Leo Featherstone
@lfeatherstone.bsky.social
Phylodynamics | The Kirby Institute & UNSW
Reposted by Leo Featherstone
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...
www.medrxiv.org/content/10.1...
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...
www.medrxiv.org
July 26, 2025 at 5:17 AM
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...
www.medrxiv.org/content/10.1...
Reposted by Leo Featherstone
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
Details and instructions for installing on the BEAST website: beast.community
July 2, 2025 at 8:32 PM
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
Details and instructions for installing on the BEAST website: beast.community
Reposted by Leo Featherstone
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...
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
academic.oup.com
June 26, 2025 at 4:23 AM
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...
Reposted by Leo Featherstone
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/10.1093/molbev/msaf130
#evobio #molbio #virus
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
doi.org
June 17, 2025 at 2:29 PM
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/10.1093/molbev/msaf130
#evobio #molbio #virus
Reposted by Leo Featherstone
🎉 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
📄 tinyurl.com/mt3sffb
🧵 1/6
May 30, 2025 at 10:02 AM
🎉 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
📄 tinyurl.com/mt3sffb
🧵 1/6
Reposted by Leo Featherstone
Please move genomes to an open pathogen platform like pathoplexus.org!
May 29, 2025 at 5:08 AM
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
1/n
May 23, 2025 at 11:36 PM
Very exciting!
Reposted by Leo Featherstone
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
1/n
May 23, 2025 at 9:02 PM
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
1/n
Reposted by Leo Featherstone
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/10.1093/molb...
#evobio #molbio
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
doi.org
April 30, 2025 at 11:29 PM
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/10.1093/molb...
#evobio #molbio
Reposted by Leo Featherstone
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...
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...
www.biorxiv.org
April 15, 2025 at 4:41 AM
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...
Reposted by Leo Featherstone
@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.
🔹 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 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...
www.sib.swiss
March 25, 2025 at 10:53 AM
@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.
🔹 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.