Reviving the Transcriptome Studies: An Insight Into the Emergence of Single-Molecule Transcriptome Sequencing von Wang, Bo, Kumar, Vivek, Olson, Andrew, Ware, Doreen

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The iPlant Collaborative: Cyberinfrastructure for Enabling Data to Discovery for the Life Sciences von Merchant, Nirav, Lyons, Eric, Goff, Stephen, Vaughn, Matthew, Ware, Doreen, Micklos, David, Antin, Parker

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Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes von Sun, Silong, Zhou, Yingsi, Chen, Jian, Shi, Junpeng, Zhao, Haiming, Zhao, Hainan, Song, Weibin, Zhang, Mei, Cui, Yang, Dong, Xiaomei, Liu, Han, Ma, Xuxu, Jiao, Yinping, Wang, Bo, Wei, Xuehong, Stein, Joshua C., Glaubitz, Jeff C., Lu, Fei, Yu, Guoliang, Liang, Chengzhi, Fengler, Kevin, Li, Bailin, Rafalski, Antoni, Schnable, Patrick S., Ware, Doreen H., Buckler, Edward S., Lai, Jinsheng

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Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline von Ou, Shujun, Su, Weija, Liao, Yi, Chougule, Kapeel, Agda, Jireh R A, Hellinga, Adam J, Lugo, Carlos Santiago Blanco, Elliott, Tyler A, Ware, Doreen, Peterson, Thomas, Jiang, Ning, Hirsch, Candice N, Hufford, Matthew B

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Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing von Wang, Bo, Tseng, Elizabeth, Regulski, Michael, Clark, Tyson A, Hon, Ting, Jiao, Yinping, Lu, Zhenyuan, Olson, Andrew, Stein, Joshua C., Ware, Doreen

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Transcriptional regulation of nitrogen-associated metabolism and growth von Gaudinier, Allison, Rodriguez-Medina, Joel, Zhang, Lifang, Olson, Andrew, Liseron-Monfils, Christophe, Bågman, Anne-Maarit, Foret, Jessica, Abbitt, Shane, Tang, Michelle, Li, Baohua, Runcie, Daniel E., Kliebenstein, Daniel J., Shen, Bo, Frank, Mary J., Ware, Doreen, Brady, Siobhan M.

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First-Generation Haplotype Map of Maize von Gore, Michael A, Chia, Jer-Ming, Elshire, Robert J, Sun, Qi, Ersoz, Elhan S, Hurwitz, Bonnie L, Peiffer, Jason A, McMullen, Michael D, Grills, George S, Ross-Ibarra, Jeffrey, Ware, Doreen H, Buckler, Edward S

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A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes von Kurtz, Stefan, Narechania, Apurva, Stein, Joshua C, Ware, Doreen

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Expression Atlas update: gene and protein expression in multiple species von 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

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Functional annotation of the transcriptome of Sorghum bicolor in response to osmotic stress and abscisic acid von Dugas, Diana V, Monaco, Marcela K, Olsen, Andrew, Klein, Robert R, Kumari, Sunita, Ware, Doreen, Klein, Patricia E

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Gene disruption by structural mutations drives selection in US rice breeding over the last century von 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.

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MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations von Campbell, Michael S., Law, MeiYee, Holt, Carson, Stein, Joshua C., Moghe, Gaurav D., Hufnagel, David E., Lei, Jikai, Achawanantakun, Rujira, Jiao, Dian, Lawrence, Carolyn J., Ware, Doreen, Shiu, Shin-Han, Childs, Kevin L., Sun, Yanni, Jiang, Ning, Yandell, Mark

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Evolution of Arabidopsis microRNA families through duplication events von Maher, Christopher, Stein, Lincoln, Ware, Doreen

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A Sorghum Mutant Resource as an Efficient Platform for Gene Discovery in Grasses von Jiao, Yinping, Burke, John, Chopra, Ratan, Burow, Gloria, Chen, Junping, Wang, Bo, Hayes, Chad, Emendack, Yves, Ware, Doreen, Xin, Zhanguo

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The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA von Regulski, Michael, Lu, Zhenyuan, Kendall, Jude, Donoghue, Mark T A, Reinders, Jon, Llaca, Victor, Deschamps, Stephane, Smith, Andrew, Levy, Dan, McCombie, W Richard, Tingey, Scott, Rafalski, Antoni, Hicks, James, Ware, Doreen, Martienssen, Robert A

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Genetic structure and domestication history of the grape von Myles, Sean, Boyko, Adam R, Owens, Christopher L, Brown, Patrick J, Grassi, Fabrizio, Aradhya, Mallikarjuna K, Prins, Bernard, Reynolds, Andy, Chia, Jer-Ming, Ware, Doreen, Bustamante, Carlos D, Buckler, Edward S

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Highly accurate long-read HiFi sequencing data for five complex genomes von Hon, Ting, Mars, Kristin, Young, Greg, Tsai, Yu-Chih, Karalius, Joseph W., Landolin, Jane M., Maurer, Nicholas, Kudrna, David, Hardigan, Michael A., Steiner, Cynthia C., Knapp, Steven J., Ware, Doreen, Shapiro, Beth, Peluso, Paul, Rank, David R.

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Gapless assembly of maize chromosomes using long-read technologies von Liu, Jianing, Seetharam, Arun S., Chougule, Kapeel, Ou, Shujun, Swentowsky, Kyle W., Gent, Jonathan, Llaca, Victor, Woodhouse, Margaret R., Manchanda, Nancy, Presting, Gernot G., Kudrna, David A., Alabady, Magdy, Hirsch, Candice N., Fengler, Kevin A., Ware, Doreen, Michael, Todd P., Hufford, Matthew B., Dawe, R. Kelly

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Role of moss and Arabidopsis zinc-finger homeodomain transcription factors in regulating plant architecture von Lee, Young Koung, Kim, Keunhwa, Ware, Doreen

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Genome-wide association study of quantitative resistance to southern leaf blight in the maize nested association mapping population von Holland, James B, Kump, Kristen L, Bradbury, Peter J, Wisser, Randall J, Buckler, Edward S, Belcher, Araby R, Oropeza-Rosas, Marco A, Zwonitzer, John C, Kresovich, Stephen, McMullen, Michael D, Ware, Doreen, Balint-Kurti, Peter J

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