Reconciling fast Hepatitis B evolutionary rates with ancient co-divergence https://www.biorxiv.org/content/10.64898/2026.06.05.730483v1

Fantastic opportunity in phylogenetics!

Rachel Warnock@rachelwarnock.bsky.social · 5mo ago

I’m looking for a post doc (up to five years) interested in phylogenetics and earth systems - please spread the word!

Fantastic opportunity!

We are recruiting two postdoc roles to work with #DeZiNetwork on dengue, Zika, and other emerging arboviruses: 🔬 Viral Computational Genomics 🔗 Apply here: lnkd.in/eq-dqCJb 🧪 Viral Genomics and Immunology 🔗 Apply here: lnkd.in/eMEKWb9b More on DeZi here: lnkd.in/edwBg-qX Deadline: 15 Jan 2026

Open science!

Pathoplexus@pathoplexus.org · 9mo ago

1/ 🚀 Big thanks to our community - since August we’ve added thousands of new sequences, rolled out major new features, and welcomed fresh faces into the #Pathoplexus world. Let’s dive into what’s new.👇🏻 Read the full update: pathoplexus.org/news/2025-11...

Very much enjoyed reading this paper!

Aaditya Narasimhan@aaditya320.bsky.social · 9mo ago

academic.oup.com/evlett/advan... So exciting to see a new method to model the evolution of G (and P) matrices on phylogenies. Another step in the direction of trying to bridge micro and macroevolution

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

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

doi.org

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!

Frederick "Erick" Matsen@matsen.bsky.social · 12mo ago

Interested in doing a PhD or postdoc in our group? Here is a letter to you: matsen.group/general/202... We are ready to recruit a trainee who can help develop the next generation of our transformer-based models of natural selection. See the "joining" tab of our website for details.

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!

Jason Moore@moorejh.bsky.social · last yr.

Yes! I graduated from the class of 6502 :) #retrocomputing

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!

Angie Rasmussen@angierasmussen.bsky.social · last yr.

Mike is both a brilliant, principled scientist & also one of the most generous, kind people I’ve worked with. His leadership & groundbreaking research has profoundly transformed how we understand pandemics. Congratulations, Mike, this is so richly deserved! 🍾🎉🇨🇦❤️ www.statnews.com/status-list/...

🚀 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

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...

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...

eur02.safelinks.protection.outlook.com

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. 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...

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...

virological.org

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...

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...

virological.org

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...

The ‘invented persona’ behind a key pandemic database

GISAID offers a safe space to post viral genomes. Peter Bogner, its perplexing creator and overseer, may be jeopardizing its future

science.org

Kristian G. Andersen@kgandersen.bsky.social · 2y ago

Can we *please* ensure that *all* H5N1 sequences generated using public funds are shared using *open* databases? GISAID is not one such database, NCBI is. If sequences are shared using the former, please ensure it is also available on the latter (and NCBI should be default).

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)