David Helekal
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David Helekal
@dhelekal.bsky.social
140 followers 340 following 65 posts
Trees, AMR, Bayes.
Current: Postdoc @ Harvard Chan SPH
Prev: PhD Maths @ Warwick
Posts Replies Media Videos
Reposted by David Helekal
evamirandag.bsky.social
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/...
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...
www.pnas.org
September 11, 2026 at 3:29 PM
#MicroSky
 David Helekal @dhelekal.bsky.social · Sep 3
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
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...
www.biorxiv.org
September 3, 2026 at 3:41 PM
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
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...
www.biorxiv.org
September 3, 2026 at 3:11 PM
Reposted by David Helekal
biorxiv-genetic.bsky.social
Bayesian adaptive experimental design for efficient microbial genome-wide association studies https://www.biorxiv.org/content/10.64898/2026.08.26.747358v1
September 1, 2026 at 4:30 AM
Reposted by David Helekal
avehtari.bsky.social
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.
June 23, 2026 at 7:37 AM
Reposted by David Helekal
andrewjroger.bsky.social
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. 🧵
June 19, 2026 at 1:24 PM
Reposted by David Helekal
johnlees.bacpop.org
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!
johannavw.bsky.social Johanna von Wachsmann @johannavw.bsky.social · Jun 16
🧬 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...
June 16, 2026 at 4:07 PM
Reposted by David Helekal
lancetmicrobe.bsky.social
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.
June 10, 2026 at 10:38 AM
Reposted by David Helekal
vcolizza.bsky.social
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.
April 19, 2026 at 2:31 PM
Reposted by David Helekal
qbiope-bot.bsky.social
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
April 15, 2026 at 7:00 AM
Reposted by David Helekal
cidrap.bsky.social
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
Image of lab scientist with test tubes.
April 7, 2026 at 8:29 PM
Reposted by David Helekal
anaignatieva.bsky.social
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...
Job Details
my.corehr.com
March 24, 2026 at 5:30 PM
Reposted by David Helekal
matthewjshepherd.bsky.social
🚨 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)
www.biorxiv.org
February 20, 2026 at 3:58 PM
Reposted by David Helekal
zaminiqbal.bsky.social
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...
February 9, 2026 at 3:28 PM
Reposted by David Helekal
bayesianstats.bsky.social
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...
February 9, 2026 at 3:22 PM
Reposted by David Helekal
yhgrad.bsky.social
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...
January 30, 2026 at 12:34 PM
Reposted by David Helekal
michaelplanknz.bsky.social
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.
January 29, 2026 at 12:19 AM
Reposted by David Helekal
yhgrad.bsky.social
Now out in NEJM. Kudos to @dhelekal.bsky.social and @tatumdmortimer.bsky.social : www.nejm.org/doi/10.1056/...
July 10, 2025 at 11:09 AM
Reposted by David Helekal
tatumdmortimer.bsky.social
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
June 26, 2025 at 2:12 PM
Reposted by David Helekal
yhgrad.bsky.social
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...
June 24, 2025 at 8:56 PM
Reposted by David Helekal
senjutisaha.bsky.social
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
June 23, 2025 at 4:19 PM
Reposted by David Helekal
vmminin.bsky.social
Looking forward to my visit @ccdd-hsph.bsky.social!
March 31, 2025 at 8:47 PM
(1/10) New preprint: Expansion of tetM-carrying Neisseria gonorrhoeae in the US, 2018-2024; Link: www.medrxiv.org/content/10.1...
March 28, 2025 at 8:43 PM
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...
www.biorxiv.org
February 7, 2025 at 9:58 PM