Readings for Functional Genomics Course

Surveys and reviews on comparative and functional genomics

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

Perspectives on functional genomics

• Genomics: Global views of biology, Lander 1996
• Genomics: Initial impact of the human genome, Lander 2011
• The future is bright: Charting a course for genomic medicine, E. Green et al, Science 2011

Browsers and analysis tools, alignments

• PSU Galaxy
• UCSC Genome Browser
• Alignment by Blast 1990, Altshul et al.
• Alignment by Blast2, Altshul et al.
• Chapter on pairwise alignment, Wheeler et al.
• Tutorial on alignments , Bill Pearson, U. VA

Human, mouse and other genomes

• Lander et al., Nature, 2001 Major paper from the public Human Genome Project
• Mouse genome paper, Waterson et al.
• Rhesus macaque genome, Gibbs et al.

Constraint (purifying selection) and function

• Ultraconserved elements, Bejerano et al.
• Review on using conserved noncoding sequences to find regulatory regions, Hardison
• phastCons: Quantitative genome-wide assessment of constraint, Seipel et al. Genome Research

Recent, adaptive, and maladaptive selection

• Review on recent and ongoing selection, Nielsen et al. Nature Reviews Genetics
• Review on positive selection, Sabeti, Lander et al., Science
• Ancestral genotypes now susceptible to diease, DiRienzo et al.
• 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.

High throughput assays for functional regions

• ChIP-seq to determine protein occupancy genome-wide , Johnson et al., Wold and Myers labs
• ENCODE pilot project analysis, Birney et al.
• ENCODE Users's Guide, ENCODE Project Consortium, 2011, PLoS Biology
• Long noncoding RNAs, Guttman et al. Rinn Lab
• "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

Genotype-phenotype associations

• GWAS catalog, Hindorff et al., Manolio, PNAS
• 1000 Genome Project, 2010 analysis, Nature

Predictions and tests of cis-regulatory modules

• Testing enhancers predicted by high constraint, Pennacchio et al.
• Testing enhancers predicted by high regulatory potential, Wang et al.
• Deletions of ultraconserved elements have no obvious phenotype, Ahituv et al. PLoS Biology

Background on molecular genetics

• Textbook, full text and free Working with Molecular Genetics