Overview

PhyloSIB is an annual workshop organised by the SIB Swiss Institute of Bioinformatics with an emphasis on molecular evolution, phylogenetics, and comparative phylogenomics. The goal of PhyloSIB is to exchange knowledge and foster discussion on current studies and recent developments in the field. Participants are typically developers of relevant analysis tools and databases, expert users of such tools and databases, as well as students and other researchers on their way to becoming experts. The 2025 PhyloSIB edition is organised as a Satellite event preceding the Biology25 Conference. Registration is open to all (limited to 50 participants) and is separate from the Biology25 registration (i.e. you do not have to be registered to attend Biology25 in order to apply to attend PhyloSIB).

Biology25 is the largest conference of organismal biology in Switzerland, and the yearly joint meeting of the Swiss Zoological Society, the Swiss Botanical Society, and the Swiss Systematics Society. The conference will be held on February 13-14, 2025 at the University of Lausanne.

PhyloSIB Scientific Organising Committee Maria Anisimova (ZHAW), Niko Beerenwinkel (ETHZ), Giulia Campli (UNIL), Louis du Plessis (ETHZ), Natasha Glover (UNIL), Evgenia Kriventseva (UNIGE), Sebastien Moretti (SIB), Richard Neher (UNIBAS), Marc Robinson-Rechavi (UNIL), & Damian Szklarczyk (UZH).

Location Amphithéâtre du Biophore at UNIL-Sorge

Application Process We will accept applications up to the deadline of January 10th whereafter we will send acceptance emails with requests for registration fee payments, as well as informing applicants if they are on the waiting list in case applications outnumber available spaces.

Schedule

Times	Sessions	Notes
10.30 - 11.00	Arrival	Welcome tea/coffee & croissants
11.00 - 11.15	Introduction	PhyloSIB
11.15 - 12.30	Session 1	5 selected talks
	Johannes Gawron - Computational Biology Group	Phylogenetic inference reveals clonal heterogeneity in circulating tumour cell clusters
	Antoine Zwaans - Computational Evolution	Leveraging single-cell lineage tracing data to reconstruct cellular processes: from CRISPR barcodes to Bayesian phylodynamics
	Nadia Neuner-Jehle - EVE Epidemiology and Virus Evolution	Phylogenetic Analysis of EV-A71, CV-A6, and CV-A16 Using Nextstrain
	Eric Ulrich - Evolutionary Microbiology	Co-evolution of four bacterial species reduces facilitative interactions
	Adrian Davin - Microbiome Research	A geological timescale for bacterial evolution
12.30 - 13.30	Lunch break	Sandwich lunch and refreshments
13.30 - 14.45	Session 2	5 selected talks
	Marco Molari - Microbial Evolution	Evolutionary dynamics of genome structure and content among closely related bacteria
	Giulia Campli - Environmental Bioinformatics	Tracing the evolutionary history of moulting genes across arthropod diversity
	Aleksandra Nivina - Evolutionary Systems Biology	Recombinational puzzle: ancestral state reconstruction in modular polyketide synthases
	Angélica Pulido - Population Genetics and Genomics	Reconstructing phylogenetic relationships of Tyto owls using museomics
	David Moi - Comparative Genomics	Foldtree2: creating and applying new structural alphabets to phylogenetics
14.45 - 15.15	Break	Tea/coffee break
15.15 - 16.30	Session 3	5 selected talks
	Cyril Malbranke - Laboratory of Computational Biology and Theoretical Biophysics	ProtMamba: a homology-aware but alignment-free protein state space model
	Alexandre Laverré - Evolutionary Bioinformatics	Detection of positive selection on regulatory sequences through genotype-to-fitness function and machine learning predictions
	Matthew Berkeley - Computational Evolutionary Genomics	OrthoDB and BUSCO update: annotation of orthologs with wider sampling of genomes
	Jūlija Pečerska - Applied Computational Genomics Team	Evolution of evolutionary methods: exploring joint tree and alignment inference
	Daniele Silvestro - Evolutionary Paleobiology	A semi-supervised learning approach for phylogenetic inference
16.30 - 16.55	Session 4	Open Discussions
16.55 - 17.00	Conclusion

Additional information

Participating SIB groups

Beerenwinkel - Computational Biology Group
Neher - Microbial Evolution
Stadler - Computational Evolution
Hodcroft - EVE Epidemiology and Virus Evolution
Bitbol - Laboratory of Computational Biology and Theoretical Biophysics
Dessimoz & Glover - Comparative Genomics
Zdobnov & Kriventseva - Computational Evolutionary Genomics
Goudet - Population Genetics and Genomics
Mitri - Evolutionary Microbiology
Robinson-Rechavi & Bastian - Evolutionary Bioinformatics
Wagner - Evolutionary Systems Biology
Waterhouse - Environmental Bioinformatics
Anisimova - Applied Computational Genomics Team
Sunagawa - Microbiome Research
Silvestro - Evolutionary Paleobiology