140. Wai, C.M., R. VanBuren, J. Zhang, L. Huang, W. Miao, P. P. Edger, W.C. Yim, H. Priest, B. Meyers, T.C.Mockler, J.A.C. Smith, J. Cushman, R. Ming. 2017. Temporal and spatial transcriptomic and microRNA dynamics of CAM photosynthesis in pineapple. The Plant Journal. DOI: 10.1111/tpj.13630

139. Qin, G., C. Xu, R. Ming, H. Tang, R. Guyot, E. M. Kramer, Y. Hu. X. Yi, Y. Qi, X. Xu, Z. Gao, H. Pan, J. Jian, Y. Tian, Z. Yue, Y. Xu. 2017. The pomegranate (Punica granatum L.) genome and the genomics of punicalagin biosynthesis. The Plant Journal. DOI: 10.1111/tpj.13625

138. Xue, X., Z. Li, M. Cai, Q. Zhang, X. Zhang, R. Ming, J. Zhang 2017. Identification and Characterization of microRNAs from Saccharum officinarum L by Deep Sequencing. Tropical Plant Biology. doi:10.1007/s12042-017-9190-y

137. Zhang, Q., M. Cai, X. Yu, L. Wang, C. Guo, R. Ming, J. Zhang 2017. Transcriptome dynamics of Camellia sinensis in response to continuous salinity and drought stress. Tree Genetics & Genomes, 13, 78.

136. Zeng, F., X. Lian, G. Zhang, X. Yu, C.A. Bradley, R. Ming. 2017. A comparative genome analysis of Cercospora sojina with other members of the pathogen genus Mycosphaerella on different plant hosts. Genomics DATA 350.

135. Zeng, F., C. Wang, G. Zhang, J. Wei, C.A. Bradley, R. Ming. 2017. Draft genome sequence of Cercospora sojina isolate S9, a fungus causing frogeye leaf spot (FLS) disease of soybean. Genomics DATA 12:79-80

134. Chen, Y., Q. Zhang, W. Hu, X. Zhang, L. Wang, X. Hua, Q. Yu, R. Ming, J. Zhang. 2017. Evolution and expression of the fructokinase gene family in Saccharum. BMC Genomics (in press).

133. Goldberg,E.E., S.P. Otto, J.C. Vamosi, I. Mayrose, N. Sabath, R. Ming, and T.-L. Ashman. 2017. Macroevolutionary synthesis of flowering plant sexual systems. Evolution. doi:10.1111/evo.13181.

132. Liao, Z., Q. Yu, R. Ming. 2017. Development of male specific markers and identification of sex reversal mutants in papaya. Euphytica. 213:1-12

131. VanBuren, R., C. M. Wai, J. Zhang, J. Han, J. Arro, Z. Lin, Z. Liao, Q. Yu, M.-L. Wang, F. Zee, R. C. Moore, D. Charlesworth, R. Ming 2016. Extremely low nucleotide diversity in the X-linked region of papaya caused by a strong selective sweep. Genome Biology. 17(1), 230.

130. Ming, R. C.M. Wai, R. Guyot. 2016. Pineapple genome: a reference for monocots and CAM photosynthesis. Trends in Genetics (in press)

129. Paull, R.E., Chen, N.J., Ming, R., Wai, C.M., Shirley, N., Schwerdt, J. and Bulone, V., 2016. Carbon Flux and Carbohydrate Gene Families in Pineapple. Tropical Plant Biology. 9:200-213.

128. Zhang, X., Liang, P. and Ming, R., 2016. Genome-Wide Identification and Characterization of Nucleotide-Binding Site (NBS) Resistance Genes in Pineapple. Tropical Plant Biology. 9:187-199.

127. Zheng, Y., Li, T., Xu, Z., Wai, C.M., Chen, K., Zhang, X., Wang, S., Ji, B., Ming, R. and Sunkar, R., 2016. Identification of microRNAs, phasiRNAs and Their Targets in Pineapple. Tropical Plant Biology. 9:176-186.

126. Wai, C.M., Powell, B., Ming, R. and Min, X.J., 2016. Genome-Wide Identification and Analysis of Genes Encoding Proteolytic Enzymes in Pineapple. Tropical Plant Biology. 9:161-175.

125. Wai, C.M., Powell, B., Ming, R. and Min, X.J., 2016. Analysis of Alternative Splicing Landscape in Pineapple (Ananas comosus). Tropical Plant Biology. 9:150-160.

124. Singh, R., Ming, R. and Yu, Q., 2016. Comparative Analysis of GC Content Variations in Plant Genomes. Tropical Plant Biology. 9:136-149.

123. Zhang, J., A. Sharma, Q. Yu, J. Wang, L. Li, L. Zhu, X. Zhang, Y, Chen, R. Ming. 2016 Comparative structural analysis of Bru1 region homeologs in Saccharum spontaneum and S. officinarum. BMC Genomics. 17:446.

122. Fang,J., A. Lin,W. Qiu,H. Cai,M. Umar,R.i Chen,R. Ming. 2016. Transcriptome profiling revealed stress-induced and disease resistance genes up-regulated in PRSV resistant transgenic papaya. Frontiers in Plant Science. 7:855.

121. Zhang, Q., Hu, W., Zhu, F., Wang, L., Yu, Q., Ming, R. and Zhang, J., 2016. Structure, phylogeny, allelic haplotypes and expression of sucrose transporter gene families in Saccharum. BMC genomics, 17:1.

120. Fang, J., C. Miao, R. Chen, R. Ming. 2016. Genome-wide comparative analysis of microsatellites in pineapple. Tropical Plant Biology. (in press).

119. Arro, J., J.-W. Park, C. M. Wai, R. VanBuren, Y.-B. Pan, C. Nagai, J. da Silva, R. Ming. 2016. Balancing selection contributed to domestication of autopolyploid sugarcane (Saccharum officinarum L.). Euphytica. DOI :10.1007/s10681-016-1672-8.

118. Fang, J., A. Woods, R. Chen, R. Ming. 2016. Molecular basis of off-type microsatellite markers in papaya. Euphytica. doi:10.1007/s10681-015-1630

117. Zhang, L., Ming, R., Zhang, J., Tao, A., Fang, P., & Qi, J. 2015. De novo transcriptome sequence and identification of major bast-related genes involved in cellulose biosynthesis in jute (Corchorus capsularis L.). BMC genomics, 16(1), 1062.

116. Ming, R., R. VanBuren, C. M. Wai, H. Tang, M.C. Schatz, J. E. Bowers, E. Lyons, M.-L. Wang, J. Chen, E. Biggers, J. Zhang, L. Huang, L. Zhang, W. Miao, J. Zhang, Z. Ye, C. Miao, Z. Lin, H. Wang, H. Zhou, W. C. Yim, H. D. Priest, C. Zheng, M. Woodhouse, P. P. Edger, R. Guyot, H.-B. Guo, H. Guo, G. Zheng, R. Singh, A. Sharma, X. Min, Y. Zheng, H. Lee, J. Gurtowski, F. J. Sedlazeck, A. Harkess, M. R. McKain, Z. Liao, J. Fang, J. Liu, X. Zhang, Q. Zhang, W. Hu, Y. Qin, K. Wang, L.-Y. Chen, N. Shirley, Y.-R. Lin, L.-Y. Liu, A. G. Hernandez, C. L. Wright, V. Bulone, G. A. Tuskan, K. Heath, F. Zee, P. H. Moore, R. Sunkar, J. H. Leebens-Mack, T. Mockler, J. L. Bennetzen, M. Freeling, D. Sankoff, A. H. Paterson, X. Zhu, X. Yang, J. A. C. Smith, J. C. Cushman, R.E. Paull, Q. Yu. 2015. The pineapple genome and the evolution of CAM photosynthesis. Nature Genetics. 47:1435-1442.

115. Sabath, N, E. Goldberg, L. Glick, M. Einhorn, T.-L. Ashman, R. Ming, S.P. Otto, J. Vamosi, I. Mayrose. 2015 Dioecy does not consistently accelerate or slow lineage diversification across multiple genera of angiosperms. New Phytologist. DOI: 10.1111/nph.13696

114. Davis, S.C., R. Ming, D. LeBauer, and S.P. Long 2015. Toward systems-level analysis of agricultural production from crassulacean acid metabolism (CAM): scaling from cell to commercial production. New Phytologist. DOI: 10.1111/nph.13522.

113. Yang, X., Cushman, J. C., Borland, A. M., Edwards, E. J., Wullschleger, S. D., Tuskan, G. A., Griffiths, H., Smith, J.A.C., De Paoli, H.C., Weston, D.J., Cottingham, R., Hartwell, J., Davis, S.C., Silveria, K., Ming, R., Schlaugh, K., Abraham, P., Stewart, R. J., Guo, H.-B., Albion, R., Ha, J., Lim, Sung D., Wone, B.W.M., Yim, W.C., Garcia, T., Mayer, J.A., Petereit, J., Nair, S. S., Casey, E., Hettich, R.L., Ceusters, J., Ranjan, P., Palla, K..J., Yin, H., Reyes-Garcia, C., Andrade, J. L., Freschi, L., Dever, L.V., Boxall, S.F., Walker, J., Davies, J., Bupphada, P., Kadu, N., Winter, K., Sage, R. F., Aguilar, C.N., Schmutz, J., Jenkins, J. & Holtum, J. A. (2015). A roadmap for research on crassulacean acid metabolism (CAM) to enhance. New Phytologist. doi:10.1111/nph.13393

112. VanBuren, R., F. Zeng, C. Chen, J Zhang, C.M. Wai, J. Han, R. Aryal, A.R. Gschwend, J. Wang, J.K. Na, L. Huang, L. Zhang, W. Miao, J. Gou, J. Arro, R. Guyot, R.C. Moore, M. Wang, F. Zee, D. Charlesworth, P.H. Moore, Q. Yu, R. Ming. 2015. Origin and domestication of papaya Yh chromosome. Genome Research, doi/10.1101/gr.183905.114.

111. Tang, H, X Zhang, C Miao, J. Zhang,R. Ming, JC Schnable, PS Schnable, E Lyons, J Lu 2015. ALLMAPS: Robust scaffold ordering based on multiple maps. Genome Biology. 16:3

110. Ming, R. C.M. Wai 2015. Assembling allopolyploid genomes: no longer formidable. Genome Biology. 16:27

109. Leisner, C, R. Ming, and E.A. Ainsworth. 2015. Distinct transcriptional profiles of ozone stress in soybean flowers, pods and leaves. BMC Plant Biology. 14:335.

108. Iovene, M, Q. Yu, R. Ming, and J. Jiang. 2015. Independent sex chromosome evolution from the same pair of autosomes inCarica papaya and Vasconcellea parviflora. Genetics doi:10.1534/genetics.114.173021.

107. Zeng, F., G. Zhang,G. Olaya, J. Wullschleger, H. Sierotzki, R. Ming, C. A. Bradley. 2014. Characterization of quinone outside inhibitor fungicide resistance in Cercospora sojina and development of diagnostic tools for its identification. Plant Disease (in press).

106. Zeng, F., Q. Yu, S. Hou, P. H. Moore, M. Alam, R. Ming. 2014. Features of transcriptome in trioecious papaya revealed by a large-scale sequencing of ESTs and comparative analysis of higher plants. Plant Omics (in press).

105. F. Denoeud, L. Carretero-Paulet, A. Dereeper, G. Droc, R. Guyot, M. Pietrella, C. Zheng, A. Alberti, F. Anthony, G. Aprea, JM. Aury, P. Bento, M. Bernard, S. Bocs, C. Campa, A. Cenci, M. Combes, D. Crouzillat, C. Da Silva, L. Daddiego, F. De Bellis, S. Dussert, O. Garsmeur, T. Gayraud, V. Guignon, K. Jahn, V. Jamilloux, T. Joët, K. Labadie, T. Lan, J. Leclercq, M. Lepelley, T. Leroy, LT. Li, P. Librado, L. Lopez, A. Muñoz, B. Noel, A. Pallavicini, G. Perrotta, V. Poncet, D. Pot, Priyono, M. Rigoreau, M. Rouard, J. Rozas, C. Tranchant-Dubreuil, R. VanBuren, Q. Zhang, AC. Andrade, X. Argout, B. Bertrand, A. de Kochko, G. Graziosi, RJ. Henry, Jayarama, R. Ming, C. Nagai, S. Rounsley, D. Sankoff, G. Giuliano, VA. Albert, P. Wincker, P. Lashermes. 2014. The coffee genome provides insight into the convergent evolution of caffeine biosynthesis. Science 345, 1181-1184 (2014).

104. The Tree of Sex Consortium. 2014. Sex determination: Why so many ways of doing it? PLoS Biology, 12(7): e1001899.

103. Zhang, Q., L. Li, R. VanBuren, Y. Liu, M. Yang, L. Xu, J. E. Bowers, C. Zhong, Y. Han, S. Li, R. Ming. 2014 Optimization of linkage mapping strategy and construction of a high-density American lotus linkage map. BMC Genomics 15: 372.

102. Berdan, E.L., Kozak, G.M., Ming, R. Rayburn, A.L., Kiehart, R., and Fuller, R.C. 2014. Insight into genomic changes accompanying divergence: genetic linkage maps and synteny of Lucania goodei and L. parva reveal a Robertsonian fusion. G3: Genes, Genomes, and Genetics. doi: 10.1534/g3.114.012096.

101. The Tree of Sex Consortium. 2014. Tree of Sex: A database of sexual systems. Scientific Data 1.

100. Zhang, J., J. Liu, R. Ming. 2014. Genomic analysis of the CAM plant pineapple. Journal of Experimental Botany (in press).

99. Zhang, J., A. Boualem, A. Bendahmane, R. Ming. 2014. Genomics of sex determination. Current Opinion in Plant Biology (in press).

98. Na, J.K., J. Wang,R. Ming. 2014. Accumulation of interspersed and sex-specific repeats in the non-recombining region of papaya sex chromosomes. BMC Genomics (in press).

97. Aryal, R., G. Jagadeeswaran, Y. Zheng, Q. Yu, R. Sunkar, R. Ming. 2014. Sex specific expression and distribution of small RNAs in papaya. BMC Genomics. 15:20.

96. Aryal, R., G. Jagadeeswaran, Y. Zheng, Q. Yu, R. Sunkar, R. Ming. 2014. Analysis of papaya small RNAs revealed a pericentric inversion triggering sex chromosome evolution. BMC Genomics (in press).

95. Han, J., J.E. Murray1, Q. Yu, P.H. Moore, R. Ming. 2014. The effects of gibberellic acid on sex expression and secondary sexual characteristics in papaya. HortScience

94. Aryal, R., R. Ming 2014. Sex determination in flowering plants: Papaya as a model system. Plant Sci.

93. Wang, J., S. Nayak, K. Koch, R. Ming. 2013. Carbon partitioning in sugarcane (Saccharum species). Frontiers in Plant Biotechnology. doi: 10.3389/fpls.2013.00201

92. Zhang, J., J. Arro, Y. Chen, R. Ming. 2013. Haplotype analysis of sucrose synthase gene family in three Saccharum species. BMC Genomics. 14:314.

91. VanBuren, R., B. Walters, R. Ming, X.J. Min. 2013. Analysis of expressed sequence tags and alternative splicing genes in sacred lotus (Nelumbo nucifera Gaertn.). Plant Omics Journal. 6:311-317.

90. Lum, G., R. VanBuren, R. Ming, X.J. Min. 2013. Secretome Prediction and Analysis in Sacred Lotus (Nelumbo nucifera Gaertn.).Tropical Plant Biology. 6:131-137.

89. Zheng, Y., G. Jagadeeswaran, K. Gowdu, N. Wang,S. Li, R. Ming, R. Sunkar. 2013. Genome-Wide Analysis of MicroRNAs in Sacred Lotus, Nelumbo nucifera (Gaertn). Tropical Plant Biology. 6:117-130.

88. Jia, R.Z., R. Ming, Y.J. Zhu. 2013. Genome-Wide Analysis of Nucleotide-Binding Site (NBS) Disease Resistance (R) Genes in Sacred Lotus (Nelumbo nucifera Gaertn.) Reveals Their Transition Role During Early Evolution of Land Plants. Tropical Plant Biology. 6:98-116.

87..Singh,R., R. Ming, Q. Yu. 2013. Nucleotide Composition of the Nelumbo nucifera Genome. Tropical Plant Biology. 6:85-97.

86. Ming R, VanBuren R, Liu Y, Yang M, Han Y, Li LT, Zhang Q, Kim MJ, Schatz MC, Campbell M, Li J, Bowers JE, Tang H, Lyons E, Ferguson AA, Narzisi G, Nelson DR, Blaby-Haas CE, Gschwend AR, Jiao Y, Der JP, Zeng F, Han J, Min X, Hudson KA, Singh R, Grennan AK, Karpowicz SJ, Watling JR, Ito K, Robinson SA, Hudson ME, Yu Q, Mockler TC, Carroll A, Zheng Y, Sunkar R,1 Jia R, Chen N, Arro J, Wai CM, Wafula E, Spence A, Han Y, Xu L, Zhang J, Peery R, Haus MJ, Xiong W, Walsh JA, Wu J, Wang ML, Zhu YJ, Paull RE, Britt AB, Du C, Downie SR, Schuler, MA, Michael TP, Long SP, Ort DR, Schopf JW, Gang DR, Jiang N, Yandell M, dePamphilis CW, Merchant SS, Paterson AH, Buchanan BB, Li S, J. Shen-Miller. 2013. Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.). Genome Biology. doi:10.1186/gb-2013-14-5-r41

85. VanBuren, R., R. Ming. 2013. Dynamic transposable element accumulation in the nascent sex chromosomes of papaya. Mobile Genetic Elements (accepted).

84. Aryal, R., X. Yang, Q. Yu, R. Sunkar, L. Li, R. Ming. 2013. Asymmetric purine-pyrimidine distribution in cellular small RNA population of papaya. BMC Genomics. 13:682

83. Gschwend, A.R., C.M.Wai, F.Zee ?A.K. Arumuganathan, R. Ming. 2013. Genome size variation among sex types in dioecious and trioecious Caricaceae species. Euphytica. DOI 10.1007/s10681-012-0815-9

82. Zhu, L., J. Zhang, Y. Chen, H. Pan, R. Ming. 2013. Identification and genes expression analysis of  ATP-dependent phosphofructokinase family members among three Saccharum species. Functional Plant Biology. DOI:10.1071/FP12182.

81. Wu J, Wang Z, Shi Z, Zhang S, Ming R, Zhu S, Khan MA, Tao S, Korban SS, Wang H, Chen NJ, Nishio T, Xu X, Cong L, Qi K, Huang X, Wang Y, Zhao X, Wu J, Deng C, Gou C, Zhou W, Yin H, Qin G, Sha Y, Tao Y, Chen H, Yang Y, Song Y, Zhan D, Wang J, Li L, Dai M, Gu C, Wang Y, Shi D, Wang X, Zhang H, Zeng L, Zheng D, Wang C, Chen M, Wang G, Xie L, Sovero V, Sha S, Huang W, Zhang S, Zhang M, Sun J, Xu L, Li Y, Liu X, Li Q, Shen J, Wang J, Paull RE, Bennetzen JL, Wang J, Zhang S. 2013. The genome of the pear (Pyrus bretschneideri Rehd.). Genomo Res. 23: 396-408.

80. Wai, C.M., P. H. Moore, R. E. Paull, R. Ming, Q. Yu. 2013. An integrated cytogenetic and physical map reveals unevenly distributed recombination spots along the papaya sex chromosomes. Chromosome Res. DOI 10.1007/s10577-012-9312-1.

79. Bradley, C. A., A. Wood, G. R. Zhang, J. E. Murray, D. V. Phillips, R. Ming. 2012. Genetic diversity of Cercospora sojina revealed by amplified fragment length polymorphism markers. Canadian Journal of Plant Pathology. 34:410?16.

78. Yang M, Han Y, VanBuren R, Ming R, Xu L, Han Y, Liu Y. 2012 Genetic linkage maps for Asian and American lotus constructed using novel SSP markers derived from the genome of sequenced cultivar. BMC genomics 13(1) 653

77. Wang, J., J.-K. Na, Q. Yu, A. R. Gschwend, J. Han, F. Zeng, R. Aryal, R. VanBuren, J.E. Murray1, W. Zhang, R.N. Pérez, F.A. Feltus, C. Lemke, E. J. Tong, C. Chen, C.M. Wai, R. Singh, M.-L. Wang, X. Min, M. Alam, D. Charlesworth, P.H. Moore, J. Jiang, A. H. Paterson, R. Ming. 2012. Sequencing papaya X and Yh chromosomes revealed molecular basis of incipient sex chromosome evolution. PNAS. 109:13710-13715.

76. Gschwend, A.R., Q. Yu, E.J. Tong, F. Zeng, J. Han, R. VanBuren, R. Aryal, D. Charlesworth, P.H. Moore, A.H. Paterson, R. Ming. 2012. Rapid divergence and expansion of the X chromosome in papaya. PNAS. 109:13716-13721.

75. Zhang, J., C. Nagai, Q. Yu, Y.-B. Pan, T. Ayala-Silva, R. J. Schnell, J. C. Comstock, A. K. Arumuganathan, R. Ming. 2012. Genome size variation in three Saccharum species. Euphytica.  185:511?19.

74. Ming, R., Q. Yu, P. H. Moore, R. E. Paull, N. J. Chen, M.-Li Wang, Y. J. Zhu, M. A. Schuler, J. Jiang, A. H. Paterson. 2012. Genome of papaya, a fast growing tropical fruit tree. Tree Genet. Genomics. 8:445?62.

73. Swaminathan, K., W. B. Chae, T. Mitros, K. Varala, L. Xie, A. Barling, K Glowacka, M. Hall, S. Jezowski, R. Ming, M. Hudson, J. A. Juvik, S. P. Moose, D. S. Rokhsar. 2012. Deep sequencing identifies markers for a framework genetic map and reveals recent allotetraploidy in Miscanthus. BMC Genomics. 13:142.

72. Gschwend, A.R., L.A. Weingartner, R.C. Moore, R. Ming. 2012. The sex-specific region of sex chromosomes in animals and plants. Chromosome Research 20:57?9.

71. James, B., C. Chen, A. Rudolph, K. Swaminathan, J. Murray, J.-K. Na, A. Spence, B. Smith, M. Hudson, S. Moose, R. Ming. 2012 Development and application of microsatellite markers in polyploid Sugarcane. Mol Breeding 30:661-119.

70. Na, J.-K., J, Wang, J. E. Murray, A. R. Gschwend, W. Zhang, Q. Yu, R. N. Pérez, F. A. Feltus, C. Chen, Z.Kubat, P. H. Moore, J. Jiang, A. H. Paterson, R. Ming 2012 Construction of physical maps for the sex-specific regions of papaya sex chromosomes. BMC Genomics. 13:176.

69. Blas, A.L., Q. Yu, O.J. Veatch, R.E. Paull, P.H. Moore, R. Ming. 2012 Genetic mapping of quantitative trait loci controlling fruit size and shape in papaya. Mol Breeding 29:457?66

68. VanBuren, R., J. Li, F. Zee, J. Zhu, C. Liu, A. K. Arumuganathan, R. Ming. 2011. Longli is not a Hybrid of Longan and Lychee as Revealed by Genome Size Analysis and Trichome Morphology. Tropical Plant Biology 4:228-236.

67. Souza G. M., A. D’Hont, B. Potier, H. Berges, J. E. Ferreira, M. Vincentz, R. Ming, R. Henry, R. Casu, M.-A. Van Sluys, A. Paterson. 2011. The Sugarcane Genome Sequencing Initiative: Strategies for Sequencing a Highly Complex Genome. Tropical Plant Biology 4:145-156.

66. Brewbaker, J. L., S. K. Kim, Y. S. So, M. Logrono, H. G. Moon, R. Ming, X. Lu, A. D. Josue. 2011. General Resistance in Maize to Souther Rust (Puccinia polysora Undeerw.).  Crop Sci. 51:1393-1409.

65. Yu, Q., R, Guyot, A. de Kochko, A. Byers, R. Navajas-Pérez, B. J. Langston, C. Dubreuil-Tranchant, A. H. Paterson, V. Poncet, C. Nagai, R. Ming. 2011. Microcolinearity and genome evolution in the vicinity of an ethylene receptor gene of cultivated diploid and allotetraploid coffee species. The Plant Journal 67:305-317.

64. Ming, R., A. Bendahmane, S. S. Renner  2011. Sex chromosomes in land plants.  Annual Review of Plant Biology 62:485-514.

63. Gschwend, A.R., P. Moore, Q. Yu, C. Saski, C. Chen, J. Wang, J.-K. Na, R. Ming. 2011.  Construction of papaya male and female BAC libraries and application in physical mapping of the sex chromosomes. Journal of Biomedicine and Biotechnology doi:10.1155/2011/929472.

62. Wu, X., J. Wang, J.-K. Na, Q. Yu, R. C. Moore, F. Zee, S. C. Huber, R. Ming. 2010. The Origin of the non-recombining region of sex chromosomes in Carica and Vasconcellea. The Plant Journal 63:801-810.

61. Zhang, W., Wai, C.M., Ming, R., Yu, Q., and  Jiang, J. 2010. Integration of genetic and cytological maps and development of a pachytene chromosome-based karyotype in papaya. Tropical Plant Biology 3:166-170.

60. Wai, C.M., Ming. R., Moore, P.H., Paull, R.E., Yu, Q. 2010. Development of chromosome-specific cytogenetic markers and merging of broken linkage groups in papaya. Tropical Plant Biology 3:171-181.

59. Wang, J., B. Roe, S. Macmil, Q. Yu, J. E. Murray, H. Tang, C. Chen, F. Najar, G. Wiley, J. Bowers, M.-A. Van Sluys, D. S. Rokhsar, M. E. Hudson, S. P. Moose, A. H. Paterson, R. Ming. 2010. Microcollinearity between autopolyploid sugarcane and diploid sorghum genomes. BMC Genomics 11(1):261.

58. Blas, A. L., R. Ming, Z. Liu, O. J. Veatch, R. E. Paull, P. H. Moore, Q. Yu. 2010. Cloning of papaya chromoplast specific lycopene β-cyclase, CpCYC-b, controlling fruit flesh color reveals conserved microsynteny and a recombination hotspot. Plant Physiology 152:2013-2022.

57. de Kochko, A,  S. Akaffou, A. Andrade, C. Campa, D. Crouzillat, R. Guyot, P. Hamon, R. Ming, L. A. Mueller, V. Poncet, C. Tranchant-Dubreuil, S. Hamon. 2010. Advances in Coffea Genomics. Advances in Botanical Research 53:24-63. 

56. Swaminathan, K., M. Alabady, K. Varala, E. De Paoli, I. Ho,  D. Rokhsar, A. K. Arumuganathan, R. Ming , P. J. Green, B. C. Meyers, S. P. Moose, M. E. Hudson. 2010. Genomic and small RNA sequencing of Miscanthus x giganteus shows the utility of sorghum as a reference genome sequence for Andropogoneae grasses. Genome Biology 11(2):R12.

55. Yu, Q., E. Tong, R. L. Skelton, J. E. Bowers, M. R. Jones, J. E. Murray, S. Hou, P. Guan, R. A. Acob, M.-C. Luo, P. H. Moore, M. Alam, A. H. Paterson, R. Ming. 2009. A physical map of the papaya genome with integrated genetic map and genome sequence. BMC Genomics 10:371.

54. Blas, A.L., Q. Yu, C. Chen, O. Veatch, P. H. Moore, R. E. Paull, R. Ming. 2009. Enrichment of a papaya high-density genetic map with AFLP markers. Genome 52:716-725.

53. Lam, E., J. Shine Jr, J. da Silva, M. Lawton, S. Bonos, M. Calvino, H. Carrer, M. C. Silva-Filho, N. Glynn, Z. Helsel, J. Ma, E. Richard Jr., G. Souza, R. Ming. 2009. Improving Sugarcane for Biofuel: Engineering for an even better feedstock. Global Change Biology Bioenergy 1:251-255.

52. Porter, B.W., M. Paidi, R. Ming, M. Alam, W.T. Nishijima, Y.J. Zhu. 2009. Genome-wide analysis of Carica papaya reveals a small NBS resistance gene family. Mol. Genet. Genomics 281:609-626.

51. Paterson, A.H. J.E. Bowers, R. Bruggmann, I. Dubchak, J. Grimwood, H. Gundlach, G. Haberer, U. Hellsten, T. Mitros, A. Poliakov, J. Schmutz, M. Spannagl, H. Tang, X. Wang, T. Wicker, A.K. Bharti, J. Chapman, F.A. Feltus, U. Gowik, I.V. Grigoriev, E. Lyons, C.A. Maher, M. Martis, A. Narechania, R.P. Otillar, B.W. Penning, A.A. Salamov, Y. Wang, L. Zhang, N.C. Carpita, M. Freeling, A.R. Gingle, C.T. Hash, B. Keller, P. Klein, S. Kresovich, M.C. McCann, R. Ming, D.G. Peterson, Mehboob-ur-Rahman, D. Ware, P. Westhoff, K. F. X. Mayer, J. Messing, D. S. Rokhsar. 2009. The Sorghum bicolor genome and the diversification of grasses. Nature 457:551-556.

50. Lyons, E., B. Pedersen, J. Kane, M. Alam, R. Ming, H. Tang, X. Wang, J. Bowers, A. Paterson, D. Lisch, M. Freeling. 2008. Finding and Comparing Syntenic Regions among Arabidopsis and the Outgroups Papaya, Poplar, and Grape: CoGe with Rosids. Plant Physiology 148:1772-1781.

49. Nelson, D. R., R. Ming, M. Alam, M. A. Schuler. 2008. Comparison of cytochrome P450 genes from six plant genomes. Tropical Plant Biology 1:216-235.

48. Paull, R. E., B. Irikura, P. Wu, H. Turano, N. J. Chen, A. Blas, J. K. Fellman, A. R. Gschwend, C. M. Wai, Q. Yu, G. Presting, M. Alam, R. Ming. 2008. Fruit development, ripening and quality related genes in the papaya genome. Tropical Plant Biology 1:246-277 (Cover article).

47. Wang, J., C. Chen, J.-K. Na, Q. Yu, S. Hou, R. E. Paull, P. H. Moore, M. Alam, R. Ming.  2008. Genome-wide comparative analysis of microsatellites in papaya. Tropical Plant Biology 1:278-292.

46. Suzuki, J. Y., S. Tripathi, G. A. Fermín, F.-J. Jan, S. Hou, H. Saw, C. M. Ackerman, Q. Yu, M. C. Schatz, K. Y. Pitz, M. Yépes, M. M. M. Fitch, R. M. Manshardt, J. L. Slightom, S. A. Ferreira, S. L. Salzberg, M. Alam, R. Ming, P. H. Moore, D. Gonsalves. 2008. Characterization of insertion sites in Rainbow papaya, the first commercialized transgenic fruit crop. Tropical Plant Biology 1:293-309.

45. Freeling, M., E. Lyon, B. Pedersen, M. Alam, R. Ming, D. Lisch. 2008. Many or most genes in Arabidopsis transposed after the origin of the order Brassicales. Genome Research 18:1924-1937.

44. Zhang, W., X. Wang, Q. Yu, R. Ming, J. Jiang. 2008. DNA methylation and heterochromatinization in the male-specific region of the primitive Y chromosome of papaya. Genome Research 18:1938-1943 (Cover article).

43. Tang, H., X. Wang, J. E. Bowers, R. Ming, M. Alam, A. H. Paterson. 2008. Unraveling ancient hexaploidy through multiply aligned angiosperm gene maps. Genome Research 18:1944-1954.

42. Nagarajan, N., R. Navajas-Pérez, M. Pop, M. Alam, R. Ming, A. H. Paterson, S. L. Salzberg. 2008. Genome-wide analysis of repetitive elements in papaya. Tropical Plant Biology 1:191-201.

41. Tang, H., J. E. Bowers, X. Wang, R. Ming, M. Alam, A. H. Paterson. 2008. Synteny and colinearity in plant genomes. Science 320:486-488.

40. Ming, R.*, S. Hou*, Y. Feng*, Q. Yu*, A. Dionne-Laporte, J. H. Saw, P. Senin, W. Wang, B. V. Ly, K. L. T. Lewis, S. L. Salzberg, L. Feng, M. R. Jones, R. L. Skelton, J. E. Murray, C. Chen, W. Qian, J. Shen, P. Du, M. Eustice, E. Tong, H. Tang, E. Lyons, R. E. Paull, T. P. Michael, K. Wall, D. Rice, H. Albert, M.-L. Wang, Y. J. Zhu, M. Schatz, N. Nagarajan, R. Acob, P. Guan, A. Blas, C. M. Wai, C. M. Ackerman, Y. Ren, C. Liu, J. Wang, J. Wang, J.-K. Na, E. V. Shakirov, B. Haas, J. Thimmapuram, D. Nelson, X. Wang, J. E. Bowers, A. R. Gschwend, A. L. Delcher, R. Singh, J. Y. Suzuki, S. Tripathi, K. Neupane, H. Wei, B. Irikura, M. Paidi, N. Jiang, W. Zhang, G. Presting, A. Windsor, R. Navajas-Pérez, M. J. Torres, F. A. Feltus, B. Porter, Y. Li, A. M. Burroughs, M.-C. Luo, L. Liu, D. A. Christopher, S. M. Mount, P. H. Moore, T. Sugimura, J. Jiang, M. A. Schuler, V. Friedman, T. Mitchell-Olds, D. E. Shippen, C. W. dePamphilis, J. D. Palmer, M. Freeling, A. H. Paterson, D. Gonsalves, L. Wang, M. Alam. 2008.  The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature 452:991-996. (*Equal contribution) (Cover article).

39. Yu, Q., D. Steiger, E. Kramer, P.H. Moore, R. Ming. 2008. Floral MADS-Box genes in trioecious papaya: Characterization of AG and AP1 subfamily genes revealed a sex-type-specific gene. Tropical Plant Biology 1:97-107.

38. Paterson, A.H, P. Felker, S. P. Hubbell, R. Ming. 2008.  The fruits of tropical plant genomics. Tropical Plant Biology 1:3-19.

37. Yu, Q., R. Navajas-Pérez, E. Tong, J. Robertson, P. H. Moore, A. H. Paterson, R. Ming. 2008. Recent origin of dioecious and gynodioecious Y chromosomes in papaya. Tropical Plant Biology 1:49-57.

36. Eustice, M., Q. Yu, C.W. Lai, S. Hou, J. Thimmapuram, L. Liu, M. Alam, P.H. Moore, G.G. Presting, R. Ming. 2008. Development and application of microsatellite markers for genomic analysis of papaya. Tree Genetics and Genomics 4:333-341.

35. Vega, F.E., A.W. Ebert, R. Ming. 2008. Coffee germplasm resources, genomics, and breeding. Plant Breeding Review 30:415-447.

34. Ackerman, C.M., Q. Yu, S. Kim, R.E. Paull, P.H. Moore, R. Ming. 2008. B-class MADS-box genes in trioecious papaya: Two TM6 paralogs, CpTM6-1 and CpTM6-2, and a PI ortholog CpPI. Planta 227:741-753.

33. Yu, Q., S. Hou, F.A. Feltus, M. R. Jones, J. Murray, O. Veatch, C. Lemke, J.H. Saw, R.C. Moore, J. Thimmapuram, L. Liu, P.H. Moore, M. Alam, J. Jiang, A. H. Paterson, R. Ming. 2008. Low X/Y divergence in four pairs of papaya sex-liked genes. The Plant Journal 53:124-132 (Cover article).

32. Chen, C., Q. Yu, S. Hou, Y. Li, M. Eustice, R. L. Skelton, O. Veatch, R. Herdes, L. Diebold, J. Saw, Y. Feng, L. Bynum, L. Wang, P. H. Moore, R. E. Paull, M. Alam, R. Ming. 2007. Construction of a sequence-tagged high density genetic map of papaya for comparative structural and evolutionary genomics in Brassicales. Genetics 177:2481-2491.

31. Yu, Q., S. Hou, R. Hobza, F.A. Feltus, X. Wang, W. Jin, R.L. Skelton, A. Blas, C. Lemke, J. H. Saw, P. H. Moore, M. Alam, J. Jiang, A. H. Paterson, B. Vyskot, R. Ming.  2007. Chromosomal location and gene paucity of the male specific region on papaya Y chromosome. Mol. Genet. Genomics 278:177-185.

30. Ming, R., Q. Yu, P.H. Moore. 2007. Sex determination in papaya. Seminars in Cell and Developmental Biology 18:401-408.

29. Ming, R., P.H. Moore. 2007. Genomics of sex chromosomes. Current Opinion in Plant Biology. 10:123-130.

28. Ming, R., J. Wang, P.H. Moore, A.H. Paterson. 2007. Sex chromosomes in flowering plants.  American Journal of Botany. 94:141-150 (Cover article).

27. Skelton, R.L., Q. Yu, R. Srinivasan, R. Manshardt, P.H. Moore, R. Ming. 2006.  Tissue differential expression of Lycopene β-cyclase gene in papaya. Cell Research 16:731-739.

26. Lai, C.W.J., Q. Yu, S. Hou, R.L. Skelton, M. R. Jones, K.L.T. Lewis, J. Murray, M. Eustice, P. Guan, R. Agbayani, P. H. Moore, R. Ming, G. Presting. 2006. Analysis of papaya BAC end sequences reveals first insights into the organization of a fruit tree genome. Mol. Genet. Genomics 276:1-12.

25. Ming, R., P. H. Moore, K. K. Wu, A. D’Hont, J. C. Glaszmann, T. L. Tew, T. E. Mirkov, J. da Silva, J. Jifon, M. Rai, R. J. Schnell, S. M. Brumbley, P. Lakshmanan, J. C. Comstock, A. H. Paterson.  2006. Sugarcane improvement through breeding and biotechnology.  Plant Breeding Review 27:15-118.

24. Yu, Q. P. H. Moore, H. H. Albert, A. H.K. Roader, R. Ming. 2005. Cloning and characterization of a FLORICAULA/LEAFY ortholog, PFL, in polygamous papaya. Cell Research 15:576-584.

23. Schenck, S., H. M. Pearl, Z. Liu, .P. H. Moore, R. Ming. 2005 Genetic Variation of Ustilago scitaminea pathotypes in Hawaii evaluated by host range and AFLP markers. Sugarcane International 23:15-19.

22. Kato, C.Y., C. Nagai, P.H. Moore, F. Zee, M.S. Kim, D.L. Steiger, R. Ming.  2004. Intra-specific DNA polymorphism in pineapple (Ananas comosus L.) assessed by AFLP markers. Genetic Resources and Crop Evolution 51:815-825.

21. Schenck, S., M.W. Crepeau, K.K. Wu, P.H. Moore, Q. Yu, R. Ming. 2004. Genetic Diversity and Relationships in Native Hawaiian Saccharum officinarum sugarcanes. J. Heredity 95: 327-331 (Cover article).

20. Pearl, H. M, C. Nagai, P. H. Moore, D. L. Steiger, R. V. Osgood, R. Ming. 2004.  Construction of a genetic map for arabica coffee. Theor. Appl. Genet. 108:829-835.

19. Ma, H., P. H. Moore, Z. Liu, M. S. Kim, Q. Yu, M. M. M. Fitch, T. Sekioka, A. H. Paterson, R. Ming.  2004. High-density genetic mapping revealed suppression of recombination at the sex determination locus in papaya. Genetics 166:419-436.

18. Liu, Z., P. H. Moore, H. Ma, C. M. Ackerman, R. Makandar, Q. Yu, H. M. Pearl, M. S. Kim, J. W. Charlton, J. I. Stiles, F. T. Zee, A. H. Paterson, R. Ming.   2004. A primitive Y chromosome in papaya marks incipient sex chromosome evolution. Nature 427:348-352.

17. Bowers, J.E., C. Abbey, S. Anderson, C. Chang, X. Draye, A. H. Lattu, R. Jessup, C. Lemke, J. Lennington, Z. Li, Y.-R. Lin, S.-C. Liu, L. Luo, B. S. Marler, R. Ming, S. E. Mitchell, D. Qiang, K. Reischmann, S.R. Schulze, D. N. Skinner, Y.-W. Wang, S. Kresovich, K. F. Schertz, A. H. Paterson.  2003. A high-density genetic recombination map of sequence-tagged sites for Sorghum, as a framework for comparative structural and evolutionary genomics of tropical grains and grasses. Genetics 165:367-386.

16. Zhou, L., C.-C. Chen, R. Ming, D.A. Christopher, R.E. Paull. 2003. Apoplastic invertase and its enhanced expression and post-translation control during fruit maturation and ripening. J. Amer. Soc. Hort. Sci. 128:628-635.

15. Yu, Q., A. M. Alvarez, P. H. Moore, F. Zee, M. S. Kim, A. de Silva, P. R. Hepperly, R. Ming. 2003. Molecular Diversity of Ralstonia solanacearum isolated from ginger in Hawaii.  Phytopathology 93:1124-1130.

14. Steiger, D.L., P.H. Moore, F. Zee, Z. Liu, R. Ming. 2003. Genetic relationships of macadamia cultivars and species revealed by AFLP markers. Euphytica 132:269-277.

13. Deputy, J. C., R. Ming, H. Ma, Z. Liu, M. Fitch, R. Manshardt, J.I. Stiles.  2002.  Molecular markers for sex determination in papaya (Carica papaya L.), Thoer. Appl. Genet. 106:107-111.

12. Ming, R., T. DelMonte, P.H. Moore, J.E. Irvine, A.H. Paterson. 2002. Comparative analysis of QTLs affecting plant height and flowering time among closely-related diploid and polyploid genomes. Genome 45:794-803.

11. Kim, M.S., P. H. Moore, F. Zee, M.M.M. Fitch, D. L. Steiger, R. M. Manshardt, R. E. Paull, R. A. Drew, T. Sekioka, R. Ming. 2002.  Genetic diversity of Carica papaya L as revealed by AFLP markers. Genome 45:503-512.

10. Ming, R., Y.-W. Wang, X. Dryer, P.H. Moore, J.E. Irvine, A.H. Paterson. 2002. Molecular dissection of complex traits in autopolyploid: Mapping QTLs influencing sugar yield and related traits in sugarcane. Thoer. Appl. Genet. 105:332-345.

9. Steiger, D.L., C. Nagai, P. H. Moore, C. W. Morden, R. V. Osgood, R. Ming.  2002. AFLP analysis of genetic diversity within and among Coffea arabica cultivars. Thoer. Appl. Genet. 105:209-215.

8. Ming, R., S.C. Liu, J.E. Bowers, P.H. Moore, J.E. Irvine, A.H. Paterson 2002 Construction of a Saccharum consensus genetic map from two interspecific crosses between S. officinarum and S. spontaneum. Crop Science 42:570-583.

7. Ming, R., S.C. Liu, P.H. Moore, J.E. Irvine, A.H. Paterson. 2001. QTL analysis in a complex autopolyploid: Genetic control of sugar content in sugarcane. Genome Research 11:2075-2084.

6. Ming, R., P.H. Moore, F.T. Zee, Abbey, C., H. Ma, A.H. Paterson.  2001. A papaya BAC library as a foundation for molecular dissection of a tree-fruit genome. Theor. Appl. Genet. 102:892-899.

5. Paterson, A.H, J.E Bowers, M.D Burow, X. Draye, C.G. Elsik , C. Jiang , C.S. Katsar , T. Lan , Y. Lin , R. Ming , R.J. Wright. 2000. Comparative genomics of plant chromosomes. Plant Cell 12:1523-1539.

4. Ming, R., J.L. Brewbaker, H.G. Moon,  T.A. Musket, R. Holley, J. K. Pataky, M.D. McMullen. 1999.  Identification of RFLP markers linked to a major gene, sw1, conferring resistance to Erwinia stewartii. Maydica 44:319-323

3. Kyetere, D.T., R. Ming, M.D. McMullen, R.C. Pratt, J.L. Brewbaker, T. Musket. 1999.  Monogenic tolerance to maize streak virus mapped on the short arm of chromosome 1. Genome 42:20-26.

2. Ming, R., S.-C. Liu, Y.-R. Lin,  D. Braga, J. da Silva, A. van Deynze, T. F. Wenslaff, K.K Wu, P. H. Moore, W. Burnquist, M. E. Sorrells, J. E. Irvine, A. H. Paterson. 1998. Alignment of Sorghum and Saccharum Chromosomes: Comparative organization of closely-related diploid and polyploid genomes. Genetics 150:1663-1882.

1. Ming, R., J.L. Brewbaker, R.C. Pratt, T. Musket, M.D. McMullen. 1997.  Molecular mapping of a major gene conferring resistance to maize mosaic virus resistance. Theor. Appl. Genet. 95:271-275.


R. Ming and P. H. Moore (eds.) 2013. Genetics and Genomics of Papaya.  Springer, Heidelberg, Germany. (in press)

P. Moore and R. Ming (eds.) 2008. Genomics of Tropical Crop Plants.  Springer, Heidelberg, Germany.

Book Chapters

Aryal. J., R. Ming. 2013. Cloning major genes controlling fruit flesh color in papaya. In: R. Ming and P. Moore (eds.) Genetics and Genomics of Papaya. pp. 341-354. Springer, Heidelberg, Germany.

Wang, J., J.-K. Na, R. Ming. 2013. Physical mapping of papaya sex chromosomes. In: R. Ming and P. Moore (eds.) Genetics and Genomics of Papaya. pp. 329-340. Springer, Heidelberg, Germany.

VanBuren, R., R. Ming. 2013. Genomics of papaya sex chromosomes. In: R. Ming and P. Moore (eds.) Genetics and Genomics of Papaya. pp. 309-328. Springer, Heidelberg, Germany.

VanBuren, R., R. Ming. 2013. Sequencing and assembly of the transgenic papaya genome. In: R. Ming and P. Moore (eds.) Genetics and Genomics of Papaya. pp. 187-204. Springer, Heidelberg, Germany.

Han. J., R. Ming. 2013 Molecular genetic mapping of papaya. In: R. Ming and P. Moore (eds.) Genetics and Genomics of Papaya. pp. 143-165. Springer, Heidelberg, Germany.

Ming, R. Q. Yu, P.H. Moore. 2012. Papaya genome and genomics. In: Raymond Schnell (ed.): Tree Genomics. Springer, Heidelberg, Germany.

Wai, C.M., J. Han, R. Singh, R. Aryal, M.-L. Wang, R. Ming. 2012. Analyzing the papaya genome. In: Karen Nelson (ed.): Genomics and the Developing World. Springer, Heidelberg, Germany.

Gschwend, A.R., R. Ming. 2011. Papaya sex chromosomes. In: Rafael Navajas Pérez (ed.): New Insights on Plant sex chromosomes. Nova Science Publishers, Inc. Hauppauge, New York.

Scheldeman, X., T. Kyndt, G. C. d'Eeckenbrugge, R. Ming, R. Drew, B. Van Droogenbroeck, P. Van Damme, P. H. Moore. 2010 Carica papaya and its close wild relatives, Vasconcellea species. In: Chittaranjan Kole (ed.): Wealth of wild species: Role in plant genome elucidation and improvement. Springer, Heidelberg, Germany.

Paterson, A. H., G. Souza, M.-A. van Sluys, R. Ming, A. D’Hont. 2010 Structural genomics and genome sequencing in sugarcane. In: Robert Henry (ed.): Sugarcane Monograph. Springer, Heidelberg, Germany.

Ming, R., Q. Yu, A. Blas, C. Chen, J.-K. Na, and Paul H. Moore 2008. Genomics of Papaya, a Common Source of Vitamins in the Tropics. In: P. Moore and R. Ming (eds.) Genomics of Tropical Crop Plants.  Springer, Heidelberg, Germany.

Peace, C., R. Ming, A. Schmidt, J. Manners, and V. Vithanage 2008. Genomics of Macadamia, a Recently Domesticated Tree Nut Crop. In: P. Moore and R. Ming (eds.) Genomics of Tropical Crop Plants.  Springer, Heidelberg, Germany.

Alvarez, A.M., Trotter, K.J., Swafford, M.B. Berestecky, J.M. Yu, Q, Ming, R. Hepperly, P.R. Zee, F.  2005.  Characterization and detection of Ralstonia solanacearum strains causing bacterial wilt of ginger in Hawaii.  In: C. Allen, P. Prior, and A.C. Hayward (eds.) Bacterial Wilt Disease and the Ralstonia solanacearum species complex. pp. 471-477. APS Press (American Phytopathological Society) St. Paul, Mn. USA

Ming, R., B. Van Droogenbroeck, P. H. Moore, F. T. Zee, T. Kyndt, X. Scheldeman, T. Sekioka, G.. Gheysen.  2005.  Molecular diversity of Carica papaya and related species. In: Arun Kumar Sharma, Archna Sharma (eds.), Plant Genome: Biodiversity and Evolution. Volume 1B: Phanerograms. pp. 229-254.  Science Publishers, Enfield, New Hampshire, USA.