Publications of Herwig Baier

Journal Article

Mearns, D. S.; Hunt, S. A.; Schneider, M.; Parker, A. V.; Stemmer, M.; Baier, H.: Diverse prey capture strategies in teleost larvae. bioRxiv: the preprint server for biology (2025)

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Parker, A. V.; Stemmer, M.; Grätsch, S.; Dorigo, A.; Rodriguez Ramirez, O.; Adel, A.; Jordan, L. A.; Baier, H.: Intrinsic timing of brood care in shell-dwelling cichlids. Current Biology 35 (3), pp. 672 - 680.e4 (2025)

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Journal Article

Shainer, I.; Kappel, J. M.; Laurell, E.; Donovan, J.; Schneider, M.; Kuehn, E.; Arnold-Ammer, I.; Stemmer, M.; Larsch, J.; Baier, H.: Transcriptomic neuron types vary topographically in function and morphology. Nature 638 (8052), pp. 1023 - 1033 (2025)

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Journal Article

Wang, Q.; Baier, H.: Eat, flee, freeze: Division of labor in the larval zebrafish visuomotor system. Proceedings of the National Academy of Sciences of the United States of America 122 (19), e2506018122 (2025)

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2024

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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. Nature Ecology & Evolution 8 (6), pp. 1165 - 1179 (2024)

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Journal Article

Huppertz, M.-C.; Wilhelm, J.; Grenier, V.; Schneider, M.; Falt, T.; Porzberg, N.; Hausmann, D.; Hoffmann, D. C.; Hai, L.; Tarnawski, M. et al.; Pino, G.; Slanchev, K.; Kolb, I.; Acuna, C.; Fenk, L. M.; Baier, H.; Hiblot, J.; Johnsson, K.: Recording physiological history of cells with chemical labeling. Science 383 (6685), pp. 890 - 897 (2024)

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Journal Article

Wullimann, M. F.; Mokayes, N.; Shainer, I.; Kuehn, E.; Baier, H.: Genoarchitectonics of the larval zebrafish diencephalon. The Journal of Comparative Neurology 532 (3), e25549 (2024)

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Journal Article

Zaupa, M.; Nagaraj, N.; Sylenko, A.; Baier, H.; Sawamiphak, S.; Filosa, A.: The Calmodulin-interacting peptide Pcp4a regulates feeding state-dependent behavioral choice in zebrafish. Neuron 112 (7), pp. 1150 - 1164.e6 (2024)

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2023

Journal Article

Hahn, J.; Monavarfeshani, A.; Qiao, M.; Kao, A.; Koelsch, Y.; Kumar, A.; Kunze, V. P.; Rasys, A. M.; Richardson, R.; Wekselblatt, J. B. et al.; Baier, H.; 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. Nature 624 (7991), pp. 415 - 424 (2023)

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Journal Article

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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Journal Article

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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Journal Article

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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2022

Journal Article

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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Journal Article

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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2021

Journal Article

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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Journal Article

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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Journal Article

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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Journal Article

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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Journal Article

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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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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Journal Article

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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Journal Article

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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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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Journal Article

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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Journal Article

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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Journal Article

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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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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Journal Article

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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Journal Article

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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Journal Article

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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2017

Journal Article

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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Journal Article

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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Journal Article

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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Journal Article

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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2016

Journal Article

Barber, D. M.; Schoenberger, M.; Burgstaller, J.; Levitz, J.; Weaver, C. D.; Isacoff, E. Y.; Baier, H.; Trauner, D.: Optical control of neuronal activity using a light-operated GIRK channel opener (LOGO). Chemical Science 7 (3), pp. 2347 - 2352 (2016)

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Journal Article

Filosa, A.; Barker, A. J.; Dal Maschio, M.; Baier, H.: Feeding state modulates behavioral choice and processing of prey stimuli in the zebrafish tectum. Neuron 90 (3), pp. 596 - 608 (2016)

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Journal Article

Hoffman, E. J.; Turner, K. J.; Fernandez, J. M.; Cifuentes, D.; Ghosh, M.; Ijaz, S.; Jain, R. A.; Kubo, F.; Bill, B. R.; Baier, H. et al.; Granato, M.; Barresi, M. J. F.; Wilson, S. W.; Rihel, J.; State, M. W.; Giraldez, A. J.: Estrogens suppress a behavioral phenotype in zebrafish mutants of the autism risk gene, CNTNAP2. Neuron 89 (4), pp. 725 - 733 (2016)

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2015

Journal Article

Auer, T. O.; Xiao, T.; Bercier, V.; Gebhardt, C.; Duroure, K.; Concordet, J.-P.; Wyart, C.; Suster, M.; Kawakami, K.; Wittbrodt, J. et al.; Baier, H.; Del Bene, F.: Deletion of a kinesin I motor unmasks a mechanism of homeostatic branching control by neurotrophin-3. eLife 4, e05061 (2015)

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Journal Article

Barker, A. J.; Baier, H.: Sensorimotor decision making in the zebrafish tectum. Current Biology 25 (21), pp. 2804 - 2814 (2015)

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Journal Article

Temizer, I.; Donovan, J. C.; Baier, H.; Semmelhack, J.: A visual pathway for looming-evoked escape in larval zebrafish. Current Biology 25 (14), pp. 1823 - 1834 (2015)

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2014

Journal Article

Goncalves, P. J.; Arrenberg, A. B.; Hablitzel, B.; Baier, H.; Machens, C. K.: Optogenetic perturbations reveal the dynamics of an oculomotor integrator. Frontiers in Neural Circuits 8, 10 (2014)

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Journal Article

Jia, S.; Muto, A.; Orisme, W.; Henson, H. E.; Parupalli, C.; Ju, B.; Baier, H.; Taylor, M. R.: Zebrafish Cacna1fa is required for cone photoreceptor function and synaptic ribbon formation. Human Molecular Genetics 23 (11), pp. 2981 - 2994 (2014)

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Journal Article

Kubo, F.; Hablitzel, B.; Dal Maschio, M.; Driever, W.; Baier, H.; Arrenberg, A. B.: Functional architecture of an optic flow-responsive area that drives horizontal eye movements in zebrafish. Neuron 81 (6), pp. 1344 - 1359 (2014)

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Journal Article

Robles, E.; Laurell, E.; Baier, H.: The retinal projectome reveals brain-area-specific visual representations generated by ganglion cell diversity. Current Biology 24 (18), pp. 2085 - 2096 (2014)

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Journal Article

Semmelhack, J. L.; Donovan, J. C.; Thiele, T. R.; Kuehn, E.; Laurell, E.; Baier, H.: A dedicated visual pathway for prey detection in larval zebrafish. eLife 3, e04878 (2014)

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