Statistics 590C (Bioinformatics II)

Instructor: Jeff Thorne

Monday, Wednesday, and Friday: 11:45A.M.-12:35P.M.

Synchronous Zoom meetings for Jan. 10 and 12 and 14 sessions

Following first week of semester, meetings are in-person in 150 Withers

Syllabus

Pairwise Alignment Review (file "bioinfintrolecture2022.pdf")
Lecture Notes on Markov models (pages 1-21, file "markov.pdf")
Lecture Notes on basic HMM algorithms (pages 22-28, file "markov2.pdf")
Lecture Notes on underflow (pages 29-31, file "markov3.pdf")
A tiny bit more on underflow
Lecture Notes on HMM miscellanea (pages 32-40, file "HMMmisc.pdf")

Lecture Notes on a few protein databases (pages 41-49, file "databases2022.pdf")

Slides on Protein Structure Prediction and CASP were distributed via email on Feb. 17, 2022

A quick tour of some techniques for obtaining random samples (pages 63-82, file "sampling2022.pdf")

An introduction to Gibbs Sampling pages 83-91, file "gibbs2022.pdf")

Dirichlet distribution and pseudocounts (pages 92-97, file "dirichlet2022.pdf")

Slides on Generative Adversarial Networks (a guest lecture by Dr. Adrian Green, April 8) were distributed via email

A little about evolutionary models and the EM algorithm (pages 98-125, file "evomodel2022.pdf")

Introduction / Background on Likelihood-Based Inference (file "basicbayesandml.pdf")

Homework #1

Homework #2

Homework #3 consists of student presentations regarding CASP (Groups A & B present on Monday April 11, Groups C & D present on Wednesday April 13, Groups E & F present on Friday April 15).

Homework #4 was emailed to students on March 21 and will be due on Monday April 18.