iiinova — where your digital self keeps evolving

Reposted by David Helekal

Eva Miranda @evamirandag.bsky.social · 11/09/2026

Before OpenAI announces the resolution of the next Millennium Prize Problem, allow me a little mathematical flex 😎. We proved that a single ball in a 2D billiard can simulate a universal Turing machine, solving a problem posed by Cris Moore.🎱🤖 Read it here @pnas.org: www.pnas.org/doi/10.1073/...

pnas.org

Two-dimensional billiards are Turing complete | PNAS

We show that two-dimensional billiard systems can simulate universal Turing machines. Billiards serve as idealized models of particle motion with e...

072

David Helekal @dhelekal.bsky.social · 03/09/2026

How do we scale bacterial GWAS to traits that require (costly) experimental measurements? In our preprint, we: (1) introduce the highly-efficient Bayesian adaptive sequential sampling GWAS (BASS-GWAS); (2) use BASS-GWAS to study the genetics of cross-resistance between two new antibiotics! /1

biorxiv.org

Bayesian adaptive experimental design for efficient microbial genome-wide association studies

Bacterial genome-wide association studies (GWAS) offer a powerful approach to identify the genetic basis of a trait measured in a set of sequenced isolates. As the number of sequenced isolates has gro...

152

Reposted by David Helekal

bioRxiv Genetics @biorxiv-genetic.bsky.social · 01/09/2026

Bayesian adaptive experimental design for efficient microbial genome-wide association studies www.biorxiv.org/content/10.64898/20…

054

Reposted by David Helekal

Aki Vehtari @avehtari.bsky.social · 23/06/2026

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/

To select or not to select: predictively
consistent priors instead of model selection

Anna Elisabeth Riha, Leevi Lindgren, David Kohns, Paul-Christian Bürkner, Aki Vehtari

Bayesian modelling workflows often consider multiple candidate models of varying complexity. Model selection is commonly used to navigate potential trade-offs between model complexity and generalisability to new data. We study when model selection is unnecessary or can even be harmful for predictive performance in finite data regimes and find that the need for selecting simpler models can depend on prior choice. We formalise predictively consistent priors, which keep prior predictive implications stable as model complexity increases. Across examples and numerical experiments, including adding covariates in linear and logistic regression, forward variable selection, and nonlinear modelling, flexible models with predictively consistent priors typically match or outperform selected simpler models in out-of-sample predictive performance. When selection helps, it can indicate poor joint prior implications, such as excessive prior mass on implausible predictive values. Based on our findings, we propose replacing the notion of sparsity or parsimony at the level of model components with specifying priors that remain sensible in predictive space as models become more complex.

110631

Reposted by David Helekal

Andrew Roger @andrewjroger.bsky.social · 19/06/2026

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. 🧵

15221

Reposted by David Helekal

John Lees @johnlees.bacpop.org · 16/06/2026

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!

13111

Reposted by David Helekal

The Lancet Microbe @lancetmicrobe.bsky.social · 10/06/2026

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

Principles of genotype-based AMR diagnostic regulation
1.
Contextualise performance claims: require stratified performance, where feasible, by geography, time window, and phylogenetic lineage, and transparent isolate sampling frames. Intended-use claims should match demonstrated coverage.
2.
Make representativeness an evidentiary criterion: treat representativeness like sample size—as a formal element of evidentiary sufficiency. For broad indications, requirement of minimum coverage across regions, lineages, or demographic groups. When gaps remain, either narrow labelling or use staged indication expansion tied to new data.
3.
Mandate prespecified post-market monitoring and re-evaluation: approval should be contingent on minimum confirmatory phenotyping rates among susceptible calls (potentially risk-stratified and geography-stratified), sentinel networks for intensive culture or phenotyping, and predefined triggers (eg, rising very major errors, detection of novel determinants) that prompt modification and review.
4.
Create pathways for iterative updates: because rules or models should evolve, regulators should provide streamlined mechanisms for updating genotype–phenotype rules and algorithms, with clear expectations for evidence and re-evaluation. These pathways for iterative updates could reduce disincentives to improve tests rapidly.
5.
Integrate with AMR surveillance systems: these diagnostics are at the intersection of clinical care and surveillance. Regulatory requirements should align with national and global AMR surveillance to support data sharing, standardised definitions, and rapid recognition of emerging mechanisms.

0119

Reposted by David Helekal

Vittoria Colizza @vcolizza.bsky.social · 19/04/2026

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.

163

Reposted by David Helekal

arXiv q-bio.PE Populations and Evolution @qbiope-bot.bsky.social · 15/04/2026

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

012

Reposted by David Helekal

CIDRAP @cidrap.bsky.social · 07/04/2026

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

22810

Reposted by David Helekal

Ana Ignatieva @anaignatieva.bsky.social · 24/03/2026

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...

my.corehr.com

Job Details

078

Reposted by David Helekal

Matthew J Shepherd @matthewjshepherd.bsky.social · 20/02/2026

🚨 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)

biorxiv.org

26533

Reposted by David Helekal

Richard Everitt @bayesianstats.bsky.social · 09/02/2026

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...

1111

Reposted by David Helekal

Yonatan Grad @yhgrad.bsky.social · 30/01/2026

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...

nature.com

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...

16531

Reposted by David Helekal

Michael Plank @michaelplanknz.bsky.social · 29/01/2026

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.

0158

Reposted by David Helekal

Tatum Mortimer @tatumdmortimer.bsky.social · 26/06/2025

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...

forms.gle

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...

055

Reposted by David Helekal

Yonatan Grad @yhgrad.bsky.social · 24/06/2025

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...

youtube.com

Harvard T.H. Chan School of Public Health

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

0203

Reposted by David Helekal

senjutisaha.bsky.social @senjutisaha.bsky.social · 23/06/2025

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/...

wwwnc.cdc.gov

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

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

136

David Helekal @dhelekal.bsky.social · 28/03/2025

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

1147

Reposted by David Helekal

Boston Bacterial Meeting @bostonbacteria.bsky.social · 01/02/2025

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.

15030

Reposted by David Helekal

Chris Mancuso @mancusosci.bsky.social · 08/05/2024

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

44329

Reposted by David Helekal

Esther Landhuis @elandhuis.bsky.social · 03/05/2024

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...

jamanetwork.com

“Super Gonorrhea” Has Arrived

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

0109

Reposted by David Helekal

Eduardo Rocha @epcrocha.bsky.social · 21/12/2023

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...

doi.org

Evo‐Scope: Fully automated assessment of correlated evolution on phylogenetic trees

01410