Fantastic opportunity in phylogenetics!

Fantastic opportunity!

Open science!

Very much enjoyed reading this paper!

Infinite Mixture Models for Improved Modeling of Across-Site Evolutionary Variation Abstract. Scientific studies in many areas of biology routinely employ evolutionary analyses based on inference of phylogenetic trees from molecular sequen

Gill, @lemeylab.bsky.social et al. develop Bayesian infinite mixture models for phylogenetic inference, finding that infinite hidden Markov models best capture complex patterns in large datasets; they implement this framework in BEAST X.

🔗 doi.org/10.1093/molbev/msaf199

#evobio #molbio

Erick is an incredible mentor, working on the most cutting-edge research at the intersection of biology, probability and computing. If I were an early-career researcher, I would jump at this opportunity -- you should too!

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

Am also a proud 6502 assembly programmer!

The OHDSI Collaborator Showcase is a chance to share your research with a global community passionate about real-world data, open science, and collaboration. Submit your abstract for a poster, demo or talk by July 1! 🌍📊 #OHDSI2025 #JoinTheJourney

🔗 https://ohdsi.org/2025-collaborator-showcase

Excited to share my new preprint developed with @matsen.bsky.social, in collaboration with Marius Brusselmans, Luiz Carvalho, @msuchard.bsky.social, and @guybaele.bsky.social, on the biological causes and impacts of tree space ruggedness in phylodynamic inference. 1/
www.biorxiv.org/content/10.1...

🚨 Calling all ATLAS users! As we continue to build an ATLAS roadmap, we ask for you to fill out Survey #2, which focuses on data sources & vocabularies. These features were discussed at our last community call (https://youtu.be/Mfi5N6NHdRA

Survey #2: https://forms.cloud.microsoft/r/NWjAG1gS33

Using administrative claims and EHR databases rates of benign tumors and thyroid #cancer were not different in 460,032 users of GLP-1RAs vs. Users of other glucose lowering agents #diabetes @hmkyale.bsky.social diabetesjournals.org/care/article...

OHDSI is on Bluesky! What is OHDSI? Glad you asked.

OHDSI (Observational Health Data Sciences and Informatics) is a global community using open-source tools & real-world data to generate reliable, reproducible evidence that improves health outcomes. Get to know us and #JoinTheJourney!

ohdsi.org

Our consortium's paper on Mpox in West Africa is finally out today: "Genomics reveals zoonotic and sustained human Mpox spread in West Africa" rdcu.be/emGKq. Extremely fortunately to get to work with such an exceptional team of African public health scientists, and our partners!

A truly amazing scientist, colleague and friend!

🚀 𝐏𝐡𝐃 𝐎𝐩𝐩𝐨𝐫𝐭𝐮𝐧𝐢𝐭𝐲 𝐚𝐭 𝐈𝐦𝐩𝐞𝐫𝐢𝐚𝐥

Looking for my first PhD student

🔬 Project: 𝐈𝐦𝐩𝐚𝐜𝐭 𝐨𝐟 𝐞𝐧𝐯𝐢𝐫𝐨𝐧𝐦𝐞𝐧𝐭𝐚𝐥, 𝐯𝐢𝐫𝐚𝐥, 𝐛𝐞𝐡𝐚𝐯𝐢𝐨𝐮𝐫𝐚𝐥 & 𝐩𝐬𝐲𝐜𝐡𝐨-𝐬𝐨𝐜𝐢𝐚𝐥 𝐞𝐱𝐩𝐨𝐬𝐮𝐫𝐞𝐬 𝐨𝐧 𝐡𝐞𝐚𝐥𝐭𝐡

Joint with LSHTM & UKHSA

See links below.

📅 𝐃𝐞𝐚𝐝𝐥𝐢𝐧𝐞: 7 March 2024

📩 Questions? DM me!

#PhD #HealthEquity #ImperialCollege

HIPSTR: highest independent posterior subtree reconstruction in TreeAnnotator X In Bayesian phylogenetic and phylodynamic studies it is common to summarise the posterior distribution of trees with a time-calibrated consensus phylogeny. While the maximum clade credibility (MCC) tr...

There is a new alternative to the MCC summary tree in BEAST X - the 'highest independent posterior sub-tree reconstruction' or HIPSTR tree. First implemented over 5 years ago (something distracted us from writing it up) we now have a preprint describing it: www.biorxiv.org/content/10.1...

Clinicians, your voice matters! 🩺 @JACCJournals & @US_FDA are teaming up to tackle urgent evidence gaps in cardiovascular care. Share the key questions you face in practice about FDA-regulated products and help shape the future of research. www.jacc.org/doi/10.1016/...

Preliminary report on genomic epidemiology of the 2024 H5N1 influenza A virus outbreak in U.S. cattle (Part 1 of 2) Due to length constraints on virological.org posts, we are splitting this report into two parts that should be read as a single report. This is Part 1, containing Background, Data, Methods, and Findi...

Preliminary report on genomic epidemiology of the 2024 H5N1 influenza A virus outbreak in U.S. cattle.

Thanks to everyone who contributed to this and, of course, first and foremost the data producers and those involved in the response.

virological.org/t/preliminar...

Note about availability of H5N1 2.3.4.4b consensus sequences from cattle and other species: On Sunday, April 21st, 2024, “in the interest of public transparency and ensuring the scientific community has access to this information as quickly as possible to encourage disease research and devel...

My colleagues and I have just posted a
"Note about availability of #H5N1 2.3.4.4b consensus sequences from cattle and other species" on virological.org.

Consensus genomes and metadata.

virological.org/t/note-about...

I want to re-emphasize how critically important it will be to not repeat our mistake from the COVID-19 pandemic of letting an opaque organization with highly questionable governance be the main source for critical, publicly funded, genomic data for H5N1.

www.science.org/content/arti...

I love that the Department of Biostatistics at UCLA still has manual pencil sharpeners on the walls.... #statistics

New paper from "SEARCH" just landed!

By sequencing 80k+ SARS2 genomes from San Diego & Baja, we looked at connectedness between waves since the start of the pandemic.

Clear heterogeneity over time and very limited effect of the US-Mexico border 'closure'.

t.co/AdtUN7VuKK

Do you want to deliver reliable evidence from observational healthcare data or develop tomorrow's hottest phylodynamics model? Find computational statistics and data science fascinating? Let me hire you as a Postdoctoral Fellow. Please email me directly ASAP! (flexible start)