Readings for Comparative Genomics Course

Surveys and reviews on comparative genomics

• Primer on Comparative Genomics in PLoS, Hardison
• Chapter from Human Genetics, Hardison
• Chapter from Annual Reviews, Miller et al.

Other readings in comparative genomics

• UCSC Genome Browser
• PSU Galaxy
• Seipel et al phastCons
• Tutorial on alignments, Pearson
• Alignment by Blast2, Altshul et al.
• Mouse genome paper, Waterson et al.
• Review on recent and ongoing selection, Nielsen et al. Nature Reviews Genetics
• Kreitman review on positive selection
• Review on positive selections, Akey et al. TIG
• McDonald-Kreitman test for non-neutral DNA
• Positive selection on human proteins, Neilsen et al.
• More on positive selection, Bustamante et al.
• Ancestral genotypes now susceptible to diease, DiRienzo et al.
• Rhesus macaque genome, Gibbs et al.
• Review on using conserved noncoding sequences to find regulatory regions, Hardison
• Ultraconserved elements, Bejerano et al.
• Testing enhancers predicted by high constraint, Pennacchio et al.
• Testing enhancers predicted by high regulatory potential, Wang et al.

High throughput assays for functional regions

• ENCODE pilot project, Birney et al.
• "What is a gene, in the post-ENCODE era? Gerstein et al.
• TAF1 binding across the human genome, Kim et al Nature
• CTCF binding across the human genome, Kim et al Cell
• Deletions of ultraconserved elements have no obvious phenotype, Ahituv et al. PLoS Biology

Basics in Genomics

• Major paper from the public Human Genome Project Lander et al., Nature, 2001

Background on molecular genetics

• Textbook, full text and free Working with Molecular Genetics