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Profile Publications (78)
XB-PERS-702

Publications By Peter D. Vize

Results 1 - 50 of 78 results

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Echinobase: a resource to support the echinoderm research community., Telmer CA, Karimi K, Chess MM, Agalakov S, Arshinoff BI, Lotay V, Wang DZ, Chu S, Pells TJ, Vize PD, Hinman VF, Ettensohn CA., Genetics. January 23, 2024;


Xenbase: key features and resources of the Xenopus model organism knowledgebase., Fisher M, 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., Genetics. May 4, 2023; 224 (1):             


The case for standardizing gene nomenclature in vertebrates., McCarthy FM, Jones TEM, Kwitek AE, Smith CL, Vize PD, Westerfield M, Bruford EA., Nature. February 1, 2023; 614 (7948): E31-E32.


A beautiful, complex simplicity: the origins of nephron segmentation uncovered by single-cell sequencing of the pronephros., Vize PD., Kidney Int. January 1, 2023; 103 (1): 23-25.


Normal Table of Xenopus development: a new graphical resource., Zahn N, James-Zorn C, Ponferrada VG, Adams DS, Grzymkowski J, Buchholz DR, Nascone-Yoder NM, Horb M, Moody SA, Vize PD, Zorn AM., Development. July 15, 2022; 149 (14):                         


Embryonic and aglomerular kidney development in the bay pipefish, Syngnathus leptorhynchus., Maters BR, Stevenson E, Vize PD., PLoS One. May 12, 2022; 17 (5): e0267932.  


The Xenopus phenotype ontology: bridging model organism phenotype data to human health and development., 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., BMC Bioinformatics. March 22, 2022; 23 (1): 99.            


Echinobase: leveraging an extant model organism database to build a knowledgebase supporting research on the genomics and biology of echinoderms., Arshinoff BI, Cary GA, Karimi K, Foley S, Agalakov S, Delgado F, Lotay VS, Ku CJ, Pells TJ, Beatman TR, Kim E, Cameron RA, Vize PD, Telmer CA, Croce JC, Ettensohn CA, Hinman VF., Nucleic Acids Res. January 7, 2022; 50 (D1): D970-D979.        


Integration of 1:1 orthology maps and updated datasets into Echinobase., Foley S, Ku C, Arshinoff B, Lotay V, Karimi K, Vize PD, Hinman V., Database (Oxford). May 19, 2021; 2021


Xenbase: deep integration of GEO & SRA RNA-seq and ChIP-seq data in a model organism database., 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., Nucleic Acids Res. January 8, 2020; 48 (D1): D776-D782.      


Seasonal temperature, the lunar cycle and diurnal rhythms interact in a combinatorial manner to modulate genomic responses to the environment in a reef-building coral., Wuitchik DM, Wang D, Pells TJ, Karimi K, Ward S, Vize PD., Mol Ecol. August 1, 2019; 28 (16): 3629-3641.            


The Pronephros; a Fresh Perspective., de Bakker BS, van den Hoff MJB, Vize PD, Oostra RJ., Integr Comp Biol. July 1, 2019; 59 (1): 29-47.


Xenbase: Facilitating the Use of Xenopus to Model Human Disease., Nenni MJ, Fisher ME, James-Zorn C, Pells TJ, Ponferrada V, Chu S, Fortriede JD, Burns KA, Wang Y, Lotay VS, Wang DZ, Segerdell E, Chaturvedi P, Karimi K, Vize PD, Zorn AM., Front Physiol. January 1, 2019; 10 154.          


Distinguishing Species Using GC Contents in Mixed DNA or RNA Sequences., Karimi K, Wuitchik DM, Oldach MJ, Vize PD., Evol Bioinform Online. July 18, 2018; 14 1176934318788866.  


De novo assembly and annotation of the Acropora gemmifera transcriptome., Oldach MJ, Vize PD., Mar Genomics. July 1, 2018; 40 9-12.


Xenbase: a genomic, epigenomic and transcriptomic model organism database., 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., Nucleic Acids Res. January 4, 2018; 46 (D1): D861-D868.        


Navigating Xenbase: An Integrated Xenopus Genomics and Gene Expression Database., James-Zorn C, Ponferrada V, Fisher ME, Burns K, Fortriede J, Segerdell E, Karimi K, Lotay V, Wang DZ, Chu S, Pells T, Wang Y, Vize PD, Zorn A., Methods Mol Biol. January 1, 2018; 1757 251-305.


Xenopus genomic data and browser resources., Vize PD, Zorn AM., Dev Biol. June 15, 2017; 426 (2): 194-199.  


Transcriptome dynamics over a lunar month in a broadcast spawning Acroporid coral., Oldach MJ, Workentine M, Matz MV, Fan TY, Vize PD., Mol Ecol. May 1, 2017;


Genome evolution in the allotetraploid frog Xenopus laevis., Session AM, Uno Y, Kwon T, Chapman JA, Toyoda A, Takahashi S, Fukui A, Hikosaka A, Suzuki A, Kondo M, van Heeringen SJ, Quigley I, Heinz S, Ogino H, Ochi H, Hellsten U, Lyons JB, Simakov O, Putnam N, Stites J, Kuroki Y, Tanaka T, Michiue T, Watanabe M, Bogdanovic O, Lister R, Georgiou G, Paranjpe SS, van Kruijsbergen I, Shu S, Carlson J, Kinoshita T, Ohta Y, Mawaribuchi S, Jenkins J, Grimwood J, Schmutz J, Mitros T, Mozaffari SV, Suzuki Y, Haramoto Y, Yamamoto TS, 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 DS, Flajnik MF, Houston DW, Shendure J, DuPasquier L, Vize PD, Zorn AM, Ito M, Marcotte EM, Wallingford JB, Ito Y, Asashima M, Ueno N, Matsuda Y, Veenstra GJ, Fujiyama A, Harland RM, Taira M, Rokhsar DS., Nature. October 20, 2016; 538 (7625): 336-343.                              


Lunar Phase Modulates Circadian Gene Expression Cycles in the Broadcast Spawning Coral Acropora millepora., Brady AK, Willis BL, Harder LD, Vize PD., Biol Bull. April 1, 2016; 230 (2): 130-42.


Xenbase: Core features, data acquisition, and data processing., James-Zorn C, Ponferrada VG, Burns KA, Fortriede JD, Lotay VS, Liu Y, Brad Karpinka J, Karimi K, Zorn AM, Vize PD., Genesis. August 1, 2015; 53 (8): 486-97.          


Model organism databases., Vize PD, Westerfield M., Genesis. August 1, 2015; 53 (8): 449.


Finding Our Way through Phenotypes., Deans AR, Lewis SE, Huala E, Anzaldo SS, Ashburner M, Balhoff JP, Blackburn DC, Blake JA, Burleigh JG, Chanet B, Cooper LD, Courtot M, Csösz S, Cui H, Dahdul W, Das S, Dececchi TA, Dettai A, Diogo R, Druzinsky RE, Dumontier M, Franz NM, Friedrich F, Gkoutos GV, Haendel M, Harmon LJ, Hayamizu TF, He Y, Hines HM, Ibrahim N, Jackson LM, Jaiswal P, James-Zorn C, Köhler S, Lecointre G, Lapp H, Lawrence CJ, Le Novère N, Lundberg JG, Macklin J, Mast AR, Midford PE, Mikó I, Mungall CJ, Oellrich A, Osumi-Sutherland D, Parkinson H, Ramírez MJ, Richter S, Robinson PN, Ruttenberg A, Schulz KS, Segerdell E, Seltmann KC, Sharkey MJ, Smith AD, Smith B, Specht CD, Squires RB, Thacker RW, Thessen A, Fernandez-Triana J, Vihinen M, Vize PD, Vogt L, Wall CE, Walls RL, Westerfeld M, Wharton RA, Wirkner CS, Woolley JB, Yoder MJ, Zorn AM, Mabee P., PLoS Biol. January 6, 2015; 13 (1): e1002033.    


Xenbase, the Xenopus model organism database; new virtualized system, data types and genomes., Karpinka JB, Fortriede JD, Burns KA, James-Zorn C, Ponferrada VG, Lee J, Karimi K, Zorn AM, Vize PD., Nucleic Acids Res. January 1, 2015; 43 (Database issue): D756-63.    


Database and Informatic Challenges in Representing Both Diploid and Tetraploid Xenopus Species in Xenbase., Vize PD, Liu Y, Karimi K., Cytogenet Genome Res. January 1, 2015; .


Separate Introns Gained within Short and Long Soluble Peridinin-Chlorophyll a-Protein Genes during Radiation of Symbiodinium (Dinophyceae) Clade A and B Lineages., Reichman JR, Vize PD., PLoS One. October 17, 2014; 9 (10): e110608.        


The Virtual Xenbase: transitioning an online bioinformatics resource to a private cloud., Karimi K, Vize PD., Database (Oxford). April 4, 2014; 2014     


Staging the self-assembly process: inspiration from biological development., Bhalla N, Bentley PJ, Vize PD, Jacob C., Artif Life. January 1, 2014; 20 (1): 29-53.


Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase., Segerdell E, Ponferrada VG, James-Zorn C, Burns KA, Fortriede JD, Dahdul WM, Vize PD, Zorn AM., J Biomed Semantics. October 18, 2013; 4 (1): 31.      


Ecological complexity of coral recruitment processes: effects of invertebrate herbivores on coral recruitment and growth depends upon substratum properties and coral species., Davies SW, Matz MV, Vize PD., PLoS One. September 3, 2013; 8 (9): e72830.            


mRNA fluorescence in situ hybridization to determine overlapping gene expression in whole-mount mouse embryos., Neufeld SJ, Zhou X, Vize PD, Cobb J., Dev Dyn. September 1, 2013; 242 (9): 1094-100.    


The Xenbase literature curation process., Bowes JB, Snyder KA, James-Zorn C, Ponferrada VG, Jarabek CJ, Burns KA, Bhattacharyya B, Zorn AM, Vize PD., Database (Oxford). January 9, 2013; 2013 bas046.    


Xenbase: expansion and updates of the Xenopus model organism database., 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., Nucleic Acids Res. January 1, 2013; 41 (Database issue): D865-70.    


Photoreception and signal transduction in corals: proteomic and behavioral evidence for cytoplasmic calcium as a mediator of light responsivity., Hilton JD, Brady AK, Spaho SA, Vize PD., Biol Bull. December 1, 2012; 223 (3): 291-9.


Multicolor fluorescent in situ mRNA hybridization (FISH) on whole mounts and sections., Lea R, Bonev B, Dubaissi E, Vize PD, Papalopulu N., Methods Mol Biol. January 1, 2012; 917 431-44.


Antibody development and use in chromogenic and fluorescent immunostaining., Dubaissi E, Panagiotaki N, Papalopulu N, Vize PD., Methods Mol Biol. January 1, 2012; 917 411-29.


Non-canonical wnt signals antagonize and canonical wnt signals promote cell proliferation in early kidney development., McCoy KE, Zhou X, Vize PD., Dev Dyn. June 1, 2011; 240 (6): 1558-66.          


Circadian Cycles of Gene Expression in the Coral, Acropora millepora., Brady AK, Snyder KA, Vize PD., PLoS One. January 1, 2011; 6 (9): e25072.      


The genome of the Western clawed frog Xenopus tropicalis., Hellsten U, Harland RM, Gilchrist MJ, Hendrix D, Jurka J, Kapitonov V, Ovcharenko I, Putnam NH, Shu S, Taher L, Blitz IL, Blumberg B, Dichmann DS, Dubchak I, Amaya E, Detter JC, Fletcher R, Gerhard DS, Goodstein D, Graves T, Grigoriev IV, Grimwood J, Kawashima T, Lindquist E, Lucas SM, Mead PE, Mitros T, Ogino H, Ohta Y, Poliakov AV, Pollet N, Robert J, Salamov A, Sater AK, Schmutz J, Terry A, Vize PD, Warren WC, Wells D, Wills A, Wilson RK, Zimmerman LB, Zorn AM, Grainger R, Grammer T, Khokha MK, Richardson PM, Rokhsar DS., Science. April 30, 2010; 328 (5978): 633-6.


Xenbase: gene expression and improved integration., Bowes JB, Snyder KA, Segerdell E, Jarabek CJ, Azam K, Zorn AM, Vize PD., Nucleic Acids Res. January 1, 2010; 38 (Database issue): D607-12.      


Transcriptome Analysis of the Circadian Regulatory Network in the Coral Acropora millepora., Vize PD., Biol Bull. April 1, 2009; 216 (2): 131-7.


Requirement of Wnt/beta-catenin signaling in pronephric kidney development., Lyons JP, Miller RK, Zhou X, Weidinger G, Deroo T, Denayer T, Park JI, Ji H, Hong JY, Li A, Moon RT, Jones EA, Vleminckx K, Vize PD, McCrea PD., Mech Dev. January 1, 2009; 126 (3-4): 142-59.        


Multichannel wholemount fluorescent and fluorescent/chromogenic in situ hybridization in Xenopus embryos., Vize PD, McCoy KE, Zhou X., Nat Protoc. January 1, 2009; 4 (6): 975-83.  


An ontology for Xenopus anatomy and development., Segerdell E, Bowes JB, Pollet N, Vize PD., BMC Dev Biol. June 23, 2008; 8 92.    


Collectrin/tmem27 is expressed at high levels in all segments of the developing Xenopus pronephric nephron and in the Wolffian duct., McCoy KE, Zhou X, Vize PD., Gene Expr Patterns. April 1, 2008; 8 (4): 271-4.        


Xenbase: a Xenopus biology and genomics resource., Bowes JB, Snyder KA, Segerdell E, Gibb R, Jarabek C, Noumen E, Pollet N, Vize PD., Nucleic Acids Res. January 1, 2008; 36 (Database issue): D761-7.    


Projecting 2D gene expression data into 3D and 4D space., Gerth VE, Katsuyama K, Snyder KA, Bowes JB, Kitayama A, Ueno N, Vize PD., Dev Dyn. April 1, 2007; 236 (4): 1036-43.        


FGF is essential for both condensation and mesenchymal-epithelial transition stages of pronephric kidney tubule development., Urban AE, Zhou X, Ungos JM, Raible DW, Altmann CR, Vize PD., Dev Biol. September 1, 2006; 297 (1): 103-17.                    


Amino acid cotransporter SLC3A2 is selectively expressed in the early proximal segment of Xenopus pronephric kidney nephrons., Zhou X, Vize PD., Gene Expr Patterns. August 1, 2005; 5 (6): 774-7.    

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