Dalhousie University
CSCI4181/6802 Bioinformatics Algorithms
Winter 2022-2023

Schedule

Lectures take place on Tuesday and Thursdays from 8:35-9:55 in Mona Campbell 1201.

  • Event
    Date
    Description
    Course Material
  • Module
    2023/01/10
    Tuesday
    Introduction
  • Lecture
    2023/01/10
    Tuesday
    01 Course Overview & Life at Resolution
    [slides] [recording (previous offering)]
  • Lecture
    2023/01/12
    Thursday
    02 Pathways & Central Dogma
    [slides] [recording]
  • Lecture
    2023/01/17
    Tuesday
    03 Molecular Evolution
    [slides] [recording]
  • Module
    2023/01/19
    Thursday
    Homology Module
  • Lecture
    2023/01/19
    Thursday
    04 Encoding DNA and Proteins
    [slides] [recording]
  • Lecture
    2023/01/24
    Tuesday
    05 Sequence Alignment - Definitions and Scoring
    [slides] [recording]
  • Lecture
    2023/01/26
    Thursday
    06 Optimal Alignment - Dynamic Programming
    [slides] [recording]
  • Lecture
    2023/01/31
    Tuesday
    07 Practical Approaches for Large Datasets: BLAST and Burrows-Wheeler Transform
    [slides] [recording]
  • Lecture
    2023/02/02
    Thursday
    08 Multiple Sequence Alignment
    [slides] [recording]
  • Assignment
    2023/02/02
    Thursday
    Assignment 1 - Alignment and Distant Homology Release
    [Assignment 1 - Alignment and Distant Homology]
  • Lecture
    2023/02/07
    Tuesday
    09 Hidden Markov Models
    [slides] [recording (previous offering)]
  • Module
    2023/02/09
    Thursday
    Assembly
  • Lecture
    2023/02/09
    Thursday
    10 Genomic Assembly
    [slides] [recording]
  • Lecture
    2023/02/09
    Thursday
    10a Bacterial Pangenomics - Dr. Ryan Fink
    [slides]
  • Due
    2023/02/09 23:59
    Thursday
    Assignment 1 Deadline
  • Lecture
    2023/02/14
    Tuesday
    11 de Bruijn Graphs and Metagenomic Assembly
    [slides] [recording]
  • Lecture
    2023/02/16
    Thursday
    12 Searching Massive Read Datasets
    [slides] [recording]
  • Assignment
    2023/02/16
    Thursday
    Assignment 2 - Genome Assembly Release
    [Assignment 2 - Genome Assembly]
  • Module
    2023/02/28
    Tuesday
    Phylogenetics
  • Lecture
    2023/02/28
    Tuesday
    13 Introduction to Phylogenetics
    [slides] [recording]
  • Lecture
    2023/03/02
    Thursday
    14 Maximum Likelihood
    [slides] [recording]
  • Due
    2023/03/02 23:59
    Thursday
    Assignment 2 Deadline
  • Lecture
    2023/03/07
    Tuesday
    15 Bayesian Phylogenetic and Statitical Support
    [slides] [recording]
  • Lecture
    2023/03/09
    Thursday
    16 Feature Selection and Visualisation
    [slides] [recording]
  • Assignment
    2023/03/09
    Thursday
    Assignment 3 - SARS-CoV-2 Genome Analysis Release
    [Assignment 3 - SARS-CoV-2 Genome Analysis]
  • Lecture
    2023/03/14
    Tuesday
    17 Networks & Lateral Gene Transfer - Prof. Robert Beiko
  • Module
    2023/03/16
    Thursday
    Machine Learning
  • Lecture
    2023/03/16
    Thursday
    18 - Pangenome Read Alignment - Prof. Travis Gagie
    [slides] [recording]
  • Due
    2023/03/16 23:59
    Thursday
    Assignment 3 Deadline
  • Lecture
    2023/03/21
    Tuesday
    19 Training ML Models
    [slides] [recording]
  • Due
    2023/03/21 23:59
    Tuesday
    Paper Selection Deadline
  • Lecture
    2023/03/23
    Thursday
    20 Classifiers - Simple to Ensembles
    [slides] [recording]
  • Assignment
    2023/03/23
    Thursday
    Assignment 4 - Machine-Learning Prediction of AMR Phenotype Release
    [Assignment 4 - Machine-Learning Prediction of AMR Phenotype]
  • Lecture
    2023/03/28
    Tuesday
    No Lecture
  • Lecture
    2023/03/30
    Thursday
    21 Artificial Neural Networks & Deep Learning - Alex Manuele
    [slides] [recording]
  • Due
    2023/03/30 23:59
    Thursday
    Assignment 4 Deadline
  • Exam
    2023/04/04 08:30
    Tuesday
    Oral Review Presentations

    In-class presentation order has been randomly assigned and shared via email. Please send your slides in PDF format to finlay.maguire@dal.ca by midnight the day befor your presentation.

  • Due
    2023/04/04 23:59
    Tuesday
    Written Paper Review Deadline
  • Exam
    2023/04/06 08:30
    Thursday
    Oral Review Presentations
  • Exam
    2023/04/11 08:30
    Tuesday
    Oral Review Presentations (if needed)