Schedule
This is a preliminary schedule that is subject to change.
15/02/18: 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.
22/02/18: Sequence alignment (Priit Adler) (slides)
- Biological concepts: Reference genomes, genetic variation.
- Computational concepts: Exact matching, hashing, edit distance, dynamic programming.
01/03/18: Gene expression (Kaur Alasoo) (slides)
- 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.
08/03/18: Transcript expression and splicing (Kaur Alasoo) (slides)
- Biological concepts: Alternative promoters, splicing, polyadenylation
- Computational concepts: Expectation-Maximisation (EM) algorithm.
15/03/18: Understanding sources of variation in data (Kaur Alasoo) (slides)
- Biological concepts: protein expression, flow cytometry
- Computational concepts: linear mixed models, variance decomposition.
22/03/18: Genetic variation (Kaur Alasoo)(slides 1,2)
- Biological concepts: SNPs, indels, LD, genotyping, CNV, Recombination
- Computational concepts: variant calling, missing data imputation
29/03/18: 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)
05/04/18: Detecting genetic associations (Leopold Parts) (slides)
12/04/18: Statistical colocalisation (Kaur Alasoo) (slides)
- Using genetics to understand gene function
- Biological concepts: linkage disequilibrium (LD), pleiotropy
- Computational concepts: Bayesian statistics, model comparison.
19/04/18: Image phenotypes (Dmytro Fishman) (slides)
Extracting meaning from microscopy images.
26/04/18: Introduction to projects (Kaur Alasoo) (slides)
03/05/18: Polygenetic risk scores and Mendellian randomisation (Krista Fischer)
Predicting complex traits from genetic variants and using genetics to understanding causal relationships.
10/05/18: CRISPR screens (Leopold Parts) (slides)
Understanding gene function by direct perturbation. Lecture starts at 16:15
17/05/18: Modelling protein structures (Alexey Morgunov) (materials)
24/05/18: Population genetics inference in reconstructing demographic history and natural selection (Mait Metspalu)
31/05/18: Project presentations
- There may be some minor changes in the schedule (due to guest lecturers or some other force majeure)