Found 18 results
Author Title Type [ Year(Desc)]
Filters: Keyword is Humans and Author is Stephen A Ramsey  [Clear All Filters]
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.
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, Gold, E. S., and Aderem, A., “A systems biology approach to understanding atherosclerosis.”, EMBO Mol Med, vol. 2, no. 3, pp. 79-89, 2010.
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.
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.
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.
2015
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.
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.
2017
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.
2018
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.
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, “A Method for Cross-Species Visualization and Analysis of RNA-Sequence Data.”, Methods Mol Biol, vol. 1702, pp. 291-305, 2018.
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.
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.
Z. Liu, Yao, Y., Wei, Q., Weeder, B., and Ramsey, S. A., “Res2s2aM: Deep residual network-based model for identifying functional noncoding SNPs in trait-associated regions.”, Pac Symp Biocomput, vol. 24, pp. 76-87, 2019.
J. - Da Lin, Nishi, H., Poles, J., Niu, X., Mccauley, C., Rahman, K., Brown, E. J., Yeung, S. T., Vozhilla, N., Weinstock, A., Ramsey, S. A., Fisher, E. A., and Loke, P. 'ng, “Single-cell analysis of fate-mapped macrophages reveals heterogeneity, including stem-like properties, during atherosclerosis progression and regression.”, JCI Insight, vol. 4, no. 4, 2019.
2020
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.
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.