Found 24 results
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Filters: Keyword is Gene Expression Regulation  [Clear All Filters]
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Y. Zhang, Bobe, G., Revel, J. S., Rodrigues, R. R., Sharpton, T. J., Fantacone, M. L., Raslan, K., Miranda, C. L., Lowry, M. B., Blakemore, P. R., Morgun, A., Shulzhenko, N., Maier, C. S., Stevens, J. F., and Gombart, A. F., “Improvements in Metabolic Syndrome by Xanthohumol Derivatives Are Linked to Altered Gut Microbiota and Bile Acid Metabolism.”, Mol Nutr Food Res, vol. 64, no. 1, p. e1900789, 2020.
D. R. Zamzow, Elias, V., Legette, L. C. L., Choi, J., J Stevens, F., and Magnusson, K. R., “Xanthohumol improved cognitive flexibility in young mice.”, Behav Brain Res, vol. 275, pp. 1-10, 2014.
Y
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.
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.
A. Yambartsev, Perlin, M. A., Kovchegov, Y., Shulzhenko, N., Mine, K. L., Dong, X., and Morgun, A., “Unexpected links reflect the noise in networks.”, Biol Direct, vol. 11, no. 1, p. 52, 2016.
X
M. Xia, Suchland, R. J., Bumgarner, R. E., Peng, T., Rockey, D. D., and Stamm, W. E., “Chlamydia trachomatis variant with nonfusing inclusions: growth dynamic and host-cell transcriptional response.”, J Infect Dis, vol. 192, no. 7, pp. 1229-36, 2005.
V
W. R. Vorachek, Bobe, G., and Hall, J. A., “Reference gene selection for quantitative PCR studies in sheep neutrophils.”, Int J Mol Sci, vol. 14, no. 6, pp. 11484-95, 2013.
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.
S
L. Louis Seifert, Si, C., Saha, D., Sadic, M., de Vries, M., Ballentine, S., Briley, A., Wang, G., Valero-Jimenez, A. M., Mohamed, A., Schaefer, U., Moulton, H. M., García-Sastre, A., Tripathi, S., Rosenberg, B. R., and Dittmann, M., “The ETS transcription factor ELF1 regulates a broadly antiviral program distinct from the type I interferon response.”, PLoS Pathog, vol. 15, no. 11, p. e1007634, 2019.
R
R. R. Rodrigues, Gurung, M., Li, Z., Garcia-Jaramillo, M., Greer, R., Gaulke, C., Bauchinger, F., You, H., Pederson, J. W., Vasquez-Perez, S., White, K. D., Frink, B., Philmus, B., Jump, D. B., Trinchieri, G., Berry, D., Sharpton, T. J., Dzutsev, A., Morgun, A., and Shulzhenko, N., “Transkingdom interactions between Lactobacilli and hepatic mitochondria attenuate western diet-induced diabetes.”, Nat Commun, vol. 12, no. 1, p. 101, 2021.
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, 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, 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, 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, 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.
O
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.
K
A. Kashyap, Rhodes, A., Kronmiller, B., Berger, J., Champagne, A., Davis, E. W., Finnegan, M. V., Geniza, M., Hendrix, D. A., Löhr, C. V., Petro, V. M., Sharpton, T. J., Wells, J., Epps, C. W., Jaiswal, P., Tyler, B. M., and Ramsey, S. A., “Pan-tissue transcriptome analysis of long noncoding RNAs in the American beaver Castor canadensis.”, BMC Genomics, vol. 21, no. 1, p. 153, 2020.
J
S. S. Jha, Danelishvili, L., Wagner, D., Maser, J., Li, Y. -jun, Moric, I., Vogt, S., Yamazaki, Y., Lai, B., and Bermudez, L. E., “Virulence-related Mycobacterium avium subsp hominissuis MAV_2928 gene is associated with vacuole remodeling in macrophages.”, BMC Microbiol, vol. 10, p. 100, 2010.
H
H. Hugejiletu, Bobe, G., Vorachek, W. R., M Gorman, E., Mosher, W. D., Pirelli, G. J., and Hall, J. A., “Selenium supplementation alters gene expression profiles associated with innate immunity in whole-blood neutrophils of sheep.”, Biol Trace Elem Res, vol. 154, no. 1, pp. 28-44, 2013.
J. A. Hall, Chinn, R. M., Vorachek, W. R., M Gorman, E., Greitl, J. L., Joshi, D. K., and Jewell, D. E., “Influence of dietary antioxidants and fatty acids on neutrophil mediated bacterial killing and gene expression in healthy Beagles.”, Vet Immunol Immunopathol, vol. 139, no. 2-4, pp. 217-28, 2011.
G
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.
D
L. Danelishvili, McGarvey, J., Li, Y. -jun, and Bermudez, L. E., “Mycobacterium tuberculosis infection causes different levels of apoptosis and necrosis in human macrophages and alveolar epithelial cells.”, Cell Microbiol, vol. 5, no. 9, pp. 649-60, 2003.
A
P. S. Askovich, Ramsey, S. A., Diercks, A. H., Kennedy, K. A., Knijnenburg, T. A., and Aderem, A., “Identifying novel transcription factors involved in the inflammatory response by using binding site motif scanning in genomic regions defined by histone acetylation.”, PLoS One, vol. 12, no. 9, p. e0184850, 2017.
D. T. Alzhanov, Weeks, S. K., Burnett, J. R., and Rockey, D. D., “Cytokinesis is blocked in mammalian cells transfected with Chlamydia trachomatis gene CT223.”, BMC Microbiol, vol. 9, p. 2, 2009.