Carlson College of Veterinary Medicine

H. R. C. Shoen, Rose, S. J., Ramsey, S. A., de Morais, H. Autran, and Bermudez, L. E., “Analysis of Staphylococcus infections in a veterinary teaching hospital from 2012 to 2015.”, Comp Immunol Microbiol Infect Dis, vol. 66, p. 101332, 2019.

A. V. Ratushny, Saleem, R. A., Sitko, K., Ramsey, S. A., and Aitchison, J. D., “Asymmetric positive feedback loops reliably control biological responses.”, Mol Syst Biol, vol. 8, p. 577, 2012.

X. Yin, Wolford, C. C., Chang, Y. - S., McConoughey, S. J., Ramsey, S. A., Aderem, A., and Hai, T., “ATF3, an adaptive-response gene, enhances TGF{beta} signaling and cancer-initiating cell features in breast cancer cells.”, J Cell Sci, vol. 123, no. Pt 20, pp. 3558-65, 2010.

E. S. Gold, Ramsey, S. A., Sartain, M. J., Selinummi, J., Podolsky, I., Rodriguez, D. J., Moritz, R. L., and Aderem, A., “ATF3 protects against atherosclerosis by suppressing 25-hydroxycholesterol-induced lipid body formation.”, J Exp Med, vol. 209, no. 4, pp. 807-17, 2012.

“The Biomedical Data Translator Program: Conception, Culture, and Community.”, Clin Transl Sci, vol. 12, no. 2, pp. 91-94, 2019.

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.

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.

Y. Vengrenyuk, Nishi, H., Long, X., Ouimet, M., Savji, N., Martinez, F. O., Cassella, C. P., Moore, K. J., Ramsey, S. A., Miano, J. M., and Fisher, E. A., “Cholesterol loading reprograms the microRNA-143/145-myocardin axis to convert aortic smooth muscle cells to a dysfunctional macrophage-like phenotype.”, Arterioscler Thromb Vasc Biol, vol. 35, no. 3, pp. 535-46, 2015.

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.

A. Z. Yu and Ramsey, S. A., “A Computational Systems Biology Approach for Identifying Candidate Drugs for Repositioning for Cardiovascular Disease.”, Interdiscip Sci, vol. 10, no. 2, pp. 449-454, 2018.

S. Prinz, Aldridge, C., Ramsey, S. A., R Taylor, J., and Galitski, T., “Control of signaling in a MAP-kinase pathway by an RNA-binding protein.”, PLoS One, vol. 2, no. 2, p. e249, 2007.

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.

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.

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.

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.

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.

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.

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.

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.

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, 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.

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.

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.

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.

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.