Carlson College of Veterinary Medicine

S. A. Ramsey, Vengrenyuk, Y., Menon, P., Podolsky, I., Feig, J. E., Aderem, A., Fisher, E. A., and Gold, E. S., “Epigenome-guided analysis of the transcriptome of plaque macrophages during atherosclerosis regression reveals activation of the Wnt signaling pathway.”, PLoS Genet, vol. 10, no. 12, p. e1004828, 2014.

P. de Atauri, Orrell, D., Ramsey, S. A., and Bolouri, H., “Evolution of 'design' principles in biochemical networks.”, Syst Biol (Stevenage), vol. 1, no. 1, pp. 28-40, 2004.

A. J. Singh, Chang, C. - N., Ma, H. - Y., Ramsey, S. A., Filtz, T. M., and Kioussi, C., “FACS-Seq analysis of Pax3-derived cells identifies non-myogenic lineages in the embryonic forelimb.”, Sci Rep, vol. 8, no. 1, p. 7670, 2018.

V. Litvak, Ramsey, S. A., Rust, A. G., Zak, D. E., Kennedy, K. A., Lampano, A. E., Nykter, M., Shmulevich, I., and Aderem, A., “Function of C/EBPdelta in a regulatory circuit that discriminates between transient and persistent TLR4-induced signals.”, Nat Immunol, vol. 10, no. 4, pp. 437-43, 2009.

M. Nykter, Price, N. D., Aldana, M., Ramsey, S. A., Kauffman, S. A., Hood, L. E., Yli-Harja, O., and Shmulevich, I., “Gene expression dynamics in the macrophage exhibit criticality.”, Proc Natl Acad Sci U S A, vol. 105, no. 6, pp. 1897-900, 2008.

S. A. Ramsey, Knijnenburg, T. A., Kennedy, K. A., Zak, D. E., Gilchrist, M., Gold, E. S., Johnson, C. D., Lampano, A. E., Litvak, V., Navarro, G., Stolyar, T., Aderem, A., and Shmulevich, I., “Genome-wide histone acetylation data improve prediction of mammalian transcription factor binding sites.”, Bioinformatics, vol. 26, no. 17, pp. 2071-5, 2010.

M. Choudhury and Ramsey, S. A., “Identifying Cell Type-Specific Transcription Factors by Integrating ChIP-seq and eQTL Data-Application to Monocyte Gene Regulation.”, Gene Regul Syst Bio, vol. 10, pp. 105-110, 2016.

P. S. Askovich, Ramsey, S. A., Diercks, A. H., Kennedy, K. A., Knijnenburg, T. A., and Aderem, A., “Identifying novel transcription factors involved in the inflammatory response by using binding site motif scanning in genomic regions defined by histone acetylation.”, PLoS One, vol. 12, no. 9, p. e0184850, 2017.

K. Rahman, Vengrenyuk, Y., Ramsey, S. A., Vila, N. Rotllan, Girgis, N. M., Liu, J., Gusarova, V., Gromada, J., Weinstock, A., Moore, K. J., Loke, P. 'ng, and Fisher, E. A., “Inflammatory Ly6Chi monocytes and their conversion to M2 macrophages drive atherosclerosis regression.”, J Clin Invest, vol. 127, no. 8, pp. 2904-2915, 2017.

T. Liang, Robinson, R., Houghtaling, J., Fridley, G., Ramsey, S. A., and Fu, E., “Investigation of Reagent Delivery Formats in a Multivalent Malaria Sandwich Immunoassay and Implications for Assay Performance.”, Anal Chem, vol. 88, no. 4, pp. 2311-20, 2016.

V. R. Babaev, Ding, L., Zhang, Y., May, J. M., Ramsey, S. A., Vickers, K. C., and Linton, M. R. F., “Loss of 2 Akt (Protein Kinase B) Isoforms in Hematopoietic Cells Diminished Monocyte and Macrophage Survival and Reduces Atherosclerosis in Ldl Receptor-Null Mice.”, Arterioscler Thromb Vasc Biol, vol. 39, no. 2, pp. 156-169, 2019.

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.

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.

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.

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.