Schedule
This is a preliminary schedule that is subject to change.
14/02/19: Introduction to the course (Kaur Alasoo) (slides)
- Aims, outline, example applications.
- Biological concepts: Central dogma of molecular biology, DNA sequencing.
- Computational concepts: Software environments, computational workflows, docker, Snakemake.
21/02/19: Sequence alignment (Priit Adler) (slides, Homework slides, video)
- Biological concepts: Reference genomes, genetic variation.
- Computational concepts: Exact matching, hashing, edit distance, dynamic programming.
28/02/19: Gene expression (Kaur Alasoo) (slides, video)
- Guilt-by-association approach to understanding gene function
- Biological concepts: RNA transcription, RNA-seq, Gene ontology
- Computational concepts: PCA, multiple testing, FDR, permutation, computational workflows.
07/03/19: Genetic variation (Kaur Alasoo)(slides 1,2) (video)
- Biological concepts: SNPs, indels, LD, genotyping, CNV, Recombination
- Computational concepts: variant calling, missing data imputation
14/03/19: Detecting genetic associations (Leopold Parts) (2018 slides)
21/03/19: Understanding sources of variation in data (Kaur Alasoo) (slides)
- Biological concepts: protein expression, flow cytometry
- Computational concepts: linear mixed models, variance decomposition.
28/03/19: Statistical colocalisation (Kaur Alasoo) (slides)
- Using genetics to understand gene function
- Biological concepts: linkage disequilibrium (LD), pleiotropy
- Computational concepts: Bayesian statistics, model comparison.
04/04/19: Transcriptional regulation (Priit Adler)(slides, notebook.pdf)
- Biological concepts: Transcription factors, Chip-seq, sequence specificities, chromatin accessibility
- Computational concepts: Peak calling, signal thresholding, pattern discovery (Gibbs sampling)
11/04/19: Transcript expression and splicing (Kaur Alasoo) (slides)
- Biological concepts: Alternative promoters, splicing, polyadenylation
- Computational concepts: Expectation-Maximisation (EM) algorithm.
18/04/19: Introduction to projects (Kaur Alasoo) (slides)
25/04/19: Mendellian randomisation (Krista Fischer) (slides)
Predicting complex traits from genetic variants and using genetics to understanding causal relationships.
02/05/19: Segmenting nuclei from microscopy images (Dmytro Fishman) (2018 slides)
Extracting meaning from microscopy images.
09/05/19: Drug repurposing (Jürgen Jänes, European Bioinformatics Institute)
16/05/19: CRISPR/Cas9 engineering and bioinformatics (Leopold Parts) (2018 slides)
Understanding gene function by direct perturbation.
23/05/19: First exam
30/05/19: Project presentations
- There may be some minor changes in the schedule (due to guest lecturers or some other force majeure)