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
| Date | Subject |
| 9/24 | Introductory Biology Primer |
| 10/1 | Introduction to Text Processing |
| 10/8 | UCSC Genome Browser Tools |
Schedule
| Date | Title | HW | |
| Related Material | |||
| 1 | 9/20 | Introduction (Serafim) | |
| 2 | 9/22 | DNA Sequencing (Serafim) | |
| 3 | 9/27 | The
Human Genome, Human Variation, Somatic Mutations, and Cancer (Gill) | |
| 4 | 9/29 | Genome
Size, Repetitive Sequences, and Genes (Gill) | HW1 out |
| 5 | 10/4 | Fragment Assembly I (Serafim) | |
| 6 | 10/6 | Fragment Assembly II (Serafim) | |
| 7 | 10/11 | Genome Evolution - Orthology, Paralogy, Chains, and Nets (Gill) | |
| 8 | 10/13 | Genome
Evolution cont., Reconstruction, Genomic Conservation (Gill) | HW2 out |
| 9 | 10/18 | Orthology, Paralogy, and Synteny (Serafim) | |
| 10 | 10/20 | Multiple Sequence Alignment (Serafim) | |
| 11 | 10/25 | Non-coding RNAs (Gill) | Halfway Feedback |
| 12 | 10/27 | Cis-regulation and cellular signaling (Gill) | Project
out HW2 Due 10/29 |
| 13 | 11/1 | Cis-regulation (cont.), GREAT (Gill subs) | |
| 14 | 11/3 | Serafim | |
| 15 | 11/8 | Ultraconserved elements (Gill) | |
| 16 | 11/10 | Ultras (cont.), hCONDELs (Gill) | Project milestone (Friday, 11/12) |
| 17 | 11/15 | Guest speaker: Nadav Ahituv, UCSF | |
| 18 | 11/17 | Guest speaker: Benedict Paten, UCSC | |
| 19 | 11/29 | Guest speaker: Nihar Nayak, Stanford | |
| 20 | 12/1 | Project presentations.aut10 | |