ZFIN Lab: Malicki Lab

ZFIN ID: ZDB-LAB-990303-4

Malicki Lab

PI/Director:	Malicki, Jarema
Contact Person:	Malicki, Jarema
Email:	J.Malicki@sheffield.ac.uk
URL:	http://cdbg.shef.ac.uk/research/malicki/
Address:	Bateson Centre Department of Biomedical Science The University of Sheffield Firth Court, Western Bank Sheffield S10 2TN UK
Country:	United Kingdom
Phone:	+44 (0)114 222-4638
Fax:	+44 (0)114 222-2787
Line Designation:	sh

GENOMIC FEATURES ORIGINATING FROM THIS LAB

Show all 36 genomic features

STATEMENT OF RESEARCH INTERESTS

Genetic basis of cellular diversity and pattern in the retina and the sensory maculae of the ear.

LAB MEMBERS

Omori, Yoshihiro Post-Doc	Pujic, Zac Post-Doc	Arslanova, Dilya Technical Staff
Avanesov, Andrei S. Technical Staff	Okafor, Obioma Technical Staff	Perez, Jean Technical Staff
Rateau, Patrice Technical Staff	Romasco, Rebecca Technical Staff

ZEBRAFISH PUBLICATIONS OF LAB MEMBERS

Leventea, E., Zhu, Z., Fang, X., Nikolaeva, Y., Markham, E., Hirst, R.A., van Eeden, F.J.M., Malicki, J.J. (2021) Ciliopathy genes are required for apical secretion of Cochlin, an otolith crystallization factor. Proceedings of the National Academy of Sciences of the United States of America. 118(28):

Fang, X., Peden, A.A., van Eeden, F.J.M., Malicki, J.J. (2021) Identification of additional outer segment targeting signals in zebrafish rod opsin. Journal of Cell Science. 134(6):

Avitan, L., Pujic, Z., Mölter, J., McCullough, M., Zhu, S., Sun, B., Myhre, A.E., Goodhill, G.J. (2020) Behavioral Signatures of a Developing Neural Code. Current biology : CB. 30(17):3352-3363.e5

Chen, Z., Omori, Y., Koren, S., Shirokiya, T., Kuroda, T., Miyamoto, A., Wada, H., Fujiyama, A., Toyoda, A., Zhang, S., Wolfsberg, T.G., Kawakami, K., Phillippy, A.M., NISC Comparative Sequencing Program, Mullikin, J.C., Burgess, S.M. (2019) De novo assembly of the goldfish (Carassius auratus) genome and the evolution of genes after whole-genome duplication. Science advances. 5:eaav0547

Elworthy, S., Savage, A.M., Wilkinson, R.N., Malicki, J.J., Chico, T.J.A. (2019) The role of endothelial cilia in post-embryonic vascular development. Developmental Dynamics : an official publication of the American Association of Anatomists. 248(6):410-425

Omori, Y., Kon, T. (2018) Goldfish: An old and new model system to study vertebrate development, evolution, and human disease. Journal of biochemistry. 165(3):209-218

van Leeuwen, L.M., Evans, R.J., Jim, K.K., Verboom, T., Fang, X., Bojarczuk, A., Malicki, J., Johnston, S.A., van der Sar, A.M. (2018) A transgenic zebrafish model for the in vivo study of the blood and choroid plexus brain barriers using claudin 5.. Biology Open. 7(2)

Radhakrishnan, U., Alsrhani, A., Sundaramoorthi, H., Khandekar, G., Kashyap, M., Fuchs, J.L., Perkins, B.D., Omori, Y., Jagadeeswaran, P. (2017) Intraflagellar transport proteins are involved in thrombocyte filopodia formation and secretion. Platelets. 29(8):811-820

Hazime, K., Malicki, J.J. (2017) Apico-basal Polarity Determinants Encoded by crumbs Genes Affect Ciliary Shaft Protein Composition, IFT Movement Dynamics, and Cilia Length.. Genetics. 207(3):1041-1051

Avitan, L., Pujic, Z., Mölter, J., Van De Poll, M., Sun, B., Teng, H., Amor, R., Scott, E.K., Goodhill, G.J. (2017) Spontaneous Activity in the Zebrafish Tectum Reorganizes over Development and Is Influenced by Visual Experience. Current biology : CB. 27(16):2407-2419.e4

Boubakri, M., Chaya, T., Hirata, H., Kajimura, N., Kuwahara, R., Ueno, A., Malicki, J., Furukawa, T., Omori, Y. (2016) Loss of ift122, a Retrograde IFT Complex Component, Leads to Slow, Progressive Photoreceptor Degeneration Due to Inefficient Opsin Transport. The Journal of biological chemistry. 291(47):24465-24474

Pooranachandran, N., Malicki, J.J. (2016) Unexpected Roles for Ciliary Kinesins and Intraflagellar Transport Proteins. Genetics. 203(2):771-85

Avitan, L., Pujic, Z., Hughes, N.J., Scott, E.K., Goodhill, G.J. (2016) Limitations of Neural Map Topography for Decoding Spatial Information. The Journal of neuroscience : the official journal of the Society for Neuroscience. 36:5385-96

Leventea, E., Hazime, K., Zhao, C., Malicki, J. (2016) Analysis of cilia structure and function in zebrafish. Methods in cell biology. 133:179-227

Malicki, J., Pooranachandran, N., Nikolaev, A., Fang, X., Avanesov, A. (2016) Analysis of the retina in the zebrafish model. Methods in cell biology. 134:257-334

Goodhill, G.J., Faville, R.A., Sutherland, D.J., Bicknell, B.A., Thompson, A.W., Pujic, Z., Sun, B., Kita, E.M., Scott, E.K. (2015) The dynamics of growth cone morphology. BMC Biology. 13:10

Jin, D., Ni, T.T., Sun, J., Wan, H., Amack, J.D., Yu, G., Fleming, J., Chiang, C., Li, W., Papierniak, A., Cheepala, S., Conseil, G., Cole, S.P., Zhou, B., Drummond, I.A., Schuetz, J.D., Malicki, J., Zhong, T.P. (2014) Prostaglandin signalling regulates ciliogenesis by modulating intraflagellar transport. Nature cell biology. 16(9):841-51

Malicki, J., and Besharse, J.C. (2012) Kinesin-2 family motors in the unusual photoreceptor cilium. Vision Research. 75:33-36

Zhao, C., Omori, Y., Brodowska, K., Kovach, P., and Malicki, J. (2012) Kinesin-2 family in vertebrate ciliogenesis. Proceedings of the National Academy of Sciences of the United States of America. 109(7):2388-2393

Avanesov, A., Honeyager, S.M., Malicki, J., and Blair, S.S. (2012) The Role of Glypicans in Wnt Inhibitory Factor-1 Activity and the Structural Basis of Wif1's Effects on Wnt and Hedgehog Signaling. PLoS Genetics. 8(2):e1002503

Zhao, C., and Malicki, J. (2011) Nephrocystins and MKS proteins interact with IFT particle and facilitate transport of selected ciliary cargos. The EMBO journal. 30(13):2532-2544

Malicki, J., Avanesov, A., Li, J., Yuan, S., and Sun, Z. (2011) Analysis of cilia structure and function in zebrafish. Methods (San Diego, Calif.). 101:39-74

den Hollander, A.I., Biyanwila, J., Kovach, P., Bardakjian, T., Traboulsi, E., Ragge, N.K., Schneider, A., and Malicki, J. (2010) Genetic defects of GDF6 in the zebrafish out of sight mutant and in human eye developmental anomalies. BMC Genetics. 11:102

Beyer, J., Zhao, X.C., Yee, R., Khaliq, S., McMahon, T.T., Ying, H., Yue, B.Y., and Malicki, J.J. (2010) The role of crumbs genes in the vertebrate cornea. Investigative ophthalmology & visual science. 51(9):4549-4556

Yang, T., Arslanova, D., Xu, X., Li, Y.M., and Xia, W. (2010) In Vivo Manifestation of Notch Related Phenotypes in Zebrafish Treated with Alzheimer's Amyloid Reducing gamma-Secretase Inhibitors. Journal of neurochemistry. 113(5):1200-1209

Chao, R., Nevin, L., Agarwal, P., Riemer, J., Bai, X., Delaney, A., Akana, M., JimenezLopez, N., Bardakjian, T., Schneider, A., Chassaing, N., Schorderet, D.F., FitzPatrick, D., Kwok, P.Y., Ellgaard, L., Gould, D.B., Zhang, Y., Malicki, J., Baier, H., and Slavotinek, A. (2010) A male with unilateral microphthalmia reveals a role for TMX3 in eye development. PLoS One. 5(5):e10565

Avanesov, A., and Malicki, J. (2010) Chapter 6 - Analysis of the retina in the zebrafish model. Methods in cell biology. 100:153-204

Jing, X., and Malicki, J. (2009) Zebrafish ale oko, an essential determinant of sensory neuron survival and the polarity of retinal radial glia, encodes the p50 subunit of dynactin. Development (Cambridge, England). 136(17):2955-2964

Zhang, Y., McCulloch, K., and Malicki, J. (2009) Lens transplantation in zebrafish and its application in the analysis of eye mutants. Journal of visualized experiments : JoVE. (28)

Kitambi, S.S., McCulloch, K.J., Peterson, R.T., and Malicki, J.J. (2009) Small molecule screen for compounds that affect vascular development in the zebrafish retina. Mechanisms of Development. 126(5-6):464-477

Kitambi, S.S., and Malicki, J.J. (2008) Spatiotemporal features of neurogenesis in the retina of medaka, Oryzias latipes. Developmental Dynamics : an official publication of the American Association of Anatomists. 237(12):3870-3881

Omori, Y., Zhao, C., Saras, A., Mukhopadhyay, S., Kim, W., Furukawa, T., Sengupta, P., Veraksa, A., and Malicki, J. (2008) elipsa is an early determinant of ciliogenesis that links the IFT particle to membrane-associated small GTPase Rab8. Nature cell biology. 10(4):437-444

Liu, T., Li, G., Nie, J., Tarokh, A., Zhou, X., Guo, L., Malicki, J., Xia, W., and Wong, S.T. (2008) An Automated Method for Cell Detection in Zebrafish. Neuroinformatics. 6(1):5-21

Li, G., Liu, T., Nie, J., Guo, L., Malicki, J., Mara, A., Holley, S.A., Xia, W., and Wong, S.T. (2007) Detection of blob objects in microscopic zebrafish images based on gradient vector diffusion. Cytometry. Part A : the journal of the International Society for Analytical Cytology. 71(10):835-845

Tsujikawa, M., Omori, Y., Biyanwila, J., and Malicki, J. (2007) Mechanism of positioning the cell nucleus in vertebrate photoreceptors. Proceedings of the National Academy of Sciences of the United States of America. 104(37):14819-14824

Schibler, A., and Malicki, J. (2007) A screen for genetic defects of the zebrafish ear. Mechanisms of Development. 124(7-8):592-604

Zhao, C., and Malicki, J. (2007) Genetic defects of pronephric cilia in zebrafish. Mechanisms of Development. 124(7-8):605-616

Zhao, X.C., Yee, R.W., Norcom, E., Burgess, H., Avanesov, A.S., Barrish, J.P., and Malicki, J. (2006) The zebrafish cornea: structure and development. Investigative ophthalmology & visual science. 47(10):4341-4348

Omori, Y., and Malicki, J. (2006) oko meduzy and Related crumbs Genes Are Determinants of Apical Cell Features in the Vertebrate Embryo. Current biology : CB. 16(10):945-957

Pujic, Z., Omori, Y., Tsujikawa, M., Thisse, B., Thisse, C., and Malicki, J. (2006) Reverse genetic analysis of neurogenesis in the zebrafish retina. Developmental Biology. 293(2):330-347

Otteson, D.C., Tsujikawa, M., Gunatilaka, T., Malicki, J., and Zack, D.J. (2005) Genomic organization of zebrafish cone-rod homeobox gene and exclusion as a candidate gene for retinal degeneration in niezerka and mikre oko. Molecular Vision. 11:986-995

Avanesov, A., Dahm, R., Sewell, W.F., and Malicki, J.J. (2005) Mutations that affect the survival of selected amacrine cell subpopulations define a new class of genetic defects in the vertebrate retina. Developmental Biology. 285(1):138-155

Tsujikawa, M., and Malicki, J. (2004) Intraflagellar transport genes are essential for differentiation and survival of vertebrate sensory neurons. Neuron. 42(5):703-716

Pujic, Z., and Malicki, J. (2004) Retinal pattern and the genetic basis of its formation in zebrafish. Seminars in cell & developmental biology. 15(1):105-114

Avanesov, A., and Malicki, J. (2004) Approaches to study neurogenesis in the zebrafish retina. The Zebrafish: Cellular and Developmental Biology,2nd Ed. Methods Cell Biol.. 76:333-384

Tsujikawa, M., and Malicki, J. (2004) Genetics of photoreceptor development and function in zebrafish. The International journal of developmental biology. 48(8-9):925-934

Malicki, J., Jo, H., and Pujic, Z. (2003) Zebrafish N-cadherin, encoded by the glass onion locus, plays an essential role in retinal patterning. Developmental Biology. 259(1):95-108

Malicki, J., Jo, H., Wei, X., Hsiung, M., and Pujic, Z. (2002) Analysis of gene function in the zebrafish retina. Methods (San Diego, Calif.). 28(4):427-438

Bang, P., Yelick, P., Malicki, J., and Sewell, W. (2002) High-throughput behavioral screening method for detecting auditory response defects in zebrafish. Journal of Neuroscience Methods. 118(2):177-187

Wei, X. and Malicki, J. (2002) nagie oko, encoding a MAGUK-family protein, is essential for cellular patterning of the retina. Nature Genetics. 31(2):150-157

Malicki, J.J., Pujic, Z., Thisse, C., Thisse, B., and Wei, X. (2002) Forward and reverse genetic approaches to the analysis of eye development in zebrafish. Vision Research. 42(4):527-533

Doerre, G. and Malicki, J. (2002) Genetic analysis of photoreceptor cell development in the zebrafish retina. Mechanisms of Development. 110(1-2):125-138

Bang, P.I., Sewell, W.F., and Malicki, J.J. (2001) Morphology and cell type heterogeneities of the inner ear epithelia in adult and juvenile zebrafish (Danio rerio). The Journal of comparative neurology. 438(2):173-190

Doerre, G. and Malicki, J. (2001) A mutation of early photoreceptor development, mikre oko, reveals cell-cell interactions involved in the survival and differentiation of zebrafish photoreceptors. The Journal of neuroscience : the official journal of the Society for Neuroscience. 21(17):6745-6757

Pujic, Z. and Malicki, J. (2001) Mutation of the zebrafish glass onion locus causes early cell-nonautonomous loss of neuroepithelial integrity followed by severe neuronal patterning defects in the retina. Developmental Biology. 234(2):454-469

Malicki, J. (2000) Harnessing the power of forward genetics – analysis of neuronal diversity and patterning in the zebrafish retina. Trends in neurosciences. 23(11):531-541

Link, B.A., Fadool, J.M., Malicki, J., and Dowling, J.E. (2000) The zebrafish young mutation acts non-cell-autonomously to uncouple differentiation from specification for all retinal cells. Development (Cambridge, England). 127(10):2177-2188

Malicki, J. (2000) Genetic analysis of eye development in zebrafish. In Vertebrate Eye Development, E. Fini, ed., in Results and Problems in Cell Differentiation.

Malicki, J. and Driever, W. (1999) oko meduzy mutations affect neuronal patterning in the zebrafish retina and reveal cell-cell interactions of the retinal neuroepithelial sheet. Development (Cambridge, England). 126:1235-1246

Malicki, J. (1999) Development of the retina. Methods in cell biology. 59:273-299

Marlow, F., Zwartkruis, F., Malicki, J., Neuhauss, S.C.F., Abbas, L., Weaver, M., Driever, W., and Solnica-Krezel, L. (1998) Functional interactions of genes mediating convergent extension, knypek and trilobite, during the partitioning of the eye primordium in zebrafish. Developmental Biology. 203:382-399

Abdelilah, S., Mountcastle-Shah, E., Harvey, M., Solnica-Krezel, L., Schier, A.F., Stemple, D.L., Malicki, J., Neuhauss, S.C., Zwartkruis, F., Stainier, D.Y., Rangini, Z., and Driever, W. (1996) Mutations affecting neural survival in the zebrafish Danio rerio. Development (Cambridge, England). 123:217-227

Driever, W., Solnica-Krezel, L., Schier, A.F., Neuhauss, S.C., Malicki, J., Stemple, D.L., Stainier, D.Y., Zwartkruis, F., Abdelilah, S., Rangini, Z., Belak, J., and Boggs, C. (1996) A genetic screen for mutations affecting embryogenesis in zebrafish. Development (Cambridge, England). 123:37-46

Malicki, J., Neuhauss, S.C., Schier, A.F., Solnica-Krezel, L., Stemple, D.L., Stainier, D.Y., Abdelilah, S., Zwartkruis, F., Rangini, Z., and Driever, W. (1996) Mutations affecting development of the zebrafish retina. Development (Cambridge, England). 123:263-273

Malicki, J., Schier, A.F., Solnica-Krezel, L., Stemple, D.L., Neuhauss, S.C., Stainier, D.Y., Abdelilah, S., Rangini, Z., Zwartkruis, F., and Driever, W. (1996) Mutations affecting development of the zebrafish ear. Development (Cambridge, England). 123:275-283

Neuhauss, S.C., Solnica-Krezel, L., Schier, A.F., Zwartkruis, F., Stemple, D.L., Malicki, J., Abdelilah, S., Stainier, D.Y., and Driever, W. (1996) Mutations affecting craniofacial development in zebrafish. Development (Cambridge, England). 123:357-367

Pack, M., Solnica-Krezel, L., Malicki, J., Neuhauss, S.C., Schier, A-, F., Stemple, D.L., Driever, W., and Fishman, M.C. (1996) Mutations affecting development of zebrafish digestive organs. Development (Cambridge, England). 123:321-328

Schier, A.F., Neuhauss, S.C., Harvey, M., Malicki, J., Solnica-Krezel, L., Stainier, D.Y., Zwartkruis, F., Abdelilah, S., Stemple, D.L., Rangini, Z., Yang, H., and Driever, W. (1996) Mutations affecting the development of the embryonic zebrafish brain. Development (Cambridge, England). 123:165-178

Solnica-Krezel, L., Stemple, D.L., Mountcastle-Shah, E., Rangini, Z., Neuhauss, S.C., Malicki, J., Schier, A.F., Stainier, D.Y., Zwartkruis, F., Abdelilah, S., and Driever, W. (1996) Mutations affecting cell fates and cellular rearrangements during gastrulation in zebrafish. Development (Cambridge, England). 123:67-80

Stainier, D.Y., Fouquet, B., Chen, J.N., Warren, K.S., Weinstein, B.M., Meiler, S.E., Mohideen, M.A., Neuhauss, S.C., Solnica-Krezel, L., Schier, A.F., Zwartkruis, F., Stemple, D.L., Malicki, J., Driever, W., and Fishman, M.C. (1996) Mutations affecting the formation and function of the cardiovascular system in the zebrafish embryo. Development (Cambridge, England). 123:285-292

Stemple, D.L., Solnica-Krezel, L., Zwartkruis, F., Neuhauss, S.C., Schier, A.F., Malicki, J., Stainier, D.Y., Abdelilah, S., Rangini, Z., Mountcastle-Shah, E., and Driever, W. (1996) Mutations affecting development of the notochord in zebrafish. Development (Cambridge, England). 123:117-128

Weinstein, B.M., Schier, A.F., Abdelilah, S., Malicki, J., Solnica-Krezel, L., Stemple, D.L., Stainier, D.Y., Zwartkruis, F., Driever, W., and Fishman, M.C. (1996) Hematopoietic mutations in the zebrafish. Development (Cambridge, England). 123:303-309

Abdelilah, S.,Driever, W., Gorn, A., Malicki,J., Neuhauss, S., Pack, M., Rangini, Z., Schier, A., Solnica-Krezel, L., Stanier, D., and Stemple, D. (1996) Anatomy of the 24, 48, 72 and 120 hours Zebrafish (Danio rerio) Embryo. ZFIN Direct Data Submission.