Extended References

Eukaryotic Gene Structure

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Chromosomal Organization of Genes and Noncoding DNA

Celniker, S. E., and G. M. Rubin. 2003. The Drosophila melanogaster genome. Ann. Rev. Genomics Hum. Genet. 4:89–117.

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Transposable (Mobile) DNA Elements

Curcio, M. J., and K. M. Derbyshire. 2003. The outs and ins of transposition: from mu to kangaroo. Nature Rev. Mol. Cell Biol. 4:865–877.

Goodier, J. L., and H. H. Kazazian, Jr. 2008. Retrotransposons revisited: the restraint and rehabilitation of parasites. Cell 135:23–35.

Jones, R. N. 2005. McClintock’s controlling elements: the full story. Cytogenet. Genome Res. 109:90–103.

Lisch, D. 2009. Epigenetic regulation of transposable elements in plants. Ann. Rev. Plant Biol. 60:43–66.

Genomics: Genome-Wide Analysis of Gene Structure and Function

BLAST Information can be found at: http://blast.ncbi.nlm.nih.gov/Blast.cgi.

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du Plessis, L., N. Skunca, and C. Dessimoz. 2011. The what, where, how and why of gene ontology—a primer for bioinformaticians. Brief Bioinform. 12:723–735.

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Lander, E. S. 2011. Initial impact of the sequencing of the human genome. Nature 470:187–197.

Mills, R. E., et al. 2011. Mapping copy number variation by population-scale genome sequencing. Nature 470:59–65.

Picardi, E., and G. Pesole. 2010. Computational methods for ab initio and comparative gene finding. Meth. Mol. Biol. 609:269–284.

Ramskold, D., et al. 2009. An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data. PLoS Comput. Biol. 5:e1000598.

Raney, B. J., et al. 2011. ENCODE whole-genome data in the UCSC genome browser (2011 update). Nucl. Acids Res. 39:D871–D875.

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Sonah, H., et al. 2011. Genomic resources in horticultural crops: status, utility and challenges. Biotechnol. Adv. 29:199–209.

Stratton, M. R. 2011. Exploring the genomes of cancer cells: progress and promise. Science 331:1553–1558.

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Structural Organization of Eukaryotic Chromosomes

Bannister, A. J., and T. Kouzarides. 2011. Regulation of chromatin by histone modifications. Cell Res. 21:381–395.

Bernstein, B. E., A. Meissner, and E. S. Lander. 2007. The mammalian epigenome. Cell 128:669–681.

Horn, P. J., and C. L. Peterson. 2006. Heterochromatin assembly: a new twist on an old model. Chromosome Res. 14:83–94.

Kurdistani, S. K. 2011. Histone modifications in cancer biology and prognosis. Prog. Drug Res. 67:91–106.

Luger, K. 2006. Dynamic nucleosomes. Chromosome Res. 14:5–16.

Luger, K., and T. J. Richmond. 1998. The histone tails of the nucleosome. Curr. Opin. Genet. Dev. 8:140–146.

Nasmyth, K., and C. H. Haering. 2005. The structure and function of SMC and kleisin complexes. Ann. Rev. Biochem. 74:595–648.

Schalch, T., et al. 2005. X-ray structure of a tetranucleosome and its implications for the chromatin fibre. Nature 436:138–141.

Woodcock, C. L., and R. P. Ghosh. 2010. Chromatin higher-order structure and dynamics. Cold Spring Harbor Perspect. Biol. 2:a000596.

Morphology and Functional Elements of Eukaryotic Chromosomes

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Belmont, A. S. 2006. Mitotic chromosome structure and condensation. Curr. Opin. Cell Biol. 18:632–638.

Blackburn, E. H. 2005. Telomeres and telomerase: their mechanisms of action and the effects of altering their functions. FEBS Lett. 579:859–862.

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MacAlpine, D. M., and S. P. Bell. 2005. A genomic view of eukaryotic DNA replication. Chromosome Res. 13:309–326.

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Tanaka, T. U. 2010. Kinetochore-microtubule interactions: steps towards bi-orientation. EMBO J. 29:4070–4082.