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Rice Gene Index: A comprehensive pan-genome database for comparative and functional genomics of Asian rice by Yu, Zhichao, Chen, Yongming, Zhou, Yong, Zhang, Yulu, Li, Mengyuan, Ouyang, Yidan, Chebotarov, Dmytro, Mauleon, Ramil, Zhao, Hu, Xie, Weibo, McNally, Kenneth L., Wing, Rod A., Guo, Weilong, Zhang, Jianwei

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Oryza glumaepatula: A wild relative to improve drought tolerance in cultivated rice by Prakash, Parthiban Thathapalli, Chebotarov, Dymetro, Zhang, Jianwei, Kudrna, David A., Torres, Rolando O., Natividad, Mignon A., Quintana, Marinell R., Song, Jiaming, Maldonado L, Carlos E., Hechanova, Sherry Lou, Jena, Kshirod, Wing, Rod A., Henry, Amelia

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A high-performance computational workflow to accelerate GATK SNP detection across a 25-genome dataset by 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.

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Rice Gene Index: A comprehensive pan-genome database for comparative and functional genomics of Asian rice by Yu, Zhichao, Chen, Yongming, Zhou, Yong, Zhang, Yulu, Li, Mengyuan, Ouyang, Yidan, Chebotarov, Dmytro, Mauleon, Ramil, Zhao, Hu, Xie, Weibo, McNally, Kenneth L., Wing, Rod A., Guo, Weilong, Zhang, Jianwei

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Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice by 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.

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Two gap-free reference genomes and a global view of the centromere architecture in rice by Song, Jia-Ming, Xie, Wen-Zhao, Wang, Shuo, Guo, Yi-Xiong, Koo, Dal-Hoe, Kudrna, Dave, Gong, Chenbo, Huang, Yicheng, Feng, Jia-Wu, Zhang, Wenhui, Zhou, Yong, Zuccolo, Andrea, Long, Evan, Lee, Seunghee, Talag, Jayson, Zhou, Run, Zhu, Xi-Tong, Yuan, Daojun, Udall, Joshua, Xie, Weibo, Wing, Rod A., Zhang, Qifa, Poland, Jesse, Zhang, Jianwei, Chen, Ling-Ling

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A platinum standard pan-genome resource that represents the population structure of Asian rice by Zhou, Yong, Chebotarov, Dmytro, Kudrna, Dave, Llaca, Victor, Lee, Seunghee, Rajasekar, Shanmugam, Mohammed, Nahed, Al-Bader, Noor, Sobel-Sorenson, Chandler, Parakkal, Praveena, Arbelaez, Lady Johanna, Franco, Natalia, Alexandrov, Nickolai, Hamilton, Ruaraidh Sackville, Leung, Hei, Mauleon, Ramil, Lorieux, Mathias, Zuccolo, Andrea, McNally, Kenneth, Zhang, Jianwei, Wing, Rod A.

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Evolution and diversity of the wild rice Oryza officinalis Complex, across continents, genome types, and ploidy levels by Shenton, Matt, Kobayashi, Masaaki, Terashima, Shin, Ohyanagi, Hajime, Copetti, Dario, Hernández-Hernández, Tania, Zhang, Jianwei, Ohmido, Nobuko, Fujita, Masahiro, Toyoda, Atsushi, Ikawa, Hiroshi, Fujiyama, Asao, Furuumi, Hiroyasu, Miyabayashi, Toshie, Kubo, Takahiko, Kudrna, David, Wing, Rod, Yano, Kentaro, Nonomura, Ken-ichi, Sato, Yutaka, Kurata, Nori

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Twelve Platinum-Standard Reference Genomes Sequences (PSRefSeq) that complete the full range of genetic diversity of Asian rice by Zhou, Yong, Chebotarov, Dmytro, Kudrna, Dave, Llaca, Victor, Lee, Seunghee, Rajasekar, Shanmugam, Mohammed, Nahed, Al-Bader, Noor, Sobel-Sorenson, Chandler, Parakkal, Praveena, Arbelaez, Lady Johanna, Franco, Natalia, Alexandrov, Nickolai, Hamilton, Ruaraidh Sackville, Leung, Hei, Mauleon, Ramil, Lorieux, Mathias, Zuccolo, Andrea, McNally, Kenneth, Zhang, Jianwei, Wing, Rod A.

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Genomic variation in 3,010 diverse accessions of Asian cultivated rice by Wang, Wensheng, Mauleon, Ramil, Hu, Zhiqiang, Chebotarov, Dmytro, Tai, Shuaishuai, Wu, Zhichao, Li, Min, Zheng, Tianqing, Fuentes, Roven Rommel, Zhang, Fan, Mansueto, Locedie, Copetti, Dario, Sanciangco, Millicent, Palis, Kevin Christian, Xu, Jianlong, Sun, Chen, Fu, Binying, Zhang, Hongliang, Gao, Yongming, Zhao, Xiuqin, Shen, Fei, Cui, Xiao, Yu, Hong, Li, Zichao, Chen, Miaolin, Detras, Jeffrey, Zhou, Yongli, Zhang, Xinyuan, Zhao, Yue, Kudrna, Dave, Wang, Chunchao, Li, Rui, Jia, Ben, Lu, Jinyuan, He, Xianchang, Dong, Zhaotong, Xu, Jiabao, Li, Yanhong, Wang, Miao, Shi, Jianxin, Li, Jing, Zhang, Dabing, Lee, Seunghee, Hu, Wushu, Poliakov, Alexander, Dubchak, Inna, Ulat, Victor Jun, Borja, Frances Nikki, Mendoza, John Robert, Ali, Jauhar, Li, Jing, Gao, Qiang, Niu, Yongchao, Yue, Zhen, Naredo, Ma.Elizabeth B., Talag, Jayson, Wang, Xueqiang, Li, Jinjie, Fang, Xiaodong, Yin, Ye, Glaszmann, Jean-Christophe, Zhang, Jianwei, Li, Jiayang, Hamilton, Ruaraidh Sackville, Wing, Rod A., Ruan, Jue, Zhang, Gengyun, Wei, Chaochun, Alexandrov, Nickolai, McNally, Kenneth L., Li, Zhikang, Leung, Hei

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Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza by Stein, Joshua C., Yu, Yeisoo, Copetti, Dario, Zwickl, Derrick J., Zhang, Li, Zhang, Chengjun, Chougule, Kapeel, Gao, Dongying, Iwata, Aiko, Goicoechea, Jose Luis, Wei, Sharon, Wang, Jun, Liao, Yi, Wang, Muhua, Jacquemin, Julie, Becker, Claude, Kudrna, Dave, Zhang, Jianwei, Londono, Carlos E. M., Song, Xiang, Lee, Seunghee, Sanchez, Paul, Zuccolo, Andrea, Ammiraju, Jetty S. S., Talag, Jayson, Danowitz, Ann, Rivera, Luis F., Gschwend, Andrea R., Noutsos, Christos, Wu, Cheng-chieh, Kao, Shu-Min, Zeng, Jhih-wun, Wei, Fu-Jin, Zhao, Qiang, Feng, Qi, El Baidouri, Moaine, Carpentier, Marie-Christine, Lasserre, Eric, Cooke, Richard, Rosa Farias, Daniel da, da Maia, Luciano Carlos, dos Santos, Railson S., Nyberg, Kevin G., McNally, Kenneth L., Mauleon, Ramil, Alexandrov, Nickolai, Schmutz, Jeremy, Flowers, Dave, Fan, Chuanzhu, Weigel, Detlef, Jena, Kshirod K., Wicker, Thomas, Chen, Mingsheng, Han, Bin, Henry, Robert, Hsing, Yue-ie C., Kurata, Nori, de Oliveira, Antonio Costa, Panaud, Olivier, Jackson, Scott A., Machado, Carlos A., Sanderson, Michael J., Long, Manyuan, Ware, Doreen, Wing, Rod A.

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Building two indica rice reference genomes with PacBio long-read and Illumina paired-end sequencing data by Zhang, Jianwei, Chen, Ling-Ling, Sun, Shuai, Kudrna, Dave, Copetti, Dario, Li, Weiming, Mu, Ting, Jiao, Wen-Biao, Xing, Feng, Lee, Seunghee, Talag, Jayson, Song, Jia-Ming, Du, Bogu, Xie, Weibo, Luo, Meizhong, Maldonado, Carlos Ernesto, Goicoechea, Jose Luis, Xiong, Lizhong, Wu, Changyin, Xing, Yongzhong, Zhou, Dao-Xiu, Yu, Sibin, Zhao, Yu, Wang, Gongwei, Yu, Yeisoo, Luo, Yijie, Hurtado, Beatriz Elena Padilla, Danowitz, Ann, Wing, Rod A., Zhang, Qifa

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Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63 by Zhang, Jianwei, Chen, Ling-Ling, Xing, Feng, Kudrna, David A., Yao, Wen, Copetti, Dario, Mu, Ting, Li, Weiming, Song, Jia-Ming, Xie, Weibo, Lee, Seunghee, Talag, Jayson, Shao, Lin, An, Yue, Zhang, Chun-Liu, Ouyang, Yidan, Sun, Shuai, Jiao, Wen-Biao, Lv, Fang, Du, Bogu, Luo, Meizhong, Maldonado, Carlos Ernesto, Goicoechea, Jose Luis, Xiong, Lizhong, Wu, Changyin, Xing, Yongzhong, Zhou, Dao-Xiu, Yu, Sibin, Zhao, Yu, Wang, Gongwei, Yu, Yeisoo, Luo, Yijie, Zhou, Zhi-Wei, Hurtado, Beatriz Elena Padilla, Danowitz, Ann, Wing, Rod A., Zhang, Qifa

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Genome Puzzle Master (GPM)-An integrated pipeline for building and editing pseudomolecules from fragmented sequences by Zhang, Jianwei, Kudrna, Dave, Mu, Ting, Li, Weiming, Copetti, Dario, Yu, Yeisoo, Goicoechea, Jose Luis, Lei, Yang, Wing, Rod A.

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DNA methylation changes facilitated evolution of genes derived from Mutator-like transposable elements by Wang, Jun, Yu, Yeisoo, Tao, Feng, Zhang, Jianwei, Copetti, Dario, Kudrna, Dave, Talag, Jayson, Lee, Seunghee, Wing, Rod A., Fan, Chuanzhu

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Oryza genome evolution through a tetraploid lens by Fornasiero, Alice, Feng, Tao, Al-Bader, Noor, Alsantely, Aseel, Mussurova, Saule, Hoang, Nam V., Misra, Gopal, Zhou, Yong, Fabbian, Leonardo, Mohammed, Nahed, Rivera Serna, Luis, Thimma, Manjula, Llaca, Victor, Parakkal, Praveena, Kudrna, David, Copetti, Dario, Rajasekar, Shanmugam, Lee, Seunghee, Talag, Jayson, Sobel-Sorenson, Chandler, Carpentier, Marie-Christine, Panaud, Olivier, McNally, Kenneth L., Zhang, Jianwei, Zuccolo, Andrea, Schranz, M. Eric, Wing, Rod A.

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