Mattingly HH*, Kamino K*, Ong Jǂ, Kottou Rǂ, Emonet T#, Machta BB#
E. coli do not count single molecules
bioRxiv 2024.07.09.602750; doi:
* contributed equally; ǂ contributed equally; # co-corresponding authors
Choi K*, Rosenbluth W*, Graf IR, Kadakia N#, Emonet T#
Bifurcation enhances temporal information encoding in the olfactory periphery

bioRxiv 2024.05.27.596086; doi:
* contributed equally
; #co-corresponding authors

Sherry DM, Graf IR#, Bryant SJ, Emonet T#, Machta BB#
Lattice ultrasensitivity produces large gain in E. coli chemosensing
bioRxiv 2024.05.28.596300; doi:
# co-corresponding authors
Moore  JP, Kamino K, Kottou R, Shimizu, TS, Emonet T
Signal integration and adaptive sensory diversity tuning in Escherichia coli chemotaxis
Cell Systems 15, 1-11 (2024), (html, PDF)

Emonet T & Vergassola M
Olfactory cues and memories in animal navigation
Nature Review Physics (2024) (html)

Phan TV*, Mattingly HH*, Vo Lam, Marvin JS, Looger LL, Emonet T
Direct measurement of dynamic attractant gradients reveals breakdown of the Patlak-Keller-Segel chemotaxis model
PNAS 121 (3) e2309251121 (2023) (html, PDF, Supp info)
* contributed equally

Vo L*, Avgidis F*, Mattingly H*, Balasubramanian R, Shimizu TS, Kazmierczak BI, Emonet T
Non-genetic adaptation by collective migration.
bioRxiv 2024.01.02.573956; (2024)  (bioRxiv)
* contributed equally

Szyszka P, Emonet T, Edwards TL
Extracting spatial information from temporal odor patterns: insights from insects.
Curr Opin Insect Sci. 59:101082 (2023)  doi: 10.1016/j.cois.2023.101082. Online ahead of print. (html)

Jayaram V*, Sehdev A*, Kadakia N, Brown EA, Emonet T
Temporal novelty detection and multiple timescale integration drive Drosophila orientation dynamics in temporally diverse olfactory environments
PLoS Comput Biol 19(5): e1010606 (2023) (html, PDF, bioRxiv)
* contributed equally
Kamino K, Kadakia N, Avgidis F, Liu Z, Aoki K, Shimizu TS, Emonet T
Optimal inference of molecular interaction dynamics in FRET microscopy
PNAS 120 (15) e2211807120 (2023) (html, PDF, Supp info)
Kadakia N, Demir M, Michaelis BT, DeAngelis, BD, Reidenbach MA, Clark DA*, Emonet T*
Odor motion sensing enhances complex plume navigation
Nature doi: 10.1038/s41586-022-05423-4 (2022) (html, PDF, Supp info)
*co-corresponding authors
Brudner S, Emonet T
Navigation: Where is that smell coming from?
eLife,  11:e82635 (2022) (html)

Mattingly H, Emonet T
Collective behavior and non-genetic inheritance allow bacterial populations to adapt to changing environments.
PNAS, 119 (26) e2117377119 (2022)  (htmlbioRxivpdf)

Jayaram V*, Kadakia N*, Emonet T
Sensing complementary temporal features of odor signals enhances navigation of diverse turbulent plumes
eLife, 11:e72415 (2022) (html)
* contributed equally

Mattingly HH*, Kamino K*, Machta BB#, Emonet T#
Escherichia coli chemotaxis is information limited
Nature Physics 17, 1426–1431 (2021) (htmlpdf, Supp Info)
* contributed equally, #co-corresponding authors

Moore JP, Kamino K, Emonet T
Non-Genetic Diversity in Chemosensing and Chemotactic Behavior
Int. J. Mol. Sci. 2021, 22(13), 6960 (html, pdf)

Lin CK, Lee DSW, McKeithen-Mead S, Emonet T, Kazmierczak B.
A Primed Subpopulation of Bacteria Enables Rapid Expression of the Type 3 Secretion System in Pseudomonas aeruginosa.
 mBio  12:e00831-21 (2021) (html , pdf )

Kamino K, Keegstra JM, Long J, Emonet T*, Shimizu TS*
Adaptive tuning of cell sensory diversity without changes in gene expression
Science Advances, Vol. 6, no. 46, eabc1087 (2020) (html, pdf, suppinfo)
* corresponding authors

Demir M*, Kadakia N*, Anderson HD, Clark DA, Emonet T
Walking Drosophila navigate complex plumes using stochastic decisions biased by the timing of odor encounters
eLife, 9:e57524 (2020) (html, pdf, figures and supplements)
* contributed equally

Schniederberend M, Johnston JF, Shine E, Shen C, Jain R, Emonet T, Kazmierczak BI
Modulation of flagellar rotation in surface-attached bacteria: a circuit for rapid surface-sensing
PLoS Pathog. Nov 19 (11):e1008149 (2019) (html)

Gorur-Shandilya S, Martelli C, Demir M, Emonet T
Controlling and measuring dynamic odorant stimuli in the laboratory
Journal of Experimental Biology,
222: jeb207787 (2019) (html)

Mattingly HH & Emonet T
A rule from bacteria to balance growth and expansion.
Nature, 153, 708–2 (2019) (html, pdf)

Kadakia N & Emonet T
Front-end Weber-Fechner gain control enhances the fidelity of combinatorial odor coding
eLife 8: e45293 (2019) (html, pdf)

Das D, Jülich D, Schwendinger-Schreck J, Guillon E, Lawton AK, Dray N, Emonet T, O’Hern CS, Shattuck MD, Holley SA.
Organization of Embryonic Morphogenesis via Mechanical Information
Developmental Cell, 17;49(6):829-839.e5 (2019) (html, pdf)

Fu X*, Kato S*,  Long J, Mattingly HH, He C, Vural DC, Zucker SW & Emonet T
Spatial Self-Organization Resolves Conflicts Between Individuality and Collective Migration
Nature Communications 9, Article number: 2177 (2018) (html, pdf, supp info)
*contributed equally

Yale News, by Bill Hathaway
preLights by Amanda Haage

Waite AJ, Frankel NW, Emonet T
Behavioral variability and phenotypic variability in bacterial chemotaxis
Annual Review of Biophysics 47:27.1–27.22 (2018) (html and pdf)

Keegstra JM, Kamino K, Anquez F, Lazova MD, Emonet T, Shimizu TS.
Phenotypic diversity and temporal variability in a bacterial signaling network revealed by single-cell FRET
eLife 6: e27455 (2017) (pdf, html, supp info)

Nesper J*, Hug I*, Kato S*, Hee C-S*, Habazettl JM, Mandredi P, Grzesiek S, Tilman S, Emonet T, Jenal U
Cyclic di-GMP differentially tunes a bacterial flagellar motor through a novel class of CheY-like regulators
eLife 6:e28842 (2017) (pdfhtml, supp info)
* contributed equally

Das D, Chatti D, Emonet T*, Holley SA*
Patterned Disordered Cell Motion Ensures Vertebral Column Symmetry
Developmental Cell, 42(2), 170-180.e5 (2017) (html, pdf, supp info)
*corresponding authors

Gorur-Shandilya S*, Demir M*, Long J, Clark DA1, Emonet T1
Olfactory receptor neurons use gain control and complementary kinetics to encode intermittent odorant stimuli
eLife, 6:e27670 (2017) DOI: 10.7554/eLife.27670 (html, pdf)
* contributed equally; 1corresponding authors

Long J, Zucker SW, Emonet T
Feedback between motion and sensation provides nonlinear boost in run-and-tumble navigation
PLoS Computational Biology, 13(3): e1005429. (2017) doi:10.1371/ journal.pcbi.1005429 (html, pdf, supp info, movie)

Waite AJ*, Frankel NW*, Dufour Y*, Johnston JF, Long J and Emonet T
Non‐genetic diversity modulates population performance
Molecular Systems Biology, 12: 895, 1-14 (2016)  (html, pdf, expanded view figures, appendix)
* contributed equally

See also News and Views: van Vliet S & Ackermann M, Stochastic gene expression: bacterial elites in chemotaxis, Molecular Systems Biology, 13: 909, 1-2 (2017) (html, pdf)

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Frankel N
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Dissertation (2014) (pdf)
Frankel N, Pontius W,Dufour Y, Long J,Hernandez-Nunez, Emonet T
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eLife 3:e03526 (2014) (html, pdf, supp. info.)
Dufour Y, Fu X, Hernandez-Nunez L, Emonet T
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PLoS Comput Biol. 10(6): e1003694 (2014)
(Note: There were several typos in the published PDF. Make sure to use this corrected version: pdf, supp. info., html)
Pontius W, Sneddon MW, Emonet T
Adaptation dynamics in densely clustered chemoreceptors.
PLoS Comput Biol. 9(9):e1003230 (2013) (pdf,, 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
Cell-Fibronectin interactions propel vertebrate trunk elongation via tissue mechanics.
Current Biology Jul 22;23(14):1335-41.(2013) (pdf, html)
Martelli C, Carlson J, and Emonet T
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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.
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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.
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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) (pdf)
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)
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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)
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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.
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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)
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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)
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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).
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Equilibrium of twisted horizontal magnetic flux tubes
Astrophysical Journal, 458, 783-801 (1996). (pdf, html)