Max Planck Institute for Biological Intelligence

Publications of the department "Genes - Circuits - Behavior"

Journal Article (72)

2023

Journal Article

Hahn, J.; Monavarfeshani, A.; Qiao, M.; Kao, A.; Koelsch, Y.; Kumar, A.; Kunze, V. P.; Rasys, A. M.; Richardson, R.; Baier, H. et al.; Lucas, R. J.; Li, W.; Meister, M.; Trachtenberg, J. T.; Yan, W.; Peng, Y.-R.; Sanes, J. R.; Shekhar, K.: Evolution of neuronal cell classes and types in the vertebrate retina. bioRxiv: the preprint server for biology (2023)

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Hellevik, A. M.; Mardoum, P.; Hahn, J.; Koelsch, Y.; D’Orazi, F. D.; Suzuki, S. C.; Godinho, L.; Lawrence, O.; Rieke, F.; Shekhar, K. et al.; Sanes, J. R.; Baier, H.; Baden, T.; Wong, R. O.; Yoshimatsu, T.: Ancient origin of the rod bipolar cell pathway in the vertebrate retina. bioRxiv: the preprint server for biology (2023)

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Jánosi, B.; Liewald, J. F.; Yu, S.-c.; Umbach, S.; Alcantara, I. C.; Bergs, A. C. F.; Schneider, M.; Shao, J.; Gottschalk, A.: RIM and RIM-binding protein localize synaptic CaV2 channels to differentially regulate transmission in neuronal circuits. bioRxiv: the preprint server for biology (2023)

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Shainer, I.; Kuehn, E.; Laurell, E.; Al Kassar, M.; Mokayes, N.; Sherman, S.; Larsch, J.; Kunst, M.; Baier, H.: A single-cell resolution gene expression atlas of the larval zebrafish brain. Science Advances 9 (8), eade9909 (2023)

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Shainer, R.; Kram, V.; Kilts, T. M.; Li, L.; Doyle, A. D.; Shainer, I.; Martin, D.; Simon, C. G. J.; Zeng-Brouwers, J.; Schaefer, L. et al.; Young, M. F.: Biglycan regulates bone development and regeneration. Frontiers in Physiology 14, 1119368 (2023)

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Sherman, S.; Arnold-Ammer, I.; Schneider, M.; Kawakami, K.; Baier, H.: Retina-derived signals control pace of neurogenesis in visual brain areas but not circuit assembly. Nature Communications 14, 6020 (2023)

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van der Plas, T. L.; Tubiana, J.; Le Goc, G.; Migault, G.; Kunst, M.; Baier, H.; Bormuth, V.; Englitz, B.; Debrégeas, G.: Neural assemblies uncovered by generative modeling explain whole-brain activity statistics and reflect structural connectivity. eLife 12, e83139 (2023)

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van der Westhuizen, C.; Botha, T. L.; Finger-Baier, K.; de Brouwer, G.; Wolmarans, D. W.: Contingency learning in zebrafish exposed to apomorphine- and levetiracetam. Behavioural Pharmacology 34 (7), pp. 424 - 436 (2023)

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2022

Journal Article

Bruckner, J. J.; Stednitz, S. J.; Grice, M. Z.; Zaidan, D.; Massaquoi, M. S.; Larsch, J.; Tallafuss, A.; Guillemin, K.; Washbourne, P.; Eisen, J. S.: The microbiota promotes social behavior by modulating microglial remodeling of forebrain neurons. PLoS Biology 20 (11), e3001838 (2022)

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Kappel, J. M.; Förster, D.; Slangewal, K.; Shainer, I.; Svara, F. N.; Donovan, J.; Sherman, S.; Januszewski, M.; Baier, H.; Larsch, J.: Visual recognition of social signals by a tectothalamic neural circuit. Nature 608 (7921), pp. 146 - 152 (2022)

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Svara, F. N.; Förster, D.; Kubo, F.; Januszewski, M.; Dal Maschio, M.; Schubert, P. J.; Kornfeld, J.; Wanner, A. A.; Laurell, E.; Denk, W. et al.; Baier, H.: Automated synapse-level reconstruction of neural circuits in the larval zebrafish brain. Nature Methods 19 (11), pp. 1357 - 1366 (2022)

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Tallafuss, A.; Stednitz, S. J.; Voeun, M.; Levichev, A.; Larsch, J.; Eisen, J.; Washbourne, P.: Egr1 is necessary for forebrain dopaminergic signaling during social behavior. eNeuro 9 (2), ENEURO.0035-22.2022 (2022)

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Vettkötter, D.; Schneider, M.; Goulden, B. D.; Dill, H.; Liewald, J.; Zeiler, S.; Guldan, J.; Ateş, Y. A.; Watanabe, S.; Gottschalk, A.: Rapid and reversible optogenetic silencing of synaptic transmission by clustering of synaptic vesicles. Nature Communications 13, 7827 (2022)

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von Bernhardi, J. E.; Biechl, D.; Miek, L.; Herget, U.; Ryu, S.; Wullimann, M. F.: A versatile transcription factor: Multiple roles of orthopedia a (otpa) beyond its restricted localization in dopaminergic systems of developing and adult zebrafish (Danio rerio) brains. The Journal of Comparative Neurology 530 (14), pp. 2537 - 2561 (2022)

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2021

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Barker, A. J.; Helmbrecht, T. O.; Grob, A. A.; Baier, H.: Functional, molecular and morphological heterogeneity of superficial interneurons in the larval zebrafish tectum. The Journal of Comparative Neurology 529 (9), pp. 2159 - 2175 (2021)

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Benito-Gutierrez, E.; Gattoni, G.; Stemmer, M.; Rohr, S. D.; Schuhmacher, L. N.; Tang, J.; Marconi, A.; Jekely, G.; Arendt, D.: The dorsoanterior brain of adult amphioxus shares similarities in expression profile and neuronal composition with the vertebrate telencephalon. BMC Biology 19 (1), 110 (2021)

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Fernandes, A. M.; Mearns, D. S.; Donovan, J. C.; Larsch, J.; Helmbrecht, T. O.; Koelsch, Y.; Laurell, E.; Kawakami, K.; Dal Maschio, M.; Baier, H.: Neural circuitry for stimulus selection in the zebrafish visual system. Neuron 109 (5), pp. 805 - 822.e6 (2021)

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Fontinha, B. M.; Zekoll, T.; Al-Rawi, M.; Gallach, M.; Reithofer, F.; Barker, A. J.; Hofbauer, M.; Fischer, R. M.; von Haeseler, A.; Baier, H. et al.; Tessmar-Raible, K.: TMT-Opsins differentially modulate medaka brain function in a context-dependent manner. PLoS Biology 19 (1), p. 31 (2021)

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Koelsch, Y.; Hahn, J.; Sappington, A.; Stemmer, M.; Fernandes, A. M.; Helmbrecht, T. O.; Lele, S.; Butrus, S.; Laurell, E.; Arnold-Ammer, I. et al.; Shekhar, K.; Sanes, J. R.; Baier, H.: Molecular classification of zebrafish retinal ganglion cells links genes to cell types to behavior. Neuron 109 (4), pp. 645 - 662.e9 (2021)

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Robles, E.; Fields, N. P.; Baier, H.: The zebrafish visual system transmits dimming information via multiple segregated pathways. The Journal of Comparative Neurology 529 (3), pp. 539 - 552 (2021)

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Shainer, I.; Stemmer, M.: Choice of pre-processing pipeline influences clustering quality of scRNA-seq datasets. BMC Genomics 22 (1), 661 (2021)

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2020

Journal Article

Antinucci, P.; Dumitrescu, A.; Deleuze, C.; Morley, H. J.; Leung, K.; Hagley, T.; Kubo, F.; Baier, H.; Bianco, I. H.; Wyart, C.: A calibrated optogenetic toolbox of stable zebrafish opsin lines. eLife 9, e54937 (2020)

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publisher-version

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DeMarco, E.; Xu, N.; Baier, H.; Robles, E.: Neuron types in the zebrafish optic tectum labeled by an id2b transgene. The Journal of Comparative Neurology 528 (7), pp. 1173 - 1188 (2020)

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Förster, D.; Helmbrecht, T. O.; Mearns, D. S.; Jordan, L.; Mokayes, N.; Baier, H.: Retinotectal circuitry of larval zebrafish is adapted to detection and pursuit of prey. eLife 9, e58596 (2020)

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supplementary-material

Journal Article

Lempka, S. F.; Capogrosso, M.; Han, X.; Baier, H.; Waddell, S.; Chiel, H. J.; Ganguly, K.: What is the key conceptual or methodological bottleneck to controlling neural biology? Cell Systems 10 (6), pp. 461 - 462 (2020)

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Mearns, D. S.; Donovan, J. C.; Fernandes, A. M.; Semmelhack, J. L.; Baier, H.: Deconstructing hunting behavior reveals a tightly coupled stimulus-response loop. Current Biology 30 (1), pp. 54 - 69.e9 (2020)

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Pantoja, C.; Larsch, J.; Laurell, E.; Marquart, G.; Kunst, M.; Baier, H.: Rapid effects of selection on brain-wide activity and behavior. Current Biology 30 (18), pp. 3647 - 3656.e3 (2020)

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van Staden, C.; de Brouwer, G.; Botha, T. L.; Finger-Baier, K.; Brand, S. J.; Wolmarans, D.: Dopaminergic and serotonergic modulation of social reward appraisal in zebrafish (Danio rerio) under circumstances of motivational conflict: Towards a screening test for anti-compulsive drug action. Behavioural Brain Research 379, 112393 (2020)

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Wu, Y.; Dal Maschio, M.; Kubo, F.; Baier, H.: An optical illusion pinpoints an essential circuit node for global motion processing. Neuron 108 (4), pp. 722 - 734.e5 (2020)

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2019

Journal Article

Kramer, A.; Wu, Y.; Baier, H.; Kubo, F.: Neuronal architecture of a visual center that processes optic flow. Neuron 103 (1), pp. 118 - 132.e7 (2019)

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supplementary-material

Journal Article

Kunst, M.; Laurell, E.; Mokayes, N.; Kramer, A.; Kubo, F.; Fernandes, A. M.; Förster, D.; Dal Maschio, M.; Baier, H.: A cellular-resolution atlas of the larval zebrafish brain. Neuron 103 (1), pp. 21 - 38.e5 (2019)

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Larsch, J.; Pantoja, C.: Learning: Complexities of habituation in escaping zebrafish larvae. Current Biology 29 (8), pp. R292 - R294 (2019)

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Marquart, G. D.; Tabor, K. M.; Bergeron, S. A.; Briggman, K. L.; Burgess, H. A.: Prepontine non-giant neurons drive flexible escape behavior in zebrafish. PLoS Biology 17 (10), e3000480 (2019)

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Shainer, I.; Michel, M.; Marquart, G. D.; Bhandiwad, A. A.; Zmora, N.; Livne, Z. B.-M.; Zohar, Y.; Hazak, A.; Mazon, Y.; Förster, D. et al.; Hollander-Cohen, L.; Cone, R. D.; Burgess, H. A.; Gothilf, Y.: Agouti-related protein 2 is a new player in the teleost stress response system. Current Biology 29 (12), pp. 2009 - 2019.e7 (2019)

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Yashina, K.; Tejero-Cantero, A.; Herz, A.; Baier, H.: Zebrafish exploit visual cues and geometric relationships to form a spatial memory. iScience 19, pp. 119 - 134 (2019)

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2018

Journal Article

Bernal Sierra, Y. A.; Rost, B. R.; Pofahl, M.; Fernandes, A. M.; Kopton, R. A.; Moser, S.; Holtkamp, D.; Masala, N.; Beed, P.; Tukker, J. J. et al.; Oldani, S.; Boenigk, W.; Kohl, P.; Baier, H.; Schneider-Warme, F.; Hegemann, P.; Beck, H.; Seifert, R.; Schmitz, D.: Potassium channel-based optogenetic silencing. Nature Communications 9, 4611 (2018)

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Journal Article

Förster, D.; Kramer, A.; Baier, H.; Kubo, F.: Optogenetic precision toolkit to reveal form, function and connectivity of single neurons. Methods 150, pp. 42 - 48 (2018)

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Haehnel-Taguchi, M.; Fernandes, A. M.; Boehler, M.; Schmitt, I.; Tittel, L.; Driever, W.: Projections of the diencephalospinal dopaminergic system to peripheral sense organs in larval zebrafish (Danio rerio). Frontiers in Neuroanatomy 12, 20 (2018)

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Helmbrecht, T. O.; Dal Maschio, M.; Donovan, J. C.; Koutsouli, S.; Baier, H.: Topography of a visuomotor transformation. Neuron 100 (6), pp. 1429 - 1445.e4 (2018)

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Larsch, J.; Baier, H.: Biological motion as an innate perceptual mechanism driving social affiliation. Current Biology 28 (22), pp. 3523 - 3532.e4 (2018)

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Nelson, J. O.; Förster, D.; Frizzell, K. A.; Luschnig, S.; Metzstein, M. M.: Multiple nonsense-mediated mRNA processes require Smg5 in Drosophila. Genetics 209 (4), pp. 1073 - 1084 (2018)

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Sparks, D. W.; Proulx, E.; Lambe, E. K.: Ready, set, go: The bridging of attention to action by acetylcholine in prefrontal cortex. Journal of Physiology-London 596 (9), pp. 1539 - 1540 (2018)

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2017

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Dal Maschio, M.; Donovan, J. C.; Helmbrecht, T. O.; Baier, H.: Linking neurons to network function and behavior by two-photon holographic optogenetics and volumetric imaging. Neuron 94 (4), pp. 774 - 789 (2017)

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Förster, D.; Arnold-Ammer, I.; Laurell, E.; Barker, A. J.; Fernandes, A. M.; Finger-Baier, K.; Filosa, A.; Helmbrecht, T. O.; Koelsch, Y.; Kuehn, E. et al.; Robles, E.; Slanchev, K.; Thiele, T. R.; Baier, H.; Kubo, F.: Genetic targeting and anatomical registration of neuronal populations in the zebrafish brain with a new set of BAC transgenic tools. Scientific Reports 7, 5230 (2017)

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Journal Article

Förster, D.; Dal Maschio, M.; Laurell, E.; Baier, H.: An optogenetic toolbox for unbiased discovery of functionally connected cells in neural circuits. Nature Communications 8, 116 (2017)

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Freifeld, L.; Odstrcil, I.; Förster, D.; Ramirez, A.; Gagnon, J. A.; Randlett, O.; Costa, E. K.; Asano, S.; Celiker, O. T.; Gao, R. et al.; Martin-Alarcon, D. A.; Reginato, P.; Dick, C.; Chen, L.; Schoppik, D.; Engert, F.; Baier, H.; Boyden, E. S.: Expansion microscopy of zebrafish for neuroscience and developmental biology studies. Proceedings of the National Academy of Sciences of the United States of America 114 (50), pp. E10799 - E10808 (2017)

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Kuechlin, S.; Schoels, M.; Slanchev, K.; Lassmann, S.; Walz, G.; Yakulov, T. A.: EpCAM controls morphogenetic programs during zebrafish pronephros development. Biochemical and Biophysical Research Communications 487 (2), pp. 209 - 215 (2017)

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Li, J.; Terry, E. E.; Fejer, E.; Gamba, D.; Hartmann, N.; Logsdon, J.; Michalski, D.; Rois, L. E.; Scuderi, M. J.; Kunst, M. et al.; Hughes, M. E.: Achilles is a circadian clock-controlled gene that regulates immune function in Drosophila. Brain, Behavior, and Immunity 61, pp. 127 - 136 (2017)

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Rahi, S. J.; Larsch, J.; Pecani, K.; Katsov, A. Y.; Mansouri, N.; Tsaneva-Atanasova, K.; Sontag, E. D.; Cross, F. R.: Oscillatory stimuli differentiate adapting circuit topologies. Nature Methods 14 (10), pp. 1010 - 1016 (2017)

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Trads, J. B.; Burgstaller, J.; Laprell, L.; Konrad, D. B.; de la Osa de la Rosa, L.; Weaver, C. D.; Baier, H.; Trauner, D.; Barber, D. M.: Optical control of GIRK channels using visible light. Organic & Biomolecular Chemistry 15 (1), pp. 76 - 81 (2017)

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