ZFIN Person: Fraser, Scott E.

ZFIN ID: ZDB-PERS-960805-187

ZFIN ID: ZDB-PERS-960805-187

Fraser, Scott E.

Email:	sefraser@caltech.edu
URL:	http://bioimaging.caltech.edu/
Affiliation:	Scott Fraser Lab
Address:	California Institute of Technology Mail Code 139-74 Pasadena, CA 91125 USA
Country:	United States
Phone:	(626) 395-2790
Fax:	(626) 449-5163
ORCID ID:

BIOGRAPHY AND RESEARCH INTERESTS

PUBLICATIONS

Chiang, H.J., Koo, D.E.S., Kitano, M., Burkitt, S., Unruh, J.R., Zavaleta, C., Trinh, L.A., Fraser, S.E., Cutrale, F. (2023) HyU: Hybrid Unmixing for longitudinal in vivo imaging of low signal-to-noise fluorescence. Nature Methods. 20(2):248-258

Djenoune, L., Mahamdeh, M., Truong, T.V., Nguyen, C.T., Fraser, S.E., Brueckner, M., Howard, J., Yuan, S. (2023) Cilia function as calcium-mediated mechanosensors that instruct left-right asymmetry. Science (New York, N.Y.). 379:717871-78

Torres-Pérez, J.V., Anagianni, S., Mech, A.M., Havelange, W., García-González, J., Fraser, S.E., Vallortigara, G., Brennan, C.H. (2022) baz1b loss-of-function in zebrafish produces phenotypic alterations consistent with the domestication syndrome. iScience. 26:105704105704

Sheardown, E., Torres-Perez, J.V., Anagianni, S., Fraser, S.E., Vallortigara, G., Butterworth, B., Miletto-Petrazzini, M.E., Brennan, C.H. (2022) Characterizing ontogeny of quantity discrimination in zebrafish. Proceedings. Biological sciences. 289:20212544

Dempsey, W.P., Du, Z., Nadtochiy, A., Smith, C.D., Czajkowski, K., Andreev, A., Robson, D.N., Li, J.M., Applebaum, S., Truong, T.V., Kesselman, C., Fraser, S.E., Arnold, D.B. (2022) Regional synapse gain and loss accompany memory formation in larval zebrafish. Proceedings of the National Academy of Sciences of the United States of America. 119(3):

Messina, A., Potrich, D., Schiona, I., Sovrano, V.A., Fraser, S.E., Brennan, C.H., Vallortigara, G. (2021) Neurons in the Dorso-Central Division of Zebrafish Pallium Respond to Change in Visual Numerosity. Cerebral cortex (New York, N.Y. : 1991). 32(2):418-428

Keomanee-Dizon, K., Fraser, S.E., Truong, T.V. (2020) A versatile, multi-laser twin-microscope system for light-sheet imaging. The Review of scientific instruments. 91:053703

Messina, A., Potrich, D., Schiona, I., Sovrano, V.A., Fraser, S.E., Brennan, C.H., Vallortigara, G. (2020) Response to change in the number of visual stimuli in zebrafish:A behavioural and molecular study. Scientific Reports. 10:5769

Truong, T.V., Holland, D.B., Madaan, S., Andreev, A., Keomanee-Dizon, K., Troll, J.V., Koo, D.E.S., McFall-Ngai, M.J., Fraser, S.E. (2020) High-contrast, synchronous volumetric imaging with selective volume illumination microscopy. Communications biology. 3:74

Shi, W., Koo, D.E.S., Kitano, M., Chiang, H.J., Trinh, L.A., Turcatel, G., Steventon, B., Arnesano, C., Warburton, D., Fraser, S.E., Cutrale, F. (2020) Pre-processing visualization of hyperspectral fluorescent data with Spectrally Encoded Enhanced Representations. Nature communications. 11:726

Simões, F.C., Cahill, T.J., Kenyon, A., Gavriouchkina, D., Vieira, J.M., Sun, X., Pezzolla, D., Ravaud, C., Masmanian, E., Weinberger, M., Mayes, S., Lemieux, M.E., Barnette, D.N., Gunadasa-Rohling, M., Williams, R.M., Greaves, D.R., Trinh, L.A., Fraser, S.E., Dallas, S.L., Choudhury, R.P., Sauka-Spengler, T., Riley, P.R. (2020) Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair. Nature communications. 11:600

Trivedi, V., Choi, H.M.T., Fraser, S.E., Pierce, N.A. (2018) Multidimensional quantitative analysis of mRNA expression within intact vertebrate embryos. Development (Cambridge, England). 145(1)

Lee, D.A., Andreev, A., Truong, T.V., Chen, A., Hill, A.J., Oikonomou, G., Pham, U., Hong, Y.K., Tran, S., Glass, L., Sapin, V., Engle, J., Fraser, S.E., Prober, D.A. (2017) Genetic and neuronal regulation of sleep by neuropeptide VF. eLIFE. 6

Chen, Y., Trinh, L.A., Fingler, J., Fraser, S.E. (2017) 3D in vivo imaging with extended-focus optical coherence microscopy. Journal of biophotonics. 10:1411-1420

Bower, D.V., Lansdale, N., Navarro, S., Truong, T.V., Bower, D.J., Featherstone, N.C., Connell, M.G., Al-Alam, D., Frey, M.R., Trinh, L.A., Fernandez, G.E., Warburton, D., Fraser, S.E., Bennett, D., Jesudason, E.C. (2017) SERCA directs cell migration and branching across species and germ layers. Biology Open. 6(10):1458-1471

Trinh, L.A., Chong-Morrison, V., Gavriouchkina, D., Hochgreb-Hägele, T., Senanayake, U., Fraser, S.E., Sauka-Spengler, T. (2017) Biotagging of Specific Cell Populations in Zebrafish Reveals Gene Regulatory Logic Encoded in the Nuclear Transcriptome. Cell Reports. 19:425-440

Cutrale, F., Trivedi, V., Trinh, L.A., Chiu, C.L., Choi, J.M., Artiga, M.S., Fraser, S.E. (2017) Hyperspectral phasor analysis enables multiplexed 5D in vivo imaging. Nature Methods. 14(2):149-152

Chen, Y., Trinh, L.A., Fingler, J., Fraser, S.E. (2016) Phase variance optical coherence microscopy for label-free imaging of the developing vasculature in zebrafish embryos. Journal of Biomedical Optics. 21:126022

Cronan, M.R., Beerman, R.W., Rosenberg, A.F., Saelens, J.W., Johnson, M.G., Oehlers, S.H., Sisk, D.M., Jurcic Smith, K.L., Medvitz, N.A., Miller, S.E., Trinh, L.A., Fraser, S.E., Madden, J.F., Turner, J., Stout, J.E., Lee, S., Tobin, D.M. (2016) Macrophage Epithelial Reprogramming Underlies Mycobacterial Granuloma Formation and Promotes Infection. Immunity. 45:861-876

Choi, H.M., Calvert, C.R., Husain, N., Huss, D., Barsi, J.C., Deverman, B.E., Hunter, R.C., Kato, M., Lee, S.M., Abelin, A.C., Rosenthal, A.Z., Akbari, O.S., Li, Y., Hay, B.A., Sternberg, P.W., Patterson, P.H., Davidson, E.H., Mazmanian, S.K., Prober, D.A., van de Rijn, M., Leadbetter, J.R., Newman, D.K., Readhead, C., Bronner, M.E., Wold, B., Lansford, R., Sauka-Spengler, T., Fraser, S.E., Pierce, N.A. (2016) Mapping a multiplexed zoo of mRNA expression. Development (Cambridge, England). 143:3632-3637

Gross, G.G., Straub, C., Perez-Sanchez, J., Dempsey, W.P., Junge, J.A., Roberts, R.W., Trinh, l.e. .A., Fraser, S.E., De Koninck, Y., De Koninck, P., Sabatini, B.L., Arnold, D.B. (2016) An E3-ligase-based method for ablating inhibitory synapses. Nature Methods. 13:673-8

Ju Shin, Y., Kyun Park, S., Jung Jung, Y., Na Kim, Y., Sung Kim, K., Kyu Park, O., Kwon, S.H., Ho Jeon, S., Trinh, l.e. .A., Fraser, S.E., Kee, Y., Joon Hwang, B. (2015) Nanobody-targeted E3-ubiquitin ligase complex degrades nuclear proteins. Scientific Reports. 5:14269

Trinh, L.A., and Fraser, S.E. (2013) Enhancer and gene traps for molecular imaging and genetic analysis in zebrafish. Development, growth & differentiation. 55(4):434-45

Palanca, A.M., Lee, S.L., Yee, L.E., Joe-Wong, C., Trinh, L.A., Hiroyasu, E., Husain, M., Fraser, S.E., Pellegrini, M., and Sagasti, A. (2013) New transgenic reporters identify somatosensory neuron subtypes in larval zebrafish. Developmental Neurobiology. 73(2):152-167

Culi-Viskota, J., Dempsey, W.P., Fraser, S.E., and Pantazis, P. (2012) Surface functionalization of barium titanate SHG nanoprobes for in vivo imaging in zebrafish. Nature Protocols. 7(9):1618-1633

Dempsey, W.P., Fraser, S.E., and Pantazis, P. (2012) PhOTO Zebrafish: A Transgenic Resource for In Vivo Lineage Tracing during Development and Regeneration. PLoS One. 7(3):e32888

Trinh, A., Hochgreb, T., Graham, M., Wu, D., Ruf-Zamojski, F., Jayasena, C.S., Saxena, A., Hawk, R., Gonzalez-Serricchio, A., Dixson, A., Chow, E., Gonzales, C., Leung, H.Y., Solomon, I., Bronner-Fraser, M., Megason, S.G., and Fraser, S.E. (2011) A versatile gene trap to visualize and interrogate the function of the vertebrate proteome. Genes & Development. 25(21):2306-20

Truong, T.V., Supatto, W., Koos, D.S., Choi, J.M., and Fraser, S.E. (2011) Deep and fast live imaging with two-photon scanned light-sheet microscopy. Nature Methods. 8(9):757-60

Hochheiser, H., Aronow, B.J., Artinger, K., Beaty, T.H., Brinkley, J.F., Chai, Y., Clouthier, D., Cunningham, M.L., Dixon, M., Donahue, L.R., Fraser, S.E., Hallgrimsson, B., Iwata, J., Klein, O., Marazita, M.L., Murray, J.C., Murray, S., de Villena, F.P., Postlethwait, J., Potter, S., Shapiro, L., Spritz, R., Visel, A., Weinberg, S.M., and Trainor, P.A. (2011) The FaceBase Consortium: a comprehensive program to facilitate craniofacial research. Developmental Biology. 355(2):175-182

Zigman, M., Trinh, L.A., Fraser, S.E., and Moens, C.B. (2011) Zebrafish Neural Tube Morphogenesis Requires Scribble-Dependent Oriented Cell Divisions. Current biology : CB. 21(1):79-86

Caneparo, L., Pantazis, P., Dempsey, W., and Fraser, S.E. (2011) Intercellular bridges in vertebrate gastrulation. PLoS One. 6(5):e20230

Quesada-Hernández, E., Caneparo, L., Schneider, S., Winkler, S., Liebling, M., Fraser, S.E., and Heisenberg, C.P. (2010) Stereotypical Cell Division Orientation Controls Neural Rod Midline Formation in Zebrafish. Current biology : CB. 20(21):1966-1972

Choi, H.M., Chang, J.Y., Trinh, L.A., Padilla, J.E., Fraser, S.E., and Pierce, N.A. (2010) Programmable in situ amplification for multiplexed imaging of mRNA expression. Nat. Biotechnol.. 28(11):1208-1212

Pantazis, P., Maloney, J., Wu, D., and Fraser, S.E. (2010) Second harmonic generating (SHG) nanoprobes for in vivo imaging. Proceedings of the National Academy of Sciences of the United States of America. 107(33):14535-14540

Vermot, J., Forouhar, A.S., Liebling, M., Wu, D., Plummer, D., Gharib, M., and Fraser, S.E. (2009) Reversing blood flows act through klf2a to ensure normal valvulogenesis in the developing heart. PLoS Biology. 7(11):e1000246

Colantonio, J.R., Vermot, J., Wu, D., Langenbacher, A.D., Fraser, S., Chen, J.N., and Hill, K.L. (2009) The dynein regulatory complex is required for ciliary motility and otolith biogenesis in the inner ear. Nature. 457(7226):205-209

Supatto, W., Fraser, S.E., and Vermot, J. (2008) An All-Optical Approach for Probing Microscopic Flows in Living Embryos. Biophysical journal. 95(4):L29-L31

Lu, J., Pereira, F., Fraser, S.E., and Gharib, M. (2008) Three-dimensional real-time imaging of cardiac cell motions in living embryos. Journal of Biomedical Optics. 13(1):014006

Liebling, M., Forouhar, A.S., Wolleschensky, R., Zimmermann, B., Ankerhold, R., Fraser, S.E., Gharib, M., and Dickinson, M.E. (2006) Rapid three-dimensional imaging and analysis of the beating embryonic heart reveals functional changes during development. Developmental Dynamics : an official publication of the American Association of Anatomists. 235(11):2940-2948

Koster, R.W., and Fraser, S.E. (2006) FGF signaling mediates regeneration of the differentiating cerebellum through repatterning of the anterior hindbrain and reinitiation of neuronal migration. The Journal of neuroscience : the official journal of the Society for Neuroscience. 26(27):7293-7304

Forouhar, A.S., Liebling, M., Hickerson, A., Nasiraei-Moghaddam, A., Tsai, H.J., Hove, J.R., Fraser, S.E., Dickinson, M.E., and Gharib, M. (2006) The embryonic vertebrate heart tube is a dynamic suction pump. Science (New York, N.Y.). 312(5774):751-753

Wang, J., Hamblet, N.S., Mark, S., Dickinson, M.E., Brinkman, B.C., Segil, N., Fraser, S.E., Chen, P., Wallingford, J.B., and Wynshaw-Boris, A. (2006) Dishevelled genes mediate a conserved mammalian PCP pathway to regulate convergent extension during neurulation. Development (Cambridge, England). 133(9):1767-1778

Rieger, S., Kulkarni, R.P., Darcy, D., Fraser, S.E., and Köster, R.W. (2005) Quantum dots are powerful multipurpose vital labeling agents in zebrafish embryos. Developmental Dynamics : an official publication of the American Association of Anatomists. 234(3):670-681

Liebling, M., Forouhar, A.S., Gharib, M., Fraser, S.E., and Dickinson, M.E. (2005) Four-dimensional cardiac imaging in living embryos via postacquisition synchronization of nongated slice sequences. Journal of Biomedical Optics. 10(5):54001

Gong, Y., Mo, C., and Fraser, S.E. (2004) Planar cell polarity signalling controls cell division orientation during zebrafish gastrulation. Nature. 430(7000):689-693

Köster, R.W., and Fraser, S.E. (2004) Time-lapse microscopy of brain development. The Zebrafish: Cellular and Developmental Biology,2nd Ed. Methods Cell Biol.. 76:207-235

Megason, S.G. and Fraser, S.E. (2003) Digitizing life at the level of the cell: high-performance laser-scanning microscopy and image analysis for in toto imaging of development. Mechanisms of Development. 120(11):1407-1420

Bak, M. and Fraser, S.E. (2003) Axon fasciculation and differences in midline kinetics between pioneer and follower axons within commissural fascicles. Development (Cambridge, England). 130(20):4999-5008

Hove, J.R., Köster, R.W., Forouhar, A.S., Acevedo-Bolton, G., Fraser, S.E., and Gharib, M. (2003) Intracardiac fluid forces are an essential epigenetic factor for embryonic cardiogenesis. Nature. 421(6919):172-177

Köster, R.W. and Fraser, S.E. (2001) Direct imaging of in vivo neuronal migration in the developing cerebellum. Current biology : CB. 11(23):1858-1863

Köster, R.W. and Fraser, S.E. (2001) Tracing transgene expression in living zebrafish embryos. Developmental Biology. 233(2):329-346

Woo, K. and Fraser, S.E. (1998) Specification of the hindbrain fate in the zebrafish. Developmental Biology. 197:283-296

Woo, K., and Fraser, S.E. (1997) Specification of the zebrafish nervous system by nonaxial signals. Science (New York, N.Y.). 277(5323):254-257

Shih, J. and Fraser, S.E. (1996) Characterizing the zebrafish organizer: microsurgical analysis at the early-shield stage. Development (Cambridge, England). 122:1313-1322

Shih, J. and Fraser, S.E. (1995) Distribution of tissue progenitors within the shield region of the zebrafish gastrula. Development (Cambridge, England). 121:2755-2765

Woo, K., Shih, J., and Fraser, S.E. (1995) Fate maps of the zebrafish embryo. Current opinion in genetics & development. 5:439-443

Woo, K. and Fraser, S.E. (1995) Order and coherence in the fate map of the zebrafish nervous system. Development (Cambridge, England). 121:2595-2609

Collazo, A., Fraser, S.E., and Mabee, P.M. (1994) A dual embryonic origin for vertebrate mechanoreceptors. Science (New York, N.Y.). 264:426-430

NON-ZEBRAFISH PUBLICATIONS