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Citing Xenbase

Citing Xenbase

The NIH requests that NIH-funded resources be cited by authors who used these publicly funded resources. Similarly, the NIH and many major publishing houses, such as Nature Publishing Group, Elsevier, Wiley, and Company of Biologists request authors use RRID numbers to accurately identify the reagents and database/software resources used in their research. Xenbase is such a resource- Please cite Xenbase in the references and in the materials and methods sections of your publications.
  • Cite Xenbase in your References:
      Xenbase: the Xenopus model organism database:
        • Karpinka et al. 2015, Nucleic Acids Research, 43(D1): D756-D763. [Xenbase / PubMed / NAR ]
      Xenbase gene expression data:
        • Bowes et al. 2010, Nucleic Acids Research, Volume 38 (suppl) 1, pp. D607-D612, doi:10.1093/nar/gkp953. [Xenbase / PubMed / NAR ]
      The XAO (Xenopus Anatomy Ontalogy):
        • Segerdell et al. 2013, Journal of Biomedical Semantics, 4:31 [Xenbase / PubMed / JMBS ]
      Xenbase software and hardware design:
        • Vize et al. 2015, Cytogenetic and Genome Research, doi:10.1159/000430427 [Xenbase / PubMed / CGR ]
  • Cite Xenbase in the Material and Methods section of your papers:
      • Xenbase (http://www.xenbase.org/, RRID:SCR_003280)
      • XAO (http://www.xenbase.org/anatomy/xao.do?method=display , RRID:SCR_004337)
  • Logo
      • This image can be used in powerpoint presentations, posters, etc. Xenbase Logo



Xenbase Publications

    2016
      • Session AM, Uno Y, Kwon T et al., Genome evolution in the allotetraploid frog Xenopus laevis, Nature, 538(7625):336-343, doi:10.1038/nature19840
      • Vize PD, Zorn AM, Xenopus genomic data and browser resources, Developmental Biology, doi:10.1016/j.ydbio.2016.03.030
    2015
      • James-Zorn C, Ponferrada VG, Burns KA, Fortriede JD, Lotay VS, Liu Y, Karpinka BJ, Karimi K, Zorn AM, Vize PD, Xenbase: Core features, data acquisition, and data processing, Genesis, 53(8):486-97
      • Vize PD, Liu Y, Karimi K, Database and Informatic Challenges in Representing Both Diploid and Tetraploid Xenopus Species in Xenbase, Cytogenet Genome Res., 145(3-4):278-82
      • Karpinka JB, Fortriede JD, Burns KA, James-Zorn C, Ponferrada VG, Lee J, Karimi K, Zorn AM, Vize PD, Xenbase, the Xenopus model organism database; new virtualized system, data types and genomes, Nucleic Acids Res., D756-63.
      • Deans AR, Lewis SE, Huala E et al., Finding Our Way through Phenotypes, PLoS Biol., 13 (1): e1002033.
      • Matsuda Y, Uno Y, Kondo M, Gilchrist MJ, Zorn AM, Rokhsar DS, Schmid M, Taira M, A New Nomenclature of Xenopus laevis Chromosomes Based on the Phylogenetic Relationship to Silurana/Xenopus tropicalis, Cytogenet Genome Res., 145 (3-4): 187-91.
      • Grant IM, Balcha D, Hao T, Shen Y, Trivedi P, Patrushev I, Fortriede JD, Karpinka JB, Liu L, Zorn AM, Stukenberg PT, Hill DE, Gilchrist MJ, The Xenopus ORFeome: A resource that enables functional genomics, Dev Biol., Volume 408, Issue 2.
    2014
      • Karimi K, Vize PD, The Virtual Xenbase: transitioning an online bioinformatics resource to a private cloud, Database, bau108
    2013
      • Segerdell E, Ponferrada VG, James-Zorn C, Burns KA, Fortriede JD, Dahdul WM, Vize PD, Zorn AM, Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase. , J Biomed Semantics., 4(1):31
      • Bowes JB, Snyder KA, James-Zorn C, Ponferrada VG, Jarabek CJ, Burns KA, Bhattacharyya B, Zorn AM, Vize PD, The Xenbase literature curation process, Database, bas046
      • James-Zorn C, Ponferrada VG, Jarabek CJ, Burns KA, Segerdell EJ, Lee J, Snyder K, Bhattacharyya B, Karpinka JB, Fortriede J, Bowes JB, Zorn AM, Vize PD, Xenbase: expansion and updates of the Xenopus model organism database, Nucleic Acids Res., D865-70.
    2010
      • Bowes JB, Snyder KA, Segerdell E, Jarabek CJ, Azam K, Zorn AM, Vize PD, Xenbase: gene expression and improved integration, Nucleic Acids Res., 38:D607-D612.
      • Hellsten U, Harland RM, Gilchrist MJ et al., The Genome of the Western Clawed Frog Xenopus tropicalis, Science, Vol. 328, Issue 5978.
    2008
      • Bowes JB, Snyder KA, Segerdell E, Gibb R, Jarabek C, Noumen E, Pollet N, Vize PD, Xenbase: a Xenopus biology and genomics resource, Nucl. Acids Res., 36 (suppl 1):D761-D767.
      • Segerdell E, Bowes JB, Pollet N, Vize PD, An ontology for Xenopus anatomy and development, BMC Dev Biol, 8 92.
    2007
      • Vize PD, Gerth VE, Adaptation of video game UVW mapping to 3D visualization of gene expression patterns, Proc. SPIE 6506 , doi:10.1117/12.714073.
      • Gerth VE, Katsuyama K, Kevin KA, Bowes JB, Atsushi K, Ueno, N, Vize PD, Projecting 2D gene expression data into 3D and 4D space, Developmental Dynamics , Volume 236, Issue 4.
    2005
      • Gerth VE, Vize PD, A Java tool for dynamic web-based 3D visualization of anatomy and overlapping gene or protein expression patterns, Bioinformatics, 21 (7):1278-1279.
    2003
      • Bowes JB, Vize PD, Xenopus Informatics, Current Genomics, Volume 4, Number 8.
    2001
      • Vize PD, Online analysis of development, BioEssays, Volume 23, Issue 6.

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