2023
Temporal novelty detection and multiple timescale integration drive Drosophila orientation dynamics in temporally diverse olfactory environments
Jayaram V, Sehdev A, Kadakia N, Brown E, Emonet T. Temporal novelty detection and multiple timescale integration drive Drosophila orientation dynamics in temporally diverse olfactory environments. PLOS Computational Biology 2023, 19: e1010606. PMID: 37167321, PMCID: PMC10205008, DOI: 10.1371/journal.pcbi.1010606.Peer-Reviewed Original Research
2022
Odour motion sensing enhances navigation of complex plumes
Kadakia N, Demir M, Michaelis B, DeAngelis B, Reidenbach M, Clark D, Emonet T. Odour motion sensing enhances navigation of complex plumes. Nature 2022, 611: 754-761. PMID: 36352224, PMCID: PMC10039482, DOI: 10.1038/s41586-022-05423-4.Peer-Reviewed Original ResearchConceptsRobot navigationVirtual agentsEffective navigationMultiple featuresMultiple streamsNavigationUncertain environmentMotion sensingVirtual reality paradigmTemporal correlationDirectional informationNavigational decisionsInformationComplex plumesSensingAlgorithmSensory inputInputParadigmSearchEnvironmentStreamsGeneralityWhere is that smell coming from?
Brudner S, Emonet T. Where is that smell coming from? ELife 2022, 11: e82635. PMID: 36125436, PMCID: PMC9489204, DOI: 10.7554/elife.82635.Commentaries, Editorials and LettersSensing complementary temporal features of odor signals enhances navigation of diverse turbulent plumes
Jayaram V, Kadakia N, Emonet T. Sensing complementary temporal features of odor signals enhances navigation of diverse turbulent plumes. ELife 2022, 11: e72415. PMID: 35072625, PMCID: PMC8871351, DOI: 10.7554/elife.72415.Peer-Reviewed Original Research
2021
Non-Genetic Diversity in Chemosensing and Chemotactic Behavior
Moore JP, Kamino K, Emonet T. Non-Genetic Diversity in Chemosensing and Chemotactic Behavior. International Journal Of Molecular Sciences 2021, 22: 6960. PMID: 34203411, PMCID: PMC8268644, DOI: 10.3390/ijms22136960.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBacteriaBacterial ProteinsChemotactic FactorsChemotaxisHumansSignal TransductionA 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. A Primed Subpopulation of Bacteria Enables Rapid Expression of the Type 3 Secretion System in Pseudomonas aeruginosa. MBio 2021, 12: 10.1128/mbio.00831-21. PMID: 34154400, PMCID: PMC8262847, DOI: 10.1128/mbio.00831-21.Peer-Reviewed Original ResearchConceptsType 3 secretion systemSecretion systemT3SS expressionVirulence traitsSpecific virulence traitsHuman disease severityComplex nanomachinesT3SS genesP. aeruginosa cellsReproductive fitnessIsogenic cellsHeterogeneous expressionCell envelopeT3SS effectorsMotility organellesReservoir of cellsCritical virulence traitsGene expressionRegulatory mechanismsSubpopulation of cellsGram-negative pathogensFluorescent reportersDivision timeP. aeruginosaPseudomonas aeruginosa
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. Walking Drosophila navigate complex plumes using stochastic decisions biased by the timing of odor encounters. ELife 2020, 9: e57524. PMID: 33140723, PMCID: PMC7609052, DOI: 10.7554/elife.57524.Peer-Reviewed Original Research
2019
Front-end Weber-Fechner gain control enhances the fidelity of combinatorial odor coding
Kadakia N, Emonet T. Front-end Weber-Fechner gain control enhances the fidelity of combinatorial odor coding. ELife 2019, 8: e45293. PMID: 31251174, PMCID: PMC6609331, DOI: 10.7554/elife.45293.Peer-Reviewed Original Research
2017
Olfactory receptor neurons use gain control and complementary kinetics to encode intermittent odorant stimuli
Gorur-Shandilya S, Demir M, Long J, Clark DA, Emonet T. Olfactory receptor neurons use gain control and complementary kinetics to encode intermittent odorant stimuli. ELife 2017, 6: e27670. PMID: 28653907, PMCID: PMC5524537, DOI: 10.7554/elife.27670.Peer-Reviewed Original ResearchFeedback 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
2013
Cell-Fibronectin Interactions Propel Vertebrate Trunk Elongation via Tissue Mechanics
Dray N, Lawton A, Nandi A, Jülich D, Emonet T, Holley SA. Cell-Fibronectin Interactions Propel Vertebrate Trunk Elongation via Tissue Mechanics. Current Biology 2013, 23: 1335-1341. PMID: 23810535, PMCID: PMC3725194, DOI: 10.1016/j.cub.2013.05.052.Peer-Reviewed Original ResearchConceptsCell migrationTrunk elongationExtracellular matrixCell-FN interactionsTransgenic rescue experimentsECM protein fibronectinElongation defectsParaxial mesodermBody elongationEmbryonic developmentTissue homeostasisTail budTissue mechanicsΑ-subunitRescue experimentsProtein fibronectinSystem-level analysisCell adhesionFN matrixIntegrin α5Concomitant lossTissue integrityCell motionITGαvFibronectinFunctional 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. Functional diversity among sensory receptors in a Drosophila olfactory circuit. Proceedings Of The National Academy Of Sciences Of The United States Of America 2013, 110: e2134-e2143. PMID: 23690583, PMCID: PMC3677458, DOI: 10.1073/pnas.1306976110.Peer-Reviewed Original ResearchConceptsOlfactory receptor neuronsFunctional diversityOdorant receptorsCognate odorantsLarval olfactory systemWeaker behavioral responsesPhysiological responsesDrosophila melanogasterSingle olfactory receptor neuronsStrong behavioral responsesDrosophila olfactory circuitStronger physiological responsesDiverse mechanismsBehavioral responsesOlfactory circuitDiverse temporal dynamicsOdor receptorsReceptor neuronsWeaker physiological responsesOlfactory codingOlfactory systemIntriguing questionDiversityReceptorsTemporal dynamicsIntensity Invariant Dynamics and Odor-Specific Latencies in Olfactory Receptor Neuron Response
Martelli C, Carlson JR, Emonet T. Intensity Invariant Dynamics and Odor-Specific Latencies in Olfactory Receptor Neuron Response. Journal Of Neuroscience 2013, 33: 6285-6297. PMID: 23575828, PMCID: PMC3678969, DOI: 10.1523/jneurosci.0426-12.2013.Peer-Reviewed Original ResearchRegulated 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 ResearchThe 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, Holley SA. The Her7 node modulates the network topology of the zebrafish segmentation clock via sequestration of the Hes6 hub. Development 2012, 139: 940-947. PMID: 22278920, PMCID: PMC3274355, DOI: 10.1242/dev.073544.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBasic Helix-Loop-Helix Transcription FactorsBiological ClocksBody PatterningComputer SimulationDimerizationDNAGene Expression Regulation, DevelopmentalGene Knockdown TechniquesGene Regulatory NetworksRecombinant Fusion ProteinsRepressor ProteinsTranscription FactorsZebrafishZebrafish ProteinsConceptsZebrafish segmentation clockSegmentation clockBinds DNACis-regulatory sequencesDNA-binding heterodimersTranscriptional negative feedbackGenetic experimentsHer7Regulatory sequencesDNA bindingHes6Vivo assaysDNAHomodimerHeterodimersDistinct preferenceEmergent functionsNetwork hubsNegative feedbackComputational analysisClockDimersSequestrationProteinRegulation
2011
Temporal coding of odor mixtures in an olfactory receptor neuron
Su CY, Martelli C, Emonet T, Carlson JR. Temporal coding of odor mixtures in an olfactory receptor neuron. Proceedings Of The National Academy Of Sciences Of The United States Of America 2011, 108: 5075-5080. PMID: 21383179, PMCID: PMC3064350, DOI: 10.1073/pnas.1100369108.Peer-Reviewed Original Research
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 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