References

References denoted by *** are especially recommended and/or heavily relied on.

References denoted by # are included in the References folder (those that are freely available, not under subscription constrictions).

454 Life Sciences (2008) At http://www.454.com. Accessed February 21, 2008.

Adams, K.L. and J.F. Wendel. 2005. Polyploidy and genome evolution in plants.  Current Opinions in Plant Biology 8: 135–141.

Aharonia, A., L.C.P. Keizerb, H.J. Bouwmeestera, Z. Suna, M. Alvarez-Huertaa, H.A. Verhoevena, J. Blaasa, A.M.M.L. van Houwelingena, R.C.H. De Vosa, H. van der Voetb, R.C. Jansenb, M. Guisa, J. Molc, R.W. Davisd, M. Schenad, A.J. van Tunena, and A.P. O'Connell. 2000. Identification of the SAAT gene involved in strawberry flavor biogenesis by use of DNA microarrays. Plant Cell 12: 647–661.

Ahn S. and S.D. Tanksley SD. 1993. Comparative linkage maps of the rice and maize genomes. Proc Natl Acad Sci USA 90:7980–7984.

Alba, R., Z. Fei, P. Payton, Y. Liu, S.L. Moore, P. Debbie, J. Cohn, M. D’Ascenzo, J.S. Gordon, J.K.C. Rose, G. Martin, S.D. Tanksley, M. Bouzayen, M.M. Jahn and J. Giovannoni. 2004. ESTs, cDNA microarrays, and gene expression profiling: tools for dissecting plant physiology and development. The Plant Journal 39 (5): 697-714. 

Altschul, S.F., W. Gish, W. Miller, E.W. Myers and D.J. Lipman. 1990. Basic local alignment search tool. J Mol Biol 215 (3):  403-410.

Andolfatto, P. 2005. Adaptive evolution of non-coding DNA in Drosophila. Nature 437:1149-1152.

Arabidopsis Genome Initiative. 2000. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796 – 815.

The Arabidopsis Information Resource (TAIR). At http://www.arabidopsis.org. Accessed February 21, 2008.

Azpiroz-Leehan, R. and K.A. Feldmann. 1997. T-DNA insertion mutagenesis in Arabidopsis: going back and forth. Trends Genet 13: 152-156.

Benson, D.A., I. Karsch-Mizrachi, D.J. Lipman, J. Ostell and D.L. Wheeler. 2005. GenBank. Nucleic Acids Research 13: 33 (Database Issue): D34-D36. Full text article available at http://www.pubmedcentral.gov/articlerender.fcgi?tool=pubmed&pubmedid=15608212

Borevitz, J.O. and M. Nordborg. 2003. The impact of genomics on the study of natural variation in Arabidopsis. Plant Physiology 132: 718–725.

Brendel, V., S. Kurtz and V. Walbot. 2002. Comparative genomics of Arabidopsis and maize: prospects and limitations. Genome Biology 3(3): reviews1005.1–1005.6 (also available at http://genomebiology.com/2002/3/3/reviews/1005).

Brent, M.R. and R. Guigo. 2004. Recent advances in gene structure prediction. Current Opinion in Structural Biology 14: 264–272.

Clark, A.G. and T.S. Whittam. 1992. Sequencing errors and molecular evolutionary analysis. Mol Biol Evol 9(4): 744-752.

Claverie, J-M. 2001. What if there are only 30,000 human genes? Science 291: 1255 – 1257. Available at http://www.sciencemag.org/cgi/content/full/291/5507/1255

***Cullis, C. 2004. Plant genomics and proteomics. Hoboken, NJ: John Wiley & Sons.

de Vicente, M.C. and T. Fulton. 2004. Using molecular marker technology effectively in plant diversity studies. Vol 1. Learning module. CD-ROM. International Plant Genetic Resources Institute, Rome, Italy and Institute for Genomic Diversity, Cornell University, Ithaca, NY, USA.

DeVries, J. and G. Toenniessen. 2001. Securing the harvest: Biotechnology, breeding and seed systems for African crops. New York: The Rockefeller Foundation.

Doerge, R.W. 2002. Mapping and analysis of quantitative trait loci in experimental populations. Nat Rev Genet 3: 43-52.

Doganlar, S., A. Frary, M-C. Daunay, R.N. Lester and S.D. Tanksley. 2002. Conservation of gene function in the Solanaceae as revealed by comparative mapping of domestication traits in eggplant. Genetics 161: 1713–1726.

Ewing, B., L. Hillier, M.C. Wendl and P. Green. 1998. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 8: 175-185.

Fowler, S. and M. Thomashow. 2002. Arabidopsis transcriptome profiling indicates that multiple regulatory pathways are activated during cold acclimation in addition to the CBF cold response pathway. Plant Cell 14: 1675–1690.

Frary Anne, T.C. Nesbitt, Amy Frary, S. Grandillo, E. van der Knaap, B. Cong, J. Liu, J. Meller, R. Elber, K.B. Alpert and S.D. Tanksley. 2000. fw2.2: A quantitative trait locus key to the evolution of tomato fruit size. Science 289: 85-88.

Friend, S.H. and R.B. Stoughton. 2002, February. The magic of microarrays. Scientific American, pp. 44-53.

Fulton, T.M., R. van der Hoeven, N.T. Eannetta and S.D. Tanksley. 2002. Identification, analysis and utilization of Conserved Ortholog Set (COS) markers for comparative genomics in higher plants. Plant Cell 14: 1457-1467.

Gale, M.D., and K.M. Devos. 1998. Comparative genetics in the grasses. Proc Natl Acad Sci  95: 1971-1974.

Genome Research Limited (GRL). 2001. http://www.yourgenome.org

Genomics: Structural and functional studies of genomes (Perspective). 1997. Genomics 45: 244-249.

Goff, S.A., D. Ricke, T.H. Lan, G. Presting, R. Wang, M. Dunn, J. Glazebrook, A. Sessions, P. Oeller, H. Varma et al. 2002. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296: 92–100.

Holland, P.W.H. 1999. The future of evolutionary developmental biology. Nature 402 (Supp): C41-C44.

Huang H, Eitan E. Winter, Huajun Wang, Keith G. Weinstock, Heming Xing, Leo Goodstadt, Peter D. Stenson, David N. Cooper, Douglas Smith, M. Mar Albà, Chris P. Ponting and Kim Fechtel. 2004. Evolutionary conservation and selection of human disease gene orthologs in the rat and mouse genomes. Genome Biol. 5(7): R47 [open access available at http://genomebiology.com/2004/5/7/R47]

 Hudson T.J., D. M. Church, S. Greenaway, H. Nguyen, A. Cook, R. G. Steen, W. J. Van Etten, A. B. Castle, M. A. Strivens, P. Trickett, C. Heuston, C. Davison, A. Southwell, R. Hardisty, A. Varela-Carver, A. R. Haynes, P. Rodriguez-Tome, H. Doi, M. S.H. Ko, J. Pontius, L. Schriml, L. Wagner, D. Maglott, S.D.M. Brown, E. S. Lander, G. Schuler and  P. Denny. 2001. A radiation hybrid map of mouse genes. Nature Genetics  29: 201 – 205

Hughes, K. Molecular Techniques. At http://web.utk.edu/~khughes/main.html. Accessed February 21, 2008.

Hunkapiller, T., R.J. Kaiser, B.F. Koop and L. Hood. 1991. Large-scale and automated DNA sequence determination. Science 253: 59-67.

Illumina, Inc. (2008) At http://www.solexa.com. Accessed February 21, 2008.

International Human Genome Sequencing Consortium. 2001. Initial sequencing and analysis of the human genome. Nature 409: 860-921.

Kamer, P.M. 2000, May 17-18. Developing a genomics/life sciences corridor in New York State: Implications for economic development. Paper presented at The Genomics Revolution: Implications for New York State, Saratoga Springs, New York.

****Koonin, E. 2005. Orthologs, paralogs, and evolutionary genomics. Annu Rev Genet 39: 309-338.

Ku, H-M., T. Vision, J. Liu and S.D. Tanksley. 2000. Comparing sequenced segments of the tomato and Arabidopsis genomes: Large-scale duplication followed by selective gene loss creates a network of synteny. Proc Natl Acad Sci USA 97: 9121– 9126.

Lander, E.S. and N.J. Schork. 1994. Genetic dissection of complex traits. Science 265: 2037–2048.

Lipman, D.J. and W.R. Pearson. 1985. Rapid and sensitive protein similarity searches.  Science 227 (4693): 1435-41.

Liu, B.H. 1998. Statistical genomics: Linkage, mapping, and QTL analysis. New York: CRC Press.

Maxam, A.M. and W. Gilbert. 1977. A new method for sequencing DNA. Proc Natl Acad Sci 74: 5463-5467.

McCallum, C.M., L. Comai, E.A. Greene and S. Henikoff. 2000. Targeted Induced Local Lesions in Genomes (TILLING) for plant functional genomics. Plant Physiology 123: 439-442.

McCook, A. 2005. The Automated DNA sequencer. The Scientist 19 (16): 15.

McKusick, V.A. and F.H. Ruddle. 1987. A new discipline, a new name, a new journal. Genomics 1 (1): 1-2.

Meagher, R. 2000. Phytoremediation of toxic elemental and organic pollutants. Current opinion in plant biology 3: 153-162.

Michelmore, R. 2000. Genomic approaches to plant disease resistance. Current Opinion in Plant Biology 3: 125-131.

***Miller, W., K.D. Makova, A. Nekrutenko and R.C. Hardison. 2004. Comparative genomics. Annu Rev Genomics Hum Genet 5:15-56.

Minorsky, P.V. 2003. Achieving the in silico plant. Systems biology and the future of plant biological research. Plant Physiology 132: 404-409.

National Center for Biotechnology Information (NCBI). At http://www.ncbi.nlm.nih.gov. Accessed February 21, 2008.

National Center for Biotechnology Information (NCBI). Blast information. At http://www.ncbi.nlm.nih.gov/Education/BLASTinfo/information3.html . Accessed February 21, 2008.

***National Center for Biotechnology Information (NCBI). A Science Primer. At http://www.ncbi.nlm.nih.gov/About/primer/index.html. Accessed February 21, 2008.

***National Institutes of Health, National Institute of General Medical Sciences. 2001. Genetics Basics. NIH Publication No. 01-662. Also available at: http://publications.nigms.nih.gov/genetics/

National Research Council. Committee on an Examination of Plant-Science Research Programs in the United States. 1992. Plant Biology Research and Training for the 21st Century. Washington, D.C.: National Academy Press. Available at: http://www.nap.edu/books/0309046793/html/

Pearson, W.R. and D.J. Lipman. 1988. Improved tools for biological sequence comparison. Proc Natl Acad Sci USA 85: 2444-48.

Peterson, D.G., S.R. Schulze, E.B. Sciara, S.A. Lee, J.E. Bowers, A. Nagel, N. Jiang, D.C. Tibbitts, S.R. Wessler and A.H. Paterson. 2002. Integration of Cot analysis, DNA cloning, and high-throughput sequencing facilitates genome characterization and gene discovery. Genome Research 12 (5): 795-807. Also available at: http://www.genome.org/cgi/content/full/12/5/795

Phillips, R.L., and M. Freeling. 1998. Plant genomics and our food supply: An introduction. Proc Natl Acad Sci 95: 1969-1970.

Pimm, S.L., M. Ayres, A. Balmford, G. Branch, K. Brandon, T. Brooks, R. Bustamante, R. Costanza, R. Cowling, L.M. Curran, A. Dobson, S. Farber, G.A.B. da Fonseca, C. Gascon, R. Kitching, J. McNeely, T. Lovejoy, R.A. Mittermeier, N. Myers, J.A. Patz, B. Raffle, D. Rapport, P. Raven, C. Roberts, J.P. Rodriguez, A.B. Rylands, C. Tucker, C. Safina, C. Samper, M.L.J. Stiassny, J. Supriatna, D.H. Wall and D. Wilcove. 2001. Can we defy Nature's end? Science 293: 2207-2208.

Pyper, W. 2003. More plastics as plants. Ecos Magazine (CSIRO) Issue 116: 35. Also available at: http://www.publish.csiro.au/ecos/

Rensink, W.A. and C.R. Buell. 2004. Arabidopsis to rice. Applying knowledge from a weed to enhance our understanding of a crop species. Plant Physiology 135: 622–629.

***Saccone, C. and G. Pesole. 2003. Handbook of comparative genomics: Principles and methodology. New Jersey:  John Wiley and Sons.

Sanger, F., S. Nicklen and A.R. Coulson. 1977. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci 74: 5463-5468.

***Schneider, D. and M. La Rota. 2000. Tutorial: Introduction to Software for the Analysis of Sequence Similarity. Tutorial prepared for the Cornell University course PL BR 607 http://cbsu.tc.cornell.edu/resources/seq_comp/TOC.html

Serageldin, I. and G.J. Persley. 2000. Promethean science: Agricultural biotechnology, the environment and the poor. Washington, D.C.: Consultative Group on International Agricultural Research (CGIAR).

Smith, T.F. 1990. The history of the genetic sequence databases. Genomics 6: 701-707.

Smith, T. and M.S. Waterman. 1981. Identification of common molecular subsequences. Journal of Molecular Biology 147: 195-197.

Somerville, C. and S. Somerville. 1999. Plant functional genomics. Science 285: 380 – 383.

Springer, N.M., X. Xu and W.B. Barbazuk. 2004. Utility of different gene enrichment approaches toward identifying and sequencing the maize gene space. Plant Physiology 136: 3023-3033.

Tang, G.L., B.J. Reinhart, D.P. Bartel and P.D. Zamore. 2003. A biochemical framework for RNA silencing in plants. Genes Dev 17: 49-63.

Van der Hoeven, R., C. Ronning, J. Giovannoni, G. Martin, S.D. Tanksley. 2002. Deductions about the Number, Organization, and Evolution of Genes in the Tomato Genome Based on Analysis of a Large Expressed Sequence Tag Collection and Selective  Genomic Sequencing. Plant Cell 14: 1441–1456.

Venter, J.C., M.D. Adams, E.W. Myers, P.W. Li, R.J. Mural, G.G. Sutton, H.O. Smith, M. Yandell, C.A. Evans, R.A. Holt, J.D. Gocayne, P. Amanatides, R.M. Ballew, D.H. Huson, J.R. Wortman, Q. Zhang, C.D. Kodira, X.H. Zheng, L. Chen, M. Skupski, G. Subramanian, P.D. Thomas, J. Zhang, G.L.G. Miklos, C. Nelson, S. Broder, A.G. Clark, J. Nadeau, V.A. McKusick, N. Zinder, A.J. Levine, R.J. Roberts, M. Simon, C. Slayman, M. Hunkapiller, R. Bolanos, A. Delcher, I. Dew, D. Fasulo, M. Flanigan, L. Florea, A. Halpern, S. Hannenhalli, S. Kravitz, S. Levy, C. Mobarry, K. Reinert, K. Remington, T.J. Abu, E. Beasley, K. Biddick, V. Bonazzi, R. Brandon, M. Cargill, I. Chandramouliswaran, R. Charlab, K. Chaturvedi, Z. Deng, V. Di Francesco, P. Dunn, K. Eilbeck, C. Evangelista, A.E. Gabrielian, W. Gan, W. Ge, F. Gong, Z. Gu, P. Guan, T.J. Heiman, M.E. Higgins, R. Ji Rui, Z. Ke, K.A. Ketchum, Z. Lai, Y. Lei, Z. Li, J. Li, Y. Liang, X. Lin, F. Lu, G.V. Merkulov, N. Milshina, H.M. Moore, A.K. Naik, V.A. Narayan, Neelam-Beena, D. Nusskern, D.B. Rusch, S. Salzberg, W. Shao, B. Shue, J. Sun, Z.Y. Wang, A. Wang, X. Wang, J. Wang, M-H. Wei, R. Wides, C. Xiao and C. Yan. 2001. The sequence of the human genome. Science 291 (5507): 1304-1351.

Vision, T.J., D.G. Brown and S.D. Tanksley. 2000. Origins of Genomic Duplications in

Arabidopsis. Science 290: 2114-2117.

Walbot, V. and D.A. Petrov. 2001. Gene galaxies in the maize genome. PNAS 98: 8163-8164.

Watson, J. and F. Crick. 1953. A structure for Deoxyribose Nucleic Acid. Nature 171: 737.

Wellcome Trust Sanger Institute. YourGenome.org. At http://www.yourgenome.org. Accessed February 21, 2008.

Wesche, P.L., D.J. Gaffney, P.D. Keightley. 2004. DNA Sequence error rates in Genbank records estimated using the mouse genome as a reference. DNA Sequence 15 (5/6): 362-364.

Wu, F., L.A. Mueller, D. Crouzillat, P. Petiard and S.D. Tanksley. 2006. Combining bioinformatics and phylogenetics to identify large sets of single copy, orthologous genes (COSII) for comparative, evolutionary and systematic studies: A test case in the Euasterid plant clade. Genetics (ahead of print) doi: 10.1534/genetics.106.062455.

Yu, J., S. Hu, J. Wang, G.K. Wong, S. Li, B. Liu, Y. Deng, L. Dai, Y. Zhou, X. Zhang et al. 2002. A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296: 79–92.

Yu, J. and E.S. Buckler. 2006. Genetic association mapping and genome organization of maize Current Opinion in Biotechnology 17:155–160.

Yu, J., G. Pressoir, W.H. Briggs, I.V. Bi, M. Yamasaki, J.F. Doebley, M.D. McMullen, B.S. Gaut, J.B. Holland, S. Kresovich and E.S. Buckler. 2006. A unified mixed-model method for association mapping accounting for multiple levels of relatedness. Nature Genetics 38: 203-208.

Zhang, M.Q. 2002. Computational prediction of eukaryotic protein-coding genes. Nat. Rev. Genet. 3: 698–709.