Weekly Schedule
Class Meetings
Tuesdays and Thursdays, 12:30pm – 1:45pm in Olsson Hall 120.
Office Hours
(29 August – 6 December)
Monday, 11am-noon: Jack (Rice 414)
Monday, 1:30-2:45pm: Dave (Rice 507)
Wednesday, noon-1pm: Ashley (Olsson 204)
Wednesday, 2-3pm: Jack (Rice 414)
Friday, 11:30am-12:30pm: Ashley (Olsson 204)
To schedule other times to meet with Dave use: https://davidevans.youcanbook.me/.
Semester Schedule
23 August: Class 1: Life
- What is Life?
- Plan for the Course
- Carbon-Based Life
25 August: Class 2: Platform for Life on Earth
- Common Platform for All Known “Life” on Earth
- DNA Replication
- DNA Interpretation
30 August: Class 3: Reading Genomes
- Completing the Platform for Life (Darwinian Evolution)
- Reading Genomes
- Genome Assembly Problem
1 September: Class 4: The Human Genome
- Instruction Alignment
- Human Genome Project
- Patenting a Gene
- “Finishing” the Human Genome
Monday, 5 September, 8:59pm: Project 1 Due
6 September: Class 5: Analyzing Genomes
- Why all the “v"s in BRCA1 patent sequence?
- GC Content
- What’s a “gene”?
- Hamming Distance
- Edit Distance
8 September: Class 6: Alignment Algorithms
- Analyzing Edit Distance
- Biological Sequence Alignment
- Needleman-Wunsch Algorithm
- What Causes Mutations
- Markov Property
- Amino Acid Swapping Costs (PAM 250)
13 September: Class 7: Estimating Evolutionary Distance
- Alignment with Affine Gaps
- Local Alignment
- BLOSUM Matrix
15 September: Class 8: Phylogeny
- Grading Philosophy (why “Gold Star"s are better than deduction points)
- Introduction to Phylogeny
- Trees in Computer Science and Biology
- Bayes' Theorem
- Parsimony Scoring
- Phootball Phylogenies
22 September: Class 9: Distance-Based Phylogeny
- Multiple Alignment
- Factors that Impact Mutation Rates (Olfactory Gene Loss)
- Tree Reconstruction
- Neighbor-Joining Algorithm
Monday, 26 September, 8:59pm: Project 2 Due
27 September: Class 10: DNA Storage
- What makes DNA (potentially) a useful computing medium
- Stability of DNA
- What’s a mole?
- Storage Density of DNA
- Crash course in Information Theory
29 September: Class 11: Implementing DNA Storage
- 455 Exabytes per gram
- Encoding for Error Correction
- Hamming Codes
- Random Access DNA Storage
Friday, 30 September: Project Idea Due
4 October: Fall Reading Days (No Classes)
6 October: Class 12: Computing with DNA
- Svente Pääblo’s Noble Prize (Neandertal DNA)
- Computing with DNA
- Complexity Classes
- Reductions
- Adleman’s DNA Computer
11 October: Class 13: Genotypes and Phenotypes
- Mendel and Inheritance
- Genome Wide Association Studies
- Quiz 1 (in class) — answers discussed in Class 15
13 October: Project Coordination
Friday, 14 October: Project Proposal Due
18 October: Class 14: Genome Editing
- Brief History of Life on Earth
- Costs and Information-Theoretic Benefits of Sex
- Recombinant DNA
20 October: Class 15: Recombinant DNA
- Quiz 1 Discussion
- Recombinant DNA
25 October: Class 16: CRISPR in Bacteria
- CRISPR mechanisms in Prokaryotes
- Capturing Invader DNA
- Designing gRNA
- Off-Target Effects
27 October: Class 17: CRISPR in Humans
- Limits on the size of the CRISPR array
- DNA Repair Mechanisms
- CRISPR for Genome Editing
- CRISPR Patent Dispute
- Applications of CRISPR
1 November: Class 18: Crispyr CRISPR
- CRISPR Recap
- Human Germline Editing
- Base Editing
Thursday, 3 November: Quiz 2
3 November: Class 19: Even Crispyr CRISPR
- Prime Editing
- Quiz 2
Monday, 7 November: Project Report Due
8 November: Election Day (No Classes)
10 November: Class 20: Death and Cancer
- What do 20-24 year olds in the United States die from?
- Cancer
17 November: Class 21: Computational Epidemiology (guest lecture by Jack Heavey)
22 November: Class 22: Programmable Pharmaceuticals
- Epidemiological Mystery: What happened with stomach cancer?
- Programmable Pharmaceuticals
24 November: Thanksgiving Break (No Classes)
29 November: Class 23: Protein Structure Prediction
- Protein Structure
- AlphaFold
1 December: Class 27: TBA
Thursday, 1 December: Quiz 3
6 December: Class 28: Project Presentations
Tuesday, 6 December: Revised Final Project Report Due