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SUMMARY:Research in the Goldman group: pandemic-scale phylogenetics\, and 
 optimizing new sequencing technologies - Nick Goldman and Nicola De Maio\,
  EMBL-European Bioinformatics Institute
DTSTART:20230208T140000Z
DTEND:20230208T150000Z
UID:TALK192041@talks.cam.ac.uk
CONTACT:Samantha Noel
DESCRIPTION:We will give a summary of the ongoing research in the Goldman 
 group at EMBL-EBI\, and of possible projects for the students. \nFirst\, w
 e will describe our work in large-scale phylogenetics\, and in particular 
 the development of a new algorithm for fast and accurate phylogenetic anal
 ysis of millions of SARS-CoV-2 genomes. \nPhylogenetic methods are essenti
 al 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 an
 alyses have however been hindered by their elevated computational demand a
 nd low reliability\, issues that we address with a new algorithm specifica
 lly developed for scenarios of low divergence between genomes. Secondly\, 
 we are working on optimizing the genome-sequencing data gathering capabili
 ties of third-generation technologies.  Nanopore sequencing devices now ha
 ve the ability to 'reject' DNA fragments they have started to read\, and w
 e have been working on methods that enable good strategies for which fragm
 ents 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
 .\n
LOCATION:CMS\, Meeting Room 15
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