Leo Featherstone

Not sure - but keen to see an answer to this 👍

This paper by Celentano et al. on scalable simulation under the birth death is one of my favourites for the year! It introduces some elegant thinning that has been sorely needed. Fantastic to pave the way forward for future simulation-heavy inference, including neural Bayes!

doi.org/10.1073/pnas...

Looks interesting!

The geospatial phylodynamics of SARS-CoV-2 in Nepal and clinical phenotype of long COVID during the Delta-Omicron waves The COVID-19 pandemic exposed gaps in global emerging infectious disease preparedness, particularly for countries with high levels of economic migration, such as Nepal. The Epidemic Intelligence proje...

Our study on SARS-CoV-2 dynamics and long COVID in Nepal has made it to preprint 🎉 Huge thanks everyone from BNMT, Center for Molecular Dynamics Nepal (CMDN), and the Centre for Pathogen Genomics at The Peter Doherty Institute for Infection and Immunity 👏👏👏

www.medrxiv.org/content/10.1...

The BEAST X logo - an octopus wrapping its noodley appendages round the letter X.

BEAST X v10.5.0 finally released – you can't just do beta releases forever. github.com/beast-dev/be...

Details and instructions for installing on the BEAST website: beast.community

Characterisation of in vitro resistance selection against second-/last-line antibiotics in methicillin-resistant Staphylococcus aureus ATCC 43300 strain AbstractBackground and objectives. The increasing occurrence of MRSA clinical isolates harbouring reduced susceptibility to mainstay antibiotics has escala

New paper from our lab in collaboration with Blaskovich lab led by former Phd student Anggia Prasetyoputri using in vitro selection to identify drug resistance conferring murations in S. aureus academic.oup.com/jacamr/artic...

Bayesian Phylodynamic Inference of Multitype Population Trajectories Using Genomic Data Abstract. Phylodynamic methods provide a coherent framework for the inference of population parameters directly from genetic data. They are an important to

Vaughan & @tanjastadler.bsky.social develop a method to infer multitype population trajectories and apply it to MERS-CoV, revealing transmission patterns between camels and humans.

🔗 doi.org/10.1093/molbev/msaf130

#evobio #molbio #virus

🎉 My PhD dissertation is now online! Traditional ODE solvers compute a single solution estimate - Probabilistic solvers also tell you how reliable they are! In my PhD, I established them as a Flexible and Efficient Framework for Probabilistic Simulation and Inference.
📄 tinyurl.com/mt3sffb

🧵 1/6

Please move genomes to an open pathogen platform like pathoplexus.org!

Very exciting!

How can one efficiently simulate phylodynamics for populations with billions of individuals, as is typical in many applications, e.g., viral evolution and cancer genomics? In this work with M. Celentano, @wsdewitt.github.io , & S. Prillo, we provide a solution. doi.org/10.1073/pnas...
1/n

Robustness of Ancestral Sequence Reconstruction to Among-site and Among-lineage Evolutionary Heterogeneity Abstract. Ancestral sequence reconstruction is typically performed using homogeneous evolutionary models, which assume that the same substitution propensit

Ancestral sequence reconstruction often assumes unrealistic homogeneous substitution models; however @rmuniztrejo.bsky.social et al. find that reconstruction accuracy is determined by phylogenetic signal, not model choice.

🔗 doi.org/10.1093/molb...

#evobio #molbio

Customizable host and viral transcript enrichment using CRISPR-Cas9 long-read sequencing for isoform discovery and validation Long-read RNA sequencing has been broadly utilized to examine the diversity of transcriptomes, understand differential expression and discover novel transcript isoforms. One of the major limitations o...

New preprint from the lab, describing an approach to enrichment of transcript isoforms for nanopore cDNA sequencing, using CRISPR-Cas9 www.biorxiv.org/content/10.1...

SIB Speaker Roadshow Initiative: Alex Zarebski on Narrow AI for Phylodynamics Alex Zarebski from the University of Cambridge will be giving two talks in Switzerland: 📍 Bern – 31 March at 15:15, at the Institute of Ecology and Evolution of the University of Bern, Baltz...

@aezarebski.bsky.social will give 2 talks in 🇨🇭:

🔹 Bern – 31/3 15:15
🔹 Basel – 16/4, 11:15

💡 Talk: Narrow AI for Phylodynamics

This visit is supported by SIB’s Speaker Roadshow Initiative, which coordinates multiple talks at partner institutions and promotes sustainable travel.