A genome resource for green millet Setaria viridis enables discovery of agronomically valuable loci
Mamidi, Sujan, Healey, Adam, Huang, Pu, Grimwood, Jane, Jenkins, Jerry, Barry, Kerrie, Sreedasyam, Avinash, Shu, Shengqiang, Lovell, John T, Feldman, Maximilian, Wu, Jinxia, Yu, Yunqing, Chen, Cindy, Johnson, Jenifer, Sakakibara, Hitoshi, Kiba, Takatoshi, Sakurai, Tetsuya, Tavares, Rachel, Nusinow, Dmitri A, Baxter, Ivan, Schmutz, Jeremy, Brutnell, Thomas P, Kellogg, Elizabeth A
Published in Nature biotechnology (01.10.2020)
Published in Nature biotechnology (01.10.2020)
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The Sorghum bicolor reference genome: improved assembly, gene annotations, a transcriptome atlas, and signatures of genome organization
McCormick, Ryan F., Truong, Sandra K., Sreedasyam, Avinash, Jenkins, Jerry, Shu, Shengqiang, Sims, David, Kennedy, Megan, Amirebrahimi, Mojgan, Weers, Brock D., McKinley, Brian, Mattison, Ashley, Morishige, Daryl T., Grimwood, Jane, Schmutz, Jeremy, Mullet, John E.
Published in The Plant journal : for cell and molecular biology (01.01.2018)
Published in The Plant journal : for cell and molecular biology (01.01.2018)
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The Peach v2.0 release: high-resolution linkage mapping and deep resequencing improve chromosome-scale assembly and contiguity
Verde, Ignazio, Jenkins, Jerry, Dondini, Luca, Micali, Sabrina, Pagliarani, Giulia, Vendramin, Elisa, Paris, Roberta, Aramini, Valeria, Gazza, Laura, Rossini, Laura, Bassi, Daniele, Troggio, Michela, Shu, Shengqiang, Grimwood, Jane, Tartarini, Stefano, Dettori, Maria Teresa, Schmutz, Jeremy
Published in BMC genomics (11.03.2017)
Published in BMC genomics (11.03.2017)
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Phytozome: a comparative platform for green plant genomics
Goodstein, David M., Shu, Shengqiang, Howson, Russell, Neupane, Rochak, Hayes, Richard D., Fazo, Joni, Mitros, Therese, Dirks, William, Hellsten, Uffe, Putnam, Nicholas , Rokhsar, Daniel S.
Published in Nucleic acids research (01.01.2012)
Published in Nucleic acids research (01.01.2012)
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AmiGO: online access to ontology and annotation data
Carbon, Seth, Ireland, Amelia, Mungall, Christopher J., Shu, ShengQiang, Marshall, Brad, Lewis, Suzanna
Published in Bioinformatics (15.01.2009)
Published in Bioinformatics (15.01.2009)
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Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure
Gordon, Sean P, Contreras-Moreira, Bruno, Woods, Daniel P, Des Marais, David L, Burgess, Diane, Shu, Shengqiang, Stritt, Christoph, Roulin, Anne C, Schackwitz, Wendy, Tyler, Ludmila, Martin, Joel, Lipzen, Anna, Dochy, Niklas, Phillips, Jeremy, Barry, Kerrie, Geuten, Koen, Budak, Hikmet, Juenger, Thomas E, Amasino, Richard, Caicedo, Ana L, Goodstein, David, Davidson, Patrick, Mur, Luis A J, Figueroa, Melania, Freeling, Michael, Catalan, Pilar, Vogel, John P
Published in Nature communications (19.12.2017)
Published in Nature communications (19.12.2017)
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The genome of cowpea (Vigna unguiculata [L.] Walp.)
Lonardi, Stefano, Muñoz‐Amatriaín, María, Liang, Qihua, Shu, Shengqiang, Wanamaker, Steve I., Lo, Sassoum, Tanskanen, Jaakko, Schulman, Alan H., Zhu, Tingting, Luo, Ming‐Cheng, Alhakami, Hind, Ounit, Rachid, Hasan, Abid Md, Verdier, Jerome, Roberts, Philip A., Santos, Jansen R.P., Ndeve, Arsenio, Doležel, Jaroslav, Vrána, Jan, Hokin, Samuel A., Farmer, Andrew D., Cannon, Steven B., Close, Timothy J.
Published in The Plant journal : for cell and molecular biology (01.06.2019)
Published in The Plant journal : for cell and molecular biology (01.06.2019)
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The Aquilegia genome provides insight into adaptive radiation and reveals an extraordinarily polymorphic chromosome with a unique history
Filiault, Danièle L, Ballerini, Evangeline S, Mandáková, Terezie, Aköz, Gökçe, Derieg, Nathan J, Schmutz, Jeremy, Jenkins, Jerry, Grimwood, Jane, Shu, Shengqiang, Hayes, Richard D, Hellsten, Uffe, Barry, Kerrie, Yan, Juying, Mihaltcheva, Sirma, Karafiátová, Miroslava, Nizhynska, Viktoria, Kramer, Elena M, Lysak, Martin A, Hodges, Scott A, Nordborg, Magnus
Published in eLife (16.10.2018)
Published in eLife (16.10.2018)
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Journal Article
A willow sex chromosome reveals convergent evolution of complex palindromic repeats
Zhou, Ran, Macaya-Sanz, David, Carlson, Craig H, Schmutz, Jeremy, Jenkins, Jerry W, Kudrna, David, Sharma, Aditi, Sandor, Laura, Shu, Shengqiang, Barry, Kerrie, Tuskan, Gerald A, Ma, Tao, Liu, Jianquan, Olson, Matthew, Smart, Lawrence B, DiFazio, Stephen P
Published in Genome Biology (14.02.2020)
Published in Genome Biology (14.02.2020)
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Fine-scale variation in meiotic recombination in Mimulus inferred from population shotgun sequencing
Hellsten, Uffe, Wright, Kevin M., Jenkins, Jerry, Shu, Shengqiang, Yuan, Yaowu, Wessler, Susan R., Schmutz, Jeremy, Willis, John H., Rokhsar, Daniel S.
Published in Proceedings of the National Academy of Sciences - PNAS (26.11.2013)
Published in Proceedings of the National Academy of Sciences - PNAS (26.11.2013)
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The Amphimedon queenslandica genome and the evolution of animal complexity
Srivastava, Mansi, Degnan, Bernard M, Rokhsar, Daniel S, Simakov, Oleg, Chapman, Jarrod, Fahey, Bryony, Gauthier, Marie E. A, Mitros, Therese, Richards, Gemma S, Conaco, Cecilia, Dacre, Michael, Hellsten, Uffe, Larroux, Claire, Putnam, Nicholas H, Stanke, Mario, Adamska, Maja, Darling, Aaron, Degnan, Sandie M, Oakley, Todd H, Plachetzki, David C, Zhai, Yufeng, Adamski, Marcin, Calcino, Andrew, Cummins, Scott F, Goodstein, David M, Harris, Christina, Jackson, Daniel J, Leys, Sally P, Shu, Shengqiang, Woodcroft, Ben J, Vervoort, Michel, Kosik, Kenneth S, Manning, Gerard
Published in Nature (London) (05.08.2010)
Published in Nature (London) (05.08.2010)
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A genome assembly and the somatic genetic and epigenetic mutation rate in a wild long-lived perennial Populus trichocarpa
Hofmeister, Brigitte T, Denkena, Johanna, Colomé-Tatché, Maria, Shahryary, Yadollah, Hazarika, Rashmi, Grimwood, Jane, Mamidi, Sujan, Jenkins, Jerry, Grabowski, Paul P, Sreedasyam, Avinash, Shu, Shengqiang, Barry, Kerrie, Lail, Kathleen, Adam, Catherine, Lipzen, Anna, Sorek, Rotem, Kudrna, Dave, Talag, Jayson, Wing, Rod, Hall, David W, Jacobsen, Daniel, Tuskan, Gerald A, Schmutz, Jeremy, Johannes, Frank, Schmitz, Robert J
Published in Genome Biology (06.10.2020)
Published in Genome Biology (06.10.2020)
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Journal Article
A new reference genome for Sorghum bicolor reveals high levels of sequence similarity between sweet and grain genotypes: implications for the genetics of sugar metabolism
Cooper, Elizabeth A, Brenton, Zachary W, Flinn, Barry S, Jenkins, Jerry, Shu, Shengqiang, Flowers, Dave, Luo, Feng, Wang, Yunsheng, Xia, Penny, Barry, Kerrie, Daum, Chris, Lipzen, Anna, Yoshinaga, Yuko, Schmutz, Jeremy, Saski, Christopher, Vermerris, Wilfred, Kresovich, Stephen
Published in BMC genomics (27.05.2019)
Published in BMC genomics (27.05.2019)
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The Reference Genome of the Halophytic Plant Eutrema salsugineum
Yang, Ruolin, Jarvis, David E, Chen, Hao, Beilstein, Mark A, Grimwood, Jane, Jenkins, Jerry, Shu, Shengqiang, Prochnik, Simon, Xin, Mingming, Ma, Chuang, Schmutz, Jeremy, Wing, Rod A, Mitchell-Olds, Thomas, Schumaker, Karen S, Wang, Xiangfeng
Published in Frontiers in plant science (2013)
Published in Frontiers in plant science (2013)
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Genome biology of the paleotetraploid perennial biomass crop Miscanthus
Mitros, Therese, Session, Adam M., James, Brandon T., Wu, Guohong Albert, Belaffif, Mohammad B., Clark, Lindsay V., Shu, Shengqiang, Dong, Hongxu, Barling, Adam, Holmes, Jessica R., Mattick, Jessica E., Bredeson, Jessen V., Liu, Siyao, Farrar, Kerrie, Głowacka, Katarzyna, Jeżowski, Stanisław, Barry, Kerrie, Chae, Won Byoung, Juvik, John A., Gifford, Justin, Oladeinde, Adebosola, Yamada, Toshihiko, Grimwood, Jane, Putnam, Nicholas H., De Vega, Jose, Barth, Susanne, Klaas, Manfred, Hodkinson, Trevor, Li, Laigeng, Jin, Xiaoli, Peng, Junhua, Yu, Chang Yeon, Heo, Kweon, Yoo, Ji Hye, Ghimire, Bimal Kumar, Donnison, Iain S., Schmutz, Jeremy, Hudson, Matthew E., Sacks, Erik J., Moose, Stephen P., Swaminathan, Kankshita, Rokhsar, Daniel S.
Published in Nature communications (28.10.2020)
Published in Nature communications (28.10.2020)
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The genomic landscape of molecular responses to natural drought stress in Panicum hallii
Lovell, John T, Jenkins, Jerry, Lowry, David B, Mamidi, Sujan, Sreedasyam, Avinash, Weng, Xiaoyu, Barry, Kerrie, Bonnette, Jason, Campitelli, Brandon, Daum, Chris, Gordon, Sean P, Gould, Billie A, Khasanova, Albina, Lipzen, Anna, MacQueen, Alice, Palacio-Mejía, Juan Diego, Plott, Christopher, Shakirov, Eugene V, Shu, Shengqiang, Yoshinaga, Yuko, Zane, Matt, Kudrna, Dave, Talag, Jason D, Rokhsar, Daniel, Grimwood, Jane, Schmutz, Jeremy, Juenger, Thomas E
Published in Nature communications (06.12.2018)
Published in Nature communications (06.12.2018)
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Journal Article
Genome sequence of the model rice variety KitaakeX
Jain, Rashmi, Jenkins, Jerry, Shu, Shengqiang, Chern, Mawsheng, Martin, Joel A, Copetti, Dario, Duong, Phat Q, Pham, Nikki T, Kudrna, David A, Talag, Jayson, Schackwitz, Wendy S, Lipzen, Anna M, Dilworth, David, Bauer, Diane, Grimwood, Jane, Nelson, Catherine R, Xing, Feng, Xie, Weibo, Barry, Kerrie W, Wing, Rod A, Schmutz, Jeremy, Li, Guotian, Ronald, Pamela C
Published in BMC genomics (27.11.2019)
Published in BMC genomics (27.11.2019)
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Journal Article
Genome sequence and evolution of Betula platyphylla
Chen, Su, Wang, Yucheng, Yu, Lili, Zheng, Tao, Wang, Sui, Yue, Zhen, Jiang, Jing, Kumari, Sapna, Zheng, Chunfang, Tang, Haibao, Li, Jun, Li, Yuqi, Chen, Jiongjiong, Zhang, Wenbo, Kuang, Hanhui, Robertson, Jon S, Zhao, Patrick X, Li, Huiyu, Shu, Shengqiang, Yordanov, Yordan S, Huang, Haijiao, Goodstein, David M, Gai, Ying, Qi, Qi, Min, JiuMeng, Xu, ChunYan, Wang, SongBo, Qu, Guan-Zheng, Paterson, Andrew H, Sankoff, David, Wei, Hairong, Liu, Guifeng, Yang, Chuanping
Published in Horticulture research (11.02.2021)
Published in Horticulture research (11.02.2021)
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The Genome of Naegleria gruberi Illuminates Early Eukaryotic Versatility
Fritz-Laylin, Lillian K., Prochnik, Simon E., Ginger, Michael L., Dacks, Joel B., Carpenter, Meredith L., Field, Mark C., Kuo, Alan, Paredez, Alex, Chapman, Jarrod, Pham, Jonathan, Shu, Shengqiang, Neupane, Rochak, Cipriano, Michael, Mancuso, Joel, Tu, Hank, Salamov, Asaf, Lindquist, Erika, Shapiro, Harris, Lucas, Susan, Grigoriev, Igor V., Cande, W. Zacheus, Fulton, Chandler, Rokhsar, Daniel S., Dawson, Scott C.
Published in Cell (05.03.2010)
Published in Cell (05.03.2010)
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