CS 594 – Algorithms of Bioinformatics (Winter 2025-26): videos
All lecture videos · module page · YouTube playlist
61 videos, 18 h 18 min
| Video | Date | Title | Length | Transcript |
|---|---|---|---|---|
| 0 | 2025-10-16 | Welcome, teaching mode, overview, assessment, academic integity, Campuswire, Slido, exam question gallery | 36:10 | transcript & video |
| 1-1 | 2025-10-16 | Protein sequencing and mass spectrometry | 15:02 | transcript & video |
| 1-2 | 2025-10-16 | The Turnpike Problem | 16:01 | transcript & video |
| 1-3 | 2025-10-16 | Backtracking algorithm for the Turnpike Problem | 9:10 | transcript & video |
| 1-4 | 2025-10-23 | Turnpike Backtracking Example | 27:58 | transcript & video |
| 1-5 | 2025-10-23 | Pseudopolynomial Turnpike algorithm | 22:05 | transcript & video |
| 1-6 | 2025-10-23 | Real Spectra | 3:50 | transcript & video |
| 2-1 | 2025-10-23 | Biology big picture | 14:47 | transcript & video |
| 2-2 | 2025-10-30 | Biomolecules | 10:38 | transcript & video |
| 2-3 | 2025-10-30 | What are genes? | 17:01 | transcript & video |
| 2-4 | 2025-10-30 | Gene detection | 7:52 | transcript & video |
| 2-5 | 2025-10-30 | Waiting for words | 32:54 | transcript & video |
| 2-6 | 2025-10-30 | Probability generating functions | 7:50 | transcript & video |
| 2-7 | 2025-11-06 | Probability generating functions part 2 | 29:31 | transcript & video |
| 2-8 | 2025-11-06 | Motifs | 22:52 | transcript & video |
| 2-9 | 2025-11-06 | Motifs finding heuristics | 22:47 | transcript & video |
| 3-1 | 2025-11-13 | Sequence alignment and edit distance | 20:42 | transcript & video |
| 3-2 | 2025-11-13 | Recap: Dynamic programming | 20:23 | transcript & video |
| 3-3 | 2025-11-13 | General alignment scores | 7:54 | transcript & video |
| 3-4 | 2025-11-13 | Local and semiglobal alignments | 12:43 | transcript & video |
| 3-5 | 2025-11-13 | Banded Alignments | 14:02 | transcript & video |
| 3-6 | 2025-11-13 | Exhaustive Tabulation Teaser | 7:26 | transcript & video |
| 3-7 | 2025-11-20 | Exhaustive Tabulation | 22:11 | transcript & video |
| 3-8 | 2025-11-20 | Linear-space alignments | 13:16 | transcript & video |
| 3-9 | 2025-11-20 | Multiple sequence alignment | 50:41 | transcript & video |
| 4-1 | 2025-11-27 | Exploding Newspapers, DNA Sequencing Technology | 25:18 | transcript & video |
| 4-2 | 2025-11-27 | De-novo sequence assembly, Overlap Graphs | 19:47 | transcript & video |
| 4-3 | 2025-11-27 | de Bruijn graph assembly, Hierholzer’s algorithm | 39:39 | transcript & video |
| 5-1 | 2025-12-04 | The read mapping problem in bioinformatics | 17:13 | transcript & video |
| 5-2 | 2025-12-04 | String matching with automata | 32:15 | transcript & video |
| 5-3 | 2025-12-04 | The Knuth-Morris-Pratt algorithm | 14:23 | transcript & video |
| 5-4 | 2025-12-04 | The Aho-Corasick algorithm | 20:00 | transcript & video |
| 5-5 | 2025-12-11 | Inexact matching via alignments | 9:00 | transcript & video |
| 5-6 | 2025-12-11 | k-Mismatch Matching, Longest common extensions | 16:12 | transcript & video |
| 5-7 | 2025-12-11 | SNPs, alignment seeds | 17:35 | transcript & video |
| 6-1 | 2025-12-11 | Suffix trees | 18:38 | transcript & video |
| 6-2 | 2025-12-11 | Suffix tree applications | 13:01 | transcript & video |
| 6-3 | 2025-12-18 | Generalized suffix trees | 25:32 | transcript & video |
| 6-4 | 2025-12-18 | Tandem repeats | 25:01 | transcript & video |
| 6-5 | 2025-12-18 | Longest common extensions and suffix trees | 7:24 | transcript & video |
| 6-6 | 2025-12-18 | Suffix arrays and string sorting | 25:27 | transcript & video |
| 6-7 | 2026-01-15 | DC3 suffix array construction: induced sorting and merging | 14:52 | transcript & video |
| 6-8 | 2026-01-15 | DC 3 suffix array construction: final algorithm | 16:10 | transcript & video |
| 6-9 | 2026-01-15 | The LCP array | 18:48 | transcript & video |
| 6-10 | 2026-01-15 | LCP array construction | 11:10 | transcript & video |
| 7-1 | 2026-01-15 | Range-minimum queries | 10:22 | transcript & video |
| 7-2 | 2026-01-15 | RMQ via sparse tables | 7:09 | transcript & video |
| 7-3 | 2026-01-22 | Cartesian trees | 20:26 | transcript & video |
| 7-4 | 2026-01-22 | String matching in enhanced suffix arrays | 15:14 | transcript & video |
| 7-5 | 2026-01-22 | The Burrows-Wheeler transform | 13:42 | transcript & video |
| 7-6 | 2026-01-22 | The Inverse BWT | 11:16 | transcript & video |
| 7-7 | 2026-01-22 | Random access in BWT-compressed texts | 7:08 | transcript & video |
| 7-8 | 2026-01-22 | String matching in BWT-compressed texts, backward search, FM Index | 9:08 | transcript & video |
| 8-1 | 2026-01-29 | Noncoding RNA | 15:08 | transcript & video |
| 8-2 | 2026-01-29 | RNA secondary structure | 20:41 | transcript & video |
| 8-3 | 2026-01-29 | Pseudoknot-free secondary structures, Nussinov algorithm | 18:19 | transcript & video |
| 8-4 | 2026-01-29 | Refined energy model, Zuker algorithm | 8:58 | transcript & video |
| 8-5 | 2026-01-29 | Grammar based secondary structure prediction | 9:24 | transcript & video |
| 8-6 | 2026-02-05 | Probabilistic context-free grammars | 23:23 | transcript & video |
| 8-6 | 2026-02-05 | Probabilistic Parsing | 20:00 | transcript & video |
| 8-6 | 2026-02-05 | RNA Grammar | 34:58 | transcript & video |