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From BTRY 4840/6840 and CS 4775: Fall 2017
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This is the course web page for "BTRY 4840/6840 & CS 4775: Computational Genetics and Genomics" – Fall 2017

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.

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: Daniel Seidman, 102F Weill Hall
  • Instructor office hours Tues 3-4pm
  • TA office hours Wed 3-4pm
  • 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 22 Introduction Lecture1
August 24 Molecular biology background; beginning probability and statistics Durbin chap. 1 and pp. 300-314 Lecture2 Problem set 1 assigned
August 29 Finish probability, maximum likelihood estimation Lecture3
August 31 Finish Bayesian statistics, hypothesis testing, model selection Lecture4
September 5 Dynamic programming, Manhattan tourist problem Durbin chap. 2 Lecture5
September 7 Global and local sequence alignment Lecture6 Problem set 1 due
Problem set 2 assigned
skeleton code 1c Python
skeleton code 1c R
scoring matrix example file
September 12 Introduction to hidden Markov models (HMMs): Viterbi algorithm Durbin chap. 3 Lecture7 HMM intro
September 14 HMMs: Forward and Backward algorithms Lecutre 8 Forward and Backward Algorithms
September 19 Continuing HMMs [Daniel lecturing] Lecture 9 Logp and Random Sampling
September 21 No class Problem set 2 due
Problem set 3 assigned
fasta sequence
example sequence with states

Section Slides