News and Events

 

Chair’s Message

pth-use-this-oneWe are moving toward our vision with a number of activities across our various programs. We have updated our strategic plan in response to the 10-year academic program review that we recently completed. For our research-oriented MS and PhD programs, we have recently added a specialization in Data Science. We are completing a curriculum revision for our on line applied clinical informatics MS which will be effective Fall 2020. The work of our fellows in the clinical informatics fellowship program has received plaudits from clinical administrators and faculty, and we are currently recruiting a new faculty member in our department to assist with this program (view position description).  We are also recruiting a faculty member in medical education to start Summer 2020 (view position description). This is the beginning of a new cycle of admissions to our graduate programs, and we look forward to another productive year, and new growth in our department.

Cordially,

Peter Tarczy-Hornoch, MD
Chair and Professor, Department of Biomedical Informatics and Medical Education

Biomedical Informatics and Medical Education Newsletter

April 18 – 22, 2022

UPCOMING LECTURES AND SEMINARS

BIME 590: Thursday, April 28st at 11:00 am

Presenter: Linda Shapiro, PhD. Professor, ENG: Computer Science and Engineering, Professor, Paul G. Allen School of Computer Science & Engineering, Adjunct Professor, Biomedical Informatics and Medical Education Professor, Electrical and Computer Engineering

Theme: Imaging Informatics

Via Zoom: https://washington.zoom.us/my/peter.th

PUBLICATIONS

Zagury-Orly Ivry MMSc; Campos-Zamora Melissa MBBS, MMSc; Cadieux Magalie MD, MMSc;

Dzara Kristina PhD, MMSc. Effectively Planning a Journal Club in Academic Medicine. ePub https://journals.lww.com/academicmedicine/Citation/9900/Effectively_Planning_a_Journal_Club_in_Academic.38.aspx

 Dr. Tom Payne is author of a chapter titled “EHR system selection and implementation.”, to appear in the book Biomedical and Health Informatics: Practical Guide, 8th Edition.  Hoyt RE and Hersh WH (eds.), 2022.

Ali M, Liu Z, Taylor M, Orcutt T, Bledsoe A, Phuong J, Stansbury LG, Arbabi S, Robinson B, Bulger E, Vavilala MS, Hess JR. Blood product availability in the Washington State trauma system. Transfusion. [Accepted for Publication on 18 Apr 2022].

Cooper Z, Herrera-Escobar JP, Phuong J, Braverman MA, Bonne S, Knudson MM, Rivara FP, Rowhani-Rahbar A, Price MA, Bulger EM, NTRAP Injury Prevention Panel. Developing a National Trauma Research Action Plan (NTRAP): Results from the Injury Prevention Research Gap Delphi Survey. J Trauma Acute Care Surg. 2022. [Accepted for Publication on 16 Apr 2022]

Joseph B, Saljuqi AT, Phuong J, Shipper E, Braverman MA, Bixby PJ, Price MA, Barraco RD, Cooper Z, Jarman M, Lack W. Developing a National Trauma Research Action Plan (NTRAP): Results from the Geriatric Research Gap Delphi Survey. Journal of Trauma and Acute Care Surgery. 2022 Apr 8:10-97. Published 8 Apr 2022. Available at: https://doi.org/10.1097/TA.0000000000003626

Phuong J, Zampino E, Dobbins N, Espinoza J, Meeker D, Spratt H, Madlock-Brown C, Weiskopf NG, Wilcox A. Extracting Patient-level Social Determinants of Health into the OMOP Common Data Model. InAMIA Annual Symposium Proceedings 2021 (Vol. 2021, p. 989). American Medical Informatics Association. Published 2022 Feb 21. Available at: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8861735/

Madlock-Brown C, Wilkens K, Weiskopf N, Cesare N, Bhattacharyya S, Riches NO, Espinoza J, Dorr D, Goetz K, Phuong J, Sule A. Clinical, social, and policy factors in COVID-19 cases and deaths: methodological considerations for feature selection and modeling in county-level analyses. BMC Public Health. 2022 Dec;22(1):1-3. Published 14 Apr 2022. Available at: https://doi.org/10.1186/s12889-022-13168-y

ANNOUNCEMENTS

Lucy Wang, PhD, a graduate of our program in 2019 will join UW faculty as an Assistant Professor in the Information School this Fall. Congratulations to Lucy and we look forward to collaborating with you in the near future!

 (in)Visibility Photo Exhibition: While often overlooked and underappreciated, custodians are the protectors of our shared spaces. Please visit a photo exhibit that features photographs taken by 16 custodial staff members who share the stories of the health impacts of their workplace, neighborhoods and homes. The exhibit will run from April 18 to June 10, 2022 and is located in the T-Wing on the 4th Floor, in the hallway adjacent to the Overpass Café. To learn more, please visit www.uwcustodianproject.com.

The Administrative Core Staff are working onsite at SLU on Thursdays and remotely the remaining days of the week. We are currently recruiting for a Graduate Program Advisor, Clinical Informatics Fellowship Administrator and a Fiscal Specialist.

 

April 10 – 15, 2022

UPCOMING LECTURES AND SEMINARS

BIME 590: Thursday, April 21st at 11:00 am

Presenter: Eric Horvitz, MD, PhD. Chief Scientific Officer, Microsoft and Affiliate Associate Professor, University of Washington

Title: People, Machines, and Intelligence: Pathways to Deeper Human-AI Synergy

Via Zoom: https://washington.zoom.us/my/peter.th

PUBLICATIONS

Estee Y Cramer, Evan L Ray, Velma K Lopez, Johannes Bracher, Andrea Brennen, Alvaro J Castro Rivadeneira, Aaron Gerding, Tilmann Gneiting, Katie H House, Yuxin Huang, Dasuni Jayawardena, Abdul H Kanji, Ayush Khandelwal, Khoa Le, Anja Mühlemann, Jarad Niemi, Apurv Shah, Ariane Stark, Yijin Wang, Nutcha Wattanachit, Martha W Zorn, Youyang Gu, Sansiddh Jain, Nayana Bannur, Ayush Deva, Mihir Kulkarni, Srujana Merugu, Alpan Raval, Siddhant Shingi, Avtansh Tiwari, Jerome White, Neil F Abernethy,

Evaluation of individual and ensemble probabilistic forecasts of COVID-19 mortality in the United States

Proceedings of the National Academy of Sciences of the United States of America 119 (15), e2113561119, 2022

ANNOUNCEMENTS

The Administrative Core Staff are working onsite at SLU on Thursdays and remotely the remaining days of the week. We are currently recruiting for a Graduate Program Advisor, Clinical Informatics Fellowship Administrator and a Fiscal Specialist.

 

April 4 – April 8, 2022

UPCOMING LECTURES AND SEMINARS

BIME 590: No Class 4/14/22

ANNOUNCEMENTS

The Administrative Core Staff are working onsite at SLU on Thursdays and remotely the remaining days of the week. We are currently recruiting for a Graduate Program Advisor, Clinical Informatics Fellowship Administrator and a Fiscal Specialist.

 

March 28 – April 1, 2022

UPCOMING LECTURES AND SEMINARS

BIME 590: Thursday, April 7th at 11:00 am

Presenter: Timothy Miller, PhD. Faculty, Computational Health Informatics Program, Boston Children’s Hospital. Assistant Professor, Department of Pediatrics, Harvard Medical School

Title: Representation Learning for Natural Language Processing of Unstructured Text in Electronic Health Records

Via Zoom: https://washington.zoom.us/my/peter.th

 

The Medical Data Science Seminar: Monday, April 4th at 1:00 pm

Presenter: Ruth Etzioni, PhD, Professor, Public Health Sciences Division, Rosalie and Harold Rea Brown Endowed Chair, Fred Hutch

Title: Using one (big) cancer data resource to help another: Recurrence using Claims And Patient-reported outcomes for SEER Enhancement

Via Zoom: https://washington.zoom.us/j/97026956385?pwd=RmZBdmFyek9ZdHFibUo0aXVrdXJPQT09

PUBLICATIONS

Backonja U, Park SE, Kurre A, Yudelman H, Heindel S, Schultz M, Whitman G, Turner AM, Marchak NT, Bekemeier B. Supporting rural public health practice to address local-level social determinants of health across Northwest states: Development of an interactive visualization dashboard. Journal of Biomedical Informatics. 129(2022):104051. https://doi.org/10.1016/j.jbi.2022.104051

Jiang S, Mathias PC, Hendrix N, Shirts BH, Tarczy-Hornoch P, Veenstra DL, et al. Implementation of pharmacogenomic clinical decision support for health systems: a cost-utility analysis. In press at The Pharmacogenomics Journal, March 2022.

ANNOUNCEMENTS

The Administrative Core Staff are working onsite at SLU on Thursdays and remotely the remaining days of the week. We are currently recruiting for a Graduate Program Advisor, Clinical Informatics Fellowship Administrator and a Fiscal Specialist.

 

March 21 – March 25, 2022

UPCOMING LECTURES AND SEMINARS

BIME 590: Thursday, March 31st at 11:00 am

Presenter: TBA

Via Zoom: https://washington.zoom.us/my/peter.th

ANNOUNCEMENTS

The Administrative Core Staff are working onsite at SLU on Thursdays and remotely the remaining days of the week. We are currently recruiting for a Graduate Program Advisor, Clinical Informatics Fellowship Administrator and a Fiscal Specialist.

 

February 28 – March 4, 2022

UPCOMING LECTURES AND SEMINARS

BIME 590: Thursday, March 10th at 11:00 am

Presenter: Patrick O’Carroll, MD, MPH, Affiliate Professor BIME, Sector Head, Health Systems Strengthening at The Task Force for Global Health

Title: Doing Better with the Next Pandemic: The CDC Data Modernization Initiative

Via Zoom: https://washington.zoom.us/my/peter.th

PUBLICATIONS AND PRESENTATIONS

Berridge, C, Turner, AM, Zaslavsky, Parsey C. Design for Dementia: A call from the health sciences. AMC Interactions. Online publication March/April 2022

Changye Li, David Knopman, Weizhe Xu, Trevor Cohen, Serguei V. S. Pakhomov. GPT-D: Inducing Dementia-related Linguistic Anomalies by Deliberate Degradation of Artificial Neural Language Models

ANNOUNCEMENTS

BHI Visit Days are virtual this year and will be held over the course of 3 days, March 9-11.

The Administrative Core Staff are working onsite at SLU on Thursdays and remotely the remaining days of the week. We are currently recruiting for a Graduate Program Advisor and Clinical Informatics Fellowship Administrator.

Trevor Cohen has been awarded an R21: Professional to Plain Language Neural Translation: A Path Toward Actionable Health Information. Gondy Leroy at UA is co-investigator (https://eller.arizona.edu/people/gondy-leroy) and Yue Guo will be the RA. The goal of the project is to develop automated methods to generate plain language summaries of the biomedical literature.

 

February 21 – 25, 2022

UPCOMING LECTURES AND SEMINARS

BIME 590: Thursday, March 3rd at 11:00 am

Presenter: Andrew Simms, MS, PhD, Senior Safety Scientist, AstraZeneca Pharmaceutical, Affiliate Assistant Professor, Biomedical Informatics and Medical Education

Title: The Patient Safety Knowledge Graph

Via Zoom: https://washington.zoom.us/my/peter.th

PUBLICATIONS AND PRESENTATIONS

Backonja U, Park SE, Kurre A, Yudelman H, Heindel S, Schultz M, Whitman G, Turner AM, Marchak NT, Bekemeier B. Supporting rural public health practice to address local-level social determinants of health across Northwest states: Development of an interactive visualization dashboard. Accepted for publication in the Journal of Biomedical Informatics.

Q. Dong, G. Luo, N.E. Lane, L. Lui, L.M. Marshall, D.M. Kado, P. Cawthon, J. Perry, S.K. Johnston, D. Haynor, J.G. Jarvik, and N.M. Cross. Deep Learning Classification of Spinal Osteoporotic Compression Fractures on Radiographs using an Adaptation of the Genant Semiquantitative Criteria. Academic Radiology, 2022.

ANNOUNCEMENTS

Congratulations to Diane Korngiebel, Affiliate Associate Professor in BIME. Diane will serve on the AMIA Ethics Committee through 2023.

 

February 14 – 18, 2022

UPCOMING LECTURES AND SEMINARS

 BIME 590: Thursday, February 24th at 11:00 am

Presenter: Daniel Capurro, MD, PhD, FAMIA: Assistant Professor, Department of Internal Medicine, Pontificia Universidad Católica de Chile, Affiliate Assistant Professor, BIME

Title: Process Mining in Healthcare

Via Zoom: https://washington.zoom.us/my/peter.th

 

WEBINAR: “Health Tech Views and Voices: Electronic health records as a catalyst for improving quality and safety of care — promises made, opportunities missed, and paths forward”

Monday, March 7, 2022 at 4:00 – 5:15 PST

The Ethical, Legal, and Social Issues (ELSI) working group of the American Medical Informatics Association (AMIA) organizes a quarterly public webinar-panel series on topics at the intersection of health technology and ethics. We invite you to join our third session in which we will discuss the use of EHR data to improve quality and safety.

The session is free of charge. Register at:

https://arizona.zoom.us/meeting/register/tZUqc-GgrzgqGtS3TsAt3zzu1J-7NePdb08i

PUBLICATIONS AND PRESENTATIONS

Masys DR, Benson DA. Don Lindberg and the Creation of the National Center for Biotechnology Information.  Stud Health Technol Inform. 2022 Feb 1;288:113-121. doi: 10.3233/SHTI210986. PMID: 35102833.

Ackerman MJ, Howe SE, Masys DR. Don Lindberg, High Performance Computing and Communications, and Telemedicine. Stud Health Technol Inform. 2022 Feb 1;288:122-133. doi: 10.3233/SHTI210987. PMID: 35102834.

Chen, A. T., Tsui, S., and Sharma, R. K. (2022). Characterizing Uncertainty in Goals-of-Care Discussions among Black and White Patients: A Qualitative Study.” BMC Palliative Care, 21(1): 24. https://doi.org/10.1186/s12904-022-00912-9.

Zaslavsky, O., Kaneshiro, J., Chu, F., Teng, A., Chen, A. T. (accepted). Virtual Intervention for Caregivers of Persons with Lewy Body Dementia (LBD). 2022 Annual Scientific Meeting of the American Geriatrics Society, May 11-14, 2022.

 

February 7 -11, 2022

UPCOMING LECTURES AND SEMINARS

BIME 590: Thursday, February 17th at 11:00 am

Presenter: David Crosslin, PhD, Associate Professor, Deming Department of Medicine,

Division of Biomedical Informatics and Genomics, Tulane University

Title: Current Precision Medicine Research Effort

Via Zoom: https://washington.zoom.us/my/peter.th

Abstract: Dr. Crosslin has been provided the unique opportunity to participate as a key contributor in multiple National Human Genome Research Institute (NHGRI) efforts that have transitioned from discovery to genetic precision medicine implementation over the last decade. He will highlight these efforts including a project to evaluate the use of genomic information (polygenic risk scores) in the health care of diverse ancestry participants at the University of Washington.

 Speaker Bio: Dr. Crosslin is an Associate Professor is the Division of Biomedical Informatics and Genomics in the John W. Deming Department of Medicine, Tulane University School of Medicine, and Co-Director of Biomedical Informatics in the Tulane University Biomedical Sciences Graduate Program. Upon his move to Tulane University School of Medicine, Dr. Crosslin received affiliate faculty appointments in the Department of Biomedical Informatics and Medical Education, Department of Genome Sciences, and the Institute for Public Health Genetics all at University of Washington. He also received an affiliate faculty appointment at Kaiser Permanente Washington Health Research Institute, Seattle, WA. Dr. Crosslin’s research program has been focused on statistical genetics and bioinformatics with applications to complex diseases, and is now focused on implementation science and precision medicine.

 

January 31 – February 4, 2022

UPCOMING LECTURES AND SEMINARS

BIME 590: Thursday, February 10th at 11:00 am

Presenter: Lydia Drumright, PhD – Research Scientist, Department of Medicine: Allergy and Infectious Diseases

Title: Leveraging Health Informatics to Facilitate Cohesiveness in Research, Healthcare, and Public Health

 

full BRiTE Center Meeting: Wednesday, February 9th at 12:00 pm (PST) featuring a special guest presentation by Dr. Serguei Pakhomov. This meeting will be recorded.

Title: Stress, affect, language and speech analysis in medicine

Via Zoom: https://washington.zoom.us/j/9594284659

 

UPCOMING FINAL EXAM

Juandalyn Burke

Friday, 2/11/2022 at 2:30 pm

Zoom: https://washington.zoom.us/s/98597577384

Title: Using Network-Based Modeling to Implement Strategies for Reducing HIV-Drug Resistance

Abstract: Mathematical models have evolved to capture epidemiological and infectious disease data and complex relationships between the disease, host, and environment. In particular, infectious disease and epidemic models serve as ethical approaches for introducing strategies intended to prevent, control, and reduce disease progression, transmission, and exposure without causing harm to any particular group or population. These models also allow researchers, clinicians, and other health professionals to explore strategies and interventions that have yet to be widely explored, either due to limited information or resources. This thesis uses a network-based, stochastic modeling system called EvoNet to capture the spread of the human immunodeficiency virus (HIV) and explore strategies that may reduce HIV drug resistance (HIV-DR), within-host and between-host. The first aim focuses on predicting the frequency and emergence of drug-resistant mutations, given the use of first-line antiretroviral treatment, patient-specific information such as drug adherence levels, and the incorporation of pharmacogenomics (PGx) and pharmacokinetic (PK) data. The second aim investigates the effect of host genetic variation and drug resistance mutations in the population, using PGx and PK study data from two sub-Saharan African populations. Lastly, in the third aim, we build a treatment-switching optimization routine and develop a method similar to the grid search optimization method, and use an R package that performs simulated annealing. The objective of using these two optimization methods is to find the best parameter values that reduce the levels of drug resistance in the simulated population and to also inform how health professionals may prioritize individuals for second-line treatment. The results of these aims include the following: (1) the inclusion of host genetic or PGx data influences the frequency of drug resistance mutations, within-host and how rapidly the drug resistance mutations emerge, (2) the presence of individuals with drug-resistant strains in the population at the start of the model simulation yields higher levels of predicted drug resistance and in particular, transmitted drug resistance, and (3) the adapted grid-search optimization approach had a higher computational time burden than simulated annealing but provided a wider range of options for group prioritization for second-line treatment conditions that dramatically reduced HIVDR in the simulated population. In all, these methodologies and results may extend to future investigations of new drugs and treatment regimens.

 

January 24-28, 2022

UPCOMING LECTURES AND SEMINARS

Note: UW is returning to largely in-person learning in February. Please be sure to check with your instructors to confirm the specifics of your courses.

BIME 590: Thursday, February 3rd at 11:00 am

Presenter: Thomas Payne, MD, FACP, FACMI

Professor, Biomedical Informatics & Medical Education

Adjunct Professor, Health Services, School of Public Health

Title: The real world of electronic health records:  A brief tour of how they are used in 2022

PUBLICATIONS AND PRESENTATIONS

M.I. Seedahmed, I. Mogilnicka, S. Zeng, G. Luo, M.A. Whooley, C.E. McCulloch, L. Koth, and M. Arjomandi. Performance of a Computational Phenotyping Algorithm for Sarcoidosis Using Diagnostic Codes in Electronic Medical Records: A Pilot Study from Two Veterans Affairs Medical Centers. JMIR Formative Research, 2022.

Weizhe Xu, Weichen Wang, Jake Portanova, Ayesha Chander, Andrew Campbell, Serguei Pakhomov, Dror Ben-Zeev, Trevor Cohen, Fully Automated Detection of Formal Thought Disorder with Time-series Augmented Representations for Detection of Incoherent Speech (TARDIS). Journal of Biomedical Informatics (126). Feb 2022. https://authors.elsevier.com/c/1eTwB5SMDQmq8G

Capurro D, Coghlan S, Pires DEV. Preventing Digital Overdiagnosis. JAMA. Published online January 21, 2022. doi:10.1001/jama.2021.22969

ANNOUNCEMENTS

Abhi Pratap, alumnus of BHI would like to share some open positions that may be of interest:

 Postdoctoral Fellow – Applied NLP in Mental Health

https://www.linkedin.com/jobs/view/2884121078/

Internships
#MLoPS– https://lnkd.in/g5p8gFgX
#ML/#AI – https://lnkd.in/g6EK2JJ7

UPCOMING FINAL EXAM

Juandalyn Burke

Friday, 2/11/2022 at 2:30 pm

Zoom: https://washington.zoom.us/s/98597577384

Title: Using Network-Based Modeling to Implement Strategies for Reducing HIV-Drug Resistance

Abstract: Mathematical models have evolved to capture epidemiological and infectious disease data and complex relationships between the disease, host, and environment. In particular, infectious disease and epidemic models serve as ethical approaches for introducing strategies intended to prevent, control, and reduce disease progression, transmission, and exposure without causing harm to any particular group or population. These models also allow researchers, clinicians, and other health professionals to explore strategies and interventions that have yet to be widely explored, either due to limited information or resources. This thesis uses a network-based, stochastic modeling system called EvoNet to capture the spread of the human immunodeficiency virus (HIV) and explore strategies that may reduce HIV drug resistance (HIV-DR), within-host and between-host. The first aim focuses on predicting the frequency and emergence of drug-resistant mutations, given the use of first-line antiretroviral treatment, patient-specific information such as drug adherence levels, and the incorporation of pharmacogenomics (PGx) and pharmacokinetic (PK) data. The second aim investigates the effect of host genetic variation and drug resistance mutations in the population, using PGx and PK study data from two sub-Saharan African populations. Lastly, in the third aim, we build a treatment-switching optimization routine and develop a method similar to the grid search optimization method, and use an R package that performs simulated annealing. The objective of using these two optimization methods is to find the best parameter values that reduce the levels of drug resistance in the simulated population and to also inform how health professionals may prioritize individuals for second-line treatment. The results of these aims include the following: (1) the inclusion of host genetic or PGx data influences the frequency of drug resistance mutations, within-host and how rapidly the drug resistance mutations emerge, (2) the presence of individuals with drug-resistant strains in the population at the start of the model simulation yields higher levels of predicted drug resistance and in particular, transmitted drug resistance, and (3) the adapted grid-search optimization approach had a higher computational time burden than simulated annealing but provided a wider range of options for group prioritization for second-line treatment conditions that dramatically reduced HIVDR in the simulated population. In all, these methodologies and results may extend to future investigations of new drugs and treatment regimens.