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Publications : Publications by year
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2018 2017 2016 2015 2014 2013 2012 2011 2010 2009 2008 2007 2006 2005 2004 2003 2002 2001-1988

Selected Publications:

Fan, C., J. Walling, J. Zhang, J. Jiang, and R.A. Wing. Conservation and purifying selection of transcribed genes in recombination-free centromeres. 2011. Plant Cell.

Ammiraju, J.S.S, X. Song, M. Luo, N. Sisneros, A. Angelova, D. Kudrna, H.R. Kim, Y. Yu, J.L. Goicoechea, M. Lorieux, N. Kurata, D. Brar, D. Ware, S. Jackson, and R.A. Wing. 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 60:536-543.

Hurwitz, B. D. Kudrna, Y. Yu, A. Sebastian, A. Zuccolo, S.A. Jackson, D. Ware, R.A. Wing*, L. Stein*. 2010. Rice structural variation: a comparative analysis of structural variation between rice and three of its closest relatives in the genus Oryza. Plant Journal 63:990-1003. (*co-corresponding authors).

Ammiraju, J.S.S., C. Fan, Y. Yu, X. Song, K.A. Cranston, A.C. Pontaroli, F.L., A. Sanyal, N. Jiang, T. Rambo, J. Currie, K. Collura, J. Talag, J.L. Bennetzen, M. Chen, S. Jackson and R.A. Wing. 2010. Spatio-temporal patterns of genome evolution in homeologous Adh1 - Adh2 regions from four allotetraploid species of the genus Oryza. Plant Journal 63:430-442.

The Maize Genome Sequencing Consortium. 2009. The B73 Maize Genome: Complexity, Diversity, and Dynamics. Science 326:1112-1115.

Wei, F., J.C. Stein, C. Liang, J. Zhang, R.S. Fulton, R.S. Baucom, E. De Paoli, S. Zhou, L. Yang, Y. Han, S. Pasternak, A. Narechania, L. Zhang, C.-T. Yeh, K. Ying, D.H. Nagel, K. Collura, D Kudrna, J. Currie, J. Lin, H.R. Kim, A. Angelova, G. Scara, M. Wissotski, W. Golser, L. C., S. Kruchowski, T.A. Graves, S.M. Rock, S. Adams, L.A. Fulton, C. Fronick, W. Courtney, M. Kramer, L. Spiegel, L. Nascimento, A. Kalyanaraman, C. Chaparro, J.-M. Deragon, P. San Miguel, N. Jiang, S.R. Wessler, P.J. Green, Y. Yu, D.C. Schwartz, B.C. Meyers, J.L. Bennetzen, R.A. Martienssen, W.R. McCombie, S. Aluru , S.W. Clifton, P.S. Schnable, D. Ware, R.K. Wilson, R.A. Wing. 2009. Detailed analysis of a contiguous 22-Mb region of the maize genome. PLoS Genet 5: e1000728.

Wei, F., J. Zhang, S. Zhou, R. He, M. Schaeffer, K. Collura, D. Kudrna, B.P. Faga, M. Wissotski, M., Golser, W., S.M. Rock, T.A. Graves, R.S. Fulton, E. Coe, P.S. Schnable, D.C. Schwartz, D. Ware, S.W. Clifton, R.K. Wilson, R.A. Wing. 2009. The physical and genetic framework of the maize B73 genome. PLoS Genet 5: e1000715

Rounsley, S., P.R. Marri, Y. Yu, R. He, N. Sisneros, J.L. Goicoechea, S.J. Lee, A. Angelova, D. Kudrna, M. Luo, J. Affourtit, B. Desany, J. Knight, F. Niazi, M. Egholm, R.A. Wing. 2009. De novo next generation sequencing of plant genomes. RICE 2:35–43

Ammiraju, JSS, F. Lu, A. Sanyal, Y. Yu, X. Song, N. Jiang, A.C. Pontaroli, T. Rambo, J. Currie, K. Collura, J. Talag, C. Fan, J.L. Goicoechea, A. Zuccolo, J. Chen, J.L. Bennetzen, M. Chen, S. Jackson, and R.A. Wing. 2008. Dynamic evolution of Oryza genomes is revealed by comparative genomic analysis of a genus-wide vertical data set. Plant Cell 20:3191-3209

Kim, H., B. Hurwitz, Y. Yu, K. Collura, N. Gill, P. SanMiguel, J.C. Mullikin, C. Maher, W. Nelson, M. Wissotski, M. Braidotti, D. Kudrna, J.L. Goicoechea, L. Stein, D. Ware, S.A. Jackson, C. Soderlund, R.A. Wing. 2008. Construction, alignment and analysis of twelve framework physical maps that represent the ten genome types of the genus Oryza. Genome Biol 9: Article R45.

Ammiraju, J.S., A. Zuccolo, Y. Yu, X. Song, B. Piegu, F. Chevalier, J.G. Walling, J. Ma, J. Talag, D.S. Brar, P.J. SanMiguel, N. Jiang, S.A. Jackson, O. Panaud, R.A. Wing. 2007. Evolutionary dynamics of an ancient retrotransposon family provides insights into evolution of genome size in the genus Oryza. Plant J 52:342-351.

Ma, J., R.A. Wing, J.L. Bennetzen, S.A. Jackson. 2007. Evolutionary history and positional shift of a rice centromere. Genetics 177:1217-1220.

Wei, F., E. Coe, W. Nelson, A.K. Bharti, F. Engler, E. Butler, H. Kim, J.L. Goicoechea, M. Chen, S. Lee, G. Fuks, H. Sanchez-Villeda, S. Schroeder, Z. Fang, M. McMullen, G. Davis, J.E. Bowers, A.H. Paterson, M. Schaeffer, J. Gardiner, K. Cone, J. Messing, C. Soderlund, R.A. Wing. 2007. Physical and genetic structure of the maize genome reflects its complex evolutionary history. PLoS Genet 3: e123.

Zuccolo, A., A. Sebastian, J. Talag, Y. Yu, H. Kim, K. Collura, D. Kudrna, R.A. Wing. 2007. Transposable element distribution, abundance and role in genome size variation in the genus Oryza. BMC Evol Biol 7: 152.

Kim, H., P. San Miguel, W. Nelson, K. Collura, M. Wissotski, J.G. Walling, J.P. Kim, S.A. Jackson, C. Soderlund, R.A. Wing. 2007. Comparative physical mapping between Oryza sativa (AA genome type) and O. punctata (BB genome type). Genetics 176:379-390.

Piegu, B., R. Guyot, N. Picault, A. Roulin, A. Saniyal, H. Kim, K. Collura, D.S. Brar, S. Jackson, R.A. Wing, O. Panaud. 2006. Doubling genome size without polyploidization: dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice. Genome Res 16:1262-1269.

Ammiraju, J.S.S., M. Luo, J.L. Goicoechea, W. Wang, D. Kudrna, C. Mueller, J. Talag, H.R. Kim, N.B. Sisneros, B. Blackmon, E. Fang, J.B. Tomkins, D. Brar, D. MacKill, S. McCouch, N. Kurata, G. Lambert, D.W. Galbraith, K. Arumuganathan, K. Rao, J.G. Walling, N. Gill , Y. Yu, P. SanMiguel, C. Soderlund, S. Jackson, R.A. Wing. (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 Res 16:140-147.

Kumar, C.S., R.A. Wing, V. Sundaresan. 2005. Efficient insertional mutagenesis in rice using maize En/Spm elements. Plant Journal 139:27-38.

The Rice Chromosome 3 Sequencing Consortium (R. Buell, W.R. McCombie & R.A. Wing – Corresponding Authors). 2005. Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species. Genome Res 15:1-10.

The International Rice Genome Sequencing Project Project. 2005. The map based sequence of the rice genome. Nature 436:793-800.

Messing, J., A.K. Bharti, W.M. Karlowski, H. Gundlach, H.R. Kim, Y. Yu, F. Wei, G. Fuks, C.A. Soderlund, K.F. Mayer, R.A. Wing. 2004. Sequence composition and genome organization of maize. Proc Natl Acad Sci USA 101:14349-14354.

Dietrich, F.S., S. Voegeli, S. Brachat, A. Lerch, K. Gates, S. Steiner, C. Mohr, R. P?hlmann, P. Luedi, S. Choi, R.A. Wing, A. Flavier, T.D. Gaffney, P. Philippsen. 2004. The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome. Science 304:304-307.

The Rice Chromosome 10 Sequencing Consortium. 2003. In-depth view of structure, activity, and evolution of rice chromosome 10. Science 300:1566-1569.

Chen M., G. Presting, Barbazuk W.B., Goicoechea J.L., Blackmon B, Fang G, Kim HR, Frisch DA, Yu Y, Higingbottom S, Phimphilai K, Phimphilai S, Thurmond S, Gaudette B, Li P, Liu J, Hatfield J, Main D, Sun S, Farrar K, Henderson C, Barnett L, Costa R, Williams B, Walser S, Atkins M, Hall C, Bancroft I, Salse J, Regad F, Mohapatra T, Singh NK, Tyagi AK, Soderlund C, Dean RA, R.A. Wing 2002. An integrated physical and genetic map of the rice genome. Plant Cell 14:537-545.

Goff, S.A., D. Ricke, R. Wang, G. Presting, D. Lan, M. Dunn, J. Glazebrook, H. Varma, D. Hadley, D Hutchison, A Sessions, C Martin, F Katagiri, P Oeller, B.M. Lange, T Moughamer, Y Xia, P Budworth, J Zhong, T Miguel, CB Ho, U Paszkowski, S Zhang, M Colbert, W Sun, L Chen, B Cooper, S Park, W Kimmerly, T.C. Wood , L. Mao, P. Quail, R.A. Wing, R. Dean, Y. Yu, S. Briggs, A. Zharkikh, R. Shen, A. Oliphant, S. Sahasrabudhe, A. Thomas, R. Cannings, A. Gutin, D. Pruss, J. Reid, S. Tavtigian, J. Mitchell, G. Eldredge, T. Scholl, R.M. Miller, S. Bhatnagar, N. Adey, T. Rubano, N. Tusneem, R. Robinson, J. Feldhaus, T. Macalma 2002. Draft sequence of the rice genome. Science 296:92-100.

Wei, F., R.A. Wing, R.P. Wise. 2002. Genome dynamics and evolution of the Mla (Powdery Mildew) resistance locus in barley. Plant Cell 14:1903-1917.

Mao, L., D. Begum, S.A. Goff, R.A. Wing. 2001. Sequence and analysis of the tomato JOINTLESS locus. Plant Physiology: 126:1331-1340.

Cheng Z., C.R. Buell, R.A. Wing , M. Gu, J. Jiang. 2001 Toward a cytological characterization of the rice genome. Genome Res, 11:2133-2141.

Mao, L., D. Begum, H.W. Chuang, M.A. Budiman, E.J. Szymkowiak, E.E. Irish, R.A. Wing. 2000. JOINTLESS is a MADS-box gene controlling tomato flower abscission zone development. Nature: 406:910-913.

Yu, Y., J.P. Tomkins, R. Waugh, D.A. Frisch, D. Kudrna, A. Kleinhofs, R.S. Brueggeman, G.J. Muehlbauer, R.P. Wise, R.A. Wing. 2000. A bacterial artificial chromosome library for barley (Hordeum vulgare L.) and the identification of clones containing putative resistance genes. Theoretical and Applied Genetics: 101:1093-1099.

Mao, L., T.C. Wood, Y. Yu, M.A. Budiman, S.S. Woo, M. Sasinowski, G. Presting, D. Frisch, S. Goff, R.A. Dean, R.A. Wing. 2000. Rice transposable elements: A survey of 73,000 sequence-tagged-connectors. Genome Res: 10:982-990.

Chen, M., Pl SanMiguel, A.X. de Oliveria, S.S. Woo, H. Zhang, R.A. Wing, J.L. Bennetzen. 1997. Microcolinearity in sh2-homologous regions of the maize, rice and sorghum genomes. Proc Natl Acad Sci USA 94:3431-3435.

Zhang, H.B., S.D. Choi, S.S. Woo, Z.K. Li, R.A. Wing. 1996. Construction and characterization of two rice bacterial artificial chromosome libraries from the parents of a permanent recombinant inbred mapping population. Molecular Breeding 2:11-24.

Woo S.-S., J. Jiang, B.S. Gill, A.H. Paterson, R.A. Wing. 1994. Construction and characterization of a bacterial artificial chromosome library for Sorghum bicolor. Nucleic Acids Res 22:4922-4931.

Chittenden, L.M., K. F. Schertz, Y.-R. Lin, R.A. Wing, A.H. Paterson. 1994. RFLP mapping of a cross between Sorghum Bicolor and S. propinquum, suitable for high-density mapping, suggests ancestral duplication of Sorghum chromosomes. Theor Appl Genet 87:925-933.

Tanksley, S.D., M.W. Ganal, J.C. Prince, M.C. deVicente, MW. Bonierbale, P. Broun, T.M Fulton, J.J. Giovannoni, S. Grandillo, G.B. Martin, R. Messequer, J.C. Miller, L. Miller, A.H. Paterson, O. Pineda, M.S. Roeder, R.A. Wing, W. Wu, N.D. Young. 1992. High-density molecular linkage maps of the tomato and potato genomes. Genetics 132:1141-1160.

J.J. Giovannoni, Wing, R.A., M. Ganal, S.D. Tanksley. 1991. Isolation of molecular markers from specific chromosomal intervals using DNA pools from existing mapping populations. Nucleic Acids Res. 23: 6553-6558.

Deng, X. W., R.A. Wing, W. Gruissem. 1989. The chloroplast genome exists in multimeric forms. Proc Natl Acad Sci USA 86:4156-4160.

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A portion of AGI's material is based upon work supported by the National Science Foundation under Grant Number 102620.