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Paper

Jiao, Yinping, Nigam, Deepti, Barry, Kerrie, Daum, Chris, Yoshinaga, Yuko, Lipzen, Anna, Khan, Adil, Parasa, Sai-Praneeth, Wei, Sharon, Lu, Zhenyuan, Tello-Ruiz, Marcela K, Dhiman, Pallavi, Burow, Gloria, Hayes, Chad, Chen, Junping, Brandizzi, Federica, Mortimer, Jenny, Ware, Doreen, Xin, Zhanguo (December 2023) A large sequenced mutant library - valuable reverse genetic resource that covers 98% of sorghum genes. The Plant Journal. ISSN 0960-7412

Zhou, Yong, Yu, Zhichao, Chebotarov, Dmytro, Chougule, Kapeel, Lu, Zhenyuan, Rivera, Luis F, Kathiresan, Nagarajan, Al-Bader, Noor, Mohammed, Nahed, Alsantely, Aseel, Mussurova, Saule, Santos, João, Thimma, Manjula, Troukhan, Maxim, Fornasiero, Alice, Green, Carl D, Copetti, Dario, Kudrna, David, Llaca, Victor, Lorieux, Mathias, Zuccolo, Andrea, Ware, Doreen, McNally, Kenneth, Zhang, Jianwei, Wing, Rod A (March 2023) Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice. Nature Communications, 14 (1). p. 1567. ISSN 2041-1723

Gladman, Nicholas, Olson, Andrew, Wei, Sharon, Chougule, Kapeel, Lu, Zhenyuan, Tello-Ruiz, Marcela, Meijs, Ivar, Van Buren, Peter, Jiao, Yinping, Wang, Bo, Kumar, Vivek, Kumari, Sunita, Zhang, Lifang, Burke, John, Chen, Junping, Burow, Gloria, Hayes, Chad, Emendack, Yves, Xin, Zhanguo, Ware, Doreen (January 2022) SorghumBase: a web-based portal for sorghum genetic information and community advancement. Planta: an international journal of plant biology, 255 (2). p. 35. ISSN 0032-0935

Wang, Liya, Lu, Zhenyuan, Van Buren, Peter, Ware, Doreen (2022) SciApps: An Automated Platform for Processing and Distribution of Plant Genomics Data. Methods in Molecular Biology, 2443. pp. 197-209. ISSN 1064-3745

Voelker, William G, Krishnan, Krittika, Chougule, Kapeel, Alexander, Louie C, Lu, Zhenyuan, Olson, Andrew, Ware, Doreen, Songsomboon, Kittikun, Ponce, Cristian, Brenton, Zachary W, Boatwright, J Lucas, Cooper, Elizabeth A (2022) Ten new high-quality genome assemblies for diverse bioenergy sorghum genotypes. Frontiers in Plant Science, 13. p. 1040909. ISSN 1664-462X

Kumari, Sunita, Kumar, Vivek, Beilsmith, Kathleen, Seaver, Samuel MD, Canon, Shane, Dehal, Paramvir, Gu, Tian, Joachimiak, Marcin, Lerma-Ortiz, Claudia, Liu, Filipe, Lu, Zhenyuan, Pearson, Eric, Ranjan, Priya, Riel, William, Henry, Christopher S, Arkin, Adam P, Ware, Doreen (November 2021) A KBase Case Study on Genome-wide Transcriptomics and Plant Primary Metabolism in response to Drought Stress in Sorghum. Current Plant Biology. p. 100229. ISSN 2214-6628

Wang, L., Lu, Z., Regulski, M., Jiao, Y., Chen, J., Ware, D., Xin, Z. (August 2020) BSAseq: an interactive and integrated web-based workflow for identification of causal mutations in bulked F2 populations. Bioinformatics. ISSN 1367-4803

Wang, L., Lu, Z., Delabastide, M., Van Buren, P., Wang, X., Ghiban, C., Regulski, M., Drenkow, J., Xu, X., Ortiz-Ramirez, C., Marco, C.F., Goodwin, S., Dobin, A., Birnbaum, K. D., Jackson, D. P., Martienssen, R. A., McCombie, W. R., Micklos, D. A., Schatz, M. C., Ware, D. H., Gingeras, T. R. (March 2020) Management, Analyses, and Distribution of the MaizeCODE Data on the Cloud. Frontiers in Plant Science, 11 (289). ISSN 1664-462X (Public Dataset)

Wang, Liya, Lu, Zhenyuan, delaBastide, Melissa, Van Buren, Peter, Wang, Xiaofei, Ghiban, Cornel, Regulski, Michael, Drenkow, Jorg, Xu, Xiaosa, Ortiz-Ramirez, Carlos, Fernandez-Marco, Cristina, Goodwin, Sara, Dobin, Alexander, Birnbaum, Kenneth, Jackson, David, Martienssen, Robert, McCombie, William, Micklos, David, Schatz, Michael, Ware, Doreen, Gingeras, Thomas (November 2019) Management, Analyses, and Distribution of the MaizeCODE Data on the Cloud. BioRxiv. (Unpublished)

Wang, L., Lu, Z., Van Buren, P., Ware, D. (June 2018) SciApps: A cloud-based platform for reproducible bioinformatics workflows. Bioinformatics, 34 (22). pp. 3917-3920. ISSN 1367-4803

Wang, B., Tseng, E., Regulski, M., Clark, T. A., Hon, T., Jiao, Y., Lu, Z., Olson, A., Stein, J. C., Ware, D. (June 2016) Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing. Nat Commun, 7. p. 11708. ISSN 2041-1723 (Electronic)2041-1723 (Linking)

Olson, A., Klein, R. R., Dugas, D. V., Lu, Z. Y., Regulski, M., Klein, P. E., Ware, D. (July 2014) Expanding and Vetting Sorghum bicolor Gene Annotations through Transcriptome and Methylome Sequencing. Plant Genome, 7 (2). p. 20. ISSN 1940-3372

Monaco, M. K., Stein, J., Naithani, S., Wei, S., Dharmawardhana, P., Kumari, S., Amarasinghe, V., Youens-Clark, K., Thomason, J., Preece, J., Pasternak, S., Olson, A., Jiao, Y., Lu, Z., Bolser, D., Kerhornou, A., Staines, D., Walts, B., Wu, G., D'Eustachio, P., Haw, R., Croft, D., Kersey, P. J., Stein, L., Jaiswal, P., Ware, D. (January 2014) Gramene 2013: comparative plant genomics resources. Nucleic Acids Research, 42 (Databa). D1193-9. ISSN 0305-1048

Regulski, M., Lu, Z., Kendall, J., Donoghue, M. T., Reinders, J., Llaca, V., Deschamps, S., Smith, A., Levy, D., McCombie, W. R., Tingey, S., Rafalski, A., Hicks, J., Ware, D., Martienssen, R. (June 2013) The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA. Genome Research, 23 (10). pp. 1651-1662. ISSN 10889051 (ISSN)

Boyle, B., Hopkins, N., Lu, Z. Y., Garay, J. A. R., Mozzherin, D., Rees, T., Matasci, N., Narro, M. L., Piel, W. H., McKay, S. J., Lowry, S., Freeland, C., Peet, R. K., Enquist, B. J. (January 2013) The taxonomic name resolution service: an online tool for automated standardization of plant names. BMC Bioinformatics, 14. ISSN 1471-2105

Book

Wang, L., Van Buren, P., Lu, Z., Ware, D. (August 2018) SciApps: A bioinformatics workflow platform powered by XSEDE and cyverse. Association for Computing Machinery, p. 138224. ISBN 9781450364461 (ISBN)