List of publications

Shainer I*, Kappel JM*, Laurell E, Donovan JC, Schneider MW, Kuehn E, Arnold-Ammer I, Stemmer M, Larsch J, Baier H. Transcriptomic neuron types vary topographically in function and morphology. Nature 638, 1023–1033 (2025). *Co-first author.

Highlighted in Nature News & Views:

Does a cell’s gene expression always reflect its function?

Featured in Nature’s 2025 Highlights:

Asteroids, antibiotics and ants: a year of remarkable science

Kawashima T, Wei Z, Haruvi R, Shainer I, Narayan S, Baier H, Ahrens MB. Voltage imaging reveals circuit computations in the raphe underlying serotonin-mediated motor vigor learning. Neuron 113, 1–16 (2025)

Haruvi R, Barbara R, Shainer I, Rosenberg AM, Moshe L, Malamud D, Toledano J, Braun D, Baier H, Kawashima T. Global and compartmentalized serotonergic control of sensorimotor integration underlying motor adaptation. BioRxiv. 2024:2024-09.

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

Elazary Y, Cheow K, Cheng RK, Ghosh R, Shainer I, Wexler Y, Crasta K, Gothilf Y, Jesuthasan SJ. Glial cells expressing visual cycle genes are vital for photoreceptor survival in the zebrafish pineal gland. Journal of Pineal Research. 2023 Apr;74(3):e12854.

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. 2023 Feb 22;9(8):eade9909. *Co-first author.

Shainer R, Kram V, Kilts TM, Li L, Doyle AD, Shainer I, Martin D, Simon CG, Zeng-Brouwers J, Schaefer L, Young MF. Biglycan regulates bone development and regeneration. Frontiers in Physiology. 2023 Feb 16;14.

Kappel JM, Förster D, Slangewal K, Shainer I, Svara F, Donovan JC, Sherman S, Januszewski M, Baier H, Larsch J. Visual recognition of social signals by a tectothalamic neural circuit. Nature. 2022 Jul 13:1-7.

Shainer I, Stemmer M. Choice of pre-processing pipeline influences clustering quality of scRNA-seq datasets. BMC genomics. 2021 Dec;22:1-3.

Shainer I, Michel M, Marquart GD, Bhandiwad AA, Zmora N, Livne ZB, Zohar Y, Hazak A, Mazon Y, Förster D, Hollander-Cohen L, Cone RD, Burgess HA, Gothilf Y. Agouti-related protein 2 is a new player in the teleost stress response system. Current Biology. 2019 17;29(12):2009-19.

Zuccarini G, D’Atri I, Cottone E, Mackie K, Shainer I, Gothilf Y, Provero P, Bovolin P, Merlo GR. Interference with the cannabinoid receptor CB1R results in miswiring of GnRH3 and AgRP1 axons in zebrafish embryos. International journal of molecular sciences. 2019 Dec 25;21(1):168.

Koch L*, Shainer I*, Gurevich T, Holzman R. The expression of agrp1, a hypothalamic appetite-stimulating neuropeptide, reveals hydrodynamic-induced starvation in a larval fish. Integrative Organismal Biology. 2019;1(1):oby003. *Co-first author.

Shainer I, Buchshtab A, Hawkins TA, Wilson SW, Cone RD, Gothilf Y. Novel hypophysiotropic AgRP2 neurons and pineal cells revealed by BAC transgenesis in zebrafish. Scientific reports. 2017 Mar 20;7(1):1-0.

Ben-Moshe Livne Z, Alon S, Vallone D, Bayleyen Y, Tovin A, Shainer I, Nisembaum LG, Aviram I, Smadja-Storz S, Fuentes M, Falcon J, Eisenberg E, Klein DC, Burgess HA, Foulkes NS, Gothilf Y. Genetically blocking the zebrafish pineal clock affects circadian behavior. PLoS genetics. 2016 Nov 21;12(11):e1006445.

Khandadash R, Machtey V, Shainer I, Gottlieb HE, Gothilf Y, Ebenstein Y, Weiss A, Byk G. Novel biocompatible hydrogel nanoparticles: generation and size-tuning of nanoparticles by the formation of micelle templates obtained from thermo-responsive monomers mixtures. Journal of nanoparticle research. 2014 Dec;16(12):1-8.

morphotypes

atlas_1

MAX_agrp2-mcherry oxt-EGFP 13dpf ventral 3.lif - pituitary