Found 61 results
Author Title Type [ Year(Asc)]
Filters: Author is Stephen A Ramsey  [Clear All Filters]
2015
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.
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.
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.
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.
2014
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.
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.
2013
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.
2012
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.
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.
2011
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.
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.
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.
2010
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.
2009
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.
2008
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.
2007
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.

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