Course documents: Reading list

Genomics

• Genome assembly:
  • Pop M (2009) Genome assembly reborn: recent computational challenges. Brief Bioinform 10(4), 354—366
  • Sommer DD, Delcher AL, Salzberg SL, Pop M (2007) Minimus: a fast, lightweight genome assembler. BMC Bioinformatics 8, 64 Huang X et al (2003) PCAP: a whole-genome assembly program. Genome Res 13(9), 2164—2170 -->
  • Salzberg SL, Yorke JA (2005) Beware of mis-assembled genomes. Bioinformatics 21(24), 4320—4321
• Read mapping
  • Trapnell C, Salzberg SL (2009) How to map billions of short reads onto genomes. Nat Biotechnol 27(5), 455—457
  • Li H, Ruan J, Durbin R (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 18(11), 1851—1858
  • Koehler R, Issac H, Cloonan N, Grimmond SM (2011) The uniqueome: a mappability resource for short-tag sequencing. Bioinformatics 27(2), 272—274
• Genome aligment
  • Blanchette M et al (2004) Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res 14(4), 708—715
• GWAS
  • McCarthy MI et al (2008) Genome-wide association studies for complex traits: consensus, uncertainty and challenges. Nat Rev Genet 9(5), 356—369
  • Wellcome Trust Case Control Consortium (2007) Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 447(7145), 661—678
  • Weedon MN et al (2008) Genome-wide association analysis identifies 20 loci that influence adult height. Nat Genet 40(5), 575—583
  • Duerr RH et al (2006) A genome-wide association study identifies IL23R as an inflammatory bowel disease gene. Science 314(5804), 1461—1463

Transcriptomics

• Wold B, Myers RM (2008) Sequence census methods for functional genomics. Nat Methods 5(1), 19—21 --> Slonim D, et al (2000) Class prediction and discovery using gene expression data. RECOMB 2000. Mortazavi A et al (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5(7), 621—628 -->
• Wang ET et al (2008) Alternative isoform regulation in human tissue transcriptomes. Nature 456(7221), 470—476
• Trapnell C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25(9), 1105—1111
• Au KF et al (2010) Detection of splice junctions from paired-end RNA-seq data by SpliceMap. Nucleic Acids Res 38(14), 4570—4578