Genome and transcriptome mechanisms driving cephalopod evolution
Albertin, Caroline B., Medina-Ruiz, Sofia, Mitros, Therese, Schmidbaur, Hannah, Sanchez, Gustavo, Wang, Z. Yan, Grimwood, Jane, Rosenthal, Joshua J. C., Ragsdale, Clifton W., Simakov, Oleg, Rokhsar, Daniel S.
Published in Nature communications (04.05.2022)
Published in Nature communications (04.05.2022)
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The barley pan-genome reveals the hidden legacy of mutation breeding
Jayakodi, Murukarthick, Padmarasu, Sudharsan, Haberer, Georg, Bonthala, Venkata Suresh, Gundlach, Heidrun, Monat, Cécile, Lux, Thomas, Kamal, Nadia, Lang, Daniel, Himmelbach, Axel, Ens, Jennifer, Zhang, Xiao-Qi, Angessa, Tefera T., Zhou, Gaofeng, Tan, Cong, Hill, Camilla, Wang, Penghao, Schreiber, Miriam, Boston, Lori B., Plott, Christopher, Jenkins, Jerry, Guo, Yu, Fiebig, Anne, Budak, Hikmet, Xu, Dongdong, Zhang, Jing, Wang, Chunchao, Grimwood, Jane, Schmutz, Jeremy, Guo, Ganggang, Zhang, Guoping, Mochida, Keiichi, Hirayama, Takashi, Sato, Kazuhiro, Chalmers, Kenneth J., Langridge, Peter, Waugh, Robbie, Pozniak, Curtis J., Scholz, Uwe, Mayer, Klaus F. X., Spannagl, Manuel, Li, Chengdao, Mascher, Martin, Stein, Nils
Published in Nature (London) (10.12.2020)
Published in Nature (London) (10.12.2020)
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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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Long-read sequence assembly: a technical evaluation in barley
Mascher, Martin, Wicker, Thomas, Jenkins, Jerry, Plott, Christopher, Lux, Thomas, Koh, Chu Shin, Ens, Jennifer, Gundlach, Heidrun, Boston, Lori B, Tulpová, Zuzana, Holden, Samuel, Hernández-Pinzón, Inmaculada, Scholz, Uwe, Mayer, Klaus F X, Spannagl, Manuel, Pozniak, Curtis J, Sharpe, Andrew G, Šimková, Hana, Moscou, Matthew J, Grimwood, Jane, Schmutz, Jeremy, Stein, Nils
Published in The Plant cell (19.07.2021)
Published in The Plant cell (19.07.2021)
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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 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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Widespread natural variation of DNA methylation within angiosperms
Niederhuth, Chad E, Bewick, Adam J, Ji, Lexiang, Alabady, Magdy S, Kim, Kyung Do, Li, Qing, Rohr, Nicholas A, Rambani, Aditi, Burke, John M, Udall, Joshua A, Egesi, Chiedozie, Schmutz, Jeremy, Grimwood, Jane, Jackson, Scott A, Springer, Nathan M, Schmitz, Robert J
Published in Genome Biology (27.09.2016)
Published in Genome Biology (27.09.2016)
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A mosaic monoploid reference sequence for the highly complex genome of sugarcane
Garsmeur, Olivier, Droc, Gaetan, Antonise, Rudie, Grimwood, Jane, Potier, Bernard, Aitken, Karen, Jenkins, Jerry, Martin, Guillaume, Charron, Carine, Hervouet, Catherine, Costet, Laurent, Yahiaoui, Nabila, Healey, Adam, Sims, David, Cherukuri, Yesesri, Sreedasyam, Avinash, Kilian, Andrzej, Chan, Agnes, Van Sluys, Marie-Anne, Swaminathan, Kankshita, Town, Christopher, Bergès, Hélène, Simmons, Blake, Glaszmann, Jean Christophe, van der Vossen, Edwin, Henry, Robert, Schmutz, Jeremy, D’Hont, Angélique
Published in Nature communications (06.07.2018)
Published in Nature communications (06.07.2018)
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A reference genome for common bean and genome-wide analysis of dual domestications
Schmutz, Jeremy, McClean, Phillip E, Mamidi, Sujan, Wu, G Albert, Cannon, Steven B, Grimwood, Jane, Jenkins, Jerry, Shu, Shengqiang, Song, Qijian, Chavarro, Carolina, Torres-Torres, Mirayda, Geffroy, Valerie, Moghaddam, Samira Mafi, Gao, Dongying, Abernathy, Brian, Barry, Kerrie, Blair, Matthew, Brick, Mark A, Chovatia, Mansi, Gepts, Paul, Goodstein, David M, Gonzales, Michael, Hellsten, Uffe, Hyten, David L, Jia, Gaofeng, Kelly, James D, Kudrna, Dave, Lee, Rian, Richard, Manon M S, Miklas, Phillip N, Osorno, Juan M, Rodrigues, Josiane, Thareau, Vincent, Urrea, Carlos A, Wang, Mei, Yu, Yeisoo, Zhang, Ming, Wing, Rod A, Cregan, Perry B, Rokhsar, Daniel S, Jackson, Scott A
Published in Nature genetics (01.07.2014)
Published in Nature genetics (01.07.2014)
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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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Assembly of the threespine stickleback Y chromosome reveals convergent signatures of sex chromosome evolution
Peichel, Catherine L, McCann, Shaugnessy R, Ross, Joseph A, Naftaly, Alice F S, Urton, James R, Cech, Jennifer N, Grimwood, Jane, Schmutz, Jeremy, Myers, Richard M, Kingsley, David M, White, Michael A
Published in Genome Biology (19.07.2020)
Published in Genome Biology (19.07.2020)
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Transposable Elements versus the Fungal Genome: Impact on Whole-Genome Architecture and Transcriptional Profiles
Castanera, Raúl, López-Varas, Leticia, Borgognone, Alessandra, LaButti, Kurt, Lapidus, Alla, Schmutz, Jeremy, Grimwood, Jane, Pérez, Gúmer, Pisabarro, Antonio G, Grigoriev, Igor V, Stajich, Jason E, Ramírez, Lucía
Published in PLoS genetics (13.06.2016)
Published in PLoS genetics (13.06.2016)
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On the origin and evolutionary consequences of gene body DNA methylation
Bewick, Adam J., Ji, Lexiang, Niederhuth, Chad E., Willing, Eva-Maria, Hofmeister, Brigitte T., Shi, Xiuling, Wang, Li, Lu, Zefu, Rohr, Nicholas A., Hartwig, Benjamin, Kiefer, Christiane, Deal, Roger B., Schmutz, Jeremy, Grimwood, Jane, Stroud, Hume, Jacobsen, Steven E., Schneeberger, Korbinian, Zhang, Xiaoyu, Schmitz, Robert J.
Published in Proceedings of the National Academy of Sciences - PNAS (09.08.2016)
Published in Proceedings of the National Academy of Sciences - PNAS (09.08.2016)
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Comparative genome structure, secondary metabolite, and effector coding capacity across Cochliobolus pathogens
Condon, Bradford J, Leng, Yueqiang, Wu, Dongliang, Bushley, Kathryn E, Ohm, Robin A, Otillar, Robert, Martin, Joel, Schackwitz, Wendy, Grimwood, Jane, MohdZainudin, NurAinizzati, Xue, Chunsheng, Wang, Rui, Manning, Viola A, Dhillon, Braham, Tu, Zheng Jin, Steffenson, Brian J, Salamov, Asaf, Sun, Hui, Lowry, Steve, LaButti, Kurt, Han, James, Copeland, Alex, Lindquist, Erika, Barry, Kerrie, Schmutz, Jeremy, Baker, Scott E, Ciuffetti, Lynda M, Grigoriev, Igor V, Zhong, Shaobin, Turgeon, B Gillian
Published in PLoS genetics (01.01.2013)
Published in PLoS genetics (01.01.2013)
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Insights into bilaterian evolution from three spiralian genomes
Simakov, Oleg, Marletaz, Ferdinand, Cho, Sung-Jin, Edsinger-Gonzales, Eric, Havlak, Paul, Hellsten, Uffe, Kuo, Dian-Han, Larsson, Tomas, Lv, Jie, Arendt, Detlev, Savage, Robert, Osoegawa, Kazutoyo, de Jong, Pieter, Grimwood, Jane, Chapman, Jarrod A., Shapiro, Harris, Aerts, Andrea, Otillar, Robert P., Terry, Astrid Y., Boore, Jeffrey L., Grigoriev, Igor V., Lindberg, David R., Seaver, Elaine C., Weisblat, David A., Putnam, Nicholas H., Rokhsar, Daniel S.
Published in Nature (London) (24.01.2013)
Published in Nature (London) (24.01.2013)
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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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The Kalanchoë genome provides insights into convergent evolution and building blocks of crassulacean acid metabolism
Yang, Xiaohan, Hu, Rongbin, Yin, Hengfu, Jenkins, Jerry, Shu, Shengqiang, Tang, Haibao, Liu, Degao, Weighill, Deborah A., Cheol Yim, Won, Ha, Jungmin, Heyduk, Karolina, Goodstein, David M., Guo, Hao-Bo, Moseley, Robert C., Fitzek, Elisabeth, Jawdy, Sara, Zhang, Zhihao, Xie, Meng, Hartwell, James, Grimwood, Jane, Abraham, Paul E., Mewalal, Ritesh, Beltrán, Juan D., Boxall, Susanna F., Dever, Louisa V., Palla, Kaitlin J., Albion, Rebecca, Garcia, Travis, Mayer, Jesse A., Don Lim, Sung, Man Wai, Ching, Peluso, Paul, Van Buren, Robert, De Paoli, Henrique Cestari, Borland, Anne M., Guo, Hong, Chen, Jin-Gui, Muchero, Wellington, Yin, Yanbin, Jacobson, Daniel A., Tschaplinski, Timothy J., Hettich, Robert L., Ming, Ray, Winter, Klaus, Leebens-Mack, James H., Smith, J. Andrew C., Cushman, John C., Schmutz, Jeremy, Tuskan, Gerald A.
Published in Nature communications (01.12.2017)
Published in Nature communications (01.12.2017)
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Journal Article
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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The Capsella rubella genome and the genomic consequences of rapid mating system evolution
Slotte, Tanja, Hazzouri, Khaled M, Ågren, J Arvid, Koenig, Daniel, Maumus, Florian, Guo, Ya-Long, Steige, Kim, Platts, Adrian E, Escobar, Juan S, Newman, L Killian, Wang, Wei, Mandáková, Terezie, Vello, Emilio, Smith, Lisa M, Henz, Stefan R, Steffen, Joshua, Takuno, Shohei, Brandvain, Yaniv, Coop, Graham, Andolfatto, Peter, Hu, Tina T, Blanchette, Mathieu, Clark, Richard M, Quesneville, Hadi, Nordborg, Magnus, Gaut, Brandon S, Lysak, Martin A, Jenkins, Jerry, Grimwood, Jane, Chapman, Jarrod, Prochnik, Simon, Shu, Shengqiang, Rokhsar, Daniel, Schmutz, Jeremy, Weigel, Detlef, Wright, Stephen I
Published in Nature genetics (01.07.2013)
Published in Nature genetics (01.07.2013)
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Journal Article
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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