I am a computational biologist in Ilya Shmulevich's research group. The focus of my research is mapping transcriptional regulatory networks by combining high-throughput experimental measurements with DNA sequence analysis. My colleagues and I are presently studying transcriptional regulation in murine macrophages by combining chromatin immunoprecipitation data with bioinformatic methods for identifying transcription factor binding from genome sequence data. This work is being carried out in collaboration with investigators in Alan Aderem's research group. I am particularly interested in the role of nuclear receptors and other transcriptional regulators in foam cell formation and atherosclerosis.
During 2003-2004, I developed a comprehensive stochastic simulation package for networks of biochemical reactions, based on an implementation of the Gillespie stochastic algorithm. The project is called Dizzy.
Institute for Systems Biology
1441 North 34th Street
Seattle, WA 98103, USA
Tel. - 206.732.1335
sramsey@systemsbiology.org
| Bibliographic information | Title | Author(s) | Electronic copy |
| Analyt Chem. (in press, 2009) | Modeling of a competitive microfluidic heterogeneous immunoassay: sensitivity of the assay response to varying system parameters | E. Fu, K. E. Nelson, S. A. Ramsey, J. O. Foley, K. Helton, P. Yager | |
| Nature Immunol. 10(4):437-43 (2009) | Function of C/EBPδ in a regulatory circuit that discriminates between transient and persistent TLR4-induced signals | V. Litvak, S. A. Ramsey, A. G. Rust, D. E. Zak, K. A. Kennedy, A. E. Lampano, M. Nykter, I. Shmulevich, A. Aderem | [DOI] |
| Proc Natl Acad Sci USA 106(10):3758-63 (2009) | Dynamic analysis of MAPK signaling using a high-throughput microfluidic single-cell imaging platform | R. J. Taylor, D. Falconnet, A. Niemistö, S. A. Ramsey, S. Prinz, I. Shmulevich, T. Galitski, C. L. Hansen | [DOI] |
| Biophys J 95(8):3715-23 (2008) | Control of transcriptional variability by overlapping feed-forward regulatory motifs | A. V. Ratushny* S. A. Ramsey*, O. Roda, Y. Wan, J. J. Smith, J. D. Aitchison | [DOI] |
| PLoS Comp Biol 4(3):e1000021 (2008) | Uncovering a macrophage transcriptional program by integrating evidence from motif scanning and expression dynamics | S. A. Ramsey, S. L. Klemm, D. E. Zak, K. A. Kennedy, V. Thorsson, B. Li, M. Gilchrist, E. S. Gold, C. D. Johnson, V. Litvak, G. Navarro, J. C. Roach, C. M. Rosenberger, A. G. Rust, N. Yudkovsky, A. Aderem, I. Shmulevich | [DOI] Corrected Table S17. |
| Proc Natl Acad Sci USA 105(6):1897-1900 (2008) | Gene expression dynamics in the macrophage exhibit criticality | M. Nykter, N. D. Price, M. Aldana, S. A. Ramsey, S. A. Kauffman, L. Hood, O. Yli-Harja, I. Shmulevich | [DOI] |
| Analyt Chim Acta 599(1):118-23 (2007) | Dependence of the signal amplification potential of colloidal gold nanoparticles on resonance wavelength in surface plasmon resonance-based detection | E. S. Fu, S. A. Ramsey, P. Yager | [DOI] |
| Mol Sys Biol 3:115 (2007) | Transcriptional responses to fatty acid are coordinated by combinatorial control | J. J. Smith, S. A. Ramsey, M. Marelli, B. Marzolf, D. Hwang, R. A. Saleem, R. A. Rachubinski, J. D. Aitchison | [DOI] |
| PLoS ONE 2:e249 (2007) | Control of signaling in a MAP-kinase pathway by an RNA-binding protein | S. Prinz, C. Aldridge, S. A. Ramsey, R. J. Taylor, T. Galitski | [DOI] |
| Sens & Act B Chem 123(10):606-13 (2007) | Resonance wavelength-dependent signal of absorptive particles in surface plasmon resonance-based detection | E. Fu, S. A. Ramsey, J. Chen, T. M. Chinowsky, B. Wiley, Y. Xia, and P. Yager | [DOI] |
| Rev Sci Inst 77:076106 (2006) | One-dimensional surface plasmon resonance imaging system using wavelength interrogation | E. Fu, S. A. Ramsey, R. Thariani, and P. Yager | [DOI] |
| Nat Genet 38(9):1082-7 (2006) | Dual feedback loops in the GAL regulon suppress cellular heterogeneity in yeast | S. A. Ramsey, J. J. Smith, D. Orrell, M. Marelli, T. W. Petersen, P. de Atauri, H. Bolouri, and J. D. Aitchison | [DOI] Corrected supplementary note. |
| Physica D 217(1):64-76 (2006) | Feedback control of stochastic noise in the yeast galactose utilization pathway | D. Orrell, S. Ramsey, M. Marelli, J. J. Smith, T. W. Petersen, P. de Atauri, J. D. Aitchison, and H. Bolouri | [DOI] |
| Phil Trans Roy Soc Lon B Biol Sci 361(1467):495-506 (2006) | Transcriptional noise and cellular heterogeneity in mammalian macrophages | S. Ramsey, A. Ozinsky, A. Clark, K. D. Smith, P. de Atauri, V. Thorsson, D. Orrell, and H. Bolouri | [DOI] |
| Proc Natl Acad Sci USA 102(48):17296-17301 (2005) | A data integration methodology for systems biology | D. Hwang, A. G. Rust, S. Ramsey, J. J. Smith, D. M. Leslie, A. D. Weston, P. de Atauri, J. D. Aitchison, L. Hood, A. F. Siegel, H. Bolouri | [DOI] |
| Proc Natl Acad Sci USA 102(48):17302-17307 (2005) | A data integration methodology for systems biology: experimental validation | D. Hwang, J. J. Smith, D. M. Leslie, A. D. Weston, A. G. Rust, S. Ramsey, P. de Atauri, A. F. Siegel, H. Bolouri, J. D. Aitchison, L. Hood. | [DOI] |
| J Bioinform Comp Biol, 3(2):415-436 (2005) | Dizzy: Stochastic simulations of large-scale genetic regulatory networks | S. Ramsey, D. Orrell, and H. Bolouri |
Article: [DOI] Supplement: [DOI] |
| Bioinform 21(2):208-217 (2005) | A method for estimating stochastic noise in large genetic regulatory networks | D. Orrell, S. Ramsey, P. de Atauri, and H. Bolouri | [DOI] |
| Biochem J 387:77-84 (2005) | Is the regulation of galactose-1-phosphate tuned against gene expression noise? | P. de Atauri, D. Orrell, S. Ramsey, and H. Bolouri | [DOI] |
| IET Sys Biol 1(1):28-40 (2004) | Evolution of "design" principles in biochemical networks | P. de Atauri, D. Orrell, S. Ramsey, and H. Bolouri | [DOI] |
| Int J Theo Phys, 40(12):2231-58 (2001) | Interacting field theories in Robertson-Walker spacetimes: analytic approximations | C. Molina-Paris, P. R. Anderson, and S. A. Ramsey | [DOI] |
| Phys Rev D 61:127501 (2000) | One-loop λφ4theory in Robertson-Walker spacetimes: adiabatic regularization and analytic approximation | C. Molina-Paris, P. R. Anderson, and S. A. Ramsey | [DOI] |
| Phys Rev D 61:125013 (2000) | Hydrodynamic transport functions from quantum kinetic theory | E. A. Calzetta, B. L. Hu, and S. A. Ramsey | [DOI] |
| Phys Rev D 59:045009 (1999) | Defect formation and Critical Dynamics in the Early Universe | G. J. Stephens, E. A. Calzetta, B. L. Hu, and S. A. Ramsey | [DOI] |
| Int J Theo Phys, 38(4):1299-1314 (1999). | Nonequilibrium dynamics of quantum fields in inflationary cosmology | S. A. Ramsey | [DOI] |
| Phys Rev D 57:6003-6021 (1998) | Nonequilibrium inflaton dynamics and reheating. II. Fermion production, noise, and stochasticity | S. A. Ramsey, B. L. Hu and A. M. Stylianopoulos | [DOI] |
| Phys Rev D 56:678-705 (1997); Erratum-ibid 57:3798 (1998) | Nonequilibrium inflaton dynamics and reheating: Back reaction of parametric particle creation and curved spacetime effects | S. A. Ramsey and B. L. Hu | [DOI] |
| Phys Rev D 56:661-677 (1997) | O(N) Quantum fields in curved spacetime | S. A. Ramsey and B. L. Hu | [DOI] |
| Brown University Physics Report BROWN-HET-922 (1993) | Some statistics for measuring large-scale structure | R. H. Brandenberger, D. H. Kaplan and S. A. Ramsey | [ArXiv] |
* indicates that these authors contributed equally.