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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.
S. A. Ramsey, A Method for Cross-Species Visualization and Analysis of RNA-Sequence Data., Methods Mol Biol, vol. 1702, pp. 291-305, 2018.
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, 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.
The Biomedical Data Translator Program: Conception, Culture, and Community., Clin Transl Sci, vol. 12, no. 2, pp. 91-94, 2019.
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. 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.
Toward A Universal Biomedical Data Translator., Clin Transl Sci, vol. 12, no. 2, pp. 86-90, 2019.
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, 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.
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.
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.
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.
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.