Research Focus

Self-organizing simple systems and the gene regulation at the single molecule level.

The Genesis of Spatial Patterns in Simple Systems

We study cell signaling in Dictyostelium, an organism where cell proliferation is cleanly separated from differentiation and morphogenesis. Our current research focuses on the molecular biology of cAMP wave propagation in uniform layers of signaling cells. Our approach is to combine the analysis of cells mutant for various components of the signaling pathway with quantitative modeling of wave speed, amplitude, and geometry. We have also initiated a high throughput genetic screen for new wave propagation mutants. Our main goal is to understand at the systems level how cell populations self-organize to give a mature organism.

Gene regulation molecule by molecule

We develop methods for studying single mRNA and protein molecules in real time in living cells, and modeling these results by comparing them to single molecule studies in vitro using near field optical methods.

Selected Publications

Kuhlman, T.E., and Cox, E.C. (2012). DNA-binding-protein inhomogeneity in E. coli modeled as biphasic facilitated diffusion. Phys. Rev. E 88, 022701. PubMed

Kuhlman TE, Cox EC. (2012) Gene location and DNA density determine transcription factor distributions in Escherichia coli. Mol Syst Biol. 8: 610. PubMed

Cooper RM, Wingreen NS, Cox EC. (2012) An excitable cortex and memory model successfully predicts new pseudopod dynamics. PLoS One 7:e33528 PubMed

Li L, Cox EC, Flyvbjerg H. (2011) 'Dicty dynamics': Dictyostelium motility as persistent random motion. Phys Biol 8: 046006 PubMed

Kinney JB, Murugan A, Callan CG Jr, Cox EC. (2010) Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequence. Proc Natl Acad Sci USA 107: 9158-9163. PubMed

Kuhlman TE, Cox EC. (2010) A place for everything: Chromosomal integration of large constructs. Bioeng Bugs. 1: 296-299. PubMed

Kuhlman TE, Cox EC. (2010) Site-specific chromosomal integration of large synthetic constructs. Nucleic Acids Res. 38: e92. PubMed

Wang Y, Guo L, Golding I, Cox EC, Ong NP. (2009) Quantitative transcription factor binding kinetics at the single-molecule level. Biophys J. 96: 609-620. PubMed

Li L, Nørrelykke SF, Cox EC. (2008) Persistent cell motion in the absence of external signals: a search strategy for eukaryotic cells. PLoS ONE. 3: e2093. PubMed

Sawai S, Guan XJ, Kuspa A, Cox EC. (2007) High-throughput analysis of spatio-temporal dynamics in Dictyostelium. Genome Biol. 8: R144. PubMed

Zhang M, Goswami M, Sawai S, Cox EC, Hereld D. (2007) Regulation of G protein-coupled cAMP receptor activation by a hydrophobic residue in transmembrane helix 3. Mol Microbiol. 65: 508-520. PubMed

Chen Y, McQuade KJ, Guan XJ, Thomason PA, Wert MS, Stock JB, Cox EC. (2007) Isoprenylcytseine carboxyl methylation is essential for development in Dictyostelium discoideum. Mol Biol Cell 18: 4106-4118. PubMed

Golding I, Cox EC. (2006) Protein synthesis molecule by molecule. Genome Biol 7: 221 PubMed

Wang YM, Austin RH, Cox EC. (2006) Single molecule measurements of repressor protein 1D diffusion on DNA. Phys Rev Lett 97: 048302. PubMed

Golding I, Cox EC. (2006) Eukaryotic transcription: What does it mean for a gene to be 'on'? Curr Biol 16: R371-373. PubMed

Thomason PA, Sawai S, Stock JB and Cox EC. (2006) The histidine kinase homologue DhkK/Sombrero controls morphogenesis in Dictyostelium. Dev Biol 292: 358-370. PubMed

Golding I, Cox EC. (2006) Physical nature of bacterial cytoplasm. Phys Rev Lett 96: 098102. PubMed

Sawai S, Thomason PA, Cox EC. (2005) An autoregulatory circuit for long-range self-organization in Dictyostelium cell populations. Nature 433: 323-326. PubMed

Chen Y, Golding I, Sawai S, Guo L, Cox EC. (2005) Population fitness and the regulation of Escherichia coli genes by bacterial viruses. PLoS Biol 3: e229. PubMed

Golding I, Paulsson J, Zawilski SM, Cox EC. (2005) Real-time kinetics of gene activity in individual bacteria. Cell 123: 1025-1036. PubMed

Samiee KT, Foquet M, Guo L, Cox EC, Craighead HG. (2005) lambda-Repressor oligomerization kinetics at high concentrations using fluorescence correlation spectroscopy in zero-mode waveguides. Biophys J 88: 2145-2153. PubMed

Huang LR, Cox EC, Austin RH, Sturm JC. (2004) Continuous particle separation through deterministic lateral displacement. Science 304: 987-990. PubMed

Golding I, Cox EC. (2004) RNA dynamics in live Escherichia coli cells. Proc Natl Acad Sci USA 101: 11310-11315. PubMed

Google Scholar Citations

https://scholar.google.com/citations?user=uH06QdMAAAAJ