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Institute for Machine Learning
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Genome Analysis & Transcriptomics (2KV)

Course no.: 365.109
Lecturer: Alois Regl (alois.regl(at)regl.net, +43 664 4502030)


It is deeply recommended to hear both lectures (Structural Bioinformatics and Genome Analysis & Transcriptomics).

All organizational details concerning GT and SBI are presented in the introductory lecture on March 8, 2022 (08:30am, HS6).

Lecture notes:

There are no lecture notes but all slides will be provided via KUSSS.

Please pay attention to the Big Picture provided in KUSSS!!!

Motivation and course outline

Bioinformatics is an interdisciplinary field at the interface of life sciences and computational sciences that deals with the development and application of methods for storing, retrieving, and, in particular, analyzing biological data. The massive data amounts produced by recent and currently emerging high-throughput biotechnologies provide unprecedented potentials, but also pose yet unseen computational challenges – making bioinformatics an essential success factor for the advancement of fields, such as, molecular biology, genetics, medicine, and pharmacology.

There are two major topics that are presented in this course:

  1. Microarray principles and data analysis
    How does the technology work that enables us to measure the level of expression of a
    set of genes? And how are expressions from several samples belonging to two or
    more groups condensed into a list of "differentially expressed genes" (= genes that
    show a stastically significant difference in expression across the groups)
  2. Sequencing principles and genome assembly
    How do sequencing machines work, what are their technical strength and
    weaknesses? What algorithms or principles do we have to come from a huge set of
    short (100 u- 200 bps) "reads" to a reconstruction of the full genome?

Transcriptomics (Microarrays):

  • Microarray Basics
  • Quality Control
  • Preprocessing
  • Differential Expression
  • Downstream analysis

Genomics (Genome assembly):

  • Sequencing technology
  • Assembly algorithms