Skip to content

citations.md

Latest commit

 

History

History
124 lines (64 loc) · 13.9 KB

citations.md

File metadata and controls

124 lines (64 loc) · 13.9 KB
layout page
title 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

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

  • 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. https://doi.org/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. https://doi.org/10.1016/j.heliyon.2023.e12974

  • 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)

  • 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)

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)

  • 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)

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)

  • 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)

  • 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)

  • 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). https://doi.org/10.1093/database/baab051 (Original work published 14 August 2021AD)

  • 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)

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)

  • 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)

  • 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)

  • 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)

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)

  • 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

  • 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

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

  • Condon, B., Almsaeed, A., Chen, M., West, J., & Staton, M. (2018). Tripal Developer Toolkit. Database, 2018. http://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)

  • 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

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)

  • 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

  • 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

  • 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

  • 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

  • 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)

  • 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)

  • 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)

  • 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)

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

  • 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

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)

  • 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)

  • 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)

  • 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

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

  • 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

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

  • 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

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

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