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2026

American science needs an executive branch constrained by checks and balances
Leifer A, Emonet T, Liu A, Nagel SR
Nature Physics 22, 1364–1365 (2026)
A behavior-environment information loop drives sensory navigation
Chen KS, Leighton MP, Clark DA, Emonet T
arXiv arXiv:2607.26295 (2026)
A neural circuit for olfactory motion detection
Santana GM*, Vashistha H*, Emonet T#, Clark DA#
bioRxiv 2026.07.13.738327 (2026)

* co-first authors; # co-last authors

On the Information Required for Feedback Control
Leighton MP, Betancourt JM, Emonet T, Machta BB, Abbott MC
arXiv arXiv:2607.16639 (2026)
Fly navigational responses exploit plume-specific odor motion and gradient cues
Brudner S*, Zhou B*, Jayaram V, Santana GM, Crimaldi JP, Clark DA#, Emonet T#
PNAS 123 (29) e2608896123 (2026)

* contributed equally; #corresponding authors

Lattice Ultrasensitivity Amplifies Signals in E. coli without Finely-Tuned Allosteric Interactions
Sherry DM, Graf IR*, Bryant SJ, Emonet T*, Machta B*
PRX Life 4, 023027 (2026)
Growth-dependent sensory bet-hedging enhances collective navigation
Avgidis F, Jurgelyte R, Emonet T, Shimizu TS
bioRxiv 2026.02.13.705748 (2026)
Discrete turn strategies emerge in information-limited navigation
Betancourt JM, Leighton MP, Emonet T, Machta BB, Abbott MC
arXiv arXiv:2602.23324 (2026)
E. coli chemosensing accuracy is not limited by stochastic molecule arrivals
Mattingly HH*, Kamino K, Ong J, Kottou R, Emonet T*, Machta B*
Nature Physics 22, 123–130 (2026)

* corresponding authors

2025

Divergent synaptic dynamics originate parallel pathways for computation and behavior in an olfactory circuit
Kim HS, Santana GM, Sancer G, Emonet T, Jeanne JM
Current Biology 35, 3146–3162 (2025)
Nongenetic adaptation by collective migration
Vo L*, Avgidis F*, Mattingly HH*, Edmonds K, Burger I, Balasubramanian R, Shimizu TS, Kazmierczak BI, Emonet T
PNAS 122 (8) e2423774122 (2025)

* co-first authors

2024

Microscopic phage adsorption assay: High-throughput quantification of virus particle attachment to host bacterial cells
Antani JD, Ward T, Emonet T, Turner PE
PNAS 121 (52) e2410905121 (2024)
Bifurcation enhances temporal information encoding in the olfactory periphery
Choi K*, Rosenbluth W*, Graf IR, Kadakia N#, Emonet T#
PRX Life 2, 043011 (2024)

* contributed equally; # co-corresponding authors

Physics of bacterial chemotaxis
Moore J, Emonet T
Current Biology 34(20), R972–R977 (2024)
Direct measurement of dynamic attractant gradients reveals breakdown of the Patlak-Keller-Segel chemotaxis model
Phan TV*, Mattingly HH*, Vo L, Marvin JS, Looger LL, Emonet T
PNAS 121 (3) e2309251121 (2024)

* contributed equally

Olfactory cues and memories in animal navigation
Emonet T & Vergassola M
Nature Reviews Physics 6, 215–216 (2024)
Signal integration and adaptive sensory diversity tuning in Escherichia coli chemotaxis
Moore JP, Kamino K, Kottou R, Shimizu TS, Emonet T
Cell Systems 15(7), 628–638.e8 (2024)

2023

Extracting spatial information from temporal odor patterns: insights from insects
Szyszka P, Emonet T, Edwards TL
Current Opinion in Insect Science 59:101082 (2023)
Temporal novelty detection and multiple timescale integration drive Drosophila orientation dynamics in temporally diverse olfactory environments
Jayaram V*, Sehdev A*, Kadakia N, Brown EA, Emonet T
PLoS Computational Biology 19(5):e1010606 (2023)

* contributed equally

Optimal inference of molecular interaction dynamics in FRET microscopy
Kamino K, Kadakia N, Avgidis F, Liu Z, Aoki K, Shimizu TS, Emonet T
PNAS 120 (15) e2211807120 (2023)

2022

Odour motion sensing enhances navigation of complex plumes
Kadakia N, Demir M, Michaelis BT, DeAngelis BD, Reidenbach MA, Clark DA*, Emonet T*
Nature 611, 754–761 (2022)

* co-corresponding authors

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

* contributed equally

Brudner S, Emonet T
eLife 11:e82635 (2022)
Collective behavior and nongenetic inheritance allow bacterial populations to adapt to changing environments
Mattingly H, Emonet T
PNAS 119 (26) e2117377119 (2022)

2021

Escherichia coli chemotaxis is information limited
Mattingly HH*, Kamino K*, Machta BB#, Emonet T#
Nature Physics 17, 1426–1431 (2021)

* contributed equally, #co-corresponding authors

A Primed Subpopulation of Bacteria Enables Rapid Expression of the Type 3 Secretion System in Pseudomonas aeruginosa
Lin CK, Lee DSW, McKeithen-Mead S, Emonet T, Kazmierczak B
mBio 12(3):e00831-21 (2021)
Non-Genetic Diversity in Chemosensing and Chemotactic Behavior
Moore JP, Kamino K, Emonet T
International Journal of Molecular Sciences 22(13):6960 (2021)

2020

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

* contributed equally

Adaptive tuning of cell sensory diversity without changes in gene expression
Kamino K, Keegstra JM, Long J, Emonet T*, Shimizu TS*
Science Advances 6(46):eabc1087 (2020)

* corresponding authors

2019

Controlling and measuring dynamic odorant stimuli in the laboratory
Gorur-Shandilya S, Martelli C, Demir M, Emonet T
Journal of Experimental Biology 222: jeb207787 (2019)
Front-end Weber-Fechner gain control enhances the fidelity of combinatorial odor coding
Kadakia N & Emonet T
eLife 8:e45293 (2019)
Organization of Embryonic Morphogenesis via Mechanical Information
Das D, Jülich D, Schwendinger-Schreck J, Guillon E, Lawton AK, Dray N, Emonet T, O’Hern CS, Shattuck MD, Holley SA
Developmental Cell 49(6):829–839.e5 (2019)
A rule from bacteria to balance growth and expansion
Mattingly HH & Emonet T
Nature 575, 602–603 (2019)
Modulation of flagellar rotation in surface-attached bacteria: A pathway for rapid surface-sensing after flagellar attachment
Schniederberend M, Johnston JF, Shine E, Shen C, Jain R, Emonet T, Kazmierczak BI
PLoS Pathogens 15(11):e1008149 (2019)

2018

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

* contributed equally

Behavioral variability and phenotypic diversity in bacterial chemotaxis
Waite AJ, Frankel NW, Emonet T
Annual Review of Biophysics 47:595–616 (2018)

2017

Olfactory receptor neurons use gain control and complementary kinetics to encode intermittent odorant stimuli
Gorur-Shandilya S*, Demir M*, Long J, Clark DA1, Emonet T1
eLife 6:e27670 (2017)

* contributed equally; 1corresponding authors

Feedback between motion and sensation provides nonlinear boost in run-and-tumble navigation
Long J, Zucker SW, Emonet T
PLoS Computational Biology 13(3):e1005429 (2017)
Phenotypic diversity and temporal variability in a bacterial signaling network revealed by single-cell FRET
Keegstra JM, Kamino K, Anquez F, Lazova MD, Emonet T, Shimizu TS
eLife 6:e27455 (2017)
Patterned Disordered Cell Motion Ensures Vertebral Column Symmetry
Das D, Chatti D, Emonet T*, Holley SA*
Developmental Cell 42(2), 170–180.e5 (2017)

* corresponding authors

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

* contributed equally

2016

Presynaptic GABA receptors mediate temporal contrast enhancement in Drosophila olfactory sensory neurons and modulate odor-driven behavioral kinetics
Raccuglia D, McCurdy LY, Demir M, Gorur-Shandilya S, Kunst M, Emonet T, Nitabach MN
eNeuro 3(4):ENEURO.0080-16.2016 (2016)
Direct correlation between motile behavior and protein abundance in single cells
Dufour YS, Gillet S, Frankel NW, Weibel DB, Emonet T
PLoS Computational Biology 12(9):e1005041 (2016)
Non‐genetic diversity modulates population performance
Waite AJ*, Frankel NW*, Dufour Y*, Johnston JF, Long J and Emonet T
Molecular Systems Biology 12:895 (2016)

* contributed equally

2015

Trade-offs in Bacterial Chemotaxis and the Adaptation of Non-Genetic Diversity
Frankel N
Dissertation Yale University (2015)

2014

Adaptability of non-genetic diversity in bacterial chemotaxis
Frankel N, Pontius W, Dufour Y, Long J, Hernandez-Nunez L, Emonet T
eLife 3:e03526 (2014)
Limits of feedback control in bacterial chemotaxis
Dufour Y, Fu X, Hernandez-Nunez L, Emonet T
PLoS Computational Biology 10(6):e1003694 (2014)

Note: There were several typos in the published PDF. Make sure to use our corrected version

2013

Intensity invariant dynamics and odor-specific latencies in olfactory receptor neuron response
Martelli C, Carlson J, Emonet T
Journal of Neuroscience 33(15):6285–6297 (2013)
Functional diversity among sensory receptors in a Drosophila olfactory circuit
Mathew D, Martelli C, Kelley-Swift E, Brusalis C, Gershow M, Samuel AD, Emonet T, Carlson JR
PNAS 110(23):E2134–E2143 (2013)
Regulated tissue fluidity steers zebrafish body elongation
Lawton AK, Nandi A, Stulberg MJ, Dray N, Sneddon MW, Pontius W, Emonet T, and Holley SA
Development 140(3):573–582 (2013)
Cell-Fibronectin interactions propel vertebrate trunk elongation via tissue mechanics
Dray N, Lawton AK, Nandi A, Jülich D, Emonet T, Holley SA
Current Biology 23(14):1335–1341 (2013)
Adaptation dynamics in densely clustered chemoreceptors
Pontius W, Sneddon MW, Emonet T
PLoS Computational Biology 9(9):e1003230 (2013)

2012

Systems Immunology: a primer for Biophysicists
Altan-Bonnet G & Emonet T
Comprehensive Biophysics, Vol. 9: Simulation and Modeling Chapter 9.16, pp. 389–413 (2012)

Edited by Edward H. Egelman

Stochastic coordination of multiple actuators reduces latency and improves chemotactic response in bacteria
Sneddon MW, Pontius W, Emonet T
PNAS 109(3):805–810 (2012)
Modeling cellular signaling: taking space into the computation
Sneddon MW and Emonet T
Nature Methods 9:239–242 (2012)
The Her7 node modulates the network topology of the zebrafish segmentation clock via sequestration of the Hes6 hub
Trofka A, Schwendinger-Schreck J, Brend T, Pontius W, Emonet T, and Holley SA
Development 139:940–947 (2012)

2011

High-throughput, subpixel precision analysis of bacterial morphogenesis and intracellular spatio-temporal dynamics
Sliusarenko O, Heinritz J, Emonet T*, Jacobs-Wagner C*
Molecular Microbiology 80(3):612–627 (2011)

* Co-corresponding authors

Temporal coding of odor mixtures in an olfactory receptor neuron
Su CY, Martelli C, Emonet T, Carlson JR
PNAS 108(12):5075–5080 (2011)
Fine-Tuning of Chemotactic Response in E. coli Determined by High-Throughput Capillary Assay
Park H, Guet CC, Emonet T, Cluzel P
Current Microbiology 62(3):764–769 (2011)
Guidelines for visualizing and annotating rule-based models
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
Molecular BioSystems 7, 2779–2795 (2011)
Thermal robustness: lessons from bacterial chemotaxis
Dufour YS, Sneddon MW, Emonet T
Current Biology 21(12):R465–R468 (2011)
Efficient modeling, simulation and coarse-graining of biological complexity with NFsim
Sneddon MW, Faeder JR, Emonet T
Nature Methods 8:177–183 (2011)

2010

The processivity of peptidoglycan synthesis provides a built-in mechanism for the robustness of straight-rod cell morphology
Sliusarenko O, Cabeen M, Wolgemuth C, Jacobs-Wagner C, Emonet T
PNAS 107(22):10086–10091 (2010)
Spatial organization of the flow of genetic information in bacteria
Llopis PM, Jackson AF, Sliusarenko O, Surovtsev I, Heinritz J, Emonet T, Jacobs-Wagner C
Nature 466(7302):77–81 (2010)
Single-cell quantification of IL-2 response by effector and regulatory T cells reveals critical plasticity in immune response
Feinerman O*, Jentsch G*, Tkach K, Coward JW, Hathorn M, Sneddon MW, Emonet T, Smith KA, Altan-Bonnet G
Molecular Systems Biology 6:437 (2010)

* Co-first author

Interdependence of behavioural variability and response to small stimuli in bacteria
Park H, Pontius W, Guet CC, Marko JF, Emonet T, Cluzel P
Nature 468(7325):819–823 (2010)

2009

RodZ, a component of the bacterial core morphogenic apparatus
Alyahya SA, Alexander R, Costa T, Henriques AO, Emonet T, and Jacobs-Wagner C
PNAS 106(4):1239–1244 (2009)
Understanding Modularity in Molecular Networks Requires Dynamics
Alexander RP, Kim PM, Emonet T*, and Gerstein MB*
Science Signaling 2(81):pe44 (2009)

* Co-corresponding author

2008

Minimally invasive determination of mRNA concentration in single living bacteria
Guet C., Bruneaux L., Min T.L., Siegal-Gaskins D., Figueroa I., Emonet T and Cluzel P
Nucleic Acids Research 36(12):e73 (2008)
Relationship between cellular response and behavioral variability in bacterial chemotaxis
Emonet T*, Cluzel P
PNAS 105(9):3304–3309 (2008)

* Corresponding author

2006

Hidden stochastic nature of a single bacterial motor
Korobkova E., Emonet T, Park H, Cluzel P
Physical Review Letters 96, 058105 (2006)
Dynamical determinants of drug-inducible gene expression in a single bacterium
Le TT, Emonet T, Harlepp S., Guet CC, Cluzel P
Biophysical Journal 90(9):3315–3321 (2006)

2005

Simulations of magneto-convection in the solar photosphere - Equations, methods, and results of the MURaM code
Vögler A, Shelyag S, Schüssler M, Cattaneo F, Emonet T, Linde T
Astronomy & Astrophysics 429, 335–351 (2005)
AgentCell: a digital single-cell assay for bacterial chemotaxis
Emonet T*, Macal CM, North MJ, Wickersham CE, Cluzel P
Bioinformatics 21(11):2714–2721 (2005)

* Corresponding author

Real-time RNA profiling within a single bacterium
Le TT, Harlepp S., Guet CC, Dittmar K, Emonet T, Pan T., Cluzel P
PNAS 102(26):9160–9164 (2005)

2004

From molecular noise to behavioural variability in a single bacterium
Korobkova E.*, Emonet T.*, Vilar J., Shimizu T. & Cluzel P
Nature 428, 574–578 (2004)

* co-first author

2003

Polarization of photospheric lines from turbulent dynamo simulations
Almeida J, Emonet T, Cattaneo F
Astrophysical Journal 585, 536–552 (2003)
On the interaction between convection and magnetic fields
Cattaneo F, Emonet T, Weiss N
Astrophysical Journal 588, 1183–1198 (2003)

2001

The zigzag path of buoyant magnetic tubes and the generation of vorticity along their periphery
Emonet T, Moreno Insertis F, Rast M
Astrophysical Journal 549, 1212–1220 (2001)
Small-scale photospheric fields: Observational evidence and numerical simulations
Emonet T, Cattaneo F
Astrophysical Journal 560, L197–L200 (2001)

1998

The physics of twisted magnetic tubes rising in a stratified medium: Two-dimensional results
Emonet T, Moreno Insertis F
Astrophysical Journal 492, 804–821 (1998)

1996

Equilibrium of twisted horizontal magnetic flux tubes
Emonet T, Moreno Insertis F
Astrophysical Journal 458, 783–801 (1996)
MHS-equilibrium of twisted magnetic tubes
Emonet T, Moreno Insertis F
Astrophysical Letters & Communications 34, 9–15 (1996)
The rise of twisted magnetic tubes in a stratified medium
Moreno Insertis F, Emonet T
Astrophysical Journal 472, L53–L56 (1996)