Course Description
Introduction to computational biology through an informatic exploration of the human genome. Topics include: genome sequencing (technologies, assembly, personalized sequencing); functional landscape (genes, gene regulation, repeats, RNA genes, epigenetics); genome evolution (comparative genomics, ultraconservation, co-option). Additional topics may include population genetics, personalized genomics, and ancient DNA. Course includes primers on molecular biology, the UCSC Genome Browser, and text processing languages. Guest lectures from genomic researchers.

Introductory Bio and CS Sessions

19/20Introduction (Serafim) 
29/22DNA Sequencing (Serafim) 
39/27The Human Genome, Human Variation,
Somatic Mutations, and Cancer (Gill)
49/29Genome Size, Repetitive Sequences,
and Genes (Gill)
HW1 out
510/4Fragment Assembly I (Serafim) 
610/6Fragment Assembly II (Serafim) 
710/11Genome Evolution - Orthology, Paralogy, Chains, and Nets (Gill) 
810/13Genome Evolution cont., Reconstruction,
Genomic Conservation (Gill)
HW2 out
910/18Orthology, Paralogy, and Synteny (Serafim) 
1010/20Multiple Sequence Alignment (Serafim) 
1110/25Non-coding RNAs (Gill)Halfway Feedback
1210/27Cis-regulation and cellular signaling (Gill)Project out
HW2 Due 10/29
1311/1Cis-regulation (cont.), GREAT (Gill subs) 
1511/8Ultraconserved elements (Gill) 
1611/10Ultras (cont.), hCONDELs (Gill)Project milestone (Friday, 11/12)
1711/15Guest speaker: Nadav Ahituv, UCSF 
1811/17Guest speaker: Benedict Paten, UCSC 
1911/29Guest speaker: Nihar Nayak, Stanford 
2012/1Project presentations.aut10