Tripal Citations

The following publications indicate use of Tripal in creation of online genome databases, development of extension modules, citation of extension modules, support in 3rd party tools, or as a recommended platform.

2024

Mihai, C. A., Bădulescu, L., Asănică, A., & Iordachescu, M. (2024). Looking in the Scaffold 22 Hotspot for Differentially Regulated Genes Genomic Sequence Variation in Romanian Blueberry Cultivars. Horticulturae, 10. http://doi.org/10.3390/horticulturae10020157

https://www.mdpi.com/2311-7524/10/2/157

2023

Volk, G., Gmitter, F., & Krueger, R. (2023). Conserving Citrus Diversity: From Vavilov’s Early Explorations to Genebanks around the World. Plants, 12. http://doi.org/10.3390/plants12040814

https://www.mdpi.com/2223-7747/12/4/814
Shrestha, N., Zhang, K., Gowda, A., Abdelraheem, A., Jones, D., & Kuraparthy, V. (2023). Identification of quantitative trait loci for fiber quality, yield, and plant height traits in Upland cotton. Crop Science. http://doi.org/https://doi.org/10.1002/csc2.20937

https://acsess.onlinelibrary.wiley.com/doi/abs/10.1002/csc2.20937
Dipta, B., Sood, S., Devi, R., Bhardwaj, V., Mangal, V., Thakur, A., et al. (2023). Digitalization of potato breeding program: Improving data collection and management. Heliyon, 9, e12974. http://doi.org/https://doi.org/10.1016/j.heliyon.2023.e12974

https://www.sciencedirect.com/science/article/pii/S2405844023001810
Lipinska, A. P., Krueger-Hadfield, S. A., Godfroy, O., Dittami, S. M., Ayres-Ostrock, L., Bonthond, G., et al. (2023). "The Rhodoexplorer Platform for Red Algal Genomics and Whole-Genome Assemblies for Several Gracilaria Species". Genome Biology And Evolution, 15, evad124. http://doi.org/10.1093/gbe/evad124 (Original work published 07AD)

https://doi.org/10.1093/gbe/evad124
Clarke, J., Cooper, L., Poelchau, M., Berardini, T., Elser, J., Farmer, A., et al. (2023). "Data sharing and ontology use among agricultural genetics, genomics, and breeding databases and resources of the Agbiodata Consortium". Database, 2023, baad076. http://doi.org/10.1093/database/baad076 (Original work published 11AD)

https://doi.org/10.1093/database/baad076

2022

Wang, Y., Wu, J., Yan, J., Guo, M., Xu, L., Hou, L., & Zou, Q. (2022). Comparative genome analysis of plant ascomycete fungal pathogens with different lifestyles reveals distinctive virulence strategies. Bmc Genomics, 23, 1-11. http://doi.org/10.1186/s12864-021-08165-1 (Original work published jan)

https://link.springer.com/article/10.1186/s12864-021-08165-1
Rolling, W. (2022). CarrotOmics: a genetics and comparative genomics database for carrot (Daucus carota). Database, 2022. http://doi.org/10.1093/DATABASE/BAAC079 (Original work published 9AD)

https://academic.oup.com/database/article/doi/10.1093/database/baac079/6693759

2021

Jung, S., Cheng, C. -H., Buble, K., Lee, T., Humann, J., Yu, J., et al. (2021). Tripal MegaSearch: a tool for interactive and customizable query and download of big data. Database, 2021. http://doi.org/10.1093/database/baab023 (Original work published 04AD)

https://doi.org/10.1093/database/baab023
Staton, M., Cannon, E., Sanderson, L. -A., Wegrzyn, J., Anderson, T., Buehler, S., et al. (2021). Tripal, a community update after 10 years of supporting open source, standards-based genetic, genomic and breeding databases. Briefings In Bioinformatics. http://doi.org/10.1093/bib/bbab238 (Original work published 07AD)

https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bbab238/6318561
Garcia, D., Wang, Z., Guan, J., Yin, L., Geng, S., Li, A., & Mao, L. (2021). WheatGene: A genomics database for common wheat and its related species. The Crop Journal, 9, 1486-1491. http://doi.org/10.1016/j.cj.2021.04.011 (Original work published dec)

https://linkinghub.elsevier.com/retrieve/pii/S2214514121001161
Sanderson, L. -A., Caron, C. T., Tan, R. L., & Bett, K. E. (2021). A PostgreSQL Tripal solution for large-scale genotypic and phenotypic data . Database, 2021(baab051). http://doi.org/https://doi.org/10.1093/database/baab051 (Original work published 14 August 2021AD)

https://academic.oup.com/database/article/doi/10.1093/database/baab051/6352209
Skern-Mauritzen, R., Malde, K., Eichner, C., Dondrup, M., Furmanek, T., Besnier, F., et al. (2021). The salmon louse genome: Copepod features and parasitic adaptations. Genomics, 113, 3666-3680. http://doi.org/10.1016/j.ygeno.2021.08.002 (Original work published nov)

https://linkinghub.elsevier.com/retrieve/pii/S0888754321003098

2020

Condon, B., Almsaeed, A., Buehler, S., Childers, C., Ficklin, S., Staton, M., & Poelchau, M. (2020). Tripal EUtils: a Tripal module to increase exchange and reuse of genome assembly metadata. Database, 2020. http://doi.org/10.1093/database/baz143 (Original work published 01AD)

https://doi.org/10.1093/database/baz143
Spoor, S., Wytko, C., Soto, B., Chen, M., Almsaeed, A., Condon, B., et al. (2020). Tripal and Galaxy: supporting reproducible scientific workflows for community biological databases. Database, 2020. http://doi.org/10.1093/database/baaa032 (Original work published 07AD)

https://doi.org/10.1093/database/baaa032
Gong, Y., Kang, N., Kim, Y., Wang, Z., Wei, L., Xin, Y., et al. (2020). The NanDeSyn database for Nannochloropsis systems and synthetic biology. The Plant Journal, 104, 1736-1745. http://doi.org/10.1111/TPJ.15025 (Original work published dec)

https://onlinelibrary.wiley.com/doi/full/10.1111/tpj.15025 https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.15025 https://onlinelibrary.wiley.com/doi/10.1111/tpj.15025
Gui, S., Yang, L., Li, J., Luo, J., Xu, X., Yuan, J., et al. (2020). ZEAMAP, a Comprehensive Database Adapted to the Maize Multi-Omics Era. Iscience, 23, 101241. http://doi.org/10.1016/j.isci.2020.101241 (Original work published jun)

https://linkinghub.elsevier.com/retrieve/pii/S2589004220304260

2019

Peace, C. P., Bianco, L., Troggio, M., van de Weg, E., Howard, N. P., Cornille, A., et al. (2019). Apple whole genome sequences: recent advances and new prospects. Horticulture Research, 6, 59. http://doi.org/10.1038/s41438-019-0141-7 (Original work published dec)

http://www.nature.com/articles/s41438-019-0141-7
Jung, S., Lee, T., Cheng, C. H., Buble, K., Zheng, P., Yu, J., et al. (2019). 15 years of GDR: New data and functionality in the Genome Database for Rosaceae. Nucleic Acids Research, 47, D1137—D1145. http://doi.org/10.1093/nar/gky1000

https://academic.oup.com/nar/article/47/D1/D1137/5144131
Zheng, Y., Wu, S., Bai, Y., Sun, H., Jiao, C., Guo, S., et al. (2019). Cucurbit Genomics Database (CuGenDB): A central portal for comparative and functional genomics of cucurbit crops. Nucleic Acids Research. http://doi.org/10.1093/nar/gky944

https://academic.oup.com/nar/article/47/D1/D1128/5128937

2018

Falk, T., Herndon, N., Grau, E., Buehler, S., Richter, P., Zaman, S., et al. (2018). Growing and cultivating the forest genomics database, TreeGenes. Database, 2018, 1-11. http://doi.org/10.1093/database/bay084

https://www.ncbi.nlm.nih.gov/pmc/PMC6146132/
Condon, B., Almsaeed, A., Chen, M., West, J., & Staton, M. (2018). Tripal Developer Toolkit. Database, 2018. http://doi.org/10.1093/database/bay099

https://dx.doi.org/10.1093/database/bay099
Moreno, L. F., Vicente, V. A., & De Hoog, S. (2018). Black yeasts in the omics era: Achievements and challenges. Medical Mycology, 56, S32—S41. http://doi.org/10.1093/mmy/myx129 (Original work published apr)

https://academic.oup.com/mmy/article/56/suppl\_1/S32/4925973
Harper, L., Campbell, J., Cannon, E. K. S., Jung, S., Poelchau, M., Walls, R., et al. (2018). AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture. Database, 2018, bay088—bay088. http://doi.org/10.1093/database/bay088

http://dx.doi.org/10.1093/database/bay088

2017

Ruas, M., Guignon, V., Sempere, G., Sardos, J., Hueber, Y., Duvergey, H., et al. (2017). MGIS: managing banana (Musa spp.) genetic resources information and high-throughput genotyping data. Database, 2017. http://doi.org/10.1093/database/bax046 (Original work published jan)

https://academic.oup.com/database/article/doi/10.1093/database/bax046/3866796
Vining, K. J., Johnson, S. R., Ahkami, A., Lange, I., Parrish, A. N., Trapp, S. C., et al. (2017). Draft Genome Sequence of Mentha longifolia and Development of Resources for Mint Cultivar Improvement. Molecular Plant, 10, 323-339. http://doi.org/https://doi.org/10.1016/j.molp.2016.10.018

https://www.sciencedirect.com/science/article/pii/S1674205216302659
Watts, N. A., & Feltus, F. A. (2017). Big Data Smart Socket (BDSS): A system that abstracts data transfer habits from end users. Bioinformatics, 33, 627-628. http://doi.org/10.1093/bioinformatics/btw679

http://dx.doi.org/10.1093/bioinformatics/btw679
Wytko, C., Soto, B., & Ficklin, S. P. (2017). Blend4php: A PHP API for galaxy. Database, 2017, baw154—baw154. http://doi.org/10.1093/database/baw154

http://dx.doi.org/10.1093/database/baw154
Chen, M., Henry, N., Almsaeed, A., Zhou, X., Wegrzyn, J., Ficklin, S., & Staton, M. (2017). New extension software modules to enhance searching and display of transcriptome data in Tripal databases. Database : The Journal Of Biological Databases And Curation, 2017. http://doi.org/10.1093/database/bax052

https://academic.oup.com/database/article/doi/10.1093/database/bax052/4049442
Vining, K. J., Johnson, S. R., Ahkami, A., Lange, I., Parrish, A. N., Trapp, S. C., et al. (2017). Draft Genome Sequence of Mentha longifolia and Development of Resources for Mint Cultivar Improvement. Molecular Plant, 10, 323-339. http://doi.org/10.1016/j.molp.2016.10.018 (Original work published feb)

https://www.sciencedirect.com/science/article/pii/S1674205216302659?via\%3Dihub
Jung, S., Lee, T., Cheng, C. -H., Ficklin, S., Yu, J., Humann, J., & Main, D. (2017). Extension modules for storage, visualization and querying of genomic, genetic and breeding data in Tripal databases. Database, 2017. http://doi.org/10.1093/database/bax092 (Original work published jan)

https://academic.oup.com/database/article/doi/10.1093/database/bax092/4718480
Andrews, R. J., Baber, L., & Moss, W. N. (2017). RNAStructuromeDB: A genome-wide database for RNA structural inference. Scientific Reports, 7, 17269. http://doi.org/10.1038/s41598-017-17510-y (Original work published dec)

http://www.nature.com/articles/s41598-017-17510-y
Nazzicari, N., Caprera, A., Rossini, L., Tartarini, S., Dondini, L., Patocchi, A., et al. (2017). FruitBreedomics phenotypes and genotypes database and tools. Acta Horticulturae, 1172, 429-434. http://doi.org/10.17660/ActaHortic.2017.1172.81 (Original work published sep)

https://www.actahort.org/books/1172/1172\_81.htm

2016

Jung, S., Lee, T., Ficklin, S., Yu, J., Cheng, C. H., & Main, D. (2016). Chado use case: Storing genomic, genetic and breeding data of Rosaceae and Gossypium crops in Chado. Database, 2016. http://doi.org/10.1093/database/baw010

https://academic.oup.com/database/article/doi/10.1093/database/baw058/2630377
Dash, S., Campbell, J. D., Cannon, E. K. S., Cleary, A. M., Huang, W., Kalberer, S. R., et al. (2016). Legume information system (LegumeInfo.org): A key component of a set of federated data resources for the legume family. Nucleic Acids Research, 44, D1181—D1188. http://doi.org/10.1093/nar/gkv1159

https://dx.doi.org/10.1093/nar/gkv1159

2015

Krishnakumar, V., Hanlon, M. R., Contrino, S., Ferlanti, E. S., Karamycheva, S., Kim, M., et al. (2015). Araport: The Arabidopsis Information Portal. Nucleic Acids Research, 43, D1003—D1009. http://doi.org/10.1093/nar/gku1200 (Original work published jan)

http://academic.oup.com/nar/article/43/D1/D1003/2439074/Araport-the-Arabidopsis-Information-Portal
Dereeper, A., Bocs, S. \ ephanie, Rouard, M., Guignon, V., Ravel, S. \ ebastien, Tranchant-Dubreuil, C., et al. (2015). The coffee genome hub: A resource for coffee genomes. Nucleic Acids Research, 43, D1028—D1035. http://doi.org/10.1093/nar/gku1108 (Original work published jan)

http://academic.oup.com/nar/article/43/D1/D1028/2437520/The-coffee-genome-hub-a-resource-for-coffee
Krishnakumar, V., Kim, M., Rosen, B. D., Karamycheva, S., Bidwell, S. L., Tang, H., & Town, C. D. (2015). MTGD: The medicago truncatula genome database. Plant And Cell Physiology, 56, e1. http://doi.org/10.1093/pcp/pcu179 (Original work published jan)

https://academic.oup.com/pcp/article-lookup/doi/10.1093/pcp/pcu179
Poelchau, M., Childers, C., Moore, G., Tsavatapalli, V., Evans, J., Lee, C. Y., et al. (2015). The i5k Workspace@NAL-enabling genomic data access, visualization and curation of arthropod genomes. Nucleic Acids Research, 43, D714—D719. http://doi.org/10.1093/nar/gku983

http://nar.oxfordjournals.org/content/43/D1/D714.abstract

2014

Yu, J., Jung, S., Cheng, C. H., Ficklin, S. P., Lee, T., Zheng, P., et al. (2014). CottonGen: A genomics, genetics and breeding database for cotton research. Nucleic Acids Research, 42, 1229-36. http://doi.org/10.1093/nar/gkt1064

http://www.ncbi.nlm.nih.gov/pubmed/24203703
Jung, S., Ficklin, S. P., Lee, T., Cheng, C. H., Blenda, A., Zheng, P., et al. (2014). The Genome Database for Rosaceae (GDR): Year 10 update. Nucleic Acids Research, 42, 1237-44. http://doi.org/10.1093/nar/gkt1012

http://www.ncbi.nlm.nih.gov/pubmed/24225320

2013

Ficklin, S. P., & Feltus, F. A. (2013). A Systems-Genetics Approach and Data Mining Tool to Assist in the Discovery of Genes Underlying Complex Traits in Oryza sativa. Plos One, 8, e68551. http://doi.org/10.1371/journal.pone.0068551

http://www.ncbi.nlm.nih.gov/pubmed/23874666
Droc, G. etan, ere, D. L. \, Guignon, V., Yahiaoui, N., This, D., Garsmeur, O., et al. (2013). The banana genome hub. Database, 2013. http://doi.org/10.1093/database/bat035

http://database.oxfordjournals.org/content/2013/bat035.abstract

2012

Wegrzyn, J. L., Main, D., Figueroa, B., Choi, M., Yu, J., Neale, D. B., et al. (2012). Uniform standards for genome databases in forest and fruit trees. Tree Genetics And Genomes, 8, 549-557. http://doi.org/10.1007/s11295-012-0494-7

https://link.springer.com/article/10.1007/s11295-012-0494-7

2011

Jung, S., Menda, N., Redmond, S., Buels, R. M., Friesen, M., Bendana, Y., et al. (2011). The Chado Natural Diversity module: A new generic database schema for large-scale phenotyping and genotyping data. Database, 2011, bar051—bar051. http://doi.org/10.1093/database/bar051

https://www.ncbi.nlm.nih.gov/pmc/PMC3225077/