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This is the course web page for "BTRY 4840/6840 & CS 4775: Computational Genetics and Genomics" – Fall 2016

Please check this page frequently throughout the semester. It will continually be updated with information you will need. Keep in mind that the schedules for lectures and problem sets are provisional.

Announcements

  • Welcome to the class!
  • For the first three weeks, Melissa's office hours will be 2pm-3pm Wed, or by appointment.

General Information

  • Lectures: Tues/Thurs, 10:10-11:25am, Weill Hall 226
  • Recitations: Fri, 12:20-1:10pm, Comstock B108
  • Instructor: Amy Williams, 102G Weill Hall
  • TA: Melissa Hubisz, 102D Weill Hall
  • Instructor office hours Tues 3-4pm
  • TA office hours Wed 1:30-2:30pm
  • Course Syllabus
  • Submission Guidelines

Discussion Forum / Q&A

Questions and answers for this course will be handled through Piazza. You can sign up for the class forum here.

Lectures and schedule

Date Topic Reading Handouts Problem sets
August 23 Introduction Large
Handouts
August 25 Molecular biology background; beginning probability and statistics Durbin chap. 1 and pp. 300-314 Large
Handouts
Problem set 1 assigned
August 30 Finish probability, maximum likelihood estimation Large
Handouts
September 1 Finish Bayesian statistics, hypothesis testing, model selection Large
Handouts
September 6 Dynamic programming, global sequence alignment Durbin chap. 2 Large
Handouts
September 8 More sequence alignment Large
Handout
Problem set 1 due
Problem set 2 assigned
September 13 Introduction to hidden Markov models (HMMs) [Melissa]: Viterbi algorithm Durbin chap. 3 Large
Handout
September 15 HMMs: Forward and Backward algorithms Large
Handout
September 20 HMMs Large
Handout
September 22 Genetic assay background, Haplotype inference (HMM application) Large
Handout
Problem set 2 due
Problem set 3 assigned
September 27 Haplotype inference (HMM application) Large
Handout
September 29 Haplotype inference (HMM application) Large
Handout
October 4 Phylogenetic reconstruction Durbin Sections 7.1-7.4, 8.1-8.3,
and Maximizing the likelihood in 8.4
Large
Handout
October 6 Phylogenetic reconstruction Large
Handout
Problem set 3 due
Problem set 4 assigned
October 13 Population structure: principal component analysis Large
Handout
October 18 Learning: Expectation Maximization, Baum-Welch Large
Handout
October 20 Molecular evolutionary models [Melissa] Large
Handout
October 25 Learning: MCMC, Gibb sampling, motif finding Andrieu et al. Large
Handout
October 27 Continuing MCMC, Gibb sampling, motif finding Large
Handout
November 1 MCMC; Generating reference genomes Large
Handout
November 3 Generating reference genomes Large
Handout
November 8 Human genome; local ancestry inference; fine scale structure Large
Handout
November 10 String matching; heuristic alignment (BLAST, BLAT) Large
Handout
November 15 Ancestral recombination graphs (ARGs) [Melissa] Large
Handout
November 17 Multiple alignment Durbin chap. 6 Large
Handout
November 22 Continuing multiple alignment Large
Handout
November 29 Neanderthal genetics Large
Handout
December 1 Neanderthal genetics Large
Handout

Problem sets

Final project

Final project details and possible projects ideas are available. Project proposals are due on November 1 by midnight.

Sections

Date Topic Handouts
August 26 Bernoulli Random Variables; is my coin fair? R code for biased coin test
Sept 2 Intro to R and LRT of normal distribution R code