ZFIN Lab: Baier Lab

ZFIN ID: ZDB-LAB-990120-1

Baier Lab

PI/Director:	Baier, Herwig
Co-PI / Senior Researcher:	Wullimann, Mario F.
Contact Person:	Cerny, Annegret
Email:	hbaier@neuro.mpg.de
URL:	http://www.neuro.mpg.de/baier
Address:	Max Planck Institute of Neurobiology Department Genes –- Circuits -– Behavior Am Klopferspitz 18 82152 Martinsried near Munich Germany
Country:	Germany
Phone:	011-49-8578-3200
Fax:	011-49-8578-3240
Line Designation:	mpn

GENOMIC FEATURES ORIGINATING FROM THIS LAB

Show first 50 of 388 genomic features

STATEMENT OF RESEARCH INTERESTS

Our current interests:
• Functional dissection of visual and visuomotor pathways at the cellular and synaptic scale.
• Neural basis of elementary cognitive processes, including decision-making, attention, memory and social affiliation.
• Innovation and refinement of optical, genetic and optogenetic methods.
• Machine learning-supported, kinematic analysis of behavior.
• Linking circuit architectures to behavioral adaptations.
• Development of a multimodal, high-resolution atlas of the zebrafish brain.
• Neuroethology and behavioral genetics of East African cichlids.

LAB MEMBERS

Foerster, Dominique Post-Doc	Grätsch, Swantje Post-Doc	Larsch, Johannes Post-Doc
Marquart, Gregory Post-Doc	Shainer, Inbal Post-Doc	Stemmer, Manuel Post-Doc
Bauer, Lisa Graduate Student	Breitzler, Lukas Graduate Student	Kappel, Johannes Graduate Student
Mearns, Duncan Graduate Student	Parker, Ashley Graduate Student	Schneider, Martin Graduate Student
Sherman, Shachar Graduate Student	Al Kassar, Mariam Research Staff	Donovan, Joseph Research Staff
Finger-Baier, Karin Research Staff	Kühn, Enrico Research Staff	Laurell, Eva Research Staff
Mokayes, Nouwar Research Staff	Robbins, Trace Research Staff	Slanchev, Krasimir Research Staff
Arnold-Ammer, Irene Technical Staff	Cerny, Annegret Administrative Staff

ZEBRAFISH PUBLICATIONS OF LAB MEMBERS

Vettkötter, D., Schneider, M., Goulden, B.D., Dill, H., Liewald, J., Zeiler, S., Guldan, J., Ateş, Y.A., Watanabe, S., Gottschalk, A. (2022) Rapid and reversible optogenetic silencing of synaptic transmission by clustering of synaptic vesicles. Nature communications. 13:78277827

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. (2022) The microbiota promotes social behavior by modulating microglial remodeling of forebrain neurons. PLoS Biology. 20:e3001838

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

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

Wullimann, M.F. (2022) The neuromeric/prosomeric model in teleost fish neurobiology. Brain, behavior and evolution. 97(6):336-360

Eugenin von Bernhardi, J., Biechl, D., Miek, L., Herget, U., Ryu, S., Wullimann, M.F. (2022) 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):2537-2561

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

Gerlach, G., Wullimann, M.F. (2021) Neural pathways of olfactory kin imprinting and kin recognition in zebrafish. Cell and tissue research. 383(1):273-287

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. (2020) Neural circuitry for stimulus selection in the zebrafish visual system. Neuron. 109(5):805-822.e6

Kölsch, Y., Hahn, J., Sappington, A., Stemmer, M., Fernandes, A.M., Helmbrecht, T.O., Lele, S., Butrus, S., Laurell, E., Arnold-Ammer, I., Shekhar, K., Sanes, J.R., Baier, H. (2020) Molecular classification of zebrafish retinal ganglion cells links genes to cell types to behavior. Neuron. 109(4):645-662.e9

Barker, A.J., Helmbrecht, T.O., Grob, A.A., Baier, H. (2020) Functional, molecular and morphological heterogeneity of superficial interneurons in the larval zebrafish tectum. The Journal of comparative neurology. 529(9):2159-2175

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

Wu, Y., Dal Maschio, M., Kubo, F., Baier, H. (2020) An Optical Illusion Pinpoints an Essential Circuit Node for Global Motion Processing. Neuron. 108(4):722-734.e5

Pantoja, C., Larsch, J., Laurell, E., Marquart, G., Kunst, M., Baier, H. (2020) Rapid Effects of Selection on Brain-wide Activity and Behavior. Current biology : CB. 30(18):3647-3656.e3

Robles, E., Fields, N.P., Baier, H. (2020) The zebrafish visual system transmits dimming information via multiple segregated pathways. The Journal of comparative neurology. 529(3):539-552

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

Zuccarini, G., D'Atri, I., Cottone, E., Mackie, K., Shainer, I., Gothilf, Y., Provero, P., Bovolin, P., Merlo, G.R. (2019) Interference with the Cannabinoid Receptor CB1R Results in Miswiring of GnRH3 and AgRP1 Axons in Zebrafish Embryos. International Journal of Molecular Sciences. 21(1):

Mearns, D.S., Donovan, J.C., Fernandes, A.M., Semmelhack, J.L., Baier, H. (2019) Deconstructing Hunting Behavior Reveals a Tightly Coupled Stimulus-Response Loop. Current biology : CB. 30(1):54-69.e9

van Staden, C., de Brouwer, G., Botha, T.L., Finger-Baier, K., Brand, S.J., Wolmarans, D. (2019) 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

Wullimann, M.F., Umeasalugo, K.E. (2019) Sonic hedgehog (shh) expression in zebrafish forebrain identifies the teleostean pallidal signaling center and shows preglomerular complex and posterior tubercular dopamine cells to arise from shh cells. The Journal of comparative neurology. 528(8):1321-1348

DeMarco, E., Xu, N., Baier, H., Robles, E. (2019) Neuron types in the zebrafish optic tectum labeled by an id2b transgene. The Journal of comparative neurology. 528(7):1173-1188

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

Yashina, K., Tejero-Cantero, Á., Herz, A., Baier, H. (2019) Zebrafish Exploit Visual Cues and Geometric Relationships to Form a Spatial Memory. iScience. 19:119-134

Shainer, I., Michel, M., Marquart, G.D., Bhandiwad, A.A., Zmora, N., Ben-Moshe Livne, Z., Zohar, Y., Hazak, A., Mazon, Y., Förster, D., Hollander-Cohen, L., Cone, R.D., Burgess, H.A., Gothilf, Y. (2019) Agouti-Related Protein 2 Is a New Player in the Teleost Stress Response System. Current biology : CB. 29(12):2009-2019.e7

Kunst, M., Laurell, E., Mokayes, N., Kramer, A., Kubo, F., Fernandes, A.M., Förster, D., Dal Maschio, M., Baier, H. (2019) A Cellular-Resolution Atlas of the Larval Zebrafish Brain. Neuron. 103(1):21-38.e5

Kramer, A., Wu, Y., Baier, H., Kubo, F. (2019) Neuronal Architecture of a Visual Center that Processes Optic Flow. Neuron. 103(1):118-132.e7

Larsch, J., Pantoja, C. (2019) Learning: Complexities of Habituation in Escaping Zebrafish Larvae. Current biology : CB. 29:R292-R294

Baeuml, S.W., Biechl, D., Wullimann, M.F. (2019) Adult islet1 Expression Outlines Ventralized Derivatives Along Zebrafish Neuraxis. Frontiers in Neuroanatomy. 13:19

Tabor, K.M., Marquart, G.D., Hurt, C., Smith, T.S., Geoca, A.K., Bhandiwad, A.A., Subedi, A., Sinclair, J.L., Rose, H.M., Polys, N.F., Burgess, H.A. (2019) Brain-wide cellular resolution imaging of Cre transgenic zebrafish lines for functional circuit-mapping. eLIFE. 8

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., Oldani, S., Bönigk, W., Kohl, P., Baier, H., Schneider-Warme, F., Hegemann, P., Beck, H., Seifert, R., Schmitz, D. (2018) Potassium channel-based optogenetic silencing. Nature communications. 9:4611

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

Larsch, J., Baier, H. (2018) Biological Motion as an Innate Perceptual Mechanism Driving Social Affiliation. Current biology : CB. 28(22):3523-3532.e4

Yakulov, T.A., Todkar, A.P., Slanchev, K., Wiegel, J., Bona, A., Groß, M., Scholz, A., Hess, I., Wurditsch, A., Grahammer, F., Huber, T.B., Lecaudey, V., Bork, T., Hochrein, J., Boerries, M., Leenders, J., de Tullio, P., Jouret, F., Kramer-Zucker, A., Walz, G. (2018) CXCL12 and MYC control energy metabolism to support adaptive responses after kidney injury. Nature communications. 9:3660

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

Tabor, K.M., Marquart, G.D., Smith, T.S., Geoca, A.K., Bhandiwad, A.A., Subedi, A., Sinclair, J.L., Burgess, H.A. (2018) Brain-wide cellular resolution imaging of Cre transgenic zebrafish lines for functional circuit-mapping. ZFIN Direct Data Submission.

Gupta, T., Marquart, G.D., Horstick, E.J., Tabor, K.M., Pajevic, S., Burgess, H.A. (2018) Morphometric analysis and neuroanatomical mapping of the zebrafish brain. Methods (San Diego, Calif.). 150:49-62

Heffer, A., Marquart, G.D., Aquilina-Beck, A., Saleem, N., Burgess, H.A., Dawid, I.B. (2017) Generation and characterization of Kctd15 mutations in zebrafish. PLoS One. 12:e0189162

Freifeld, L., Odstrcil, I., Förster, D., Ramirez, A., Gagnon, J.A., Randlett, O., Costa, E.K., Asano, S., Celiker, O.T., Gao, R., Martin-Alarcon, D.A., Reginato, P., Dick, C., Chen, L., Schoppik, D., Engert, F., Baier, H., Boyden, E.S. (2017) 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):E10799-E10808

Köhler, A., Collymore, C., Finger-Baier, K., Geisler, R., Kaufmann, L., Pounder, K.C., Schulte-Merker, S., Valentim, A., Varga, Z.M., Weiss, J., Strähle, U. (2017) Report of Workshop on Euthanasia for Zebrafish-A Matter of Welfare and Science. Zebrafish. 14(6):547-551

Marquart, G.D., Tabor, K.M., Horstick, E.J., Brown, M., Geoca, A.K., Polys, N.F., Nogare, D.D., Burgess, H.A. (2017) High-precision registration between zebrafish brain atlases using symmetric diffeomorphic normalization. GigaScience. 6:1-15

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

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

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

Dal Maschio, M., Donovan, J.C., Helmbrecht, T.O., Baier, H. (2017) Linking Neurons to Network Function and Behavior by Two-Photon Holographic Optogenetics and Volumetric Imaging. Neuron. 94:774-789.e5

Biechl, D., Tietje, K., Ryu, S., Grothe, B., Gerlach, G., Wullimann, M.F. (2017) Identification of accessory olfactory system and medial amygdala in the zebrafish. Scientific Reports. 7:44295

Richardson, R., Metzger, M., Knyphausen, P., Ramezani, T., Slanchev, K., Kraus, C., Schmelzer, E., Hammerschmidt, M. (2016) Re-epithelialization of cutaneous wounds in adult zebrafish uses a combination of mechanisms at play during wound closure in embryonic and adult mammals. Development (Cambridge, England). 143(12):2077-88

Filosa, A., Barker, A.J., Dal Maschio, M., Baier, H. (2016) Feeding State Modulates Behavioral Choice and Processing of Prey Stimuli in the Zebrafish Tectum. Neuron. 90(3):596-608

Biechl, D., Dorigo, A., Köster, R.W., Grothe, B., Wullimann, M.F. (2016) Eppur Si Muove: Evidence for an External Granular Layer and Possibly Transit Amplification in the Teleostean Cerebellum. Frontiers in Neuroanatomy. 10:49

Biechl, D., Tietje, K., Gerlach, G., Wullimann, M.F. (2016) Crypt cells are involved in kin recognition in larval zebrafish. Scientific Reports. 6:24590

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., Granato, M., Barresi, M.J., Wilson, S.W., Rihel, J., State, M.W., Giraldez, A.J. (2016) Estrogens Suppress a Behavioral Phenotype in Zebrafish Mutants of the Autism Risk Gene, CNTNAP2. Neuron. 89(4):725-33

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

Donovan, J. (2016) Exploring behavioral circuits with holographic optogenetics and network imaging.. Ph.D. Thesis.

Marquart, G.D., Tabor, K.M., Brown, M., Strykowski, J.L., Varshney, G.K., LaFave, M.C., Mueller, T., Burgess, S.M., Higashijima, S., Burgess, H.A. (2015) A 3D Searchable Database of Transgenic Zebrafish Gal4 and Cre Lines for Functional Neuroanatomy Studies. Frontiers in neural circuits. 9:78

Barker, A.J., Baier, H. (2015) Sensorimotor Decision Making in the Zebrafish Tectum. Current biology : CB. 25:2804-14

Marquart, G.D., Tabor, K.M., Brown, M., Strykowski, J.L., Varshney, G.K., LaFave, M.C., Mueller, T., Burgess, S.H., Higashijima, S., and Burgess, H.A. (2015) Enhancer Trap Transgenics. ZFIN Direct Data Submission.

Temizer, I., Donovan, J.C., Baier, H., Semmelhack, J.L. (2015) A Visual Pathway for Looming-Evoked Escape in Larval Zebrafish. Current biology : CB. 25(14):1823-34

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

Epting, D., Slanchev, K., Boehlke, C., Hoff, S., Loges, N.T., Yasunaga, T., Indorf, L., Nestel, S., Lienkamp, S.S., Omran, H., Kuehn, E.W., Ronneberger, O., Walz, G., Kramer-Zucker, A. (2015) The Rac1 regulator ELMO controls basal body migration and docking in multiciliated cells through interaction with Ezrin. Development (Cambridge, England). 142:174-84

Semmelhack, J.L., Donovan, J.C., Thiele, T.R., Kuehn, E., Laurell, E., Baier, H. (2014) A dedicated visual pathway for prey detection in larval zebrafish. eLIFE. 4:299-307

Robles, E., Laurell, E., Baier, H. (2014) The Retinal Projectome Reveals Brain-Area-Specific Visual Representations Generated by Ganglion Cell Diversity. Current biology : CB. 24(18):2085-96

Schoetz, U., Deliolanis, N.C., Ng, D., Pauli, J., Resch-Genger, U., Kühn, E., Heuer, S., Beisker, W., Köster, R.W., Zitzelsberger, H., Caldwell, R.B. (2014) Usefulness of a Darwinian System in a Biotechnological Application: Evolution of Optical Window Fluorescent Protein Variants under Selective Pressure. PLoS One. 9:e107069

Thiele, T.R., Donovan, J.C., Baier, H. (2014) Descending Control of Swim Posture by a Midbrain Nucleus in Zebrafish. Neuron. 83(3):679-691

Jia, S., Muto, A., Orisme, W., Henson, H.E., Parupalli, C., Ju, B., Baier, H., and Taylor, M.R. (2014) Zebrafish Cacna1fa is required for cone photoreceptor function and synaptic ribbon formation. Human molecular genetics. 23(11):2981-94

Skugor, A., Slanchev, K., Torgersen, J.S., Tveiten, H., and Andersen, O. (2014) Conserved Mechanisms for Germ Cell-Specific Localization of nanos3 Transcripts in Teleost Species with Aquaculture Significance. Marine biotechnology (New York, N.Y.). 16(3):256-64

Herget, U., Wolf, A., Wullimann, M.F., and Ryu, S. (2014) Molecular neuroanatomy and chemoarchitecture of the neurosecretory preoptic-hypothalamic area in zebrafish larvae. The Journal of comparative neurology. 522(7):1542-64

Kubo, F., Hablitzel, B., Dal Maschio, M., Driever, W., Baier, H., Arrenberg, A.B. (2014) Functional architecture of an optic flow-responsive area that drives horizontal eye movements in zebrafish. Neuron. 81:1344-59

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

Wullimann M.F. (2013) Ancestry of basal ganglia circuits: new evidence in teleosts. The Journal of comparative neurology. 522(9):2013-2018

Muto, A., Taylor, M.R., Suzawa, M., Korenbrot, J.I., and Baier, H. (2013) Glucocorticoid receptor activity regulates light adaptation in the zebrafish retina. Frontiers in neural circuits. 7:145

Kim, Y.H., Epting, D., Slanchev, K., Engel, C., Walz, G., and Kramer-Zucker, A. (2013) A Complex of BBS1 and NPHP7 Is Required for Cilia Motility in Zebrafish. PLoS One. 8(9):e72549

Gebhardt, C., Baier, H., and Bene, F.D. (2013) Direction selectivity in the visual system of the zebrafish larva. Frontiers in neural circuits. 7:111

Richardson, R., Slanchev, K., Kraus, C., Knyphausen, P., Eming, S., and Hammerschmidt, M. (2013) Adult zebrafish as a model system for cutaneous wound healing research. The Journal of investigative dermatology. 133(6):1655-65

Ziv, L., Muto, A., Schoonheim, P.J., Meijsing, S.H., Strasser, D., Ingraham, H.A., Schaaf, M.J., Yamamoto, K.R., and Baier, H. (2013) An affective disorder in zebrafish with mutation of the glucocorticoid receptor. Molecular psychiatry. 18(6):681-91

Barker, A.J., and Baier, H. (2013) SINs and SOMs: neural microcircuits for size tuning in the zebrafish and mouse visual pathway. Frontiers in neural circuits. 7:89

Grisham, R.C., Kindt, K., Finger-Baier, K., Schmid, B., and Nicolson, T. (2013) Mutations in ap1b1 Cause Mistargeting of the Na(+)/K(+)-ATPase Pump in Sensory Hair Cells. PLoS One. 8(4):e60866

Robles, E., Filosa, A., and Baier, H. (2013) Precise lamination of retinal axons generates multiple parallel input pathways in the tectum. The Journal of neuroscience : the official journal of the Society for Neuroscience. 33(11):5027-5039

Kress, S., and Wullimann, M.F. (2012) Correlated basal expression of immediate early gene egr1 and tyrosine hydroxylase in zebrafish brain and downregulation in olfactory bulb after transitory olfactory deprivation. Journal of chemical neuroanatomy. 46(1-2):51-66

Griffiths, B.B., Schoonheim, P.J., Ziv, L., Voelker, L., Baier, H., and Gahtan, E. (2012) A zebrafish model of glucocorticoid resistance shows serotonergic modulation of the stress response. Frontiers in behavioral neuroscience. 6:68

Akerboom, J., Chen, T.W., Wardill, T.J., Tian, L., Marvin, J.S., Mutlu, S., Calderón, N.C., Esposti, F., Borghuis, B.G., Sun, X.R., Gordus, A., Orger, M.B., Portugues, R., Engert, F., Macklin, J.J., Filosa, A., Aggarwal, A., Kerr, R.A., Takagi, R., Kracun, S., Shigetomi, E., Khakh, B.S., Baier, H., Lagnado, L., Wang, S.S., Bargmann, C.I., Kimmel, B.E., Jayaraman, V., Svoboda, K., Kim, D.S., Schreiter, E.R., and Looger, L.L. (2012) Optimization of a GCaMP Calcium Indicator for Neural Activity Imaging. The Journal of neuroscience : the official journal of the Society for Neuroscience. 32(40):13819-13840

Robles, E., and Baier, H. (2012) Assembly of synaptic laminae by axon guidance molecules. Current opinion in neurobiology. 22(5):799-804

Warp, E., Agarwal, G., Wyart, C., Friedmann, D., Oldfield, C.S., Conner, A., Del Bene, F., Arrenberg, A.B., Baier, H., and Isacoff, E.Y. (2012) Emergence of Patterned Activity in the Developing Zebrafish Spinal Cord. Current biology : CB. 22(2):93-102

Miri, A., Daie, K., Arrenberg, A.B., Baier, H., Aksay, E., and Tank, D.W. (2011) Spatial gradients and multidimensional dynamics in a neural integrator circuit. Nature Neuroscience. 14(9):1150-9

Slanchev, K., Pütz, M., Schmitt, A., Kramer-Zucker, A., and Walz, G. (2011) Nephrocystin-4 is required for pronephric duct-dependent cloaca formation in zebrafish. Human molecular genetics. 20(16):3119-28

Xiao, T., Staub, W., Robles, E., Gosse, N.J., Cole, G.J., and Baier, H. (2011) Assembly of Lamina-Specific Neuronal Connections by Slit Bound to Type IV Collagen. Cell. 146(1):164-176

Nevin, L.M., Xiao, T., Staub, W., and Baier, H. (2011) Topoisomerase II{beta} is required for lamina-specific targeting of retinal ganglion cell axons and dendrites. Development (Cambridge, England). 138(12):2457-2465

Wullimann, M.F., Mueller, T., Distel, M., Babaryka, A., Grothe, B., and Köster, R.W. (2011) The long adventurous journey of rhombic lip cells in jawed vertebrates: a comparative developmental analysis. Frontiers in Neuroanatomy. 5:27

Robles, E., Smith, S.J., and Baier, H. (2011) Characterization of genetically targeted neuron types in the zebrafish optic tectum. Frontiers in neural circuits. 5:1

Yamamoto, K., Ruuskanen, J.O., Wullimann, M.F., and Vernier, P. (2011) Differential expression of dopaminergic cell markers in the adult zebrafish forebrain. The Journal of comparative neurology. 519(3):576-598

Arrenberg, A.B., Stainier, D.Y., Baier, H., and Huisken, J. (2010) Optogenetic control of cardiac function. Science (New York, N.Y.). 330(6006):971-974

Del Bene, F., Wyart, C., Robles, E., Tran, A., Looger, L., Scott, E.K., Isacoff, E.Y., and Baier, H. (2010) Filtering of visual information in the tectum by an identified neural circuit. Science (New York, N.Y.). 330(6004):669-673

Nevin, L.M., Robles, E., Baier, H., and Scott, E.K. (2010) Focusing on optic tectum circuitry through the lens of genetics. BMC Biology. 8:126

Volkmann, K., Chen, Y.Y., Harris, M.P., Wullimann, M.F., and Köster, R.W. (2010) The zebrafish cerebellar upper rhombic lip generates tegmental hindbrain nuclei by long-distance migration in an evolutionary conserved manner. The Journal of comparative neurology. 518(14):2794-2817

Neumann-Haefelin, E., Kramer-Zucker, A., Slanchev, K., Hartleben, B., Noutsou, F., Martin, K., Wanner, N., Ritter, A., Gödel, M., Pagel, P., Fu, X., Müller, A., Baumeister, R., Walz, G., and Huber, T.B. (2010) A Model organism approach: Defining the role of Neph proteins as regulators of neuron and kidney morphogenesis. Human molecular genetics. 19(12):2347-2359

Schoonheim, P.J., Arrenberg, A.B., Del Bene, F., and Baier, H. (2010) Optogenetic localization and genetic perturbation of saccade-generating neurons in zebrafish. The Journal of neuroscience : the official journal of the Society for Neuroscience. 30(20):7111-7120

Chao, R., Nevin, L., Agarwal, P., Riemer, J., Bai, X., Delaney, A., Akana, M., JimenezLopez, N., Bardakjian, T., Schneider, A., Chassaing, N., Schorderet, D.F., FitzPatrick, D., Kwok, P.Y., Ellgaard, L., Gould, D.B., Zhang, Y., Malicki, J., Baier, H., and Slavotinek, A. (2010) A male with unilateral microphthalmia reveals a role for TMX3 in eye development. PLoS One. 5(5):e10565

Carney, T.J., Feitosa, N.M., Sonntag, C., Slanchev, K., Kluger, J., Kiyozumi, D., Gebauer, J.M., Coffin Talbot, J., Kimmel, C.B., Sekiguchi, K., Wagener, R., Schwarz, H., Ingham, P.W., and Hammerschmidt, M. (2010) Genetic analysis of fin development in zebrafish identifies furin and hemicentin1 as potential novel Fraser Syndrome disease genes. PLoS Genetics. 6(4):e1000907

Yamamoto, K., Ruuskanen, J.O., Wullimann, M.F., and Vernier, P. (2010) Two tyrosine hydroxylase genes in vertebrates: New dopaminergic territories revealed in the zebrafish brain. Molecular and cellular neurosciences. 43(4):394-402

Osório, J., Mueller, T., Rétaux, S., Vernier, P., and Wullimann, M.F. (2010) Phylotypic expression of the bHLH genes Neurogenin2, Neurod, and Mash1 in the mouse embryonic forebrain. The Journal of comparative neurology. 518(6):851-871

Kühn, E., and Köster, R.W. (2010) Analysis of gene expression by in situ hybridization on adult zebrafish brain sections. CSH protocols. 2010(2):pdb.prot5382

Arrenberg, A.B., Del Bene, F., and Baier, H. (2009) Optical control of zebrafish behavior with halorhodopsin. Proceedings of the National Academy of Sciences of the United States of America. 106(42):17968-17973

Scott, E.K., and Baier, H. (2009) The cellular architecture of the larval zebrafish tectum, as revealed by gal4 enhancer trap lines. Frontiers in neural circuits. 3:13

Baier, H., and Scott, E.K. (2009) Genetic and optical targeting of neural circuits and behavior-zebrafish in the spotlight. Current opinion in neurobiology. 19(5):553-560

Wyart, C., Bene, F.D., Warp, E., Scott, E.K., Trauner, D., Baier, H., and Isacoff, E.Y. (2009) Optogenetic dissection of a behavioural module in the vertebrate spinal cord. Nature. 461(7262):407-410

Distel, M., Wullimann, M.F., and Köster, R.W. (2009) Optimized Gal4 genetics for permanent gene expression mapping in zebrafish. Proceedings of the National Academy of Sciences of the United States of America. 106(32):13365-13370

Seipold, S., Priller, F.C., Goldsmith, P., Harris, W.A., Baier, H., and Abdelilah-Seyfried, S. (2009) Non-SMC condensin I complex proteins control chromosome segregation and survival of proliferating cells in the zebrafish neural retina. BMC Developmental Biology. 9:40

Slanchev, K., Carney, T.J., Stemmler, M.P., Koschorz, B., Amsterdam, A., Schwarz, H., and Hammerschmidt, M. (2009) The epithelial cell adhesion molecule EpCAM is required for epithelial morphogenesis and integrity during zebrafish epiboly and skin development. PLoS Genetics. 5(7):e1000563

Kurrasch, D.M., Nevin, L.M., Wong, J., Baier, H., and Ingraham, H.A. (2009) Neuroendocrine transcriptional programs adapt dynamically to the supply and demand for neuropeptides as revealed in NSF mutant zebrafish. Neural Development. 4:22

Maddison, L.A., Lu, J., Victoroff, T., Scott, E., Baier, H., and Chen, W. (2009) A gain-of-function screen in zebrafish identifies a guanylate cyclase with a role in neuronal degeneration. Molecular genetics and genomics : MGG. 281(5):551-563

Wullimann, M.F. (2009) Secondary neurogenesis and telencephalic organization in zebrafish and mice: a brief review. Integrative Zoology. 4(1):123-133

Mason, L., Scott, E.K., Staub, W., Finger-Baier, K., and Baier, H. (2009) Expression patterns from GAL4 enhancer trap screen. ZFIN Direct Data Submission.

Slanchev, K., Stebler, J., Goudarzi, M., Cojocaru, V., Weidinger, G., and Raz, E. (2009) Control of Dead end localization and activity – Implications for the function of the protein in antagonizing miRNA function. Mechanisms of Development. 126(3-4):270-277

Gosse, N.J., and Baier, H. (2009) An essential role for Radar (Gdf6a) in inducing dorsal fate in the zebrafish retina. Proceedings of the National Academy of Sciences of the United States of America. 106(7):2236-2241

Babaryka, A., Kuhn, E., and Koster, R.W. (2009) In vivo synthesis of meganuclease for generating transgenic zebrafish Danio rerio. Journal of Fish Biology. 74(2):452-457

Lillesaar, C., Stigloher, C., Tannhäuser, B., Wullimann, M.F., and Bally-Cuif, L. (2009) Axonal projections originating from raphe serotonergic neurons in the developing and adult zebrafish, Danio rerio, using transgenics to visualize raphe-specific pet1 expression. The Journal of comparative neurology. 512(2):158-182

Mueller, T., and Wullimann, M.F. (2009) An evolutionary interpretation of teleostean forebrain anatomy. Brain, behavior and evolution. 74(1):30-42

Nevin, L.M., Taylor, M.R., and Baier, H. (2008) Hardwiring of fine synaptic layers in the zebrafish visual pathway. Neural Development. 3:36

Sumbre, G., Muto, A., Baier, H., and Poo, M.M. (2008) Entrained rhythmic activities of neuronal ensembles as perceptual memory of time interval. Nature. 456(7218):102-106

Del Bene, F., Wehman, A.M., Link, B.A., and Baier, H. (2008) Regulation of neurogenesis by interkinetic nuclear migration through an apical-basal notch gradient. Cell. 134(6):1055-1065

Chi, N.C., Shaw, R.M., Jungblut, B., Huisken, J., Ferrer, T., Arnaout, R., Scott, I., Beis, D., Xiao, T., Baier, H., Jan, L.Y., Tristani-Firouzi, M., and Stainier, D.Y. (2008) Genetic and Physiologic Dissection of the Vertebrate Cardiac Conduction System. PLoS Biology. 6(5):e109

Gosse, N.J., Nevin, L.M., and Baier, H. (2008) Retinotopic order in the absence of axon competition. Nature. 452(7189):892-895

Mueller, T., Wullimann, M.F., and Guo, S. (2008) Early teleostean basal ganglia development visualized by Zebrafish Dlx2a, Lhx6, Lhx7, Tbr2 (eomesa), and GAD67 gene expression. The Journal of comparative neurology. 507(2):1245-1257

Kedde, M., Strasser, M.J., Boldajipour, B., Oude Vrielink, J.A., Slanchev, K., le Sage, C., Nagel, R., Voorhoeve, P.M., van Duijse, J., Andersson Ørom, U., Lund, A.H., Perrakis, A., Raz, E., and Agami, R. (2007) RNA-Binding Protein Dnd1 Inhibits MicroRNA Access to Target mRNA. Cell. 131(7):1273-1286

Xiao, T., and Baier, H. (2007) Lamina-specific axonal projections in the zebrafish tectum require the type IV collagen Dragnet. Nature Neuroscience. 10(12):1529-1537

Campbell, D.S., Stringham, S.A., Timm, A., Xiao, T., Law, M.Y., Baier, H., Nonet, M.L., and Chien, C.B. (2007) Slit1a inhibits retinal ganglion cell arborization and synaptogenesis via Robo2-dependent and -independent pathways. Neuron. 55(2):231-245

Jin, S.W., Herzog, W., Santoro, M.M., Mitchell, T.S., Frantsve, J., Jungblut, B., Beis, D., Scott, I.C., D'Amico, L.A., Ober, E.A., Verkade, H., Field, H.A., Chi, N.C., Wehman, A.M., Baier, H., and Stainier, D.Y. (2007) A transgene-assisted genetic screen identifies essential regulators of vascular development in vertebrate embryos. Developmental Biology. 307(1):29-42

Szobota, S., Gorostiza, P., Del Bene, F., Wyart, C., Fortin, D.L., Kolstad, K.D., Tulyathan, O., Volgraf, M., Numano, R., Aaron, H.L., Scott, E.K., Kramer, R.H., Flannery, J., Baier, H., Trauner, D., and Isacoff, E.Y. (2007) Remote control of neuronal activity with a light-gated glutamate receptor. Neuron. 54(4):535-545

Davison, J.M., Akitake, C.M., Goll, M.G., Rhee, J.M., Gosse, N., Baier, H., Halpern, M.E., Leach, S.D., and Parsons, M.J. (2007) Transactivation from Gal4-VP16 transgenic insertions for tissue-specific cell labeling and ablation in zebrafish. Developmental Biology. 304(2):811-824

Scott, E.K., Mason, L., Arrenberg, A.B., Ziv, L., Gosse, N.J., Xiao, T., Chi, N.C., Asakawa, K., Kawakami, K., and Baier, H. (2007) Targeting neural circuitry in zebrafish using GAL4 enhancer trapping. Nature Methods. 4(4):323-326

Scott, I.C., Masri, B., D'Amico, L.A., Jin, S.W., Jungblut, B., Wehman, A.M., Baier, H., Audigier, Y., and Stainier, D.Y. (2007) The G protein-coupled receptor agtrl1b regulates early development of myocardial progenitors. Developmental Cell. 12(3):403-413

Wehman, A.M., Staub, W., and Baier, H. (2007) The anaphase-promoting complex is required in both dividing and quiescent cells during zebrafish development. Developmental Biology. 303(1):144-156

Smear, M.C., Tao, H.W., Staub, W., Orger, M.B., Gosse, N.J., Liu, Y., Takahashi, K., Poo, M.M., and Baier, H. (2007) Vesicular Glutamate Transport at a Central Synapse Limits the Acuity of Visual Perception in Zebrafish. Neuron. 53(1):65-77

Mumm, J.S., Williams, P.R., Godinho, L., Koerber, A., Pittman, A.J., Roeser, T., Chien, C.B., Baier, H., and Wong, R.O. (2006) In vivo imaging reveals dendritic targeting of laminated afferents by zebrafish retinal ganglion cells. Neuron. 52(4):609-621

Sive, H., Mueller, T., Wullimann, M.F., Kuwada, J.Y., Moorman, S.J., Haendel, M.A. (2006) ZFIN Anatomy Working Group: Nervous System. Manually curated data.

Mueller, T., Vernier, P., and Wullimann, M.F. (2006) A phylotypic stage in vertebrate brain development: GABA cell patterns in zebrafish compared with mouse. The Journal of comparative neurology. 494(4):620-634

Slanchev, K.I. (2006) Molecular mechanisms governing germ line development in zebrafish and the role of this lineage in sexual differentiation. Ph.D. Thesis.

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Gahtan. E., Tanger. P., and Baier, H. (2005) Visual prey capture in larval zebrafish is controlled by identified reticulospinal neurons downstream of the tectum. The Journal of neuroscience : the official journal of the Society for Neuroscience. 25(40):9294-9303

Beis, D., Bartman, T., Jin, S.W., Scott, I.C., D'Amico, L.A., Ober, E.A., Verkade, H., Frantsve, J., Field, H.A., Wehman, A., Baier, H., Tallafuss, A., Bally-Cuif, L., Chen, J.N., Stainier, D.Y., and Jungblut, B. (2005) Genetic and cellular analyses of zebrafish atrioventricular cushion and valve development. Development (Cambridge, England). 132(18):4193-4204

Wullimann, M.F., Rink, E., Vernier, P., and Schlosser, G. (2005) Secondary neurogenesis in the brain of the African clawed frog, Xenopus laevis, as revealed by PCNA, Delta-1, Neurogenin-related-1, and NeuroD expression. The Journal of comparative neurology. 489(3):387-402

Mueller, T., and Wullimann, M.F. (2005) Atlas of Early Zebrafish Brain Development: A Tool for Molecular Neurogenetics. Elsevier Science. :183p

Xiao, T., Roeser, T., Staub, W., and Baier, H. (2005) A GFP-based genetic screen reveals mutations that disrupt the architecture of the zebrafish retinotectal projection. Development (Cambridge, England). 132(13):2955-2967

Chen, P.Y., Manninga, H., Slanchev, K., Chien, M., Russo, J.J., Ju, J., Sheridan, R., John, B., Marks, D.S., Gaidatzis, D., Sander, C., Zavolan, M., and Tuschl, T. (2005) The developmental miRNA profiles of zebrafish as determined by small RNA cloning. Genes & Development. 19(11):1288-1293

Kay, J.N., Link, B.A., and Baier, H. (2005) Staggered cell-intrinsic timing of ath5 expression underlies the wave of ganglion cell neurogenesis in the zebrafish retina. Development (Cambridge, England). 132(11):2573-2585

Orger, M.B., and Baier, H. (2005) Channeling of red and green cone inputs to the zebrafish optomotor response. Visual neuroscience. 22(3):275-281

Wehman, A.M., Staub, W., Meyers, J.R., Raymond, P.A., and Baier, H. (2005) Genetic dissection of the zebrafish retinal stem-cell compartment. Developmental Biology. 281(1):53-65

Hua, J.Y., Smear, M.C., Baier, H., and Smith, S.J. (2005) Regulation of axon growth in vivo by activity-based competition. Nature. 434(7036):1022-1026

Slanchev, K., Stebler, J., de la Cueva-Mendez, G., and Raz, E. (2005) Development without germ cells: The role of the germ line in zebrafish sex differentiation. Proceedings of the National Academy of Sciences of the United States of America. 102(11):4074-4079

Seiler, C., Finger-Baier, K.C., Rinner, O., Makhankov, Y.V., Schwarz, H., Neuhauss, S.C., and Nicolson, T. (2005) Duplicated genes with split functions: independent roles of protocadherin15 orthologues in zebrafish hearing and vision. Development (Cambridge, England). 132(3):615-623

Baraban, S.C., Taylor, M.R., Castro, P.A., and Baier, H. (2005) Pentylenetetrazole induced changes in zebrafish behavior, neural activity and c-fos expression. Neuroscience. 131(3):759-768

Page-McCaw, P.S., Chung, S.C., Muto, A., Roeser, T., Staub, W., Finger-Baier, K.C., Korenbrot, J.I., and Baier, H. (2004) Retinal network adaptation to bright light requires tyrosinase. Nature Neuroscience. 7(12):1329-1336

Wullimann, M.F., and Mueller, T. (2004) Teleostean and mammalian forebrains contrasted: Evidence from genes to behavior. The Journal of comparative neurology. 475(2):143-162

Mueller, T., Vernier, P., and Wullimann, M.F. (2004) The adult central nervous cholinergic system of a neurogenetic model animal, the zebrafish Danio rerio. Brain research. 1011(2):156-169

Rink, E., and Wullimann, M.F. (2004) Connections of the ventral telencephalon (subpallium) in the zebrafish (Danio rerio). Brain research. 1011(2):206-220

Gahtan, E., and Baier, H. (2004) Of lasers, mutants, and see-through brains: Functional neuroanatomy in zebrafish. Journal of neurobiology. 59(1):147-161

Wullimann, M.F., and Mueller, T. (2004) Identification and morphogenesis of the eminentia thalami in the zebrafish. The Journal of comparative neurology. 471(1):37-48

Kay, J.N., Roeser, T., Mumm, J.S., Godinho, L., Mrejeru, A., Wong, R.O., and Baier, H. (2004) Transient requirement for ganglion cells during assembly of retinal synaptic layers. Development (Cambridge, England). 131(6):1331-1342

Orger, M.B., Gahtan, E., Muto, A., Page-McCaw, P., Smear, M.C., and Baier, H. (2004) Behavioral screening assays in zebrafish. The Zebrafish: Genetics, Genomics and Informatics, 2nd ed., Methods Cell Biol.. 77:53-68

Goldsmith, P., Baier, H., and Harris, W.A. (2003) Two zebrafish mutants, ebony and ivory, uncover benefits of neighborhood on photoreceptor survival. Journal of neurobiology. 57(3):235-245

Loosli, F., Staub, W., Finger-Baier, K.C., Ober, E.A., Verkade, H., Wittbrodt, J., and Baier, H. (2003) Loss of eyes in zebrafish caused by mutation of chokh/rx3. EMBO reports. 4(9):894-899

Weidinger, G., Stebler, J., Slanchev, K., Dumstrei, K., Wise, C., Lovell-Badge, R., Thisse, C., Thisse, B., and Raz, E. (2003) dead end, a novel vertebrate germ plasm component, is required for zebrafish primordial germ cell migration and survival. Current biology : CB. 13(16):1429-1434

Roeser, T. and Baier, H. (2003) Visuomotor behaviors in larval zebrafish after GFP-guided laser ablation of the optic tectum. The Journal of neuroscience : the official journal of the Society for Neuroscience. 23(9):3726-3734

Mueller, T., and Wullimann, M.F. (2003) Anatomy of neurogenesis in the early zebrafish brain. Brain research. Developmental brain research. 140(1):137-155

Wullimann, M.F., and Mueller, T. (2002) Expression of Zash-1a in the postembryonic zebrafish brain allows comparison to mouse Mash1 domains. Gene expression patterns : GEP. 1(3-4):187-192

Mueller, T., and Wullimann, M. (2002) BrdU-, neuroD (nrd)- and Hu-studies reveal unusual non-ventricular neurogenesis in the postembryonic zebrafish forebrain. Mechanisms of Development. 117(1-2):123-135

Rink, E. and Wullimann, M.F. (2002) Development of the catecholaminergic system in the early zebrafish brain: an immunohistochemical study. Brain research. Developmental brain research. 137(1):89-100

Mueller, T., and Wullimann, M.F. (2002) Expression domains of neuroD (nrd) in the early postembryonic zebrafish brain. Brain research bulletin. 57(3-4):377-379

Rink, E. and Wullimann, M.F. (2002) Connections of the ventral telencephalon and tyrosine hydroxylase distribution in the zebrafish brain (Danio rerio) lead to identification of an ascending dopaminergic system in a teleost. Brain research bulletin. 57(3-4):385-387

Wullimann, M.F. and Rink, E. (2002) The teleostean forebrain: a comparative and developmental view based on early proliferation, Pax6 activity and catecholaminergic organization. Brain research bulletin. 57(3-4):363-370

Baraban, S., Castro, P., and Baier, H. (2002) Identification of seizure-resistant zebrafish mutants. Epilepsia. 43(7):238

Wullimann, M.F. and Rink, E. (2001) Detailed immunohistology of Pax6 protein and tyrosine hydroxylase in the early zebrafish brain suggests role of Pax6 gene in development of dopaminergic diencephalic neurons. Brain research. Developmental brain research. 131(1-2):173-191

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Rink, E. and Wullimann, M.F. (2001) The teleostean (zebrafish) dopaminergic system ascending to the subpallium (striatum) is located in the basal diencephalon (posterior tuberculum). Brain research. 889:316-330

Wullimann, M.F. (2001) Brain phenotypes and early regulatory genes: the bauplanof the metazoan central nervous system. In Brain Evolution and Cognition, G. Roth and M.F. Wullimann, eds., New York and Heidelberg: Spektrum Akademischer Verlag and J. Wiley & Sons. :11-39

Orger, M.B., Smear, M.C., Anstis, S.M., and Baier, H. (2000) Perception of Fourier and non-Fourier motion by larval zebrafish. Nature Neuroscience. 3(11):1128-1133

Wullimann, M.F. and Knipp, S. (2000) Proliferation pattern changes in the zebrafish brain from embryonic through early postembryonic stages. Anatomy and embryology. 202:385-400

Baier, H. (2000) Zebrafish on the move: towards a behavior-genetic analysis of vertebrate vision. Current opinion in neurobiology. 10(4):451-455

Baier, H. and Copenhagen, D. (2000) Combining physiology and genetics in the zebrafish retina. The Journal of physiology. 524(1):1

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Wullimann M.F., Puelles, L., and Wicht, H. (1999) Early postembryonic neural development in the zebrafish: a 3-D reconstruction of forebrain proliferation zones shows their relationship to prosomeres. Eur. J. Morphol.. 37:117-121

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