gene regulation in mouse macrophages

Ramsey Laboratory:  Computational Systems Biology at Oregon State University

gene icon We use the tools of bioinformatics, artificial intelligence, and systems biology to understand the molecular basis of diseases and to advance precision medicine. We are currently working on research projects in the areas of cancer, wound healing, drug repositioning, and genomics. We sincerely thank 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.

gene icon At OSU, we are actively collaborating on research projects with Matt Johnston (COE), Elain Fu (COE), Dan Rockey (CVM), Brian Dolan (CVM), Jennifer Johns (CVM), and Kaitlin Fogg (COE). More broadly, through the NIH NCATS Biomedical Data Translator project, we are collaborating with researchers at Penn State University, Institute for Systems Biology, Drexel University, University of North Carolina Chapel Hill, and University of Alabama Birmingham.

Team members

Stephen Ramsey
Associate Professor
 
 
 
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
Amy Glen
Postdoctoral Scholar
 
 
 
Amy is a postdoctoral scholar working on the NCATS Translator project. She has a PhD in CS from Oregon State University.
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.
Matthew Taylor
Graduate Student
 
 
 
Matt is majoring in Statistics. He is working on the chlamydia 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.
Sydney Bolaños
Graduate Student
 
 
 
Sydney is a DVM-MS student whose MS project is co-advised by Dr. Ramsey and Dr. Jennifer Johns. She has a bachelors degree in biology from Grand Canyon University. She is working on an immunology project using single-cell transcriptome analysis.

Collaborators

We work with researchers across OSU and at the Institute for Systems Biology, Penn State, OHSU, and UAB.

Lab members have gone on to work at

Lab News

Dec 10, 2024
Akshay Mulgund has passed his MS final exam! Congratulations, Akshay! The title of his MS project report was A Retrieval-Augmented Generation Framework for Rare Disease Knowledge Dissemination Using LLMs.
Nov 23, 2024
San gave a talk on his work on the epilepsy drug monitoring project, at the ACM Conference on Bioinformatics, Computational Biology, and Health Informatics in Shenzhen, China.
Nov 15, 2024
San gave a talk on his work on the epilepsy drug monitoring project, at the Oregon Bioengineering Symposium at OHSU in Portland.
Oct 25, 2024
San gave a poster presentation on his work on the epilepsy drug monitoring project, at the annual meeting of the Biomedical Engineering Society in Baltimore.
Sep 25, 2024
Steve gave a presentation on ARAX and RTX-KG2 at the CyPsy27 conference in Tempe, Arizona.
Sep 16, 2024
We welcome post-bac students Guy Cohen and Dominick Tucker to the lab!
Sep 24, 2024
Our collaborative paper with Prof. Elain Fu and graduate students Sangam Buddhacharya and Noël Lefevre using machine-learning for electrochemical voltammogram data processing (for carbamazepine detection in saliva) has been accepted into the ACM Conference on Bioinformatics, Computational Biology, and Health Informatics! San will present the work on behalf of our team at the conference in Shenzhen, China in November. Thank you to the OSU Foundation, the OSU College of Engineering, and the China Experience Fund for your support!
Sep 12, 2024
A preprint of our comparative study of human and canine prostate cancer (with George Thomas and Marcela Riveros Angel at OHSU and with Christiane Löhr at OSU) has been accepted for publication in Veterinary and Comparative Oncology and is now available on bioRxiv.

Current and future teaching and seminar presentations

Spring 2025
Instructor
VMB 652
Cancer systems biology
Winter 2025
Instructor
CS 446/546
Networks in computational biology
Winter 2025
Guest Speaker
PHAR 507
Seminar
Fall 2025
Guest Instructor
VMB 671
Molecular Tools

Graduate programs that I work with

 

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.

Phenotyping activity based on tasting phenylthiocarbamide.
Learn about chromosomes by reconstructing a karyotype.
Learn about genetic conditions by playing Genetic4.
Sequence proteins in fossils using Mass Spectrometry!
What types of protein are in this dinosaur fossil?
Compare dinosaur proteins to modern organisms'
Should we bring back extinct species? An ethics activity.
A Mendelian genetics activity, for elementary school students.
A forensic genomics activity, for middle school students.
A genetics activity, for high school students.
A genetics activity, for elementary school students.

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

 
Oregon State University
106 Dryden Hall
Corvallis, OR 97331-4801
 
Oregon State University
105 Magruder Hall
Corvallis, OR 97331-4801