Carlson College of Veterinary Medicine

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.

J. Meznarich, Malchodi, L., Helterline, D., Ramsey, S. A., Bertko, K., Plummer, T., Plawman, A., Gold, E., and Stempien-Otero, A., “Urokinase plasminogen activator induces pro-fibrotic/m2 phenotype in murine cardiac macrophages.”, PLoS One, vol. 8, no. 3, p. e57837, 2013.

S. A. Ramsey, Klemm, S. L., Zak, D. E., Kennedy, K. A., Thorsson, V., Li, B., Gilchrist, M., Gold, E. S., Johnson, C. D., Litvak, V., Navarro, G., Roach, J. C., Rosenberger, C. M., Rust, A. G., Yudkovsky, N., Aderem, A., and Shmulevich, I., “Uncovering a macrophage transcriptional program by integrating evidence from motif scanning and expression dynamics.”, PLoS Comput Biol, vol. 4, no. 3, p. e1000021, 2008.

E. Fu, Ramsey, S. A., Kauffman, P., Lutz, B., and Yager, P., “Transport in two-dimensional paper networks.”, Microfluid Nanofluidics, vol. 10, no. 1, pp. 29-35, 2011.

J. J. Smith, Ramsey, S. A., Marelli, M., Marzolf, B., Hwang, D., Saleem, R. A., Rachubinski, R. A., and Aitchison, J. D., “Transcriptional responses to fatty acid are coordinated by combinatorial control.”, Mol Syst Biol, vol. 3, p. 115, 2007.

S. A. Ramsey, Ozinsky, A., Clark, A., Smith, K. D., de Atauri, P., Thorsson, V., Orrell, D., and Bolouri, H., “Transcriptional noise and cellular heterogeneity in mammalian macrophages.”, Philos Trans R Soc Lond B Biol Sci, vol. 361, no. 1467, pp. 495-506, 2006.

“Toward A Universal Biomedical Data Translator.”, Clin Transl Sci, vol. 12, no. 2, pp. 86-90, 2019.

S. A. Ramsey, Gold, E. S., and Aderem, A., “A systems biology approach to understanding atherosclerosis.”, EMBO Mol Med, vol. 2, no. 3, pp. 79-89, 2010.

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.

D. B. Burdick, Cavnor, C. C., Handcock, J., Killcoyne, S., Lin, J., Marzolf, B., Ramsey, S. A., Rovira, H., Bressler, R., Shmulevich, I., and Boyle, J., “SEQADAPT: an adaptable system for the tracking, storage and analysis of high throughput sequencing experiments.”, BMC Bioinformatics, vol. 11, p. 377, 2010.

X. Dong, Yambartsev, A., Ramsey, S. A., Thomas, L. D., Shulzhenko, N., and Morgun, A., “Reverse enGENEering of Regulatory Networks from Big Data: A Roadmap for Biologists.”, Bioinformatics and biology insights, vol. 9, pp. 61-74, 2015.

X. Dong, Yambartsev, A., Ramsey, S. A., Thomas, L. D., Shulzhenko, N., and Morgun, A., “Reverse enGENEering of Regulatory Networks from Big Data: A Roadmap for Biologists.”, Bioinform Biol Insights, vol. 9, pp. 61-74, 2015.

E. Fu, Ramsey, S. A., Chen, J., Chinowsky, T. M., Wiley, B., Xia, Y., and Yager, P., “Resonance wavelength-dependent signal of absorptive particles in surface plasmon resonance-based detection.”, Sens Actuators B Chem, vol. 123, no. 1, pp. 606-613, 2007.

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.

P. de Atauri, Orrell, D., Ramsey, S. A., and Bolouri, H., “Is the regulation of galactose 1-phosphate tuned against gene expression noise?”, Biochem J, vol. 387, no. Pt 1, pp. 77-84, 2005.

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.

J. V. Brady, Troyer, R. M., Ramsey, S. A., Leeper, H., Yang, L., Maier, C. S., Goodall, C. P., Ruby, C. E., Albarqi, H. A. M., Taratula, O., and Bracha, S., “A Preliminary Proteomic Investigation of Circulating Exosomes and Discovery of Biomarkers Associated with the Progression of Osteosarcoma in a Clinical Model of Spontaneous Disease.”, Transl Oncol, vol. 11, no. 5, pp. 1137-1146, 2018.

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.

T. A. Knijnenburg, Ramsey, S. A., Berman, B. P., Kennedy, K. A., Smit, A. F. A., Wessels, L. F. A., Laird, P. W., Aderem, A., and Shmulevich, I., “Multiscale representation of genomic signals.”, Nat Methods, vol. 11, no. 6, pp. 689-94, 2014.

E. Fu, Nelson, K. E., Ramsey, S. A., Foley, J. O., Helton, K., and Yager, P., “Modeling of a competitive microfluidic heterogeneous immunoassay: sensitivity of the assay response to varying system parameters.”, Anal Chem, vol. 81, no. 9, pp. 3407-13, 2009.

D. Orrell, Ramsey, S. A., de Atauri, P., and Bolouri, H., “A method for estimating stochastic noise in large genetic regulatory networks.”, Bioinformatics, vol. 21, no. 2, pp. 208-17, 2005.

S. A. Ramsey, “A Method for Cross-Species Visualization and Analysis of RNA-Sequence Data.”, Methods Mol Biol, vol. 1702, pp. 291-305, 2018.

S. D. Farris, Hu, J. Hong, Krishnan, R., Emery, I., Chu, T., Du, L., Kremen, M., Dichek, H. L., Gold, E., Ramsey, S. A., and Dichek, D. A., “Mechanisms of urokinase plasminogen activator (uPA)-mediated atherosclerosis: role of the uPA receptor and S100A8/A9 proteins.”, J Biol Chem, vol. 286, no. 25, pp. 22665-77, 2011.

A. V. Ratushny, Ramsey, S. A., and Aitchison, J. D., “Mathematical modeling of biomolecular network dynamics.”, Methods Mol Biol, vol. 781, pp. 415-33, 2011.

M. A. Gillespie, Gold, E. S., Ramsey, S. A., Podolsky, I., Aderem, A., and Ranish, J. A., “An LXR-NCOA5 gene regulatory complex directs inflammatory crosstalk-dependent repression of macrophage cholesterol efflux.”, EMBO J, vol. 34, no. 9, pp. 1244-58, 2015.