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Xenbase Publications
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 D776âD782, 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
2018
• 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,
doi:10.1093/nar/gkx936
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.