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Leo Featherstone

@lfeatherstone.bsky.social
55 followers 195 following 4 posts

Phylodynamics | The Kirby Institute & UNSW

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Wytamma @wytamma.bsky.social · 06/05/2026
@lfeatherstone.bsky.social and I have just released v1.10.2 of clockor2.github.io 🎉 including several performance upgrades. Here we reproduce the results of McBride et al 2023, showing accelerated evolution of SARS-CoV-2 in white-tailed deer transmission clusters 🦌🦠 go.unimelb.edu.au/ydo2
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Leo Featherstone @lfeatherstone.bsky.social · 21/12/2025
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...
doi.org
PNAS
Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
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Leo Featherstone @lfeatherstone.bsky.social · 04/12/2025
Looks interesting!
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Reposted by Leo Featherstone
Wytamma @wytamma.bsky.social · 26/07/2025
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...
medrxiv.org
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...
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Reposted by Leo Featherstone
Andrew Rambaut (🐏🎀) @arambaut.bsky.social · 02/07/2025
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
The BEAST X logo - an octopus wrapping its noodley appendages round the letter X.
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Lachlan Coin @lachlanjmc.bsky.social · 26/06/2025
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...
academic.oup.com
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
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Reposted by Leo Featherstone
Molecular Biology and Evolution @molbioevol.bsky.social · 17/06/2025
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
doi.org
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
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Nathanael Bosch @nathanaelbosch.de · 30/05/2025
🎉 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
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Wytamma @wytamma.bsky.social · 29/05/2025
Please move genomes to an open pathogen platform like pathoplexus.org!
pathoplexus.org
Pathoplexus | Home
Pathoplexus is a new, open-source database dedicated to the efficient sharing of human viral pathogen genomic data, fostering global collaboration and public health response.
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Leo Featherstone @lfeatherstone.bsky.social · 24/05/2025
Very exciting!
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Reposted by Leo Featherstone
Yun S. Song @yun-s-song.bsky.social · 23/05/2025
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
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Molecular Biology and Evolution @molbioevol.bsky.social · 01/05/2025
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
doi.org
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
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Lachlan Coin @lachlanjmc.bsky.social · 15/04/2025
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...
biorxiv.org
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...
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SIB Swiss Institute of Bioinformatics @sib.swiss · 25/03/2025
@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.
sib.swiss
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...
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