Lectures for CS 581, Fall 2020
 August 25, 2020
(Overview of course)

August 27, 2020
(Chapters 1, 5.1, 5.35.5, and 8.18.2)

September 1, 2020

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 1015, 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 DistanceBased Phylogenetic Placement with or without Alignments",
Systematic Biology, Volume 69, Issue 3, May 2020, Pages 566578,
(HTML)

October 6: Review of course, and discussion of course projects

October 8: Presentation of the takehome 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 ElKebir.
Mohammed will talk about:
Weber LL, Aguse N, Chia N, ElKebir M. PhyDOSE: Design of followup singlecell sequencing experiments of tumors. Nagarajan N, ed. PLoS Comput Biol. 2020;16(10):e1008240. doi:10.1371/journal.pcbi.1008240. Presentation
(PDF)
 November 2129, 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