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modeling
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Book
Peter D. Vize, Adrian S. Woolf &
Jonathan Bard (Editors).
The Kidney; From Normal Development to Congenital Disease.
Academic Press, Amsterdam. ISBN: 0127224416. Published February, 2003. Check it out on Google Books
To view a sample download
Chapter 1
For independent reviews of this book see:
New Eng. J.Med. 349: 2176
Am. J.Kid. Diseases 42: 427 (I like
this one!)
Dev. Dyn. 230: 389.
Trends Endocrinol. Metab. 15: 250.
Hoppler, S and Vize, P.D. (Editors). Xenopus Protocols, Second Edition. Methods in Molecular Biology Series, Springer 2012.
Papers
Hilton. D., Brady, A.K., Spapho, S. and Vize, P.D. (2012). Photoreception and signal transduction in corals; proteomic and behavioral evidence for cytoplasmic calcium as a mediator of light responsivity. Biological Bulletin 223: 291-299.
Dubaissi, E., Panagiotaki, N., Papalopulu, N. and Vize P.D. (2012) Antibody development and use in chromogenic and fluorescent immunostaining. In Hoppler, S and Vize, P.D. (Editors). Xenopus Protocols, Second Edition. Methods in Molecular Biology series, Springer 2012.
Lea, R., Bonev, B., Dubaissi, E., Vize, P.D. and Papalopulu, N. (2012) Triple fluorescent in situ hybridization (FISH) on whole mounts and sections. In Hoppler, S and Vize, P.D. (Editors). Xenopus Protocols, Second Edition. Methods in Molecular Biology series, Springer 2012.
Bhalla, N., Bentley, P.J., Vize, P.D. and Jacob, C. (2012). Programming and evolving physical self-assembling systems in three dimensions. Natural Computing Journal. DOI 10.1007/s11047-011-9293-6
Brady. A.K., Snyder, K. and Vize, P.D. (2011). Circadian cycles of gene expression in the coral, Acropora millepora. PLoS One 6(9): e25072
McCoy, K.E., Zhou, X. and Vize, P.D. (2011). Non-canonical wnt signals antagonize and canonical wnt signals promote cell proliferation in early kidney development. Developmental Dynamics 240; 1558-1566
Bhalla, N., Bentley, P.J., Vize, P. D. and Jacob, C. (2011). Staging the self-assembly process using morphological information. European Conference on Artificial Life (ECAL 2011) Proceedings of the Eleventh European Conference on the Synthesis and Simulation of Living Systems. Edited by Tom Lenaerts, Mario Giacobini, Hugues Bersini, Paul Bourgine, Marco Dorigo and René Doursat. Download (13.5 mb).
Hellsten, U, Harland, R.M., Gilchrist, M.J., Hendrix, D., Jurka, J., Kapitonov, V., Ovcharenko, I., Putnam, N.H., Shu, S., Taher, L, Blitz, I.L., Blumberg, B., Dichmann, D.S., Dubchak, I., Amaya, E., Detter, J.C., Fletcher, R., Gerhard, D.S., Goodstein, D., Graves, T., Grigoriev, I.V., Grimwood, .J, Kawashima, T., Lindquist, E., Lucas, S.M., Mead, P.E., Mitros, T., Ogino, H., Ohta, Y., Poliakov, A.V., Pollet, N., Robert, J., Salamov, A., Sater, A.K., Schmutz, J., Terry, A., Vize, P.D., Warren, W.C., Wells, D., Wills, A., Wilson, R.K., Zimmerman, L.B., Zorn, A.M., Grainger, R., Grammer, T., Khokha, M.K., Richardson, P.M. and Rokhsar, D.S. (2010) The genome of the western clawed frog Xenopus tropicalis. Science 328: 633-636.
Jeff B. Bowes, Kevin A. Snyder, Erik Segerdell, Chris J. Jarabek, Kenan Azam, Aaron M. Zorn and Peter D. Vize (2009). Xenbase: Gene expression and improved integration. Nucl. Acids Res. doi:10.1093/nar/gkp953
Peter D. Vize, Kyle E. McCoy and Zhou, X. (2009) Multichannel wholemount fluorescent and fluorescent/ chromogenic in situ hybridization of Xenopus embryos. Nature Protocols 4: 975-983
Lyons, J.P., Miller, R.K., Zhou, X., Weidinger, G., Denayer, T., Park, J-I., Ji, H., Deroo, T., Jones, E.A. Moon, R.T., Vleminckx, K., Vize, P.D. and McCrea, P.D. (2009) Canonical wnt signaling is required for pronephric tubule development. Mechanisms of Development 126, 142-159.
A.K.Brady, J.D. Hilton and Peter D. Vize (2009). Coral spawn timing is a direct response to solar light cycles and is not an entrained circadian response. Coral Reefs 28: 677-680
Vize, P.D. (2009) Transcriptome analysis of the circadian regulatory network in the coral, Acropora millepora. Biological Bulletin 216; 131-137. (Editors pick- free full content)
Davies, S.W. and Vize, P.D. (2008). Effects of herbivore grazing on juvenile coral growth in the Gulf of Mexico. Proc. 11th ICRS, 23: 1220-1222.
Vize, P.D., Hilton, J.D., Brady, A.K. and Davies, S.W. (2008). Light sensing and the coordination of coral broadcast spawning behavior. Proc. 11th ICRS, 11: 385-388.
Segerdell, E., Bowes, J.B., Pollet, N. and Vize, P.D. (2008) The Xenopus Anatomical Ontology: a comprehensive map of development in a model vertebrate. BMC Developmental Biology 2008, 8: 92-98.
McCoy, K., Zhou, X., and Vize, P.D. (2008). Collectrin/tmem27 is expressed at high levels in all segments of the developing Xenopus pronephric nephron and in the Wolffian duct. Gene Exp. Patterns, 8: 271-274.
Bowes, J.B., Snyder, K.. Segerdell, E., Gibb, R., Jarabek, C., Noumen, E., Pollet, N. and Vize, P.D. (2008). Xenbase: a Xenopus biology and genomics resource. Nucl. Acids. Res. 36: D761-D767.
Vize, P.D. and Gerth, V.E. (2007). Adaptation of videogame UVW mapping to 3D visualization of gene expression patterns. Proc. SPIE.
Urban, A., Zhou, X. Ungoss, J., Raible, D.W., Altmann, C.R. and Vize, P.D. (2006). FGF is essential for both condensation and mesenchymal-epithelial transition stages of pronephric kidney tubule development.. Developmental Biology 297, 103-117.
Vize, P.D. (2006). Deep water broadcast spawning by Montastraea cavernosa, M. franksi and Diploria strigosa at the Flower Garden Banks, Gulf of Mexico. Coral Reefs, 25; 169-171.
Vize, P.D., Embesi, J.A., Nickell, M., Brown, D.P. and Hagman, D.K. (2005). Tight temporal consistency of coral mass spawning at the Flower Garden Banks, Gulf of Mexico, from 1997 - 2003. Gulf of Mexico Science 23: 107-114.
Zhou, X. and Vize,
P.D. (2005a). Amino acid cotransporter SLC3A2 is selectively expressed in
the early proximal segment of Xenopus pronephric kidney nephrons.
MOD Gene Exp. Patterns, 5: 774-777.
Gerth, V.E., Zhou, X. and Vize, P.D. (2005). Nephrin expression and 3D morphogenesis
of the Xenopus pronephric glomus. Developmental
Dynamics, 233: 1131-1139. View the 3D
models and movies from this paper.
Zhou, X. and Vize, P.D. (2005b). Pronephric regulation of acid-base balance;
coexpression of carbonic anhydrase type 2 and sodium-bicarbonate cotransporter-1
in the late distal segment. Developmental
Dynamics, 232: 142-144.
Gerth, V.E. and Vize, P.D. (2005). A Java tool for
dynamic web-based 3D visualization of anatomy and overlapping gene or protein
expression patterns. Bioinformatics
21; 1278-1279.
Download pdf (no login).
Zhou, X. and Vize, P.D. (2004). Proximo-distal specialization of epithelial
transport processes within the Xenopus pronephric tubules. Developmental
Biology 271: 322-338.
Vize, P.D. and Smith, H.W. (2004). A Homeric view of kidney evolution. Anatomical Record 277: 344-354.
Vize, P.D., Carroll., T.J. and Wallingfrod, J.B. (2003). Induction, development and physiology of the pronephric tubules. In The Kidney: From Normal Development to Congenital Disease. Peter D. Vize, Adrian S. Woolf & Jonathan Bard (Editors). Academic Press, San Diego.
Hallgr’msson, B, Benediktsson, H & Vize, P.D. (2003) Anatomy and histology of the human urinary system. In The Kidney: From Normal Development to Congenital Disease. Peter D. Vize, Adrian S. Woolf & Jonathan Bard (Editors). Academic Press, San Diego.
Vazquez, M.D., Bouchet, P. and Vize, P.D. (2003). 3-Dimensional anatomy of mammalian mesonephroi. In The Kidney: From Normal Development to Congenital Disease. Peter D. Vize, Adrian S. Woolf & Jonathan Bard (Editors). Academic Press, San Diego.
Vize, P.D. (2003). The embryonic kidneys and other nephrogenic models. In The Kidney: From Normal Development to Congenital Disease. Peter D. Vize, Adrian S. Woolf & Jonathan Bard (Editors). Academic Press, San Diego.
Bowes, J.B. and Vize, P.D. (2003). Xenopus informatics. Current Genomics 4: 653-664.
Reichman, J.R., Wilcox, T.P. and Vize, P.D. (2003). Characterization and organization of the PCP gene family in Symbiodinium from Hippopus hippopus: low levels of concerted evolution among PCP genes contribute to predicted isoform diversity and spectral tuning of chromophores. Mol. Biol. Evol. 20: 2143-2154.
Vize, P.D. (2003). The chloride conductance channel ClC-K is a specific marker for the Xenopus pronephric distal tubule and duct. Gene Exp. Patterns 3: 347-350.
Gerth, V.E. and Vize, P.D. (2003). Interactive 3D Gene Expression Viewer. Siggraph "Best software of 2003"
Hagman, D.K. and Vize, P.D. (2003). Mass spawning by two brittle star species, Ophioderma rubicundum and O. squamosissimum, at the Flower Garden Banks, Gulf of Mexico. Bulletin Marine Sci. 72(3): 871-876. (download pdf)
Vize, P.D. (2001). On-line analysis of development. Bioessays, 23: 549-554.
Seufert, D.W., Brennan, H., DeGuire, J., Jones, E.A. and Vize, P.D. (1999). Developmental basis of pronephric defects in Xenopus body plan phenotypes. Developmental Biology 215: 233-242.
Matsumura, I., Wallingford, J.B., Surana, N., Vize, P.D. and Ellington, A.D. (1999). Directed evolution of the surface chemistry of the reporter enzyme, ß-glucuronidase. Nature Biotechnology 17: 696-701.
Carroll, T.J. and Vize, P.D. (1999) Synergism between Pax-8 and lim-1 in embryonic kidney development. Developmental Biology 214: 46-59.
Carroll, T.J., Wallingford, J.B. and Vize, P.D. (1999). Dynamic patterns of gene expression in the developing pronephros of Xenopus laevis. Developmental Genetics , 24: 199-207.
Carroll, T.J., Wallingford, J.B., Seufert, D.W. and Vize, P.D. (1999). Molecular regulation of pronephric development. Current Topics in Developmental Biology . 44: 67-100.
Wallingford, J.B., Carroll, T.J. and Vize, P.D. (1998). Precociuos expression of the Wilms' tumor gene xWT1 inhibits embryonic kidney development in Xenopus laevis. Developmental Biology, 202: 103-112.
Hagman, D.K., Gittings, S. and Vize, P.D. (1998). Fertilization in broadcast-spawning corals of the Flower Garden Banks National Marine Sanctuary. Gulf Mexico Sci. 16: 180-187 (Download pdf)
Wallingford, J.B., Seufert, D.W., Virta, V. and Vize, P.D. (1997) p53 activity is essential for normal development in Xenopus. Current Biology 7: 747-757.
Vize, P.D., Seufert, D.W., Carroll, T.J. and Wallingford, J.B. (1997) Model systems for the study of kidney development; use of the pronephros in the analysis of organ induction and patterning. Developmental Biology 188: 189-204.
Vize, P.D. (1996) DNA sequences mediating the transcriptional response of the Mix.2 homeobox gene to mesoderm induction. Developmental Biology 177: 226-231.
Carroll, T.J. and Vize, P.D. (1996) The Wilms' tumor suppressor gene is involved in the development of disparate kidney forms: evidence from expression in the Xenopus pronephros. Developmental Dynamics 206: 131-138.
Huang, H.C., Murtaugh, L.C., Vize, P.D. and Whitman, M. (1995) Identification of a potential regulator of early transcriptional responses to mesoderm inducers in the frog embryo. EMBO J. 14: 5965-5973.
Vize, P.D., Jones, E.A. and Pfister, R. (1995) Development of the Xenopus pronephros. Developmental Biology 171, 531-540.
Vize, P.D. and Thomsen, G.H. (1994) Vg1 and regional specification in vertebrates; a new role for an old molecule. Trends. Genet. 10: 371-376
Fischer-Vize, J.A., Vize, P.D. and Rubin, G. (1992). A unique mutation in the Enhancer of Split complex affects the fate of the mystery cells in the developing Drosophila eye disc. Development 115: 89-101.
Vize, P.D., Hemmati-Brivanlou, A.,
Harland, R. and Melton, D.A. (1991). Assays for gene function in developing
Xenopus embryos, in Methods
in Cell Biology , vol. 36. B.K.Kay and H.B.Peng eds. Academic Press Inc.,
Florida.
Vize, P.D., Vaughan, A. and Krieg, P.A. (1990). Expression of the N-myc proto-oncogene
during the early development of Xenopus laevis. Development
110: 885-896.