publications
( ... = lab member )

Pontius W, Sneddon MW, Emonet T
Adaptation dynamics in densely clustered chemoreceptors.
PLoS Computational Biology 9(9):e1003230. (2013) (pdf, supp.info., html)
Mathew D, Martelli C, Kelley-Swift E, Brusalis C, Gershow M, Samuel AD, Emonet T, Carlson JR.
Functional diversity among sensory receptors in a Drosophila olfactory circuit.
Proc. Natl. Acad. Sci.,110(23):E2134-43 (2013) (pdf, supplement, data, html)
Dray N, Lawton AK, Nandi A, D. Jülich, Emonet T, Holley SA
Integrin α5 and αV promote vertebrate trunk elongation not via cell migration but through tissue mechanics and inter-tissue adhesion.
Current Biology Jul 22;23(14):1335-41.(2013) (pdf, html)
Martelli C, Carlson J, and Emonet T
Intensity invariant dynamics and odor-specific latencies in olfactory receptor neuron response.
Journal of Neuroscience, 33(15):6285-6297 (2013) (pdf, html)
Lawton AK, Nandi A, Stulberg MJ, Dray N, Sneddon MW, Pontius W, Emonet T, and Holley SA.
Regulated tissue fluidity steers zebrafish body elongation.
Development, 140(3):573-82(2013) (pdf, html, supp. info.)
Trofka A, Schwendinger-Schreck J, Brend T, Pontius W, Emonet T, and Holley SA.
The Her7 node modulates the network topology of the zebrafish segmentation clock via sequestration of the Hes6 hub.
Development, 139:940-947(2012) (pdf, html, supp. info.)
Sneddon MW and Emonet T.
Modeling cellular signaling: taking space into the computation.
Nature Methods, 9:239–242 (2012) (pdf, html)
Sneddon MW, Pontius W, Emonet T.
Stochastic coordination of multiple actuators reduces latency and improves chemotactic response in bacteria.
Proc. Natl. Acad. Sci., 109(3): 805-810 (2012) (pdf, html, supp. info.)
Dufour YS, Sneddon MW, Emonet T.
Thermal robustness: lessons from bacterial chemotaxis.
Curr. Biol., 21(12):R465-8 (2011) (pdf, html)
Chylek LA, Hu B, Blinov ML, Emonet T, Faeder JR, Goldstein Byron, Gutenkunst RN, Haugh JM, Lipniacki T, Posner RG, Yang J and Hlavacek WS.
Guidelines for visualizing and annotating rule-based models.

Mol. BioSyst., (2011) (pdf, html, supp. info.)
Emonet T & Altan-Bonnet G,
“Systems Immunology: a primer for Biophysicists”, Section: “Mathematical Modeling of Complex Systems: from genes and molecules to organs and organisms: immune system”
,
Chapter 9:26 for “Comprehensive Biophysics” (Edited by Edward Egelman)(April 12 2012)
Sliusarenko O, Heinritz J, Emonet T*, Jacobs-Wagner C.*,
High-throughput, subpixel precision analysis of bacterial morphogenesis and intracellular spatio-temporal dynamics.
Mol. Micro., 80(3):612–627, May 2011 (pdf, html, supp. info., supp. movies, source code)
 * Co-corresponding authors
Su CY, Martelli C, Emonet T, Carlson JR.
Temporal coding of odor mixtures in an olfactory receptor neuron.,
Proc. Natl. Acad. Sci., 108(12):5075-80 (2011). (pdf, html, supp. info.)
Sneddon MW, Faeder JR, Emonet T.
Efficient modeling, simulation and coarse-graining of biological complexity with NFsim,
Nature Methods, 8:177-183 (2011). (pdf, html, supp. info., supp. video 1, supp. video 2, source code)
see also News & Views by Bachman and Sorger Nature Methods, 8:130-131 (2011) (pdf, html)
Park H, Pontius W, Guet CC, Marko JF, Emonet T, Cluzel P.
Interdependence of behavioural variability and response to small stimuli in bacteria,
Nature, 468(7325):819-823 (2010). (pdf, html, supp. info.)
Feinerman O*, Jentsch G*, Tkach K, Coward JW, Hathorn M, Sneddon MW, Emonet T, Smith KA, Altan-Bonnet G,
Single-cell quantification of IL-2 response by effector and regulatory T cells reveals critical plasticity in immune response
,
Molecular Systems Biology, 6:437 (2010). (pdf, html, supp. info., SBML model)  * Co-first authors
Park H, Guet CC, Emonet T, Cluzel P.
Fine-Tuning of Chemotactic Response in E. coli Determined by High-Throughput Capillary Assay,
Current Microbiology 62(3):764-769 (2011) (pdf, html)
Llopis PM, Jackson AF, Sliusarenko O, Surovtsev I, Heinritz J, Emonet T, Jacobs-Wagner C.
Spatial organization of the flow of genetic information in bacteria,
Nature, 466(7302):77-81 (2010). (pdf, html, supp. info.)
Sliusarenko O, Cabeen M, Wolgemuth C, Jacobs-Wagner C, Emonet T.
The processivity of peptidoglycan synthesis provides a built-in mechanism for the robustness of straight-rod cell morphology,
Proc. Natl. Acad. Sci., 107(22):10086-91 (2010). (pdf, html, supp. info.)
Alexander RP, Kim PM, Emonet T*, and Gerstein MB*
Understanding Modularity in Molecular Networks Requires Dynamics
Sci. Signal., 81(2):44 (2009). (pdf, html)  * Co-corresponding authors
Alyahya SA, Alexander R, Costa T, Henriques AO, Emonet T, and Jacobs-Wagner C.,
RodZ, a component of the bacterial core morphogenic apparatus,
Proc. Natl. Acad. Sci., 106(4):1239-44 (2009). (pdf, html, supp. info.)
Emonet T*, Cluzel P.
Relationship between cellular response and behavioral variability in bacterial chemotaxis,
Proc. Natl. Acad. Sci., 105(9):3304-9(2008). (pdf, html, supp. info.)  * Corresponding author
Guet C., Bruneaux L., Min T.L., Siegal-Gaskins D., Figueroa I., Emonet T and Cluzel P.
Minimally invasive determination of mRNA concentration in single living bacteria,
Nucleic Acids Research, 36(12):1-8 (2008). (pdf, html, supp. info. file 1, supp. info. file 2)
Le TT, Emonet T, Harlepp S., Guet CC, Cluzel P.
Dynamical determinants of inducible gene expression in a single bacterium
Biophysical J., 90(9):3315-21 (2006). (pdf, html, supp. info.)
Korobkova E., Emonet T, Park H, Cluzel P.
Hidden stochastic nature of a single bacterial motor
Phys. Rev. Letters, 96, 58105 (2006). (pdf, html)
Le TT, Harlepp S., Guet CC, Dittmar K, Emonet T, Pan T., Cluzel P.
Real-time RNA profiling within a single bacterium
Proc. Natl. Acad. Sci., 102 (26):9160-4 (2005). (pdf, html, supp. info.)
Emonet T*, Macal CM, North MJ, Wickersham CE, Cluzel P.
AgentCell: a digital single-cell assay for bacterial chemotaxis
Bioinformatics, 1; 21(11):2714-21 (2005). (pdf, html, supp. info.)  * Corresponding author
Vogler A., Shelyag S., Schussler M., Cattaneo F. Emonet, T. & Linde T.
Simulations of magneto-convection in the solar photosphere - Equations, methods, and results of the MURaM code,
Astronomy & Astrophysics, 429, 335-U113 (2005). (pdf, html)
Korobkova E.*, Emonet T.*, Vilar J., Shimizu T. & Cluzel P.
From molecular noise to behavioral variability in a single bacterium
Nature, 428, 574-578 (2004). (pdf, html, supp. info.)  * co-first authors
Cattaneo F., Emonet, T. & Weiss N.
On the interaction between convection and magnetic fields,
Astrophysical Journal, 588, 1183-1198 (2003). (pdf, html)
Almeida J., Emonet, T. & Cattaneo F.
Polarization of photospheric lines from turbulent dynamo simulations
Astrophysical Journal, 585, 536-552 (2003). (pdf, html)
Emonet, T. & Cattaneo, F.
Small-scale photospheric fields: Observational evidence and numerical simulations
Astrophysical Journal, 560, L197-L200 (2001). (pdf, html)
Emonet, T., Moreno Insertis, F. & Rast M.
The zigzag path of buoyant magnetic tubes and the generation of vorticity along their periphery
Astrophysical Journal, 549, 1212-1220 (2001). (pdf, html)
Emonet, T. & Moreno Insertis, F.
The physics of twisted magnetic tubes rising in a stratified medium: Two-dimensional results
Astrophysical Journal, 492, 804-821 (1998). (pdf, html)
Moreno Insertis, F. & Emonet, T.
The rise of twisted magnetic tubes in a stratified medium
Astrophysical Journal, 472, L53-& (1996). (pdf, html)
Emonet, T. & Moreno-Insertis, F.
MHS-equilibrium of twisted magnetic tubes
Astrophysical Letters & Communications, 34, 9-15 (1996).
Emonet, T. & Moreno Insertis, F.
Equilibrium of twisted horizontal magnetic flux tubes
Astrophysical Journal, 458, 783-801 (1996). (pdf, html)