Arvutiteaduse instituut
  1. Kursused
  2. 2020/21 kevad
  3. Bioinformaatika (MTAT.03.239)
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Bioinformaatika 2020/21 kevad

  • Main
  • Schedule
  • Assignments
  • Introductory biology
  • Projects

Schedule

The lecture recordings are available from Panopto.

You can download the slides from OwnCloud

08/02/21: Introduction I (Erik Abner, Kaur Alasoo)

  • Aims, outline, example applications.
  • Biological concepts: Central dogma of molecular biology, DNA sequencing.
  • Computational concepts:

15/02/21: Introduction II (Erik Abner)

22/02/21: Sequence alignment (Priit Adler)

  • Biological concepts: Reference genomes, genetic variation.
  • Computational concepts: Exact matching, hashing, edit distance, dynamic programming.

01/03/21: Gene expression (Kaur Alasoo)

  • 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.

08/03/21: Genetic variation (Kaur Alasoo)

  • Biological concepts: SNPs, indels, LD, genotyping, CNV, Recombination
  • Computational concepts: variant calling, missing data imputation

11/03/21: Developing scientific workflows with Nextflow (Nurlan Kerimov) + consultation session.

15/03/21: Protein expression and variance decomposition (Kaur Alasoo)

  • Biological concepts: protein expression, flow cytometry
  • Computational concepts: linear mixed models, variance decomposition.

22/03/21: Detecting genetic associations (Leopold Parts/Kaur Alasoo)

29/03/21: Statistical colocalisation and fine mapping (Kaur Alasoo)

  • Using genetics to understand gene function
  • Biological concepts: linkage disequilibrium (LD), pleiotropy
  • Computational concepts: Bayesian statistics, model comparison.

05/04/21: Transcriptional regulation and functional fine mapping (Kaur Alasoo)

  • Biological concepts: Transcription factors, Chip-seq, sequence specificities, chromatin accessibility
  • Computational concepts: Peak calling, signal thresholding

12/04/21: Transcript expression and splicing (Kaur Alasoo)

  • Biological concepts: Alternative promoters, splicing, polyadenylation
  • Computational concepts: Expectation-Maximisation (EM) algorithm.

31/05/21: Project presentations - CANCELLED

  • There may be some minor changes in the schedule (due to guest lecturers or some other force majeure)
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