Genome Informatics Research Seminar

392188 Stoye, Wittler Summer 2013 Thursday 16-18 in U10-146 ekvv

Course Description

In this seminar, current topics of the Genome Informatics research group are presented.

(In dieser Veranstaltung wird in Vorträgen über aktuelle Themen aus der Forschung der Arbeitsgruppe Genominformatik berichtet.)


Date Topic Name
11.04.2013 Organization of the seminar Jens Stoye
18.04.2013 The Algebraic Theory of Genome Rearrangement Pedro Feijão
25.04.2013 BREW rehearsals and one MS kickoff Linda Sundermann, Kai Bernd Stadermann, Christoph Brinkrolf, Maureen Smith
02.05.2013 MS and BS kickoffs Mark Ugarov, Malte Mattheis, Nina Luhmann, Christian Bender
09.05.2013 (Himmelfahrt)
16.05.2013 Metabolic Networks Fábio Martinez
23.05.2013 (Jens away)
30.05.2013 (Fronleichnam)
06.06.2013 Gene Clusters Daniel Dörr
13.06.2013 My Next Generation Nature Paper Sebastian Jünemann
20.06.2013 Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ) Martin Mascher
26.06.2013, 10am c.t. The Supercool Supermarket Project Tina Zekic and Annelyse Thévenin
27.06.2013 Netzwerkbasierte Analysen genetischer Assoziationen zur Identifikation krankheitsrelevanter biologischer Prozesse Andreas Klötgen
04.07.2013 (Jens away)
11.07.2013 (Swines and other balls) everybody
17.07.2013, 11am c.t. Methods for sequencing data: from genome assembly parameters to Ion Torrent base calling Paul Medvedev
18.07.2013 (BI-Vancouver DiDy Application Workshop)
01.08.2013 The Potential of Family-Free Genome Comparison Jens Stoye
10.09.2013, 2pm c.t. Master Thesis Presentation Nina Luhmann
19.09.2013 BS presentations B.S students
26.09.2013 An Overview of Genomic Distances Modeled with Indels Marília D. V. Braga
t.b.a. The Ottawa Project Katharina Jahn
t.b.a. Jumping Chimeras Linda Sundermann
t.b.a. Next Generation Immunomics Spectratyping Pina Krell
t.b.a. Recent Results in Computational Metabolomics Nils Hoffmann


Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ)
Martin Mascher

Next-generation, whole genome shotgun (WGS) assemblies of complex genomes are highly enabling, but fail to link nearby sequence contigs with each other or provide a linear order of contigs along individual chromosomes. Here, we introduce a strategy based on sequencing progeny of a segregating population that allows the de novo production of a genetically anchored, linear assembly of the gene space of an organism. We demonstrate the power of the approach by reconstructing the chromosomal organization of the gene space of barley, a large, complex and highly repetitive 5.1-Gb genome. We evaluate the robustness of the new assembly by comparison to a recently released physical and genetic framework of the barley genome, and to different genetically ordered sequence-based genotypic datasets. The method is independent of the need for any prior sequence resources and will enable the rapid and cost efficient establishment of powerful genomic information for many species.

An Overview of Genomic Distances Modeled with Indels
Marília D. V. Braga

The genomic distance typically describes the minimum number of large-scale mutations that transform one genome into another. Classical approaches to compute the genomic distance are usually limited to genomes with the same content and take into consideration only rearrangements that change the organization of the genome (i.e., positions and orientation of pieces of DNA, and number of chromosomes). In order to handle genomes with distinct contents, also insertions and deletions of pieces of DNA—named indels—must be allowed. Some extensions of the classical approaches lead to models that allow rearrangements and indels. In this work we introduce a new graph structure that gives a unified view of these approaches, present an overview of their results and point out some open problems related to them.

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