Translational Bioinformatics Working Group
2022–Present	National Institutes of Health, National Heart, Lung, and Blood Institute, BioData Catalyst® Data Management Core, Data Standards Team
University of Utah
2018–2021	Department of Biomedical Informatics, Curriculum Committee
2018	Department of Biomedical Informatics, Reed Gardner Teaching Excellence Award Committee
2020	Department of Biomedical Informatics, Industry Advisory Board Steering Committee
2020	Department of Biomedical Informatics, PhD Admissions Committee
University of Chicago
2022	Comprehensive Cancer Center, EYES on Cancer, Research Team
2022	Data Science Institute, Summer Lab Program

Review Boards / Panels

2021–Present	American Medical Informatics Association / Health Level Seven International, FHIR App Competition
Ad hoc review	Americal Medical Informatics Association Annual Symposium, BMC Med Informatics Dec Making

Associations and Memberships

Health Level Seven International (HL7)
American Medical Informatics Association (AMIA)

Teaching

BMI 6030	Graduate, “Foundations of Bioinformatics”, Course Developer, Co-Instructor, 2017–2020
BMI 7902	Graduate, “FHIR Practicum”, Course Developer, Co-Instructor, 2018–2021
Workshop	Graduate, “Data Modeling Using FHIR”, Content Developer, Instructor, 2019–2020
Workshop	Corporate, “HL7® FHIR® 101 for Developers”, Content Developer, Co-Instructor, 2019–2021
Workshop	Corporate, “SMART on FHIR and CDS Hooks”, Content Developer, Instructor, 2020–2021
Workshop	Corporate, “Introduction to CQL”, Content Developer, Instructor, 2020–2021

Mentorship / Advising

Masters Students

Alex Au, MD, MS, Eccles School of Medicine, University of Utah
Bradley Carlson, MD, MS, Pritzker School of Medicine, University of Chicago
David Chen, MS, Pritzker School of Medicine, University of Chicago

Undergraduate Students

Loreen Tumeh, BS, Comprehensive Cancer Center, University of Chicago
Zoey Zhou, BS, Data Science Institute, University of Chicago
Shuhan Liu, BS, Data Science Institute, University of Chicago
Xuerong Shang, BS, Data Science Institute, University of Chicago

Talks and Presentations

2018	Invited speaker, “Precision medicine and its emerging app development landscape”, University of Utah Industry Advisory Board (IABTalks), Salt Lake City, UT
2018	Invited speaker, “FHIR queries and creating a FHIR-based medical calculator”, University of Utah School of Medicine DeCART Summer Program, Salt Lake City, UT
2018	Invited speaker, “Using genomic data in CDS via FHIR”, University of Utah Translational Research Informatics Special Interest Group, Salt Lake City, UT
2018	Invited speaker, “Biomedical Informatics and Graduate Studies”, Brigham Young University Life Sciences Career Exploration, Provo, UT
2019	Plenary talk, “Use of Infobuttons to find answers to clinicians’ questions in clinical genomics”, National Library of Medicine Informatics Training Conference, Indianapolis, IN
2019	Invited speaker, “FHIR, SMART, and Social Determinants of Health”, Pan American Health Organization (PAHO) and the Peruvian Ministry of Health, Lima, Peru
2019	Invited speaker, “Genomic Infobuttons—Matching info needs to electronic knowledge resources”, University of Utah Translational Research Informatics Special Interest Group, Salt Lake City, UT
2019	Invited speaker, “Creating a SMART on FHIR application and deploying it with CDS Hooks”, University of Utah IT Exchange (ITX) Group, Salt Lake City, UT
2019	Plenary talk, “Implementing the VMC specification to reduce ambiguity in genomic variant representation”, American Medical Informatics Association, Annual Symposium, Washington, DC
2019	Invited speaker, “How using the GA4GH VR-Spec can improve and promote data sharing”, University of Utah Molecular Data Warehouse (MDW) Group, Salt Lake City, UT
2020	Invited speaker, “GA4GH VR-spec overview and implementation in HCI”, Huntsman Cancer Institute, Population Sciences Variant Data Team, Salt Lake City, UT
2020	Plenary talk, “FHIR Lab Reports: using SMART on FHIR and CDS Hooks to increase the clinical utility of pharmacogenomic laboratory test results”, American Medical Informatics Association, Virtual Summit
2020	Plenary talk, “A SMART on FHIR and CDS-Hooks enabled approach to the exchange and review of genomic test results”, National Library of Medicine Informatics Training Conference, Indianapolis, ID
2020	Invited speaker, “IAB Student Lightning Talk”, University of Utah Industry Advisory Board (IABTalks), Salt Lake City, UT
2021	Plenary talk, “ResultsMyWay: combining Fast Healthcare Interoperability Resources (FHIR), Clinical Quality Language (CQL), and informational resources to create a newborn screening application”, American Medical Informatics Association, Virtual Summit
2021	Invited speaker, “FHIR Lab Reports: using SMART on FHIR and CDS Hooks to increase the clinical utility of pharmacogenomic laboratory test results”, University of Utah Morgan Award Acceptance, Salt Lake City, UT
2022	Invited speaker, “Genetic Analysis Elements for the PCDC Rhabdomyosarcoma Data Dictionary”, International Soft Tissue Sarcoma Consortium (INSTRuCT) Executive Committee Meeting, Virtual
2022	Invited speaker, “Pediatric Oncology and mCODE”, Childhood Cancer–Data Integration for Research, Education, Care, and Clinical Trials Partnership (CC-DIRECT), Virtual
2022	Plenary talk, “LocalVar: a local variant collection manager to asynchronously detect synonyms, HGVS expression changes, and variant interpretation changes from ClinVar”, American Medical Informatics Association, Annual Symposium, Washington, DC
2023	Invited speaker, “Some ‘Growing Pains’ of Health Data Interoperability”, Brigham Young University Life Sciences Graduate Seminary Series, Provo, UT
2023	Invited speaker, “AYA Represention in The Cancer Moonshot Initiative”, Teen Cancer America Moonshot Initiative Roundtable, Los Angeles, CA
2023	Invited speaker, “Genomic Alteration Modeling in Neuroblastoma”, International Neuroblastoma Risk Group (INRG) Annual Meeting, Amsterdam, Netherlands
2024	Invited speaker, “Developing Pediatric Cancer Data Standards”, National Cancer Institute Childhood Cancer Data Initiative (CCDI) Webinar Series, Virtual
2024	Invited speaker, “Pediatric Cancer Common Data Elements (CDEs)”, North American Association of Central Cancer Registries (NAACCR) Site-Specific Data Item (SSDI) Working Group Meeting, Virtual

Publications

Watkins M, Fujimoto MS, Clement M. (2016) A Simplified Framework for Neural Networks [poster]. BIOT.

Watkins M, Rynearson S, Henrie A, Eilbeck K. (2019) Implementing the VMC specification to reduce ambiguity in genomic variant representation. AMIA Annu Symp Proc. 2019:1226-1235.

Watkins M, Eilbeck K. (2020) FHIR Lab Reports: using SMART on FHIR and CDS Hooks to increase the clinical utility of pharmacogenomic laboratory test results. AMIA Jt Summits Transl Sci Proc. 2020:683-692.

Watkins M, Viernes B, Nguyen V, Rojas Mezarina L, Silva Valencia J, Borbolla D. (2020) Translating social determinants of health into standardized clinical entities. Stud Health Technol Inform. 70:474-478. doi: 10.3233/SHTI200205.

Watkins M, Au A, Vuong T, Wallis H, Hart K, Rohrwasser A, Eilbeck K. (2021) ResultsMyWay: combining FHIR, Clinical Quality Language (CQL), and informational resources to create a newborn screening application. AMIA Annu Symp Proc.; 2021:615–623.

Watkins M, Au A, Eilbeck K, Ruiz-Schultz N, Rohrwasser A, Hart K, Williams M. (2022) A comprehansive newborn screening data interface for Utah providers, parents, and guardians [poster]. APHL.

Watkins M, Furner B, Li M, Cohen E, Carlson B, Leary S, Hettmer S, Kamihara J, Wyatt K, Volchenboum S. (2022) Harmonizing Genetic Data Element Modeling Across Cancer Trials [poster]. 54th Congress of the International Society of Paediatric Oncology (SIOP).

Watkins M, Kohlmann W, Berry T, Sama N, Koptiuch C, Rynearson S, Eilbeck K. (2023) LocalVar: a local variant collection manager to asynchronously detect synonyms, HGVS expression changes, and variant interpretation changes from ClinVar. AMIA Annu Symp Proc. ; 2023:1145-1152.

Carlson B, Watkins M, Li M, Furner B, Cohen E, Volchenboum S. (2023) Using A Standardized Nomenclature to Semantically Map Oncology-Related Concepts from Common Data Models to a Pediatric Cancer Data Model. AMIA Annu Symp Proc. ; 2023: 874–883.

Furner B, Cheng A, Desai A, Benedetti D, Friedman D, Wyatt K, Watkins M, Volchenboum S, Cohn S. (2024) Extracting Electronic Health Record Neuroblastoma Treatment Data with High Fidelity Using the REDCap Clinical Data Interoperability Services Module. JCO Clinical Cancer Informatics vol. 8 (2024): e2400009.

Wyatt K, Birz S, Castellino S, Henderson T, Lucas J, Pei Q, Zhou Y, Volchenboum S, Furner B, Watkins M, Kelly K, Flerlage J. (2024) Accelerating pediatric Hodgkin lymphoma research: the Hodgkin lymphoma data collaboration (NODAL). Journal of the National Cancer Institute. 2024;, djae013.

Watkins M, Christensen E, Eilbeck K (2024) Categorizing Genomic Concepts from Clinical and Research Terminologies Commonly Used in Cancer Reporting. AMIA Annu Symp Proc. 2024; Submitted Mar 2024.