Publications

2026

Journal Article

Grätsch, S.; Dorigo, A.; Agarwal, V.; Parker, A. V.; Stemmer, M.; Hernandez Murcia, I.; Adel, A.; Jordan, A.; Baier, H.: Cognitive ethology of nest building in a shell-dwelling cichlid. bioRxiv: the preprint server for biology (2026)

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Journal Article

Slangewal, K.; Aimon, S.; Capelle, M. Q.; Kämpf, F.; Naumann, H.; Baier, H.; Slanchev, K.; Bahl, A.: Parallel and convergent pathways for multifeature visual processing in larval zebrafish sensorimotor decision-making. bioRxiv: the preprint server for biology (2026)

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2025

Journal Article

Bakker, S.; ten Donkelaar, H. J.; Voogd, J.; Nicholson, C.; Bannister, L. H.; Medina, L.; Desfilis, E.; Wullimann, M. F.; Meek, J.; Puelles, L. et al.; Broere, C. A. J.; Turner, R.; Cerliani, L.; Glasser, M. F.: Rudolf Nieuwenhuys (11 June 1927 – 4 November 2024): A scholarly life. Brain Structure & Function 230 (6), 90 (2025)

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Journal Article

Kawashima, T.; Wei, Z.; Haruvi, R.; Shainer, I.; Narayan, S.; Baier, H.; Ahrens, M. B.: Voltage imaging reveals circuit computations in the raphe underlying serotonin-mediated motor vigor learning. Neuron 113 (16), pp. 2692 - 2707 (2025)

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Journal Article

Mearns, D. S.; Hunt, S. A.; Schneider, M. W.; Parker, A. V.; Stemmer, M.; Baier, H.: Diverse prey capture strategies in teleost larvae. eLife 13, RP98347 (2025)

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Journal Article

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 (2025)

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Journal Article

Shainer, I.; Kappel, J. M.; Laurell, E.; Donovan, J.; Schneider, M. W.; 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

Slanchev, K.; Laurell, E.; Arnold-Ammer, I.; Kuehn, E.; Pandiarajan, U.; Baier, H.: Molecular delineation of a retina-dependent photoneuroendocrine pathway in zebrafish. Current Biology 35 (23), pp. 5890 - 5896 (2025)

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Journal Article

Spreen, A.; Sadanandan, N. P.; Schneider, M. W.; Kuehn, E.; Leemisa, A. N.; Zio, R. D.; Meyer, N.; Busse, W.; Erlinghagen, B.; Adenauer, L. et al.; Opitz, T.; Bönigk, W.; Schiewer, E.; Heer, J.; Schmitz, D.; Vierock, J.; Beck, H.; Hegemann, P.; Baier, H.; Schneider-Warme, F.; Bernal Sierra, Y. A.; Seifert, R.: Optogenetic silencing by combining a rhodopsin cyclase with an engineered cGMP-gated potassium channel. Science Advances 11 (48), eadx1195 (2025)

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Journal Article

van Staden, C.; Finger-Baier, K.; Weinshenker, D.; Botha, T. L.; Brand, L.; Wolmarans, D. W.: The number of conspecific alarm substance donors notably influences the behavioural responses of zebrafish subjected to a traumatic stress procedure. Fish Physiology and Biochemistry 51 (2), 55 (2025)

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Journal Article

van Staden, C.; Weinshenker, D.; Finger-Baier, K.; Botha, T. L.; Brand, L.; de Wolmarans, W.: Posttraumatic anxiety-like behaviour in zebrafish is dose-dependently attenuated by the alpha-2A receptor agonist, guanfacine. Behavioural Pharmacology 36 (1), pp. 47 - 59 (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

Journal Article

Hellevik, A. M.; Mardoum, P.; Hahn, J.; Kölsch, 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. W.; 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

Smith, K.; Pilger, A.; Amorim, M. L. M.; Mircic, S.; Reining, Z.; Ristow, N.; Miller, D.; Leonhardt, A.; Donovan, J.; Meier, M. et al.; Marzullo, T. C.; Serbe-Kamp, E.; Steiner, A. P.; Gage, G. J.: Low-cost classroom and laboratory exercises for investigating both wave and event-related electroencephalogram potentials. Journal of undergraduate neuroscience education: JUNE: A publication of FUN, Faculty for Undergraduate Neuroscience 22 (3), pp. A197 - A206 (2024)

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Journal Article

Sneddon, L. U.; Schroeder, P.; Roque, A.; Finger-Baier, K.; Fleming, A.; Tinman, S.; Collet, B.: Pain management in zebrafish: Report from a FELASA Working Group. Laboratory Animals 58 (3), pp. 261 - 276 (2024)

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Journal Article

Wullimann, M. F.: Good heavens! Finally a landslide analysis of basal ganglia circuitry in teleosts. Cell Reports 43 (3), 113915 (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 (2024)

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2023

Journal Article

Hahn, J.; Monavarfeshani, A.; Qiao, M.; Kao, A.; Kölsch, 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

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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Journal Article

Sherman, S.; Arnold-Ammer, I.; Schneider, M. W.; 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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Journal Article

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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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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Journal Article

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), 0035-22.2022 (2022)

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Journal Article

Vettkötter, D.; Schneider, M. W.; 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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Journal Article

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

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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Full

Journal Article

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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Journal Article

Fernandes, A. M.; Mearns, D. S.; Donovan, J. C.; Larsch, J.; Helmbrecht, T. O.; Kölsch, 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), e3001012 (2021)

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Journal Article

Kölsch, 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 (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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Journal Article

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

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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publisher-version

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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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 (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

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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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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publisher-version

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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publisher-version

Journal Article

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

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Journal Article

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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publisher-version

Publications of the department "Genes - Circuits - Behavior"

Journal Article (89)