Additional materials of the author at
CSHL Institutional Repository

Lee, YK, Kim, K , Ware, D (2024) Role of moss and Arabidopsis zinc-finger homeodomain transcription factors in regulating plant architecture. Plant Biotechnology Reports, 18(2) pp. 223-231.

Koren, Sergey, Bao, Zhigui, Guarracino, Andrea, Ou, Shujun, Goodwin, Sara, Jenike, Katharine M, Lucas, Julian, McNulty, Brandy, Park, Jimin, Rautianinen, Mikko, Rhie, Arang, Roelofs, Dick, Schneiders, Harrie, Vrijenhoek, Ilse, Nijbroek, Koen, Ware, Doreen, Schatz, Michael C, Garrison, Erik, Huang, Sanwen, McCombie, William Richard, Miga, Karen H, Wittenberg, Alexander HJ , Phillippy, Adam M (2024) Gapless assembly of complete human and plant chromosomes using only nanopore sequencing. bioRxiv,

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 (2024) A high-performance computational workflow to accelerate GATK SNP detection across a 25-genome dataset. BMC Biology, 22(1) pp. 13.

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 (2023) A large sequenced mutant library - valuable reverse genetic resource that covers 98% of sorghum genes. The Plant Journal,

George, Nancy, Fexova, Silvie, Fuentes, Alfonso Munoz, Madrigal, Pedro, Bi, Yalan, Iqbal, Haider, Kumbham, Upendra, Nolte, Nadja Francesca, Zhao, Lingyun, Thanki, Anil S, Yu, Iris D, Marugan Calles, Jose C, Erdos, Karoly, Vilmovsky, Liora, Kurri, Sandeep R, Vathrakokoili-Pournara, Anna, Osumi-Sutherland, David, Prakash, Ananth, Wang, Shengbo, Tello-Ruiz, Marcela K, Kumari, Sunita, Ware, Doreen, Goutte-Gattat, Damien, Hu, Yanhui, Brown, Nick, Perrimon, Norbert, Vizcaíno, Juan Antonio, Burdett, Tony, Teichmann, Sarah, Brazma, Alvis , Papatheodorou, Irene (2023) Expression Atlas update: insights from sequencing data at both bulk and single cell level. Nucleic Acids Research (NAR), pp. gkad1021.

Harrison, Peter W, Amode, M Ridwan, Austine-Orimoloye, Olanrewaju, Azov, Andrey G, Barba, Matthieu, Barnes, If, Becker, Arne, Bennett, Ruth, Berry, Andrew, Bhai, Jyothish, Bhurji, Simarpreet Kaur, Boddu, Sanjay, Branco Lins, Paulo R, Brooks, Lucy, Ramaraju, Shashank Budhanuru, Campbell, Lahcen I, Martinez, Manuel Carbajo, Charkhchi, Mehrnaz, Chougule, Kapeel, Cockburn, Alexander, Davidson, Claire, De Silva, Nishadi H, Dodiya, Kamalkumar, Donaldson, Sarah, El Houdaigui, Bilal, Naboulsi, Tamara El, Fatima, Reham, Giron, Carlos Garcia, Genez, Thiago, Grigoriadis, Dionysios, Ghattaoraya, Gurpreet S, Martinez, Jose Gonzalez, Gurbich, Tatiana A, Hardy, Matthew, Hollis, Zoe, Hourlier, Thibaut, Hunt, Toby, Kay, Mike, Kaykala, Vinay, Le, Tuan, Lemos, Diana, Lodha, Disha, Marques-Coelho, Diego, Maslen, Gareth, Merino, Gabriela Alejandra, Mirabueno, Louisse Paola, Mushtaq, Aleena, Hossain, Syed Nakib, Ogeh, Denye N, Sakthivel, Manoj Pandian, Parker, Anne, Perry, Malcolm, Piližota, Ivana, Poppleton, Daniel, Prosovetskaia, Irina, Raj, Shriya, Pérez-Silva, José G, Salam, Ahamed Imran Abdul, Saraf, Shradha, Saraiva-Agostinho, Nuno, Sheppard, Dan, Sinha, Swati, Sipos, Botond, Sitnik, Vasily, Stark, William, Steed, Emily, Suner, Marie-Marthe, Surapaneni, Likhitha, Sutinen, Kyösti, Tricomi, Francesca Floriana, Urbina-Gómez, David, Veidenberg, Andres, Walsh, Thomas A, Ware, Doreen, Wass, Elizabeth, Willhoft, Natalie L, Allen, Jamie, Alvarez-Jarreta, Jorge, Chakiachvili, Marc, Flint, Bethany, Giorgetti, Stefano, Haggerty, Leanne, Ilsley, Garth R, Keatley, Jon, Loveland, Jane E, Moore, Benjamin, Mudge, Jonathan M, Naamati, Guy, Tate, John, Trevanion, Stephen J, Winterbottom, Andrea, Frankish, Adam, Hunt, Sarah E, Cunningham, Fiona, Dyer, Sarah, Finn, Robert D, Martin, Fergal J , Yates, Andrew D (2023) Ensembl 2024. Nucleic Acids Research, pp. gkad1049.

Lee, Eun Song, Heo, Jung, Bang, Woo Young, Chougule, Kapeel M, Waminal, Nomar Espinosa, Hong, Nguyen Thi, Kim, Min Ji, Beak, Hong Kwan, Kim, Yong Jun, Priatama, Ryza A, Jang, Ji In, Cha, Kang Il, Son, Seung Han, Rajendran, Sujeevan, Choo, Young-Kug, Bae, Jong Hyang, Kim, Chul Min, Lee, Young Koung, Bae, Sangsu, Jones, Jonathan DG, Sohn, Kee Hoon, Lee, Jiyoung, Kim, Hyun Hee, Hong, Jong Chan, Ware, Doreen, Kim, Keunhwa , Park, Soon Ju (2023) Engineering homoeologs provide a fine scale for quantitative traits in polyploid. Plant Biotechnology Journal, pp. 1-15.

Velt, Amandine, Frommer, Bianca, Blanc, Sophie, Holtgräwe, Daniela, Duchêne, Éric, Dumas, Vincent, Grimplet, Jérôme, Hugueney, Philippe, Kim, Catherine, Lahaye, Marie, Matus, José Tomás, Navarro-Payá, David, Orduña, Luis, Tello-Ruiz, Marcela K, Vitulo, Nicola, Ware, Doreen , Rustenholz, Camille (2023) An improved reference of the grapevine genome reasserts the origin of the PN40024 highly homozygous genotype. Whiteman, N (Ed.). G3: Genes, Genomes, Genetics, 13(5) pp. jkad067.

Shi, Xiaoya, Cao, Shuo, Wang, Xu, Huang, Siyang, Wang, Yue, Liu, Zhongjie, Liu, Wenwen, Leng, Xiangpeng, Peng, Yanling, Wang, Nan, Wang, Yiwen, Ma, Zhiyao, Xu, Xiaodong, Zhang, Fan, Xue, Hui, Zhong, Haixia, Wang, Yi, Zhang, Kekun, Velt, Amandine, Avia, Komlan, Holtgräwe, Daniela, Grimplet, Jérôme, Matus, José Tomás, Ware, Doreen, Wu, Xinyu, Wang, Haibo, Liu, Chonghuai, Fang, Yuling, Rustenholz, Camille, Cheng, Zongming, Xiao, Hua , Zhou, Yongfeng (2023) The complete reference genome for grapevine (Vitis vinifera L.) genetics and breeding. Horticulture Research, 10(5) pp. uhad061.

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 (2023) Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice. Nature Communications, 14(1) pp. 1567.

Gladman, Nicholas, Goodwin, Sara, Chougule, Kapeel, Richard McCombie, William , Ware, Doreen (2023) Era of gapless plant genomes: innovations in sequencing and mapping technologies revolutionize genomics and breeding. Current Opinion in Biotechnology, 79 pp. 102886.

Lee, YK, Olson, A, Kim, K, Ohme-Takagi, M , Ware, D (2023) HB31 and HB21 regulate floral architecture through miRNA396/GRF modules in Arabidopsis. Plant Biotechnology Reports,

Zhang, Lifang, Braynen, Janeen, Fahey, Audrey, Chopra, Kriti, Cifani, Paolo, Tadesse, Dimiru, Regulski, Michael, Hu, Fangle, van Dam, Hubertus JJ, Xie, Meng, Ware, Doreen , Blaby-Haas, Crysten E (2023) Two related families of metal transferases, ZNG1 and ZNG2, are involved in acclimation to poor Zn nutrition in Arabidopsis. Frontiers in Plant Science, 14 pp. 1237722.

Fahlgren, Noah, Kapoor, Muskan, Yordanova, Galabina, Papatheodorou, Irene, Waese, Jamie, Cole, Benjamin, Harrison, Peter, Ware, Doreen, Tickle, Timothy, Paten, Benedict, Burdett, Tony, Elsik, Christine G, Tuggle, Christopher K , Provart, Nicholas J (2022) Toward a Data Infrastructure for the Plant Cell Atlas. Plant Physiology,

Lee, Young Koung, Kumari, Sunita, Olson, Andrew, Hauser, Felix , Ware, Doreen (2022) Role of a ZF-HD Transcription Factor in miR157-Mediated Feed-Forward Regulatory Module That Determines Plant Architecture in Arabidopsis. International Journal of Molecular Sciences, 23(15) pp. 8665.

Gladman, Nicholas, Hufnagel, Barbara, Regulski, Michael, Liu, Zhigang, Wang, Xiaofei, Chougule, Kapeel, Kochian, Leon, Magalhães, Jurandir , Ware, Doreen (2022) Sorghum root epigenetic landscape during limiting phosphorus conditions. Plant Direct, 6(5) pp. e393.

Brady, Siobhan (2022) Transcriptional regulation of primary and specialized metabolism. The FASEB Journal, 36(S1)

Ferrero-Serrano, Ángel, Sylvia, Megan M, Forstmeier, Peter C, Olson, Andrew J, Ware, Doreen, Bevilacqua, Philip C , Assmann, Sarah M (2022) Experimental demonstration and pan-structurome prediction of climate-associated riboSNitches in Arabidopsis. Genome Biology, 23(1) pp. 101.

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 (2022) SorghumBase: a web-based portal for sorghum genetic information and community advancement.. Planta: an international journal of plant biology, 255(2) pp. 35.

Tello-Ruiz, Marcela Karey, Jaiswal, Pankaj , Ware, Doreen (2022) Gramene: A Resource for Comparative Analysis of Plants Genomes and Pathways. Methods in Molecular Biology, 2443 pp. 101-131.

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 pp. 1040909.

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.

Moreno, Pablo, Fexova, Silvie, George, Nancy, Manning, Jonathan R, Miao, Zhichiao, Mohammed, Suhaib, Muñoz-Pomer, Alfonso, Fullgrabe, Anja, Bi, Yalan, Bush, Natassja, Iqbal, Haider, Kumbham, Upendra, Solovyev, Andrey, Zhao, Lingyun, Prakash, Ananth, García-Seisdedos, David, Kundu, Deepti J, Wang, Shengbo, Walzer, Mathias, Clarke, Laura, Osumi-Sutherland, David, Tello-Ruiz, Marcela Karey, Kumari, Sunita, Ware, Doreen, Eliasova, Jana, Arends, Mark J, Nawijn, Martijn C, Meyer, Kerstin, Burdett, Tony, Marioni, John, Teichmann, Sarah, Vizcaíno, Juan Antonio, Brazma, Alvis , Papatheodorou, Irene (2021) Expression Atlas update: gene and protein expression in multiple species. Nucleic Acids Research,

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 (2021) Ensembl Genomes 2022: an expanding genome resource for non-vertebrates.. Nucleic Acids Research,

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 (2021) A KBase Case Study on Genome-wide Transcriptomics and Plant Primary Metabolism in response to Drought Stress in Sorghum.. Current Plant Biology, pp. 100229-100229.

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 (2021) De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes.. Science, 373(6555) pp. 655-662.

Olson, Andrew J , Ware, Doreen (2021) Ranked Choice Voting for Representative Transcripts with TRaCE. Bioinformatics,

Vaughn, Justin N, Korani, Walid, Stein, Joshua C, Edwards, Jeremy D, Peterson, Daniel G, Simpson, Sheron A, Youngblood, Ramey C, Grimwood, Jane, Chougule, Kapeel, Ware, Doreen H, McClung, Anna M , Scheffler, Brian E (2021) Gene disruption by structural mutations drives selection in US rice breeding over the last century.. PLoS Genetics, 17(3) pp. e1009389.

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. (2021) Gramene 2021: harnessing the power of comparative genomics and pathways for plant research. Nucleic Acids Res, 49(D1) pp. D1452-d1463.

Xu, X., Crow, M., Rice, B. R., Li, F., Harris, B., Liu, L., Demesa-Arevalo, E., Lu, Z., Wang, L., Fox, N., Wang, X., Drenkow, J., Luo, A., Char, S. N., Yang, B., Sylvester, A. W., Gingeras, T. R., Schmitz, R. J., Ware, D., Lipka, A. E., Gillis, J. , Jackson, D. (2020) Single-cell RNA sequencing of developing maize ears facilitates functional analysis and trait candidate gene discovery. Dev Cell, S1534-(20) pp. 31021-31022.

Diniz, A. L., da Silva, D. I. R., Lembke, C. G., Costa, M. D. L., Ten-Caten, F., Li, F., Vilela, R. D., Menossi, M., Ware, D., Endres, L. , Souza, G. M. (2020) Amino Acid and Carbohydrate Metabolism Are Coordinated to Maintain Energetic Balance during Drought in Sugarcane. Int J Mol Sci, 21(23) pp. 9124.

Hon, T., Mars, K., Young, G., Tsai, Y. C., Karalius, J. W., Landolin, J. M., Maurer, N., Kudrna, D., Hardigan, M. A., Steiner, C. C., Knapp, S. J., Ware, D., Shapiro, B., Peluso, P. , Rank, D. R. (2020) Highly accurate long-read HiFi sequencing data for five complex genomes. Sci Data, 7(1) pp. 399.

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

Parry, G, Provart, NJ, Brady, SM, Uzilday, B, Adams, K, Araújo, W, Aubourg, S, Baginsky, S, Bakker, E, Bärenfaller, K, Batley, J, Beale, M, Beilstein, M, Belkhadir, Y, Mendel, G, Berardini, T, Bergelson, J, Blanco-Herrera, F, Brady, S, Braun, HP, Briggs, S, Brownfield, L, Cardarelli, M, Castellanos-Uribe, M, Coruzzi, G, Dassanayake, M, De Jaeger, G, Dilkes, B, Doherty, C, Ecker, J, Edger, P, Edwards, D, El Kasmi, F, Eriksson, M, Exposito-Alonso, M, Falter-Braun, P, Fernie, A, Ferro, M, Fiehn, O, Friesner, J, Greenham, K, Guo, Y, Hamann, T, Hancock, A, Hauser, MT, Heazlewood, J, Ho, CH, Hõrak, H, Huala, E, Hwang, I, Iuchi, S, Jaiswal, P, Jakobson, L, Jiang, Y, Jiao, Y, Jones, A, Kadota, Y, Khurana, J, Kliebenstein, D, Knee, E, Kobayashi, M, Koch, M, Krouk, G, Larson, T, Last, R, Lepiniec, L, Li, S, Lurin, C, Lysak, M, Maere, S, Malinowski, R, Maumus, F, May, S, Mayer, K, Mendoza-Cozatl, D, Mendoza-Poudereux, I, Micol, JL, Millar, H, Mock, HP, Mukhtar, K, Mukhtar, S, Murcha, M, Nakagami, H, Nakamura, Y, Nicolov, L, Nikolau, B, Nowack, M, Nunes-Nesi, A, Palmgren, M, Parry, G, Patron, N, Peck, S, Pedmale, U, Perrot-Rechenmann, C, Pieruschka, R, Pío-Beltrán, J, Pires, JC, Provart, N, Rajjou, L , Reiser, L (2020) Current status of the multinational Arabidopsis community. Plant Direct, 4(7)

Liu, J., Seetharam, A.S., Chougule, K., Ou, S., Swentowsky, K.W., Gent, J.I., Llaca, V., Woodhouse, M.R., Manchanda, N., Presting, G.G., Kudrna, D., Alabady, M., Hirsch, C.N., Fengler, K.A., Ware, D., Michael, T.P., Hufford, M. B. , Dawe, R.K. (2020) Gapless Assembly of Maize Chromosomes Using Long-Read Technologies. Genome Biology, 21(1) pp. 121.

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. (2020) Effect of sequence depth and length in long-read assembly of the maize inbred NC358. Nature Communications, 11(1) pp. 2288. Nature.

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. (2020) Management, Analyses, and Distribution of the MaizeCODE Data on the Cloud. Frontiers in Plant Science, 11(289)

Wang, B., Tseng, E., Baybayan, P., Eng, K., Regulski, M., Jiao, Y., Wang, L., Olson, A., Chougule, K., Buren, P. V. , Ware, D. (2020) Variant phasing and haplotypic expression from long-read sequencing in maize. Commun Biol, 3(1) pp. 78.

Zou, C., Karn, A., Reisch, B., Nguyen, A., Sun, Y., Bao, Y., Campbell, M. S., Church, D., Williams, S., Xu, X., Ledbetter, C. A., Patel, S., Fennell, A., Glaubitz, J. C., Clark, M., Ware, D., Londo, J. P., Sun, Q. , Cadle-Davidson, L. (2020) Haplotyping the Vitis collinear core genome with rhAmpSeq improves marker transferability in a diverse genus. Nat Commun, 11(1) pp. 413.

Howe, K. L., Contreras-Moreira, B., De Silva, N., Maslen, G., Akanni, W., Allen, J., Alvarez-Jarreta, J., Barba, M., Bolser, D. M., Cambell, L., Carbajo, M., Chakiachvili, M., Christensen, M., Cummins, C., Cuzick, A., Davis, P., Fexova, S., Gall, A., George, N., Gil, L., Gupta, P., Hammond-Kosack, K. E., Haskell, E., Hunt, S. E., Jaiswal, P., Janacek, S. H., Kersey, P. J., Langridge, N., Maheswari, U., Maurel, T., McDowall, M. D., Moore, B., Muffato, M., Naamati, G., Naithani, S., Olson, A., Papatheodorou, I., Patricio, M., Paulini, M., Pedro, H., Perry, E., Preece, J., Rosello, M., Russell, M., Sitnik, V., Staines, D. M., Stein, J., Tello-Ruiz, M. K., Trevanion, S. J., Urban, M., Wei, S., Ware, D., Williams, G., Yates, A. D. , Flicek, P. (2020) Ensembl Genomes 2020-enabling non-vertebrate genomic research. Nucleic Acids Res, 48(1) pp. 689-695.

Ou, S., Su, W., Liao, Y., Chougule, K., Agda, J. R. A., Hellinga, A. J., Lugo, C. S. B., Elliott, T. A., Ware, D., Peterson, T., Jiang, N., Hirsch, C. N. , Hufford, M. B. (2019) Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline. Genome Biol, 20(1) pp. 275.

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 (2019) Management, Analyses, and Distribution of the MaizeCODE Data on the Cloud. BioRxiv,

Knauer, S., Javelle, M., Li, L., Li, X., Ma, X., Wimalanathan, K., Kumari, S., Johnston, R., Leiboff, S., Meeley, R., Schnable, P. S., Ware, D., Lawrence-Dill, C., Yu, J., Muehlbauer, G. J., Scanlon, M. J. , Timmermans, M. C. P. (2019) A high-resolution gene expression atlas links dedicated meristem genes to key architectural traits. Genome Res, 29(12) pp. 1962-1973.

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. (2019) Plant Reactome: a knowledgebase and resource for comparative pathway analysis. Nucleic Acids Res, 48 pp. 1093-1103.

Chen, J. P., Jiao, Y. P., Laza, H., Payton, P., Ware, D. , Xin, Z. G. (2019) Identification of the First Nuclear Male Sterility Gene (Male-sterile 9) in Sorghum. Plant Genome, 12(3) pp. Article No 190020.

Dampanaboina, L., Jiao, Y., Chen, J., Gladman, N., Chopra, R., Burow, G., Hayes, C., Christensen, S. A., Burke, J., Ware, D. , Xin, Z. (2019) Sorghum MSD3 Encodes an omega-3 Fatty Acid Desaturase that Increases Grain Number by Reducing Jasmonic Acid Levels. Int J Mol Sci, 20(21)

Tello-Ruiz, M. K., Marco, C. F., Hsu, F. M., Khangura, R. S., Qiao, P., Sapkota, S., Stitzer, M. C., Wasikowski, R., Wu, H., Zhan, J., Chougule, K., Barone, L. C., Ghiban, C., Muna, D., Olson, A. C., Wang, L., Ware, D. , Micklos, D. A. (2019) Double triage to identify poorly annotated genes in maize: The missing link in community curation. PLoS ONE, 14(10) pp. Article number e0224086.

Gladman, N., Jiao, Y., Lee, Y. K., Zhang, L., Chopra, R., Regulski, M., Burow, G., Hayes, C., Christensen, S. A., Dampanaboina, L., Chen, J., Burke, J., Ware, D. , Xin, Z. (2019) Fertility of Pedicellate Spikelets in Sorghum Is Controlled by a Jasmonic Acid Regulatory Module. Int J Mol Sci, 20(19)

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

Wittmeyer, K., Cui, J., Chatterjee, D., Lee, T. F., Tan, Q., Xue, W., Jiao, Y., Wang, P. H., Gaffoor, I., Ware, D., Meyers, B. C. , Chopra, S. (2018) The Dominant and Poorly Penetrant Phenotypes of Maize Unstable factor for orange1 Are Caused by DNA Methylation Changes at a Linked Transposon. Plant Cell, 30(12) pp. 3006-3023.

Gaudinier, A., Rodriguez-Medina, J., Zhang, L., Olson, A., Liseron-Monfils, C., Bagman, A. M., Foret, J., Abbitt, S., Tang, M., Li, B., Runcie, D. E., Kliebenstein, D. J., Shen, B., Frank, M. J., Ware, D. , Brady, S. M. (2018) Transcriptional regulation of nitrogen-associated metabolism and growth. Nature, 563(7730) pp. 259-264.

Chougule, K. M., Wang, L., Stein, J. C., Wang, X., Devisetty, U. K., Klein, R. R. , Ware, D. (2018) Improved RNA-seq Workflows Using CyVerse Cyberinfrastructure. Curr Protoc Bioinformatics, pp. e53.

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. (2018) The maize W22 genome provides a foundation for functional genomics and transposon biology. Nat Genet, 50(9) pp. 1282-1288.

Sun, S., Zhou, Y., Chen, J., Shi, J., Zhao, H., Zhao, H., Song, W., Zhang, M., Cui, Y., Dong, X., Liu, H., Ma, X., Jiao, Y., Wang, B., Wei, X., Stein, J. C., Glaubitz, J. C., Lu, F., Yu, G., Liang, C., Fengler, K., Li, B., Rafalski, A., Schnable, P. S., Ware, D. H., Buckler, E. S. , Lai, J. (2018) Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes. Nat Genet, 50(9) pp. 1289-1295.

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 (2018) KBase: The United States Department of Energy Systems Biology Knowledgebase.. Nature Biotechnology, 36(7) pp. 566-569.

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

Wang, B., Regulski, M., Tseng, E., Olson, A., Goodwin, S., McCombie, W. R. , Ware, D. (2018) A comparative transcriptional landscape of maize and sorghum obtained by single-molecule sequencing. Genome Res, 28(6) pp. 921-932.

Majoros, W. H., Holt, C., Campbell, M. S., Ware, D., Yandell, M. , Reddy, T. E. (2018) Predicting Gene Structure Changes Resulting from Genetic Variants via Exon Definition Features. Bioinformatics, 34(21) pp. 3616-3623.

Bukowski, R., Guo, X., Lu, Y., Zou, C., He, B., Rong, Z., Wang, B., Xu, D., Yang, B., Xie, C., Fan, L., Gao, S., Xu, X., Zhang, G., Li, Y., Jiao, Y., Doebley, J. F., Ross-Ibarra, J., Lorant, A., Buffalo, V., Romay, M. C., Buckler, E. S., Ware, D., Lai, J., Sun, Q. , Xu, Y. (2018) Construction of the third generation Zea mays haplotype map. Gigascience, 7(4) pp. 1-12.

Jiao, Y., Lee, Y. K., Gladman, N., Chopra, R., Christensen, S. A., Regulski, M., Burow, G., Hayes, C., Burke, J., Ware, D. , Xin, Z. (2018) MSD1 regulates pedicellate spikelet fertility in sorghum through the jasmonic acid pathway. Nat Commun, 9(1) pp. 822.

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. (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.

Jiao, Y. P., Burow, G., Gladman, N., Acosta-Martinez, V., Chen, J. P., Burke, J., Ware, D. , Xin, Z. G. (2018) Efficient Identification of Causal Mutations through Sequencing of Bulked F-2 from Two Allelic Bloomless Mutants of Sorghum bicolor. Frontiers in Plant Science, 8 pp. 2267.

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. (2018) Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species. Nucleic Acids Res, 46(D1) pp. D802-D808.

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. (2018) Gramene 2018: unifying comparative genomics and pathway resources for plant research. Nucleic Acids Res, 46(D1) pp. D1181-D1189.

Harper, L., Campbell, J., Cannon, E. K. S., Jung, S., Poelchau, M., Walls, R., Andorf, C., Arnaud, E., Berardini, T. Z., Birkett, C., Cannon, S., Carson, J., Condon, B., Cooper, L., Dunn, N., Elsik, C. G., Farmer, A., Ficklin, S. P., Grant, D., Grau, E., Herndon, N., Hu, Z. L., Humann, J., Jaiswal, P., Jonquet, C., Laporte, M. A., Larmande, P., Lazo, G., McCarthy, F., Menda, N., Mungall, C. J., Munoz-Torres, M. C., Naithani, S., Nelson, R., Nesdill, D., Park, C., Reecy, J., Reiser, L., Sanderson, L. A., Sen, T. Z., Staton, M., Subramaniam, S., Tello-Ruiz, M. K., Unda, V., Unni, D., Wang, L., Ware, D., Wegrzyn, J., Williams, J., Woodhouse, M., Yu, J. , Main, D. (2018) AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture. Database (Oxford), 2018

Friesner, J., Assmann, S. M., Bastow, R., Bailey-Serres, J., Beynon, J., Brendel, V., Buell, C. R., Bucksch, A., Busch, W., Demura, T., Dinneny, J. R., Doherty, C. J., Eveland, A. L., Falter-Braun, P., Gehan, M. A., Gonzales, M., Grotewold, E., Gutierrez, R., Kramer, U., Krouk, G., Ma, S., Markelz, R. J. C., Megraw, M., Meyers, B. C., Murray, J. A. H., Provart, N. J., Rhee, S., Smith, R., Spalding, E. P., Taylor, C., Teal, T. K., Torii, K. U., Town, C., Vaughn, M., Vierstra, R., Ware, D., Wilkins, O., Williams, C. , Brady, S. M. (2017) The Next Generation of Training for Arabidopsis Researchers: Bioinformatics and Quantitative Biology. Plant Physiol, 175(4) pp. 1499-1509.

Majsec, K., Bhuiyan, N. H., Sun, Q., Kumari, S., Kumar, V., Ware, D. , van Wijk, K. J. (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.

Jiao, Y., Peluso, P., Shi, J., Liang, T., Stitzer, M. C., Wang, B., Campbell, M. S., Stein, J. C., Wei, X., Chin, C. S., Guill, K., Regulski, M., Kumari, S., Olson, A., Gent, J., Schneider, K. L., Wolfgruber, T. K., May, M. R., Springer, N. M., Antoniou, E., McCombie, W. R., Presting, G. G., McMullen, M., Ross-Ibarra, J., Dawe, R. K., Hastie, A., Rank, D. R. , Ware, D. (2017) Improved maize reference genome with single-molecule technologies. Nature, 546(7659) pp. 524-527.

Majoros, W. H., Campbell, M. S., Holt, C., DeNardo, E., Ware, D., Allen, A. S., Yandell, M. , Reddy, T. E. (2017) High-throughput interpretation of gene structure changes in human and nonhuman resequencing data, using ACE. Bioinformatics, 33(10) pp. 1437-1446.

Turco, G. M., Kajala, K., Kunde-Ramamoorthy, G., Ngan, C. Y., Olson, A., Deshphande, S., Tolkunov, D., Waring, B., Stelpflug, S., Klein, P., Schmutz, J., Kaeppler, S., Ware, D., Wei, C. L., Etchells, J. P. , Brady, S. M. (2017) DNA methylation and gene expression regulation associated with vascularization in Sorghum bicolor. New Phytol, 214(3) pp. 1213-1229.

Adam-Blondon, A. F., Alaux, M., Pommier, C., Cantu, D., Cheng, Z. M., Cramer, G. R., Davies, C., Delrot, S., Deluc, L., Di Gaspero, G., Grimplet, J., Fennell, A., Londo, J. P., Kersey, P., Mattivi, F., Naithani, S., Neveu, P., Nikolski, M., Pezzotti, M., Reisch, B. I., Topfer, R., Vivier, M. A., Ware, D. , Quesneville, H. (2016) Towards an open grapevine information system. Horticulture Research, 3 pp. 16056.

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 (2016) Gramene Database: Navigating Plant Comparative Genomics Resources. Current Plant Biology, 7-8 pp. 10-15.

Naithani, S., Preece, J., D'Eustachio, P., Gupta, P., Amarasinghe, V., Dharmawardhana, P. D., Wu, G., Fabregat, A., Elser, J. L., Weiser, J., Keays, M., Fuentes, A. M., Petryszak, R., Stein, L. D., Ware, D. , Jaiswal, P. (2016) Plant Reactome: a resource for plant pathways and comparative analysis. Nucleic Acids Res, 45(D1) pp. D1029-D1039.

Jiao, Y., Burke, J. J., Chopra, R., Burow, G., Chen, J., Wang, B., Hayes, C., Emendack, Y., Ware, D. , Xin, Z. (2016) A Sorghum Mutant Resource as an Efficient Platform for Gene Discovery in Grasses. Plant Cell, 28(7) pp. 1551-1562.

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

He, F., Yoo, S., Wang, D., Kumari, S., Gerstein, M., Ware, D. , Maslov, S. (2016) Large-scale atlas of microarray data reveals the distinct expression landscape of different tissues in Arabidopsis. Plant J, 86(6) pp. 472-80.

Wang, L., Van Buren, P. , Ware, D. (2016) Architecting a distributed bioinformatics platform with iRODS and iPlant agave API. 2015 International Conference on Computational Science and Computational Intelligence (CSCI), pp. 420-423. IEEE.

Merchant, N., Lyons, E., Goff, S., Vaughn, M., Ware, D., Micklos, D. , Antin, P. (2016) The iPlant Collaborative: Cyberinfrastructure for Enabling Data to Discovery for the Life Sciences. PLoS Biol, 14(1) pp. e1002342.

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. (2016) Ensembl Genomes 2016: more genomes, more complexity. Nucleic Acids Res, 44(D1) pp. D574-80.

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. (2016) Gramene 2016: comparative plant genomics and pathway resources. Nucleic Acids Res, 44(D1) pp. D1133-40.

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

Liu, H., Niu, Y., Gonzalez-Portilla, P. J., Zhou, H., Wang, L., Zuo, T., Qin, C., Tai, S., Jansen, C., Shen, Y., Lin, H., Lee, M., Ware, D., Zhang, Z., Lubberstedt, T. , Pan, G. (2015) An ultra-high-density map as a community resource for discerning the genetic basis of quantitative traits in maize. BMC Genomics, 16(1) pp. 1078.

Liseron-Monfils, Christophe , Ware, Doreen (2015) Revealing gene regulation and associations through biological networks. Current Plant Biology, 3-4 pp. 30-39.

Noutsos, C., Perera, A. M., Nikolau, B. J., Seaver, S. M. , Ware, D. H. (2015) Metabolomic Profiling of the Nectars of Aquilegia pubescens and A. Canadensis. PLoS One, 10(5) pp. e0124501.

Smedley, D., Haider, S., Durinck, S., Pandini, L., Provero, P., Allen, J., Arnaiz, O., Awedh, M. H., Baldock, R., Barbiera, G., Bardou, P., Beck, T., Blake, A., Bonierbale, M., Brookes, A. J., Bucci, G., Buetti, I., Burge, S., Cabau, C., Carlson, J. W., Chelala, C., Chrysostomou, C., Cittaro, D., Collin, O., Cordova, R., Cutts, R. J., Dassi, E., Genova, A. D., Djari, A., Esposito, A., Estrella, H., Eyras, E., Fernandez-Banet, J., Forbes, S., Free, R. C., Fujisawa, T., Gadaleta, E., Garcia-Manteiga, J. M., Goodstein, D., Gray, K., Guerra-Assuncao, J. A., Haggarty, B., Han, D. J., Han, B. W., Harris, T., Harshbarger, J., Hastings, R. K., Hayes, R. D., Hoede, C., Hu, S., Hu, Z. L., Hutchins, L., Kan, Z., Kawaji, H., Keliet, A., Kerhornou, A., Kim, S., Kinsella, R., Klopp, C., Kong, L., Lawson, D., Lazarevic, D., Lee, J. H., Letellier, T., Li, C. Y., Lio, P., Liu, C. J., Luo, J., Maass, A., Mariette, J., Maurel, T., Merella, S., Mohamed, A. M., Moreews, F., Nabihoudine, I., Ndegwa, N., Noirot, C., Perez-Llamas, C., Primig, M., Quattrone, A., Quesneville, H., Rambaldi, D., Reecy, J., Riba, M., Rosanoff, S., Saddiq, A. A., Salas, E., Sallou, O., Shepherd, R., Simon, R., Sperling, L., Spooner, W., Staines, D. M., Steinbach, D., Stone, K., Stupka, E., Teague, J. W., Dayem Ullah, A. Z., Wang, J. , Ware, D. (2015) The BioMart community portal: an innovative alternative to large, centralized data repositories. Nucleic Acids Res, 43(W1) pp. W589-W598.

Wang, L., Ware, D., Lushbough, C., Merchant, N. , Stein, L. (2015) A genome-wide association study platform built on iPlant cyber-infrastructure. Concurrency Computation, 27(2) pp. 420-432.

Law, M., Childs, K. L., Campbell, M. S., Stein, J. C., Olson, A. J., Holt, C., Panchy, N., Lei, J., Jiao, D., Andorf, C. M., Lawrence, C. J., Ware, D., Shiu, S. H., Sun, Y., Jiang, N. , Yandell, M. (2015) Automated Update, Revision, and Quality Control of the Maize Genome Annotations Using MAKER-P Improves the B73 RefGen_v3 Gene Models and Identifies New Genes. Plant Physiol, 167(1) pp. 25-39.

Taylor-Teeples, M., Lin, L., de Lucas, M., Turco, G., Toal, T. W., Gaudinier, A., Young, N. F., Trabucco, G. M., Veling, M. T., Lamothe, R., Handakumbura, P. P., Xiong, G., Wang, C., Corwin, J., Tsoukalas, A., Zhang, L., Ware, D., Pauly, M., Kliebenstein, D. J., Dehesh, K., Tagkopoulos, I., Breton, G., Pruneda-Paz, J. L., Ahnert, S. E., Kay, S. A., Hazen, S. P. , Brady, S. M. (2015) An Arabidopsis gene regulatory network for secondary cell wall synthesis. Nature, 517(7536) pp. 571-575.

Schatz, M. C., Maron, L. G., Stein, J. C., Hernandez Wences, A., Gurtowski, J., Biggers, E., Lee, H., Kramer, M., Antoniou, E., Ghiban, E., Wright, M. H., Chia, J. M., Ware, D., McCouch, S. R. , McCombie, W. R. (2014) Whole genome de novo assemblies of three divergent strains of rice, Oryza sativa, document novel gene space of aus and indica. Genome Biol, 15(11) pp. 506.

Law, M., Childs, K. L., Campbell, M. S., Stein, J. C., Holt, C., Panchy, N., Lei, J., Jao, D., Andorf, C. M., Lawrence, C. J., Ware, D., Shiu, S. H., Sun, Y., Jiang, N. , Yandell, M. (2014) Automated update, revision and quality control of the Zea mays genome annotations using MAKER-P improves the B73 RefGen_v3 gene models and identifies new genes. Plant Physiology,

Zwickl, D. J., Stein, J. C., Wing, R. A., Ware, D. , Sanderson, M. J. (2014) Disentangling methodological and biological sources of gene tree discordance on Oryza (Poaceae) chromosome 3. Systematic Biology, 63(5) pp. 645-659.

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

Seaver, S. M., Gerdes, S., Frelin, O., Lerma-Ortiz, C., Bradbury, L. M., Zallot, R., Hasnain, G., Niehaus, T. D., El Yacoubi, B., Pasternak, S., Olson, R., Pusch, G., Overbeek, R., Stevens, R., de Crecy-Lagard, V., Ware, D., Hanson, A. D. , Henry, C. S. (2014) High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource. Proceedings of the National Academy of Sciences of the United States of America, 111(26) pp. 9645-9650.

Campbell, M. S., Law, M., Holt, C., Stein, J. C., Moghe, G. D., Hufnagel, D. E., Lei, J., Achawanantakun, R., Jiao, D., Lawrence, C. J., Ware, D., Shiu, S. H., Childs, K. L., Sun, Y., Jiang, N. , Yandell, M. (2014) MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations. Plant Physiol, 164(2) pp. 513-24.

Kersey, P. J., Allen, J. E., Christensen, M., Davis, P., Falin, L. J., Grabmueller, C., Hughes, D. S., Humphrey, J., Kerhornou, A., Khobova, J., Langridge, N., McDowall, M. D., Maheswari, U., Maslen, G., Nuhn, M., Ong, C. K., Paulini, M., Pedro, H., Toneva, I., Tuli, M. A., Walts, B., Williams, G., Wilson, D., Youens-Clark, K., Monaco, M. K., Stein, J., Wei, X., Ware, D., Bolser, D. M., Howe, K. L., Kulesha, E., Lawson, D. , Staines, D. M. (2014) Ensembl Genomes 2013: scaling up access to genome-wide data. Nucleic Acids Research, 42(Databa) pp. D546-52.

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. (2014) Gramene 2013: comparative plant genomics resources. Nucleic Acids Research, 42(Databa) pp. D1193-9.

Eveland, A. L., Goldshmidt, A., Pautler, M., Morohashi, K., Liseron-Monfils, C., Lewis, M. W., Kumari, S., Hiraga, S., Yang, F., Unger-Wallace, E., Olson, A., Hake, S., Vollbrecht, E., Grotewold, E., Ware, D. , Jackson, D. (2014) Regulatory modules controlling maize inflorescence architecture. Genome Research, 24(3) pp. 431-443.

Kumari, S. , Ware, D. (2013) Genome-Wide Computational Prediction and Analysis of Core Promoter Elements across Plant Monocots and Dicots. PLoS ONE, 8(10) pp. Art no. e79011.

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. (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.

Luo, M. C., Gu, Y. Q., You, F. M., Deal, K. R., Ma, Y., Hu, Y., Huo, N., Wang, Y., Wang, J., Chen, S., Jorgensen, C. M., Zhang, Y., McGuire, P. E., Pasternak, S., Stein, J. C., Ware, D., Kramer, M., McCombie, W. R., Kianian, S. F., Martis, M. M., Mayer, K. F. X., Sehgal, S. K., Li, W., Gill, B. S., Bevan, M. W., Šimková, H., Doležel, J., Weining, S., Lazo, G. R., Anderson, O. D. , Dvorak, J. (2013) A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor. Proceedings of the National Academy of Sciences of the United States of America, 110(19) pp. 7940-7945.

Dharmawardhana, P., Ren, L. Y., Amarasinghe, V., Monaco, M., Thomason, J., Ravenscroft, D., McCouch, S., Ware, D. , Jaiswal, P. (2013) A genome scale metabolic network for rice and accompanying analysis of tryptophan, auxin and serotonin biosynthesis regulation under biotic stress. Rice, 6(1) pp. 1-15.

Monaco, M. K., Sen, T. Z., Dharmawardhana, P. D., Ren, L., Schaeffer, M., Naithani, S., Amarasinghe, V., Thomason, J., Harper, L., Gardiner, J., Cannon, E. K. S., Lawrence, C. J., Ware, D. , Jaiswal, P. (2013) Maize Metabolic Network Construction and Transcriptome Analysis. Plant Genome, 6(1)

Hung, H. Y., Shannon, L. M., Tian, F., Bradbury, P. J., Chen, C., Flint-Garcia, S. A., McMullen, M. D., Ware, D., Buckler, E. S., Doebley, J. F. , Holland, J. B. (2012) ZmCCT and the genetic basis of day-length adaptation underlying the postdomestication spread of maize. Proceedings of the National Academy of Sciences of the United States of America, 109(28) pp. E1913-E1921.

Hufford, M. B., Xu, X., van Heerwaarden, J., Pyhajarvi, T., Chia, J. M., Cartwright, R. A., Elshire, R. J., Glaubitz, J. C., Guill, K. E., Kaeppler, S. M., Lai, J. S., Morrell, P. L., Shannon, L. M., Song, C., Springer, N. M., Swanson-Wagner, R. A., Tiffin, P., Wang, J., Zhang, G. Y., Doebley, J., McMullen, M. D., Ware, D., Buckler, E. S., Yang, S. , Ross-Ibarra, J. (2012) Comparative population genomics of maize domestication and improvement. Nature Genetics, 44(7) pp. 808-811.

Liu, Z. J., Kumari, S., Zhang, L. F., Zheng, Y. L. , Ware, D. (2012) Characterization of miRNAs in Response to Short-Term Waterlogging in Three Inbred Lines of Zea mays. PLoS ONE, 7(6) pp. e39786.

Chia, J. M., Song, C., Bradbury, P. J., Costich, D., de Leon, N., Doebley, J., Elshire, R. J., Gaut, B., Geller, L., Glaubitz, J. C., Gore, M., Guill, K. E., Holland, J., Hufford, M. B., Lai, J., Li, M., Liu, X., Lu, Y., McCombie, R., Nelson, R., Poland, J., Prasanna, B. M., Pyhajarvi, T., Rong, T., Sekhon, R. S., Sun, Q., Tenaillon, M. I., Tian, F., Wang, J., Xu, X., Zhang, Z., Kaeppler, S. M., Ross-Ibarra, J., McMullen, M. D., Buckler, E. S., Zhang, G., Xu, Y. , Ware, D. (2012) Maize HapMap2 identifies extant variation from a genome in flux. Nat Genet, 44(7) pp. 803-U238.

Baerenfaller, K., Bastow, R., Beynon, J., Brady, S., Brendel, V., Donaldson, S., Dooley, R., Forster, M., Friesner, J., Gifford, D., Grotewold, E., Gutierrez, R., Huala, E., Jaiswal, P., Joshi, H., Kersey, P., Liu, L., Loraine, A., Lyons, E., May, S., Mayer, K., MacLean, D., Meyers, B., Mueller, L., Muller, R., Muller, H. M., Ouellette, F., Pires, J. C., Provart, N., Staiger, D., Stanzione, D., Taylor, J., Taylor, C., Town, C., Toyoda, T., Vaughn, M., Walsh, S., Ware, D., Weckwerth, W. , Int Arabidopsis, Informatics (2012) Taking the Next Step: Building an Arabidopsis Information Portal. Plant Cell, 24(6) pp. 2248-2256.

The Tomato Genome Consortium, (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature, 485(7400) pp. 635-41.

Spooner, W., Youens-Clark, K., Staines, D. , Ware, D. (2012) GrameneMart: the BioMart data portal for the Gramene project. Database (Oxford), 2012(0)

Consortium, Arabidopsis Interactome Mapping (2011) Evidence for Network Evolution in an Arabidopsis Interactome Map. Science, 333(6042) pp. 601-607.

Myles, S., Boyko, A. R., Owens, C. L., Brown, P. J., Grassi, F., Aradhya, M. K., Prins, B., Reynolds, A., Chia, J. M., Ware, D. H., Bustamante, C. D. , Buckler, E. S. (2011) Genetic structure and domestication history of the grape. Proceedings of the National Academy of Sciences of the United States of America, 108(9) pp. 3530-3535.

Chia, J. M. , Ware, D. H. (2011) Sequencing for the cream of the crop. Nature Biotechnology, 29(2) pp. 138-9.

Brady, S. M., Zhang, L., Megraw, M., Martinez, N. J., Jiang, E., Yi, C. S., Liu, W., Zeng, A., Taylor-Teeples, M., Kim, D., Ahnert, S., Ohler, U., Ware, D. H., Walhout, A. J. M. , Benfey, P. N. (2011) A stele-enriched gene regulatory network in the Arabidopsis root. Molecular Systems Biology, 7 pp. 459.

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. (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. (2011) Gramene database in 2010: updates and extensions. Nucleic Acids Res, 39 pp. D1085-D1094.

Goff, S. A, Vaughn, M., McKay, S., Lyons, E., Stapleton, A. E, Gessler, D., Matasci, N., Wang, L., Hanlon, M., Lenards, A., Muir, A., Merchant, N., Lowry, S., Mock, S., Helmke, M., Kubach, A., Narro, M., Hopkins, N., Micklos, D., Hilgert, U., Gonzales, M, Jordan, C., Skidmore, E., Dooley, R., Cazes, J., McLay, R., Lu, Z., Pasternak, S., Koesterke, L., Piel, W. H., Grene, R., Noutsos, C., Gendler, K., Feng, X., Tang, C., Lent, M., Kim, S. J., Kvilekval, K., Manjunath, B.S., Tannen, V., Stamatakis, A., Sanderson, M. J., Welch, S. M., Cranston, K., Soltis, P., Soltis, D., O'Meara, B., Ane, C., Brutnell, T., Kleibenstein, D. J., White, J. W., Leebens-Mack, J., Donoghue, M. J., Spalding, E. P., Vision, T. J., Myers, C. R., Lowenthal, D., Enquist, B. J., Boyle, B., Akoglu, A., Andrews, G., Ram, S., Ware, D., Stein, L. , Stanzione, D. (2011) The iPlant Collaborative: Cyberinfrastructure for Plant Biology. Frontiers in Plant Science, 2

Gill, N., SanMiguel, P., Dhillon, B. D. S., Abernathy, B., Kim, H., Stein, L. D., Ware, D. H., Wing, R. , Jackson, S. A. (2010) Dynamic Oryza Genomes: Repetitive DNA Sequences as Genome Modeling Agents. Rice, 3(4) pp. 251-269.

Swanson-Wagner, R. A., Eichten, S. R., Kumari, S., Tiffin, P., Stein, J. C., Ware, D. H. , Springer, N. M. (2010) Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor. Genome Research, 20(12) pp. 1689-1699.

Eveland, A. L., Satoh-Nagasawa, N., Goldschmidt, A., Meyer, S., Beatty, M., Sakai, H., Ware, D. H. , Jackson, D. P. (2010) Digital Gene Expression Signatures for Maize Development. Plant Physiology, 154(3) pp. 1024-1039.

Myles, S., Chia, J. M., Hurwitz, B. L., Simon, C., Zhong, G. Y., Buckler, E. , Ware, D. H. (2010) Rapid Genomic Characterization of the Genus Vitis. PLoS ONE, 5(1)

Ammiraju, J. S. S., Song, X., Luo, M., Sisneros, N., Angelova, A., Kudrna, D., Kim, H., Yu, Y., Goicoechea, J. L., Lorieux, M., Kurata, N., Brar, D., Ware, D. H., Jackson, S. , Wing, R. A. (2010) The Oryza BAC resource: A genus-wide and genome scale tool for exploring rice genome evolution and leveraging useful genetic diversity from wild relatives. Breeding Science, 60(5) pp. 536-543.

Cranston, K. A., Hurwitz, B. L., Sanderson, M. J., Ware, D. H., Wing, R. A. , Stein, L. D. (2010) Phylogenomic analysis of BAC-end sequence libraries in Oryza (Poaceae). Systematic Botany, 35(3) pp. 512-523.

Hurwitz, B. L., Kudrna, D., Yu, Y., Sebastian, A., Zuccolo, A., Jackson, S. A., Ware, D. H., Wing, R. A. , Stein, L. D. (2010) Rice structural variation: A comparative analysis of structural variation between rice and three of its closest relatives in the genus Oryza. Plant Journal, 63(6) pp. 990-1003.

Jordan, C., Stanzione, D., Ware, D. H., Lu, J. , Noutsos, C. (2010) Comprehensive data infrastructure for plant bioinformatics. 2010 IEEE International Conference on Cluster Computing Workshops and Posters, Cluster Workshops 2010. 2010 IEEE International Conference on Cluster Computing Workshops and Posters, IEEE.

Gore, M. A., Chia, J. M., Elshire, R. J., Sun, Q., Ersoz, E. S., Hurwitz, B. L., Peiffer, J. A., McMullen, M. D., Grills, G. S., Ross-Ibarra, J., Ware, D. H. , Buckler, E. S. (2009) A first-generation haplotype map of maize. Science, 326(5956) pp. 1115-1117.

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. (2009) The B73 maize genome: complexity, diversity, and dynamics. Science, 326(5956) pp. 1112-5.

Youens-Clark, K., Faga, B. P., Yap, I. V., Stein, L. D. , Ware, D. H. (2009) CMap 1.01: A comparative mapping application for the Internet. Bioinformatics, 25(22) pp. 3040-3042.

Wei, F., Stein, J. C., Liang, C., Zhang, J., Fulton, R. S., Baucom, R. S., De Paoli, E., Zhou, S., Yang, L., Han, Y., Pasternak, S., Narechania, A., Zhang, L., Yeh, C. T., Ying, K., Nagel, D. H., Collura, K., Kudrna, D., Currie, J., Lin, J., Kim, H., Angelova, A., Scara, G., Wissotski, M., Golser, W., Courtney, L., Kruchowski, S., Graves, T. A., Rock, S. M., Adams, S., Fulton, L. A., Fronick, C., Courtney, W., Kramer, M., Spiegel, L., Nascimento, L., Kalyanaraman, A., Chaparro, C., Deragon, J. M., Miguel, P. S., Jiang, N., Wessler, S. R., Green, P. J., Yu, Y., Schwartz, D. C., Meyers, B. C., Bennetzen, J. L., Martienssen, R. A., McCombie, W. R., Aluru, S., Clifton, S. W., Schnable, P. S., Ware, D., Wilson, R. K. , Wing, R. A. (2009) Detailed analysis of a contiguous 22-Mb region of the maize genome. PLoS genetics, 5(11) pp. e1000728.

Wei, F., Zhang, J., Zhou, S., He, R., Schaeffer, M., Collura, K., Kudrna, D., Faga, B. P., Wissotski, M., Golser, W., Rock, S. M., Graves, T. A., Fulton, R. S., Coe, E., Schnable, P. S., Schwartz, D. C., Ware, D. H., Clifton, S. W., Wilson, R. K. , Wing, R. A. (2009) The physical and genetic framework of the maize b73 genome. PLoS Genet, 5(11) pp. e1000715.

Zhang, L., Chia, J. M., Kumari, S., Stein, J. C., Liu, Z., Narechania, A., Maher, C. A., Guill, K., McMullen, M. D. , Ware, D. H. (2009) A Genome-Wide Characterization of MicroRNA Genes in Maize. PLoS Genet, 5(11) pp. e1000716.

Zhou, S., Wei, F., Nguyen, J., Bechner, M., Potamousis, K., Goldstein, S., Pape, L., Mehan, M. R., Churas, C., Pasternak, S., Forrest, D. K., Wise, R., Ware, D. H., Wing, R. A., Waterman, M. S., Livny, M. , Schwartz, D. C. (2009) A single molecule scaffold for the maize genome. PLoS Genet, 5(11) pp. e1000711.

Cranston, K. A., Hurwitz, B. L., Ware, D. H., Stein, L. D. , Wing, R. A. (2009) Species Trees from Highly Incongruent Gene Trees in Rice. Systematic Biology, 58(5) pp. 489-500.

Liang, C., Mao, L., Ware, D. H. , Stein, L. D. (2009) Evidence-based gene predictions in plant genomes. Genome Res, 19(10) pp. 1912-1923 .

Buckler, E. S., Holland, J. B., Bradbury, P. J., Acharya, C. B., Brown, P. J., Browne, C., Ersoz, E., Flint-Garcia, S., Garcia, A., Glaubitz, J. C., Goodman, M. M., Harjes, C., Guill, K., Kroon, D. E., Larsson, S., Lepak, N. K., Li, H., Mitchell, S. E., Pressoir, G., Peiffer, J. A., Rosas, M. O., Rocheford, T. R., Romay, M. C., Romero, S., Salvo, S., Sanchez Villeda, H., da Silva, H. S., Sun, Q., Tian, F., Upadyayula, N., Ware, D. H., Yates, H., Yu, J., Zhang, Z., Kresovich, S. , McMullen, M. D. (2009) The genetic architecture of maize flowering time. Science, 325(5941) pp. 714-8.

McMullen, M. D., Kresovich, S., Villeda, Hector S., Bradbury, P. J., Li, H., Sun, Q., Flint-Garcia, S., Thornsberry, J., Acharya, C. B., Bottoms, C., Brown, P. J., Browne, C., Eller, M., Guill, K., Harjes, C., Kroon, D. E., Lepak, N.., Mitchell, S. E., Peterson, B., Pressoir, G., Romero, S., Rosas, M. O., Salvo, S., Yates, H., Hanson, M., Jones, E. G., Smith, S., Glaubitz, J. C., Goodman, M. M., Ware, D. H., Holland, J. B. , Buckler, E. S. (2009) Genetic Properties of the Maize Nested Association Mapping Population. Science, 325(5941) pp. 737-740.

Ni, J., Pujar, A., Youens-Clark, K., Yap, I. V., Jaiswal, P., Tecle, I., Tung, C.-W., Ren, L., Spooner, W., Wei, X, Avraham, S, Ware, D. H., Stein, L. D. , McCouch, S. (2009) Gramene QTL database: development, content and applications. Database, 2009(0) pp. bap005.

Brooks, L., Strable, J., Zhang, X., Ohtsu, K., Zhou, R., Sarkar, A., Hargreaves, S., Elshire, R. J., Eudy, D., Pawlowska, T., Ware, D. H., Janick-Buckner, D., Buckner, B., Timmermans, M. C. P., Schnable, P. S., Nettleton, D. , Scanlon, M. J. (2009) Microdissection of shoot meristem functional domains. PLoS Genet, 5(5) pp. e1000476.

Paterson, A. H., Bowers, J. E., Bruggmann, R., Dubchak, I., Grimwood, J., Gundlach, H., Haberer, G., Hellsten, U., Mitros, T., Poliakov, A., Schmutz, J., Spannagl, M., Tang, H., Wang, X., Wicker, T., Bharti, A. K., Chapman, J., Feltus, F. A., Gowik, U., Grigoriev, I. V., Lyons, E., Maher, C. A., Martis, M., Narechania, A., Otillar, R. P., Penning, B. W., Salamov, A. A., Wang, Y., Zhang, L., Carpita, N. C., Freeling, M., Gingle, A. R., Hash, C. T., Keller, B., Klein, P., Kresovich, S., McCann, M. C., Ming, R., Peterson, D. G., Mehboob ur, R., Ware, D. H., Westhoff, P., Mayer, K. F. X., Messing, J. , Rokhsar, D. S. (2009) The Sorghum bicolor genome and the diversification of grasses. Nature, 457(7229) pp. 551-556.

Kurtz, S., Narechania, A., Stein, J. C. , Ware, D. H. (2008) A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes. BMC Genomics, 9 pp. 517.

Wicker, T., Narechania, A., Sabot, F., Stein, J. C., Vu, G. T. H., Graner, A., Ware, D. H. , Stein, N. (2008) Low-pass shotgun sequencing of the barley genome facilitates rapid identification of genes, conserved non-coding sequences and novel repeats. BMC Genomics, 9 pp. 518.

Kim, H. R., Hurwitz, B. L., Yu, Y., Collura, K., Gill, N., SanMiguel, P., Mullikin, J. C., Maher, C., Nelson, W., Wissotski, M., Braidotti, M., Kudrna, D., Goigochia, J. L., Stein, L. D., Ware, D. H., Jackson, S., Soderlund, C. , Wing, R. (2008) Construction, alignment and analysis of 12 framework physical maps that represent the 10 genome types of the genus Oryza. Genome Biology, 9(2) pp. R45.

Avraham, S., Tung, C. W., Ilic, K., Jaiswal, P., Kellogg, E. A., McCouch, S., Pujar, A., Reiser, L., Rhee, S. Y., Sachs, M. M., Schaeffer, M., Stein, L. D., Stevens, P., Vincent, L., Zapata, F. , Ware, D. H. (2008) The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations. Nucleic Acids Res, 36(Databa) pp. D449-54.

Liang, C., Jaiswal, P., Hebbard, C., Avraham, S., Buckler, E. S., Casstevens, T., Hurwitz, B. L., McCouch, S., Ni, J., Pujar, A., Ravenscroft, D., Ren, L., Spooner, W., Tecle, I., Thomason, J., Tung, C. W., Wei, X., Yap, I., Youens-Clark, K., Ware, D. H. , Stein, L. D. (2008) Gramene: a growing plant comparative genomics resource. Nucleic Acids Res, 36(Databa) pp. D947-53.

Canaran, P., Buckler, E. S., Glaubitz, J. C., Stein, L. D., Sun, Q., Zhao, W. , Ware, D. H. (2008) Panzea: an update on new content and features. Nucleic Acids Res, 36(Databa) pp. D1041-3.

Hufford, K. M., Canaran, P., Ware, D. H., McMullen, M. D. , Gaut, B. S. (2007) Patterns of selection and tissue-specific expression among maize domestication and crop improvement loci. Plant Physiology, 144(3) pp. 1642-1653.

Ilic, K., Kellogg, E. A., Jaiswal, P., Zapata, F., Stevens, P. F., Vincent, L. P., Avraham, S., Reiser, L., Pujar, A., Sachs, M. M., Whitman, N. T., McCouch, S. R., Schaeffer, M. L., Ware, D. H., Stein, L. D. , Rhee, S. Y. (2007) The plant structure ontology, a unified vocabulary of anatomy and morphology of a flowering plant. Plant Physiology, 143(2) pp. 587-599.

Ware, D. H. (2007) Gramene. In: Methods Mol Biol. Methods Mol Biol, 406 pp. 315-329. Humana.

Pujar, An., Jaiswal, P., Kellogg, E. A., Ilic, K., Vincent, L., Avraham, Sh., Stevens, P., Zapata, F., Reiser, L., Rhee, S. Y., Sachs, M. M., Schaeffer, M., Stein, L. D., Ware, D. H. , McCouch, S. (2006) Whole-plant growth stage ontology for angiosperms and its application in plant biology. Plant Physiology, 142(2) pp. 414-428.

Canaran, P., Stein, L. D. , Ware, D. H. (2006) Look-Align: an interactive web-based multiple sequence alignment viewer with polymorphism analysis support. Bioinformatics, 22(7) pp. 885-6.

Maher, C., Stein, L. D. , Ware, D. (2006) Evolution of Arabidopsis microRNA families through duplication events. Genome Res, 16(4) pp. 510-9.

Zhao, W., Canaran, P., Jurkuta, R., Fulton, T., Glaubitz, J., Buckler, E., Doebley, J., Gaut, B., Goodman, M., Holland, J., Kresovich, S., McMullen, M., Stein, L. D. , Ware, D. (2006) Panzea: a database and resource for molecular and functional diversity in the maize genome. Nucleic Acids Res, 34(Databa) pp. D752-7.

Hass-Jacobus, B. L., Futrell-Griggs, M., Abernathy, B., Westerman, R., Goicoechea, J. L., Stein, J., Klein, P., Hurwitz, B., Zhou, B., Rakhshan, F., Sanyal, A., Gill, N., Lin, J. Y., Walling, J. G., Luo, M. Z., Ammiraju, J. S. S., Kudrna, D., Kim, H. R., Ware, D., Wing, Rod A., San Miguel, P. , Jackson, S. A. (2006) Integration of hybridization-based markers (overgos) into physical maps for comparative and evolutionary explorations in the genus Oryza and in Sorghum. BMC Genomics, 7 pp. 199.

Jaiswal, P., Avraham, S., Ilic, K., Kellogg, E. A., McCouch, S., Pujar, A., Reiser, L., Rhee, S. Y., Sachs, M. M., Schaeffer, M., Stein, L., Stevens, P., Vincent, L. D., Ware, D. H. , Zapata, F. (2005) Plant Ontology (PO): a Controlled Vocabulary of Plant Structures and Growth Stages. Comp Funct Genomics, 6(7-8) pp. 388-97.

Kresovich, S., Barbazuk, B., Bedell, J. A., Borrell, A., Buell, C. R., Burke, J., Clifton, S., Cordonnier-Pratt, M. M., Cox, S., Dahlberg, J., Erpelding, J., Fulton, T. M., Fulton, B., Fulton, L., Gingle, A. R., Hash, C. T., Huang, Y., Jordan, D., Klein, P. E., Klein, R. R., Magalhaes, J., McCombie, R., Moore, P., Mullet, J. E., Ozias-Akins, P., Paterson, A. H., Porter, K., Pratt, L., Roe, B., Rooney, W., Schnable, P. S., Stelly, D. M., Tuinstra, M., Ware, D. , Warek, U. (2005) Toward sequencing the sorghum genome. A U.S. National Science Foundation-sponsored workshop report. Plant Physiology, 138(4) pp. 1898-1902.

Ware, D. , Stein, L. (2003) Comparison of genes among cereals. Current Opinion in Plant Biology, 6(2) pp. 121-7.

Scholl, R., Sachs, M. M. , Ware, D. (2003) Maintaining collections of mutants for plant functional genomics. Methods in Molecular Biology, 236 pp. 311-26.

Yu, Y., Rambo, T., Currie, J., Saski, C., Kim, H. R., Collura, K., Thompson, S., Simmons, J., Yang, T. J., Nah, G., Patel, A. J., Thurmond, S., Henry, D., Oates, R., Palmer, M., Pries, G., Gibson, J., Anderson, H., Paradkar, M., Crane, L., Dale, J., Carver, M. B., Wood, T., Frisch, D., Engler, F., Soderlund, C., Palmer, L. E., Tetylman, L., Nascimento, L., de la Bastide, M., Spiegel, L., Ware, D., O'Shaughnessy, A., Dike, S., Dedhia, N., Preston, R., Huang, E., Ferraro, K., Kuit, K., Miller, B., Zutavern, T., Katzenberger, F., Muller, S., Balija, V., Martienssen, R. A., Stein, L., Minx, P., Johnson, D., Cordum, H., Mardis, E., Cheng, Z., Jiang, J., Wilson, R., McCombie, W. R., Wing, R. A., Yuan, Q., Ouyang, S., Liu, J., Jones, K. M., Gansberger, K., Moffat, K., Hill, J., Tsitrin, T., Overton, L., Bera, J., Kim, M., Jin, S., Tallon, L., Ciecko, A., Pai, G., van Aken, S., Utterback, T., Reidmuller, S., Bormann, J., Feldblyum, T., Hsiao, J., Zismann, V., Blunt, S., de Vazeilles, A., Shaffer, T., Koo, H., Suh, B., Yang, Q., Haas, B., Peterson, J., Pertea, M., Volfovsky, N., Wortman, J., White, O., Salzberg, S. L., Fraser, C. M., Robin Buell, C., Messing, J., Song, R., Fuks, G., Llaca, V., Kovchak, S., Young, S., Bowers, J. E. , Paterson, A. H. (2003) In-depth view of structure, activity, and evolution of rice chromosome 10. Science, 300(5625) pp. 1566-1569.

Ware, D. H., Jaiswal, P. J., Ni, J. J., Yap, I., Pan, X. K., Clark, K. Y., Teytelman, L., Schmidt, S. C., Zhao, W., Chang, K., Cartinhour, S., Stein, L. D. , McCouch, S. R. (2002) Gramene, a tool for grass Genomics. Plant Physiology, 130(4) pp. 1606-1613.

Bruskiewich, R., Coe, E. H., Jaiswal, P., McCouch, S., Polacco, M., Stein, L., Vincent, L. , Ware, D. (2002) The Plant Ontology (TM) Consortium and plant ontologies. Comparative and Functional Genomics, 3(2) pp. 137-142.

Jaiswal, P., Ware, D., Ni, J. J., Chang, K., Zhao, W., Schmidt, S., Pan, X. K., Clark, K., Teytelman, L., Cartinhour, S., Stein, L. , McCouch, S. (2002) Gramene: development and integration of trait and gene ontologies for rice. Comparative and Functional Genomics, 3(2) pp. 132-136.

Ware, D., Jaiswal, P., Ni, J. J., Pan, X. K., Chang, K., Clark, K., Teytelman, L., Schmidt, S., Zhao, W., Cartinhour, S., McCouch, S. , Stein, L. (2002) Gramene: a resource for comparative grass genomics. Nucleic Acids Research, 30(1) pp. 103-105.

Li, H., Wu, G., Ware, D., Davis, K. R. , Yang, Z. (1998) Arabidopsis Rho-related GTPases: differential gene expression in pollen and polar localization in fission yeast. Plant Physiology, 118(2) pp. 407-17.

Wanner, L. A., Li, G., Ware, D., Somssich, I. E. , Davis, K. R. (1995) The phenylalanine ammonia-lyase gene family in Arabidopsis thaliana. Plant Mol Biol, 27(2) pp. 327-38.