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
The following is a list of introductory sessions for students unfamiliar with (or just wanting a refresher lecture on) biology and computer science to the depth necessary to make the course enjoyable. All sessions will take place in Beckman B-302 (the lecture room) from 10:00am-11:00am.
| Date | Subject |
| 9/30 | Introductory Biology Primer |
| 10/7 | Introduction to Text Processing |
| 10/14 | UCSC Genome Browser Tools |
Schedule
As the quarter progresses, the following schedule will be updated accordingly. Please check back often for the latest material. Homework related materials require a SUNet ID and password for registered students. If you are auditing the class and want access to these materials, please email the staff mailing list.
| Date | Title | HW | |
| Related Material | |||
| 1 | 9/26 | Gill: Introduction | |
| 2 | 9/28 | Serafim: DNA Sequencing Part I | |
| 3 | 10/3 | Serafim: DNA Sequencing Part II | |
| 4 | 10/5 | Gill: Human Genomic Variation | HW1 out |
| 5 | 10/10 | Gill: Genome Size, Repeats & Genes | |
| 6 | 10/12 | Gill: Genome Evolution, Chromosomal Mutations, Paralogy & Orthology, Chains & Nets | |
| 7 | 10/17 | Gill: Chains & Nets, Genome Reconstruction, Conservation | |
| 8 | 10/19 | Serafim: Human Population Genomics I | HW2 out |
| 9 | 10/24 | Serafim: Human Population Genomics II | |
| 10 | 10/26 | Serafim: Cancer Genomics | |
| 11 | 10/31 | Gill: Conservation & Non-Coding RNAs | Halfway Feedback |
| 12 | 11/2 | Gill: Gene Regulation | Project out HW2 Due 11/4 |
| 13 | 11/7 | Gill: GREAT.stanford.edu & The search for what makes us human | |
| 14 | 11/9 | Serafim: Sequencing extinct human ancestors I | |
| 15 | 11/14 | Serafim: Sequencing extinct human ancestors II | |
| 16 | 11/16 | Serafim: Batzoglou Lab Projects | Project milestone (Monday, 11/21) |
| 17 | 11/28 | Serafim/Gill: Guest #1 | |
| 18 | 11/30 | Serafim/Gill: Guest #2 | |
| 19 | 12/5 | Serafim/Gill: Guest #3 | |
| 20 | 12/7 | Serafim+Gill+CAs: Project Presentations | |