DMICE Faculty to Play Major Role in New OHSU-Led National Center for Data to Health

Oregon Health & Science University (OHSU) is the lead institution in a new award from the National Center for Advancing Translational Sciences (NCATS) to establish a National Center for Data to Health (CD2H). The center emanates from the National Institutes of Health (NIH) Clinical and Translational Science Award (CTSA) Program and its major goal is to support the use of health data, algorithms and information systems to bridge basic science and clinical research.

The contact PI of the project is Melissa Haendel, PhD, associate professor in the Department of Medical Informatics & Clinical Epidemiology (DMICE). Dr. Haendel co-director of the NCATS-funded Biomedical Data Translator, the Monarch Initiative, and the OHSU Library.

The newly awarded grant provides $25 million over five years to establish the new center, which aims to foster collaboration across more than 50 premier medical research institutions within the CTSA network. According to Dr. Haendel, “The goal is to unlock and coordinate the unique wealth of technologies and innovation that each participating institution brings. Team science, data sharing, use of informatics to integrate and analyze data and collaboration will ultimately improve the care of patients.”

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The specific aims of the center are to (1) harmonize the data ecosystem, (2) realize a software tool ecosystem, (3) synthesize a people ecosystem, and (4) catalyze technical and cultural evolution. The center’s “Idea to Implementation (I2I)” pipeline will leverage the above aims, develop community, and demonstrate translational impact in diverse domains, such as Rare Disease and Lifespan and aging.

Partners in the project include Northwestern University, University of Washington, Johns Hopkins University School of Medicine, Sage Bionetworks, Scripps Research Institute, Washington University, the University of Iowa, and the Jackson Laboratory. The governance structure of the project is shown in the figure from the grant proposal.


A number of DMICE faculty will play major roles in the project as follows.

In addition to serving as an overall project leader, Dr. Haendel will lead Policy for Ontologies/Standards, Operations for Rare disease, Operations for People & Attribution, and will participate in Data and Engagement teams.

Rob Schuff, MS, instructor, will also instantiate the use case elements more directly related to standardization of common clinical data elements against research data warehouses and provide guidance to others working to improve their data and software interfaces and standardization. He will be pivotal in assisting with the technical requirements, development, implementation in Software, clinical data systems expertise in Data and domain application expertise for Rare Disease and Lifespan.

Ted Laderas, PhD, assistant professor, will assist with the development and assessment of materials in Education, as well as participate in Data, Software and Lifespan

David Dorr, MD, MS, will serve as the Coordination Lead for Lifespan and participate in Data, Evaluation and Education.

Shannon McWeeney, PhD, professor and vice chair, will serve as the Policy lead for Education as well as participate in Evaluation, Engagement, Software and Lifespan.

Nicole Weiskopf, PhD, assistant professor, will participate in Data, Engagement, and Lifespan.

Beth Wilmot, PhD, assistant professor, will participate in Data, Software, Lifespan and Rare Disease, providing her domain expertise as well as her experience in diverse methodologies for analysis of complex traits and management, integration and visualization of large, multi-omic, multi-site data sets.

William Hersh, MD, professor and chair, will serve as the Operations Lead in Education and participate in Engagement and People, Expertise and Attribution.

Michael Chiang, MD Elected to American College of Medical Informatics

Chiang-Michael-_CaseyEye_0211-e1507579378734-209x300DMICE Professor Michael Chiang, MD has been elected to the American College of Medical Informatics (ACMI).  He will be inducted into the College on November 5 during the 2017 American Medical Informatics Association (AMIA) Annual Symposium. ACMI is an honorary College of elected fellows from the United States and abroad selected for significant and sustained contributions to the field. Dr. Chiang joins four other DMICE faculty who are fellows of ACMI: Joan Ash, PhD, professor and vice chair; David Dorr, MD, MS, professor and vice chair; Paul Gorman, MD, professor; and William Hersh, MD, professor and chair.

Dr. Chiang is Knowles Professor of Ophthalmology and Medical Informatics and Clinical Epidemiology at OHSU and is vice chair in the Department of Ophthalmology. He also leads the Oregon State Elks Center for Ophthalmic Informatics. As a clinician-scientist, he conducts research in the application of biomedical informatics to clinical ophthalmology. Dr. Chiang’s clinical practice focuses on pediatric ophthalmology and adult strabismus. His research examines telemedicine for diagnosis of retinopathy of prematurity and other ophthalmic diseases, implementation and evaluation of electronic health record systems, modeling of clinical workflow and computer-based image analysis for clinical diagnosis.

Dr. Chiang directs aNational Institutes of Health (NIH)-funded T32 training program in translational visual science for graduate students and postdoctoral fellows, teaches in both the ophthalmology and biomedical informatics departments, and has directly mentored over 40 graduate students, medical students, and postdoctoral fellows. His research has been continuously funded by the NIH since 2003 and his group has published over 100 peer-reviewed journal papers.

(Adapted from OHSU Research News.)

September Brings 10 New Grants and Contracts for DMICE

The month of September was highly productive for the Department of Medical Informatics and Clinical Epidemiology (DMICE), with 7 new grants funded within the department and 3 more larger OHSU grants funded that include DMICE collaborators.

Two faculty received career development grants from the National Library of Medicine (NLM), the institute within the National Institutes of Health (NIH) that funds research and training in biomedical informatics.

Michelle Hribar, Ph.D., assistant professor, was awarded an R00 grant, Modeling and Optimization of Clinical Processes Using EHR Data. This research grant provides 3 years of funding with total costs of $672,297.

Nicole Weiskopf, Ph.D., assistant professor, has been awarded a K01 grant, Measuring and Improving Data Quality for Clinical Quality Measure Reliability. The career development grant provides 3 years of funding with total costs of $462,128.

Another grant was awarded by the Agency for Healthcare Research and Quality (AHRQ) to DMICE faculty Jeff Gold, M.D., professor; Vishnu Mohan, M.D., M.B.I., associate professor; and Joan Ash, Ph.D,. professor and vice chair. Entitled, Creation and Validation of a Training Toolkit to Ensure Safe and Proficient Use of EHR by Medical Scribes, the grant is for 5 years with total costs of $2 million.

In addition, Annette Totten, Ph.D., assistant professor, and Eilis Boudreau, M.D., Ph.D., associate professor, have been awarded a contract from the Department of Veterans Affairs on sleep study data analytics. Their project will evaluate the Office of Rural Health Pathway to Partnership Sleep-Telemedicine Project to determine whether e-consultation, telehealth, and virtual care models result in equivalent care outcomes when compared to traditional face-to-face care. They will also look at Veterans’ satisfaction with care and cost-effectiveness. The amount of funding for the base year of the contract is $156,210. The VA can choose to exercise two option periods, which would bring the total amount of funding to $424,120.

The Pacific Northwest Evidence-based Practice Center (PNWEPC) within DMICE also received new funding. Roger Chou, M.D., professor and EPC director, will be on a grant from the National Center for Complementary & Integrative Health, Clinical Coordinating Center for Spinal Manipulation and Patient Self-Management for Preventing Acute to Chronic Back Pain. The grant is based at the University of Minnesota, with Dr. Gert Bronfort as principal investigator, and Dr. Chou a co-investigator at OHSU.  In addition, the PNWEPC will be providing guideline support development to the American Urological Association on the topic of recurrent urinary tract infections, with Dr. Chou as the principal investigator.

The department was also awarded an administrative supplement for its NLM biomedical informatics and data science training grant, now in its 26th year. A total of $100,000 has been provided for one year to advance faculty and curriculum development in data science. This adds to the five-year, $4.4 million award that was funded earlier this summer to fund predoctoral and postdoctoral positions from the NLM and the National Institute for Environmental and Health Sciences (NIEHS). The latter positions will facilitate collaboration between the department and the new OHSU-PSU School of Public Health.

A number of DMICE faculty are also part of 3 larger grants awarded to OHSU.

Melissa Haendel, Ph.D,. associate professor, has been awarded a large, multi-institution grant under the CTSA Data to Health (CD2H) initiative of the National Center for Advancing Translational Science (NCATS). Entitled, A National Center for Digital Health Informatics Innovation, the grant involves 9 institutions and includes 5 other DMICE faculty: Shannon McWeeney, Ph.D., professor and Vice Chair; Ted Laderas, Ph.D,, assistant professor; David Dorr, M.D., M.S., professor; Nicole Weiskopf, Ph.D., assistant professor; Robert Schuff, M.S., instructor; and William Hersh, M.D., professor and chair.

Annette Totten, Ph.D., assistant professor, is principal investigator of a contract awarded to the Oregon Rural Practice-based Research Network (ORPRN) by the Patient-Centered Outcomes Research Institute (PCORI). Entitled A Cluster-Randomized Trial Comparing Team-Based versus Primary Care Clinician-Focused Advance Care Planning in Practice-Based Research Networks, the award will provide 4 years of funding with total costs of $8 million. This award has been approved pending completion of a business and programmatic review by PCORI staff and issuance of a formal award contract.

Cynthia Morris, Ph.D., M.P.H., professor and vice chair, is Senior Associate Director, Education & Career Development; Shannon McWeeney, Ph.D., professor and vice chair, is Associate Director, Translational Bioinformatics; and Rob Schuff, M.S., instructor, is Associate Director, Clinical Research Informatics for OHSU’s Oregon Clinical & Translational Research Institute (OCTRI), which had its 5-year, $37 million grant renewed as part of the NIH Clinical and Translational Science Award (CTSA) program.

Learn About Career and Educational Opportunities in Biomedical Informatics at Prospective Student Open House Saturday October 14, 2017

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Discover One of the Leading Programs in Biomedical Informatics!

Please join us to learn more about careers and educational opportunities in biomedical informatics – the field at the intersection of health, biomedicine, computer science, and data science – at the annual Open House of the OHSU Biomedical Informatics Graduate Program. The Open House will take place this year on Saturday, October 14th from 11:30 am to 2:30 pm. Participants can register and look at the schedule here: DMICE Open House.

The Open House is a great opportunity to learn about our programs and be part of discussions with DMICE Chair William Hersh, Vice Chair Shannon McWeeney, and current students and faculty in the program.

DMICE Bringing Informatics Education to India

bill4The Oregon Health & Science University (OHSU) Department of Medical Informatics & Clinical Epidemiology (DMICE), in collaboration with Krishmatics, will be delivering a new online course, Health Informatics and Analytics, to an audience in India. The course will be led by DMICE Chair and well-known informatics educator, Dr. William Hersh. At the end of the online portion of the course, Dr. Hersh will conduct an in-person session in India.

The course adapts and combines components of OHSU’s well-known curricula in both health informatics and data analytics. The overall goal of the course is to provide a deep introduction to the application of information technology and data analytics in healthcare. Students will learn about clinical data, electronic health records, data standards and interoperability, clinical decision support, quality measurement, and information retrieval, and how they are employed in healthcare data analytics.

The course is offered in two parts:

  • An 8-unit Web-based component provided through on-line lectures, readings, interactive discussion, and self-assessment tests accessed via OHSU’s Sakai Learning Management System
  • An intensive one-day in-person session bringing participants together to integrate the material, allow presentation of course projects, and meet the instructor as well as other students in person

The course uses the following teaching modalities:

  • Voice-over-PowerPoint lectures – The key material is delivered using Flash, HTML 5, or a special iPad player. As such, the content is easily accessed by any type of connection to the Internet.
  • Interactive threaded discussion – Students engage in discussion on important issues using the on-line threaded discussion forums. An on-line faculty moderator helps keep the discussion on track.
  • Reading assignments – The course uses a variety of readings made available to students.
  • Homework/quizzes – Each of the units is accompanied by a 10-question multiple-choice self-assessment that aims to have the student apply the knowledge from the unit.

The topics of the course include:

1. Overview of Field and Problems Motivating It
1.1 What is Biomedical and Health Informatics?
1.2 A Discipline Whose Time has Come
1.3 Problems in Healthcare Motivating Biomedical and Health Informatics
1.4 Who Does Biomedical and Health Informatics?
1.5 Seminal Documents and Reports

2. Electronic and Personal Health Records (EHR, PHR)
2.1 Clinical Data
2.2 History and Perspective of the Health (Medical) Record
2.3 Definitions and Key Attributes of the EHR
2.4 Benefits and Challenges of the EHR
2.5 EHR Examples
2.6 Personal Health Records

3. Health Care Data Analytics
3.1 General Health Care Data Analytics
3.2 Extracting and Working with Data
3.3 Population Health and the Application of Health IT
3.4 Applying Health IT to Improve Population Health at the Community Level
3.5 Identifying Risk and Segmenting Populations: Predictive Analytics for Population Health
3.6 Big Data, Interoperability, and Analytics for Population Health
3.7 Data Analytics in Clinical Settings
3.8 Risk Adjustment and Predictive Modeling

4. Standards and Interoperability
4.1 Standards and Interoperability: Basic Concepts
4.2 Identifier and Transaction Standards
4.3 Message Exchange Standards
4.4 Terminology Standards
4.5 Natural Language Processing of Clinical Text

5. Advancing Care With the EHR
5.1 Healthcare Quality
5.2 Clinical Decision Support (CDS)
5.3 Computerized Provider Order Entry (CPOE)
5.4 Clinical Workflow Analysis and Redesign
5.5 System Selection and Implementation
5.6 Evaluation of Usage, Outcomes and Cost
5.7 Public Health Informatics

6. Protection and Analytical Use of Data
6.1 Privacy, Confidentiality, and Security
6.2 HIPAA Privacy and Security Regulations
6.3 Evidence-based Medicine
6.4 Clinical Practice Guidelines
6.5 Digital Imaging
6.6 Telemedicine: Definitions, Uses, and Barriers

7. Research Informatics
7.1 Clinical Research Informatics
7.2 Bioinformatics – The Big Picture
7.3 Overview of Basic Molecular Biology
7.4 From Clinical Genetics and Genomics to Precision Medicine
7.5 Genomics Data in the EHR and Other Information Systems

8. Information Retrieval (Search)
8.1 Information Retrieval
8.2 Knowledge-based Information
8.3 Content
8.4 Indexing
8.5 Retrieval
8.6 Research: Evaluation and Future Directions

9. Informatics and Analytics in the Indian context (in person)
9.1 Age of digitization in India
9.2 Health Informatics and Analytics in India
9.3 Employment and entrepreneurship opportunities
9.4 Global opportunities
9.5 Course content and expectations
9.6 Technical help

DMICE NLM Biomedical Informatics & Data Science Training Grant Renewed for Five Years

The Department of Medical Informatics & Clinical Epidemiology has been awarded $3.8 million for five years from the NIH National Library of Medicine (NLM) to renew its Training Grant in Biomedical Informatics & Data Science.

The grant will provide annual funding for seven PhD students, four postdoctoral fellows, and four short-term training positions for diversity students.

This award is a competitive renewal of this training grant that has been held by OHSU since 1992, making it one of the longest and most established programs in the field. Many alumni of the program have gone on to successful careers in academia and industry. Current trainees in the program recently attended the annual meeting for NLM trainees held this year at the University of California San Diego on June 5-6. The picture below shows trainees and faculty who attended the event, some of whom presented papers and posters (see legend below).


Front: Mitzi Boardman, Bill Hersh, Aurora Blucher*, Eric Feczko, Kristen Stevens
Middle: Julian Egger, Steve Chamberlin+, Aaron Coyner, Josh Burkhart, Eric Leung*
Back: Dana Womack+, James Jacobs*, Geoff Schau
(Not pictured: Shannon McWeeney, Erin Hickman*)
(*gave oral presentation, +gave poster presentation)

DMICE Hosts Inaugural Cascadia-R Conference

The inaugural Cascadia-R Conference was held June 3, 2017 in the OHSU Collaborative Life Sciences Building (CLSB) on the South Waterfront. The morning featured two workshops. The first was a beginner/intermediate workshop introducing data wrangling and visualization using tidyverse, by Chester Ismay and Department of Medical Informatics & Clinical Epidemiology (DMICE) faculty Ted Laderas, PhD (see photo). The second was a more advanced programming workshop about the functional programming package purr by Charlotte Wickham. There was such great feedback and enthusiasm for the workshops that the organizers are considering having a whole day just dedicated to workshops for future conferences.


In attendance were 190 R users and programmers from all parts of the west coast: Oregon, Washington, California and British Columbia (see photo). There were several stimulating speakers, including a keynote from OHSU Medical Oncology Professor Vinay Prasad, MD about big data and medical reversal. Gabriela de Quieroz, of R Ladies Global, gave a keynote to encourage women R users to start their own chapter of R-Ladies. OHSU was well represented, including DMICE faculty Lisa Karstens, PhD and alumnus Mark Danes giving talks. The day ended with short-form lightning talks that covered authoring manuscripts in R, automated User Interface Testing, and mentoring new R-users.


The entire program can be seen at, with workshop material, talks, and other information. The organizers were thrilled to help connect data science enthusiasts, R users, and programmers and look forward to hosting future Cascadia-R conferences at OHSU. More insights into conference organization can be found on Dr. Laderas’ blog.

DMICE Chair Elected to International Informatics Academy

bill4DMICE Chair William Hersh, MD, FACMI, FACP has been elected to the inaugural group of 121 international leaders in biomedical informatics. Dr. Hersh was elected to the International Academy of Health Sciences Informatics (IAHSI). He will be inducted into the group with his colleagues at the MEDINFO 2017 meeting in August in Hangzhou, China. Dr. Hersh has won numerous other awards in the informatics field. At the national level, he received the 2015 HIMSS Physician IT Leadership Award and the 2007 AMIA Donald AB Lindberg Innovation in Informatics Award. Locally, he received the OHSU Faculty Senate Award for Teaching in 2008. Dr. Hersh is also a Fellow of both the American College of Medicine Informatics and the American College of Physicians.

Celebrating Twenty Years of Graduates of the OHSU Biomedical Informatics Graduate Program

Each June, we are pleased to announce students who take part in OHSU Commencement as graduates of the degree and certificate programs of the Biomedical Informatics Graduate Program. This weekend’s OHSU Convocation marks the 20th year of graduates from the program, and there are 48 graduates, distributed among our four graduate programs:

  • PhD – 3
  • Master of Science – 6
  • Master of Biomedical Informatics – 20
  • Graduate Certificate – 19

This group brings the total number of alumni of our program to around 700, dating back to the first graduates in 1998.

(NOTE: The individuals listed below are in the graduation program but this does not indicate they will be receiving their diplomas, as some are still completing graduation requirements and will receive their diplomas soon. Also, pictures from the department banquet and convocation will appear in separate postings in this blog soon.)

Graduates by degree/certificate and track

PhD – Clinical Informatics Track

  • Olubumi Akiwumi
  • Nathan Bahr
  • Bryan Gamble

Master of Science – Bioinformatics and Computational Biology Track

  • Benjamin Cordier
  • Jeffrey Hunter
  • Brandon Keibler
  • Raviteja Madhira
  • Nasim Sanati

Master of Science – Clinical Informatics Track

  • Erin Hickman

Master of Biomedical Informatics – Bioinformatics and Computational Biology Track

  • Ashley Choi
  • Prerna Das
  • Annika Eriksson
  • Thomas Meyer
  • Melissa Yan

Master of Biomedical Informatics – Clinical Informatics Track

  • Benjamin Barsotti
  • Keith Boone
  • Cinthia Feldman
  • Katharine Fultz-Hollis
  • Kenneth Gridley
  • Christopher Hoekstra
  • Ilya Ivlev
  • Arthur Knepper
  • James Morrison
  • Dustin Pezall
  • Eric Shelov
  • Amy Wang

Master of Biomedical Informatics – Health Information Management Track

  • Ashley Armijo
  • Leslie DeYoung
  • Hanna Nelson

Graduate Certificate – Clinical Informatics Track

  • Dale Cox
  • Sarah Gebauer
  • Nathan Gerstmann
  • Carrie Grinstead
  • Umar Iqbal
  • Inho Kim
  • Michael Kopinsky
  • J Edward Maddela
  • Naveen Muthu
  • Lucas Newman
  • Jennifer Pacheco
  • Ellen Provost
  • Gene Ren
  • Sarah Schultz

Graduate Certificate – Health Information Management Track

  • Sang Pak
  • Erleen Palmer
  • Skyler Sommers
  • Crystal Vargas
  • Laura Zukowski

DMICE Professor Karen Eden Receives 2017 School of Medicine Service Award


Congratulations to Karen Eden, Ph.D., professor of medical informatics and clinical epidemiology, who received the 2017 Service Award for the OHSU School of Medicine, as part of the Distinguished Faculty Awards sponsored by the OHSU Faculty Senate. The award was announced on May 25, 2017.

Dr. Eden was one of four nominees for outstanding service within the school. According to the nomination, “Dr. Karen Eden volunteers for service on committees not with the aim of fulfilling her obligations as a faculty member, or for personal accolades, but to truly improve our environment.”

Upon receiving the award, Dr. Eden said, “It was a great honor to be selected to receive the School of Medicine Service Award. I want to recognize the incredible DMICE educational staff, graduate students and my colleagues who made this possible.”

Dr. Eden currently serves on the Faculty Senate, Diversity Advisory Council, OHSU Graduate Council, and Graduate Program Steering Committee. She also continues to serve as ex-Officio on the Women in Academic Medicine committee as a past co-chair.. She is also the associate director of the Patient Centered-Outcomes Research K12 career development program. Within DMICE, Dr. Eden is associate director of the pre- and post-doctoral programs and directs the health and clinical informatics track of the biomedical informatics graduate program.

Last year, Dr. Eden was honored to be selected by DMICE graduates to serve as an usher at graduation. This graduation she will assist with the hooding of DMICE graduates.

“We are thrilled for Dr. Eden,” said DMICE Chair William Hersh, M.D. “Karen’s service at the departmental, school, university, and national levels is unparalleled. That she is able to provide this while maintaining a busy portfolio of research and activities is all the more impressive.”

The Distinguished Faculty Awards program was established by the Faculty Senate to recognize outstanding performance by members of the faculty. There are six categories that rotate among the schools on an annual basis: teaching, leadership, excellence, services, research, and collaboration.


The Department of Medical Informatics & Clinical Epidemiology (DMICE) is one of 27 academic departments in the School of Medicine at Oregon Health & Science University (OHSU). The mission of DMICE is to provide leadership, discovery and dissemination of knowledge in clinical informatics, clinical epidemiology, and bioinformatics / computational biology. This mission is fulfilled through programs of research, education, and service. For more information, visit

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