Stephen Ramsey, PhD, MS, ScB

Associate Professor, Department of Biomedical Sciences and School of Electrical Engineering and Computer Science
Stephen.Ramsey@oregonstate.edu

Office: 541-737-5609

Dryden Hall

Dryden Hall 208A

450 SW 30th Street

450 SW 30th Street
Corvallis, OR 97331
Education: 
NIH K25 Fellowship, Institute for Systems Biology and Seattle Biomedical Research Institute Postdoctoral Fellow, University of Washington Ph.D., University of Maryland M.S., University of Maryland Sc.B., Brown University
Location: 
Building: 

Profile Field Tabs

At OSU
Affiliated with: 
Veterinary Medicine
Headquarters: 
OSU Main Campus
Research/Career Interests: 

My lab's research program combines computational and experimental approaches to map and functionally characterize gene regulatory networks. Our aim is to develop data-driven approaches to “reverse engineer” the regulatory networks that control immune responses in host defense against pathogens and in chronic inflammatory diseases. A comprehensive understanding of these networks is a gateway to being able to predict how the immune system will respond to novel therapies, pathogens, and vaccines. On the computational side, we use integrative machine-learning methods to both identify the genomic regulatory elements that mediate transcriptional control in specific cell types, and to leverage information from genetic epidemiology and from molecular networks to uncover novel molecular regulators of inflammatory responses. On the experimental side, we have been studying the mammalian macrophage (a key constituent of the innate immune system) as both a primary application area and a “test-bed” for integrative methods development. Together with collaborators, we are also employing this systems biology approach in studies of gene regulation in other cell types such as smooth muscle cells and cancer cells.

Ramsey Lab Information

Publications

 

My Publications

2021

Journal Article

M. Sinha, Tadepalli, P., and Ramsey, S. A., “Voting-based integration algorithm improves causal network learning from interventional and observational data: An application to cell signaling network inference.”, PLoS One, vol. 16, no. 2, p. e0245776, 2021.

2020

Journal Article

C. Parachini-Winter, Bracha, S., Ramsey, S. A., Yang, L., Ho, E., Leeper, H., and Curran, K. M., “Prospective evaluation of the lymph node proteome in dogs with multicentric lymphoma supplemented with sulforaphane.”, J Vet Intern Med, vol. 34, no. 5, pp. 2036-2047, 2020.
S. A. Ramsey, Liu, Z., Yao, Y., and Weeder, B., “Combining eQTL and SNP Annotation Data to Identify Functional Noncoding SNPs in GWAS Trait-Associated Regions.”, Methods Mol Biol, vol. 2082, pp. 73-86, 2020.
Y. Yao and Ramsey, S. A., “CERENKOV3: Clustering and molecular network-derived features improve computational prediction of functional noncoding SNPs.”, Pac Symp Biocomput, vol. 25, pp. 535-546, 2020.
A. Kashyap, Rhodes, A., Kronmiller, B., Berger, J., Champagne, A., Davis, E. W., Finnegan, M. V., Geniza, M., Hendrix, D. A., Löhr, C. V., Petro, V. M., Sharpton, T. J., Wells, J., Epps, C. W., Jaiswal, P., Tyler, B. M., and Ramsey, S. A., “Pan-tissue transcriptome analysis of long noncoding RNAs in the American beaver Castor canadensis.”, BMC Genomics, vol. 21, no. 1, p. 153, 2020.

2019

Journal Article

Y. Yao, Liu, Z., Wei, Q., and Ramsey, S. A., “CERENKOV2: improved detection of functional noncoding SNPs using data-space geometric features.”, BMC Bioinformatics, vol. 20, no. 1, p. 63, 2019.
J. - Da Lin, Nishi, H., Poles, J., Niu, X., Mccauley, C., Rahman, K., Brown, E. J., Yeung, S. T., Vozhilla, N., Weinstock, A., Ramsey, S. A., Fisher, E. A., and Loke, P. 'ng, “Single-cell analysis of fate-mapped macrophages reveals heterogeneity, including stem-like properties, during atherosclerosis progression and regression.”, JCI Insight, vol. 4, no. 4, 2019.
“The Biomedical Data Translator Program: Conception, Culture, and Community.”, Clin Transl Sci, vol. 12, no. 2, pp. 91-94, 2019.
“Toward A Universal Biomedical Data Translator.”, Clin Transl Sci, vol. 12, no. 2, pp. 86-90, 2019.
Z. Liu, Yao, Y., Wei, Q., Weeder, B., and Ramsey, S. A., “Res2s2aM: Deep residual network-based model for identifying functional noncoding SNPs in trait-associated regions.”, Pac Symp Biocomput, vol. 24, pp. 76-87, 2019.

Pages