Leo Lahti

🎉 The Nordic CompBio Conference is coming soon to Tallinn, Estonia 🇪🇪
📅 Thursday-Friday 23-24th of October (10:30-17:15 EEST)
📢 Abstract submissions and registration are open
🔗 nordic-compbio.org/ncb-week

#NordicCompBio #ComputationalBiology #Bioinformatics #Nordics

Come join us 2-4th March 2026 for a cracking #microbiome conference in Hinxton UK! Speaker line up is AMAZING and lots of opportunities for ECRs for selected talks, flash talks and posters.

Bursaries are also available!

See details below 👇

Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols.
Thread 1/n

New ERC funded computational postdoc position in my lab! We are looking for someone who will study the genomics of bacterial evolution using samples from experimental evolution and clinical trials. Lots of opportunities for interesting and fun collaboration!
my.corehr.com/pls/uoxrecru...

Research security All applicants must include an appendix with their application that contains a self-assessment of research security issues and, if necessary, a more detailed description of the risks and a risk manage...

New fun stuff for those applying for RCF funding:
www.aka.fi/en/research-...

Nothing is inevitable. In either direction. Hope and work.

Orchestrating Microbiome Analysis with Bioconductor 2–6 February 2026

🌱 New course: Orchestrating Microbiome Analysis with @bioconductor.bsky.social (2–6 Feb 2026, online). Learn from @antagomir.bsky.social & Toumas Borman how to analyse microbiome & multi-omics data in R/Bioconductor.

www.physalia-courses.org/courses-work...

A quick reminder to all those who care about open research to consider joining us for the FOR2026 Conference in the Future of Open Research at the Technical University of Munich in May 4-6, 2026! Deadline for paper and poster proposals: 30 September

opensciencestudies.eu/for-2026-con...

TIA Seed 2025 -rahoitushaku avautuu 15.9. – ilmoittaudu info-webinaariin! - www.vaikuttavuussaatio.fi Vaikuttavuussäätiö avaa tänä syksynä Tandem Industry Academia (TIA) Seed -rahoitushaun, joka on suunnattu hiljattain suomalaisen tutkimusrahoitusjärjestelmän piiriin tulleille professoritasoisille tut...

TIA Seed 2025 -rahoitushaku avautuu 15.9. Rahoitusta voivat hakea professorit, jotka ovat olleet palkattuna suomalaisessa korkeakoulussa tai tutkimuslaitoksessa enintään kolme vuotta ja jotka ovat asuneet vähintään viisi vuotta yhtäjaksoisesti Suomen ulkopuolella ennen Suomeen tuloaan.

An arrow with a LaTeX equation

Trigonometric functions and a unit circle

A bivariate change model with structured residuals

A hierarchical model of cognitive abilities

Now on CRAN, ggdiagram is a #ggplot2 extension that draws diagrams programmatically in #Rstats. Allows for precise control in how objects, labels, and equations are placed in relation to each other.
wjschne.github.io/ggdiagram/ar...

Race by other names: critiquing population categories in microbiome research | mSystems Behind the façade of scientific objectivity, race continues to haunt modern science. Contemporary biomedical research often employs categories of human difference that have recently come under critici...

Race by other names: critiquing population categories in microbiome research

#mSystems MiniReview by Marta Scaglioni

journals.asm.org/doi/10.1128/...

Chronological age estimation from human microbiomes with transformer-based Robust Principal Component Analysis - Communications Biology An interpretable Transformer-based model accurately predicts chronological age across body site and identifies key microbial signatures of aging.

Chronological age estimation from human microbiomes with transformer-based Robust Principal Component Analysis www.nature.com/articles/s42...

The Journal of Open Source Software (@joss-openjournals.bsky.social‬) is looking for editors. Come join our team!

I've only been an editor for a few months, but I love working with JOSS. Our peer review process is actually collaborative, and we're Diamond Open Access.

#AcademicSky 🧪 ⚗️ #CompChem

Green Algorithms Towards environmentally sustainable computational science

IMHO green computing & green software engineering are becoming even very important.

Check out our Green Algorithms Initiative for more tools and information www.green-algorithms.org

And the GREENER Principles which lay the foundation for a sustainability roadmap www.nature.com/articles/s43...

Beeswarm plot of the prediction error across different methods of double perturbations showing that all methods (scGPT, scFoundation, UCE, scBERT, Geneformer, GEARS, and CPA) perform worse than the additive baseline.

Line plot of the true positive rate against the false discovery proportion showing that none of the methods is better at finding non additive interactions than simply predicting no change.

Our paper benchmarking foundation models for perturbation effect prediction is finally published 🎉🥳🎉

www.nature.com/articles/s41...

We show that none of the available* models outperform simple linear baselines. Since the original preprint, we added more methods, metrics, and prettier figures!

🧵

support firehose · Issue #23 · JBGruber/atrrr See: https://docs.bsky.app/docs/advanced-guides/firehose I tried it at some point and the socket part works fine. However, decoding the CBOR event data is a bigger challenge. The Python package use...

The next version of the #rstats 📦 {atrrr} will likely contain a function to stream from the Bluesky Firehose! Looking for people to test and comment now:

github.com/JBGruber/atr...

Metagenomic estimation of absolute bacterial biomass in the mammalian gut through host-derived read normalization | mSystems In this study, we asked whether normalization by host reads alone was sufficient to estimate absolute bacterial biomass directly from stool metagenomic data, without the need for synthetic spike-ins, ...

You can get an accurate estimate of total bacterial biomass from stool metagenomes by simply normalizing by host read count, without needing any additional measurements.

Excellent work by UW Master's student Gechlang Tang in @asm.org #mSystems Journal.

journals.asm.org/doi/10.1128/...
🧵

EurIPS is coming! 📣 Mark your calendar for Dec. 2-7, 2025 in Copenhagen 📅

EurIPS is a community-organized conference where you can present accepted NeurIPS 2025 papers, endorsed by @neuripsconf.bsky.social and @nordicair.bsky.social and is co-developed by @ellis.eu

eurips.cc

Need to update your data? Follow these five tips Researchers engaged in long-term projects often need to update their data sets over time. Here’s how to do it while maintaining reproducibility.

"Long-term ecological research is not the only area that needs to maintain and update data for future use. Many researchers add to, revise or overhaul their data sets over the course of their projects or careers, all while continuing to publish articles." www.nature.com/articles/d41... #OpenData

Bioconductor nominations graphic with CAB and TAB illustrations and www.bioconductor.org

🌟 Bioconductor 2025 CAB & TAB nominations are open!

Join our advisory boards to support community growth or guide technical strategy.

📅 Apply by Aug 31
CAB: forms.gle/8NYxRGhprfuN...
TAB: forms.gle/eqef9ThpUypc...

#Bioconductor #RStats

Integrative genomic reconstruction reveals heterogeneity in carbohydrate utilization across human gut bifidobacteria - Nature Microbiology A comprehensive genomic analysis reveals species- and strain-level heterogeneity in carbohydrate utilization potential across bifidobacteria of human origin.

New RESOURCE!

Integrative genomic reconstruction reveals heterogeneity in carbohydrate utilization across human gut bifidobacteria

@arzamasovalex.bsky.social @drlarsbode.bsky.social Andrei Osterman, Jeff Gordon & co

#microbiomesky #microsky

www.nature.com/articles/s41...

Interested in an international #PhD at the intersection of computational & environmental microbiome research (Finland + Australia)?

PM/email for more details.

Antibiotic resistance predicts higher mortality risk in 17-year follow-up – linked to diet and gender A population-based study led by the University of Turku, Finland, investigated factors associated with the prevalence of antibiotic resistance.

Press release: www.utu.fi/en/news/pres...

Antimicrobial resistance: a silent pandemic SPONSOR FEATURES

Part of the special issue “Antimicrobial resistance: a silent pandemic” www.nature.com/immersive/an...

Variation and prognostic potential of the gut antibiotic resistome in the FINRISK 2002 cohort - Nature Communications Here, in a representative cohort of 7,095 Finnish adults, the authors reveal that gut antibiotic resistance is shaped not only by antibiotic use but also by the microbiome, diet, lifestyle, household ...

Read the study: doi.org/10.1038/s414... - /w @katammp.bsky.social @begia.bsky.social Guilhem Sommeria-Klein, Ville Laitinen, Pyry Kantanen, @gmeric.bsky.social @gazollavolpiano.bsky.social Michael Inouye, Rob Knight, Veikko Salomaa, Aki S. Havulinna, Teemu Niiranen, @antagomir.bsky.social

High resistance gene load predicted a similar level increase in the relative risk of all-cause mortality as high blood pressure or type 2 diabetes. Thus, #resistome profiling may serve as a novel biomarker for long-term health risk influenced by #socio-demographic factors.

To understand clinical relevance, we linked resistome data to national health registers. The #resistance gene load was associated with remarkably elevated relative risk of sepsis and all-cause #mortality during the 17-year follow-up.

The resistomes exhibited vast individual variation but were systematically linked to age, sex, diet, medication use, and lifestyle factors as well as individual gut #microbiome composition. These all associated with resistome composition, diversity and resistance gene load.

The resistome profile - the set of antibiotic resistance genes (ARGs) - was profiled with #metagenomics sequencing of stool samples and linked to individual-level information from national health registers.

We carried out a large-scale analysis of the gut antibiotic #resistome in FINRISK 2002, a representative population cohort of over 6,500 Finnish adults who were prospectively followed up for 17 years after the sample collection.