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Home
Publications
Found 61 results
Author
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Type
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Year
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Stephen A Ramsey
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2004
P. de Atauri
,
Orrell, D.
,
Ramsey, S. A.
, and
Bolouri, H.
,
“
Evolution of 'design' principles in biochemical networks.
”
,
Syst Biol (Stevenage)
, vol. 1, no. 1, pp. 28-40, 2004.
2005
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.
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.
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.
P. de Atauri
,
Orrell, D.
,
Ramsey, S. A.
, and
Bolouri, H.
,
“
Is the regulation of galactose 1-phosphate tuned against gene expression noise?
”
,
Biochem J
, vol. 387, no. Pt 1, pp. 77-84, 2005.
2006
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
,
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.
2007
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.
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.
E. Fu
,
Ramsey, S. A.
,
Chen, J.
,
Chinowsky, T. M.
,
Wiley, B.
,
Xia, Y.
, and
Yager, P.
,
“
Resonance wavelength-dependent signal of absorptive particles in surface plasmon resonance-based detection.
”
,
Sens Actuators B Chem
, vol. 123, no. 1, pp. 606-613, 2007.
J. J. Smith
,
Ramsey, S. A.
,
Marelli, M.
,
Marzolf, B.
,
Hwang, D.
,
Saleem, R. A.
,
Rachubinski, R. A.
, and
Aitchison, J. D.
,
“
Transcriptional responses to fatty acid are coordinated by combinatorial control.
”
,
Mol Syst Biol
, vol. 3, p. 115, 2007.
2008
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.
M. Nykter
,
Price, N. D.
,
Aldana, M.
,
Ramsey, S. A.
,
Kauffman, S. A.
,
Hood, L. E.
,
Yli-Harja, O.
, and
Shmulevich, I.
,
“
Gene expression dynamics in the macrophage exhibit criticality.
”
,
Proc Natl Acad Sci U S A
, vol. 105, no. 6, pp. 1897-900, 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.
2009
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.
V. Litvak
,
Ramsey, S. A.
,
Rust, A. G.
,
Zak, D. E.
,
Kennedy, K. A.
,
Lampano, A. E.
,
Nykter, M.
,
Shmulevich, I.
, and
Aderem, A.
,
“
Function of C/EBPdelta in a regulatory circuit that discriminates between transient and persistent TLR4-induced signals.
”
,
Nat Immunol
, vol. 10, no. 4, pp. 437-43, 2009.
E. Fu
,
Nelson, K. E.
,
Ramsey, S. A.
,
Foley, J. O.
,
Helton, K.
, and
Yager, P.
,
“
Modeling of a competitive microfluidic heterogeneous immunoassay: sensitivity of the assay response to varying system parameters.
”
,
Anal Chem
, vol. 81, no. 9, pp. 3407-13, 2009.
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
,
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.
D. B. Burdick
,
Cavnor, C. C.
,
Handcock, J.
,
Killcoyne, S.
,
Lin, J.
,
Marzolf, B.
,
Ramsey, S. A.
,
Rovira, H.
,
Bressler, R.
,
Shmulevich, I.
, and
Boyle, J.
,
“
SEQADAPT: an adaptable system for the tracking, storage and analysis of high throughput sequencing experiments.
”
,
BMC Bioinformatics
, vol. 11, p. 377, 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.
A. V. Ratushny
,
Ramsey, S. A.
, and
Aitchison, J. D.
,
“
Mathematical modeling of biomolecular network dynamics.
”
,
Methods Mol Biol
, vol. 781, pp. 415-33, 2011.
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