Lectures for CS 581, Spring 2020
- January 21, 2020.
(Overview of course)
-
January 23, 2020.
(Chapters 1, 5.1, 5.3-5.5, and 8.1-8.2)
-
January 28, 2020.
(Chapters 2 and 3.1-3.3)
- Guest lecture: Erin Molloy
(PPTX)
-
January 30, 2020.
(Chapters 3.4, 3.5, 4.1-4.4, 4.7, and 8.8)
- February 4, 2020 (Chapters 4.1-4.4, 4.7, 8.6, and 8.8)
- Vote on midterm: in class, or take-home?
- Review of prior material (including
Sankoff algorithm and other
assigned reading)
-
(PPTX)
(PDF)
- February 6, 2020 (Chapter 10.1-10.6)
- Review questions from Chapters 1-5, 8
- Species tree estimation given ILS, part I
(PDF)
- Note: Homework #2 due today by 10 PM, in Moodle
- February 11, 2020
- Species tree estimation given ILS, part II
(Continuing where we left off on Feb 6)
- February 13, 2020 (Chapter 7)
- February 18, 2020
- Introduction to MSA.
(PDF)
- February 20, 2020.
- Continuing MSA (where we left off on Feb 18).
Also, what we learn about MSA from data
(PPTX)
(PDF)
- February 25-27, 2020 (Chapter 9.1-9.5, 9.12): Vladimir Smirnov lectures
-
Profile HMMs
(PDF)
-
Using profile HMMs to compute alignments
- March 3, 2020
-
Review of course so far
(preparation for midterm)
- March 5, 2020
-
Midterm distributed in class (due Sunday March 8, 5 pm)
- March 10, 2020
- March 12, 2020
- Course project discussion
(Note: HW 7, which is your course project proposal, is due
10 PM March 11.)
-
March 24, 2020
- Shayan, presenting Zhang, Chao, et al. "ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees." BMC bioinformatics 19.6 (2018): 153
(HTML).
Discussants: Binghui and Payam
Presentation: (PDF)
- Payam, presenting Yin, John, Chao Zhang, and Siavash Mirarab. "ASTRAL-MP: scaling ASTRAL to very large datasets using randomization and parallelization." Bioinformatics 35.20 (2019): 3961-3969.
(HTML).
Discussants: Binghui, Shayan.
Presentation: (PDF)
- March 26, 2020
- Martin,
presenting Zou et al. (2019),
"Deep residual neural networks resolve quartet molecular phylogenies",
Molecular Biology and Evolution, msz307,
(HTML).
Discussants: Shayan, Timothy, and Marc.
Presentation: (PDF)
- Marc, presenting
De Maio, Nicola, Dominik Schrempf, and Carolin Kosiol. "PoMo: an allele frequency-based approach for species tree estimation." Systematic biology 64.6 (2015): 1018-1031
(HTML).
Discussants: Leah and Martin.
Presentation: (PDF).
-
March 31, 2020
- Tanvi, presenting
"Quartets MaxCut: A Divide and Conquer Quartets Algorithm," in IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 7, no. 4, pp. 704-718, October 2010.
(HTML).
Discussants: Binghui, Martin, and Yufeng.
Presentation:
(PDF)
- Tim, presenting
Berry et al.,
"Quartet Cleaning: Improved Algorithms and Simulations",
European Symposium on Algorithms 1999, LNCS 1643, pp. 313-324,
(PDF).
Discussants: Minghao, Martin.
Presentation: (PDF)
- April 2, 2020
- Minghao, presenting Roch, S., and Snir, S. 2013.
"Recovering the tree-like trend of evolution despite extensive lateral genetic transfer: a probabilistic analysis." Journal of Computational Biology, 20, 93-112
(HTML)
Discussants: Tanvi, Leah, and Marc.
Presentation: (PDF)
- Leah, presenting Galtier, "A model of horizontal
gene transfer and the bacterial phylogeny problem",
Syt. Biol. 56(4):633-642, 2007.
(HTML).
Discussants: Tanvi, Shayan, Minghao, and Marc.
Presentation: (PDF)
-
April 7, 2020
- WanXian,
presenting Wheeler and Kececioglu (2007),
"Multiple alignment by aligning alignments",
Bioinformatics 23 (13), i559-i568
(HTML).
Discussants: Minhyuk, Maya, Yufeng, and Leah.
(PDF)
-
Yufeng, presenting
Kececioglu and Starrett,
"Aligning alignments exactly",
RECOMB 2004, pp. 85-86,
(HTML)
Discussants: Tanvi, WanXian, Maya, and Minhyuk.
(PDF)
- April 9, 2020
- Min, presenting
Benjamin P. Blackburne and Simon Whelan,
"Class of Multiple Sequence Alignment Algorithm Affects Genomic Analysis,"
Molecular Biology and Evolution, Volume 30, Issue 3, March 2013,
Pages 642-653
(HTML).
Discussant: Payam, Maya, Yufeng, and WanXian.
Presentation:
(PDF)
- Maya, presenting Loytynoja and Goldman, 2008.
"Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis", Science, 320(5883), 1632-1635.
(PDF).
Discussants: WanXian, Minghao, and Timothy.
Presentation: (PDF)
-
April 14, 2020
- Binghui, presenting
Price, Morgan N., Paramvir S. Dehal, and Adam P. Arkin. "FastTree 2--approximately maximum-likelihood trees for large alignments." PloS one 5.3 (2010)
(PDF).
Discussant: Minhyuk, Timothy, and Payam.
Presentation: (PDF)
- April 16, 2020
-
April 21, 2020
-
Vlad Smirnov, presents new research
(PPTX)
- April 23, 2020
-
April 28, 2020
- Course project presentations:
Maya (PDF) and Leah
(PPTX)
- April 30, 2020
-
Course project presentations:
group discussion
(or Tandy will talk about absolute fast
converging methods, (PDF))
-
May 5, 2020 (last day)
-
Course project presentations