Recent Publications by QBio Faculty

2022

Barrasso K., Chac D., Debela M.D., Geigel C., Steenhaut A., Rivera Seda A., Dunmire C.N., Harris J.B., LaRocque R.C., Midani F.S., Qadri F., Yan J., Weil A.A., Ng W.-L. (2022). Impact of a human gut microbe on Vibrio cholerae host colonization through biofilm enhancement. ELife, 11, e73010.

Gonzalez-Suarez, A. D., Zavatone-Veth, J. A., Chen, J., Matulis, C. A., Badwan, B. A., and Clark, D. A. (2022). Excitatory and inhibitory neural dynamics jointly tune motion detection. Accepted, Current Biology.

Henzel T., Nijjer J., Senthilnathan C., Wahdat H., Crosby A.J., Yan J., Cohen T. (2022). Interfacial cavitation. Under review.

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

Kadakia, N., Demir, M., Michaelis, B. T., Reidenbach, M. A., DeAngelis, B. D., Clark, D. A.*, Emonet T.* (2022). Odor motion sensing enables complex plume navigation. Accepted, Nature. (* co-corresponding authors)

Li J., Kothari M., Senthilnathan C., Henzel T., Zhang Q., Li X., Yan J., Cohen T. (2022). Nonlinear inclusion theory with application to the growth and morphogenesis of a confined body. Journal of the Mechanics and Physics of Solids, 159, 104709.

Marris J.C., Collins M.S., Huang P., Schramm C.M., Nero T., Yan J., Murray T.S. (2022). Bacterial surface detachment during nebulization with contaminated reusable home nebulizers. Microbiology Spectrum, 10, e02535-21.

Mattingly H. & Emonet T. (2022). Collective behavior and non-genetic inheritance allow bacterial populations to adapt to changing environments . Proceedings of the National Academy of Sciences, 119(26), e2117377119.

Tai J.-S. B., Mukherjee S., Nero T., Olson R., Tithof J., Nadell C.D., Yan J. (2022 Social evolution of shared biofilm matrix components. Proceedings of the National Academy of Sciences, 119, e2123469119. Highlighted by Burroughs Welcome Fund and Yale News.

Tanaka, R. & Clark, D. A. (2022). Identifying inputs to visual projection neurons in Drosophila lobula by analyzing connectomic data. ENeuro 9(2).

Tanaka, R. & Clark, D. A. (2022). Neural mechanisms to exploit positional geometry for collision avoidance. Current Biology 32(11): 2357-2374.

Zhang Q., Nguyen D., Tai J.-S. B., Xu X., Nijjer J., Huang X., Li Y., Yan J. (2022). Mechanical resilience of biofilms toward environmental perturbations mediated by extracellular matrix. Advanced Functional Materials, 32, 2110699.

Zhou B., Li Z., Kim, S. S. Y., Lafferty J., Clark D. A. (2022). Shallow neural networks trained to detect collisions recover features of visual loom-selective neurons. ELife, 11, e72076.

2021

Jiang Z., Nero T., Mukherjee S., Olson S., Yan J. (2021). Searching for the secret of stickiness: How biofilms adhere to surfaces. Frontiers in Microbiology, 12, 686793 (Invited review).

Lin C.K., Lee D.S.W., McKeithen-Mead S., Emonet T., Kazmierczak B. (2021). A primed subpopulation of bacteria enables rapid expression of the type 3 secretion system in Pseudomonas aeruginosa. MBio 12(3), e00831-21.

Liu W., Feke A., Leung C. C., Tarte D., Yuan W., Vanderwall M., Sager G. C., Wu X., Schear A., Clark D. A., Thines B.C., Gendron J. G. (2021). A metabolic daylength measurement system mediates winter photoperiodism in plants. Developmental Cell, 56(17), 2501-2515.

Mano, O., Creamer, M. S., Badwan, B. A., Clark, D. A. (2021). Predicting individual neuron responses with anatomically constrained task optimization. Current Biology 31(18), 4062-4075.

Mattingly H.H.*, Kamino K.*, Machta B.B.#, Emonet T#. (2021). Behavioral variability and phenotypic variability in bacterial chemotaxis. Nature Physics, 17, 1426–1431. (*contributed equally, # co-corresponding authors)

Moore J.P., Kamino K., Emonet T. (2021). Non-genetic diversity in chemosensing and chemotactic behavior. International Journal of Molecular Sciences, 22(13), 6960.

Nijjer J., Li C., Zhang Q., Lu H., Zhang S., Yan J. (2021). Mechanical forces drive a reorientation cascade leading to biofilm self-patterning. Nature Communications, 12(1), 1-9. Highlighted by Nature Communications Editor.

Zhang Q., Li J., Nijjer J., Lu H, Kothari M., Alert R., Cohen T., Yan J. (2021). Morphogenesis and cell ordering in confined bacterial biofilms. Proceedings of the National Academy of Sciences, 118(31), e2107107118.

2020

Agrochao, M.*, Tanaka, R.*, Salazar-Gatzimas, E., Clark, D. A. (2020). Mechanism for analogous illusory motion perception in flies and humans. Proceedings of the National Academy of Sciences, 117(37), 23044-23053. (* contributed equally)

DeAngelis, B. D.*, Zavatone-Veth, J. A.*, Gonzalez-Suarez A. D., Clark, D. A. (2020). Spatiotemporally precise optogenetic activation of sensory neurons in freely walking Drosophila. ELife, 9, e54183. (*contributed equally)

Demir M.*, Kadakia N.*, Anderson H.D., Clark D.A., Emonet T. (2020) Walking Drosophila navigate complex plumes using stochastic decisions biased by the timing of odor encounters. ELife, 9, e57524. (*contributed equally)

Kamino K., Keegstra J.M., Long J., Emonet T.*, Shimizu T.S.* (2020). Adaptive tuning of cell sensory diversity without changes in gene expression. Science Advances 6(46), eabc1087. (*corresponding authors)

Matulis, C. A., Chen, J., Gonzalez-Saurez, A. D., Behnia, R., Clark, D. A. (2020). Heterogeneous temporal contrast adaptation in Drosophila direction-selective circuits. Current Biology 30(2), 222-236.

Shook B. A., Wasko R. R., Mano O., Rutenberg-Schoenberg M., Rudolph M. C., Zirak B. Rivera-Gonzalez G. C., López-Giráldez F., Zarini, S., Rezza A., Clark D. A., Rendl M., Rosenblum M. D., Gerstein M. B., Horsley V. (2020). Dermal adipocyte lipolysis and myofibroblast conversion are required for efficient skin repair. Cell Stem Cell 26(6), 880-895.

Tanaka, R. & Clark, D. A. (2020). Object displacement-sensitive visual neurons drive freezing in Drosophila. Current Biology 30(13), 2532-2550.

Zavatone-Veth, J. A., Badwan, B. A., Clark, D. A. (2020). A minimal synaptic model for direction selective neurons in Drosophila. Journal of Vision, 22(2), 1-22.

2019

Badwan, B. A., Creamer, M. S., Zavatone-Veth, J. A., Clark, D. A. (2019). Dynamic nonlinearities enable direction-opponency in Drosophila elementary motion detectors. Nature Neuroscience 22(8), 1318-1326.

Chen, J., Mandel, H. M., Fitzgerald, J. E.*, Clark, D. A.* (2019). Asymmetric ON-OFF processing of visual motion cancels variability induced by the structure of natural scenes. ELife, 8, e47579. (* corresponding authors)

Creamer, M. S., Mano, O., Tanaka, R., Clark, D. A. (2019). A flexible geometry for panoramic visual and optogenetic stimulation during behavior and physiology. Journal of Neuroscience Methods, 323, 48-55.

Das D., Jülich D., Schwendinger-Schreck J., Guillon E., Lawton A.K., Dray N., Emonet T., O’Hern C.S., Shattuck M.D., Holley S.A. (2019). Organization of Embryonic Morphogenesis via mechanical information. Developmental Cell, 49(6), 829-839.

DeAngelis, B. D.*, Zavatone-Veth, J. A.*, Clark, D. A. (2019). The manifold structure of limb coordination in walking Drosophila. ELife, 8, e46409. (* contributed equally)

Gorur-Shandilya S., Martelli C., Demir M., Emonet T. (2019). Controlling and measuring dynamic odorant stimuli in the laboratory. Journal of Experimental Biology, 222(23), jeb207787.

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

Mano, O., Creamer, M. S., Matulis, C. A., Salazar-Gatzimas, E., Chen, J., Zavatone-Veth, J. A., Clark, D. A. (2019). Using slow frame rate imaging to extract fast receptive fields. Nature Communications, 10, 1-13.

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

Schniederberend M., Johnston J.F., Shine E., Shen C., Jain R., Emonet T., Kazmierczak B.I. (2019). Modulation of flagellar rotation in surface-attached bacteria: a circuit for rapid surface-sensing. PLoS Pathogens, 15(11), e1008149.

2018

Astigarraga, S., Douthit, J., Tarnogorska, D., Creamer, M. S., Mano, O., Clark, D. A., Meinertzhagen, I., Treisman, J. E. (2018). Drosophila Sidekick is required in developing photoreceptors to enable visual motion detection. Development, 145(3), dev158246.

Creamer, M. S., Mano, M., Clark, D. A. (2018). Visual control of walking speed in Drosophila. Neuron, 100(6), 1460-1473.

Fu X.*, Kato S.*, Long J., Mattingly H.H., He C., Vural D.C., Zucker S.W., Emonet T. (2018). Spatial self-organization resolves conflicts between individuality and collective migration. Nature Communications 9(1), 1-12. (*contributed equally)

Salazar-Gatzimas, E., Agrochao, M., Fitzgerald, J. E., Clark, D. A. (2018). The neuronal basis of an illusory motion percept is explained by decorrelation of parallel motion pathways. Current Biology, 28(23), 3748-3762.

Shook, B. A., Wasko, R. R., Rivera-Gonzalez, G. C., Salazar-Gatzimas, E., López-Giráldez, F., Dash, B. C., Munoz-Rojas, A. R., Aultman, K. D., Zwick, R. K., Lei, V., Arbiser, J. L., Miller-Jensen, K., Clark, D. A., Hsia, H. C., Horsley, V. (2018). Myofibroblast proliferation and heterogeneity are supported by macrophages during skin repair. Science 362(6417), eaar2971.

Waite A.J., Frankel N.W., Emonet T. (2018). Behavioral variability and phenotypic variability in bacterial chemotaxis. Annual Review of Biophysics 47, 595.

2017

Das D., Chatti D., Emonet T.*, Holley S.A.* (2017). Patterned disordered cell motion ensures vertebral column symmetry. Developmental Cell, 42(2), 170-180. (*corresponding authors)

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

Keegstra J.M., Kamino K., Anquez F., Lazova M.D., Emonet T., Shimizu T.S. (2017). Phenotypic diversity and temporal variability in a bacterial signaling network revealed by single-cell FRET. ELife, 6, e27455.

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

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