Ramsey Laboratory:  Computational Systems Biology at Oregon State University

We use the tools of bioinformatics, artificial intelligence (AI), and systems biology to understand the molecular basis of diseases and to advance precision medicine. We are working on projects in the areas of drug repositioning, point-of-care diagnostics, and genomics. In the area of AI for rare disease, we have developed a prototype chat agent, called Radiant, that can answer questions about rare disease causes, symptoms, management, and treatments; for more information about our rare disease work, please see our white paper. In the area of AI for translational science, we work on the NIH-sponsored Biomedical Data Translator project. We work with researchers across OSU and at the Institute for Systems Biology, Penn State, OHSU, and UAB. We thank and acknowledge our current and past research sponsors, which include NIH (NHLBI, NIBIB, NIDCR, NIAID, NIGMS, and NCATS), NSF, PhRMA, Amazon.com, the Medical Research Foundation, the Animal Cancer Foundation, the Valley Foundation, and the Research to the People Foundation.

Team members

Stephen Ramsey

Associate Professor

 

 

 

 
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Stephen studied physics and mathematics, earning an ScB from Brown University and a PhD from the University of Maryland. Building on his computational modeling experience, Stephen trained in bioinformatics, first with Maynard Olson at the University of Washington and then with Hamid Bolouri and Ilya Shmulevich at the Institute for Systems Biology. Next, Stephen worked in Alan Aderem's laboratory on computational methods for mapping gene regulatory networks. At OSU, Stephen holds a split appointment in the Department of Biomedical Sciences and in the School of Electrical Engineering and Computer Science. Stephen's research has been recognized with an NIH Career Development Award, a PhRMA New Investigator Award, an NSF CAREER award, and the Zoetis Award.

• Associate Professor, OSU Department of Biomedical Sciences
• Associate Professor, OSU School of Electrical Engineering and Computer Science
• Affiliate Member, OHSU Knight Cancer Institute
• Faculty Affiliate, OSU Center for Quantitative Life Sciences
• Senior Member, International Society for Computational Biology
• Wayne & Gladys Valley Foundation Fellow in Biohealth

Adilbek Bazarkulov

Graduate Student

 

 

 

 
Adilbek ("Adil") Bazarkulov is a MS CS student. He has a BS CS degree from Oregon State University. He is working on the NCATS Translator project.

Frank Hodges

Graduate Student

 

 

 

 
Frank ("Frankie") Hodges is a PhD student in AI. He has a BA in biology from Ohio State University and completed the CS post-bac program at OSU. He is working on a project to develop an AI system for repurposing drugs for rare diseases.

Guy Cohen

Post-Bac Student

 

 

 

 
Guy is a post-bac student in CS. He has a Bachelors of Commerce from Toronto Metropolitan University. He is working on the rare disease project.

Sangam Buddhacharya

Graduate Student

 

 

 

 
Sangam is a graduate student in artificial intelligence. He has a bachelor's in electronics and communication engineering from Tribhuvan University in Nepal. He is working on the epilepsy project.

Sundareswar Pullela

Graduate Student

 

 

 

 
Sundareswar ("Sundar") is a graduate student in computer science. He has a bachelor's in CS from Raghu Engineering College. He is working on the NCATS Translator project.

Current and future teaching and seminar presentations

Graduate programs that I work with

• Comparative Health Sciences (CHS)
• Computer Science (CS)
• Artificial Intelligence (AI)
• Bioengineering (BIOE)
• Biological Data Sciences (BDS) — graduate minor

Outreach

In partnership with the Science & Math Investigative Learning Experiences (SMILE) organization at Oregon State University, we have developed a series of one-hour science activities for high school students. The student guides and teacher guides for these activities are freely distributed here under the Creative Commons (CC-BY) license.

Developed by: Dr. Dominique Brooks, Dr. Jay Well, Morgan McCarthy, Demi Butler, Emma Cushing, Lexi Wilson, Dane Besser, Baylee Goodwin, and Stephen Ramsey.

Impact

We have hosted four high school summer interns and 17 undergraduate researchers in our lab. We have also hosted science activities at three SMILE teacher training workshops.

Open source

We generally open-source the software that we have developed in our projects; see our lab GitHub page.

Contact