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Home
Publications
Found 61 results
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Stephen A Ramsey
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A
H. R. C. Shoen
,
Rose, S. J.
,
Ramsey, S. A.
,
de Morais, H. Autran
, and
Bermudez, L. E.
,
“
Analysis of Staphylococcus infections in a veterinary teaching hospital from 2012 to 2015.
”
,
Comp Immunol Microbiol Infect Dis
, vol. 66, p. 101332, 2019.
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.
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.
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.
B
“
The Biomedical Data Translator Program: Conception, Culture, and Community.
”
,
Clin Transl Sci
, vol. 12, no. 2, pp. 91-94, 2019.
C
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.
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.
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. 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.
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.
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.
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.
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.
D
D. Hwang
,
Rust, A. G.
,
Ramsey, S. A.
,
Smith, J. J.
,
Leslie, D. M.
,
Weston, A. D.
,
de Atauri, P.
,
Aitchison, J. D.
,
Hood, L.
,
Siegel, A. F.
, and
Bolouri, H.
,
“
A data integration methodology for systems biology.
”
,
Proc Natl Acad Sci U S A
, vol. 102, no. 48, pp. 17296-301, 2005.
D. Hwang
,
Smith, J. J.
,
Leslie, D. M.
,
Weston, A. D.
,
Rust, A. G.
,
Ramsey, S. A.
,
de Atauri, P.
,
Siegel, A. F.
,
Bolouri, H.
,
Aitchison, J. D.
, and
Hood, L.
,
“
A data integration methodology for systems biology: experimental verification.
”
,
Proc Natl Acad Sci U S A
, vol. 102, no. 48, pp. 17302-7, 2005.
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.
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
,
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
,
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.
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.
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.
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.
E
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.
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.
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.
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