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Bioinformatics and Genomics for the Biologist

Module: 
6
Section: 
D

Instructor: David MacAlpine
Summary: Computational biology and genomics are a mainstay of modern biology. For example, sequence alignments, identification of gene orthologs and paralogs by blast searches, and motif identification are now routine practices in the laboratory. In addition, the explosion of whole genome sequencing in the last decade has led to a variety of genomic approaches (many based on microarray technology and next-generation sequencing) to phenotype the cell at the level of gene expression and identify networks of co-regulated genes. These computational tools and genomic approaches are likely to be integral components of many research projects.
In this module, we will explore the tools and approaches to analyze next-generation sequencing data. We will make extensive use of Unix, bash scripting, and the R environment for statistical computing. The student will not only learn to critically evaluate these complex genomic experiments, but will also gain first hand experience at analyzing primary data.

Readings: 

Unix Tutorial
http://www.ee.surrey.ac.uk/Teaching/Unix/

R Tutorial
http://www.cyclismo.org/tutorial/R/

Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc. 2012 Mar 1;7(3):562-78. doi: 10.1038/nprot.2012.016. PubMed PMID: 22383036; PubMed Central PMCID: PMC3334321.