Computational Pangenomics: Algorithms & Applications @ ECCB 2020

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Link to the Workshop

Date: Friday, 4th September

Time: 17:00 to 20:00 (CEST)


  • Solon P. Pissis, Centrum Wiskunde & Informatica (CWI and VU), The Netherlands
  • Yuri Pirola, Università degli Studi di Milano-Bicocca (UNIMIB), Italy

Invited Speakers

  • Valentina Boeva, ETH Zürich, Switzerland
  • Tobias Marshall, Universität Düsseldorf, Germany


Computational Pangenomics encompasses different research efforts for transitioning the existing paradigm from a sequence-based reference genome to a pan-genome, i.e., an evolutionarily coherent collections of genomes. Such a transition is urgently needed to effectively exploit the data masses produced by the technical advances and the widespread adoption of sequencing technologies. Graph-based representations of collections of genomes and diploid-aware assemblers have been recently proposed, but a large amount of work is still needed to shift to a pan-genomic view into the current research practice.

Computational Pangenomics is at its infancy and, to better sustain its full (and possibly, rapid) development, an interdisciplinary collaboration between Bioinformatics, Theoretical Computer Science, and Medicine is of crucial importance. As such, the workshop aims to provide an occasion for researchers of these disciplines to know the recent advances of the topic and the questions that will drive the future research efforts in this area.

This virtual workshop is articulated in two keynote talks focusing on algorithms (graph and string algorithms, indexing) and on applications (genome assembly, variant calling, comparative and evolutionary genomics) and in several invited talks given by researchers from the EU Project PANGAIA’s partners.

Target audience

The workshop aims to strengthen the interdisciplinary collaborations between computer scientists and bioinformaticians as well as practitioners of the field of computational genomics that are interested to deal with the complexity of data related to genomes at population scale. The workshop is open to everyone who wants to share their ideas and work about algorithms and applications related to computational pangenomics.


Time (CEST)Details
17:00 – 17:45Tobias Marschall: Sequence-to-Graph Alignment and Pangenome-based Genome Inference
17:45 – 18:30Valentina Boeva: Machine learning approaches for cancer survival prediction
18:30 – 18:50Cedric Chauve: Annotation free isoform discovery from long reads
18:50 – 19:10Paul Medvedev: Reference-free error correction of Oxford Nanopore transcriptome data
19:10 – 19:30Iman Hajirasouliha: Novel methods for Structural Variation detection and assembly using long-range DNA sequencing
19:30 – 20:00Q&A with all the speakers

For registration details please visit