Overview: 

Bentley, D. R. (2006) Whole-genome re-sequencing, Current Opinion in Genetics & Development, 16:545-552. 

Dohm et al. (2008) Substantial biases in ultra-short read data sets from high-throughput DNA sequencing, Nucleic Acids Research 36:e105.  

454 sequencing:

Meyer, M., Stenzel, U., Hofreiter, M. (2008) Parallel tagged sequencing on the 454 platform, Nature Protocols 3:267-278.  

Margulies et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors, Nature 437:376-380. 

Vera et al. (2008) Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing, Molecular Ecology 17:1636-1647.

Green et al. (2008) A Complete Neandertal Mitochondrial Genome Sequence Determined by High-Throughput Sequencing, Cell 134: 416-426.

Other methods (e.g Solexa and Sanger):

Campbell et al. (2008) Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing, Nature Genetics 40:722-729. 

Levy et al. (2007) The diploid genome sequence of an individual human, PLoS Biology 5:e254. 

Gene annotation:

Emrich et al. (2007) Gene discovery and annotation using LCM-454 transcriptome sequencing, Genome Research 17:69-73. 

Alternative splicing:

Barbazuk et al. (2008) Genome-wide analyses of alternative splicing in plants: Opportunities and challenges, Genome Research 18:1381-1392. 

Xiao et al. (2007) Coevolutionary networks of splicing cis-regulatory elements, PNAS 104:18583-18588. 

microRNA:

O. Hobert (2008) Gene regulation by transcription factors and micro RNAs, Science 319:1785-1786. 

Makeyev et al. (2008) Multilevel regulation of gene expression by microRNAs, Science 319:1789-1790. 

Friedländer et al. (2008) Discovering microRNAs from deep sequencing data using miRDeep, Nature Biotechnology 26:407-415.

Morin et al. (2008) Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells, Genome Research 18:610-621. 

Epigenetics:

Zhu, J-K. (2008) Epigenome sequencing comes of age, Cell 133:395-397.

Bock, C., Lengauer, T. (2008) Computational epigenetics, Bioinformatics 24:1-10. 

Lister et al. (2008) Highly integrated single-base resolution maps of the epigenome in arabidopsis, Cell 133:523-536. 

Polymorphism in local populations:

Korbel et al. (2007) Paired-end mapping reveals extensive structural variation in the human genome, Science 318:420-426. 

Ross-Ibarra et al. (2008) Patterns of polymorphism and demographic history in natural populations of Arabidopsis lyrata, PLoS ONE, 3:e2411. 

Evolution of gene regulatory networks:

Crombach, A., Hogeweg, P. (2008) Evolution of evolvability in gene regulatory networks, PLoS Computational Biology 4:e1000112.

Gene family evolution:

Roth et al. (2006) Evolution after gene duplication: models, mechanisms, sequences, systems, and organisms, Journal of Experimental Zoology Part B: Molecular and Developmental Evolution 308B:58-73.

Arvestad et al.(2004) Gene tree reconstruction and orthology analysis based on an integrated model for duplications and sequence evolution, RECOMB'04.

Gorecki et al. (2006) DLS-trees: A model of evolutionary scenarios, Theoretical Computer Science 359:378-399. 

Gene expression:

Torres et al. (2008) Gene expression profiling by massively parallel sequencing, Genome research 18:172-177. 

Segal et al. (2008) Predicting expression patterns from regulatory sequence in Drosophila segmentation, Nature 451: 535-540. 

Chang et al. (2008) Computational identification of the normal and perturbed genetic networks involved in myeloid differentiation and acute promyelotic leukemia, Genome Biology 9:R38.

Sharon et al. (2008) A feature-based approach to modeling protein-DNA interactions, PLoS Computational Biology 4:e1000154.