2017
Feedback between motion and sensation provides nonlinear boost in run-and-tumble navigation
Long J, Zucker SW, Emonet T. Feedback between motion and sensation provides nonlinear boost in run-and-tumble navigation. PLOS Computational Biology 2017, 13: e1005429. PMID: 28264023, PMCID: PMC5358899, DOI: 10.1371/journal.pcbi.1005429.Peer-Reviewed Original ResearchConceptsNon-normal dynamicsRelevant parameter spaceFundamental nonlinearityParameter spaceInternal statesRandom reorientationDrift speedClassical drawbacksDynamics implicitStraight motionLarge transientsMotionAnalytical approachLarge fluctuationsDynamicsProbabilityNonlinearitySignal levelGradientFeedbackSpaceSpeedFluctuationsDirection
2014
Limits of Feedback Control in Bacterial Chemotaxis
Dufour YS, Fu X, Hernandez-Nunez L, Emonet T. Limits of Feedback Control in Bacterial Chemotaxis. PLOS Computational Biology 2014, 10: e1003694. PMID: 24967937, PMCID: PMC4072517, DOI: 10.1371/journal.pcbi.1003694.Peer-Reviewed Original ResearchConceptsFeedback controlIntegral feedback controlOperational regimesOptimal operational regimeComplex statisticsDrift velocityRobust performanceFuture inputsAdaptation rateProper information transferChemotactic driftAnalytical modelInput signalOptimal regimeActuatorsSteep gradientsProper couplingWide rangeChemotactic performanceRegimeBifurcation
2013
Regulated tissue fluidity steers zebrafish body elongation
Lawton AK, Nandi A, Stulberg MJ, Dray N, Sneddon MW, Pontius W, Emonet T, Holley SA. Regulated tissue fluidity steers zebrafish body elongation. Development 2013, 140: 573-582. PMID: 23293289, PMCID: PMC3561786, DOI: 10.1242/dev.090381.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAnimals, Genetically ModifiedBiomechanical PhenomenaBody PatterningCadherinsCell AdhesionCell CountCell MovementCell PolarityComputer SimulationEmbryo, NonmammalianEmbryonic DevelopmentFibroblast Growth FactorsGene Expression Regulation, DevelopmentalModels, BiologicalTailTime FactorsWnt Signaling PathwayZebrafishZebrafish Proteins
2012
Modeling cellular signaling: taking space into the computation
Sneddon MW, Emonet T. Modeling cellular signaling: taking space into the computation. Nature Methods 2012, 9: 239-242. PMID: 22373909, PMCID: PMC4713026, DOI: 10.1038/nmeth.1900.Peer-Reviewed Original Research
2011
Stochastic coordination of multiple actuators reduces latency and improves chemotactic response in bacteria
Sneddon MW, Pontius W, Emonet T. Stochastic coordination of multiple actuators reduces latency and improves chemotactic response in bacteria. Proceedings Of The National Academy Of Sciences Of The United States Of America 2011, 109: 805-810. PMID: 22203971, PMCID: PMC3271881, DOI: 10.1073/pnas.1113706109.Peer-Reviewed Original Research
2010
Efficient modeling, simulation and coarse-graining of biological complexity with NFsim
Sneddon MW, Faeder JR, Emonet T. Efficient modeling, simulation and coarse-graining of biological complexity with NFsim. Nature Methods 2010, 8: 177-183. PMID: 21186362, DOI: 10.1038/nmeth.1546.Peer-Reviewed Original ResearchProcessivity of peptidoglycan synthesis provides a built-in mechanism for the robustness of straight-rod cell morphology
Sliusarenko O, Cabeen MT, Wolgemuth CW, Jacobs-Wagner C, Emonet T. Processivity of peptidoglycan synthesis provides a built-in mechanism for the robustness of straight-rod cell morphology. Proceedings Of The National Academy Of Sciences Of The United States Of America 2010, 107: 10086-10091. PMID: 20479277, PMCID: PMC2890421, DOI: 10.1073/pnas.1000737107.Peer-Reviewed Original ResearchSingle‐cell quantification of IL‐2 response by effector and regulatory T cells reveals critical plasticity in immune response
Feinerman O, Jentsch G, Tkach KE, Coward JW, Hathorn MM, 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 2010, 6: msb201090. PMID: 21119631, PMCID: PMC3010113, DOI: 10.1038/msb.2010.90.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCells, CulturedCoculture TechniquesEnzyme-Linked Immunosorbent AssayImmunity, CellularInterleukin-2Interleukin-2 Receptor alpha SubunitMiceMice, Inbred C57BLMice, TransgenicModels, BiologicalSingle-Cell AnalysisStaining and LabelingT-Lymphocytes, Helper-InducerT-Lymphocytes, RegulatoryConceptsInterleukin-2T cellsImmune responseSingle-cell quantificationSingle-cell measurementsEffector T cellsRegulatory T cellsIL-2 responseSurvival signalsReceptor expression levelsIndividual cellsSuppressive capacityCytokine regulationExpression levelsImmune systemHeterogeneous cellsSpecific suppressionSilico modelingPopulation levelCellsEffectorsResponseCritical plasticityPopulationSuppression
2009
Understanding Modularity in Molecular Networks Requires Dynamics
Alexander RP, Kim PM, Emonet T, Gerstein MB. Understanding Modularity in Molecular Networks Requires Dynamics. Science Signaling 2009, 2: pe44. PMID: 19638611, PMCID: PMC4243459, DOI: 10.1126/scisignal.281pe44.Peer-Reviewed Original ResearchConceptsMolecular networksBiological networksMolecular network analysisAnalysis of modularityCellular machinesMolecular partsSystems biologyFunctional analysisGenome sequencingCellular behaviorCollective functionsMolecular interactionsSmall moleculesNetwork analysisRecent advancesIntense researchBiologyFundamental goalSequencingMajor advancesMoleculesInteractionIsolationModularity
2006
Hidden Stochastic Nature of a Single Bacterial Motor
Korobkova EA, Emonet T, Park H, Cluzel P. Hidden Stochastic Nature of a Single Bacterial Motor. Physical Review Letters 2006, 96: 058105. PMID: 16486999, DOI: 10.1103/physrevlett.96.058105.Peer-Reviewed Original Research
2005
AgentCell: a digital single-cell assay for bacterial chemotaxis
Emonet T, Macal CM, North MJ, Wickersham CE, Cluzel P. AgentCell: a digital single-cell assay for bacterial chemotaxis. Bioinformatics 2005, 21: 2714-2721. PMID: 15774553, DOI: 10.1093/bioinformatics/bti391.Peer-Reviewed Original ResearchConceptsBacterial chemotaxisSingle-cell biologySingle-cell assaysSingle-cell levelChemotaxis networkCellular behaviorBacterial populationsIntracellular processesIndividual cellsSingle cellsSwimming cellsMolecular interactionsChemotaxis assaysBiological systemsNew computational approachCellsComputational approachChemotaxisAssaysFlagellaBiologyBacterium
2004
From molecular noise to behavioural variability in a single bacterium
Korobkova E, Emonet T, Vilar JM, Shimizu TS, Cluzel P. From molecular noise to behavioural variability in a single bacterium. Nature 2004, 428: 574-578. PMID: 15058306, DOI: 10.1038/nature02404.Peer-Reviewed Original ResearchConceptsChemotaxis networkSingle-cell levelSignal transductionPopulation measurementsIntracellular networksMolecular noiseBehavioral variationMolecular eventsBiological complexityIndividual bacteriaNon-stimulated cellsEscherichia coliBehavioral variabilitySingle bacteriumTemporal fluctuationsStatistical fluctuationsTransductionSuch variabilityTemporal variationBacteriumColiGeneral understandingCertain propertiesBacteriaPathway