Publications

  • Karimi, K., Fortriede, J.D., Lotay, V.S., Burns, K.A., Wang, D.Z., Fisher, M.E., Pells, T.J., James-Zorn, C., Wang, Y., Ponferrada, V.G., Chu, S., Chaturvedi, P., Zorn A.M. and Vize, P.D. (2018). Xenbase: a genomic, epigenomic and transcriptomic model organism database. Nucleic Acids Res. 46(D1):D861-D868.
  • Session, A.M., Uno. Y., Kwon, T., Chapman, J.A., Toyoda, A., Takahashi, S., Fukui, A., Hikosaka, A., Suzuki, A., Kondo, M., van Heeringen, S.J., Quigley, I., Heinz, S., Ogino, H., Ochi, H., Hellsten, U., Lyons, J.B., Simakov, O., Putnam, N., Stites, J., Kuroki, Y., Tanaka, T., Michiue, T., Watanabe, M., Bogdanovic, O., Lister, R., Georgiou, G., Paranjpe, S.S., van Kruijsbergen, I., Shu, S., Carlson, J., Kinoshita, T., Ohta, Y., Mawaribuchi, S., Jenkins, J., Grimwood, J., Schmutz, J., Mitros, T., Mozaffari, S.V., Suzuki, Y., Haramoto, Y., Yamamoto, T.S., Takagi, C., Heald, R., Miller, K., Haudenschild, C., Kitzman, J., Nakayama, T., Izutsu, Y., Robert, J., Fortriede, J., Burns, K., Lotay, V., Karimi, K., Yasuoka, Y., Dichmann, D.S., Flajnik, M.F., Houston, D.W., Shendure, J., DuPasquier, L., Vize, P.D., Zorn, A.M., Ito, M., Marcotte EM, Wallingford JB, Ito Y, Asashima M, Ueno N, Matsuda Y, Veenstra GJ, Fujiyama A, Harland RM, Taira M, Rokhsar DS. (2016) Genome evolution in the allotetraploid frog Xenopus laevis. Nature 538(7625): 336-343.
  • Vize, P.D. and Zorn, A.M. (2016) Xenopus genomic data and browser resources. Dev. Biol.  doi: 10.1016/j.ydbio.2016.03.030
  • Vize, P.D. and Westerfield, M. (2015) Model Organism Databases. Genesis 53: 449.
  • James-Zorn, C., Ponferrada, V.G., Burns, K., Fortreide, J., Lotay, V., Liu, Y., Karpinka, J.B., Karimi, K., Zorn, A.M. and Vize P.D. (2015). Xenbase; core features, data acquisition and data processing. Genesis 53: 486-497
  • Vize, P.D., Liu, Y. and Karimi, K. (2015). Database and informatic challenges in representing both diploid and tetraploid Xenopus species in Xenbase. Cytogenet. Genome Res. 145: 278-282
  • A.R.Deans et al. (inc. P.D. Vize), the Phenoscape Consortium. (2015) Finding our way through phenotypes. PLoS Biology, 13: e1002033.
  • Karpinka, J.B., Fortreide, J.D., Burns, K.A., James-Zorn, C., Ponferrada, V.G., Lee, Jacqueline, Karimi, K., Zorn, A.M. and Vize, P.D. (2015). Xenbase, the Xenopus model organism database; new virtualized system, data types and genomes. Nucleic Acids Res. 43: D756-763
  • Karimi, K. and Vize, P.D. (2014). The virtual Xenbase. Database 2014 ; doi: 10.1093/database/bau108
  • Bhalla, N., Bentley, P.J., Vize, P.D. and Jacob, C. (2014). Staging the self-assembly process: inspiration from biological development. Artif. Life 20: 29-59.
  • Segerdell, E., Ponferrada V.G., James-Zorn C., Burns, K., Fortriede J., Dahdul W., Vize, P.D. and Zorn, A.M. (2013) XAO: an enhanced ontology of Xenopus anatomy and development.  Journal of Biological Semantics 4:31 doi:10.1186/2041-1480-4-31
  • Neufeld, S.J., Zhou, X, Vize, P.D. and Cobb, J. (2013). mRNA fluorescence in situ hybridization to determine overlapping gene expression in whole-mount mouse embryos. Dev. Dyn. 242; 1094-1100
  • James-Zorn C , Ponferrada VG, Jarabek CJ, Segerdell EJ, Lee J, Snyder K, Bhattacharyya B, Karpinka JB, Bowes JB, Zorn AM and Vize PD. (2013) Xenbase; expansion and updates of the Xenopus model organism database. Nucleic Acids Res. 41: D865-870.
  • Bowes, J., Snyder, K., James-Zorn, C., Ponferrada, V.G., Jarabek, C.J., Burns, K.A., Bhattacharyya, B., Zorn, A.M. and Vize, P.D. (2013). The Xenbase literature curation process. Database 2013: bas046 doi:10.1093/database/bas046
  • Bhalla, N., Bentley, P.J., Vize, P.D. and Jacob, C. (2012). Programming and evolving physical self-assembling systems in three dimensions. Natural Computing 11:475-498
  • 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). pp 93-100.
  • 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 (2010). Xenbase: Gene expression and improved integration. Nucl. Acids Res. 38 (Database issue): D607-612
  • Vize, P.D., McCoy, K.E. and Zhou, X. (2009) Multichannel wholemount fluorescent and fluorescent/ chromogenic in situ hybridization of Xenopus embryos. Nature Protocols 4: 975-983
  • 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.
  • 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.