Book Chapters
Yu, Yanchun, Wing, Rod A. and Li, Jiayang (2013). Grain quality. Genetics and genomics of rice. (pp. 237-254) edited by Qifa Zhang and Rod A. Wing. New York, NY, United States: Springer New York. doi: 10.1007/978-1-4614-7903-1_16
Wing, Rod A. and Zhang, Qifa (2013). Perspective rice 2020 revised: An urgent call to mobilize and coordinate rice functional genomics research worldwide. Genetics and Genomics of Rice. (pp. 387-390) New York, NY, United States: Springer New York. doi: 10.1007/978-1-4614-7903-1
Wing, Rod A., Kim, Hyeran, Goicoechea, Jose Luis, Yu, Yeisoo, Kudrna, Dave, Zuccolo, Andrea, Ammiraju, Jetty Siva S., Luo, Meizhong, Nelson, Will, Ma, Jianxin, Sanmiguel, Phillip, Hurwitz, Bonnie, Ware, Doreen, Brar, Darshan, Mackill, David, Soderlund, Cari, Stein, Lincoln and Jackson, Scott (2007). The oryza map alignment project (OMAP): a new resource for comparative genome studies within oryza. Rice Functional Genomics: Challenges, Progress and Prospects. (pp. 395-409) New York, NY, United States: Springer New York. doi: 10.1007/0-387-48914-2_15
Journal Articles
Athiyannan, Naveenkumar, Abrouk, Michael, Boshoff, Willem H. P., Cauet, Stéphane, Rodde, Nathalie, Kudrna, David, Mohammed, Nahed, Bettgenhaeuser, Jan, Botha, Kirsty S., Derman, Shannon S., Wing, Rod A., Prins, Renée and Krattinger, Simon G. (2022). Long-read genome sequencing of bread wheat facilitates disease resistance gene cloning. Nature Genetics, 54 (3), 227-231. doi: 10.1038/s41588-022-01022-1
Fornasiero, Alice, Wing, Rod A. and Ronald, Pamela (2022). Rice domestication. Current Biology, 32 (1), R20-R24. doi: 10.1016/j.cub.2021.11.025
Park, Hyun-Seung, Jayakodi, Murukarthick, Lee, Sae Hyun, Jeon, Jae-Hyeon, Lee, Hyun-Oh, Park, Jee Young, Moon, Byeong Cheol, Kim, Chang-Kug, Wing, Rod A., Newmaster, Steven G., Kim, Ji Yeon and Yang, Tae-Jin (2021). Author Correction: Mitochondrial plastid DNA can cause DNA barcoding paradox in plants (Scientific Reports, (2020), 10, 1, (6112), 10.1038/s41598-020-63233-y). Scientific Reports, 11 (1) 9599, 9599. doi: 10.1038/s41598-021-89266-5
Janner de Freitas, Karine E., Dos Santos, Railson Schreinert, Busanello, Carlos, Victoria, Filipe de Carvalho, Lopes, Jennifer Luz, Wing, Rod A. and de Oliveira, Antonio Costa (2021). Starch synthesis-related genes (SSRG) evolution in the genus oryza. Plants, 10 (6) 1057, 1-15. doi: 10.3390/plants10061057
Tian, Peng, Zhang, Xuemei, Xia, Rui, Liu, Yang, Wang, Meijiao, Li, Bo, Liu, Tieyan, Shi, Jinfeng, Wing, Rod A., Meyers, Blake C. and Chen, Mingsheng (2021). Evolution and diversification of reproductive phased small interfering RNAs in Oryza species. New Phytologist, 229 (5), 2970-2983. doi: 10.1111/nph.17035
Paritosh, Kumar, Yadava, Satish Kumar, Singh, Priyansha, Bhayana, Latika, Mukhopadhyay, Arundhati, Gupta, Vibha, Bisht, Naveen Chandra, Zhang, Jianwei, Kudrna, David A., Copetti, Dario, Wing, Rod A., Reddy Lachagari, Vijaya Bhasker, Pradhan, Akshay Kumar and Pental, Deepak (2021). A chromosome-scale assembly of allotetraploid Brassica juncea (AABB) elucidates comparative architecture of the A and B genomes. Plant Biotechnology Journal, 19 (3), 602-614. doi: 10.1111/pbi.13492
Lovell, John T., MacQueen, Alice H., Mamidi, Sujan, Bonnette, Jason, Jenkins, Jerry, Napier, Joseph D., Sreedasyam, Avinash, Healey, Adam, Session, Adam, Shu, Shengqiang, Barry, Kerrie, Bonos, Stacy, Boston, LoriBeth, Daum, Christopher, Deshpande, Shweta, Ewing, Aren, Grabowski, Paul P., Haque, Taslima, Harrison, Melanie, Jiang, Jiming, Kudrna, Dave, Lipzen, Anna, Pendergast, Thomas H., Plott, Chris, Qi, Peng, Saski, Christopher A., Shakirov, Eugene V., Sims, David, Sharma, Manoj ... Schmutz, Jeremy (2021). Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass. Nature, 590 (7846), 438-444. doi: 10.1038/s41586-020-03127-1
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 and Schmitz, Robert J. (2020). A genome assembly and the somatic genetic and epigenetic mutation rate in a wild long-lived perennial Populus trichocarpa. Genome Biology, 21 (1) 259. doi: 10.1186/s13059-020-02162-5
Mussurova, Saule, Al-Bader, Noor, Zuccolo, Andrea and Wing, Rod A. (2020). Potential of platinum standard reference genomes to exploit natural variation in the wild relatives of rice. Frontiers in Plant Science, 11 579980. doi: 10.3389/fpls.2020.579980
Fan, Guangyi, Song, Yue, Yang, Liandong, Huang, Xiaoyun, Zhang, Suyu, Zhang, Mengqi, Yang, Xianwei, Chang, Yue, Zhang, He, Li, Yongxin, Liu, Shanshan, Yu, Lili, Chu, Jeffery, Seim, Inge, Feng, Chenguang, Near, Thomas J, Wing, Rod A, Wang, Wen, Wang, Kun, Wang, Jing, Xu, Xun, Yang, Huanming, Liu, Xin, Chen, Nansheng and He, Shunping (2020). Initial data release and announcement of the 10,000 Fish Genomes Project (Fish10K). GigaScience, 9 (8). doi: 10.1093/gigascience/giaa080
Park, Hyun-Seung, Jayakodi, Murukarthick, Lee, Sae Hyun, Jeon, Jae-Hyeon, Lee, Hyun-Oh, Park, Jee Young, Moon, Byeong Cheol, Kim, Chang-Kug, Wing, Rod A., Newmaster, Steven G., Kim, Ji Yeon and Yang, Tae-Jin (2020). Mitochondrial plastid DNA can cause DNA barcoding paradox in plants. Scientific Reports, 10 (1) 6112, 6112. doi: 10.1038/s41598-020-63233-y
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, N. Ruaraidh Sackville, Leung, Hei, Mauleon, Ramil, Lorieux, Mathias, Zuccolo, Andrea, McNally, Kenneth, Zhang, Jianwei and Wing, Rod A. (2020). A platinum standard pan-genome resource that represents the population structure of Asian rice. Scientific Data, 7 (1) 113, 113. doi: 10.1038/s41597-020-0438-2
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 and Kurata, Nori (2020). Evolution and Diversity of the Wild Rice Oryza officinalis Complex, across Continents, Genome Types, and Ploidy Levels. Genome Biology and Evolution, 12 (4), 413-428. doi: 10.1093/gbe/evaa037
Flynn, Jullien M., Long, Manyuan, Wing, Rod A. and Clark, Andrew G. (2020). Evolutionary dynamics of abundant 7-bp satellites in the genome of Drosophila virilis. Molecular Biology and Evolution, 37 (5), 1362-1375. doi: 10.1093/molbev/msaa010
Hazzouri, Khaled M., Gros-Balthazard, Muriel, Flowers, Jonathan M., Copetti, Dario, Lemansour, Alain, Lebrun, Marc, Masmoudi, Khaled, Ferrand, Sylvie, Dhar, Michael I., Fresquez, Zoë A., Rosas, Ulises, Zhang, Jianwei, Talag, Jayson, Lee, Seunghee, Kudrna, David, Powell, Robyn F., Leitch, Ilia J., Krueger, Robert R., Wing, Rod A., Amiri, Khaled M. A. and Purugganan, Michael D. (2019). Genome-wide association mapping of date palm fruit traits. Nature Communications, 10 (1) 4680. doi: 10.1038/s41467-019-12604-9
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 and Ronald, Pamela C. (2019). Genome sequence of the model rice variety KitaakeX. BMC Genomics, 20 (1) 905. doi: 10.1186/s12864-019-6262-4
Mangu, Venkata R., Ratnasekera, Disna, Yabes, Jonalyn C., Wing, Rod A. and Baisakh, Niranjan (2019). Functional screening of genes from a halophyte wild rice relative Porteresia coarctata in Arabidopsis model identifies candidate genes involved in salt tolerance. Current Plant Biology, 18 100107, 100107. doi: 10.1016/j.cpb.2019.100107
Fuentes, Roven Rommel, Chebotarov, Dmytro, Duitama, Jorge, Smith, Sean, De la Hoz, Juan Fernando, Mohiyuddin, Marghoob, Wing, Rod A., McNally, Kenneth L., Tatarinova, Tatiana, Grigoriev, Andrey, Mauleon, Ramil and Alexandrov, Nickolai (2019). Structural variants in 3000 rice genomes. Genome Research, 29 (5), 870-880. doi: 10.1101/gr.241240.118
Chen, Erwang, Huang, Xuehui, Tian, Zhixi, Wing, Rod A. and Han, Bin (2019). The Genomics of Oryza Species Provides Insights into Rice Domestication and Heterosis. Annual Review of Plant Biology, 70 (1), 639-665. doi: 10.1146/annurev-arplant-050718-100320
Scheben, Armin, Chan, Chon-Kit Kenneth, Mansueto, Locedie, Mauleon, Ramil, Larmande, Pierre, Alexandrov, Nickolai, Wing, Rod A., McNally, Kenneth L., Quesneville, Hadi and Edwards, David (2019). Progress in single-access information systems for wheat and rice crop improvement. Briefings in Bioinformatics, 20 (2), 565-571. doi: 10.1093/bib/bby016
Zhang, Li, Ren, Yan, Yang, Tao, Li, Guangwei, Chen, Jianhai, Gschwend, Andrea R., Yu, Yeisoo, Hou, Guixue, Zi, Jin, Zhou, Ruo, Wen, Bo, Zhang, Jianwei, Chougule, Kapeel, Wang, Muhua, Copetti, Dario, Peng, Zhiyu, Zhang, Chengjun, Zhang, Yong, Ouyang, Yidan, Wing, Rod A., Liu, Siqi and Long, Manyuan (2019). Rapid evolution of protein diversity by de novo origination in Oryza. Nature Ecology & Evolution, 3 (4), 679-690. doi: 10.1038/s41559-019-0822-5
Kim, Nam-Hoon, Jayakodi, Murukarthick, Lee, Sang-Choon, Choi, Beom-Soon, Jang, Woojong, Lee, Junki, Kim, Hyun Hee, Waminal, Nomar E., Lakshmanan, Meiyappan, van Nguyen, Binh, Lee, Yun Sun, Park, Hyun-Seung, Koo, Hyun Jo, Park, Jee Young, Perumal, Sampath, Joh, Ho Jun, Lee, Hana, Kim, Jinkyung, Kim, In Seo, Kim, Kyunghee, Koduru, Lokanand, Kang, Kyo Bin, Sung, Sang Hyun, Yu, Yeisoo, Park, Daniel S., Choi, Doil, Seo, Eunyoung, Kim, Seungill, Kim, Young-Chang ... Yang, Tae-Jin (2018). Genome and evolution of the shade-requiring medicinal herb Panax ginseng. Plant Biotechnology Journal, 16 (11), 1904-1917. doi: 10.1111/pbi.12926
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 ... Wing, Rod A. (2018). Publisher Correction: Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza. Nature Genetics, 50 (11), 1618-1618. doi: 10.1038/s41588-018-0261-2
Wing, Rod A., Purugganan, Michael D. and Zhang, Qifa (2018). The rice genome revolution: from an ancient grain to Green Super Rice. Nature Reviews Genetics, 19 (8), 505-517. doi: 10.1038/s41576-018-0024-z
Liao, Yi, Zhang, Xuemei, Li, Bo, Liu, Tieyan, Chen, Jinfeng, Bai, Zetao, Wang, Meijiao, Shi, Jinfeng, Walling, Jason G., Wing, Rod A., Jiang, Jiming and Chen, Mingsheng (2018). Comparison of Oryza sativa and Oryza brachyantha genomes reveals selection-driven gene escape from the centromeric Regions. The Plant Cell, 30 (8), 1729-1744. doi: 10.1105/tpc.18.00163
Lv, Shuwei, Wu, Wenguang, Wang, Muhua, Meyer, Rachel S., Ndjiondjop, Marie-Noelle, Tan, Lubin, Zhou, Haiying, Zhang, Jianwei, Fu, Yongcai, Cai, Hongwei, Sun, Chuanqing, Wing, Rod A. and Zhu, Zuofeng (2018). Genetic control of seed shattering during African rice domestication. Nature Plants, 4 (6), 331-337. doi: 10.1038/s41477-018-0164-3
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 ... Leung, Hei (2018). Genomic variation in 3,010 diverse accessions of Asian cultivated rice. Nature, 557 (7703), 43-49. doi: 10.1038/s41586-018-0063-9
Bhatia, Dharminder, Wing, Rod A., Yu, Yeisoo, Chougule, Kapeel, Kudrna, Dave, Lee, Seunghee, Rang, Allah and Singh, Kuldeep (2018). Genotyping by sequencing of rice interspecific backcross inbred lines identifies QTLs for grain weight and grain length. Euphytica, 214 (2) 41. doi: 10.1007/s10681-018-2119-1
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 ... Wing, Rod A. (2018). Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza. Nature Genetics, 50 (2), 285-296. doi: 10.1038/s41588-018-0040-0
dos Santos, Railson Schreinert, Farias, Daniel da Rosa, Pegoraro, Camila, Rombaldi, Cesar Valmor, Fukao, Takeshi, Wing, Rod A. and de Oliveira, Antonio Costa (2017). Evolutionary analysis of the SUB1 locus across the Oryza genomes. Rice, 10 (1) 4. doi: 10.1186/s12284-016-0140-3
Copetti, Dario, Búrquez, Alberto, Bustamante, Enriquena, Charboneau, Joseph L. M., Childs, Kevin L., Eguiarte, Luis E., Lee, Seunghee, Liu, Tiffany L., McMahon, Michelle M., Whiteman, Noah K., Wing, Rod A., Wojciechowski, Martin F. and Sanderson, Michael J. (2017). Extensive gene tree discordance and hemiplasy shaped the genomes of North American columnar cacti. Proceedings of the National Academy of Sciences of the United States of America, 114 (45), 12003-12008. doi: 10.1073/pnas.1706367114
Harkess, Alex, Zhou, Jinsong, Xu, Chunyan, Bowers, John E, Van der Hulst, Ron, Ayyampalayam, Saravanaraj, Mercati, Francesco, Riccardi, Paolo, McKain, Michael R, Kakrana, Atul, Tang, Haibao, Ray, Jeremy, Groenendijk, John, Arikit, Siwaret, Mathioni, Sandra M, Nakano, Mayumi, Shan, Hongyan, Telgmann-Rauber, Alexa, Kanno, Akira, Yue, Zhen, Chen, Haixin, Li, Wenqi, Chen, Yanling, Xu, Xiangyang, Zhang, Yueping, Luo, Shaochun, Chen, Helong, Gao, Jianming, Mao, Zichao ... Chen, Guangyu (2017). The asparagus genome sheds light on the origin and evolution of a young Y chromosome. Nature Communications, 8 (1) 1279, 1279. doi: 10.1038/s41467-017-01064-8
Eizenga, G. C., Sanchez, P. L., Jackson, A. K., Edwards, J. D., Hurwitz, B. L., Wing, R. A. and Kudrna, D. (2017). Genetic variation for domestication-related traits revealed in a cultivated rice, Nipponbare (Oryza sativa ssp. japonica) × ancestral rice, O. nivara, mapping population. Molecular Breeding, 37 (11) 135. doi: 10.1007/s11032-017-0734-5
Brozynska, Marta, Copetti, Dario, Furtado, Agnelo, Wing, Rod A., Crayn, Darren, Fox, Glen, Ishikawa, Ryuji and Henry, Robert J. (2017). Sequencing of Australian wild rice genomes reveals ancestral relationships with domesticated rice. Plant Biotechnology Journal, 15 (6), 765-774. doi: 10.1111/pbi.12674
Wu, Wenguang, Liu, Xiaoyun, Wang, Muhua, Meyer, Rachel S., Luo, Xiaojin, Ndjiondjop, Marie-Noelle, Tan, Lubin, Zhang, Jianwei, Wu, Jianzhong, Cai, Hongwei, Sun, Chuanqing, Wang, Xiangkun, Wing, Rod A. and Zhu, Zuofeng (2017). A single-nucleotide polymorphism causes smaller grain size and loss of seed shattering during African rice domestication. Nature Plants, 3 (6) 17064, 17064. doi: 10.1038/nplants.2017.64
Lee, Cheng-Ruei, Wang, Baosheng, Mojica, Julius P., Mandáková, Terezie, Prasad, Kasavajhala V. S. K., Goicoechea, Jose Luis, Perera, Nadeesha, Hellsten, Uffe, Hundley, Hope N., Johnson, Jenifer, Grimwood, Jane, Barry, Kerrie, Fairclough, Tephen, Jenkins, Jerry W., Yu, Yeisoo, Kudrna, Dave, Zhang, Jianwei, Talag, Jayson, Golser, Wolfgang, Ghattas, Kathryn, Schranz, M. Eric, Wing, Rod, Lysak, Martin A., Schmutz, Jeremy, Rokhsar, Daniel S. and Mitchell-Olds, Thomas (2017). Young inversion with multiple linked QTLs under selection in a hybrid zone. Nature Ecology and Evolution, 1 (5) 0119. doi: 10.1038/s41559-017-0119
Choi, Jae Young, Platts, Adrian E., Fuller, Dorian Q., Hsing, Yue-Ie, Wing, Rod A., Purugganan, Michael D. and Kim, Yuseob (2017). The rice paradox: multiple origins but single domestication in Asian Rice. Molecular Biology and Evolution, 34 (4), 969-979. doi: 10.1093/molbev/msx049
Thakare, Dhiraj, Zhang, Jianwei, Wing, Rod A., Cotty, Peter J. and Schmidt, Monica A. (2017). Aflatoxin-free transgenic maize using host-induced gene silencing. Science Advances, 3 (3) e1602382, e1602382. doi: 10.1126/sciadv.1602382
Mansueto, Locedie, Fuentes, Roven Rommel, Borja, Frances Nikki, Detras, Jeffery, Abrio-Santos, Juan Miguel, Chebotarov, Dmytro, Sanciangco, Millicent, Palis, Kevin, Copetti, Dario, Poliakov, Alexandre, Dubchak, Inna, Solovyev, Victor, Wing, Rod A., Hamilton, Ruaraidh Sackville, Mauleon, Ramil, McNally, Kenneth L. and Alexandrov, Nickolai (2017). Rice SNP-seek database update: New SNPs, indels, and queries. Nucleic Acids Research, 45 (D1), D1075-D1081. doi: 10.1093/nar/gkw1135
Copetti, Dario and Wing, Rod A. (2016). The dark side of the genome: revealing the native transposable element/repeat content of Eukaryotic genomes. Molecular Plant, 9 (12), 1664-1666. doi: 10.1016/j.molp.2016.09.006
Gan, Xiangchao, Hay, Angela, Kwantes, Michiel, Haberer, Georg, Hallab, Asis, Ioio, Raffaele Dello, Hofhuis, Hugo, Pieper, Bjorn, Cartolano, Maria, Neumann, Ulla, Nikolov, Lachezar A., Song, Baoxing, Hajheidari, Mohsen, Briskine, Roman, Kougioumoutzi, Evangelia, Vlad, Daniela, Broholm, Suvi, Hein, Jotun, Meksem, Khalid, Lightfoot, David, Shimizu, Kentaro K., Shimizu-Inatsugi, Rie, Imprialou, Martha, Kudrna, David, Wing, Rod, Sato, Shusei, Huijser, Peter, Filatov, Dmitry, Mayer, Klaus F. X. ... Tsiantis, Miltos (2016). The Cardamine hirsuta genome offers insight into the evolution of morphological diversity. Nature Plants, 2 (11) 16167. doi: 10.1038/nplants.2016.167
Zhang, Jianwei, Kudrna, Dave, Mu, Ting, Li, Weiming, Copetti, Dario, Yu, Yeisoo, Goicoechea, Jose Luis, Lei, Yang and Wing, Rod A. (2016). Genome puzzle master (GPM): An integrated pipeline for building and editing pseudomolecules from fragmented sequences. Bioinformatics, 32 (20), 3058-3064. doi: 10.1093/bioinformatics/btw370
Van Andel, Tinde R., Meyer, Rachel S., Aflitos, Saulo A., Carney, Judith A., Veltman, Margaretha A., Copetti, Dario, Flowers, Jonathan M., Havinga, Reinout M., Maat, Harro, Purugganan, Michael D., Wing, Rod A. and Schranz, M. Eric (2016). Tracing ancestor rice of Suriname Maroons back to its African origin. Nature Plants, 2 (10) 16149. doi: 10.1038/nplants.2016.149
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. and Zhang, Qifa (2016). Building two indica rice reference genomes with PacBio long-read and Illumina paired-end sequencing data. Scientific Data, 3 (1) 160076. doi: 10.1038/sdata.2016.76
Wicker, Thomas, Yu, Yeisoo, Haberer, Georg, Mayer, Klaus F. X., Marri, Pradeep Reddy, Rounsley, Steve, Chen, Mingsheng, Zuccolo, Andrea, Panaud, Olivier, Wing, Rod A. and Roffler, Stefan (2016). DNA transposon activity is associated with increased mutation rates in genes of rice and other grasses. Nature Communications, 7 (1) 12790. doi: 10.1038/ncomms12790
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 ... Zhang, Qifa (2016). Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63. Proceedings of the National Academy of Sciences, 113 (35), E5163-E5171. doi: 10.1073/pnas.1611012113
Ray, Soham, Bose, Lotan K., Ray, Joshitha, Ngangkham, Umakanta, Katara, Jawahar L., Samantaray, Sanghamitra, Behera, Lambodar, Anumalla, Mahender, Singh, Onkar N., Chen, Meingsheng, Wing, Rod A. and Mohapatra, Trilochan (2016). Development and validation of cross-transferable and polymorphic DNA markers for detecting alien genome introgression in Oryza sativa from Oryza brachyantha. Molecular Genetics and Genomics, 291 (4), 1783-1794. doi: 10.1007/s00438-016-1214-z
Wang, Jun, Yu, Yeisoo, Tao, Feng, Zhang, Jianwei, Copetti, Dario, Kudrna, Dave, Talag, Jayson, Lee, Seunghee, Wing, Rod A. and Fan, Chuanzhu (2016). DNA methylation changes facilitated evolution of genes derived from Mutator-like transposable elements. Genome Biology, 17 (1) 92. doi: 10.1186/s13059-016-0954-8
Wendel, Jonathan F., Jackson, Scott A., Meyers, Blake C. and Wing, Rod A. (2016). Evolution of plant genome architecture. Genome Biology, 17 (37) 37. doi: 10.1186/s13059-016-0908-1
Bai, Zetao, Chen, Jinfeng, Liao, Yi, Wang, Meijiao, Liu, Rong, Ge, Song, Wing, Rod A. and Chen, Mingsheng (2016). The impact and origin of copy number variations in the Oryza species. BMC Genomics, 17 (1) 261. doi: 10.1186/s12864-016-2589-2
De Vega, Jose J., Ayling, Sarah, Hegarty, Matthew, Kudrna, Dave, Goicoechea, Jose L., Ergon, Åshild, Rognli, Odd A., Jones, Charlotte, Swain, Martin, Geurts, Rene, Lang, Chunting, Mayer, Klaus F. X., Rössner, Stephan, Yates, Steven, Webb, Kathleen J., Donnison, Iain S., Oldroyd, Giles E. D., Wing, Rod A., Caccamo, Mario, Powell, Wayne, Abberton, Michael T. and Skøt, Leif (2015). Red clover (Trifolium pratense L.) draft genome provides a platform for trait improvement. Scientific Reports, 5 (1) 17394. doi: 10.1038/srep17394
Zhang, Yesheng, Zhang, Shilai, Liu, Hui, Fu, Binying, Li, Lijuan, Xie, Min, Song, Yue, Li, Xin, Cai, Jing, Wan, Wenting, Kui, Ling, Huang, Hui, Lyu, Jun, Dong, Yang, Wang, Wensheng, Huang, Liyu, Zhang, Jing, Yang, Qinzhong, Shan, Qinli, Li, Qiong, Huang, Wangqi, Tao, Dayun, Wang, Muhua, Chen, Mingsheng, Yu, Yeisoo, Wing, Rod A., Wang, Wen and Hu, Fengyi (2015). Genome and comparative transcriptomics of African wild rice Oryza longistaminata provide insights into molecular mechanism of rhizomatousness and self-incompatibility. Molecular Plant, 8 (11), 1683-1686. doi: 10.1016/j.molp.2015.08.006
Wicker, Thomas, Wing, Rod A. and Schubert, Ingo (2015). Recurrent sequence exchange between homeologous grass chromosomes. Plant Journal, 84 (4), 747-759. doi: 10.1111/tpj.13040
Kim, Kyunghee, Lee, Sang-Choon, Lee, Junki, Yu, Yeisoo, Yang, Kiwoung, Choi, Beom-Soon, Koh, Hee-Jong, Waminal, Nomar Espinosa, Choi, Hong-Il, Kim, Nam-Hoon, Jang, Woojong, Park, Hyun-Seung, Lee, Jonghoon, Lee, Hyun Oh, Joh, Ho Jun, Lee, Hyeon Ju, Park, Jee Young, Perumal, Sampath, Jayakodi, Murukarthick, Lee, Yun Sun, Kim, Backki, Copetti, Dario, Kim, Soonok, Kim, Sunggil, Lim, Ki-Byung, Kim, Young-Dong, Lee, Jungho, Cho, Kwang-Su, Park, Beom-Seok ... Yang, Tae-Jin (2015). Complete chloroplast and ribosomal sequences for 30 accessions elucidate evolution of Oryza AA genome species. Scientific Reports, 5 (1) 15655. doi: 10.1038/srep15655
Wing, Rod A. (2015). Harvesting rice's dispensable genome. Genome Biology, 16 (1) 217. doi: 10.1186/s13059-015-0787-x
Copetti, Dario, Zhang, Jianwei, El Baidouri, Moaine, Gao, Dongying, Wang, Jun, Barghini, Elena, Cossu, Rosa M., Angelova, Angelina, Maldonado L., Carlos E., Roffler, Stefan, Ohyanagi, Hajime, Wicker, Thomas, Fan, Chuanzhu, Zuccolo, Andrea, Chen, Mingsheng, Costa de Oliveira, Antonio, Han, Bin, Henry, Robert, Hsing, Yue-ie, Kurata, Nor, Wang, Wen, Jackson, Scott A., Panaud, Olivier and Wing, Rod A. (2015). RiTE database: A resource database for genus-wide rice genomics and evolutionary biology. BMC Genomics, 16 (1) 538, 538-538. doi: 10.1186/s12864-015-1762-3
Sanderson, Michael J., Copetti, Dario, Búrquez, Alberto, Bustamante, Enriquena, Charboneau, Joseph L. M., Eguiarte, Luis E., Kumar, Sudhir, Lee, Hyun Oh, Lee, Junki, McMahon, Michelle, Steele, Kelly, Wing, Rod, Yang, Tae-Jin, Zwickl, Derrick and Wojciechowski, Martin F. (2015). Exceptional reduction of the plastid genome of saguaro cactus (Carnegiea gigantea): loss of the ndh gene suite and inverted repeat 1. American Journal of Botany, 102 (7), 1115-1127. doi: 10.3732/ajb.1500184
Gao, Dongying, Jiang, Ning, Wing, Rod A., Jiang, Jiming and Jackson, Scott A. (2015). Transposons play an important role in the evolution and diversification of centromeres among closely related species. Frontiers in Plant Science, 6 (APR) 216. doi: 10.3389/fpls.2015.00216
Muñoz-Amatriaín, María, Lonardi, Stefano, Luo, Mingcheng, Madishetty, Kavitha, Svensson, Jan T., Moscou, Matthew J., Wanamaker, Steve, Jiang, Tao, Kleinhofs, Andris, Muehlbauer, Gary J., Wise, Roger P., Stein, Nils, Ma, Yaqin, Rodriguez, Edmundo, Kudrna, Dave, Bhat, Prasanna R., Chao, Shiaoman, Condamine, Pascal, Heinen, Shane, Resnik, Josh, Wing, Rod, Witt, Heather N., Alpert, Matthew, Beccuti, Marco, Bozdag, Serdar, Cordero, Francesca, Mirebrahim, Hamid, Ounit, Rachid, Wu, Yonghui ... Close, Timothy J. (2015). Sequencing of 15 622 gene-bearing BACs clarifies the gene-dense regions of the barley genome. Plant Journal, 84 (1), 216-227. doi: 10.1111/tpj.12959
Geering, Andrew D. W., Maumus, Florian, Copetti, Dario, Choisne, Nathalie, Zwickl, Derrick J., Zytnicki, Matthias, McTaggart, Alistair R., Scalabrin, Simone, Vezzulli, Silvia, Wing, Rod A., Quesneville, Hadi and Teycheney, Pierre-Yves (2014). Endogenous florendoviruses are major components of plant genomes and hallmarks of virus evolution. Nature Communications, 5 (1) 5269, 5269.1-5269.11. doi: 10.1038/ncomms6269
Wang, Muhua, Yu, Yeisoo, Haberer, Georg, Marri, Pradeep Reddy, Fan, Chuanzhu, Goicoechea, Jose Luis, Zuccolo, Andrea, Song, Xiang, Kudrna, Dave, Ammiraju, Jetty S.S., Cossu, Rosa Maria, Maldonado, Carlos, Chen, Jinfeng, Lee, Seunghee, Sisneros, Nick, De Baynast, Kristi, Golser, Wolfgang, Wissotski, Marina, Kim, Woojin, Sanchez, Paul, Ndjiondjop, Marie-Noelle, Sanni, Kayode, Long, Manyuan, Carney, Judith, Panaud, Olivier, Wicker, Thomas, MacHado, Carlos A., Chen, Mingsheng, Mayer, Klaus F.X. ... Wing, Rod A. (2014). The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication. Nature Genetics, 46 (9), 982-988. doi: 10.1038/ng.3044
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. ... Jackson, Scott A. (2014). A reference genome for common bean and genome-wide analysis of dual domestications. Nature Genetics, 46 (7), 707-713. doi: 10.1038/ng.3008
Wang, Xiaoming, Kudrna, David A., Pan, Yonglong, Wang, Hao, Liu, Lin, Lin, Haiyan, Zhang, Jianwei, Song, Xiang, Goicoechea, Jose Luis, Wing, Rod A., Zhang, Qifa and Luo, Meizhong (2014). Global genomic diversity of Oryza sativa varieties revealed by comparative physical mapping. Genetics, 196 (4), 937-949. doi: 10.1534/genetics.113.159970
Jacquemin, Julie, Ammiraju, Jetty S.S., Haberer, Georg, Billheimer, Dean D., Yu, Yeisoo, Liu, Liana C., Rivera, Luis F., Mayer, Klaus, Chen, Mingsheng and Wing, Rod A. (2014). Fifteen million years of evolution in the Oryza genus shows extensive gene family expansion. Molecular Plant, 7 (4), 642-656. doi: 10.1093/mp/sst149
Pan, Yonglong, Deng, Ying, Lin, Haiyan, Kudrna, David A., Wing, Rod A., Li, Lijia, Zhang, Qifa and Luo, Meizhong (2014). Comparative BAC-based physical mapping of Oryza sativa ssp. indica var. 93-11 and evaluation of the two rice reference sequence assemblies. Plant Journal, 77 (5), 795-805. doi: 10.1111/tpj.12412
Ortiz, Marianyoly, Legatzki, Antje, Neilson, Julia W., Fryslie, Brandon, Nelson, William M., Wing, Rod A., Soderlund, Carol A., Pryor, Barry M. and Maier, Raina M. (2014). Making a living while starving in the dark: metagenomic insights into the energy dynamics of a carbonate cave. ISME Journal, 8 (2), 478-491. doi: 10.1038/ismej.2013.159
Zwickl, Derrick J., Stein, Joshua C., Wing, Rod A., Ware, Doreen and Sanderson, Michael J. (2014). Disentangling methodological and biological sources of gene tree discordance on Oryza (Poaceae) chromosome 3. Systematic Biology, 63 (5), 645-659. doi: 10.1093/sysbio/syu027
Chamala, Srikar, Chanderbali, Andre S., Der, Joshua P., Lan, Tianying, Walts, Brandon, Albert, Victor A., DePamphilis, Claude W., Leebens-Mack, Jim, Rounsley, Steve, Schuster, Stephan C., Wing, Rod A., Xiao, Nianqing, Moore, Richard, Soltis, Pamela S., Soltis, Douglas E. and Barbazuk, W. Brad (2013). Assembly and validation of the genome of the nonmodel basal angiosperm Amborella. Science, 342 (6165), 1516-1517. doi: 10.1126/science.1241130
DePamphilis, Claude W., Palmer, Jeffrey D., Rounsley, Steve, Sankoff, David, Schuster, Stephan C., Ammiraju, Jetty S. S., Barbazuk, W. Bradley, Chamala, Srikar, Chanderbali, Andre S., Determann, Ronald, Hong, Ma., Ralph, Paula, Talag, Jason, Tomsho, Lynn, Walts, Brandon, Wanke, Stefan, Wing, Rod A., Chang, Tien-Hao, Lan, Tianying, Soltis, Douglas E., Arikit, Siwaret, Axtell, Michael J., Ayyampalayam, Saravanaraj, Burnette III, James M., De Paoli, Emanuele, Farrell, Nina P., Harkess, Alex, Jiao, Yuannian, Leebens-Mack, James ... Soltis, Pamela S. (2013). The Amborella genome and the evolution of flowering plants. Science, 342 (6165) 1241089, 1241089-1241089. doi: 10.1126/science.1241089
Wang, Chao, Shi, Xue, Liu, Lin, Li, Haiyan, Ammiraju, Jetty S.S., Kudrna, David A., Xiong, Wentao, Wang, Hao, Dai, Zhaozhao, Zheng, Yonglian, Lai, Jinsheng, Jin, Weiwei, Messing, Joachim, Bennetzen, Jeffrey L., Wing, Rod A. and Luo, Meizhong (2013). Genomic resources for gene discovery, functional genome annotation, and evolutionary studies of maize and its close relatives. Genetics, 195 (3), 723-737. doi: 10.1534/genetics.113.157115
Dereeper, Alexis, Guyot, Romain, Tranchant-Dubreuil, Christine, Anthony, François, Argout, Xavier, de Bellis, Fabien, Combes, Marie-Christine, Gavory, Frederick, de Kochko, Alexandre, Kudrna, Dave, Leroy, Thierry, Poulain, Julie, Rondeau, Myriam, Song, Xiang, Wing, Rod and Lashermes, Philippe (2013). BAC-end sequences analysis provides first insights into coffee (Coffea canephora P.) genome composition and evolution. Plant Molecular Biology, 83 (3), 177-189. doi: 10.1007/s11103-013-0077-5
Singh, Rajinder, Ong-Abdullah, Meilina, Low, Eng-Ti Leslie, Manaf, Mohamad Arif Abdul, Rosli, Rozana, Nookiah, Rajanaidu, Ooi, Leslie Cheng-Li, Ooi, Siew-Eng, Chan, Kuang-Lim, Halim, Mohd Amin, Azizi, Norazah, Nagappan, Jayanthi, Bacher, Blaire, Lakey, Nathan, Smith, Steven W., He, Dong, Hogan, Michael, Budiman, Muhammad A., Lee, Ernest K., Desalle, Rob, Kudrna, David, Goicoechea, Jose Luis, Wing, Rod A., Wilson, Richard K., Fulton, Robert S., Ordway, Jared M., Martienssen, Robert A. and Sambanthamurthi, Ravigadevi (2013). Oil palm genome sequence reveals divergence of interfertile species in Old and New worlds. Nature, 500 (7462), 335-339. doi: 10.1038/nature12309
Horvath, David P., Kudrna, David, Talag, Jayson, Anderson, James V., Chao, Wun S., Wing, Rod, Foley, Michael E. and Doǧramaci, Münevver (2013). BAC library development and clone characterization for dormancy-responsive DREB4A, DAM, and FT from leafy spurge (Euphorbia esula) identifies differential splicing and conserved promoter motifs. Weed Science, 61 (2), 303-309. doi: 10.1614/WS-D-12-00175.1
Matsuba, Yuki, Nguyen, Thuong T.H., Wiegert, Krystle, Falara, Vasiliki, Gonzales-Vigil, Eliana, Leong, Bryan, Schäfer, Petra, Kudrna, David, Wing, Rod A., Bolger, Anthony M., Usadel, Björn, Tissier, Alain, Fernie, Alisdair R., Barry, Cornelius S. and Pichersky, Eran (2013). Evolution of a complex locus for terpene biosynthesis in Solanum. Plant Cell, 25 (6), 2022-2036. doi: 10.1105/tpc.113.111013
Zhang, Qifa and Wing, Rod (2013). Genome studies and molecular genetics: Understanding the functional genome based on the rice model. Current Opinion in Plant Biology, 16 (2), 129-132. doi: 10.1016/j.pbi.2013.04.003
Zhang, Chengjun, Wang, Jun, Marowsky, Nicholas C., Long, Manyuan, Wing, Rod A. and Fan, Chuanzhu (2013). High occurrence of functional new chimeric genes in survey of rice chromosome 3 short arm genome sequences. Genome Biology and Evolution, 5 (5), 1038-1048. doi: 10.1093/gbe/evt071
Jacquemin, Julie, Bhatia, Dharminder, Singh, Kuldeep and Wing, Rod A. (2013). The International Oryza Map Alignment Project: development of a genus-wide comparative genomics platform to help solve the 9 billion-people question. Current Opinion in Plant Biology, 16 (2), 147-156. doi: 10.1016/j.pbi.2013.02.014
Maron, Lyza G., Guimarães, Claudia T., Kirst, Matias, Albert, Patrice S., Birchler, James A., Bradbury, Peter J., Buckler, Edward S., Coluccio, Alison E., Danilova, Tatiana V., Kudrna, David, Magalhaes, Jurandir V., Piñeros, Miguel A., Schatz, Michael C., Wing, Rod A. and Kochian, Leon V. (2013). Aluminum tolerance in maize is associated with higher MATE1 gene copy number. Proceedings of the National Academy of Sciences of the United States of America, 110 (13), 5241-5246. doi: 10.1073/pnas.1220766110
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. and Wang, Xiangfeng (2013). The reference genome of the halophytic plant Eutrema salsugineum. Frontiers in Plant Science, 4 (MAR) 46. doi: 10.3389/fpls.2013.00046
Chen, Jinfeng, Huang, Quanfei, Gao, Dongying, Wang, Junyi, Lang, Yongshan, Liu, Tieyan, Li, Bo, Bai, Zetao, Luis Goicoechea, Jose, Liang, Chengzhi, Chen, Chengbin, Zhang, Wenli, Sun, Shouhong, Liao, Yi, Zhang, Xuemei, Yang, Lu, Song, Chengli, Wang, Meijiao, Shi, Jinfeng, Liu, Geng, Liu, Junjie, Zhou, Heling, Zhou, Weili, Yu, Qiulin, An, Na, Chen, Yan, Cai, Qingle, Wang, Bo, Liu, Binghang ... Chen, Mingsheng (2013). Whole-genome sequencing of Oryza brachyantha reveals mechanisms underlying Oryza genome evolution. Nature Communications, 4 (1) 1595. doi: 10.1038/ncomms2596
Koo, Hyun Jo, McDowell, Eric T., Ma, Xiaoqiang, Greer, Kevin A., Kapteyn, Jeremy, Xie, Zhengzhi, Descour, Anne, Kim, HyeRan, Yu, Yeisoo, Kudrna, David, Wing, Rod A., Soderlund, Carol A. and Gang, David R. (2013). Ginger and turmeric expressed sequence tags identify signature genes for rhizome identity and development and the biosynthesis of curcuminoids, gingerols and terpenoids. BMC Plant Biology, 13 (1) 27. doi: 10.1186/1471-2229-13-27
Zhang, Qifa and Wing, Rod A. (2013). Preface. Genetics and Genomics of Rice, 7-7. doi: 10.1007/978-1-4614-7903-1
Ortiz, Marianyoly, Neilson, Julia W., Nelson, William M., Legatzki, Antje, Byrne, Andrea, Yu, Yeisoo, Wing, Rod A., Soderlund, Carol A., Pryor, Barry M., Pierson III, Leland S. and Maier, Raina M. (2013). Profiling Bacterial Diversity and Taxonomic Composition on Speleothem Surfaces in Kartchner Caverns, AZ. Microbial Ecology, 65 (2), 371-383. doi: 10.1007/s00248-012-0143-6
Mayer, Klaus F. X., Waugh, Robbie, Langridge, Peter, Close, Timothy J., Wise, Roger P., Graner, Andreas, Matsumoto, Takashi, Sato, Kazuhiro, Schulman, Alan, Ariyadasa, Ruvini, Schulte, Daniela, Poursarebani, Naser, Zhou, Ruonan, Steuernagel, Burkhard, Mascher, Martin, Scholz, Uwe, Shi, Bujun, Madishetty, Kavitha, Svensson, Jan T., Bhat, Prasanna, Moscou, Matthew, Resnik, Josh, Muehlbauer, Gary J., Hedley, Pete, Liu, Hui, Morris, Jenny, Frenkel, Zeev, Korol, Avraham, Bergès, Hélène ... Stein, Nils (2012). A physical, genetic and functional sequence assembly of the barley genome. Nature, 491 (7426), 711-716. doi: 10.1038/nature11543
Yang, Lu, Liu, Tieyan, Li, Bo, Sui, Yi, Chen, Jinfeng, Shi, Jinfeng, Wing, Rod A. and Chen, Mingsheng (2012). Comparative Sequence Analysis of the Ghd7 Orthologous Regions Revealed Movement of Ghd7 in the Grass Genomes. PLoS ONE, 7 (11) e50236. doi: 10.1371/journal.pone.0050236
Sato, Shusei, Tabata, Satoshi, Hirakawa, Hideki, Asamizu, Erika, Shirasawa, Kenta, Isobe, Sachiko, Kaneko, Takakazu, Nakamura, Yasukazu, Shibata, Daisuke, Aoki, Koh, Egholm, Michael, Knight, James, Bogden, Robert, Li, Changbao, Shuang, Yang, Xu, Xun, Pan, Shengkai, Cheng, Shifeng, Liu, Xin, Ren, Yuanyuan, Wang, Jun, Albiero, Alessandro, Dal Pero, Francesca, Todesco, Sara, Van Eck, Joyce, Buels, Robert M., Bombarely, Aureliano, Gosselin, Joseph R., Huang, Minyun ... The Tomato Genome Consortium (2012). The tomato genome sequence provides insights into fleshy fruit evolution. Nature, 485 (7400), 635-641. doi: 10.1038/nature11119
Figueira, Thais Rezende E Silva, Okura, Vagner, Rodrigues Da Silva, Felipe, Jose Da Silva, Marcio, Kudrna, Dave, Ammiraju, Jetty S.S., Talag, Jayson, Wing, Rod and Arruda, Paulo (2012). A BAC library of the SP80-3280 sugarcane variety (saccharum sp.) and its inferred microsynteny with the sorghum genome. BMC Research Notes, 5 (1) 185. doi: 10.1186/1756-0500-5-185
Neilson, Julia W., Quade, Jay, Ortiz, Marianyoly, Nelson, William M., Legatzki, Antje, Tian, Fei, LaComb, Michelle, Betancourt, Julio L., Wing, Rod A., Soderlund, Carol A. and Maier, Raina M. (2012). Life at the hyperarid margin: novel bacterial diversity in arid soils of the Atacama Desert, Chile. Extremophiles, 16 (3), 553-566. doi: 10.1007/s00792-012-0454-z
Ha, Jungmin, Abernathy, Brian, Nelson, William, Grant, David, Wu, Xiaolei, Nguyen, Henry T., Stacey, Gary, Yu, Yeisoo, Wing, Rod A., Shoemaker, Randy C. and Jackson, Scott A. (2012). Integration of the draft sequence and physical map as a framework for genomic research in soybean (Glycine max (l.) merr.) and wild soybean (Glycine soja Sieb. and Zucc.). G3: Genes, Genomes, Genetics, 2 (3), 321-329. doi: 10.1534/g3.111.001834
Lin, Haiyan, Xia, Peng, Wing, Rod A., Zhang, Qifa and Luo, Meizhong (2012). Dynamic intra-japonica subspecies variation and resource application. Molecular Plant, 5 (1), 218-230. doi: 10.1093/mp/ssr085
Li, Hong-Jing, Li, Xiang-Hua, Xiao, Jing-Hua, Wing, Rod A. and Wang, Shi-Ping (2012). Ortholog alleles at Xa3/Xa26 locus confer conserved race-specific resistance against xanthomonas oryzae in rice. Molecular Plant, 5 (1), 281-290. doi: 10.1093/mp/ssr079
Jacquemin, J., Chaparro, C., Laudié, M., Berger, A., Gavory, F., Goicoechea, J. L., Wing, R. A. and Cooke, R. (2011). Long-range and targeted ectopic recombination between the two homeologous chromosomes 11 and 12 in Oryza species. Molecular Biology and Evolution, 28 (11), 3139-3150. doi: 10.1093/molbev/msr144
Fan, Chuanzhu, Walling, Jason G., Zhang, Jianwei, Hirsch, Cory D., Jiang, Jiming and Wing, Rod A. (2011). Conservation and purifying selection of transcribed genes located in a rice centromere. Plant Cell, 23 (8), 2821-2830. doi: 10.1105/tpc.111.085605
Piegu, Benoit, Guyot, Romain, Picault, Nathalie, Roulin, Anne, Sanyal, Abhijit, Kim, Hyeran, Collura, Kristi, Brar, Darshan S., Jackson, Scott, Wing, Rod A. and Panaud, Olivier (2011). Doubling genome size without polyploidization: dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice (Genome Research (2006) 16, (1262-1269)). Genome Research, 21 (7)
Zuccolo, Andrea, Bowers, John E., Estill, James C., Xiong, Zhiyong, Luo, Meizhong, Sebastian, Aswathy, Goicoechea, José L., Collura, Kristi, Yu, Yeisoo, Jiao, Yuannian, Duarte, Jill, Tang, Haibao, Ayyampalayam, Saravanaraj, Rounsley, Steve, Kudrna, Dave, Paterson, Andrew H., Pires, J C., Chanderbali, Andre, Soltis, Douglas E., Chamala, Srikar, Barbazuk, Brad, Soltis, Pamela S., Albert, Victor A., Ma, Hong, Mandoli, Dina, Banks, Jody, Carlson, John E., Tomkins, Jeffrey, dePamphilis, Claude W. ... Leebens-Mack, Jim (2011). A physical map for the Amborella trichopoda genome sheds light on the evolution of angiosperm genome structure. Genome Biology, 12 (5) R48. doi: 10.1186/gb-2011-12-5-r48
Song, Xiang, Goicoechea, Jose Luis, Ammiraju, Jetty S. S., Luo, Meizhong, He, Ruifeng, Lin, Jinke, Lee, So-Jeong, Sisneros, Nicholas, Watts, Tom, Kudrna, David A., Golser, Wolfgang, Ashley, Elizabeth, Collura, Kristi, Braidotti, Michele, Yu, Yeisoo, Matzkin, Luciano M., McAllister, Bryant F., Markow, Therese Ann and Wing, Rod A. (2011). The 19 genomes of Drosophila: a BAC library resource for genus-wide and genome-scale comparative evolutionary research. Genetics, 187 (4), 1023-1030. doi: 10.1534/genetics.111.126540
Blair, Matthew W., Hurtado, Natalia, Chavarro, Carolina M., Muñoz-Torres, Monica C., Giraldo, Martha C., Pedraza, Fabio, Tomkins, Jeff and Wing, Rod (2011). Gene-based SSR markers for common bean (Phaseolus vulgaris L.) derived from root and leaf tissue ESTs: an integration of the BMc series. BMC Plant Biology, 11 50. doi: 10.1186/1471-2229-11-50
Wing, Rod A., Lin, Jinke and Kudrna, Dave (2011). Construction, characterization, and preliminary BAC-end sequence analysis of a bacterial artificial chromosome library of the tea plant (Camellia sinensis). Journal of Biomedicine and Biotechnology, 2011 476723, 1-8. doi: 10.1155/2011/476723
Tian, Zhixi, Yu, Yanjun, Lin, Feng, Yu, Yeisoo, SanMiguel, Phillip J., Wing, Rod A., McCouch, Susan R., Ma, Jianxin and Jackson, Scott A. (2011). Exceptional lability of a genomic complex in rice and its close relatives revealed by interspecific and intraspecific comparison and population analysis. BMC Genomics, 12 (1) 142. doi: 10.1186/1471-2164-12-142
Paiva, Jorge A. P., Prat, Elisa, Vautrin, Sonia, Santos, Mauro D., San-Clemente, Hélène, Brommonschenkel, Sérgio, Fonseca, Paulo G. S., Grattapaglia, Dario, Song, Xiang, Ammiraju, Jetty S. S., Kudrna, David, Wing, Rod A., Freitas, Ana T., Bergès, Hélène and Grima-Pettenati, Jacqueline (2011). Advancing Eucalyptus genomics: identification and sequencing of lignin biosynthesis genes from deep-coverage BAC libraries. BMC Genomics, 12 (1) 137. doi: 10.1186/1471-2164-12-137
Den Camp, Rik Op, Streng, Arend, De Mita, Stéphane, Cao, Qingqin, Polone, Elisa, Liu, Wei, Ammiraju, Jetty S. S., Kudrna, Dave, Wing, Rod, Untergasser, Andreas, Bisseling, Ton and Geurts, René (2011). LysM-type mycorrhizal receptor recruited for rhizobium symbiosis in nonlegume Parasponia. Science, 331 (6019), 909-912. doi: 10.1126/science.1198181
Argout, Xavier, Salse, Jerome, Aury, Jean-Marc, Guiltinan, Mark J., Droc, Gaetan, Gouzy, Jerome, Allegre, Mathilde, Chaparro, Cristian, Legavre, Thierry, Maximova, Siela N., Abrouk, Michael, Murat, Florent, Fouet, Olivier, Poulain, Julie, Ruiz, Manuel, Roguet, Yolande, Rodier-Goud, Maguy, Barbosa-Neto, Jose Fernandes, Sabot, Francois, Kudrna, Dave, Ammiraju, Jetty Siva S., Schuster, Stephan C., Carlson, John E., Sallet, Erika, Schiex, Thomas, Dievart, Anne, Kramer, Melissa, Gelley, Laura, Shi, Zi ... Lanaud, Claire (2011). The genome of Theobroma cacao. Nature Genetics, 43 (2), 101-108. doi: 10.1038/ng.736
Gill, Navdeep, SanMiguel, Phillip, Dhillon, Braham Deep Singh, Abernathy, Brian, Kim, HyeRan, Stein, Lincoln, Ware, Doreen, Wing, Rod and Jackson, Scott A. (2010). Dynamic Oryza genomes: repetitive DNA sequences as genome modeling agents. Rice, 3 (4), 251-269. doi: 10.1007/s12284-010-9054-7
Zuccolo, Andrea, Sebastian, Aswathy, Yu, Yeisoo, Jackson, Scott, Rounsley, Steve, Billheimer, Dean and Wing, Rod A. (2010). Assessing the extent of substitution rate variation of retrotransposon Long Terminal Repeat sequences in Oryza sativa and Oryza glaberrima. Rice, 3 (4), 242-250. doi: 10.1007/s12284-010-9046-7
Ammiraju, Jetty S.S., Song, Xiang, Luo, Meizhong, Sisneros, Nicholas, Angelova, Angelina, Kudrna, David, Kim, Hyeran, Yu, Yeisoo, Goicoechea, Jose Luis, Lorieux, Mathias, Kurata, Nori, Brar, Darshan, Ware, Doreen, Jackson, Scott and Wing, Rod 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), 536-543. doi: 10.1270/jsbbs.60.536
Henry, Robert J., Rice, Nicole, Waters, Daniel L. E., Kasem, Shabana, Ishikawa, Ryuji, Hao, Yin, Dillon, Sally, Crayn, Darren, Wing, Rod and Vaughan, Duncan (2010). Australian Oryza: utility and conservation. Rice, 3 (4), 235-241. doi: 10.1007/s12284-009-9034-y
Febrer, Melanie, Goicoechea, Jose Luis, Wright, Jonathan, McKenzie, Neil, Song, Xiang, Lin, Jinke, Collura, Kristi, Wissotski, Marina, Yu, Yeisoo, Ammiraju, Jetty S. S., Wolny, Elzbieta, Idziak, Dominika, Betekhtin, Alexander, Kudrna, Dave, Hasterok, Robert, Wing, Rod A. and Bevan, Michael W. (2010). An integrated physical, genetic and cytogenetic map of Brachypodium distachyon, a model system for grass research. PLoS ONE, 5 (10) e13461, e13461. doi: 10.1371/journal.pone.0013461
Sanyal, Abhijit, Ammiraju, Jetty S. S., Lu, Fei, Yu, Yeisoo, Rambo, Teri, Currie, Jennifer, Kollura, Kristi, Kim, Hye-Ran, Chen, Jinfeng, Ma, Jianxin, San Miguel, Phillip, Mingsheng, Chen, Wing, Rod A. and Jackson, Scott A. (2010). Orthologous comparisons of the Hd1 region across genera reveal hd1 gene lability within diploid oryza species and disruptions to microsynteny in sorghum. Molecular Biology and Evolution, 27 (11), 2487-2506. doi: 10.1093/molbev/msq133
Geraldes, Armando, Rambo, Teri, Wing, Rod A., Ferrand, Nuno and Nachman, Michael W. (2010). Extensive gene conversion drives the concerted evolution of paralogous copies of the SRY gene in European rabbits. Molecular Biology and Evolution, 27 (11), 2437-2440. doi: 10.1093/molbev/msq139
Ammiraju, Jetty S. S., Fan, Chuanzhu, Yu, Yeisoo, Song, Xiang, Cranston, Karen A., Pontaroli, Ana Clara, Lu, Fei, Sanyal, Abhijit, Jiang, Ning, Rambo, Teri, Currie, Jennifer, Collura, Kristi, Talag, Jayson, Bennetzen, Jeffrey L., Chen, Mingsheng, Jackson, Scott and Wing, Rod A. (2010). Spatio-temporal patterns of genome evolution in allotetraploid species of the genus Oryza. Plant Journal, 63 (3), 430-442. doi: 10.1111/j.1365-313X.2010.04251.x
Schmutz, Jeremy, Cannon, Steven B., Schlueter, Jessica, Ma, Jianxin, Mitros, Therese, Nelson, William, Hyten, David L., Song, Qijian, Thelen, Jay J., Cheng, Jianlin, Xu, Dong, Hellsten, Uffe, May, Gregory D., Yu, Yeisoo, Sakurai, Tetsuya, Umezawa, Taishi, Bhattacharyya, Madan K., Sandhu, Devinder, Valliyodan, Babu, Lindquist, Erika, Peto, Myron, Grant, David, Shu, Shengqiang, Goodstein, David, Barry, Kerrie, Futrell-Griggs, Montona, Abernathy, Brian, Du, Jianchang, Tian, Zhixi ... Jackson, Scott A. (2010). Erratum: Genome sequence of the palaeopolyploid soybean (Nature (2010) 463 (178-183)). Nature, 465 (7294), 120-120. doi: 10.1038/nature08957
Schmutz, Jeremy, Cannon, Steven B., Schlueter, Jessica, Ma, Jianxin, Mitros, Therese, Nelson, William, Hyten, David L., Song, Qijian, Thelen, Jay J., Cheng, Jianlin, Xu, Dong, Hellsten, Uffe, May, Gregory D., Yu, Yeisoo, Sakurai, Tetsuya, Umezawa, Taishi, Bhattacharyya, Madan K., Sandhu, Devinder, Valliyodan, Babu, Lindquist, Erika, Peto, Myron, Grant, David, Shu, Shengqiang, Goodstein, David, Barry, Kerrie, Futrell-Griggs, Montona, Abernathy, Brian, Du, Jianchang, Tian, Zhixi ... Jackson, Scott A. (2010). Genome sequence of the palaeopolyploid soybean. Nature, 463 (7278), 178-183. doi: 10.1038/nature08670
Gao, Dongying, Gill, Navdeep, Kim, Hye-Ran, Walling, Jason G, Zhang, Wenli, Fan, Chuanzhu, Yu, Yeisoo, Ma, Jianxin, Sanmiguel, Phillip, Jiang, Ning, Cheng, Zhukuan, Wing, Rod A., Jiang, Jiming and Jackson, Scott A. (2009). A lineage-specific centromere retrotransposon in Oryza brachyantha. Plant Journal, 60 (5), 820-831. doi: 10.1111/j.1365-313X.2009.04005.x
Schnable, Patrick S., Ware, Doreen, Fulton, Robert S., Stein, Joshua C., Wei, Fusheng, Pasternak, Shiran, Liang, Chengzhi, Zhang, Jianwei, Fulton, Lucinda, Graves, Tina A., Minx, Patrick, Reily, Amy Denise, Courtney, Laura, Kruchowski, Scott S., Tomlinson, Chad, Strong, Cindy, Delehaunty, Kim, Fronick, Catrina, Courtney, Bill, Rock, Susan M., Belter, Eddie, Du, Feiyu, Kim, Kyung, Abbott, Rachel M., Cotton, Marc, Levy, Andy, Marchetto, Pamela, Ochoa, Kerri, Jackson, Stephanie M. ... Wilson, Richard K. (2009). The B73 maize genome: Complexity, diversity, and dynamics. Science, 326 (5956), 1112-1115. doi: 10.1126/science.1178534
Zhou, Shiguo, Wei, Fusheng, Nguyen, John, Bechner, Mike, Potamousis, Konstantinos, Goldstein, Steve, Pape, Louise, Mehan, Michael R., Churas, Chris, Pasternak, Shiran, Forrest, Dan K., Wise, Roger, Ware, Doreen, Wing, Rod A., Waterman, Michael S., Livny, Miron and Schwartz, David C. (2009). A single molecule scaffold for the maize genome. PLoS Genetics, 5 (11) e1000711, e1000711. doi: 10.1371/journal.pgen.1000711
Wei, Fusheng, Zhang, Jianwei, Zhou, Shiguo, He, Ruifeng, Schaeffer, Mary, Collura, Kristi, Kudrna, David, Faga, Ben P., Wissotski, Marina, Golser, Wolfgang, Rock, Susan M., Graves, Tina A., Fulton, Robert S., Coe, Ed, Schnable, Patrick S., Schwartz, David C., Ware, Doreen, Clifton, Sandra W., Wilson, Richard K. and Wing, Rod A. (2009). The physical and genetic framework of the maize B73 genome. PLoS Genetics, 5 (11) e1000715, e1000715. doi: 10.1371/journal.pgen.1000715
Wei, Fusheng, Stein, Joshua C., Liang, Chengzhi, Zhang, Jianwei, Fulton, Robert S., Baucom, Regina S., De Paoli, Emanuele, Zhou, Shiguo, Yang, Lixing, Han, Yujun, Pasternak, Shiran, Narechania, Apurva, Zhang, Lifang, Yeh, Cheng-Ting, Ying, Kai, Nagel, Dawn H., Collura, Kristi, Kudrna, David, Currie, Jennifer, Lin, Jinke, Kim, HyeRan, Angelova, Angelina, Scara, Gabriel, Wissotski, Marina, Golser, Wolfgang, Courtney, Laura, Kruchowski, Scott, Graves, Tina A., Rock, Susan M. ... Wing, Rod A. (2009). Detailed analysis of a contiguous 22-Mb region of the maize genome. PLoS Genetics, 5 (11) e1000728, e1000728. doi: 10.1371/journal.pgen.1000728
Cranston, Karen A., Hurwitz, Bonnie, Ware, Doreen, Stein, Lincoln and Wing, Rod A. (2009). Species trees from highly incongruent gene trees in rice. Systematic Biology, 58 (5), 489-500. doi: 10.1093/sysbio/syp054
Nah, Gyoungju, Pagliarulo, Christopher L., Mohr, Peter G., Luo, Meizhong, Sisneros, Nick, Yu, Yeisoo, Collura, Kristi, Currie, Jennifer, Goicoechea, Jose Luis, Wing, Rod A. and Schumaker, Karen S. (2009). Comparative sequence analysis of the SALT OVERLY SENSITIVE1 orthologous region in Thellungiella halophila and Arabidopsis thaliana. Genomics, 94 (3), 196-203. doi: 10.1016/j.ygeno.2009.05.007
Degnan, Patrick H., Yu, Yeisoo, Sisneros, Nicholas, Wing, Rod A. and Moran, Nancy A. (2009). Hamiltonella defensa, genome evolution of protective bacterial endosymbiont from pathogenic ancestors. Proceedings of the National Academy of Sciences of the United States of America, 106 (22), 9063-9068. doi: 10.1073/pnas.0900194106
Rounsley, Steve, Marri, Pradeep Reddy, Yu, Yeisoo, He, Ruifeng, Sisneros, Nick, Goicoechea, Jose Luis, Lee, So Jeong, Angelova, Angelina, Kudrna, Dave, Luo, Meizhong, Affourtit, Jason, Desany, Brian, Knight, James, Niazi, Faheem, Egholm, Michael and Wing, Rod A. (2009). De novo next generation sequencing of plant genomes. Rice, 2 (1), 35-43. doi: 10.1007/s12284-009-9025-z
Lu, Fei, Ammiraju, Jetty S. S., Sanyal, Abhijit, Zhang, Shengli, Son, Rentao, Chen, Jinfeng, Li, Guisheng, Sui, Yi, Song, Xiang, Cheng, Zhukuan, De Oliveira, Antonio Costa, Bennetzen, Jeffrey L., Jackson, Scott A., Wing, Rod A. and Chena, Mingsheng (2009). Comparative sequence analysis of MONOCULM1-orthologous regions in 14 Oryza genomes. Proceedings of the National Academy of Sciences of the United States of America, 106 (6), 2071-2076. doi: 10.1073/pnas.0812798106
Nelson, William, Luo, Meizhong, Ma, Jianxin, Estep, Matt, Estill, James, He, Ruifeng, Talag, Jayson, Sisneros, Nicholas, Kudrna, David, Kim, HyeRan, Ammiraju, Jetty S.S., Collura, Kristi, Bharti, Arvind K., Messing, Joachim, Wing, Rod A., SanMiguel, Phillip, Bennetzen, Jeffrey L. and Soderlund, Carol (2008). Methylation-sensitive linking libraries enhance gene-enriched sequencing of complex genomes and map DNA methylation domains. BMC Genomics, 9 (1) 621. doi: 10.1186/1471-2164-9-621
Meier, Stuart, Gehring, Chris, MacPherson, Cameron Ross, Kaur, Mandeep, Maqungo, Monique, Reuben, Sheela, Muyanga, Samson, Shih, Ming-Der, Wei, Fu-Jin, Wanchana, Samart, Mauleon, Ramil, Radovanovic, Aleksandar, Bruskiewich, Richard, Tanaka, Tsuyoshi, Mohanty, Bijayalaxmi, Itoh, Takeshi, Wing, Rod, Gojobori, Takashi, Sasaki, Takuji, Swarup, Sanjay, Hsing, Yue-ie and Bajic, Vladimir B. (2008). The promoter signatures in rice LEA genes can be used to build a co-expressing LEA gene network. Rice, 1 (2), 177-187. doi: 10.1007/s12284-008-9017-4
Ammiraju, Jetty S. S., Lu, Fei, Sanyal, Abhijit, Yu, Yeisoo, Song, Xiang, Jiang, Ning, Pontaroli, Ana Clara, Rambo, Teri, Currie, Jennifer, Collura, Kristi, Talag, Jayson, Fan, Chuanzhu, Goicoechea, Jose Luis, Zuccolo, Andrea, Chen, Jinfeng, Bennetzen, Jeffrey L., Chen, Mingsheng, Jackson, Scott and Wing, Rod A. (2008). Dynamic evolution of Oryza genomes is revealed by comparative genomic analysis of a genus-wide vertical data set. Plant Cell, 20 (12), 3191-3209. doi: 10.1105/tpc.108.063727
Zuccolo, Andrea, Ammiraju, Jetty S. S., Kim, HyeRan, Sanyal, Abhijit, Jackson, Scott and Wing, Rod A. (2008). Rapid and differential proliferation of the Ty3-Gypsy LTR retrotransposon Atlantys in the genus Oryza. Rice, 1 (1), 85-99. doi: 10.1007/s12284-008-9002-y
Le Cunff, Loïc, Garsmeur, Olivier, Raboin, Louis Marie, Pauquet, Jérome, Telismart, Hugues, Selvi, Athiappan, Grivet, Laurent, Philippe, Romain, Begum, Dilara, Deu, Monique, Costet, Laurent, Wing, Rod, Glaszmann, Jean Christophe and D'Hont, Angélique (2008). Diploid/polyploid syntenic shuttle mapping and haplotype-specific chromosome walking toward a rust resistance gene (Bru1) in highly polyploid sugarcane (2n ∼ 12x ∼ 115). Genetics, 180 (1), 649-660. doi: 10.1534/genetics.108.091355
Fan, Chuanzhu, Zhang, Yong, Yu, Yeisoo, Rounsley, Steve, Long, Manyuan and Wing, Rod A. (2008). The subtelomere of Oryza sativa chromosome 3 short arm as a hot bed of new gene origination in rice. Molecular Plant, 1 (5), 839-850. doi: 10.1093/mp/ssn050
Wei, Fusheng and Wing, Rod A. (2008). A fruitful outcome to the papaya genome project. Genome Biology, 9 (6) 227. doi: 10.1186/gb-2008-9-6-227
Shoemaker, Randy C., Grant, David, Olson, Terry, Warren, Wesley C., Wing, Rod, Yu, Yeisoo, Kim, Hyeran, Cregan, Perry, Joseph, Bindu, Futrell-Griggs, Montona, Nelson, Will, Davito, Jon, Walker, Jason, Wallis, John, Kremitski, Colin, Scheer, Debbie, Clifton, Sandra W., Graves, Tina, Nguyen, Henry, Wu, Xiaolei, Luo, Mingcheng, Dvorak, Jan, Nelson, Rex, Cannon, Steven, Tomkins, Jeff, Schmutz, Jeremy, Stacey, Gary and Jackson, Scott (2008). Microsatellite discovery from BAC end sequences and genetic mapping to anchor the soybean physical and genetic maps. Genome, 51 (4), 294-302. doi: 10.1139/G08-010
Soltis, Douglas E., Albert, Victor A., Leebens-Mack, Jim, Palmer, Jeffrey D., Wing, Rod A., dePamphilis, Claude W., Ma, Hong, Carlson, John E., Altman, Naomi, Kim, Sangtae, Kerr, P. Kerr, Zuccolo, Andrea and Soltis, Pamela S. (2008). The Amborella genome: An evolutionary reference for plant biology. Genome Biology, 9 (3) 402. doi: 10.1186/gb-2008-9-3-402
Kim, HyeRan, Hurwitz, Bonnie, Yu, Yeisoo, Collura, Kristi, Gill, Navdeep, SanMiguel, Phillip, Mullikin, James C., Maher, Christopher, Nelson, William, Wissotski, Marina, Braidotti, Michele, Kudrna, David, Goicoechea, José Luis, Stein, Lincoln, Ware, Doreen, Jackson, Scott A., Soderlund, Carol and Wing, Rod A. (2008). Construction, alignment and analysis of twelve framework physical maps that represent the ten genome types of the genus Oryza. Genome Biology, 9 (2) R45. doi: 10.1186/gb-2008-9-2-r45
Qu, Shaohong, Desai, Aparna, Wing, Rod and Sundaresan, Venkatesan (2008). A versatile transposon-based activation tag vector system for functional genomics in cereals and other monocot plants. Plant Physiology, 146 (1), 189-199. doi: 10.1104/pp.107.111427
Clark, Andrew G., Eisen, Michael B., Smith, Douglas R., Bergman, Casey M., Oliver, Brian, Markow, Therese A., Kaufman, Thomas C., Kellis, Manolis, Gelbart, William, Iyer, Venky N., Pollard, Daniel A., Sackton, Timothy B., Larracuente, Amanda M., Singh, Nadia D., Abad, Jose P., Abt, Dawn N., Adryan, Boris, Aguade, Montserrat, Akashi, Hiroshi, Anderson, Wyatt W., Aquadro, Charles F., Ardell, David H., Arguello, Roman, Artieri, Carlo G., Barbash, Daniel A., Barker, Daniel, Barsanti, Paolo, Batterham, Phil, Batzoglou, Serafim ... MacCallum, Iain (2007). Evolution of genes and genomes on the Drosophila phylogeny. Nature, 450 (7167), 203-218. doi: 10.1038/nature06341
Zuccolo, Andrea, Sebastian, Aswathy, Talag, Jayson, Yu, Yeisoo, Kim, HyeRan, Collura, Kristi, Kudrna, Dave and Wing, Rod A. (2007). Transposable element distribution, abundance and role in genome size variation in the genus Oryza. BMC Evolutionary Biology, 7 (1) 152. doi: 10.1186/1471-2148-7-152
Chen, Kai-Yi, Cong, Bin, Wing, Rod, Vrebalov, Julia and Tanksley, Steven D. (2007). Changes in regulation of a transcription factor lead to autogamy in cultivated tomatoes. Science, 318 (5850), 643-645. doi: 10.1126/science.1148428
Ma, Jianxin, Wing, Rod A., Bennetzen, Jeffrey L. and Jackson, Scott A. (2007). Evolutionary history and positional shift of a rice centromere. Genetics, 177 (2), 1217-1220. doi: 10.1534/genetics.107.078709
Liang, Haiying, Fang, Eric G., Tomkins, Jeffrey P., Luo, Meizhong, Kudrna, David, Kim, Hye Ran, Arumuganathan, K., Zhao, Shaying, Leebens-Mack, James, Schlarbaum, Scott E., Banks, Jo Ann, Depamphilis, Claude W., Mandoli, Dina F., Wing, Rod A. and Carlson, John E. (2007). Development of a BAC library for yellow-poplar (Liriodendron tulipifera) and the identification of genes associated with flower development and lignin biosynthesis. Tree Genetics and Genomes, 3 (3), 215-225. doi: 10.1007/s11295-006-0057-x
Wei, Fusheng, Coe, Ed, Nelson, William, Bharti, Arvind K., Engler, Fred, Butler, Ed, Kim, HyeRan, Goicoechea, Jose Luis, Chen, Mingsheng, Lee, Seunghee, Fuks, Galina, Sanchez-Villeda, Hector, Schroeder, Steven, Fang, Zhiwei, McMullen, Michael, Davis, Georgia, Bowers, John E., Paterson, Andrew H., Schaeffer, Mary, Gardiner, Jack, Cone, Karen, Messing, Joachim, Soderlund, Carol and Wing, Rod A. (2007). Physical and genetic structure of the maize genome reflects its complex evolutionary history. PLoS Genetics, 3 (7), 1254-1263. doi: 10.1371/journal.pgen.0030123
Grover, Corrinne E., Kim, Hyeran, Wing, Rod A., Paterson, Andrew H. and Wendel, Jonathan F. (2007). Microcolinearity and genome evolution in the AdhA region of diploid and polyploid cotton (Gossypium). Plant Journal, 50 (6), 995-1006. doi: 10.1111/j.1365-313X.2007.03102.x
Kim, HyeRan, San Miguel, Phillip, Nelson, William, Collura, Kristi, Wissotski, Marina, Walling, Jason G., Jun, Pyo Kim, Jackson, Scott A., Soderlund, Carol and Wing, Rod A. (2007). Comparative physical mapping between Oryza sativa (AA genome type) and O. punctata (BB genome type). Genetics, 176 (1), 379-390. doi: 10.1534/genetics.106.068783
Gowda, Malali, Venu, R. C., Li, Huameng, Jantasuriyarat, Chatchawan, Chen, Songbiao, Bellizzi, Maria, Pampanwar, Vishal, Kim, Hyeran, Dean, Ralph A., Stahlberg, Eric, Wing, Rod, Soderlund, Cari and Wang, Guo-Liang (2007). Magnaporthe grisea infection triggers RNA variation and antisense transcript expression in rice. Plant Physiology, 144 (1), 524-533. doi: 10.1104/pp.107.095653
Ma, Jianxin, Wing, Rod A., Bennetzen, Jeffrey L. and Jackson, Scott A. (2007). Plant centromere organization: a dynamic structure with conserved functions. Trends in Genetics, 23 (3), 134-139. doi: 10.1016/j.tig.2007.01.004
Jung, Jinwook, Won, So Youn, Suh, Seok Cheol, Kim, Hyeran, Wing, Rod, Jeong, Yeonhwa, Hwang, Ingyu and Kim, Minkyun (2007). The barley ERF-type transcription factor HvRAF confers enhanced pathogen resistance and salt tolerance in Arabidopsis. Planta, 225 (3), 575-588. doi: 10.1007/s00425-006-0373-2
Itoh, Takeshi, Tanaka, Tsuyoshi, Barrero, Roberto A., Yamasaki, Chisato, Fujii, Yasuyuki, Hilton, Phillip B., Antonio, Baltazar A., Aono, Hideo, Apweiler, Rolf, Bruskiewich, Richard, Bureau, Thomas, Burr, Frances, De Oliveira, Antonio Costa, Fuks, Galina, Habara, Takuya, Haberer, Georg, Han, Bin, Harada, Erimi, Hiraki, Aiko T., Hirochika, Hirohiko, Hoen, Douglas, Hokari, Hiroki, Hosokawa, Satomi, Hsing, Yue-Ie, Ikawa, Hiroshi, Ikeo, Kazuho, Imanishi, Tadashi, Ito, Yukiyo, Jaiswal, Pankaj ... Sasaki, Takuji (2007). Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana: The Rice Annotation Project. Genome Research, 17 (2), 175-183. doi: 10.1101/gr.5509507
Nelson, William M., Dvorak, Jan, Luo, Ming-Cheng, Messing, Joachim, Wing, Rod A. and Soderlund, Carol (2007). Efficacy of clone fingerprinting methodologies. Genomics, 89 (1), 160-165. doi: 10.1016/j.ygeno.2006.08.008
Gowda, Malali, Venu, Reddyvari-Channa, Raghupathy, Mohan B., Nobuta, Kan, Li, Huameng, Wing, Rod, Stahlberg, Eric, Couglan, Sean, Haudenschild, Christian D., Dean, Ralph, Nahm, Baek-Hie, Meyers, Blake C. and Wang, Guo-Liang (2006). Deep and comparative analysis of the mycelium and appressorium transcriptomes of Magnaporthe grisea using MPSS, RL-SAGE, and oligoarray methods. BMC Genomics, 7 (1) 310. doi: 10.1186/1471-2164-7-310
Hawkins, Jennifer S., Kim, HyeRan, Nason, John D., Wing, Rod A. and Wendel, Jonathan F. (2006). Differential lineage-specific amplification of transposable elements is responsible for genome size variation in Gossypium. Genome Research, 16 (10), 1252-1261. doi: 10.1101/gr.5282906
Soderlund, Carol, Haller, Karl, Pampanwar, Vishal, Ebbole, Daniel, Farman, Mark, Orbach, Marc J., Wang, Guo-Liang, Wing, Rod, Xu, Jin-Rong, Brown, Doug, Mitchell, Thomas and Dean, Ralph (2006). MGOS: a resource for studying Magnaporthe grisea and Oryza sativa interactions. Molecular Plant-Microbe Interactions, 19 (10), 1055-1061. doi: 10.1094/MPMI-19-1055
Cunningham, Charles, Hikima, Jun-Ichi, Jenny, Matthew J., Chapman, Robert W., Fang, Guang-Chen, Saski, Chris, Lundqvist, Mats L., Wing, Rod A., Cupit, Pauline M., Gross, Paul S., Warr, Greg W. and Tomkins, Jeff P. (2006). New resources for marine genomics: Bacterial artificial chromosome libraries for the eastern and pacific oysters (Crassostrea virginica and C. gigas). Marine Biotechnology, 8 (5), 521-533. doi: 10.1007/s10126-006-6013-9
Piegu, Benoit, Guyot, Romain, Picault, Nathalie, Roulin, Anne, Saniyal, Abhijit, Kim, Hyeran, Collura, Kristi, Brar, Darshan S., Jackson, Scott, Wing, Rod A. and Panaud, Olivier (2006). Doubling genome size without polyploidization: dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice. Genome Research, 16 (10), 1262-1269. doi: 10.1101/gr.5290206
Yan, Huihuang, Ito, Hidetaka, Nobuta, Kan, Ouyang, Shu, Jin, Weiwei, Tian, Shulan, Lu, Cheng, Venu, R. C., Wang, Guo-Liang, Green, Pamela J., Wing, Rod A., Buell, C. Robin, Meyers, Blake C. and Jiang, Jiming (2006). Genomic and genetic characterization of rice Cen3 reveals extensive transcription and evolutionary implications of a complex centromere. Plant Cell, 18 (9), 2123-2133. doi: 10.1105/tpc.106.043794
Hass-Jacobus, Barbara L., Futrell-Griggs, Montona, Abernathy, Brian, Westerman, Rick, Goicoechea, Jose-Luis, Stein, Joshua, Klein, Patricia, Hurwitz, Bonnie, Zhou, Bin, Rakhshan, Fariborz, Sanyal, Abhijit, Gill, Navdeep, Lin, Jer-Young, Walling, Jason G., Luo, Mei Zhong, Ammiraju, Jetty Siva S., Kudrna, Dave, Kim, Hye Ran, Ware, Doreen, Wing, Rod A., San Miguel, Phillip and Jackson, Scott 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 (1) 199. doi: 10.1186/1471-2164-7-199
Luo, Meizhong, Kim, HyeRan, Kudrna, Dave, Sisneros, Nicholas B., Lee, So-Jeong, Mueller, Christopher, Collura, Kristi, Zuccolo, Andrea, Buckingham, Bryan, Grim, Suzanne M., Yanagiya, Kazuyo, Inoko, Hidetoshi, Shiina, Takashi, Flajnik, Martin F., Wing, Rod A. and Ohta, Yuko (2006). Construction of a nurse shark (Ginglymostoma cirratum) bacterial artificial chromosome (BAC) library and a preliminary genome survey. BMC Genomics, 7 (1) 106. doi: 10.1186/1471-2164-7-106
Luo, Meizhong, Yu, Yeisoo, Kim, Hyeran, Kudrna, Dave, Itoh, Yuichiro, Agate, Robert J., Melamed, Esther, Goicoechea, José L., Talag, Jayson, Mueller, Christopher, Wang, Wenming, Currie, Jennifer, Sisneros, Nicholas B., Wing, Rod A. and Arnold, Arthur P. (2006). Utilization of a zebra finch BAC library to determine the structure of an avian androgen receptor genomic region. Genomics, 87 (1), 181-190. doi: 10.1016/j.ygeno.2005.09.005
Vroh Bi, I., McMullen, M. D., Sanchez-Villeda, H., Schroeder, S., Gardiner, J., Polacco, M., Soderlund, C., Wing, R., Fang, Z. and Coe Jr., E. H. (2006). Single nucleotide polymorphisms and insertion-deletions for genetic markers and anchoring the maize fingerprint contig physical map. Crop Science, 46 (1), 12-21. doi: 10.2135/cropsci2004.0706
Ammiraju, Jetty S.S., Luo, Meizhong, Goicoechea, José L., Wang, Wenming, Kudrna, Dave, Mueller, Christopher, Talag, Jayson, Kim, HyeRan, Sisneros, Nicholas B., Blackmon, Barbara, Fang, Eric, Tomkins, Jeffery B., Brar, Darshan, MacKill, David, McCouch, Susan, Kurata, Nori, Lambert, Georgina, Galbraith, David W., Arumuganathan, K., Rao, Kiran, Walling, Jason G., Gill, Navdeep, Yu, Yeisoo, SanMiguel, Phillip, Soderlund, Carol, Jackson, Scott and Wing, Rod A. (2006). The Oryza bacterial artificial chromosome library resource: Construction and analysis of 12 deep-coverage large-insert BAC libraries that represent the 10 genome types of the genus Oryza. Genome Research, 16 (1), 140-147. doi: 10.1101/gr.3766306
Nelson, William M., Bharti, Arvind K., Butler, Ed, Wei, Fusheng, Fuks, Galina, Kim, HyeRan, Wing, Rod A., Messing, Joachim and Soderlund, Carol (2005). Whole-genome validation of high-information-content fingerprinting. Plant Physiology, 139 (1), 27-38. doi: 10.1104/pp.105.061978
Jantasuriyarat, Chatchawan, Gowda, Malali, Haller, Karl, Hatfield, Jamie, Lu, Guodong, Stahlberg, Eric, Zhou, Bo, Li, Huameng, Kim, HyRan, Yu, Yeisoo, Dean, Ralph A., Wing, Rod A., Soderlund, Carol and Wang, Guo-Liang (2005). Large-scale identification of expressed sequence tags involved in rice and rice blast fungus interaction. Plant Physiology, 138 (1), 105-115. doi: 10.1104/pp.104.055624
Haberer, Georg, Young, Sarah, Bharti, Arvind K., Gundlach, Heidrun, Raymond, Christina, Fuks, Galina, Butler, Ed, Wing, Rod A., Rounsley, Steve, Birren, Bruce, Nusbaum, Chad, Mayer, Klaus F.X. and Messing, Joachim (2005). Structure and architecture of the maize genome. Plant Physiology, 139 (4), 1612-1624. doi: 10.1104/pp.105.068718
Ammiraju, Jetty S. S., Yu, Yeisoo, Luo, Meizhong, Kudrna, Dave, Kim, HyeRan, Goicoechea, Jose L., Katayose, Yuichi, Matsumoto, Takashi, Wu, Jianzhong, Sasaki, Takuji and Wing, Rod A. (2005). Random sheared fosmid library as a new genomic tool to accelerate complete finishing of rice (Oryza sativa spp. Nipponbare) genome sequence: sequencing of gap-specific fosmid clones uncovers new euchromatic portions of the genome. Theoretical and Applied Genetics, 111 (8), 1596-1607. doi: 10.1007/s00122-005-0091-3
Pratt, Lee H., Liang, Chun, Shah, Manish, Sun, Feng, Wang, Haiming, Reid, St. Patrick, Gingle, Alan R., Paterson, Andrew H., Wing, Rod, Dean, Ralph, Klein, Robert, Nguyen, Henry T., Ma, Hong-Mei, Zhao, Xin, Morishige, Daryl T., Mullet, John E. and Cordonnier-Pratt, Marie-Michèle (2005). Sorghum expressed sequence tags identify signature genes for drought, pathogenesis, and skotomorphogenesis from a milestone set of 16,801 unique transcripts. Plant Physiology, 139 (2), 869-884. doi: 10.1104/pp.105.066134
Choisne, Nathalie, Demange, Nadia, Orjeda, Gisela, Samain, Sylvie, D'Hont, Angélique, Cattolico, Laurence, Pelletier, Eric, Couloux, Arnaud, Segurens, Béatrice, Wincker, Patrick, Scarpelli, Claude, Weissenbach, Jean, Salanoubat, Marcel, Singh, Nagendra K., Mohapatra, Trilochan, Sharma, Tilak R., Gaikwad, Kishor, Singh, Archana, Dalal, Vivek, Srivastava, Subodh K., Dixit, Anupam, Pal, Ajit K., Ghazi, Irfan A., Yadav, Mahavir, Pandit, Awadhesh, Bhargava, Ashutosh, Sureshbabu, K., Dixit, Rekha, Singh, Harvinder ... Messing, Joachim (2005). The sequence of rice chromosomes 11 and 12, rich in disease resistance genes and recent gene duplications. BMC Biology, 3 (1) 20. doi: 10.1186/1741-7007-3-20
Buell, C. Robin, McCombie, W. Richard, Wing, Rod A., Yuan, Qiaoping, Ouyang, Shu, Liu, Jia, Zhu, Wei, Wang, Aihui, Maiti, Rama, Haas, Brian, Wortman, Jennifer, Pertea, Mihaela, Jones, Kristine M., Kim, Mary, Overton, Larry, Tsitrin, Tamara, Fadrosh, Douglas, Bera, Jayati, Weaver, Jayati, Jin, Shaohua, Johri, Shivani, Reardon, Matt, Webb, Kristen, Hill, Jessica, Moffat, Kelly, Tallon, Luke, Van Aken, Susan, Lewis, Matthew, Utterback, Teresa ... Jackson, Scott (2005). Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species. The Rice Chromosome 3 Sequencing Consortium. Genome Research, 15 (9), 1284-1291. doi: 10.1101/gr.3869505
Wing, Rod (2005). Plant Molecular Biology: Editorial. Plant Molecular Biology, 59 (1), vii-vii. doi: 10.1007/s11103-005-2196-0
Wing, Rod A., Ammiraju, Jetty S.S., Luo, Meizhong, Kim, HyeRan, Yu, Yeisoo, Kudrna, Dave, Goicoechea, Jose L., Wang, Wenming, Nelson, Will, Rao, Kiran, Brar, Darshan, Mackill, Dave J., Han, Bin, Soderlund, Cari, Stein, Lincoln, SanMiguel, Phillip and Jackson, Scott (2005). The Oryza map alignment project: The golden path to unlocking the genetic potential of wild rice species. Plant Molecular Biology, 59 (1), 53-62. doi: 10.1007/s11103-004-6237-x
Matsumoto, Takashi, Wu, Jianzhong, Kanamori, Hiroyuki, Katayose, Yuichi, Fujisawa, Masaki, Namiki, Nobukazu, Mizuno, Hiroshi, Yamamoto, Kimiko, Antonio, Baltazar A., Baba, Tomoya, Sakata, Katsumi, Nagamura, Yoshiaki, Aoki, Hiroyoshi, Arikawa, Koji, Arita, Kohei, Bito, Takahito, Chiden, Yoshino, Fujitsuka, Nahoko, Fukunaka, Rie, Hamada, Masao, Harada, Chizuko, Hayashi, Akiko, Hijishita, Saori, Honda, Mikiko, Hosokawa, Satomi, Ichikawa, Yoko, Idonuma, Atsuko, Iijima, Masumi, Ikeda, Michiko ... Burr, Benjamin (2005). The map-based sequence of the rice genome. Nature, 436 (7052), 793-800. doi: 10.1038/nature03895
Yang, Tae-Jin, Yu, Yeisoo, Chang, Song-Bin, De Jong, Hans, Oh, Chang-Sik, Ahn, Sang-Nag, Fang, Eric and Wing, Rod A. (2005). Toward closing rice telomere gaps: Mapping and sequence characterization of rice subtelomere regions. Theoretical and Applied Genetics, 111 (3), 467-478. doi: 10.1007/s00122-005-2034-4
Yang, Tae-Jin, Lee, Seunghee, Chang, Song-Bin, Yu, Yeisoo, de Jong, Hans and Wing, Rod A. (2005). In-depth sequence analysis of the tomato chromosome 12 centromeric region: Identification of a large CAA block and characterization of pericentromere retrotranposons. Chromosoma, 114 (2), 103-117. doi: 10.1007/s00412-005-0342-8
Wang, Wenming, Tanurdzic, Milos, Luo, Meizhong, Sisneros, Nicholas, Kim, Hye Ran, Weng, Jing-Ke, Kudrna, Dave, Mueller, Christopher, Arumuganathan, K., Carlson, John, Chapple, Clint, de Pamphilis, Claude, Mandoli, Dina, Tomkins, Jeff, Wing, Rod A. and Banks, Jo Ann (2005). Construction of a bacterial artificial chromosome library from the spikemoss Selaginella moellendorffii: a new resource for plant comparative genomics. BMC Plant Biology, 5 (1) 10, 10.1-10.8. doi: 10.1186/1471-2229-5-10
Horn, Renate, Lecouls, Anne-Claire, Callahan, Ann, Dandekar, Abhaya, Garay, Lilibeth, McCord, Per, Howad, Werner, Chan, Helen, Verde, Ignazio, Main, Doreen, Jung, Sook, Georgi, Laura, Forrest, Sam, Mook, Jennifer, Zhebentyayeva, Tatyana, Yu, Yeisoo, Hye, Ran Kim, Jesudurai, Christopher, Sosinski, Bryon, Arús, Pere, Baird, Vance, Parfitt, Dan, Reighard, Gregory, Scorza, Ralph, Tomkins, Jeffrey, Wing, Rod and Abbott, Albert Glenn (2005). Candidate gene database and transcript map for peach, a model species for fruit trees. Theoretical and Applied Genetics, 110 (8), 1419-1428. doi: 10.1007/s00122-005-1968-x
Conference Paper
Adema, Coen M., Luo, Mei-Zhong, Hanelt, Ben, Hertel, Lynn A., Marshall, Jennifer J., Zhang, Si-Ming, DeJong, Randall J., Kim, Hye-Ran, Kudrna, David, Wing, Rod A., Soderlund, Cari, Knight, Matty, Lewis, Fred A., Caldeira, Roberta Lima, Jannotti-Passos, Liana K., Carvalho, Omar Dos Santos and Loker, Eric S. (2006). A bacterial artificial chromosome library for Biomphalaria glabrata, intermediate snail host of Schistosoma mansoni. Fundacao Oswaldo Cruz. doi: 10.1590/S0074-02762006000900027