There are ~8 small groups, each with 4-5 students. For the first day, students are responsible for reading their assigned paper (labeled A, B, C, D below) prior to class and then discussing the paper with their small group during class (participation grade). For the second day, one of the two small groups assigned the same paper will present it to the entire class (~12 minutes; see the presentation schedule on ELMS).

Sept 16,18: Multiple Sequence Alignment (MSA) and Whole Genome Alignment (WGA)

  1. Smirnov and Warnow, 2020, MAGUS: Multiple sequence Alignment using Graph clUStering, Bioinformatics. [link]
  2. Shen et al., 2022, WITCH: Improved Multiple Sequence Alignment Through Weighted Consensus Hidden Markov Model Alignment, Journal of Computational Biology. [link] (note there is a related bioRxiv preprint available)
  3. Garriga et al., 2019, Large multiple sequence alignments with a root-to-leaf regressive method, Nature Biotechnology. [link]
  4. Armstrong et al., 2020, Progrssive Cactus is a multiple-genome aligner for the thousand-genome era, Nature. [link]

Sept 23,25: WGA and pangenomics

  1. Armstrong et al., 2019, Whole-Genome Alignment and Comparative Annotation, Annual Review of Animal Biosciences. [link]
  2. Angiuoli and Salzberg, 2011, Mugsy: fast multiple alignment of closely related whole genomes, Bioinformatics. [link]
  3. Garrison and Guarracino, 2023, Unbiased pangenome graphs, Bioinformatics. [link]
  4. Guarracino et al., 2022, ODGI: understanding pangenome graphs, Bioinformatics. [link]

Nov 13,18: Species trees

  1. Colijn and Plazzotta, 2017, A Metric on Phylogenetic Tre Shapes, Systematic Biology. [link]
  2. Rabiee and Mirarab, 2018, Multi-allele species reconstruction using ASTRAL, Molecular Phylogenetics and Evolution. [link]
  3. Zhang et al., 2020, ASTRAL-Pro: Quartet-Based Species-Tree Inference despite Paralogy, Molecular Biology and Evolution. [link]
  4. Han and Molloy, 2024, Improved robustness to gene tree incompleteness, estimation errors, and systematic homology errors with weighted TREE-QMC, bioRxiv. [link] (use PDF on ELMS)

Nov 20,25: Protein Structure and Phylogenetics

  1. Rajapaksa et al., 2023, Sequence and structure alignments in post-AlphaFold era, Current Opinion in Structural Biology. [link]
  2. Zhang et al., 2024, Protein language models learn evolutionary statistics of interacting sequence motifs, PNAS. [link]
  3. Malik et al., 2020, Structural Phylogenetics with Confidence, Molecular Biology and Evolution. [link]
  4. Puente-Lelievre et al., 2024, Tertiary-interaction characters enable fast, model-based structural phylogenetics beyond the twilight zone, bioRix. [link]