Orchestrating Microbiome Analysis with Bioconductor https://www.biorxiv.org/content/10.1101/2025.10.29.685036v1

Greetings from Brisbane, Int'l Data Week #IDW2025, SciDataCon25 & CODATA ExComm this week - - Looking fwd to catch up! Also check this one: "Open data science and responsible research" summarizing the national policy work on open methods in #Finland (Wed 2pm) lnkd.in/d7zBrNNn

15 years in the making, we confirmed that mitochondria - the powerhouse of the cell - have an unusual localization in patients who experience psychosis (including schizophrenia and bipolar disorders). You’ll never guess what kind of patient cells we used to make this discovery… 🧵

Just published an interactive article about a magical algorithm known as the Burrows-Wheeler Transform, which powers sequence alignment tools like bowtie and bwa: sandbox.bio/concepts/bwt It's also notoriously unintuitive so I'm hoping this article helps you build that intuition.

🎉 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...

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

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

🌱 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. 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.

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 MiniReview by Marta Scaglioni journals.asm.org/doi/10.1128/...

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

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...

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! 🧵

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...

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

"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 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

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.

Antimicrobial resistance ( #AMR ) is a silent pandemic that has been attributed to over a million deaths per year worldwide. Socio-demographic factors contribute to the emergence and spread of AMR.🧵

That time of the year again! summer course Brain, Bacteria and Behavior @tulipantricolor.bsky.social @eugenianatasha.bsky.social @daniquemulder.bsky.social Rochellys Diaz Heijtz @antagomir.bsky.social Thomaz Bastiaanse Aletta Kraneveld Tuomas Bormann Annemarie Boleij Maartje van Kessel ea! 🧠 🦠 🧫

Tuomas Borman from @antagomir.bsky.social lab demonstrating why data containers are so useful (book >> loose pages) Online book for microbiome analysis: microbiome.github.io/OMA/docs/dev... #GBCC2025

This is wild! Engineering E. coli bacteria to turn plastic waste into paracetamol (Tylenol) www.nature.com/articles/s41... www.nature.com/articles/s41...

📣 Late-breaking poster call for #EuroBioC2025 is now open! Submit by July 11 to present your work in Barcelona this September. 🔗 forms.gle/ewTGdKzB2xyE... 📅 Notifications by July 15 #Bioconductor #Bioinformatics

International comparison reveals gender differences in antimicrobial resistance - an analysis of more than 14,000 open gut metagenomes indicates that in high-income countries women had more antibiotic resistance than men www.utu.fi/en/news/pres... /w @katammp.bsky.social @mahkamehsalehi.bsky.social

Biome-specific genome catalogues reveal functional potential of shallow sequencing with BioSIFTR - a biorXiv preprint www.biorxiv.org/content/10.1...

"Validating and Extracting Information from National Identification Numbers in #R: The Case of Finland and Sweden" journal.r-project.org/articles/RJ-... (The R Journal, 2025 - the "hetu" rOpenGov package) #rstats #ropengov

Turtle Mutual Aid:

New tenure track assistant professor position in molecular microbiology in our department @dmf-unil.bsky.social @unil.bsky.social! We are casting a wide net for an experimental molecular microbiologist. Apply here: wwwfbm.unil.ch/releve/appli...

If you missed StanBio live-stream, the full day recording of Bayesian Stan goodness is available at stanbio.org

Assessing the #safety of #microbiome perturbations www.microbiologyresearch.org/content/jour...

How does the adoption of preprinting differ between European countries? Preprint adoption is significantly higher in Western and Northern European countries than in their Southern and Eastern European neighbors. Switzerland has the highest preprint adoption in Europe.

Our "goal is to create a stable, independent non-profit organization that ensures [bioRxiv & medRxiv] remain open...governed by and for the research community, not a single funder...or any one stakeholder." Some common questions about openRxiv answered: openrxiv.org/qa-governanc...

Did you know that the female #microbiome is unique in many ways, and antibiotic resistance in the gut microbiome varies between genders? See npj Biofilms and Microbiomes special issue, Women and their microbes, to learn more! www.nature.com/collections/...

US brain drain: Nature’s guide to the initiatives drawing scientists abroad www.nature.com/articles/d41...

Insights from @geomblog.bsky.social on recent (lack of) AI legislation. Dr. Venkatasubramanian *deeply* understands the complex interplay of ethics, regulation, and technology, having worked in government and in academia on precisely these issues. I trust his views more than most.

Are you a US-based academic that has prior ties to Sweden? Are you also 7-12 years from your PhD? If so, the Foundation for Strategic Research is providing funds of up to $1.5 mil (15m SEK) to bring you back to Sweden! Application deadline Sep 23. strategiska.se/pressmeddela...

📊 Now published in Bioinformatics Advances: “iSEEtree: Interactive explorer for hierarchical data” Explore the full paper here: https://doi.org/10.1093/bioadv/vbaf107 Authors include: @antagomir.bsky.social

Lehti kerää apc-maksuja, toimitusprosessin läpi kulkee iso määrä artikkeleita, jotka myöhemmin vedetään pois. Mitä se kertoo toimitusprosessin laadusta? Eli mistä maksetaan? retractionwatch.com/2025/05/07/j... 1/

A GO for studying the microbiology of the human #Microbiome! Congrats @tclavel.bsky.social, Tom’s team and collaborators. www.nature.com/articles/s41...

I like this paper: not only does it review of all the reasons standardized coefficients are bad, actually, It also then goes on to show how test statistics can be used as measures of unique contribution/ effect size! - something that just sounds so so wrong! #stats doi.org/10.1080/0003...

What if your gut bacteria could tell you how old your body is? A 14-year study of wild baboons links #microbiome makeup to biological ageing, hinting at new ways to measure and maybe even slow it in humans. #Ageing #MachineLearning elifesciences.org/digests/1021...

Dethlefsen and Relman new #microbiome article is always an event www.nature.com/articles/s41...