Carlson College of Veterinary Medicine

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.

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.

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.

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.

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.

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. 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.

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.

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.

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.

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.

E. Fu, Liang, T., Houghtaling, J., Ramachandran, S., Ramsey, S. A., Lutz, B., and Yager, P., “Enhanced sensitivity of lateral flow tests using a two-dimensional paper network format.”, Anal Chem, vol. 83, no. 20, pp. 7941-6, 2011.

S. A. Ramsey, “An Empirical Prior Improves Accuracy for Bayesian Estimation of Transcription Factor Binding Site Frequencies within Gene Promoters.”, Bioinform Biol Insights, vol. 9, no. Suppl 4, pp. 59-69, 2015.

Q. Wei, Ramsey, S. A., Larson, M. K., Berlow, N. E., Ochola, D., Shiprack, C., Kashyap, A., Séguin, B., Keller, C., and Löhr, C. V., “Elucidating the transcriptional program of feline injection-site sarcoma using a cross-species mRNA-sequencing approach.”, BMC Cancer, vol. 19, no. 1, p. 311, 2019.

R. J. Taylor, Falconnet, D., Niemistö, A., Ramsey, S. A., Prinz, S., Shmulevich, I., Galitski, T., and Hansen, C. L., “Dynamic analysis of MAPK signaling using a high-throughput microfluidic single-cell imaging platform.”, Proc Natl Acad Sci U S A, vol. 106, no. 10, pp. 3758-63, 2009.

S. A. Ramsey, Smith, J. J., Orrell, D., Marelli, M., Petersen, T. W., de Atauri, P., Bolouri, H., and Aitchison, J. D., “Dual feedback loops in the GAL regulon suppress cellular heterogeneity in yeast.”, Nat Genet, vol. 38, no. 9, pp. 1082-7, 2006.

J. Yang and Ramsey, S. A., “A DNA shape-based regulatory score improves position-weight matrix-based recognition of transcription factor binding sites.”, Bioinformatics, vol. 31, no. 21, pp. 3445-50, 2015.

S. A. Ramsey, Orrell, D., and Bolouri, H., “Dizzy: stochastic simulation of large-scale genetic regulatory networks (supplementary material).”, J Bioinform Comput Biol, vol. 3, no. 2, pp. 437-54, 2005.

S. A. Ramsey, Orrell, D., and Bolouri, H., “Dizzy: stochastic simulation of large-scale genetic regulatory networks.”, J Bioinform Comput Biol, vol. 3, no. 2, pp. 415-36, 2005.

A. J. Singh, Ramsey, S. A., Filtz, T. M., and Kioussi, C., “Differential gene regulatory networks in development and disease.”, Cell Mol Life Sci, vol. 75, no. 6, pp. 1013-1025, 2018.

E. Fu, Ramsey, S. A., and Yager, P., “Dependence of the signal amplification potential of colloidal gold nanoparticles on resonance wavelength in surface plasmon resonance-based detection.”, Anal Chim Acta, vol. 599, no. 1, pp. 118-23, 2007.

D. Hwang, Smith, J. J., Leslie, D. M., Weston, A. D., Rust, A. G., Ramsey, S. A., de Atauri, P., Siegel, A. F., Bolouri, H., Aitchison, J. D., and Hood, L., “A data integration methodology for systems biology: experimental verification.”, Proc Natl Acad Sci U S A, vol. 102, no. 48, pp. 17302-7, 2005.

D. Hwang, Rust, A. G., Ramsey, S. A., Smith, J. J., Leslie, D. M., Weston, A. D., de Atauri, P., Aitchison, J. D., Hood, L., Siegel, A. F., and Bolouri, H., “A data integration methodology for systems biology.”, Proc Natl Acad Sci U S A, vol. 102, no. 48, pp. 17296-301, 2005.

S. A. Ramsey, Xu, T., Goodall, C., Rhodes, A. C., Kashyap, A., He, J., and Bracha, S., “Cross-species analysis of the canine and human bladder cancer transcriptome and exome.”, Genes Chromosomes Cancer, vol. 56, no. 4, pp. 328-343, 2017.

A. V. Ratushny, Ramsey, S. A., Roda, O., Wan, Y., Smith, J. J., and Aitchison, J. D., “Control of transcriptional variability by overlapping feed-forward regulatory motifs.”, Biophys J, vol. 95, no. 8, pp. 3715-23, 2008.