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 will take you to the publication reprint.)

Visualizing Functional Divergence and Conservation in Gene Families with TBrowse - (Abstract Only)
Olson, A., Chougule, K., Kumari, S., Lu, Z., Van Buren, P., Wei, S., Gladman, N.P., Ware, D. 2025. Visualizing Functional Divergence and Conservation in Gene Families with TBrowse. Conference on Genome Informatics . Conference on Genome Informatics.

Propagating rsIDs Across Crop Pan-Genomes in Gramene Platform Using the Ensembl Variant Remapping Pipeline - (Abstract Only)
Chougule, K., Kim, S., Wei, S., Olson, A., Lu, Z., Tello-Ruiz, M., Ware, D. 2025. Propagating rsIDs Across Crop Pan-Genomes in Gramene Platform Using the Ensembl Variant Remapping Pipeline. Meeting Abstract. Genome Informatics Conference.

Gramene 2025: expanded comparative genomics resources, integrated search, and pan-genome portals for crop research - (Peer Reviewed Journal)

Unifying Rice Diversity: The GrameneOryza 2025 Pan-Genome Platform for Research and Community Engagement - (Abstract Only)
Wei, S., Chougule, K., Lu, Z., Olson, A., Tello-Ruiz, M., Gladman, N.P., Zhang, L., Kumar, V., Kumari, S., Ware, D., Kim, S., Dooling, K., Olson, C., Assmann, S., Dyer, S., Jaiswal, P. 2025. Unifying Rice Diversity: The GrameneOryza 2025 Pan-Genome Platform for Research and Community Engagement . Meeting Abstract. 2025 International Symposium on Rice Functional Genomics (ISRFG).

SorghumBase is a Knowledgebase for Sorghum Genomic Data and Community Interaction - (Abstract Only)
Braynen, J., Gladman, N.P., Gladman, N., Chougule, K., Wei, S., Lu, Z., Tello-Ruiz, M., Olson, A., Kumari, S., Ware, D., Kumar, V., Van Buren, P. 2025. SorghumBase is a Knowledgebase for Sorghum Genomic Data and Community Interaction. Meeting Abstract. American Society of Plant Biologists - Plant Biology 2025 Meeting.

Accelerating Agricultural Research Through Interoperable Genetic and Phenotypic Variation Data - (Abstract Only)
Tello-Ruiz, M.K., Wei, S., Kumar, V., Olson, A., Harrison, M.L., Cezard, T., Gladman, N.P., Ware, D. 2025. Accelerating Agricultural Research Through Interoperable Genetic and Phenotypic Variation Data. Meeting Abstract. 18th Annual International Biocuration Conference.

Understanding nitrogen adaptation in maize and sorghum through gene networks - (Abstract Only)
Braynen, J., Kumari, S., Zhang, L., Olson, A., Kumar, V., Regulski, M., Liseron-Monfils, C., Gaudinier, A., Frank, M., Ware, D., Shen, B., Abbitt, S., Bagman, A., Rooney, W.L., Klein, R.R., Correa, E., Boerman, N.A., Kochian, L., Brady, S. 2025. Understanding nitrogen adaptation in maize and sorghum through gene networks. Advances in Genome Biology and Technology. dvances in Genome Biology and Technology Agricultural meeting.

Unlocking genomic diversity through comparative and pan-genome analysis for crop research communities - (Abstract Only)
Kumari, S., Braynen, J., Chougule, K., Kumar, V., Lu, Z., Olson, A., Tello-Ruiz, M., Wei, S., Van Buren, P., Ware, D., Gladman, N.P. 2025. Unlocking genomic diversity through comparative and pan-genome analysis for crop research communities. Advances in Genome Biology and Technology. Advances in Genomie Biology and Technology Agriculutral meeting.

Characterization of key regulators in microRNA-mediated responses to phosphate deficiency during Arabidopsis root development - (Abstract Only)
Zhang, L., Olson, A., Fahey, A., Hu, F., Regulski, M., Bagman, A., Brady, S.M., Ware, D. 2025. Characterization of key regulators in microRNA-mediated responses to phosphate deficiency during Arabidopsis root development . Meeting Abstract. Network Biology Meeting.

Understanding iron response mechanisms and carbon partitioning strategies in sorghum under Fe stress - (Abstract Only)
Braynen, J., Kumari, S., Chougule, K., Regulski, M., Dooling, K., Olson, C., Bhat, A., Tesesse, D., Paape, T., Ware, D., Xie, M., Cooper, E. 2025. Understanding iron response mechanisms and carbon partitioning strategies in sorghum under Fe stress. Meeting Abstract. Network Biology Meeting.

Genomic strategies to improve nitrogen use efficiency and reduce nitrate levels in sorghum forage lines - (Abstract Only)
Braynen, J., Kumari, S., Regulski, M., Zhang, L., Olson, A., Kumar, V., Rooney, W.L., Klein, R.R., Correa, E., Ware, D., Boerman, N.A. 2025. Genomic strategies to improve nitrogen use efficiency and reduce nitrate levels in sorghum forage lines. Meeting Abstract. Network Biology Meeting.

Pan-transcriptome of delevoping sorghum meristems reveal putative regulatory targets for mature seed traits - (Abstract Only)
Gladman, N.P., Fahey, A., Regulski, M., Ware, D. 2025. Pan-transcriptome of delevoping sorghum meristems reveal putative regulatory targets for mature seed traits. Meeting Abstract. Network Biology Meeting.

Gramene plants: empowering agricultural research from genomic diversity through pan-genome analysis - (Abstract Only)
Lu, Z., Chougule, K., Kumar, V., Kumari, S., Olson, A., Tello-Ruiz, M., Wei, S., Van Buren, P., Gladman, N.P., Ware, D. 2025. Gramene plants: empowering agricultural research from genomic diversity through pan-genome analysis. Maize Genetics Conference Abstracts. Maize Genetics Conference.

Maize data for biology, breeding, and genomics: the pan maize gramene database - (Abstract Only)
Ware, D., Chougule, K., Kumar, V., Kumar, S., Lu, Z., Olson, A., Tello-Ruiz, M., Wei, S., Van Buren, P., Gladman, N.P. 2025. Maize data for biology, breeding, and genomics: the pan maize gramene database. Maize Genetics Conference Abstracts. Maize Genetics Conference.

GrameneOryza: A Comprehensive Resource for Oryza Genomes, Genetic Variation, and Functional Data - (Peer Reviewed Journal)
Wei, S., Chougule, K., Olson, A., Lu, Z., Tello-Ruiz, M.K., Kumar, V., Kumari, S., Zhang, L., Olson, A., Ware, D., Kim, C., Gladman, N.P. 2025. GrameneOryza: A Comprehensive Resource for Oryza Genomes, Genetic Variation, and Functional Data. Database: The Journal of Biological Databases and Curation. 2025. https://doi.org/10.1093/database/baaf021 .

Using Pan-genomes, Databases, and Genomics to Advance Agriculture - (Proceedings)
Gladman, N.P., Olson, A., Tello-Ruiz, M., Wei, S., Chougule, K., Kamari, S., Lu, Z., Kumar, V., Olson, A., Ware, D., Van Buren, P. 2025. Using Pan-genomes, Databases, and Genomics to Advance Agriculture. Symposium Proceedings. Center for Sorghum Improvement.

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/.

MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication - (Peer Reviewed Journal)
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.R. 2024. MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication. Nature Communications. 15, 10854 (2024). https://doi.org/10.1038/s41467-024-55195-w.

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

Building a FAIR data ecosystem for incorporating single-cell transcriptomics data into agricultural genome to phenome research - (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. 15. https://doi.org/10.3389/fgene.2024.1460351.

Functional diversification within the heme-binding split-barrel family - (Peer Reviewed Journal)
Grosjean, N., Zhang, L., Kumaran, D., Xie, M., Fahey, A., Santiago, K., Hu, F., Regulski, M., Blaby, I.K., Blaby-Haas, C.E., Ware, D. 2024. Functional diversification within the heme-binding split-barrel family. Journal of Biological Chemistry. 2024 Nov;300(11):107888. https://doi.org/10.1016/j.jbc.2024.107888.

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)

SorghumBase: A Public Genetic and Genomic Resource for the Sorghum Community - (Abstract Only)
Gladman, N.P., Tello-Ruiz, M.K., Chougule, K., Kumar, V., Kumari, S., Lu, Z., Olson, A., Olson, A., Van Buren, P., Ware, D., Wei, S. 2024. SorghumBase: A Public Genetic and Genomic Resource for the Sorghum Community. Meeting Abstract. CROPS Conference 2024.

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 - (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. - (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 - (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 - (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 - (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.