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 29: 659-670,

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 8: e42138 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 Chem. Biol. 25: 1-8


Oteiza P*, Odstrcil I*, Lauder G, Portugues R#, Engert F# (2017). A novel mechanism for mechanosensory-based rheotaxis in larval zebrafish. Nature 547: 445-448, doi:10/1038/nature23014
*denotes co-first author, #denotes co-senior author

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
*denotes co-first author

Knogler LD, Markov AD, Dragomir EI, Stih 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

Colbourn Hildebrand DG, 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 WA, Jeong W, Lichtman JW, Engert F (2017) Whole-brain serial-secton electron microscopy in larval zebrafish. Nature doi:10.1038/nature22356


Lopes SS, Distel M, Linker C, Fior R, Monteiro R, Bianco IH, Portugues R, Strähle S, Saúde L (2016). Report of the 4th European Zebrafish Principal Investigator Meeting. Zebrafish 13: 590-595. doi:10.1089/zeb.2016.1364

Orger MB, Portugues R (2016). Correlating Whole Brain Neural Activity with Behavior in Head-Fixed Larval Zebrafish Methods. Mol Biol 1451: 307


Randlett O, Wee C, Naumann E, Nnaemeka O, Schoppik D, Fitzgerald J, Portugues R, Lacoste AMB, Riegler C, Engert F, Schier AF (2015). Whole-brain activity mapping onto a zebrafish brain atlas. Nat Meth 12:1039-46

Lacoste AMB, Schoppik D, Robson DN, Haesemeyer M, Portugues R, Li JM, Randlett O, Wee CL, Engert F, Schier AF (2015). A convergent and essential interneuron pathway for Mauthner-cell-mediated escapes. Curr Biol 25: 1526-1534

Portugues R*, Haesemeyer M*, Blum ML, Engert F (2015). Whole-field visual motion drives swimming in larval zebrafish via a stochastic process. J Exp Biol 218: 1433-1443
*denotes co-first author

Feierstein CE, Portugues R, Orger MB (2015). Seeing the whole picture: A comprehensive imaging approach to functional mapping of circuits in behaving zebrafish. Neurosci 296: 26-38


Rose T, Goltstein PM, Portugues R, Griesbeck O (2014). Putting a finishing touch on GECIs. Front Mol Neurosci 7: 88

Severi KE*, Portugues R*#, Marques JC, O'Malley DM, Orger MB, Engert F# (2014). Neural control and modulation of swimming speed in the larval zebrafish. Neuron 83: 692-707
*denotes co-first author
#denotes co-senior author

Portugues R*, Feierstein CE*, Engert F, Orger MB (2014). Whole-brain activity maps reveal stereotyped, distributed networks for visuomotor behavior. Neuron 81: 1328–1343
*denotes co-first author


Portugues R, Severi KE, Wyart C, Ahrens MB (2013). Optogenetics in a transparent animal: circuit function in the larval zebrafish. Curr Opin Neurobiol 23: 119-216


Akerboom J, Chen T-W, Wardill TJ, Tian L, Marvin JS, Mutlu S, Calderón NC, Esposti F, Borghuis BG, Sun XR, et al. (2012). Optimization of a GCaMP calcium indicator for neural activity imaging. J Neurosci 32: 13819–13840

Ahrens MB, Li JM, Orger MB, Robson DN, Schier AF, Engert F, Portugues R (2012). Brain-wide neuronal dynamics during motor adaptation in zebrafish. Nature 485: 471–477

Valente A*, Huang K-HH*, Portugues R, Engert F (2012). Ontogeny of classical and operant learning behaviors in zebrafish. Learn Mem 19: 170–177
*denotes co-first author


Portugues R, Engert F (2011). Adaptive locomotor behavior in larval zebrafish. Front Syst Neurosci 5: 72


Portugues R, Engert F (2009) The neural basis of visual behaviors in the larval zebrafish. Curr Opin Neurobiol 19: 644-647



Papers in theoretical physics (authors in alphabetical order)


Portugues, R (2009). "Magnetic monopoles in electromagnetism and gravity"
published inQuantum 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 (2006). Gauge/string duality in confining theories. Fortsch Phys 54: 525-579, HEP-TH 0602021

Bunster C, Cnockaert S, Henneaux M, Portugues R (2006). Monopoles for gravitation and for higher spin fields. Phys Rev D73:105014, HEP-TH 0601222 

Hartnoll SA, Portugues R (2004). Deforming baryons into confining strings. Phys Rev D70:066007, HEP-TH 0405214 

Portugues R (2004). Membrane solitons in eight-dimensional hyperkahler backgrounds.  JHEP 0403:051, HEP-TH 0311099

Gursoy U, Hartnoll SA, Portugues R (2004). The chiral anomaly from M theory. Phys Rev D69:086003, HEP-TH 0311088

Portugues R, Townsend PK (2002). Sigma model soliton intersections from exceptional calibrations. JHEP 0204:039, HEP-TH 0203181

Portugues R, Townsend PK (2002). Intersoliton forces in the Wess-Zumino model. Phys Lett B530:227-234, HEP-TH 0112077

Gauntlett JP, Portugues R, Tong D, Townsend PK (2001). D-brane solitons in supersymmetric sigma models. Phys Rev D63:085002, HEP-TH 0008221


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