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Similarly, the NIH and many major publishing houses, such as Nature Publishing Group, Elsevier, Wiley,
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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.
Please cite Xenbase in your References:
Xenbase: Fisher et al. 2023, Xenbase: key features and resources of the Xenopus model organism knowledgebase,
Genetics, Volume 224, Issue 1, May 2023, iyad018, doi:10.1093/genetics/iyad018
(Xenbase / PubMed / Genetics)
Disease research: Nenni et al. 2019, Xenbase: Facilitating the use of Xenopus to Model Human Disease,
Frontiers in Physiology, Volume 10, doi:10.3389/fphys.2019.00154
(Xenbase / PubMed / Front Physiol)
The XAO (Xenopus Anatomy Ontology): Segerdell et al. 2013, Enhanced XAO: the ontology of Xenopus anatomy and development underpins more
accurate annotation of gene expression and queries on Xenbase, Journal of Biomedical Semantics, 4:31
(Xenbase / PubMed / JMBS)
The XPO (Xenopus Phenotype Ontology): Fisher et al. 2022, The Xenopus phenotype ontology: bridging model organism phenotype data to human
health and development, BMC Bioinformatics, 23,99
(Xenbase / PubMed / BMC Bioinform)
• Vize et al. 2015, Database and Informatic Challenges in Representing Both Diploid and Tetraploid Xenopus Species in Xenbase,
Cytogenetic and Genome Research, doi:10.1159/000430427
(Xenbase / PubMed / CGR)
Reference Xenbase in the Material and Methods section of your papers:
Logo: can be used in powerpoint presentations, posters, etc.
Xenbase Publications
2023
• Fisher ME, James-Zorn C, Ponferrada V, Bell AJ, Sundararaj N, Segerdell E, Chaturvedi P, Bayyari N, Chu S, Pells T,
Lotay V, Agalakov S, Wang DZ, Arshinoff BI, Foley S, Karimi K, Vize PD, Zorn AM,
Xenbase: key features and resources of the Xenopus model organism knowledgebase,
Genetics, Volume 224, Issue 1, May 2023, iyad018, doi:10.1093/genetics/iyad018
• Dimitrakopoulou D, Khwatenge CN, James-Zorn C, Paiola M, Bellin EW, Tian Y, Sundararaj N, Polak EJ, Grayfer L,
Barnard D, Ohta Y, Horb M, Sang Y, Robert J.
Advances in the Xenopus immunome: Diversification, expansion, and contraction,
J. Dev Comp Immunol., 2023 Aug;145:104734, doi:10.1016/j.dci.2023.104734
• McCarthy, FM, Jones, TEM, Kwitek, AE, Smith CL, Vize PD, Westerfield M, Bruford EA,
The case for standardizing gene nomenclature in vertebrates,
Nature 614, E31-E32 (2023), doi:10.1038/s41586-022-05633-w
• Gene Ontology Consortium; Aleksander SA , et al.,
The Gene Ontology knowledgebase in 2023, Genetics, 2023 May 4;224(1):iyad031, doi:10.1093/genetics/iyad031
2022
• Zahn N, James-Zorn C, Ponferrada VG, Adams DS, Grzymkowski J, Buchholz DR, Nascone-Yoder NM, Horb M, Moody SA, Vize PD, Zorn AM,
Normal Table of Xenopus development: a new graphical resource,
Development, 2022 Jul 15;149(14):dev200356, doi:10.1242/dev.200356
• Fisher ME, Segerdell E, Matentzoglu N, Nenni MJ, Fortriede JD, Chu S, Pells TJ, Osumi-Sutherland D, Chaturvedi P, James-Zorn C, Sundararaj N,
Lotay VS, Ponferrada V, Wang DZ, Kim E, Agalakov S, Arshinoff BI, Karimi K, Vize PD, Zorn AM,
The Xenopus phenotype ontology: bridging model organism phenotype data to human health and development,
BMC Bioinformatics, 2022 Mar 22;23(1):99, doi:10.1186/s12859-022-04636-8
2021
• Karimi K, Agalakov S, Telmer CA, Beatman TR, Pells TJ, Arshinoff BI, Ku CJ, Foley S,
Hinman VF, Ettensohn CA, Vize PD, Classifying domain-specific text documents containing ambiguous keywords,
Database (Oxford), Volume 2021, baab062, doi:10.1093/database/baab062
2020
• 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, doi:10.1093/nar/gkz933
2019
• 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, doi:10.1101/571174
• 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
• Horb M, Wlizla M, Abu-Daya A, McNamara S, Gajdasik D, Igawa T, Suzuki A, Ogino H, Noble A, Robert J, James-Zorn C, Guille M.,
Xenopus Resources: Transgenic, Inbred and Mutant Animals, Training Opportunities, and Web-Based Support,
Front Physiol., 2019 Apr 25;10:387, doi:10.3389/fphys.2019.00387
2018
• 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,
doi:10.1093/nar/gkx936
• 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
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
• 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,
doi:10.1002/dvg.22873
• 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,
doi:10.1159/000430427
• 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
2014
• Karimi K, Vize PD,
The Virtual Xenbase: transitioning an online bioinformatics resource to a private cloud, Database (Oxford),
doi:10.1093/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, 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
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
can be used in powerpoint presentations, posters, etc.