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Manuel Zimmer

One of the prime goals pursued by current neuroscientists is to gain a comprehensive understanding of how networks of neurons operate as a single brain to produce sensations, thoughts, and behaviour. This is a challenging endeavour because of the sheer complexity of mammalian nervous systems. To address this problem, we study at our lab the nematode C. elegans which is equipped with a simple and anatomically well-defined nervous system of just 302 neurons. Specifically, we combine worm genetics, quantitative behavioural assays, novel functional imaging techniques, and theoretical modelling to elucidate the neural circuits that control locomotion and chemosensory behaviours.



Fieseler, C., Zimmer, M., Kutz, JN. (2020)

Unsupervised learning of control signals and their encodings in Caenorhabditis elegans whole-brain recordings.

J R Soc Interface. 17(173):20200459
Kaplan, HS., Salazar Thula, O., Khoss, N., Zimmer, M. (2020)

Nested Neuronal Dynamics Orchestrate a Behavioral Hierarchy across Timescales.

Neuron. 105(3):562-576.e9
Kaplan, HS., Zimmer, M. (2020)

Brain-wide representations of ongoing behavior: a universal principle?

Curr Opin Neurobiol. 64:60-69


Uzel, K., Zimmer, M. (2019)

Imaging the Emergence of Behavior.

Cell. 179(2):285-286


Kaplan, HS., Nichols, ALA., Zimmer, M. (2018)

Sensorimotor integration in Caenorhabditis elegans: a reappraisal towards dynamic and distributed computations.

Philos Trans R Soc Lond B Biol Sci. 373(1758)
Kaplan, HS., Zimmer, M. (2018)

Sensorimotor Integration for Decision Making: How the Worm Steers.

Neuron. 97(2):258-260
Rojo Romanos, T., Ng, L., Pocock, R. (2018)

Behavioral Assays to Study Oxygen and Carbon Dioxide Sensing in Caenorhabditis elegans.

Bio Protoc. 8(1)
Rouse, T., Aubry, G., Cho, Y., Zimmer, M., Lu, H. (2018)

A programmable platform for sub-second multichemical dynamic stimulation and neuronal functional imaging in C. elegans.

Lab Chip. 18(3):505-513
Skora, S., Mende, F., Zimmer, M. (2018)

Energy Scarcity Promotes a Brain-wide Sleep State Modulated by Insulin Signaling in C. elegans.

Cell Rep. 22(4):953-966


Jang, H., Levy, S., Flavell, SW., Mende, F., Latham, R., Zimmer, M., Bargmann, CI. (2017)

Dissection of neuronal gap junction circuits that regulate social behavior in Caenorhabditis elegans.

Proc Natl Acad Sci U S A. 114(7):E1263-E1272
Nichols, ALA., Eichler, T., Latham, R., Zimmer, M. (2017)

A global brain state underlies C. elegans sleep behavior.

Science. 356(6344)


Drexel, T., Mahofsky, K., Latham, R., Zimmer, M., Cochella, L. (2016)

Neuron type-specific miRNA represses two broadly expressed genes to modulate an avoidance behavior in C. elegans.

Genes Dev. 30(18):2042-2047
Hums, I., Riedl, J., Mende, F., Kato, S., Kaplan, HS., Latham, R., Sonntag, M., Traunmüller, L., Zimmer, M. (2016)

Regulation of two motor patterns enables the gradual adjustment of locomotion strategy in Caenorhabditis elegans.

Elife. 5
Moreno, E., McGaughran, A., Rödelsperger, C., Zimmer, M., Sommer, RJ. (2016)

Oxygen-induced social behaviours in Pristionchus pacificus have a distinct evolutionary history and genetic regulation from Caenorhabditis elegans.

Proc Biol Sci. 283(1825):20152263
Witham, E., Comunian, C., Ratanpal, H., Skora, S., Zimmer, M., Srinivasan, S. (2016)

C. elegans Body Cavity Neurons Are Homeostatic Sensors that Integrate Fluctuations in Oxygen Availability and Internal Nutrient Reserves.

Cell Rep. 14(7):1641-54


Kato, S., Kaplan, HS., Schrödel, T., Skora, S., Lindsay, TH., Yemini, E., Lockery, S., Zimmer, M. (2015)

Global brain dynamics embed the motor command sequence of Caenorhabditis elegans.

Cell. 163(3):656-69


Prevedel, R., Yoon, YG., Hoffmann, M., Pak, N., Wetzstein, G., Kato, S., Schrödel, T., Raskar, R., Zimmer, M., Boyden, ES., Vaziri, A. (2014)

Simultaneous whole-animal 3D imaging of neuronal activity using light-field microscopy.

Nat Methods. 11(7):727-30
Yapici, N., Zimmer, M., Domingos, AI. (2014)

Cellular and molecular basis of decision-making.

EMBO Rep. 15(10):1023-35


Gramstrup Petersen, J., Rojo Romanos, T., Juozaityte, V., Redo Riveiro, A., Hums, I., Traunmüller, L., Zimmer, M., Pocock, R. (2013)

EGL-13/SoxD specifies distinct O2 and CO2 sensory neuron fates in Caenorhabditis elegans.

PLoS Genet. 9(5):e1003511
Schrödel, T., Prevedel, R., Aumayr, K., Zimmer, M., Vaziri, A. (2013)

Brain-wide 3D imaging of neuronal activity in Caenorhabditis elegans with sculpted light.

Nat Methods. 10(10):1013-20


McGrath, PT., Rockman, MV., Zimmer, M., Jang, H., Macosko, EZ., Kruglyak, L., Bargmann, CI. (2009)

Quantitative mapping of a digenic behavioral trait implicates globin variation in C. elegans sensory behaviors.

Neuron. 61(5):692-9
Zimmer, M., Gray, JM., Pokala, N., Chang, AJ., Karow, DS., Marletta, MA., Hudson, ML., Morton, DB., Chronis, N., Bargmann, CI. (2009)

Neurons detect increases and decreases in oxygen levels using distinct guanylate cyclases.

Neuron. 61(6):865-79


Essmann, CL., Martinez, E., Geiger, JC., Zimmer, M., Traut, MH., Stein, V., Klein, R., Acker-Palmer, A. (2008)

Serine phosphorylation of ephrinB2 regulates trafficking of synaptic AMPA receptors.

Nat Neurosci. 11(9):1035-43


Chronis, N., Zimmer, M., Bargmann, CI. (2007)

Microfluidics for in vivo imaging of neuronal and behavioral activity in Caenorhabditis elegans.

Nat Methods. 4(9):727-31


Zimmer, M., Palmer, A., Köhler, J., Klein, R. (2003)

EphB-ephrinB bi-directional endocytosis terminates adhesion allowing contact mediated repulsion.

Nat Cell Biol. 5(10):869-78


Palmer, A., Zimmer, M., Erdmann, KS., Eulenburg, V., Porthin, A., Heumann, R., Deutsch, U., Klein, R. (2002)

EphrinB phosphorylation and reverse signaling: regulation by Src kinases and PTP-BL phosphatase.

Mol Cell. 9(4):725-37


Kullander, K., Croll, SD., Zimmer, M., Pan, L., McClain, J., Hughes, V., Zabski, S., DeChiara, TM., Klein, R., Yancopoulos, GD., Gale, NW. (2001)

Ephrin-B3 is the midline barrier that prevents corticospinal tract axons from recrossing, allowing for unilateral motor control.

Genes Dev. 15(7):877-88


Watty, A., Neubauer, G., Dreger, M., Zimmer, M., Wilm, M., Burden, SJ. (2000)

The in vitro and in vivo phosphotyrosine map of activated MuSK.

Proc Natl Acad Sci U S A. 97(9):4585-90