Bioinformatics - Next generation genomics

Seminar: Next generation genomics

Relatively recent "next-generation sequencing" techniques have resulted in a new approach to genome analyses. This seminar will elucidate the novelty of these techniques w.r.t. traditional sequencing methods. These new methods generate vast amounts of sequence data that result in new algorithmic problems. We will explore the tools and algorithms that have emerged in the past few years in response to these problems. Furthermore, the impact of these new methods in genome research will be examined.

Veranstalter :

• Rolf Backofen
• Steffen Heyne
• Sita Lange

Typ der Veranstaltung:

• Blockseminar: Tuesday 26.01. - Thursday 28.01.2010 from 16:00 until ca. 19:00!
• Hand-in presentation draft by 18.01.2010.
• If you are interested in a topic, contact us until 06.11.2009.
• Please let us know if you decide not to do the seminar as EARLY AS POSSIBLE!.

Themenliste:

Next-generation sequencing technologies

• Presentation 1.1. Summary of next-generation sequencing methods (COMPULSORY):
  Bettina Huebner (Sita)
  Give an introduction to next generation sequencing techniques and highlight the differences to traditional methods. What are the novel challenges that have to be overcome when developing tools and algorithms for this data. Furthermore, summarize the advantages and deficits of each method. Note: The given references are only guidelines as this is more a research topic. The difficulty lies in giving a concise presentation relevant to bioinformatics, so not to get delayed in biological details.
  REFERENCES:
  Impact of the next generation DNA sequencers
  The impact of next-generation sequencing technology on genetics
  



Developments in genome assembly

• Presentation 2.1. Introduction to assembly (COMPULSORY):
  Jonas Seherr-Thoss (Sita)
  Define what genome assembly is and give an introduction to the algorithms used to address this problem. Give an outline about what has changed and where particular attention is needed.
  REFERENCES:
  Genome assembly reborn: recent computational challenges
  Parametric complexity of sequence assembly: Theory and applications to next generation sequencing
  


• Presentation 2.2. Practical demo:
  Kiran Kumar Telukunta (Sita)
  Use the assembly viewer EagleView to give a practical demonstration of what is involved in an assembly project. The audience should be given an example of real data and shown where errors often occur. This topic involves installing the viewer and playing around with the given test datasets to find good examples. It also involves doing some research on the topic, so that the person doing the presentation knows what assembly is and where the pitfalls lie.
  REFERENCES:
  EagleView: A genome assembly viewer for next-generation sequencing technologies
  


• Presentation 2.3. De novo short read assembly using de Bruijn graphs:
  Summarise paper.
  REFERENCES:
  Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
  


• Presentation 2.4. De novo fragment assembly using mate pairs:
  Summarise paper.
  REFERENCES:
  De novo fragment assembly with short mate-paired reads: Does the read length matter?
  


• Presentation 2.5. Comparative genome assembly:
  Give an initial description of the comparative genome assembly problem and then use the algorithm in the paper as an example.
  REFERENCES:
  A new pheromone trail-based genetic algorithm for comparative genome assembly
  Comparative genome assembly
  


• Presentation 2.6. De novo transcriptome assembly with ABySS:
  Summarise paper.
  REFERENCES:
  De novo transcriptome assembly with ABySS
  



Methods for (short-) read mapping (one topic is compulsory)

• Presentation 3.1. Mapping with hash tables and quality scores:
  Philipp Wollermann (Steffen)
  Summarise paper.
  REFERENCES:
  Mapping short DNA sequencing reads and calling variants using mapping quality scores.
  


• Presentation 3.2. Mapping with mismatches and gaps:
  Waldemar Wittmann (Steffen)
  Summarise paper.
  REFERENCES:
  Fast and accurate short read alignment with Burrows-Wheeler transform.
  


• Presentation 3.3. Mapping with index data structures:
  Kerstin Schmatzer (Steffen)
  Summarise paper.
  REFERENCES:
  Fast mapping of short sequences with mismatches, insertions and deletions using index structures.
  



Metagenomics

• Presentation 4.1. The challenges of metagenomics (COMPULSORY):
  Kyanoush Seyed Yahosseini (Sita)
  Describe the challenges of metagenomics and follow the references in the paper to go into the topics into more detail than it is done here.
  REFERENCES:
  The next meta-challenge for bioinformatics
  


• Presentation 4.2. ESPRIT:
  Summarise paper.
  REFERENCES:
  ESPRIT: estimation species richness using large collections of 16S rRNA pyrosequences
  


• Presentation 4.3. Taxonomic classification of metagenomic datasets:
  Present the problem and summarise the two publications. Choose one of the two to go into more detail, i.e. present the algorithm/methods used. Compare the results.
  REFERENCES:
  TACOA - Taxonomic classification of environmental genomic fragments using a kernalized nearest neighbor approach
  Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models
  



Postgenomics (one topic is compulsory)

• Presentation 5.1. Detecting structural variations:
  Benjamin Schulz (Steffen)
  Summarise paper.
  REFERENCES:
  Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes
  


• Presentation 5.2. Detecting indels and single nucleotide polymorphisms:
  Summarise paper for PolyScan. The other papers give an overview about the general problem.
  REFERENCES:
  PolyScan: an automatic indel and SNP detection approach to the analysis of human resequencing data
  Next-generation sequencing methods: impact of sequencing accuracy on SNP discovery
  Mining SNPs from DNA Sequence Data; Computational Approaches to SNP Discovery and Analysis
  


• Presentation 5.3. Detecting splice sites:
  Summarise paper.
  REFERENCES:
  Optimal spliced alignments of short sequence reads
  

Durchführung

1. Vortrag des Seminarthemas:
   Dauer 30 Minuten, Deutsch/Englisch, Folienpräsentation, anschauliche Darstellung mit vielen Bildern
Richtlinien für Seminarvorträge
Abgabe der Vortragspräsentation eine Woche vor Präsentationstermin

Voraussetzungen

• Teilnahme an mindestens einer Bioinformatik-Vorlesung der vergangenen Semester
• grundlegende molekularbiologische Kenntnisse und entsprechendes Interesse an biologisch relevanten Fragestellungen

Leistungsnachweis

Voraussetzung ist die aktive Teilnahme am (Block-)Seminar sowie die Präsentation eines Themas in Form eines 30-minütigen Vortrags (benotet).

Literatur

• wissenschaftliche Fachartikel zur Ausarbeitung der Seminarthemen werden bei der Vorbesprechung zur Verfügung gestellt
• weiterführende selbstständige Literaturrecherche in Fachliteratur wird erwartet