DMICE Postdoctral Fellow, Ilya Ivlev, MD, PhD Publishes Systematic Review

_thumb_35291Postdoctral Fellow, Ilya Ivlev, MD, PhD, has published a study in Journal of General Internal Medicine, Use of Patient Decision Aids Increased Younger Women’s Reluctance to Begin Screening Mammography: A Systematic Review and Meta-Analysis, that is also featured in the journal’s Capsule Commentary section as well as on the OHSU News site. The systematic review reports that evidence-based breast cancer screening decision aids reduces by 77 percent the number of women who plan to undergo screening mammography. It is one of the first to examine the effects of these aids on women’s intentions to be screened.

DMICE Student Wins Second Place in Research Week Three-Minute Thesis Competition

Prerna Das, a student in the OHSU Master of Science in Biomedical Informatics program, won second place in the OHSU Research Week Three-Minute Thesis (3MT) competition, held May 3, 2017. Das presented her thesis topic, In Pursuit of Genetic Risk Factors for Alzheimer’s.  She also presented a poster on this topic at the May 1 poster session. The three winners of the 3MT will represent OHSU at the statewide competition at the University of Oregon on May 12th.

Overall at Research Week, there were five oral presentations from Department of Medical Informatics & Clinical Epidemiology (DMICE) faculty, staff, fellows and/or students as authors, while 15 posters at the Monday evening poster session featured DMICE-affiliated authors.

Below are some pictures from the event:

Eric Leung, pre-doctoral fellow, viewed MBI student Prerna Das’s poster, Aggregating Common, Rare, and Private Variants in Alzheimer’s Disease Genes.

Das Leung Research Week 217 cropped

Pre-doctoral fellow Dana Womack, M.S., discussed her poster, Exploration of Operational Data Streams as a Source of Actionable Insight, with Research Week judge Virginia Tilden, PhD., R.N., F.A.A.N., professor and senior associate dean for research affairs in the School of Nursing.

Womack Tilden Res Week 2017 cropped

Mark Klick, master of science student, presented a poster on Elucidating Gut Microbiota-Immune Interactions in an Animal Model of Ankylosing Spondylitis.

Mark Klick Research Week Cropped

Erin Hickman, M.D., post-doctoral fellow, and Eric Leung, pre-doctoral fellow, reviewed Julian Egger’s poster on Transcriptome Characterization of the Collaborative Cross Founder Strains Using RNA-Seq K-mer Content.  Julian is a pre-doctoral fellow.

Hickman Leung Egger RW 2017 cropped

Steve Chamberlin, N.D., post-doctoral fellow, created a poster on Natural Product Targetome in Cancer: Definition and Application.

Chamberlin Research Week 2017 cropped

DMICE Faculty and Fellows Present at Inaugural OHSU Symposium on Educational Excellence

Several faculty and trainees from the Department of Medical Informatics & Clinical Epidemiology (DMICE) presented panels and posters at the inaugural OHSU Symposium on Educational Excellence on Friday, April 14, 2017.

A panel, Innovation in Teaching Cross-Cutting Disciplines: Case Study of Biomedical Informatics & Data Science, was presented by William Hersh, MD; David Dorr, MD, MS; Ted Laderas, PhD; and Vishnu Mohan, MD, MBI.


Heidi D. Nelson, MD, MPH was part of a panel, Developing Effective Faculty Mentors for Student Scholarly Projects in the New MD Curriculum.

Several DMICE faculty took part in the poster session in the BICC Gallery.


Heidi D. Nelson, MD, MPH was also among authors of a poster, Preparedness of Pre-Clinical Medical Students to Plan and Conduct a Scholarly Project.


Paul Gorman, MD was among authors of a poster, Health Systems Science: Integrating the ‘Third Science’ into the Undergraduate Medical Curriculum.


Gretchen Scholl and Anirudh Chintalapani, MD presented a poster, co-authored by Vishnu Mohan, MD, MBI and Jeffrey Gold, MD, Creating and deploying online CME activities featuring the safe, efficient and effective use of the electronic health record.


William Hersh, MD was among authors of a poster, creativeIDEAS: A Vision for Training the Next Generation of PhD scientists in the School of Medicine.



DMICE-Affiliated Faculty, Staff, Fellows, and Students Presenting Their Research During OHSU Research Week 2017, May 1-3, 2017

The DMICE-affiliated faculty, staff, fellows, and students listed below(presenter underlined) are presenting their research as part of OHSU’s 2017 Research Week, which takes place May 1-3, 2017. For the full Research Week schedule, see:

Oral Presentation Session 4 

Monday, 01/May/2017:2:30pm – 4:00pm Location: Old Library room 211

A Computational Framework to Analyze Surgical Experience

Mark Engelstad, Quinn Walker, James Morrison

Oral Presentation Session 6 

Monday, 01/May/2017:2:30pm – 4:00pm Location: Old Library room 221

The Evolving Role of Medical Scribe: Variation and Implications for Organizational Effectiveness and Safety

Deborah V Woodcock, Robert Pranaat, Karess McGrath, Joan S Ash

Poster Session A 

Monday, 01/May/2017:4:30pm – 5:30pm Location: OHSU Library / BICC

FIOncoNet: A software tool for localizing somatic mutations within protein-protein binding interfaces

Joshua Garrison Burkhart

Natural Product Targetome in Cancer: Definition and Application

Steve Chamberlin, Aurora Blucher, Gabrielle Choonoo, Molly Kulesz-Martin, Shannon McWeeney

Aggregating common, rare and private variants in Alzheimer’s disease genes

Prerna Das, Beth Wilmot

Transcriptome Characterization of the Collaborative Cross Founder Strains Using RNA-Seq K-mer Content

Julian Egger, Christina Zheng

Controlling for contaminants in low-biomass microbiome experiments

Lisa Karstens, Rahel Nardos, Mark Asquith, Shannon McWeeney

Elucidating Gut Microbiota-immune Interactions in an Animal Model of Ankylosing Spondylitis

Mark T Klick, Lisa Karstens, Sean Davin, Patrick Stauffer, Mark Asquith

Co-targeting epidermal growth factor receptor (EGFR) and anaplastic lymphoma kinase (ALK) overcomes EGFR inhibitor resistance in head and neck squamous cell carcinoma patient-derived models

Xiaoming Ouyang, Ashley Barling, Jeff Tyner, Shannon McWeeney, Molly Kulesz-Martin

LSD1 promotes castration-resistant prostate cancer cell survival independently of the androgen receptor and of histone demethylation

Archana Sehrawat, Lina Gao, Junior Tayou, Armand Bankhead, Laura Heiser, Carly King, Yuliang Wang, Jacob Schwartzman, Joshua Urrutia, Daniel Coleman, Sheila Weinmann, Bhaskar Kallakury, Deborah Berry, Reina Haque, Stephen Eeden, Tomasz Beer, George Thomas, Shannon McWeeney, Joshi Alumkal

Resident Attitudes, Confidence, and Experiences in Leadership: Results from the National Leadership Survey

Jeanne-Marie Guise, Barbara Skarica, Tabria Harrod, Matthew Hansen, Elizabeth Kinsey

Exploration of Operational Data Streams as a Source of Actionable Insight

Dana Womack, Michelle Hribar, Paul Gorman

Improving Retrieval of Datasets: OHSU Participation in the bioCADDIE Evaluation Challenge

Theodore Brady Wright, David Ball, William Hersh

Narratives of Residents’ Experiences of Unconscious Bias: Results of the National Leadership Survey

Jeanne-Marie Guise, Shammarie Mathis, Tabria Harrod, Matthew Hansen

A proof of concept study evaluating the variability and accuracy among scribes’ transcribed notes using EHR integrated simulation

Robert Pranaat, Jeff Gold, Vishnu Mohan, Deborah Woodcock, Maxwell Hirsh, Karess McGrath, Gretchen Scholl, Meg O’Reilly

Poster Session B 

Monday, 01/May/2017:6:00pm – 7:00pm Location: OHSU Library / BICC

Identifying novel biomarkers for Systemic Exertion Intolerance Disease/Chronic Fatigue Syndrome through community profiling of the intestinal microbiota by 16S rRNA gene sequencing

Eric T Leung, Lisa Karstens, Mark Asquith, Beth Smith

A Validated 7-minute Tool to Examine Pediatric Safety & Quality: The Pediatric prehospital safety Event Detection System (PEDS)

Nicole Ovregaard, Carl Eriksson, Garth Meckler, Matt Hansen, Barbara Skarica, Jeanne-Marie Guise

Oral Presentation Session 8 

Tuesday, 02/May/2017:10:00am – 11:30am Location: Old Library room 217

Chromosome Elimination from the Primate Pre-Implantation Embryo Revealed by Single-Cell Sequencing

Brittany L. Daughtry, Jimi L. Rosenkrantz, Nathan Lazar, Suzanne S. Fei, Nash Redmayne, Kristóf Törkenczy, Andrew Adey, Geoffrey Schau, Kimberly A. Nevonen, Lucia Carbone, Shawn L. Chavez

Oral Presentation Session 13 

Wednesday, 03/May/2017:1:00pm – 2:30pm Location: Old Library room 211

Synthetic lethality of TNK2 inhibition in PTPN11-mutant AML

Chelsea Jenkins, Samuel Luty, Julia Maxson, Christopher Eide, Melissa Abel, Corinne Togiai, Eneida Nemecek, Daniel Bottomly, Shannon McWeeney, Beth Wilmot, Marc Loriaux, Bill Chang, Jeffrey Tyner

OHSU News Hub Features Blog Posting from DMICE Chair on March for Science

bill-loresDMICE Chair William Hersh, MD wrote a posting to his Informatics Professor blog that has been featured on the OHSU News Hub. In the posting, Dr. Hersh described his rationale for participating in the March for Science Portland.

School of Medicine Selects Journal Article from Evidence-based Practice Center as Paper of the Month

One of the systematic reviews from the Pacific Northwest Evidence-based Practice Center, previously highlighted in Health Data, Information and Action, was selected as the OHSU School of Medicine Paper of the Month for March 2017. The journal article on low back pain was published in the February 14, 2017 issue of Annals of Internal Medicine. Congratulations, Dr. Roger Chou and team!

Informatics Fellows Win Award from Society for Imaging Informatics in Medicine (SIIM) for FHIR-Based Application

Morrison_and_TeamDMICE Clinical Informatics Fellow James Morrison, M.D., received a $10,000 prize in the first Innovation Challenge of the Society for Imaging Informatics in Medicine. Dr. Morrison, an interventional radiologist, and his team from OHSU presented their project, Voice Enabling the Imaging Enterprise, a voice interface going directly into the electronic health record (EHR) that allows quick, seamless data access through voice commands.

In addition to Dr. Morrison, the winning team included Steven Kassakian, M.D., former National Library of Medicine (NLM) post-doctoral fellow and now medical director of Clinical Informatics and assistant professor, DMICE; Eric Leung, Ph.D. student and NLM pre-doctoral fellow; and Jonathan Steinberger, M.D., assistant professor of interventional radiology.

The project uses Amazon Echo voice-activated hardware and connects with the EHR via the HL7 Fast Health Interoperability resources (FHIR) standard. The OHSU team envisions this technology as an optimal solution for getting information out of the EHR and other resources while allowing users to maintain focus on the task at hand, whether that is reading imaging studies in radiology, operating in the OR, or talking to a patient in clinic.

“The inaugural SIIM Innovation Challenge was an ideal venue to get feedback and exposure for our idea of bringing a more robust voice-activated interface in to the radiology reading room and outpatient clinic.,” said Dr. Morrison.

“Winning the Grand Prize and People’s Choice Award was validation of the underlying concept, and the $10,000 gave my co-founders and me the capital we needed to take our prototype to the next level. It’s fair to say that without SIIM’s support our idea may never have made it out of the dreamer phase.”

Dr. Morrison plans to use the funds to obtain additional hardware for development and testing.

The SIIM meeting was held in July 2016 in Portland, Ore., and the OHSU team will report on their progress at the 2017 meeting in June in Pittsburgh, Pa.

A video about the project can be viewed at Photo above provided by Society for Imaging Informatics in Medicine (SIIM).

Biomedical Informatics Graduate Program Renames Tracks, Reflecting Evolution of Field

The OHSU Biomedical Informatics Graduate Program has received university approval to rename the two tracks of its program to reflect changes in the field and evolving content in the curriculum.

Since 2006, the program has had two “tracks,” which we have called Clinical Informatics (CI) and Bioinformatics & Computational Biology (BCB). We have chosen to call these two pathways through our programs “tracks” because they represent two different foci within the larger field of biomedical informatics, which is the discipline that acquires, organizes, and uses data, information, and knowledge to advance health-related sciences. Historically, the differences between the tracks represented their informatics focus, in particular people, populations, and healthcare (clinical informatics) vs. cellular and molecular biology, genomics, and imaging (bioinformatics).

In recent years, however, these distinctions have blurred as “omics” science has worked its way into clinical medicine. At the same time, health, healthcare, and public health have become much more data-driven, due in no small part to the large-scale adoption of electronic health records. As such, the two tracks have begun to represent different but still distinct foci, mostly in their depth of quantitative methods (deep vs. applied) but also in coverage of other topics (e.g., system implementation, especially in complex health environments; usability; and clinical data quality and standards).

We believe that both tracks possess a set of common competencies at a high level that reflect the essential knowledge and skills of individuals who work in biomedical informatics. Our curriculum organizes these competencies into “domains,” which are groups of required and elective courses that comprise the core curriculum of each track. To reflect the evolution of the program, we have renamed the BCB track to Bioinformatics and Computational Biomedicine (still abbreviated BCB) and the CI track to Health and Clinical Informatics (now to be abbreviated HCI). The table lists below lists the common competencies and the names of the domains for each track. Each of the domains contains required courses, individual competency courses (where students are required to select a certain number of courses from a larger list, which we used to call “k of n” courses), and elective courses.


The program will continue the overall structure of the curriculum with the “knowledge base” that represents the core curriculum of the master’s degree and the base curriculum for advanced study in the PhD program. A thesis or capstone is added to the knowledge base to qualify for the MS or MBI (latter in the HCI Track only) degrees, respectively. Additional courses are required for the PhD, ultimately culminating in a dissertation.

We are in the process of updating the materials and Web site for our program to reflect the new names. We will also be evolving our course content as well as introducing new courses to reflect the foci of the new tracks. The program still fundamentally aims to train future researchers and leaders in the field of biomedical informatics.

Evidence-based Practice Center publishes two systematic reviews related to low back pain in Annals of Internal Medicine

Chou PhotoThe Pacific Northwest Evidence-based Practice Center (EPC), based in the Department of Medical Informatics and Clinical Epidemiology, had two systematic reviews related to low back pain published in the February 14, 2017 issue of Annals of Internal Medicine. The papers were published in conjunction with a clinical guideline on noninvasive treatments for subacute, and chronic low back pain, issued by the American College of Physicians (ACP).

Roger Chou, M.D., director of the EPC and professor of medical informatics and clinical epidemiology and medicine, was first author of the systematic review on systemic pharmacologic therapies for low pain. The review was conducted by EPC investigators and staff at OHSU along with EPC partners, the University of Washington CHASE Alliance and Spectrum Research, Inc. Among the co-authors were DMICE staff Tracy Dana, M.L.S., Jessica Griffin, M.S., and Sara Grusing, B.A.

The second systematic review focused on nonpharmacologic therapies for low back pain. Dr. Chou served as first author, with DMICE staff Ms. Tracy, Ms. Griffin and Ms. Grusing as co-authors, along with others at OHSU, the University of Washington, and Spectrum Research.

“Low back pain is a common problem and it continues to be a challenge for primary care and specialist providers,” said Dr. Chou. “The EPC evidence reviews to support the ACP guideline required a huge effort to gather and assess the abundance of evidence on nonpharmacological therapies as well as prescription and over-the-counter medications, and I’m grateful to our EPC investigators for their excellent teamwork.”

The ACP guideline on low back pain was prepared by the ACP Clinical Guidelines Committee. Linda Humphrey, M.D., M.P.H., professor of medicine and medical informatics and clinical epidemiology, and Devan Kansagara, M.D., M.C.R., associate professor of medicine and medical informatics and clinical epidemiology, served on the guidelines committee. Both physicians also work at the VA Portland Health Care System.

“The guidelines emphasize nonpharmacological treatments as first-line therapy for chronic LBP. In particular, they emphasize the limited role of opioids for LBP,” added Dr. Chou.

The EPC reviews are available from the Annals Web site:

Extension of Clinical Informatics Subspecialty Grandfathering Period Provides New Options for Physician Certification

In November, the American Board of Preventive Medicine (ABPM) announced that the “grandfathering period” for physicians to become board-certified in the new subspecialty of clinical informatics would be extended for five additional years, from 2017 to 2022 (see also). This means that physicians can become board-certified in the subspecialty through either the practice pathway or via “non-traditional” fellowships that include both the OHSU National Library of Medicine (NLM) fellowship as well as our master’s degree program, the latter of which is available online.

OHSU has developed an ACGME-accredited clinical informatics fellowship and we believe this is the gold standard for training in clinical informatics. However, we also recognize that a two-year on-site fellowship is not possible for all who desire to achieve certification in the subspecialty, especially those who are mid-career and not easily able to relocate for a full-time fellowship.

The requirements for board eligibility include board certification in a primary specialty and qualification via the practice pathway or a non-traditional fellowship. The practice pathway requires one to have “practiced” clinical informatics for 25% or more time over three of the last five years. Education time counts as half of the time of practice time, i.e., 50% or more time over three years, which is comparable to the duration of a one-and-a-half-year full-time master’s degree.

All practice pathway time is additive, so a combination of practice and/or educational activities can reach the threshold. In addition, a recent master’s degree from an established program (the actual list is not known but includes long-standing programs, including ours at OHSU) has been enough to achieve board eligibility. Those eligible for the exam can then apply to ABPM to take the exam, which is offered annually each October.

About 40 graduates of the OHSU Biomedical Informatics Graduate Program have achieved eligibility in the subspecialty since its inception, and we look forward to working with those physicians who aim to achieve eligibility via our online education or clinical fellowship programs.


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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