====== Genome Informatics Research Seminar ======
\\ 


|392188 |Stoye, Wittler |Summer 2013 |Thursday 16-18 in U10-146 |[[http://ekvv.uni-bielefeld.de/kvv_publ/publ/vd?id=36919830|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.) 



===== Schedule =====

|  **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 |

===== Abstracts: =====
**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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