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Citing Xenbase

How to cite 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:
        • Karimi et al. 2018, Nucleic Acids Research, Volume 46, Issue D1, pp. D861-D868, doi:10.1093/nar/gkx936 (Xenbase / PubMed / NAR)
      GEO RNA-Seq and ChIP-Seq data integration:
        • Fortriede et al. 2020, Nucleic Acids Research, Volume 48, Issue D1, Pages D776–D782, doi:10.1093/nar/gkz933 (Xenbase / PubMed / NAR)
      Disease research:
      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 (, RRID:SCR_003280)
      • XAO ( , RRID:SCR_004337)
  • Logo: Xenbase Logocan be used in powerpoint presentations, posters, etc.

Xenbase Publications

      • Fortriede JD, Pells TJ, Chu S, Chaturvedi P, Wang D, Fisher ME, James-Zorn C, Wang Y, Nenni MJ, Burns KA, Lotay VS, Ponferrada VG, Karimi K, Zorn AM, Vize PD, Xenbase: deep integration of GEO & SRA RNA-seq and ChIP-seq data in a model organism database, Nucleic Acids Res., Volume 48, Issue D1, Pages D776–D782
      • Peshkin L, Lukyanov A, Kalocsay A, Gage RM, Wang D, Pells TJ, Karimi K, Vize PD, Wuhr M, Kirschner MW, The protein repertoire in early vertebrate embryogenesis, bioRxiv,
      • Nenni MJ, Fisher ME, James-Zorn C, Pells TJ, Ponferrada VG, Chu S, Fortriede JD, Burns KA, Wang Y, Lotay VS, Wang DZ, Segerdell E, Chaturvedi P, Karimi K, Vize PD, Zorn AM. Xenbase: Facilitating the use of Xenopus to Model Human Disease, Frontiers in Physiology, Volume 10, doi:10.3389/fphys.2019.00154
      • Patrushev I, James-Zorn C, Ciau-Uitz A, Patient R., Gilchrist MJ, New methods for computational decomposition of whole-mount in situ images enable effective curation of a large, highly redundant collection of Xenopus images, PLoS Comput. Biol., DOI:10.1371/journal.pcbi.1006077
      • Karimi K, Wuitchik DM, Oldach MJ, Vize PD. Distinguishing Species Using GC Contents in Mixed DNA or RNA Sequences, Evolutionary Bioinformatics, Volume 14, doi:10.1177/1176934318788866
      • James-Zorn C, Ponferrada VG, Fisher ME, Burns KA, Fortriede JD, Segerdell E, Karimi K, Lotay VS, Wang DZ, Chu S, Pells TJ, Wang Y, Vize PD, Zorn AM. Navigating Xenbase: An Integrated Xenopus Genomics and Gene Expression Database, Eukaryotic Genomic Databases: Methods and Protocols, Volume 1757, Chapter 10, pp. 251-305, doi:10.1007/978-1-4939-7737-6
      • Karimi K, Fortriede JD, Lotay VS, Burns KA, Wang DZ, Fisher ME, Pells TJ, James-Zorn C, Wang Y, Ponferrada VG, Chu S, Chaturvedi P, Zorn AM, Vize PD. Xenbase: a genomic, epigenomic and transcriptomic model organism database, Nucleic Acids Res., Volume 46, Issue D1, pp. D861-D868
      • 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
      • 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., Volume 43, Issue D1, pp. D756-D763
      • 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
      • Karimi K, Vize PD, The Virtual Xenbase: transitioning an online bioinformatics resource to a private cloud, Database (Oxford), doi:10.1093/database/bau108
      • 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, doi:10.1093/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., Volume 41, Issue D1, pp. D865-D870
      • 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
      • 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
      • 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
      • 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
      • Bowes JB, Vize PD, Xenopus Informatics, Current Genomics, Volume 4, Number 8
      • Vize PD, Online analysis of development, BioEssays, Volume 23, Issue 6
Xenbase: The Xenopus laevis and X. tropicalis resource.
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Major funding for Xenbase is provided by grant P41 HD064556