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Zhou, Yong, Kathiresan, Nagarajan, Yu, Zhichao, Rivera, Luis F, Yang, Yujian, Thimma, Manjula, Manickam, Keerthana, Chebotarov, Dmytro, Mauleon, Ramil, Chougule, Kapeel, Wei, Sharon, Gao, Tingting, Green, Carl D, Zuccolo, Andrea, Xie, Weibo, Ware, Doreen, Zhang, Jianwei, McNally, Kenneth L, Wing, Rod A (January 2024) A high-performance computational workflow to accelerate GATK SNP detection across a 25-genome dataset. BMC Biology, 22 (1). p. 13. ISSN 1741-7007

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

Hufford, Matthew B, Seetharam, Arun S, Woodhouse, Margaret R, Chougule, Kapeel M, Ou, Shujun, Liu, Jianing, Ricci, William A, Guo, Tingting, Olson, Andrew, Qiu, Yinjie, Della Coletta, Rafael, Tittes, Silas, Hudson, Asher I, Marand, Alexandre P, Wei, Sharon, Lu, Zhenyuan, Wang, Bo, Tello-Ruiz, Marcela K, Piri, Rebecca D, Wang, Na, Kim, Dong Won, Zeng, Yibing, O'Connor, Christine H, Li, Xianran, Gilbert, Amanda M, Baggs, Erin, Krasileva, Ksenia V, Portwood, John L, Cannon, Ethalinda KS, Andorf, Carson M, Manchanda, Nancy, Snodgrass, Samantha J, Hufnagel, David E, Jiang, Qiuhan, Pedersen, Sarah, Syring, Michael L, Kudrna, David A, Llaca, Victor, Fengler, Kevin, Schmitz, Robert J, Ross-Ibarra, Jeffrey, Yu, Jianming, Gent, Jonathan I, Hirsch, Candice N, Ware, Doreen, Dawe, R Kelly (August 2021) De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes. Science, 373 (6555). pp. 655-662. ISSN 0036-8075

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

Ou, S. J., Liu, J. N., Chougule, K. M., Fungtammasan, A., Seetharam, A.S., Stein, J. C., Llaca, V., Manchanda, N., Gilbert, A. M., Wei, S. R., Chin, C. S., Hufnagel, D. E., Pedersen, S., Snodgrass, S. J., Fengler, K., Woodhouse, M., Walenz, B. P., Koren, S., Phillippy, A. M., Hannigan, B. T., Dawe, R. K., Hirsch, C. N., Hufford, M. B., Ware, D. (May 2020) Effect of sequence depth and length in long-read assembly of the maize inbred NC358. Nature Communications, 11 (1). p. 2288. ISSN 2041-1723

Naithani, S., Gupta, P., Preece, J., D'Eustachio, P., Elser, J. L., Garg, P., Dikeman, D. A., Kiff, J., Cook, J., Olson, A., Wei, S., Tello-Ruiz, M. K., Mundo, A. F., Munoz-Pomer, A., Mohammed, S., Cheng, T., Bolton, E., Papatheodorou, I., Stein, L., Ware, D., Jaiswal, P. (November 2019) Plant Reactome: a knowledgebase and resource for comparative pathway analysis. Nucleic Acids Res, 48. pp. 1093-1103. ISSN 0305-1048 (Public Dataset)

Springer, N. M., Anderson, S. N., Andorf, C. M., Ahern, K. R., Bai, F., Barad, O., Barbazuk, W. B., Bass, H. W., Baruch, K., Ben-Zvi, G., Buckler, E. S., Bukowski, R., Campbell, M. S., Cannon, E. K. S., Chomet, P., Dawe, R. K., Davenport, R., Dooner, H. K., Du, L. H., Du, C., Easterling, K. A., Gault, C., Guan, J. C., Hunter, C. T., Jander, G., Jiao, Y., Koch, K. E., Kol, G., Kollner, T. G., Kudo, T., Li, Q., Lu, F., Mayfield-Jones, D., Mei, W., McCarty, D. R., Noshay, J. M., Portwood, J. L., Ronen, G., Settles, A. M., Shem-Tov, D., Shi, J., Soifer, I., Stein, J. C., Stitzer, M. C., Suzuki, M., Vera, D. L., Vollbrecht, E., Vrebalov, J. T., Ware, D., Wei, S., Wimalanathan, K., Woodhouse, M. R., Xiong, W., Brutnell, T. P. (July 2018) The maize W22 genome provides a foundation for functional genomics and transposon biology. Nat Genet, 50 (9). pp. 1282-1288. ISSN 1061-4036

Stein, J. C., Yu, Y., Copetti, D., Zwickl, D. J., Zhang, L., Zhang, C., Chougule, K., Gao, D., Iwata, A., Goicoechea, J. L., Wei, S., Wang, J., Liao, Y., Wang, M., Jacquemin, J., Becker, C., Kudrna, D., Zhang, J., Londono, C. E. M., Song, X., Lee, S., Sanchez, P., Zuccolo, A., Ammiraju, J. S. S., Talag, J., Danowitz, A., Rivera, L. F., Gschwend, A. R., Noutsos, C., Wu, C. C., Kao, S. M., Zeng, J. W., Wei, F. J., Zhao, Q., Feng, Q., El Baidouri, M., Carpentier, M. C., Lasserre, E., Cooke, R., Rosa Farias, D. D., da Maia, L. C., Dos Santos, R. S., Nyberg, K. G., McNally, K. L., Mauleon, R., Alexandrov, N., Schmutz, J., Flowers, D., Fan, C., Weigel, D., Jena, K. K., Wicker, T., Chen, M., Han, B., Henry, R., Hsing, Y. C., Kurata, N., de Oliveira, A. C., Panaud, O., Jackson, S. A., Machado, C. A., Sanderson, M. J., Long, M., Ware, D., Wing, R. A. (January 2018) Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza. Nat Genet, 50 (2). pp. 285-296. ISSN 1061-4036

Kersey, P. J., Allen, J. E., Allot, A., Barba, M., Boddu, S., Bolt, B. J., Carvalho-Silva, D., Christensen, M., Davis, P., Grabmueller, C., Kumar, N., Liu, Z., Maurel, T., Moore, B., McDowall, M. D., Maheswari, U., Naamati, G., Newman, V., Ong, C. K., Paulini, M., Pedro, H., Perry, E., Russell, M., Sparrow, H., Tapanari, E., Taylor, K., Vullo, A., Williams, G., Zadissia, A., Olson, A., Stein, J., Wei, S., Tello-Ruiz, M., Ware, D., Luciani, A., Potter, S., Finn, R. D., Urban, M., Hammond-Kosack, K. E., Bolser, D. M., De Silva, N., Howe, K. L., Langridge, N., Maslen, G., Staines, D. M., Yates, A. (January 2018) Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species. Nucleic Acids Res, 46 (D1). D802-D808. ISSN 0305-1048

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

Gupta, Parul, Naithani, Sushma, Tello-Ruiz, Marcela Karey, Chougule, Kapeel, D’Eustachio, Peter, Fabregat, Antonio, Jiao, Yinping, Keays, Maria, Lee, Young Koung, Kumari, Sunita, Mulvaney, Joseph, Olson, Andrew, Preece, Justin, Stein, Joshua, Wei, Sharon, Weiser, Joel, Huerta, Laura, Petryszak, Robert, Kersey, Paul, Stein, Lincoln D., Ware, Doreen, Jaiswal, Pankaj (November 2016) Gramene Database: Navigating Plant Comparative Genomics Resources. Current Plant Biology, 7-8. pp. 10-15. ISSN 2214-6628

Kersey, P. J., Allen, J. E., Armean, I., Boddu, S., Bolt, B. J., Carvalho-Silva, D., Christensen, M., Davis, P., Falin, L. J., Grabmueller, C., Humphrey, J., Kerhornou, A., Khobova, J., Aranganathan, N. K., Langridge, N., Lowy, E., McDowall, M. D., Maheswari, U., Nuhn, M., Ong, C. K., Overduin, B., Paulini, M., Pedro, H., Perry, E., Spudich, G., Tapanari, E., Walts, B., Williams, G., Tello-Ruiz, M., Stein, J., Wei, S., Ware, D., Bolser, D. M., Howe, K. L., Kulesha, E., Lawson, D., Maslen, G., Staines, D. M. (January 2016) Ensembl Genomes 2016: more genomes, more complexity. Nucleic Acids Res, 44 (D1). D574-80. ISSN 1362-4962 (Electronic)0305-1048 (Linking)

Tello-Ruiz, M. K., Stein, J., Wei, S., Preece, J., Olson, A., Naithani, S., Amarasinghe, V., Dharmawardhana, P., Jiao, Y., Mulvaney, J., Kumari, S., Chougule, K., Elser, J., Wang, B., Thomason, J., Bolser, D. M., Kerhornou, A., Walts, B., Fonseca, N. A., Huerta, L., Keays, M., Tang, Y. A., Parkinson, H., Fabregat, A., McKay, S., Weiser, J., D'Eustachio, P., Stein, L., Petryszak, R., Kersey, P. J., Jaiswal, P., Ware, D. (January 2016) Gramene 2016: comparative plant genomics and pathway resources. Nucleic Acids Res, 44 (D1). D1133-40. ISSN 1362-4962 (Electronic)0305-1048 (Linking)

Tello-Ruiz, M. K., Stein, J., Wei, S., Youens-Clark, K., Jaiswal, P., Ware, D. (January 2016) Gramene: A Resource for Comparative Analysis of Plants Genomes and Pathways. Methods Mol Biol, 1374. pp. 141-63. ISSN 1940-6029 (Electronic)1064-3745 (Linking)

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

Youens-Clark, K., Buckler, E., Casstevens, T., Chen, C., DeClerck, G., Derwent, P., Dharmawardhana, P., Jaiswal, P., Kersey, P., Karthikeyan, A. S., Lu, J., McCouch, S. R., Ren, L., Spooner, W., Stein, J. C., Thomason, J., Wei, S., Ware, D. H. (January 2011) Gramene database in 2010: Updates and extensions. Nucleic Acids Research, 39 (SUPPL.).

Youens-Clark, K., Buckler, E., Casstevens, T., Chen, C., Declerck, G., Derwent, P., Dharmawardhana, P., Jaiswal, P., Kersey, P., Karthikeyan, A. S., Lu, J., McCouch, S. R., Ren, L., Spooner, W., Stein, J. C., Thomason, J., Wei, S., Ware, D. H. (January 2011) Gramene database in 2010: updates and extensions. Nucleic Acids Res, 39. D1085-D1094. ISSN 1362-4962 (Electronic) 0305-1048 (Linking)

Schnable, P. S., Ware, D., Fulton, R. S., Stein, J. C., Wei, F., Pasternak, S., Liang, C., Zhang, J., Fulton, L., Graves, T. A., Minx, P., Reily, A. D., Courtney, L., Kruchowski, S. S., Tomlinson, C., Strong, C., Delehaunty, K., Fronick, C., Courtney, B., Rock, S. M., Belter, E., Du, F., Kim, K., Abbott, R. M., Cotton, M., Levy, A., Marchetto, P., Ochoa, K., Jackson, S. M., Gillam, B., Chen, W., Yan, L., Higginbotham, J., Cardenas, M., Waligorski, J., Applebaum, E., Phelps, L., Falcone, J., Kanchi, K., Thane, T., Scimone, A., Thane, N., Henke, J., Wang, T., Ruppert, J., Shah, N., Rotter, K., Hodges, J., Ingenthron, E., Cordes, M., Kohlberg, S., Sgro, J., Delgado, B., Mead, K., Chinwalla, A., Leonard, S., Crouse, K., Collura, K., Kudrna, D., Currie, J., He, R., Angelova, A., Rajasekar, S., Mueller, T., Lomeli, R., Scara, G., Ko, A., Delaney, K., Wissotski, M., Lopez, G., Campos, D., Braidotti, M., Ashley, E., Golser, W., Kim, H., Lee, S., Lin, J., Dujmic, Z., Kim, W., Talag, J., Zuccolo, A., Fan, C., Sebastian, A., Kramer, M., Spiegel, L., Nascimento, L., Zutavern, T., Miller, B., Ambroise, C., Muller, S., Spooner, W., Narechania, A., Ren, L., Wei, S., Kumari, S., Faga, B., Levy, M. J., McMahan, L., Van Buren, P., Vaughn, M. W. (November 2009) The B73 maize genome: complexity, diversity, and dynamics. Science, 326 (5956). pp. 1112-5. ISSN 1095-9203 (Electronic)0036-8075 (Linking)

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.