Publications for Peter D. Vize

Publications(19)

ECB-PERS-702

Publications By Peter D. Vize

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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;
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.
Classifying domain-specific text documents containing ambiguous keywords., Karimi K, Agalakov S, Telmer CA, Beatman TR, Pells TJ, Arshinoff BI, Ku CJ, Foley S, Hinman VF, Ettensohn CA, Vize PD., Database (Oxford). September 29, 2021; 2021
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;
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. February 26, 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.
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.
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.
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.
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.
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; 145 (3-4): 278-82.
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.
The Virtual Xenbase: transitioning an online bioinformatics resource to a private cloud., Karimi K, Vize PD., Database (Oxford). November 7, 2014; 2014
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.
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.
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.
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. January 1, 2013; 8 (9): e72830.

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;

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.

Classifying domain-specific text documents containing ambiguous keywords., Karimi K, Agalakov S, Telmer CA, Beatman TR, Pells TJ, Arshinoff BI, Ku CJ, Foley S, Hinman VF, Ettensohn CA, Vize PD., Database (Oxford). September 29, 2021; 2021

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;

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. February 26, 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.

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.

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.

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.

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.

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; 145 (3-4): 278-82.

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.

The Virtual Xenbase: transitioning an online bioinformatics resource to a private cloud., Karimi K, Vize PD., Database (Oxford). November 7, 2014; 2014

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.

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.

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.

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. January 1, 2013; 8 (9): e72830.

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