Zeller Publications

Chen JS, Revilla AC, Guerrero M, Gumbayan AM, Zeller RW (2015). Properties and kinetics of microRNA regulation through canonical seed sites. J RNAi Gene Silencing 11: 506-514. Paper

Chen, JS, Gumbayan, AM, Zeller, RW and Mahaffy, JM. (2014). An Expanded Notch-Delta Model Exhibiting Long-Range Patterning and Incorporating microRNA Regulation. PLoS Comput Biol 10(6): e1003655. doi:10.1371/journal.pcbi.1003655

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Chen, JS and Zeller, RW. (2014). Using Engineered microRNAs as Vectors for Animal RNA Interference: Promises and Challenges. Advances in Bioscience and Biotechnology. doi:10.4236/abb.2014.54037

Aihara, H., Katikala, L., Zeller, RW., Di Gregorio, A., and Nibu, Y. (2013). Optimization of a method for chromatin immunoprecipitation assays in the marine invertebrate chordate Ciona. Marine Biotechnology 15:520-525. doi:10.1007/s10126-013-9504-5

Tang, W.J, Chen, J.S., and Zeller, RW. (2013). Transcriptional Regulation of the Peripheral Nervous System in Ciona intestinalis. Developmental Biology 378:183-193. doi:10.1016/j.ydbio.2013.03.016

Chen, JS, San Pedro, M, and Zeller, RW. (2011). miR-124 function during Ciona intestinalis neuronal development includes extensive interaction with the Notch signaling pathway. Development 138:4943-4953. doi:10.1242/dev.068049

Zeller RW. (2010). Computational Analysis of Ciona intestinalis Operons Integrative and Comparative Biology 50(1):75-85. doi:10.1093/icb/icq040

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Matsumoto J, Dewar K, Wasserscheid J, Wiley GB, Macmil SL, Roe BA, Zeller RW, Satou Y, Hastings KE. (2010). High-throughput sequence analysis of Ciona intestinalis SL trans-spliced mRNAs: alternative expression modes and gene function correlates. Genome Research 20(5):636-645. doi:10.1101/gr.100271.109

Virata MJ, and Zeller RW. (2010). Ascidians: an invertebrate chordate model to study Alzheimer's disease pathogenesis. Disease Models and Mechanisms 3(5-6):377-385. doi:10.1242/dmm.003434

Keshavan R, Virata M, Keshavan A, Zeller RW. (2010). Computational identification of Ciona intestinalis microRNAs. Zoological Science 27(2):162-170. doi:10.2108/zsj.27.162

Satou Y, Mineta K, Ogasawara M, Sasakura Y, Shoguchi E, Ueno K, Yamada L, Matsumoto J, Wasserscheid J, Dewar K, Wiley GB, Macmil SL, Roe BA, Zeller RW, Hastings KE, Lemaire P, Lindquist E, Endo T, Hotta K, Inaba K. (2008). Improved genome assembly and evidence-based global gene model set for the chordate Ciona intestinalis: new insight into intron and operon populations. Genome Biology Oct.14; 9(10):R152. doi:10.1186/gb-2008-9-10-r152

Leoni LM, Bailey B, Reifert J, Bendall HH, Zeller RW, Corbeil J, Elliott G, Niemeyer CC. (2008). Bendamustine (Treanda) displays a distinct pattern of cytotoxicity and unique mechanistic features compared with other alkylating agents. Clincal Cancer Research 14(1) 309-317. doi:10.1158/1078-0432.CCR-07-1061

Zeller RW, Virata MJ, Cone AC. (2006). Predictable mosaic transgene expression in ascidian embryos using a simple electroporation device. Developmental Dynamics 235(7) 1921-1932. doi:10.1002/dvdy.20815

Zeller, R.W., Weldon, D., Pellatiro, M. and Cone, A. C. (2006). Optimized GFP variants provide single cell resolution of transgene expression in ascidian embryos. Developmental Dynamics 235(2) 456-467. doi:10.1002/dvdy.20644

Cone, A.C. and Zeller, R.W. (2005). Using Ascidian Embryos to Study the Evolution of Developmental Gene Regulatory Networks. Canadian Journal of Zoology 83(1): 75-89. doi:10.1139/z04-165

Zeller, R.W. (2004). Generation and use of transgenic ascidian embryos. Methods in Cell Biology 74: 713-730. doi:10.1016/S0091-679X(04)74029-7

Bower KE, Zeller R.W., Wachsman W, Martinez T, McGuire KL. (2002) Correlation of transcriptional repression by p21SNFT with changes in DNA/NF-AT complex interactions. J. Biol Chem. 277(38):34967-34977. doi:10.1074/jbc.M205048200

Takahashi, H., Hotta, K., Erives, A., Di Gregorio, A., Zeller, R.W., Levine, M., and Satoh, N. (1999) Brachyury downstream notochord differentiation in the ascidian embryo. Genes & Dev. 13: 1519-1523.

Corbo, J.C., Levine, M. and Zeller,R.W. (1997). Characterization of a notochord-specific enhancer from the Brachyury promoter region of the ascidian, Ciona intestinalis. Development 124: 589-602.

Zeller, R.W., Griffith, J.D., Moore, J.G., Kirchhamer, C.V., Britten, R.J.and Davidson, E.H. (1995). A multimerizing transcription factor of sea urchin embryos capable of looping DNA. Proc. Nat. Acad. Sci. USA. 92:2989-2993.

Zeller, R.W., Coffman, J.A., Harrington, M.G., Britten, R.J. and Davidson, E.H. (1995). SpGCF1, a sea urchin embryo DNA binding protein, exists as five nested variants encoded by a single mRNA. Dev. Biol. 169: 713-727.

Zeller, R.W., Britten, R.J. and Davidson, E.H. (1995). Developmental utilization of SpP3a1 and SpP3a2: Two proteins which recognize the same DNA target site in several sea urchin gene regulatory regions. Dev. Biol. 170: 75-82.

Zeller, R.W., Cameron, R.A., Franks, R.R., Britten, R.J. and Davidson, E.H. (1992). Territorial expression of 3 different trans-genes in early sea urchin embryos detected by a whole-mount fluorescence procedure. Dev. Biol. 151:382-390.

Calzone, F.J., Hoog, C., Teplow, D.B., Cutting, A.E., Zeller, R.W., Britten, R.J. and Davidson, E.H. (1991). Gene regulatory factors of the sea urchin embryo. I. Purification by affinity-chromatography and cloning of P3A2, a novel sea urchin DNA binding protein. Development 112:335-350.

Hough-Evans, B.R., Franks, R.R., Zeller, R.W., Britten, R.J. and Davidson, E.H. (1990). Negative spatial regulation of the lineage-specific CyIIIa actin gene in the sea urchin embryo. Development 110:41-50.

Costello, J.H., Strickler, J.R., Marrase, C., Trager, G. and Zeller, R. (1990). Grazing in a turbulent environment - behavioral response of a calanoid copepod, Centropages hamatus. Proc. Nat. Acad. Sci. USA. 87:1648-1652.

Book Chapters

Zeller, R.W. and Cameron, R.A (2008). Chapter 30, Lower Deuterostomes as Models of the Developmental Process. In Oceans and Human Health. . PJ Walsh, S Smith, L Fleming, H Solo-Gabriele and WH Gerwich, Editors. Elsevier Press.

Zeller, R.W. (2004). Chapter 29, Generation and Use of Transgenic Ascidian Embryos. In Development of Sea Urchins, Ascidians, and Other Invertebrate Deuterostomes: Experimental Approaches. Methods in Cell Biology Vol. 74. C.A. Ettensohn, G.A. Wray, and G.M. Wessel, Editors. Elsevier Press.

Zeller, R.W. (1997). Chapter 23, Marine Invertebrate Eggs. In Cells: A laboratory manual. D.L. Spector, R. Goldman, L. Leinwand, Editors. Cold Spring Harbor Laboratory Press.

Cameron, R.A., Zeller, R.W., Coffman, J.A. and Davidson, E.H. (1996). The analysis of lineage specific gene activity during sea urchin development. In Molecular Zoology: Advances, Strategies, and Protocols. Joan D. Ferraris and Stephen R. Palumbi, Editors. New York : Wiley-Liss.