Lecture 1: Welcome!
Lecture 2: BLAST is a Microcosm of All that is Wrong in Bioinformatics
Lecture 3: Mapping. References:
Flicek, P., & Birney, E. (2009). Sense from sequence reads: methods
for alignment and assembly. Nature Methods, 6(11 Suppl), S6?S12.
doi:10.1038/nmeth.1376
http://www.ncbi.nlm.nih.gov/pubmed?term=19844229
Glenn, T. C. (2011). Field guide to next-generation DNA sequencers.
Molecular Ecology Resources. doi:10.1111/j.1755-0998.2011.03024.x
http://www.ncbi.nlm.nih.gov/pubmed/21592312
Hudson, M. E. (2008). Sequencing breakthroughs for genomic ecology and
evolutionary biology. Molecular Ecology Resources, 8(1), 3?17.
doi:10.1111/j.1471-8286.2007.02019.x
http://www.ncbi.nlm.nih.gov/pubmed?term=21585713
Li, H., & Homer, N. (2010). A survey of sequence alignment algorithms
for next-generation sequencing. Briefings in bioinformatics, 11(5),
473?483. doi:10.1093/bib/bbq015
http://www.ncbi.nlm.nih.gov/pubmed?term=20460430
Lecture 4: Assembly. Reference:
Lecture 5: ChIP-Seq Studies.
Lecture 6: Designing experiments and thinking about statistics:
Paul L. Auer and R.W. Doerge 2010. Statistical Design and Analysis of
RNA-Seq Data. Genetics. 10.1534/genetics.110.114983
PMID: 20439781
Bullard, J. H., Purdom, E., Hansen, K. D., & Dudoit, S. (2010).
Evaluation of statistical methods for normalization and differential
expression in mRNA-Seq experiments. BMC Bioinformatics, 11, 94.
doi:10.1186/1471-2105-11-94