Eukaryotic Gene Structure

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Davuluri, R. V., et al. 2008. The functional consequences of alternative promoter use in mammalian genomes. Trends Genet. 24:167–177.

Wang, E. T., et al. 2008. Alternative isoform regulation in human tissue transcriptomes. Nature 456:470–476.

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.

Crook, Z. R., and D. Housman. 2011. Huntington’s disease: can mice lead the way to treatment? Neuron 69:423–435.

Feuillet, C., et al. 2011. Crop genome sequencing: lessons and rationales. Trends Plant Sci. 16:77–88.

Giardina, E., A. Spinella, and G. Novelli. 2011. Past, present and future of forensic DNA typing. Nanomedicine (Lond.) 6:257–270.

Hannan, A. J. 2010. TRPing up the genome: tandem repeat polymorphisms as dynamic sources of genetic variability in health and disease. Discov. Med. 10:314–321.

International Human Genome Sequencing Consortium. 2004. Finishing the euchromatic sequence of the human genome. Nature 431:931–945.

Jobling, M. A., and P. Gill. 2004. Encoded evidence: DNA in forensic analysis. Nature Rev. Genet. 5:739–751.

Lander, E. S., et al. 2001. Initial sequencing and analysis of the human genome. Nature 409:860–921.

Todd, P. K., and H. L. Paulson. 2010. RNA-mediated neurodegeneration in repeat expansion disorders. Ann. Neurol. 67:291–300.

Venter, J. C., et al. 2001. The sequence of the human genome. Science 291:1304–1351.

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.

1000 Genomes Project Consortium. 2010. A map of human genome variation from population-scale sequencing. Nature 467:1061–1073.

Alkan, C., B. P. Coe, and E. E. Eichler. 2011. Genome structural variation discovery and genotyping. Nature Rev. Genet. 12:363–376.

Chimpanzee Sequencing and Analysis Consortium. 2005. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437:69–87.

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.

Ideker, T., J. Dutkowski, and L. Hood. 2011. Boosting signal-to-noise in complex biology: prior knowledge is power. Cell 144:860–863.

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.

Sleator, R. D. 2010. An overview of the current status of eukaryote gene prediction strategies. Gene 461:1–4.

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.

Venter, J. C. 2011. Genome-sequencing anniversary. The human genome at 10: successes and challenges. Science 331:546–547.

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.

Cvetic, C., and J. C. Walter. 2005. Eukaryotic origins of DNA replication: could you please be more specific? Semin. Cell Dev. Biol. 16:343–353.

Froenicke, L. 2005. Origins of primate chromosomes as delineated by Zoo-FISH and alignments of human and mouse draft genome sequences. Cytogenet. Genome Res. 108:122–138.

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

Ohta, S., et al. 2011. Building mitotic chromosomes. Curr. Opin. Cell Biol. 23:114–121.

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