Claudi F, Tyson AL, Petrucco L, Margrie TW, Portugues R, Branco T

Visualizing anatomically registered data with Brainrender

eLife (in press)

Valera G*, Markov DA, Bijari K, Randlett O, Asgharsharghi A, Baudoin J-P, Ascoli GA, Portugues R, López-Schier H

A neuronal blueprint for directional mechanosensation in larval zebrafish

Current Biology (in press)

Jafari M*, Schumacher A-M*, Snaidero N*, Ullrich Gavilanes EM,Neziraj T, Kocsis-Jutka V, Engels D, Jürgens T, Wagner I, Flórez Weidinger JD, Schmidt SS, Beltrán E, Hagan N, Woodworth L, Ofengeim D, Gans J, Wolf F, Kreutzfeldt M, Portugues R, Merkler D#, Misgeld T#, Kerschensteiner M#

Phagocyte-mediated synapse removal in cortical neuroinflammation is promoted by local calcium accumulation

Nature Neuroscience volume 24, pages 355–367 (2021)


Claudi F, Petrucco L, Tyson AL, Branco T, Margrie TW, Portugues R (2020)

BrainGlobe Atlas API: a common interface for neuroanatomical atlases

Journal of Open Source Software, 5(54), 2668

Yildizoglu T, Riegler C, Fitzgerald JE#, Portugues R# (2020)

A neural representation of naturalistic motion-guided behavior in the zebrafish brain

Current Biology, Volume 30, Issue 12, pages 2321-2333.e6

KP Siju, Štih V, Aimon S, Gjorgjieva J, Portugues R, Grunwald Kadow IC (2020)

Valence and state-dependent population coding in dopaminergic neurons in the fly mushroom body

Current Biology, Volume 30, Issue 11, pages 2104-2115.e4

Barykina NV, Sotskov VP, Gruzdeva AM, Wu YK, Portugues R, Subach OM, Chefanova ES, Plusnin VV, Ivashkina OI, Anokhin KV, Vlaskina AV, Korzhenevskiy DA, Nikolaeva AY, Boyko KM, Rakitina TV, Varizhuk AM, Pozmogova GE, Subach FV

FGCaMP7, an improved version of fungi-based ratiometric calcium indicator for in vivo visualization of neuronal activity

Int. J. Mol. Sci. 2020, 21(8), 3012

Dragomir EI, Štih V, Portugues R (2020)

Evidence accumulation during a sensorimotor decision task revealed by whole-brain imaging

Nature Neuroscience volume 23, pages 85–93(2020)


Kist AM, Portugues R (2019)

Optomotor swimming in larval zebrafish Is driven by global whole-field visual motion and local light-dark transitions

Cell Reports, doi:10.1016/j.celrep.2019.09.024

Štih V, Petrucco L, Kist AM, Portugues R (2019)

Stytra: An open-source, integrated system for stimulation, tracking and closed-loop behavioral experiments

PLOS Computational Biology, doi:10.1371/journal.pcbi.1006699

Knogler LD, Kist AM, Portugues R (2019)

Motor context dominates output from purkinje cell functional regions during reflexive visuomotor behaviours

eLife, doi:10.7554/eLife.42138


Fabritius A, Ng D, Kist AM, Erdogan M, Portugues R, Griesbeck O (2018)

Imaging-based screening platform assists protein engineering

Cell Chemical Biology, doi:10.1016/j.chembiol.2018.08.008


Oteiza P*, Odstrcil I*, Lauder G, Portugues R#, Engert F# (2017)

A novel mechanism for mechanosensory-based rheotaxis in larval zebrafish

Nature 547 27: 445-448, doi:10/1038/nature23014

News & views: “Biomechanics: how fish feel the flow”, Dabiri JO, Nature 547, 406-407, 2017.

Knogler LD, Markov AD, Dragomir EI, Štih V, Portugues R (2017)

Sensorimotor representations in cerebellar granule cells in larval zebrafish are dense, spatially organized, and non-temporally patterned

Curr Biol 27: 1288-1302, doi: 10.1016/j.cub.2017.03.029

Dispatch: “Cerebellar granule cells: dense, rich and evolving representations” , Badura and De Zeeuw, Curr Biol 27: R415-R418, 2017.

Hildebrand DGC, Cicconet M, Torres RM, Choi W, Quan TM, Moon J, Wetzel AW, Champion AS, Graham BJ, Randlett O, Plummer GS, Portugues R, Bianco IH, Saalfeld S, Baden AD, Lillaney K, Burns R, Vogelstein JT, Schier AF, Lee WCA, Jeong WK, Lichtman JW, Engert F (2017)

Whole-brain serial-section electron microscopy in larval zebrafish

Nature 545, 345-349, doi:10.1038/nature22356

Kist AM, Knogler LD, Markov DA, Yildizoglu T, Portugues R (2017)

Whole-brain imaging using genetically encoded activity sensors in vertebrates

Decoding neural circuit structure and function, Springer.


Lopes SS, Distel M, Linker C, Fior R, Monteiro R, Bianco IH, Portugues R, Strähle U, Saúde L. (2016)

Report of the 4th European Zebrafish Principal Investigator Meeting


Orger MB, Portugues R.

Correlating whole brain neural activity with behavior in head-fixed larval zebrafish

Methods Mol Biol 1451: 307 (2016)


Randlett O, Wee C, Naumann E, Nnaemeka O, Schoppik D, Fitzgerald J, Portugues R, Lacoste AMB, Riegler C, Engert F, Schier AF.

Whole-brain activity mapping onto a zebrafish brain atlas

Nat Meth 12, 1039-1046 (2015)

Lacoste AMB, Schoppik D, Robson DN, Haesemeyer M, Portugues R, Li JM, Randlett O, Wee CL, Engert F, Schier AF.

A convergent and essential interneuron pathway for Mauthner-cell-mediated escapes

Curr Biol 25(11): 1526-1534 (2015)

Portugues R*, Haesemeyer M*, Blum ML, Engert F.

Whole-field visual motion drives swimming in larval zebrafish via a stochastic process

J Exp Biol 218: 1433-1443 (2015)

Feierstein CE, Portugues R, Orger MB.

Seeing the whole picture: A comprehensive imaging approach to functional mapping of circuits in behaving zebrafish

Neurosci 296: 26-38 (2015)


Rose T, Goltstein PM, Portugues R, Griesbeck O.

Putting a finishing touch on GECIs

Front Mol Neurosci 7: 88 (2014)

Severi KE*, Portugues R*#, Marques JC, O’Malley DM, Orger MB, Engert F#.

Neural control and modulation of swimming speed in the larval zebrafish

Neuron 83: 692-707 (2014)

Portugues R*, Feierstein CE*, Engert F, Orger MB.

Whole-brain activity maps reveal stereotyped, distributed networks for visuomotor behavior

Neuron 81: 1328-1343 (2014)


Portugues R, Severi KE, Wyart C, Ahrens MB.

Optogenetics in a transparent animal: circuit function in the larval zebrafish

Curr Opin Neurobiol 23: 119-216 (2013)


Akerboom J, Chen T-W, Wardill TJ, Tian L, Marvin JS, Mutlu S, Calderon NC, Esposti F, Borghuis BG, Sun XR, et al.

Optimization of a GCaMP calcium indicator for neural activity imaging

J Neurosci 32: 13819-13840 (2012)

Ahrens MB, Li JM, Orger MB, Robson DN, Schier AF, Engert F, Portugues R.

Brain-wide neuronal dynamics during motor adaptation in zebrafish

Nature 485: 471-477 (2012)

Valente A*, Huang K-H*, Portugues R, Engert F.

Ontogeny of classical and operant learning behaviors in zebrafish

Learn Mem 19: 170-177 (2012)


Portugues R, Engert F.

Adaptive locomotor behavior in larval zebrafish

Front Syst Neurosci 5: 72 (2011)


Portugues R, Engert F.

The neural basis of visual behaviors in the larval zebrafish

Curr Opin Neurobiol 19: 644-647 (2009)


(authors in alphabetical order)

Portugues, R.

Magnetic monopoles in electromagnetism and gravity

Published in Quantum Mechanics of Fundamental Systems: The Quest for Beauty and Simplicity – Claudio Bunster Festschrift, Henneaux, M; Zanelli, J (Eds.), Springer Verlag 2009.

Edelstein JD, Portugues R.

Gauge/string duality in confining theories

Fortsch Phys 54: 525-579, HEP-TH 0602021 (2006)

Bunster C, Cnockaert S, Henneaux M, Portugues R.

Monopoles for gravitation and for higher spin fields

Phys Rev D73:105014, HEP-TH 0601222 (2006)

Hartnoll SA, Portugues R.

Deforming baryons into confining strings

Phys Rev D70:066007, HEP-TH 0405214 (2004)

Portugues R.

Membrane solitons in eight-dimensional hyperkaehler backgrounds

JHEP 0403:051, HEP-TH 0311099 (2004)

Gursoy U, Hartnoll SA, Portugues R.

The chiral anomaly from M theory

Phys Rev D69:086003, HEP-TH 0311088 (2004)

Portugues R, Townsend PK.

Sigma model soliton intersections from exceptional calibrations

JHEP 0204:039, HEP-TH 0203181 (2002)

Portugues R, Townsend PK.

Intersoliton forces in the Wess-Zumino model

Phys Lett B530:227-234, HEP-TH 0112077 (2002)

Gauntlett JP, Portugues R, Tong D, Townsend PK.

D-brane solitons in supersymmetric sigma models

Phys Rev D63:085002, HEP-TH 0008221 (2001)

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