Publications

AgBioData Publications:

• Cabugos, L., Buble, K., Daenzer, J., Jung. S., Main, D., Marrano, A., ..., Reiser L. 2025. AgBioDatabase Finder: an online tool to help researchers find and submit agricultural genomic, genetic, and breeding data. microPublication Biology, https://doi.org/10.17912/micropub.biology.001896
   
• Callwood, J., Celebioglu, B., Gladman, N., Jung, J., Lachowiec, J., Quezada-Rodriguez, EH., McNamara, J., Clarke, J. (2025) The need for robust, FAIR phenomic databases supporting agricultural efficiency and resiliency, Science and Public Policy, scaf039, https://doi.org/10.1093/scipol/scaf039
   
• Marrano, A., Cabugos, L., Hafner, A., Kapoor, B., McNamara, J., O'Donnell, M., Reiser, L., Tello-Ruiz, M.K., Zhang, H., Staton, M. (2025) A teaching and training framework to promote findable, accessible, interoperable, and reusable data generation in agriculture. Database, Volume 2025, 2025, baaf034, https://doi.org/10.1093/database/baaf034
   
• Cannon, E.K.S., Molik, D.C., Wright, A.J., Zhang, H., Honaas, L., Chougule, K., Dyer, S. (2025) Guidelines for Gene and Genome Assembly Nomenclature. Genetics, iyaf006. https://doi.org/10.1093/genetics/iyaf006
   
• Hafner, A., DeLeo, V., Deng, C., Elsik, C. G., Fleming, D., Harrison, P. W., Kalbfleisch, T. S., Petry, B., Pucker, B., Quezada-Rodríguez, E. H., Tuggle, C. K., Koltes, J. (2025) Data Reuse in Agricultural Genomics Research: Present Challenges and Future Solutions. GigaScience, Volume 14, giae106. PDF
   
• Kapoor, M., Ventura, E.S., Walsh, A., Sokolov, A., George, N., Kumari, S., Provart, N.J., Cole, B., Libault, M., Tickle, T., Warren, W.C., Koltes, J.E., Papatheodorou, I., Ware, D., Harrison, P.W., Elsik, C., Yordanova, G., Burdett, T., Tuggle, C.K. (2024)Building a FAIR data ecosystem for incorporating single-cell transcriptomics data into agricultural genome to phenome research. Front. Genet., 15: 1460351. PDF
   
• Clarke, J.L., Cooper, L.D., Poelchau, M.F., Berardini, T.Z., Elser, J., Farmer, A.D., Ficklin, S., Kumari, S., Laporte, M.A., Nelson, R.T., Sadohara, R. (2023) Data sharing and ontology use among agricultural genetics, genomics, and breeding databases and resources of the AgBioData Consortium. Database, 1-16. PDF
   
• Deng, C.H., Naithani, S., Kumari, S., Cobo-Simon, I., Quezada-Rodriguez, E.H., Skrabisova, M., Gladman, N., Correll, M.J., Sikiru, A.B., Afuwape, O.O., Marrano, A., Rebollo, I., Zhang, W., Jung, S. (2023) Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences. Database, 1-17 PDF
   
• Saha, S., Cain, S., Cannon, E.K., Dunn, N. Farmer, A., Hu, Z., Maslen, G., Moxon, S., Mungall, C.J., Nelson, R., Poelchau, M.F. (2022). Recommendations for extending the GFF3 specification for improved interoperability of genomic data. arXiv.
   
• Harper, L., Campbell, J., Cannon, E.K., Jung, S., Poelchau, M., Walls, R., ... & Cannon, S. (2018). AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture. Database, 1-32. PDF.
   
• Reiser, L., Harper, L., Freeling, M., Han, B., Luan, S. (2018). FAIR: A Call to Make Published Data More Findable, Accessible, Interoperable, and Reusable. Molecular Plant, 11(9):1105-1108. PDF.

AgBioData at conferences:

2025

• Kumari, S. (AgBioData Ambassador). Building FAIR Workflows for Integrating Single-Cell Data into Agricultural Genomics" at The Single-Cell Approaches in Plant Biology Gordon Research Conference. 10-15 August 2025, Portland, ME. Poster.

• Tello-Ruiz, M. K. (AgBioData Ambassador). The AgBioData Curriculum for Ag FAIR Data & Standards for Genetic Variation in Agriculture. Global Bioinformatics Education Summit 2025 (GBES25). 19-23 May 2025, Mexico City and online. Products include:

  • Matimba, A., Nikolic, D., Bingöl, E. N., van Geest, G., Heil, K. F., Paladin, L., Burke, M., Palopoli, N., Carvajal-López, P., Julius, R., Maracaja-Coutinho, V. with card contributions from 27 resources including AgBioData, represented by M.K. Tello-Ruiz. "Bioinformatics training on different scales - sharing knowledge and leveraging global connections". https://doi.org/10.5281/zenodo.17373244

• Tello-Ruiz MK, Wei S, Kumar V et al. Accelerating agricultural research through interoperable genetic and phenotypic variation data [version 1, not peer reviewed]. F1000Research 2025, 14:348. 18th Annual International Biocuration Conference, 5-9 April, Kansas City, MO. Poster. https://doi.org/10.7490/f1000research.1120115.1. 

• Reiser L, Bakker E, Chen X et al. How the Arabidopsis Information Resource (TAIR)and AgBioData Consortium contribute to the FAIRification of Arabidopsis data [version 1; not peer reviewed]. F1000Research 2025, 14:342. 18th Annual International Biocuration Conference, 5-9 April, Kansas City, MO. Poster.  https://doi.org/10.7490/f1000research.1120113.1.

2024

• Marrano, A. "The AgBioData journey towards best practices of data sharing and management in agricultural research and education." Workshop "Plant Bioinformatics Resources for FAIR Agricultural Data Discovery and Reuse" at the Plant Biology 2024 Conference (June 21, 2024). Oral Presentation.

• Reiser, L. "Update: AgBioData Consortium." Workshop “Beyond the National Plant Genome Initiative: New Frontiers and Grand Challenges in Plant Genomics” at PAG 31 (January 14, 2024). Invited oral presentation.

2023

• O'Donnell, M. "Building a Community Lead FAIR Data Curriculum for Agricultural Biology Data." Research Data Access and Preservation (RDAP) Summit 2023 (March 28-30, 2023). Poster presentation. 

• Marrano, A., Campbell, D., Campbell, J., Cannon, E., Cooper, L., Harrison, P., Harper, L., Huala, E., Jung, S., Kumari, S., McNamara, J., Naithani, S., Poelchau, M., Reiser, L., Staton, M., Tello-Ruiz, M.K. "Can we make phenomic, genetic, and genomic data FAIR? The AgBioData road trip towards best practices of data sharing and management in agricultural research and education." The NAPPN Annual Conference 2023 (February 13-17, 2023). Poster presentation.

• Marrano, A. "The AgBioData Research Coordination Network: creating community-based standards for more findable, accessible, and reusable agricultural data". The Plant Bioinformatics Resources for FAIR Agricultural Data Discovery and Reuse Workshop at the Plant Biology conference 2023 (August 5-9, 2023). Invited oral presentation.

2022

• Reiser, L., Campbell, D., Campbell, J., Cannon, E., Cooper, L., Harper, L., Huala, E., Jung, S., Marrano, A., Poelchau, M., Staton, M., Tello-Ruiz, M.K. "The AgBioData Research Coordination Network: Ensuring FAIR agricultural data through community-based standards." AG2PI Workshop “Harnessing the Ag Genomics Data Torrent: A Community-driven Discussion on Best Practices for Using and Reusing Genomics Data” (February 9, 2022). Invited oral presentation.

• Marrano, A., Campbell, D., Campbell, J., Cannon, E., Cooper, L., Harper, L., Huala, E., Jung, S., Poelchau, M., Reiser, L., Staton, M., Tello-Ruiz, M.K., "The AgBioData Research Coordination Network: Ensuring FAIR agricultural data through community-based standards." The 2022 North American Plant Phenotyping Network Annual Conference (February 22-25, 2022). Oral presentation.

• Jung, S. "AgBioData: Reimagining a Sustainable Data Network to Accelerate Agricultural Research and Discovery." The Genomics Aotearoa seminar series (March 25, 2022). Invited seminar.

• Marrano, A., Campbell, D., Campbell, J., Cannon, E., Cooper, L., Harper, L., Huala, E., Kumari, S., Jung, S., Poelchau, M., Reiser, L., Staton, M., Tello-Ruiz, M.K. "The AgBioData Research Coordination Network: Ensuring FAIR agricultural data through community-based standards." The 2022 Plant Genome Online Conference (April 27-28, 2022). Oral presentation. 

• Marrano, A., Campbell, D., Campbell, J., Cannon, E., Cooper, L., Harper, L., Huala, E., Kumari, S., Naithani, S., Jung, S., Poelchau, M., Reiser, L., Staton, M., Tello-Ruiz, M.K. "The AgBioData Research Coordination Network: Ensuring FAIR agricultural data through community-based standards." The Arthropod Genomics Symposium 2022 (July 9-11, 2022). Poster presentation. 

• Marrano, A. "The AgBioData Research Coordination Network: creating community-based standards for more findable, accessible, and reusable agricultural data." The Bioinformatics Resources For Plant Biologists Workshop at the ASPB Plant Biology conference 2022 (July 9-13, 2022). Invited oral presentation.

• Jung, S. "Complementary Efforts By Other Databases, Initiatives and Networks to Facilitate Use of the Existing Genetic Diversity in the NPGS System and Other Collections (GDV, GDR, AgBioData)." The American Society for Horticultural Science 2022 Annual Conference (July 30-August 3, 2022). Oral presentation.