New paper "To select or not to select: predictively consistent priors instead of model selection" with Anna Elisabeth Riha, Leevi Lindgren, @davidkohns.bsky.social, @paulbuerkner.com arxiv.org/abs/2606.22850 Model selection is not a substitute for building good models in the first place 1/

1/ Deep-time phylogenetics is hard: overly simplistic substitution models can mislead tree estimation at the billion year timescale. Our new preprint introduces GTRspmix, a protein modeling framework designed to more realistically model site-to-site heterogeneity in amino acid replacement. 🧵

We've been looking at how to compare and cluster large numbers of genomes, such as those in large isolate databases such as AllTheBacteria, and metagenome assemblies (e.g. SPIRE, MGnify). On a combined dataset of 5.6 million assemblies, we can now cluster/dereplicate everything in under a day!

New comment Genotype-based antimicrobial resistance tests need a new regulatory framework www.thelancet.com/journals/lan... #IDSky #ClinMicro #AMR #OpenAccess #OA

Great discussion with @billhanage.bsky.social and the audience at #ESCMIDGlobal2026 during our session “Pathogens and people: modelling epidemics for preparedness”. Strong focus on how to improve preparedness in collaboration with public health institutes - lots to take forward.

Ian Braga, Lucas Wardil, Ricardo Martinez-Garcia: Fixation probabilities for multi-allele Moran dynamics with weak selection https://arxiv.org/abs/2604.12004 https://arxiv.org/pdf/2604.12004 https://arxiv.org/html/2604.12004

The European Commission will invest $34.7 million in the two public-private partnerships to boost the pipeline for new antibiotics and other AMR medical countermeasures. Read more: ow.ly/Sap850YFgir

We (with @yanwong.bsky.social) are advertising a 3 year postdoc position for a project on ARG inference and methods! Based at Oxford stats. Closing date noon 7 April, full details at my.corehr.com/pls/uoxrecru...

🚨 New pre-print! 🚨 In the largest study of its kind to-date, we investigate the ecological and evolutionary mechanisms driving within-patient evolution of antimicrobial resistance (AMR). Read here: www.biorxiv.org/content/10.6... , and follow along with this thread, discussing our findings (1/21)

We're also happy to see a second paper out today, led by Nicola de Maio, which develops methods to identify and account for mutation rate variation and recurrent errors. www.nature.com/articles/s41...

Ian Roberts published his first paper "Bayesian Inference of Pathogen Phylogeography using the Structured Coalescent Model" with me, Jere Koskela and Xavier Didelot. We describe an efficient reversible jump MCMC method for inference for the structured coalescent. journals.plos.org/pl...

Now published: our work using phylodynamics from surveillance data to quantify and experimentally validate the fitness impact of antibiotic resistance determinants & how this changes with patterns of antibiotic use: www.nature.com/articles/s41...

Very happy to have had the opportunity to contribute to this work. Thanks to Robin Thompson for leading, the amazing team of co-authors and the INI for hosting us.

Now out in NEJM. Kudos to @dhelekal.bsky.social and @tatumdmortimer.bsky.social : www.nejm.org/doi/10.1056/...

If you are an early career research attending @stihiv2025.org and interested in learning more about data visualization in R, @odileharrison.bsky.social , Sim Dabee, and I are organizing a workshop during the conference (11:30am-1:30pm on Wednesday). Register here: forms.gle/e4UL1NG62PUD...

A fun conversation with Carl this afternoon about his excellent book AIR-BORNE--the recording is available at the HSPH youtube site: www.youtube.com/user/Harvard...

One ceftriaxone-resistant #typhoid case last year set us on a path that is now live on Emerging Infectious Diseases. 47 cases in months, resistance rose from 0 to 5%. We spoke with patients, sequenced samples. 4.3.1.2.B1 lineage+blaCTX-M-15 on pCROB1. #AMR #PublicHealth wwwnc.cdc.gov/eid/article/...

Looking forward to my visit @ccdd-hsph.bsky.social!

(1/10) New preprint: Expansion of tetM-carrying Neisseria gonorrhoeae in the US, 2018-2024; Link: www.medrxiv.org/content/10.1...

How do changes in antibiotic use, various pathways to resistance, multiple drug resistance, and more come together to shape the success and failure of bacterial lineages in a real-world epidemic? #AMR #microsky A preprint: www.biorxiv.org/content/10.1... (1/15)

SAVE THE DATE ‼️ 📆 📢 BBM 2025 will be held on June 9-10th at the Harvard Science Center feat. the one and only Dr. Petra Levin as keynote! We can't wait to see you there. Registration and scholarship applications open next week.

Why don’t people who live together have the same strains of microbes? Tami Lieberman (@contaminatedsci.bsky.social) and I put forward one underexplored reason in our new preprint: Intraspecies warfare restricts strain coexistence in human skin microbiomes

My latest for JAMA. Dire headline but focuses on solutions - eg PCR test showing if patient responds to "older" antibiotic, modeling study suggesting how to deploy new drugs w/ national surveillance on shoestring budget. @yhgrad.bsky.social @jenabbasi.bsky.social jamanetwork.com/journals/jam...

Fully automated assessment of correlated evolution on phylogenetic trees: now out in OA: doi.org/10.1111/2041... Thanks to all authors (not yet here). This explains the methodological basis of our recent work on epistatic interactions in the evolution of quinolone resistance: doi.org/10.1093/molb...