OHSU Bioinformatics and Computational Biology

As part of the School of Medicine’s strategic reorganization, we are announcing that, as of March 31, 2025, the Division of Bioinformatics and Computational Biomedicine (BCB) and its parent department, the Department of Medical Informatics and Clinical Epidemiology (DMICE) no longer exist as a standalone entity. DMICE is now fully integrated into the Department of Medicine as the Division of Informatics, Clinical Epidemiology and Translational Data Science (DICE) reflecting OHSU’s commitment to evolving with the times and fostering interdisciplinary collaboration.

This integration aligns with OHSU’s strategic vision to advance science and optimize health worldwide through innovation and partnership. By embedding DMICE within the broader Department of Medicine, we aim to enhance our focus on data science and biomedical informatics, creating new opportunities for impactful research and education.
While organizational structures may change, our faculty remain steadfast in their dedication to advancing our educational and research missions. We will continue to train future leaders in biomedical informatics and computational biomedicine while driving discovery in health data science. This transition represents an exciting opportunity to deepen collaboration across disciplines and strengthen our collective impact on improving human health.

We thank our community for their continued support as we embrace this change and look forward to building an integrated future together.

The KCVI Epigenetics Consortium is pleased to offer the first OHSU Epigenetics Symposium. We are excited to host two keynote speakers: Dr. Marisa Bartolomei (University of Pennsylvania) and Dr. Joe Ecker (UC San Diego).

The program will include talks from investigators whose research focuses on epigenetics and posters from graduate students, postdocs, and research staff. A reception will follow. We hope to see you there!

Please, register using the link on the flyer or here: https://lp.constantcontactpages.com/ev/reg/7n3hr8f

Fantastic highlight of the work of OHSU Bioinformatics and Computational Biology faculty Dr. Michael Mooney and colleagues ! Neuroimaging studies of ADHD have been hindered by small sample sizes, small effects, and differences among study methods. They demonstrate that an ADHD polyneuro risk score (PNRS), representing brain-wide connectivity patterns, was robustly associated with ADHD symptoms in the Adolescent Brain Cognitive Development Study and the Oregon-ADHD-1000 cohort. The findings highlight the promise of approaches examining cumulative, brain-wide effects, and the importance of using large samples for improving reproducibility of neuroimaging studies. Coverage: https://news.ohsu.edu/2024/01/30/ohsu-researchers-confirm-cumulative-brain-wide-effects-of-adhd

Congratulations to our graduates ! We are all so proud of you !

*Graduates 2023*

Graduate Certificate
Biomedical Informatics
• Lawrence Ham

Health & Clinical Informatics
• Mohammed Mirghani Ahmed Abdelaziz
• Christine Anne Doyle
• Teja Ganta
• Kevin Edward Kindler
• Nikhil Tej Kurapati
• Matthew John Molloy
• Kelly K. O'Malia
• Marie Pelzer
• Alyssa D Rapp
• Andrew G Ten Have
• John Glenn Williams
• Amy Woods

Master of Science

Bioinformatics & Computational Biomedicine
• Sedigheh Fazli
• Matthew Jordan Hammer
• Maclean Elizabeth Oviatt

Health & Clinical Informatics
• Marshall Healy
• Roheet Kakaday
• Samuel Alan Lindner
• Christina Anne Winter Malone
• Steven Donald McGaughey
• Chengda Zhang

Fantastic upcoming symposium in April on machine learning in medical imaging - can attend virtually. Register at https://dfci.zoom.us/meeting/register/tJUkdu2pqDMuHNCVZgCSt0B9putExhrLM-JX

Congrats to the Reactome Knowledgebase (www.reactome.org)
and OHSU Bioinformatics and Computational Biology faculty Dr. Guanming Wu on Reactome being selected as part of the inaugural cohort of global core biodata resources. More info at: https://globalbiodata.org/global-biodata-coalition-announces-the-first-set-of-global-core-biodata-resources/

Register for an Upcoming Free Virtual Workshop: The Importance of EHR Data in Clinical Care and Research

The Childhood Cancer Data Initiative (CCDI) is hosting a workshop where we will bring together scientific stakeholders and leaders from academia, government, industry, and advocacy to gain a common understanding of the current issues and opportunities related to electronic health record (EHR) extraction in childhood cancer research. These insights will help drive future CCDI EHR activities.

During the event, you will have the opportunity to listen to the panel discussions and submit questions for panelists.

The Importance of EHR Data in Clinical Care and Research
Date: Wednesday, November 2, 2022
Time: 10:00am–3:30pm

This event is open to the public and free to attend, but registration is required to obtain the event link. Register at: https://events.cancer.gov/nci/ccdi?cid=eb_govdel_ccdi_events

Congratulations to the Bioinformatics and Computational Biomedicine Graduates! So wonderful to be in person with you today and so proud of all you achieved. We couldn't resist posting screenshots from the livestream recording (the official photos will be available in the next few days).

Today Thursday 4/28 at 11:30 am PT OHSU BCB faculty and National Microbiome Data Collaborative ambassador Dr. Lisa Karstens presents an online seminar "Introduction to Urobiome Metadata Standards".
It will provide an overview about metadata standards for microbiome research with a focus on the human urinary microbiome (urobiome). This presentation will also serve as a primer for the upcoming hands-on urobiome metadata workshop, scheduled for May 11, 2022 at 8 am PT / 11 am ET. This is open to all interested in learning about metadata standards for human microbiome research. The presentation will be recorded and available on the OHSU informatics You Tube channel

Upcoming ISCB Academy tutorial: “Integrating gene expression and biological knowledge for drug discovery and repurposing” on the 22nd of April at 8:00am EDT.

Description of the Tutorial:
Screening for potential cancer therapies using existing large datasets of drug perturbations requires expertise and resources not available to all. This is often a barrier for lab scientists to tap into these valuable resources. To address these issues, one can take advantage of prior knowledge especially those coded in standard formats such as causal biological networks (CBN). Large datasets can be converted into appropriate structures, analyzed once and the results made freely available in easy-to-use formats. In these three parts tutorial, we will give a full description of one large scale analysis of using this approach, one case study of building a network of metastasis suppressors from scratch, and a walkthrough example code to perform and adapt these tools for different use cases.

Part One: a talk describing the construction of a database for cancer-cell-specific perturbations of biological networks (LINPS). We pre-computed cancer-cell-specific perturbation amplitudes of several biological networks and made the output available in a database with an interactive web interface.
Part Two: a talk describing the building of a functional network model of the metastasis suppressor RKIP and its regulators in breast cancer cells. In this case study, we applied text mining and a manual literature search to extract known interactions between several metastasis suppressors and their regulators. Then we adopted a reverse causal reasoning approach to evaluate and prioritize pathways that are most consistent and responsive to drugs that inhibit cell growth. We further validated some of the predicted regulatory links in the breast cancer cell line MCF7 experimentally and highlighted the points of uncertainty in our model.
Part Three: a code walkthrough encoding directed interactions into the biological expression language (BEL), computing the network perturbation amplitudes (NPA), and interpreting the output.

Pre-requisites:
● Knowledge of the mechanisms of transcriptional regulation
● Familiarity with high-throughput gene expression data
● Basic knowledge of R and Bioconductor
● Familiarity with Docker and Git (This is only required to execute the code on a local machine)
Register 👉

Main ISCB - International Society for Computational Biology

OHSU's BioData Club is partnering with PREreview to bring the PREreview Open Reviewers Workshop Series to OHSU. Learn how to give constructive feedback and address bias in the peer review process. All OHSU schools and OHSU partners are welcome to participate. Register by July 25

Register for PREreview Open Reviewers Workshop Series BioData Club: PREreview Open Reviewers Workshop Series

New course offering - faculty Dr. Ted Laderas is teaching an R programming course for Oregon Health & Science University (OHSU) / Portland State University School of Public Health in Winter 2021 See course website here: https://sph-r-programming.netlify.app/