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!

Johanna von Wachsmann@johannavw.bsky.social · 2mo ago

🧬 New preprint! We clustered 5.6 million bacterial genomes into genomically cohesive units (GCUs) 500× faster than existing tools. (In just 14 hours, 16.5 GB RAM using 48 CPUs). 🦠🐙Meet gemsparcl 💎✨! www.biorxiv.org/content/10.6...

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...

Rate variation and recurrent sequence errors in pandemic-scale phylogenetics - Nature Methods

Performing pandemic-scale phylogenetic analysis poses multifaceted challenges. This study develops methods for identifying and accounting for mutation rate variation and recurrent sequence errors, lea...

nature.com

Zamin Iqbal@zaminiqbal.bsky.social · 6mo ago

A long time ago in a galaxy far away, there was a SARS-CoV-2 pandemic. Our paper, led by @martibartfast.bsky.social a) correcting errors in 4.5 million genomes & their phylogeny b) improving representation of the Global South in public data www.nature.com/articles/s41... (thread 1/n)

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...

Quantifying the real-world impact of antibiotic use and genetic determinants of resistance on gonococcal dynamics

Nature Microbiology - Phylodynamic modelling shows how the changing antibiotic landscape and genetic determinants of resistance shape real-world gonococcal dynamics. Experiments validated that...

nature.com

Yonatan Grad@yhgrad.bsky.social · last yr.

New preprint! How much does antibiotic use shape bacterial lineage dynamics, and how does that relate to the fitness costs/benefits of resistance determinants? All sorts of fun findings and a method that we hope will be broadly useful. See @dhelekal.bsky.social's thread and the preprint!

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.

Thomas House@tah-sci.com · 6mo ago

New paper! "Infectious disease outbreak controllability: biological, social and public health factors" - we provide a modelling-informed discussion of what 'controllability' means for an infectious disease outbreak. royalsocietypublishing.org/rspb/article...

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

Expansion of tetM-Carrying Neisseria gonorrhoeae in the United States, 2018–2024 | NEJM

During 2018–2024, the percentage of N. gonorrhoeae isolates carrying tetM, which confers tetracycline resistance, increased from less than 10% to more than 30% across the United States.

nejm.org

Yonatan Grad@yhgrad.bsky.social · last yr.

New preprint, as described by David below. There's been an increase in doxycycline use for prevention and treatment of bacterial STIs. What's happened to resistance in Neisseria gonorrhoeae? Here we track tetM, a tetracycline-resistance gene, looking at both proportion and phylogenetics.

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...

ECR Data Visualisation Workshop

Please complete this application to attend the Data Viz workshop. This event will be held at the 2025 STI & HIV World Congress in Montreal, Canada on Wednesday, July 30th from 11:30-13:30. Effective...

forms.gle

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...

Harvard T.H. Chan School of Public Health

Sharing diverse perspectives on public health. Speakers do not speak for Harvard.

youtube.com

Carl Zimmer@carlzimmer.com · last yr.

Looking forward to talking about AIR-BORNE at 1 pm at @hsph.harvard.edu Watch online here: hsph.harvard.edu/events/whats...

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/...

Outbreak of Ceftriaxone-Resistant <em>Salmonella enterica</em> Serovar Typhi, Bangladesh, 2024

Ceftriaxone-Resistant <em>Salmonella</em> Typhi, Bangladesh

wwwnc.cdc.gov

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

kermit the frog is dancing in front of a red curtain with the words i 'm so excited !

ALT: kermit the frog is dancing in front of a red curtain with the words i 'm so excited !

media.tenor.com

CCDD@ccdd-hsph.bsky.social · last yr.

Join us this Thursday (4/3) at 1PM ET for our #IDEpi Seminar by Prof @vmminin.bsky.social, Professor of Statistics, Assoc Director of the Infectious Disease Science Initiative, at University of California, Irvine. Register at hsph.me/IDEPI25

(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)

Quantifying the impact of antibiotic use and genetic determinants of resistance on bacterial lineage dynamics

The dynamics of antimicrobial resistance in bacteria are informed by the fitness advantages conferred by genetic determinants of resistance in the presence of antibiotic pressure and the potential fit...

biorxiv.org

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

bioRxiv Microbiology@biorxiv-microbiol.bsky.social · 2y ago

Intraspecies warfare restricts strain coexistence in human skin microbiomes https://www.biorxiv.org/content/10.1101/2024.05.07.592803v1

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...

“Super Gonorrhea” Has Arrived

This Medical News article discusses approaches to slow the spread of antimicrobial resistance in Neisseria gonorrhoeae.

jamanetwork.com

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...