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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.
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.