Publications of Ruben Portugues

Journal Article (40)

2022
Journal Article
Odstrcil, I.; Petkova, M. D.; Haesemeyer, M.; Boulanger-Weill, J.; Nikitchenko, M.; Gagnon, J. A.; Oteiza, P.; Schalek, R.; Peleg, A.; Portugues, R. et al.; Lichtman, J. W.; Engert, F.: Functional and ultrastructural analysis of reafferent mechanosensation in larval zebrafish. Current Biology 32 (1), pp. 176 - 189.e5 (2022)
Journal Article
Xiao, Y.; Petrucco, L.; Hoodless, L. J.; Portugues, R.; Czopka, T.: Oligodendrocyte precursor cells sculpt the visual system by regulating axonal remodeling. Nature Neuroscience 25 (3), pp. 280 - 284 (2022)
2021
Journal Article
Claudi, F.; Tyson, A. L.; Petrucco, L.; Margrie, T. W.; Portugues, R.; Branco, T.: Visualizing anatomically registered data with brainrender. eLife 10, e65751 (2021)
Journal Article
Jafari, M.; Schumacher, A.-M.; Snaidero, N.; Ullrich Gavilanes, E. M.; Neziraj, T.; Kocsis-Jutka, V.; Engels, D.; Jürgens, T.; Wagner, I.; Weidinger, J. D. F. et al.; Schmidt, S. S.; Beltran, 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 24 (3), pp. 355 - 367 (2021)
Journal Article
Markov, D. A.; Petrucco, L.; Kist, A. M.; Portugues, R.: A cerebellar internal model calibrates a feedback controller involved in sensorimotor control. Nature Communications 12, 6694 (2021)
Journal Article
Valera, G.; Markov, D. A.; Bijari, K.; Randlett, O.; Asgharsharghi, A.; Baudoin, J.-P.; Ascoli, G. A.; Portugues, R.; Lopez-Schier, H.: A neuronal blueprint for directional mechanosensation in larval zebrafish. Current Biology 31 (7), pp. 1463 - 1475.e6 (2021)
2020
Journal Article
Barykina, N. V.; Sotskov, V. P.; Gruzdeva, A. M.; Wu, Y. K.; Portugues, R.; Subach, O. M.; Chefanova, E. S.; Plusnin, V. V.; Ivashkina, O. I.; Anokhin, K. V. et al.; Vlaskina, A. V.; Korzhenevskiy, D. A.; Nikolaeva, A. Y.; Boyko, K. M.; Rakitina, T. V.; Varizhuk, A. M.; Pozmogova, G. E.; Subach, F. V.: FGCaMP7, an improved version of fungi-based ratiometric calcium indicator for in vivo visualization of neuronal activity. International Journal of Molecular Sciences 21 (8), 3012 (2020)
Journal Article
Claudi, F.; Petrucco, L.; Tyson, A. L.; Branco, T.; Margrie, T. W.; Portugues, R.: BrainGlobe Atlas API: A common interface for neuroanatomical atlases. The Journal of Open Source Software 5 (54), 2668 (2020)
Journal Article
Dragomir, E. I.; Štih, V.; Portugues, R.: Evidence accumulation during a sensorimotor decision task revealed by whole-brain imaging. Nature Neuroscience 23 (1), pp. 85 - 93 (2020)
Journal Article
Siju, K. P.; Štih, V.; Aimon, S.; Gjorgjieva, J.; Portugues, R.; Grunwald Kadow, I. C.: Valence and state-dependent population coding in dopaminergic neurons in the fly mushroom body. Current Biology 30 (11), pp. 2104 - 2115.e4 (2020)
Journal Article
Yildizoglu, T.; Riegler, C.; Fitzgerald, J. E.; Portugues, R.: A neural representation of naturalistic motion-guided behavior in the zebrafish brain. Current Biology 30 (12), pp. 2321 - 2333.e6 (2020)
2019
Journal Article
Kist, A. M.; Portugues, R.: Optomotor swimming in larval zebrafish is driven by global whole-field visual motion and local light-dark transitions. Cell Reports 29 (3), pp. 659 - 670.e3 (2019)
Journal Article
Knogler, L. D.; Kist, A. M.; Portugues, R.: Motor context dominates output from purkinje cell functional regions during reflexive visuomotor behaviours. eLife 8, e42138 (2019)
Journal Article
Štih, V.; Petrucco, L.; Kist, A. M.; Portugues, R.: Stytra: An open-source, integrated system for stimulation, tracking and closed-loop behavioral experiments. PLoS Computational Biology 15 (4), e1006699 (2019)
2018
Journal Article
Fabritius, A.; Ng, D.; Kist, A. M.; Erdogan, M.; Portugues, R.; Griesbeck, O.: Imaging-based screening platform assists protein engineering. Cell Chemical Biology 25 (12), pp. 1554 - 1561.e8 (2018)
2017
Journal Article
Hildebrand, D. G. C.; Cicconet, M.; Iguel Torres, R. M.; Choi, W.; Quan, T. M.; Moon, J.; Wetzel, A. W.; Champion, A. S.; Graham, B. J.; Randlett, O. et al.; Plummer, G. S.; Portugues, R.; Bianco, I. H.; Saalfeld, S.; Baden, A. D.; Lillaney, K.; Burns, R.; Vogelstein, J. T.; Schier, A. F.; Lee, W.-C. A.; Jeong, W.-K.; Lichtman, J. W.; Engert, F.: Whole-brain serial-section electron microscopy in larval zebrafish. Nature 545 (7654), pp. 345 - 349 (2017)
Journal Article
Knogler, L. D.; Markov, D. A.; Dragomir, E. I.; Štih, V.; Portugues, R.: Sensorimotor representations in cerebellar granule cells in larval zebrafish are dense, spatially organized, and non-temporally patterned. Current Biology 27 (9), pp. 1288 - 1302 (2017)
Journal Article
Oteiza, P.; Odstrcil, I.; Lauder, G.; Portugues, R.; Engert, F.: A novel mechanism for mechanosensory-based rheotaxis in larval zebrafish. Nature 547 (7664), pp. 445 - 448 (2017)
2016
Journal Article
Lopes, S. S.; Distel, M.; Linker, C.; Fior, R.; Monteiro, R.; Bianco, I. H.; Portugues, R.; Straehle, U.; Saude, L.: Report of the 4th European zebrafish principal investigator meeting. Zebrafish 13 (6), pp. 590 - 595 (2016)
2015
Journal Article
Feierstein, C. E.; Portugues, R.; Orger, M. B.: Seeing the whole picture: A comprehensive imaging approach to functional mapping of circuits in behaving zebrafish. Neuroscience 296, pp. 26 - 38 (2015)
Journal Article
Lacoste, A. M. B.; Schoppik, D.; Robson, D. N.; Haesemeyer, M.; Portugues, R.; Li, J. M.; Randlett, O.; Wee, C. L.; Engert, F.; Schier, A. F.: A convergent and essential interneuron pathway form Mauthner-cell-mediated escapes. Current Biology 25 (11), pp. 1526 - 1534 (2015)
Journal Article
Portugues, R.; Haesemeyer, M.; Blum, M. L.; Engert, F.: Whole-field visual motion drives swimming in larval zebrafish via a stochastic process. The Journal of Experimental Biology 218 (9), pp. 1433 - 1443 (2015)
Journal Article
Randlett, O.; Wee, C. L.; Naumann, E. A.; Nnaemeka, O.; Schoppik, D.; Fitzgerald, J. E.; Portugues, R.; Lacoste, A. M. B.; Riegler, C.; Engert, F. et al.; Schier, A. F.: Whole-brain activity mapping onto a zebrafish brain atlas. Nature Methods 12 (11), pp. 1039 - 1046 (2015)
2014
Journal Article
Portugues, R.; Feierstein, C. E.; Engert, F.; Orger, M. B.: Whole-brain activity maps reveal stereotyped, distributed networks for visuomotor behavior. Neuron 81 (6), pp. 1328 - 1343 (2014)
Journal Article
Rose, T.; Goltstein, P. M.; Portugues, R.; Griesbeck, O.: Putting a finishing touch on GECI's. Frontiers in Molecular Neuroscience 7, 88 (2014)
Journal Article
Severi, K. E.; Portugues, R.; Marques, J. C.; O'Malley, D. M.; Orger, M. B.; Engert, F.: Neural control and modulation of swimming speed in the larval zebrafish. Neuron 83 (3), pp. 692 - 707 (2014)
2013
Journal Article
Portugues, R.; Severi, K. E.; Wyart, C.; Ahrens, M. B.: Optogenetics in a transparent animal: Circuit function in the larval zebrafish. Current Opinion in Neurobiology 23 (1), pp. 119 - 126 (2013)
2012
Journal Article
Ahrens, M. B.; Li, J. M.; Orger, M. B.; Robson, D. N.; Schier, A. F.; Engert, F.; Portugues, R.: Brain-wide neuronal dynamics during motor adaptation in zebrafish. Nature 485 (7399), pp. 471 - 477 (2012)
Journal Article
Akerboom, J.; Chen, T. W.; Wardill, T. J.; Tian, L.; Marvin, J. S.; Mutlu, S.; Calderon, N. C.; Esposti, F.; Borghuis, B. G.; Sun, X. R. et al.; 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. H.; Bargmann, C. I.; Kimmel, B. E.; Jayaraman, V.; Svoboda, K.; Kim, D. S.; Schreiter, E. R.; Looger, L. L.: Optimization of a GCaMP calcium indicator for neural activity imaging. The Journal of Neuroscience 32 (40), pp. 13819 - 13840 (2012)
Journal Article
Valente, A.; Huang, K. H.; Portugues, R.; Engert, F.: Ontogeny of classical and operant learning behaviors in zebrafish. Learning & memory 19 (4), pp. 170 - 177 (2012)
2011
Journal Article
Portugues, R.; Engert, F.: Adaptive locomotor behavior in larval zebrafish. Frontiers in Systems Neuroscience 5, 72 (2011)
2009
Journal Article
Portugues, R.; Engert, F.: The neural basis of visual behaviors in the larval zebrafish. Current Opinion in Neurobiology 19 (6), pp. 644 - 647 (2009)
2006
Journal Article
Bunster, C.; Portugues, R.; Cnockaert, S.; Henneaux, M.: Monopoles for gravitation and for higher spin fields. Physical Review D 73 (10), 105014 (2006)
Journal Article
Edelstein, J. D.; Portugues, R.: Gauge/string duality in confining theories. Fortschritte der Physik/Progress of Physics 54 (7), pp. 525 - 579 (2006)
2004
Journal Article
Gursoy, U.; Hartnoll, S. A.; Portugues, R.: The chiral anomaly from M theory. Physical Review D 69 (8), 086003 (2004)
Journal Article
Hartnoll, S. A.; Portugues, R.: Deforming baryons into confining strings. Physical Review D 70 (6), 066007 (2004)
Journal Article
Portugues, R.: Membrane solitons in eight-dimensional hyper-Kahler backgrounds. Journal of High Energy Physics (3), p. 14 (2004)
2002
Journal Article
Portugues, R.; Townsend, P. K.: Sigma-model soliton intersections from exceptional calibrations. Journal of High Energy Physics (4), p. 19 (2002)
Journal Article
Portugues, R.; Townsend, P. K.: Intersoliton forces in the Wess-Zumino model. Physics Letters B 530 (1-4), pp. 227 - 234 (2002)
2001
Journal Article
Gauntlett, J. P.; Portugues, R.; Tong, D.; Townsend, P. K.: D-brane solitons in supersymmetric sigma models. Physical Review D 63 (8), 085002 (2001)

Book Chapter (2)

2017
Book Chapter
Kist, A. M.; Knogler, L. D.; Markov, D. A.; Yildizoglu, T.; Portugues, R.: Whole-brain imaging using genetically encoded activity sensors in vertebrates. In: Decoding Neural Circuit Structure and Function, pp. 321 - 341 (Eds. Çelik, A.; Wernet, M.). Springer, Cham (2017)
2016
Book Chapter
Orger, M. B.; Portugues, R.: Correlating whole brain neural activity with behavior in head-fixed larval zebrafish. In: Zebrafish. Methods and protocols, pp. 307 - 320 (Eds. Kawakami, K.; Patton, E. E.; Orger, M.). Humana Press, New York (2016)

Conference Paper (1)

2008
Conference Paper
Portugues, R.: Magnetic monopoles in electromagnetism and gravity. In: Quantum Mechanics of Fundamental Systems: The Quest for Beauty and Simplicity, pp. 197 - 212 (Eds. Zanelli, J.; Henneaux, M.). Meeting on Quantum Mechanics of Fundanental Systems - The Quest for Beauty and Simplicitt. Claudio Bunster Festschrift, Valdivua, Chile, January 10, 2008 - January 11, 2008. Springer, New York (2008)
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