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Paper

Wang, Bo, Chougule, Kapeel, Jiao, Yinping, Olson, Andrew, Kumar, Vivek, Gladman, Nicholas, Huang, Jian, Llaca, Victor, Fengler, Kevin, Wei, Xuehong, Wang, Liya, Wang, Xiaofei, Regulski, Michael, Drenkow, Jorg, Gingeras, Thomas, Hayes, Chad, Armstrong, J Scott, Huang, Yinghua, Xin, Zhanguo, Ware, Doreen (September 2024) High-quality chromosome scale genome assemblies of two important Sorghum inbred lines, Tx2783 and RTx436. NAR Genomics and Bioinformatics, 6 (3). lqae097. ISSN 2631-9268 (Public Dataset)

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

Yates, Andrew D, Allen, James, Amode, Ridwan M, Azov, Andrey G, Barba, Matthieu, Becerra, Andrés, Bhai, Jyothish, Campbell, Lahcen I, Carbajo Martinez, Manuel, Chakiachvili, Marc, Chougule, Kapeel, Christensen, Mikkel, Contreras-Moreira, Bruno, Cuzick, Alayne, Da Rin Fioretto, Luca, Davis, Paul, De Silva, Nishadi H, Diamantakis, Stavros, Dyer, Sarah, Elser, Justin, Filippi, Carla V, Gall, Astrid, Grigoriadis, Dionysios, Guijarro-Clarke, Cristina, Gupta, Parul, Hammond-Kosack, Kim E, Howe, Kevin L, Jaiswal, Pankaj, Kaikala, Vinay, Kumar, Vivek, Kumari, Sunita, Langridge, Nick, Le, Tuan, Luypaert, Manuel, Maslen, Gareth L, Maurel, Thomas, Moore, Benjamin, Muffato, Matthieu, Mushtaq, Aleena, Naamati, Guy, Naithani, Sushma, Olson, Andrew, Parker, Anne, Paulini, Michael, Pedro, Helder, Perry, Emily, Preece, Justin, Quinton-Tulloch, Mark, Rodgers, Faye, Rosello, Marc, Ruffier, Magali, Seager, James, Sitnik, Vasily, Szpak, Michal, Tate, John, Tello-Ruiz, Marcela K, Trevanion, Stephen J, Urban, Martin, Ware, Doreen, Wei, Sharon, Williams, Gary, Winterbottom, Andrea, Zarowiecki, Magdalena, Finn, Robert D, Flicek, Paul (November 2021) Ensembl Genomes 2022: an expanding genome resource for non-vertebrates. Nucleic Acids Research. ISSN 0305-1048

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

Tello-Ruiz, M. K., Naithani, S., Gupta, P., Olson, A., Wei, S., Preece, J., Jiao, Y., Wang, B., Chougule, K., Garg, P., Elser, J., Kumari, S., Kumar, V., Contreras-Moreira, B., Naamati, G., George, N., Cook, J., Bolser, D., D'Eustachio, P., Stein, L. D., Gupta, A., Xu, W., Regala, J., Papatheodorou, I., Kersey, P. J., Flicek, P., Taylor, C., Jaiswal, P., Ware, D. (January 2021) Gramene 2021: harnessing the power of comparative genomics and pathways for plant research. Nucleic Acids Res, 49 (D1). D1452-d1463. ISSN 0305-1048 (Print)0305-1048

Wang, B., Kumar, V., Olson, A., Ware, D. (April 2019) Reviving the Transcriptome Studies: An Insight Into the Emergence of Single-Molecule Transcriptome Sequencing. Front Genet, 10. Article no.384. ISSN 1664-8021 (Print)1664-8021

Arkin, Adam P, Cottingham, Robert W, Henry, Christopher S, Harris, Nomi L, Stevens, Rick L, Maslov, Sergei, Dehal, Paramvir, Ware, Doreen, Perez, Fernando, Canon, Shane, Sneddon, Michael W, Henderson, Matthew L, Riehl, William J, Murphy-Olson, Dan, Chan, Stephen Y, Kamimura, Roy T, Kumari, Sunita, Drake, Meghan M, Brettin, Thomas S, Glass, Elizabeth M, Chivian, Dylan, Gunter, Dan, Weston, David J, Allen, Benjamin H, Baumohl, Jason, Best, Aaron A, Bowen, Ben, Brenner, Steven E, Bun, Christopher C, Chandonia, John-Marc, Chia, Jer-Ming, Colasanti, Ric, Conrad, Neal, Davis, James J, Davison, Brian H, DeJongh, Matthew, Devoid, Scott, Dietrich, Emily, Dubchak, Inna, Edirisinghe, Janaka N, Fang, Gang, Faria, José P, Frybarger, Paul M, Gerlach, Wolfgang, Gerstein, Mark, Greiner, Annette, Gurtowski, James, Haun, Holly L, He, Fei, Jain, Rashmi, Joachimiak, Marcin P, Keegan, Kevin P, Kondo, Shinnosuke, Kumar, Vivek, Land, Miriam L, Meyer, Folker, Mills, Marissa, Novichkov, Pavel S, Oh, Taeyun, Olsen, Gary J, Olson, Robert, Parrello, Bruce, Pasternak, Shiran, Pearson, Erik, Poon, Sarah S, Price, Gavin A, Ramakrishnan, Srividya, Ranjan, Priya, Ronald, Pamela C, Schatz, Michael C, Seaver, Samuel MD, Shukla, Maulik, Sutormin, Roman A, Syed, Mustafa H, Thomason, James, Tintle, Nathan L, Wang, Daifeng, Xia, Fangfang, Yoo, Hyunseung, Yoo, Shinjae, Yu, Dantong (July 2018) KBase: The United States Department of Energy Systems Biology Knowledgebase. Nature Biotechnology, 36 (7). pp. 566-569. ISSN 1087-0156

Tello-Ruiz, M. K., Naithani, S., Stein, J. C., Gupta, P., Campbell, M., Olson, A., Wei, S., Preece, J., Geniza, M. J., Jiao, Y., Lee, Y. K., Wang, B., Mulvaney, J., Chougule, K., Elser, J., Al-Bader, N., Kumari, S., Thomason, J., Kumar, V., Bolser, D. M., Naamati, G., Tapanari, E., Fonseca, N., Huerta, L., Iqbal, H., Keays, M., Munoz-Pomer Fuentes, A., Tang, A., Fabregat, A., D'Eustachio, P., Weiser, J., Stein, L. D., Petryszak, R., Papatheodorou, I., Kersey, P. J., Lockhart, P., Taylor, C., Jaiswal, P., Ware, D. (January 2018) Gramene 2018: unifying comparative genomics and pathway resources for plant research. Nucleic Acids Res, 46 (D1). D1181-D1189. ISSN 0305-1048

Majsec, K., Bhuiyan, N. H., Sun, Q., Kumari, S., Kumar, V., Ware, D., van Wijk, K. J. (November 2017) The Plastid and Mitochondrial Peptidase Network in Arabidopsis thaliana: A Foundation for Testing Genetic Interactions and Functions in Organellar Proteostasis. Plant Cell, 29 (11). pp. 2687-2710. ISSN 1040-4651

Conference or Workshop Item

Tello-Ruiz, Marcela Karey, Wei, Sharon, Olson, Andrew, Gupta, Parul, Naithani, Sushma, Chougule, Kapeel, Kumari, Sunita, Kumar, Vivek, D'Eustachio, Peter, Papatheodorou, Irene, Contreras-Moreira, Bruno, Jaiswal, Pankaj, Ware, Doreen (September 2021) Gramene's Reference Genomes and Comparative Resources for Horticultural Species. In: Abstracts of Presentations from American Society of Horticultural Science 2021 Annual Conference.

Tello-Ruiz, Marcela Karey, Wei, Sharon, Olson, Andrew, Preece, Justin, Gupta, Parul, Stein, Joshua, Naithani, Sushma, Jiao, Yinping, Wang, Bo, Kumari, Sunita, Lee, Young Koung, Kumar, Vivek, Muna, Demitri, Bolser, Daniel, D'Eustachio, Peter, Papatheodorou, Irene, Kersey, Paul, Jaiswal, Pankaj, Ware, Doreen (September 2018) Gramene's Reference Genomes and Comparative Resource for Horticultural Species. In: American Society of Horticultural Science.