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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Research Project #445304

Research Project: Championing Improvement of Sorghum and Other Agriculturally Important Species through Data Stewardship and Functional Dissection of Complex Traits

Location: Plant, Soil and Nutrition Research

Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)

Empowering Sorghum Research: SorghumBase as a Hub for Genomic Data and Community Collaboration - (Abstract Only)
Ware, D., Gladman, N.P., Olson, A., Chougule, K., Wei, S., Lu, Z., Tello-Ruiz, M., Olson, A., Kumari, S., Kumar, V., Van Buren, P. 2025. Empowering Sorghum Research: SorghumBase as a Hub for Genomic Data and Community Collaboration. Plant and Animal Genome Conference. https://intlpag.org/PAG32/.

Building a FAIR data ecosystem for incorporating single-cell transcriptomics data into agricultural genome to phenome research Reprint Icon - (Peer Reviewed Journal)
Kapoor, M., Ventrua, E., Walsh, A., Sokolov, A., George, N., Kumari, S., Provart, N.J., Cole, B., Libault, M., Tuggle, C.K., Tickle, T., Warren, W.C., Koltes, J., Papatheodorou, I., Ware, D., Harisson, P., Elsik, C., Yordanova, G., Burdett, T. 2024. Building a FAIR data ecosystem for incorporating single-cell transcriptomics data into agricultural genome to phenome research. Frontiers in Genetics. Vol. 15. https://doi.org/10.3389/fgene.2024.1460351.

Advancing agricultural genomics: Integrating rsIDs for standardized genetic variation and enhanced breeding strategies - (Abstract Only)

Functional diversification within the heme-binding split-barrel family - (Peer Reviewed Journal)

GrameneOryza 2024: A Collaborative Pan-Genome Resource for Rice Diversity, Knowledge Discovery, and Community Engagement - (Abstract Only)
Chougule, K., Wei, S., Lu, Z., Olson, A., Tello-Ruiz, M.K., Gladman, N.P., Zhang, L., Kumar, V., Kumari, S., Ware, D., Kim, S., Dooling, K., Olson, C., Assmann, S., Dyer, S., Jaiswal, P. 2024. GrameneOryza 2024: A Collaborative Pan-Genome Resource for Rice Diversity, Knowledge Discovery, and Community Engagement. International Symposium on Rice Germplasm Evaluation and Enhancement. International Symposium on Rice Functional Genomics Conference, September 9, 2024.

Catalyzing Genomic Discoveries: Leveraging rsIDs for Enhanced Trait-Driven Interoperability and Genomic Function Transfer - (Abstract Only)

Crop Improvement Through Genomics - (Abstract Only)

Characterization of key regulators in microRNA-mediated responses to phosphate deficiency in Arabidopsis root development - (Abstract Only)

Gramene 2024: A comparative resource on plant reference genomes, pan-genomes, and pathways - (Abstract Only)

Gramene Plants And Pan Genome Resources for Plant Communities - (Abstract Only)

SorghumBase 2024: Building Partnerships and Integrating Genetic Knowledge for the Sorghum Community - (Abstract Only)

Decoding Nitrogen Use Efficiency in Maize and Sorghum: Insights from Comparative Gene Regulatory Networks for Sustainable Agriculture - (Abstract Only)

Catalyzing Genomic Discoveries: Leveraging rsIDs for Enhanced Trait-Driven Interoperability and Genomic Function Transfer - (Abstract Only)

Binding Behaviors of Diverse GRAS Family Transcription Factors in Monocots - (Abstract Only)

Transcriptomic Profiles of Developing Meristems Across Sorghum Accessions Reveal Nuanced Regulatory Pathways Towards Panicle Morphology and Grain Content - (Abstract Only)

Gramene: A comparative resource on plant reference genomes, pan-genomes and pathways - (Abstract Only)

Swift Pan-Genomic Methods for Comprehensive Genome Annotation in Crop Genomes. - (Abstract Only)

Sorghum Pan-Transcriptome Reveals Divergent and Constrained Modules for Inflorescence Morphology - (Abstract Only)

Elucidating Nitrogen Use Efficiency in Crops through Comparative Analysis of Gene Regulatory Networks in Maize and Sorghum - (Abstract Only)

Evaluating Nitrate Tolerance in Male Sterile Sorghum Lines for implications for safe forage Production - (Abstract Only)

Genome-wide Response to Iron Availability and Identification of Leaf-level Metal Acclimation Factors in Four Sorghum Carbon Partitioning NAM Populations. - (Abstract Only)

Genetic variation standardization (rsIDs) enhances Trait-Driven Interoperability and Genomic Function Transfer - (Abstract Only)

Binding Site Preferences of Sorghum GRAS Transcription Factors Across Monocots - (Abstract Only)

Characterization of Transcription Factor Family’s Functional Role in Arabidopsis thaliana Primary Root Growth - (Abstract Only)

Unlocking Genomic Diversity: Harnessing the Power of FAIR Principles in SorghumBase - (Abstract Only)

SorghumBase: Fostering Community Engagement for Sustainable Sorghum Research - (Abstract Only)

SorghumBase: Public Genetic and Genomic Database for the Sorghum Research and Breeding Community - (Abstract Only)

Sorghum 2.4K SNP panel: a cost-effective, high sample throughput genotyping resource for US sorghum breeding and research community - (Abstract Only)

Gapless assembly of complete humannand plant chromosomes using only nanopore sequencing - (Pre-print Publication)

Role of moss and Arabidopsis zinc-fnger homeodomain transcription factors in regulating plant architecture Reprint Icon - (Peer Reviewed Journal)
Lee, Y., Kim, K., Ware, D. 2024. Role of moss and Arabidopsis zinc-fnger homeodomain transcription factors in regulating plant architecture. Plant Biotechnology Reports. 18:223-231. https://doi.org/10.1007/s11816-024-00897-2.

Maize Data For Biology, Breeding, and Genomics: The PanMaize Gramene Database - (Abstract Only)

Transcriptomic Profiles of Developing Meristems Across Sorghum Accessions Reveal Nuanced Regulatory Pathways Towards Panicle Morphology - (Abstract Only)

Decoding Nitrogen Use Efficiency in Maize and Sorghum: Insights from Comparative Gene Regulatory Networks for Sustainable Agriculture - (Abstract Only)

Gramene PanMaize: One-Stop Pan-Genome Browser for Exploring the Rich Genetic Diversity in Maize - (Abstract Only)

Gramene 2024: A comparative resource on plant reference genomes, pan-genomes and pathways - (Abstract Only)

MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication. Reprint Icon - (Pre-print Publication)
Cahn, J., Regulski, M., Lynn, J., Ernst, E., De Santis Alves, C., Ramakrishnan, S., Chougule, K., Wei, S., Lu, Z., Martienssen, R.A., Xiaosa, X., Drenkow, J., Kramer, M., Mccombie, R., Ware, D., Jackson, D., Schatz, M., Gingeras, T. 2024. MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication.. bioRxiv. https://doi.org/10.1101/2024.02.22.581585.

Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences Reprint Icon - (Peer Reviewed Journal)
Deng, C.H., Naithani, S., Kuamri, S., Cobo-Simón, I., Quezada-Rodríguez, E.H., Skrabisova, M., Gladman, N.P., Correll, M.J., Sikiru, A., Jung, S., Afuwape, O., Marrano, A., Rebollo, I., Zhang, W. 2023. Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences. Database: The Journal of Biological Databases and Curation. https://doi.org/10.1093/database/baad088.

Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences Reprint Icon - (Peer Reviewed Journal)
Deng, C.H., Naithani, S., Kumari, S., Cobo-Simon, I., Quezada-Rodriquez, E.H., Skrabisova, M., Gladman, N.P., Correl, M.J., Sikiru, A., Jung, S., Afuwape, O., Marrano, A., Rebollo, I., Zhang, W. 2023. Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences. Database: The Journal of Biological Databases and Curation. https://doi.org/10.1093/database/baad088.

Leveraging Biomedicine Resources to Understand Single-Cell Data in Agriculture: The Faang Experience - (Abstract Only)

Long-read sequencing broadens access to genetic and transcript diversity for high-value traits in sorghum - (Abstract Only)

Unlocking genomic diversity: harnessing the power of FAIR principles in gramene - (Abstract Only)

Standardizing biocuration of genetic variation data to promote FAIRification - (Abstract Only)

CLIMtools: A web-based suite of tools for exploring genotype by environment (GxE) associations - (Abstract Only)

Sorghum eFP browser to view gene expression anatomograms in gramene - (Abstract Only)

Swift pan-genomic methods for comprehensive genome annotation in crop genomes - (Abstract Only)

Ensembl 2024 Reprint Icon - (Peer Reviewed Journal)
Harrison, P.W., Amode, R., Austine-Orimoloye, O., Aziv, A.G., Barba, M., Barnes, I., Becker, A., Bennett, R., Berry, A., Yates, A.D., Bhai, J., Bhurji, S., Boddu, S., Branco Lins, P.R., Brooks, L., Budhanuru Ramaraju, S., Campbell, L.I., Carbajo Martinez, M., Charkhchi, M., Chougule, K., Cockburn, A., Davidson, C.E., De Silva, N.H., Dodiya, K., Donaldson, S., El Houdaigui, B., El Naboulsi, T., Fatima, R., Garcia Giron, C., Genez, T., Grigoriadis, D., Ghattaoraya, G., Gonzalez Martinez, J., Gurbich, T.A., Hardy, M.E., Hollis, Z., Hourlier, T.E., Hunt, T., Kay, M., Kaykala, V., Le, T., Lelmos, D., Lodha, D., Marques-Coelho, D., Maslen, G., Merino, G.A., Mirabueno, L., Mushtaq, A.E., Nakib Hossain, S., Ogeh, D.N., Pandian Sakthivel, M., Parker, A., Perry, M., Pilizota, I., Poppleton, D., Prosovetskaia, I., Raj, S., Perez-Silva, J.G., Salam, A.A., Saraf, S., Saraiva-Agostinho, N., Sheppard, D., Sinha, S., Sipos, B., Sitnik, V., Stark, W., Steed, E., Suner, M., Surapaneni, L., Sutinen, K., Tricomi, F.F., Urbina-Gomez, D., Veidenberg, A.E., Walsh, T.A., Ware, D., Wass, E., Willhoft, N.L., Allen, J., Alvarez-Jarreta, J., Chakiachvili, M., Flint, B., Giorgetti, S., Haggerty, L., Ilsley, G.R., Keatley, J., Loveland, J.E., Moore, B., Mudge, J.M., Naamati, G., Tate, J., Trevanion, S.J., Winterbottom, A., Frankish, A., Hunt, S.E., Cunningham, F.E., Dyser, S., Finn, R.D., Martin, F. 2023. Ensembl 2024. Nucleic Acids Research. Vol.52, p. D891-899. https://doi.org/10.1093/nar/gkad1049.