Bailey Lab Publications
 
   
 
 
 
Publications and PDFs (use PDF hyperlinks to access the article for one time use as a reprint)
  • Vlad, D., D. Kierzkowski, M.I. Rast, F. Vuolo, R.D. Ioio, C. Galinha, X. Gan, M. Hajheidari, A. Hay, R.S. Smith, P. Huijser, C.D. Bailey, M. Tsiantis. 2014. Leaf shape evolution through duplication, regulatory diversification and loss of a homeobox gene. Science 343:780-783. short video description

  • Urban, L. and C. D. Bailey. 2013. Phylogeny of Leavenworthia and Selenia (Brassicaceae) . Systematic Botany 38: 723-736.

  • Alexander, P. J., M. D. Windham, J. B. Beck, I. A. Al-Shehbaz, L. Allphin, and C. D. Bailey. 2013. Molecular phylogenetics and taxonomy of the genus Boechera and related genera (Brassicaceae: Boechereae). Systematic Botany 38: 192-209.

  • Churbanov, A., R. Ryan, N. A. Hasan, C. D. Bailey, H. Chen, and B. G. Milligan. 2012. HighSSR software: High throughput SSR characterization and locus development from next gen sequencing data. Bioinformatics 28: 2797-2803.

  • Beck, J. B., P. A. Alexander, L. Allphin, I. A. Al-Shehbaz, C. Rushworth, C. D. Bailey, and M. D. Windham. 2012. Does hybridization drive the transition to asexuality in diploid Boechera? Evolution 66: 985-995. PDF
  • Govindarajulu, R., C. E. Hughes, P. J. Alexander, and C. D. Bailey. 2011a. The complex evolutionary dynamics of ancient and recent polyploidy in Leucaena (Leguminosae; Mimosoideae). American Journal of Botany 98: 2064-2076. PDF

  • Govindarajulu, R., C. E. Hughes, and C. D. Bailey. 2011b. Phylogenetic and population genetic analyses of diploid Leucaena (Leguminosae; Mimosoideae) reveal cryptic species diversity and patterns of divergent allopatric speciation. American Journal of Botany 98: 2049-2063. PDF

  • Alexander, P. J., M. D. Windham, R. Govindarajulu, I. A. Al-Shehbaz, and C. D. Bailey. 2010. Molecular phylogenetics and taxonomy of the genus Thysanocarpus (Brassicaceae). Systematic Botany 35: 559-577. PDF

  • Cervantes, S. D., P. Tonne, R. Govindarajulu, P. A. Alexander, and C. D. Bailey. 2010. Population genetic analysis of Argemone pleiacantha subsp. pinnatisecta sacramento prickly poppy, Papaveraceae) and re-evaluation of its taxonomic status. Journal of the Botantical Research Institute of Texas 4: 261 – 269. PDF

  • Hasan, N. A., K. Mummenhoff, C. F. Quiros, C. D. Tay, and C. D. Bailey. 2010. Polymorphic chloroplast microsatellite markers in octoploid Lepidium meyenii (Brassicaceae) and cross-species amplification in Lepidium. American Journal of Botany Primer Notes: doi:10.3732/ajb.1000225. PDF

  • Piazza, P., C. D. Bailey, M. Cartolano, J. Krieger, J. Cao, S. Ossowski, K. Schneeberger, F. He, J. de Meaux, N. Hall, N. MacLeod, D. Filatov, A. Hay, and M. Tsiantis. 2010. Arabidopsis thaliana Leaf Form Evolved via Loss of KNOX Expression in Leaves in Association with a Selective Sweep. Current Biology 20: 2223-2228. PDF

  • Cibrián-Jaramillo, A., C. D. Bacon, N. Garwood, R. M. Bateman, M. M. Thomas, S. Russell, C. D. Bailey, W. J. Hahn, S. G. M. Bridgewater, and R. DeSalle. 2009. Population genetics of the understory fishtail palm Chamaedorea ernesti-augusti in Belize: high genetic connectivity with local differentiation. BMC Genetics 10: 65. PDF

  • Bacon, C. D., F. A. Feltus, A. H. Paterson, and C. D. Bailey. 2008. Developing intron-spanning primer sets for low-copy nuclear genes: novel tools for Arecaceae systematics. Molecular Ecology Notes 8: 211-214. PDF

  • Bailey, C. D. 2008. Book Review: Plant Systematics, a phylogenetic approach. Cladistics: 848-850. PDF

  • Bailey, C. D., I. A. Al-Shehbaz, and G. Rajanikanth. 2007. Generic limits in the tribe Halimolobeae and the description of the new genus Exhalimolobos (Brassicaceae). Systematic Botany 32: 140-156. PDF

  • Hughes, C. E., R. Govindarajulu, A. Robertson, S. A. Harris, and C. D. Bailey. 2007. Serendipitous backyard hybridization and the origin of crops. Proceedings of the National Academy of Sciences 104: 14389-14394. PDF

  • Lohithaswa, H. C., F. A. Feltus, H. P. Singh, C. D. Bacon, C. D. Bailey, and A. H. Paterson. 2007. Leveraging the rice genome sequence for monocot comparative and translational genomics. Theoretical and Applied Genetics 115: 237-243. PDF

  • Alexander, P. J., G. Rajanikanth, C. Bacon, and C. D. Bailey. 2006. Rapid inexpensive recovery of high quality plant DNA using a reciprocating saw and silica-based columns. Molecular Ecology Notes 7: 5-9. PDF - note correction, 80 ul of lysis buffer not 320 ul!

  • Bacon, C. D. and C. D. Bailey. 2006. Taxonomy and Conservation: a case study from Chamaedorea alternans. Annals of Botany 98: 775-763. PDF

  • Bailey, C. D., M. G. Fain, and P. Houde. 2006a. On conditioned reconstruction, gene content data, and the recovery of fusion genomes. Molecular Phylogenetics and Evolution 39: 263-270. PDF

  • Bailey, C. D., M. Koch, M. S. Mayer, K. Mummenhoff, S. L. O'Kane, Jr. , S. I. Warwick, M. D. Windham, and I. A. Al-Shehbaz. 2006b. Toward a global phylogeny of the Brassicaceae. Molecular Biology and Evolution 23: 2142–2160. PDF

  • Hughes, C. E., R. J. Eastwood, and C. D. Bailey. 2006. From famine to feast? Selecting nuclear DNA sequence loci for plant species-level phylogeny reconstruction. Philosophical Transactions of the Royal Society B 361: 211-225. PDF

  • Bailey, C. D., C. E. Hughes, and S. A. Harris. 2004. Using RAPDs to identify DNA sequence loci for species level phylogeny reconstruction: an example from Leucaena (Fabaceae). Systematic Botany 29: 4-14. PDF

  • Bailey, C. D., T. G. Carr, S. A. Harris, and C. E. Hughes. 2003. Characterization of angiosperm nrDNA polymorphism, paralogy, and pseudogenes. Molecular Phylogenetics and Evolution 29: 435-455. PDF

  • Hughes, C. E., C. D. Bailey, S. Krosnick, and M. Luckow. 2003. Relationships among genera of the informal Dichrostachys and Leucaena groups (Mimosoideae) inferred from nuclear ribosomal ITS sequences in Klitgaard, B. and A. Bruneau, eds. Advances in Legume Systematics, Part 10, Higher Level Systematics. Royal Botanic Gardens, Kew. PDF

  • Scotland, R., C. E. Hughes, C. D. Bailey, and A. Wortley. 2003. The Big Machine and the Much-Maligned Taxonomist. Systematics and Biodiversity 1: 139-143. PDF

  • Bailey, C. D., R. A. Price, and J. J. Doyle. 2002. Systematics of the Halimolobine Brassicaceae: evidence from three loci and morphology. Systematic Botany 27: 318-332. PDF

  • Hughes, C. E., C. D. Bailey, and S. A. Harris. 2002. Divergent and reticulate species relationships in Leucaena (Fabaceae) inferred from multiple data sources: insights into polyploid origins and nrDNA polymorphism. American Journal of Botany 89: 1057-1073. PDF

  • Bailey, C. D. 2001. Systematics of Sphaerocardamum (Brassicaceae) and related genera. Cornell University Dissertation.

  • Kajita, T., H. Ohashi, Y. Tateishi, C. D. Bailey, and J. J. Doyle. 2001. rbcL and legume phylogeny, with particular reference to phaseoleae, millettieae, and allies. Systematic Botany 26: 515-536. PDF

  • Price, R. A., C. D. Bailey, and I. A. Al-Shehbaz. 2001. Transfer of the cupulate-flowered Arabis microsperma and A. tricornuta (Brassicaceae) to Pennellia. Novon 11: 337-340.

  • Doyle, J. J., J. A. Chappill, C. D. Bailey, and T. Kajita. 2000. Towards a  comprehensive phylogeny of Legumes:  evidence from rbcL sequences and non-molecular data. Pp. 1-20 in Herendeen, P. S. and A. BRUNEAU, eds. Advances in Legume Systematics. The Royal Botanic Gardens, Kew, London.

  • Simmons, M. P., C. D. Bailey, and K. C. Nixon. 2000. Phylogeny reconstruction using duplicate genes. Molecular Biology and Evolution 17: 469-473.

  • Bailey, C. D. and J. J. Doyle. 1999. Potential phylogenetic utility of the low-copy nuclear gene pistillata in dicotyledonous plants: comparison to nrDNA ITS and trnL intron in Sphaerocardamum and other Brassicaceae. Molecular Phylogenetics and Evolution 13: 20-30. PDF

  • Bailey, C. D., J. J. Doyle, T. Kajita, T. Nemoto, and H. Ohashi. 1997. The chloroplast rpl2 intron and ORF184 as phylogenetic markers in the legume tribe Desmodieae. Systematic Botany 22: 133-138. PDF