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Research
General Information
ZIRC
ZFIN ID: ZDB-PERS-960805-349
Malicki, Jarema (Deceased)
Email: J.Malicki@sheffield.ac.uk
URL: http://cdbg.shef.ac.uk/research/malicki/
Affiliation: Malicki Lab
Address: MRC Centre for Developmental and Biomedical Genetics Department of Biomedical Science, The University of Sheffield Firth Court, Western Bank Sheffield S10 2TN UK
Country: United States
Phone: +44 (0)114 222-4638
Fax: +44 (0)114 222-2787
Orcid ID:


BIOGRAPHY AND RESEARCH INTERESTS
Genetic basis of neuronal identity and pattern in the zebrafish retina.


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

NON-ZEBRAFISH PUBLICATIONS
1. Settleman, J., Fazeli, A., Malicki, J., Horwitz, B. H. and DiMaio, D. (1989). Genetic evidence that acute morphologic transformation, induction of cellular DNA synthesis, and focus formation are mediated by a single activity of the bovine papillomavirus E5 protein. Mol Cell Biol 9, 5563-72.

2. Malicki, J., Schughart, K. and McGinnis, W. (1990). Mouse Hox-2.2 specifies thoracic segmental identity in Drosophila embryos and larvae. Cell 63, 961-967.

3. Malicki, J., Cianetti, L. C., Peschle, C. and McGinnis, W. (1992). A human HOX4B regulatory element provides head-specific expression in Drosophila embryos. Nature 358, 345-347.

4. Malicki, J., Bogarad, L. D., Martin, M. M., Ruddle, F. H. and McGinnis, W. (1993). Functional analysis of the mouse homeobox gene HoxB9 in Drosophila development. Mech Dev 42, 139-150.