Arvutiteaduse instituut
  1. Kursused
  2. 2017/18 kevad
  3. Bioinformaatika (MTAT.03.239)
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Bioinformaatika 2017/18 kevad

  • Main
  • Schedule
  • Homework
  • Additional reading
  • Introductory biology
  • Projects

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)
  • Arvutiteaduse instituut
  • Loodus- ja täppisteaduste valdkond
  • Tartu Ülikool
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