Bioinformatik der Infektionsforschung

Die Arbeitsgruppe “Bioinformatik der Infektionsforschung” erforscht mit computergestützten Techniken das menschliche Mikrobiom, virale und bakterielle Pathogene sowie menschliche Zelllinien anhand von großen biologischen und epidemiologischen Datensätzen. Durch die Analyse von Metaom-, Populationsgenom- und Einzelzellgenomdaten erzeugen wir experimentell überprüfbare Hypothesen,  wie z.b. welche Veränderungen an Proteinen oder welche Gene assoziiert sind mit dem Auftreten einer Krankheit, von Antibiotikaresistenzen oder dem Ausweichen des Immunschutzes durch Pathogene. Wir arbeiten mit experimentellen Kollaborationspartnern zusammen, um unsere Erkenntnisse zu verifizieren und deren Translation in die medizinische Diagnostik und Behandlung zu fördern. Um die Forschungsziele zu erreichen, entwickelt die Arbeitsgruppe auch neue Algorithmen und Bioinformatik-Software.

Leitung

Fachseminar: Sequence search and analysis

The seminar "Sequence search and analysis" is hosted by the department "Computational Biology of Infection Research" at the HZI headed by Prof. Alice McHardy.

Kick-off meeting time: Wednesday, 7.10.2020, 10 am
Kick-off meeting room: BRICS, room 207
Date: one-day block during semester break (tba)
Room: tba
Modus: 30 minutes presentation and discussion; 3-5 page written summary
Language: English
Maximum of 10 participants
Designated for Bachelor and Master students in computer science and related

In case you have any questions about the seminar and related topics, feel free to contact Andreas Klötgen

Description

Sequence analysis is a broad problem not only restricted to bioinformatics but common to various computer science fields. Google’s success comes from its Search Engine developed in the late 1990’s dealing with information from a giant space of websites, made available via complicated sequence search algorithms. In bioinformatics, sequence analysis is a key field dealing with the comparison of two or more (genome or gene) sequences. Most importantly, the breakthrough of next generation sequencing techniques, allowing to sequence an individual’s genome and uncover all potentially disease-relevant mutations in an unprecedented fast and potentially personalized manner, was enabled via bioinformatics improvements in large scale sequence analysis algorithms.

This seminar will cover the basics of sequence analysis, from comparing two strings for (dis-)similarities to building complex algorithms analyzing millions of sequences within minutes. It will also discuss appropriate data structures to handle a big search space of sequences such as suffix trees.

Topics

  • Sequence alignment (how to compare strings)
  • De-novo genome assembly
  • Sequencing read alignment (e.g. using suffix trees) of millions of reads
  • Protein sequence alignments (e.g. in Pfam database using hidden markov models)
  • Taxonomic binning / profiling of metagenomes
  • Gene prediction in novel genome sequences
  • Google’s Search Engine

Video

  • Kann man die nächste Grippe-Epidemie vorhersagen?

    Es antwortet Dr. Andreas Bremges, stellv. Abteilungsleiter Bioinformatik der Infektionsforschung am HZI in Braunschweig.

Kontakt

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