Syllabus

Video recordings for some of the lectures is available on this playlist

Week Date Topic Slides Assignment Resources Video
01 07-31 (Wed)
  1. Introduction to the course: Finding the faults in our DNA
 1 All biology is computational biology
01 08-02 (Fri)
  1. Sequences: Probability and Statistics
 2U;2A Code for GC content
02 08-07 (Wed)
  1. Sequence : Statistics II
 3U;3A
02 08-09 (Fri)
  1. Sequences: Statistics III and Alignment
 4U;4A
  • Assignment 01 released
03 08-14 (Wed)
  1. Global and Local Alignment
 5
03 08-16 (Fri)
  1. Genome search engines and Sequencing by synthesis
 6A;6B
  • Assignment 01 due
  • Assignment 02 released
 Genomes 5 Ch 4
04 08-21 (Wed)
  1. DNA mapping algorithms
 7 Bioinformatics Algorithms 2nd Ed Ch 7 🎥
04 08-23 (Fri)
  1. Hands on DNA-seq
 8
  • Assignment 02 due
  • Assignment 03 released
 HandsOn 02 🎥
05 08-28 (Wed)
  1. RNA-seq: Quantification
 9

Genomes 5 Ch 12

EM notes

Dempster1977

Splicing video

Translation video

Coin Toss Python

 🎥
05 08-30 (Fri)
  1. Sequencing review
 10
  • Assignment 03 due
  • Assignment 04 released
 🎥
06 09-04 (Wed)
  1. RNA-seq normalization
 11 🎥
06 09-06 (Fri)
  1. Models for counts and variance stabilization
 12
  • Assignment 04 due
07 09-11 (Wed)
  1. Dimensionality reduction (PCA/SVD)
 13 🎥
07 09-13 (Fri)
  1. Multiple hypothesis testing
 14 🎥
08 09-18 (Wed) Mid-semester Week (NO CLASS)
08 09-20 (Fri) Mid-semester Week(NO CLASS) Exam on 21st September, Saturday 11 AM - 1 PM, Venue: LC 202, LT 203
09 09-25 (Wed)
  1. Multiple Hypothesis testing
 15 🎥
09 09-27 (Fri)
  1. Single cell transcriptomics: technologies
 16
  • Assignment 05 released
 🎥
10 10-02 (Wed) No class (institute holiday)
10 10-04 (Fri)
  1. Hands on RNA-seq analysis
 17
  • Assignment 05 due
 Data 🎥
11 10-09 (Wed)
  1. Single cell normalization and clustering
 18 🎥
11 10-11 (Fri)
  1. Single-cell Hands on
 19-Raw;19-html
  • Assignment 06 released
 Paper 🎥
12 10-16 (Wed)
  1. Sequencing the epigenome
 20 🎥
12 10-18 (Fri)
  1. ‘CRISPRing’ the genome
 21
  • Assignment 06 due
  • Assignment 07 released
 🎥
13 10-23 (Wed)
  1. Genome wide association studies
 22 🎥
13 10-25 (Fri)
  1. Q & A
 Q & A
14 10-30 (Wed)
  1. Let’s go back to the start
 24!
  • Assignment 07 due

Suggested readings

  1. Molecular Biology for Computer Scientists by Lawerence Hunter
  2. Genomes by TA Brown
  3. Computational Genome Analysis by Richard C. Deonier , Michael S. Waterman , and Simon Tavaré
  4. Bioinformatics Algorithms by Phillip Compeau and Pavel A. Pevzner
  5. Modern Statistics for Modern Biology by Susan Holmes and Wolfgang Huber
  6. Data Analysis for the Life Sciences by Rafael A Irizarry and Michael I Love