Research in the Goldman group: pandemic-scale phylogenetics, and optimizing new sequencing technologies

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• Nick Goldman and Nicola De Maio, EMBL-European Bioinformatics Institute
• Wednesday 08 February 2023, 14:00-15:00
• CMS, Meeting Room 15.

If you have a question about this talk, please contact Samantha Noel.

Our intention is to deliver all Seminars in person. Seminars are aimed mainly at MPhil CompBio students, but are open to anyone who wishes to attend by pre-booking with the Administrator

We will give a summary of the ongoing research in the Goldman group at EMBL -EBI, and of possible projects for the students. First, we will describe our work in large-scale phylogenetics, and in particular the development of a new algorithm for fast and accurate phylogenetic analysis of millions of SARS -CoV-2 genomes. Phylogenetic methods are essential in studying evolution, as exemplified by their use during the SARS -CoV-2 pandemic to identify new variants, reconstruct the origin of the virus, and trace transmission, among many other applications. Phylogenetic analyses have however been hindered by their elevated computational demand and low reliability, issues that we address with a new algorithm specifically developed for scenarios of low divergence between genomes. Secondly, we are working on optimizing the genome-sequencing data gathering capabilities of third-generation technologies. Nanopore sequencing devices now have the ability to ‘reject’ DNA fragments they have started to read, and we have been working on methods that enable good strategies for which fragments to read in their entirety and which to reject. We will describe two experimental contexts in which our methods can be useful, one of which is working and recently published and one of which is still work-in-progress.

This talk is part of the Computational and Systems Biology Seminar Series 2023 - 24 series.

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