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.

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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.

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The entire program can be seen at http://cascadiarconf.com, 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

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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.

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.

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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.

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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.

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

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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.

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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.

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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: https://www.conftool.pro/research-week-2017/sessions.php

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!

About DMICE

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 http://www.ohsu.edu/informatics

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