Kamran Karimi - Publications

Publications (15)

XB-PERS-2300

Publications By Kamran Karimi

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

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 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.

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.

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.

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; .

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

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