Lectures for CS 581, Fall 2020

• August 25, 2020 (Overview of course)
  • (PPTX) (PDF)
• August 27, 2020 (Chapters 1, 5.1, 5.3-5.5, and 8.1-8.2)
  • (PPTX) (PDF)
• September 1, 2020
  • (PPTX) (PDF)
• September 3, 2020
  • (PPTX) (PDF)
  • Note: Homework #1 due today by 10 PM, in Moodle.
• September 8, 2020
  • Discuss homoplasy, compatibility, etc., and review prior material.
  • (PPTX) (PDF)
• September 10-15, 2020
  • Species tree estimation given ILS (PDF)
• September 17, 2020
  • Constrained optimization tree construction (PDF)
• September 22 to October 1, 2020
  • Discussion of HW3 (PDF)
  • Introduction to Multiple Sequence Alignment (PDF)
  • Introduction to Profile Hidden Markov Models (PDF)
  • What we learn from data (PDF)
  • Discussion of paper by Balaban, Sarmashghi, and Mirarab, "APPLES: Scalable Distance-Based Phylogenetic Placement with or without Alignments", Systematic Biology, Volume 69, Issue 3, May 2020, Pages 566--578, (HTML)
• October 6: Review of course, and discussion of course projects
• October 8: Presentation of the take-home midterm (due October 11, 10 PM)
• October 13: Review of midterm, and introduction to Ensembles of Hidden Markov Models (PDF)
• October 15: Introduction to Disjoint Tree Mergers and the Guide Tree Merger in particular
• October 20: Sarah Christensen presentation about TRACTION. Then, presentation of project ideas (5 minutes per team: 3 minute presentation with a single slide, and 2 minutes for Q&A) (PDF)
• October 22: Discussion of course projects (how to design them)
• October 27: Presentation of papers by (1) James and Mrinmoy (PDF) and (2) Baqiao (PDF)
• October 29: Presentation of papers by (1) Kathie and Eleanor (PDF) and (2) Grant and Vishal (PPTX)
• November 3: HOLIDAY
• November 5: Presentation of papers by (1) Elizabeth and Malachi (PDF)and (2) Qikai (PDF)
• November 10: Presentations of papers by (1) Gillian (PDF) and (2) Chengze and Qinghui (PPTX)
• November 12: Guest lecture by Jian Peng (PPTX)
• November 17: Guest lecture by Payam and Shayan.
• November 19: Guest lecture by Mohammed El-Kebir. Mohammed will talk about: Weber LL, Aguse N, Chia N, El-Kebir M. PhyDOSE: Design of follow-up single-cell sequencing experiments of tumors. Nagarajan N, ed. PLoS Comput Biol. 2020;16(10):e1008240. doi:10.1371/journal.pcbi.1008240. Presentation (PDF)
• November 21-29, Fall break
• December 1 Course project presentations (short): (1) Chengze & Qinghui, (2) Mrinmoy and James, (3) Baqiao
• December 3 Course project presentations (short): (1) Elizabeth & Malachi, (2) Kathie & Eleanor, (3) Grant & Vishal
• December 8 Course project presentations (short) LAST DAY of class: (1) Qikai and (2) Gillian