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Algorithmische Bioinformatik (ALGBIOINF)5 ECTS
(englische Bezeichnung: Algorithmic Bioinformatics)

Modulverantwortliche/r: David B. Blumenthal
Lehrende: David B. Blumenthal, und Mitarbeiter/innen


Startsemester: WS 2021/2022Dauer: 1 SemesterTurnus: jährlich (WS)
Präsenzzeit: 60 Std.Eigenstudium: 90 Std.Sprache:

Lehrveranstaltungen:


Empfohlene Voraussetzungen:

Since the lecture will be accompanied by programming exercises in Python, prior knowledge of this programming language is recommended. For students without prior experience, a very brief introduction to Python will be provided in the first two exercise sessions.

Inhalt:

With the growing amount of readily available molecular profiling data, algorithms for analyzing these data are getting more and more important. This lecture provides a close-up view on a selection of these algorithms and introduces the biomedical problems which are addressed by them. In particular, the lecture will cover the following topics:

  • A very brief introduction to molecular biology.

  • Algorithms for global and local sequence alignment.

  • Algorithms for de novo sequence assembly.

  • Algorithms for secondary RNA structure prediction.

  • Algorithms for exploratory omics data analysis.

  • Algorithms for network alignment.

  • Algorithms for disease mechanism mining in biological networks.

Lernziele und Kompetenzen:

Students will

  • get familiar with the basics of molecular biology,

  • acquire a thorough understanding of fundamental algorithms used in the field,

  • learn how to use paradigms of algorithm design such as dynamic programming, local search, and ant colony optimization in concrete application scenarios,

  • be able to reimplement the covered algorithms,

  • be able to provide detailed, technical explanations of the covered algorithms.

Literatur:

Pointers to relevant papers will be provided throughout the lecture and be made available on StudOn (https://www.studon.fau.de/crs3922912.html). As optional accompanying literature, the following textbooks are recommended:

  • Phillip Compeau & Pavel Pevzner: Bioinformatics Algorithms: An Active Learning Approach, Active Learning Publishers, 2018.

  • Patrick Siarry (Ed.): Metaheuristics, Springer International Publishing, 2016.


Studien-/Prüfungsleistungen:

Algorithmische Bioinformatik (Prüfungsnummer: 76781)

(englischer Titel: Algorithmic Bioinformatics)

Prüfungsleistung, mündliche Prüfung, Dauer (in Minuten): 30, benotet, 5 ECTS
Anteil an der Berechnung der Modulnote: 100.0 %
Prüfungssprache: Deutsch oder Englisch

Erstablegung: WS 2021/2022, 1. Wdh.: SS 2022
1. Prüfer: David B. Blumenthal

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