Mining viral genomes to improve clinical diagnostics

What you will learn: how to mine viral genomes to improve clinical diagnostics using V-pipe, a new SIB bioinformatics pipeline for analyzing viral sequencing data (https://cbg-ethz.github.io/V-pipe/)

Target audience: scientists who analyze virus sequencing data in basic research or clinical settings, e.g. bioinformaticians embedded in clinical research groups, staff of bioinformatics core units, etc.

Speaker: Niko Beerenwinkel, Group Leader, Computational Biology Group, SIB Swiss Institute of Bioinformatics & ETH Zurich (see biography below)

Click to access specific sections of the talk:
1. Why analyzing viral genomes 00:34
2. What is V-Pipe 04:04
3. Can I build my own pipeline 10:24
4. How can I get started using V-Pipe 11:54

Any question about this talk? Contact the team: [email protected]
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More about the speaker: Niko Beerenwinkel is a full professor of computational biology at ETH Zurich and a Group Leader at the SIB Swiss Institute of Bioinformatics. His research is at the interface of mathematics, statistics and computer science with biology and medicine. His interests range from the mathematical foundations of biostatistical models to evolutionary modelling and clinical applications in oncology and infectious diseases. He has developed several computational methods for the analysis of deep sequencing data to infer the genetic composition of virus populations.

Further reading...
... on global haplotype reconstruction:
Töpfer A, Marschall T, Bull RA, Luciani F, Schönhuth A, et al. (2014) Viral Quasispecies Assembly via Maximal Clique Enumeration. PLOS Computational Biology
https://doi.org/10.1371/journal.pcbi....

... on local haplotype reconstruction:
Osvaldo Zagordi, Lukas Geyrhofer, Volker Roth, and Niko Beerenwinkel (2010) Deep Sequencing of a Genetically Heterogeneous Sample: Local Haplotype Reconstruction and Read Error Correction. Journal of Computational Biology
https://doi.org/10.1089/cmb.2009.0164

…on the software components used in V-Pipe:
Osvaldo Zagordi, Arnab Bhattacharya, Nicholas Eriksson and Niko Beerenwinkel (2011) ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data. BMC Bioinformatics
https://doi.org/10.1186/1471-2105-12-119

…on methods for viral diversity estimation:
Susana Posada-Cespedes, David Seifert and Niko Beerenwinkel (2017) Recent advances in inferring viral diversity from high-throughput sequencing data. Virus research
https://doi.org/10.1016/j.virusres.20...

Other resources about V-Pipe
- Flyer: https://polybox.ethz.ch/index.php/s/C...
- Slide deck: https://polybox.ethz.ch/index.php/s/m...

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Funding
V-Pipe is supported by ETH Zurich, SIB, SNF, SHCS, SystemsX.ch, ERASysAPP, Swiss Cancer League, EC Horizon 2020, ERC Synergy

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