Genomics and bioinformatics

BIO-463

Media

This file is part of the content downloaded from Genomics and bioinformatics.

The course starts on Tuesday 18 February.


Course: 15:15 - 17:00, BCH2201
Exercises: 17:15 - 19:00, AAC231

Bibliography

Background:

Bioinformatics:

R language:

Week 1

Course:
  • Genomics and Bioinformatics: overview, historical perspective, structure of the course
  • Sequencing DNA and the Human Genome Project

Exercises:
  • Install R and R studio
  • First exercises in R

Week 2

Course:
  • Basic genome assembly algorithms
  • Sequence alignments

Exercises:
  • Assemble and analyse a (tiny) genome in R

Week 3

Course:
  • Annotating genomes by modelling features: Hidden Markov Models (HMM)
Exercises:
  • HMM

Week 4

Course:
  • Molecular evolution
  • Phylogeny
  • Homology
Exercises:
  • Analyze sequence data, in particular evolutionary distances
  • Construct phylogenetic trees
  • Identify orthologs

Week 5

Course:
  • Mutations
  • Population genetics: genetic drift and natural selection
Exercises:
  • Fluctuation test
  • Wright-Fisher model
  • Mutations, genetic drift and natural selection

Week 6

Course:
  • Population genetics, beyond mutation, selection and drift
Exercises:
  • Graded problem set

Week 7

Course:

  • RNA molecules

  • Bulk RNA-sequencing

  • Unsupervised clustering analysis


Week 8

Course:
  • Dimensionality reduction
  • Singular Value Decomposition analysis

Week 9

Course:
  • Pre-processing of single-cell RNA-sequencing data
  • Unsupervised clustering analysis

The material for the exercise can downloaded on Zenodo:

 https://zenodo.org/records/11032235

Holidays

Week 10

Course:
  • Alternative polyadenylation analysis
  • scRNA-seq clustering and cell type identification

Week 11

Course:
  • Transcriptional regulation
  • ChIP-seq and related techniques

Week 12

Course:
  • Regulatory networks and modules

Week 13

Course:
  • Chromosome conformation

Week 14