Schedule
This is a preliminary schedule that is subject to change.
10/02/20: Introduction I (Erik Abner, Kaur Alasoo) (Kaur's slides, Erik's slides)
- Aims, outline, example applications.
- Biological concepts: Central dogma of molecular biology, DNA sequencing.
- Computational concepts:
17/02/20: Introduction II (Erik Abner) (slides)
26/02/20: Sequence alignment (Priit Adler) (on Wednesday)(slides, Homework slides)
- Biological concepts: Reference genomes, genetic variation.
- Computational concepts: Exact matching, hashing, edit distance, dynamic programming.
02/03/20: Gene expression (Kaur Alasoo) (slides, HPC 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.
09/03/20: Genetic variation (Kaur Alasoo)(slides)(video)
- Biological concepts: SNPs, indels, LD, genotyping, CNV, Recombination
- Computational concepts: variant calling, missing data imputation
11/03/20: Developing scientific workflows with Nextflow (Nurlan Kerimov) + consultation session. (slides)
16/03/20: No lecture or practice session on this week.
23/03/20: Detecting genetic associations (Leopold Parts) (2018 slides)
06/04/20: Protein expression and variance decomposition (Kaur Alasoo) (video )
- Biological concepts: protein expression, flow cytometry
- Computational concepts: linear mixed models, variance decomposition.
13/04/20: Statistical colocalisation and finemapping (Kaur Alasoo) (slides)
- Using genetics to understand gene function
- Biological concepts: linkage disequilibrium (LD), pleiotropy
- Computational concepts: Bayesian statistics, model comparison.
20/04/20: 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)
27/04/20: Transcript expression and splicing (Kaur Alasoo) (slides)
- Biological concepts: Alternative promoters, splicing, polyadenylation
- Computational concepts: Expectation-Maximisation (EM) algorithm.
01/06/20: Project presentations
- There may be some minor changes in the schedule (due to guest lecturers or some other force majeure)