Carlson College of Veterinary Medicine

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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, 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.

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.

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.

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.

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.

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.

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.

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.

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.

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.