For Fall 2022, CMSC892A meets on Tuesdays and Thursdays from 11:00am - 12:15pm. A tentative course schedule is below.
Week | Day | Date | Class | Notes | Associated Reading |
---|---|---|---|---|---|
1 | Tu | Aug 30th | Preliminaries 1 | Lecture: Class overview and some biological background [1_biol.pdf] | CP Appendix B (for those looking to review algorithms) |
Th | Sep 1st | Preliminaries 2 | Lecture: Inputs, Outputs, and Data Processing as well as Basic Definitions for Phylogenetic Trees (e.g., clade, bipartition, contraction, refinement, etc.) [2_data.pdf] [3_trees.pdf] | CP Sections 2.1-2.2.2, 2.3-2.3.4, 2.5-2.6, and 2.10 | |
2 | Tu | Sep 6th | Genome Assembly and Metagenomics | Guest lecture by Prof. Mihai Pop | NA (Not on exam) |
Th | Sep 8th | Profiling Structural Variants in Cancer | Guest lecture by Dr. Mikhail (Misha) Kolmogorov [5_cancer_svs.pdf] | NA (Not on exam) | |
3 | Tu | Sep 13th | Multiple Sequence Alignment | Lecture: Pairwise alignment (review) and then multiple sequence alignment, specifically generalized tree alignment problem, sum-of-pairs (SOP) alignment problem, STAR alignment [6_msa_part1.pdf] | CP Sections 9.1-9.5.3 and 9.12 |
Th | Sep 15th | Modern MSA | Lecture: Consistency and maximum weight trace (MWT) problem, sequence profiles, aligning alignments, progressive alignment, iterative refinement, divide-and-conquer, popular MSA methods (Clustal W/Omega, T-Coffee, MAFFT, MUSCLE, PASTA) [7_msa_part2.pdf] | CP Sections 9.6-9.74, 9.10-9.16 | |
4 | Tu | Sep 20th | Profile Hidden Markov Models (HMMs) | Lecture: Supervised training (Maximum Likelihood), decoding (Viterbi algorithm) (also of interest is unsupervised training with Baum-Welch algorithm and posterior decoding with Forward and Background algorithms) [8_profile_hmms.pdf] | BSA Sections 5.1-5.8 |
Th | Sep 22nd | Reading Group (MSA) |
Small group discussion
Homework assignment released! |
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5 | Tu | Sep 27th | Presentations and large group discussion | ||
Th | Sep 29th | Compatibility | Lecture: Constructing trees from clades (Hasse diagram approach), clade compatibility, bipartition compatibility, homoplasy, character compatibility, perfect phylogeny problem, maximum compatibility problem, infinite sites assumption [9_compatibility.pdf] | CP Sections 2.1-2.5, 4.4 | |
6 | Tu | Oct 4th | Parsimony | Lecture: Maximum parsimony problem (small and large), Fitch's algorithm, branch-and-bound, randomized taxon addition, search moves (NNI, SPR, TBR), consensus trees [10_parsimony.pdf] | CP Sections 4.1-4.3, 4.6-4.7, 6.1-6.2.3, Example 6.7 |
Th | Oct 6th | CFN model and Maximum likelihood | Lecture: How to generate data under Cavendar-Farris-Neyman (CFN) model, How to compute probability of characters under CFN model, Felsenstein's Pruning Algorithm, Maximum Likelihood problem, statistical consistency [11_finite_sites.pdf] | CP Sections 1.1-1.4, 8.1, 8.5-8.6, 8.8 | |
7 | Tu | Oct 11th | Practice Talk | Lecture: Recent advances and open challenges in estimating evolutionary histories from low-homoplasy markers | NA (Not on exam) |
Deadline | Homework assignment due today (Tuesday, October 11th at 11:59 PM ET)! | ||||
Th | Oct 13th | Molecular Sequence Evolution Models and Applications (Class on Zoom!) | Lecture: Time-continuous Markov Chains, Jukes-Cantor model, Generalized Time Reversible (GTR) model, SHR assumptions as well as practical issues: insertions/deletions (missing data), model violations, varying rates across sites (CAT and GAMMA models), taxon sampling, uncertainty quantification (bootstrapping vs. Bayesian), phylogenetic placement and applications to taxonomic identification | CP Sections 8.2, | |
8 | Tu | Oct 18th | Population-level processes | Lecture: Population-level processes (coalescent and recombination), Multi-Species Coalescent (MSC) model, concatenation vs. coalescent methods, practical issues (recombination ratchet, gene tree estimation error, missing data, etc.) [12_species_tree_msc.pdf] | CP Sections 10.1-10.5.2 (skipping 10.5.1) |
Th | Oct 20th | Reading Group (SARS-CoV-2) | Small group discussion | ||
9 | Tu | Oct 25th | Presentations and large group discussion | ||
Th | Oct 27th | Triplet Methods | Lecture: Triplet methods for species tree estimation under MSC model - includes tree edit operations, compatibility supertrees, ASSU algorithm, STELAR, MP-EST [13_triplet_methods.pdf] | CP Section 10.5.1 | |
Deadline | Project proposal due today (Tuesday, October 27th at 11:59 PM ET)! | ||||
10 | Tu | Nov 1st | Distance and Quartet Methods | Lecture: Quartet methods for species tree estimation under MSC model (includes All Quartets algorithm and ASTRAL), average gene tree internode distances, p-distances and model-corrected distances), additive and nearly additive, ultrametric, Naive Quartet method, UPGMA, and Neighbor Joining [14_quartet_and_distance_methods.pdf] | CP Sections 10.5.1 (quartet methods), 7.7, 10.5.1 (distance methods) 5.1, 5.3-5.5.1, 8.4, 5.2, 5.6-5.10 |
Th | Nov 3rd | Reading group (tumor phylogeny) | Small group discussion | ||
11 | Tu | Nov 8th | Presentations and large group discussion | ||
Th | Nov 10th | Exam Review | A running list of review questions and practice problems can be downloaded here: [exam-study-guide.pdf]. | ||
12 | Tu | Nov 15th | Exam | In-class today (Tuesday, November 15th in IRB-2207 from 11:00am-12:15pm ET)! | |
Th | Nov 17th | Logistics | Check in about exam, projects, etc. | ||
13 | Tu | Nov 22nd | Hybridization and admixture | Lecture: Phylogenetic networks, Wright-Fisher model, admixture graphs (Note this will be 30-minute lecture to prepare for reading groups. After I will have office hours about class projects.) | |
Th | Nov 24th | No class! | |||
14 | Tu | Nov 29th | Reading group (phylogenetic networks) | Small group discussion | |
Th | Dec 1st | Presentations and large-group discussion | |||
15 | Tu | Dec 6th | Project Presentations | ||
Th | Dec 8th | Project Presentations | |||
17 | Su | Dec 18th | Deadline | Project reports due today (Sunday, December 18th at 11:59PM ET)! |