Lectures
- Lecture 1 : Course introduction, policies and prospective topics & basic bio
- Lecture 2 : Basic bio (part 2) & computational approaches to biological problems
- Lecture 3 : Sequencing by synthesis and “short read” technology
- Lecture 4 : Pairwise sequence alignment
- Lecture 5 : General and affine gap penalties
- Lecture 6 : Optimal alignment in linear space
- Lecture 7 : Multiple Sequence Alignment
- Lecture 8 & 9 : Phylogenomics; small & large phylogeny problem
- Presentation of final project options
- Lecture 10 : Exact pattern matching with KMP
- Lecture 11 : Suffix Tries and Suffix Trees
- Lecture 12 : Suffix Arrays
- Lecture 13 : BWT & FM-index
- Lecture 14 : Overlap, Layout, Consensus assembly
- Lecture 15 : De Bruijn graph (DBG)-based assembly
- Lecture 16 : Exact and approximate representation of k-mers
- Lecture 17 : (Hidden) Markov Models & Inference I
- Lecture 18 : Ab initio gene finding & Inference II
- Lecture 19 : Evidence-based modeling & reference-guided transcript assembly
- Lecture 20 : Fast Algorithms for Improved Transcriptome Analysis I : Transcriptomic Mapping
- Lecture 21 : Fast Algorithms for Improved Transcriptome Analysis II : Quantification
Other links
- Least Common Ancestor (via RMQ) in linear space and constant time
- List of final project options
- Molecular Biology of the Cell
- Transcription
- Translation
Assignments for waitlisted students
- Assignment 1 - academic honesty review — due Tues. Sept 6 by midnight EST.