Starting this week, I set aside one hour each week to meet ECRs outside my group who want to discuss career development, mentorship, or any non-technical professional questions. Here is a blog that explains my motivation for this and how to schedule a meeting: merenlab.org/2025/11/16/E...

Know metagenomics and could spare 2 mins? I'm applying for funding to build a visual repository for metagenomic classification data (not sequence data). To support the application, I have a short 2 minute survey and it would be a big help if you could fill it in: docs.google.com/forms/d/e/1F...

Orchestrating Microbiome Analysis with Bioconductor. #Microbiome #DataAnalysis #Bioconductor @biorxivpreprint.bsky.social www.biorxiv.org/content/10.1...

Do you teach #rstats? Do your students complain about how lame and old-fashioned dplyr is? Don't worry: I have the solution for you: github.com/hadley/genzp.... genzplyr is dplyr, but bussin fr fr no cap.

The abstract deadline for Nordic AMR Conference 2026 has been extended. Also see the list of keynote speakers. More information at www.helsinki.fi/en/conferenc...

Newly released Stockholm Declaration recommends the following reforms to publishing: 1. Academia resumes control of publishing 2. Incentive systems to merit quality, not quantity 3. Independent fraud detection and prevention 4. Legislation and policies to protect science quality and integrity

This year the sequencing was not perfect, but we got one circular (hopefully complete) genome. On Wednesday we continue with more in depth annotations and will learn more.

Great to see this finally published! Metalog: curated and harmonised contextual data for global metagenomics samples now out in @narjournal.bsky.social academic.oup.com/nar/advance-...

📣 Open position: We are looking for a new #ScientificLead for the #SILVA database 🧬🖥️, who will be responsible for guiding the development of this important resource and for curating the #SILVA taxonomy🌳. Read and share! 👉 www.dsmz.de/dsmz/career/... 🧪🦠🌱🦋💽

Kun pidät tieteellisen seminaarin jossa tarjolla ”pientä purtavaa”, pidä se ravitsemustieteilijöiden kanssa. Koska TOTTA KAI niiden väitöskirjatutkija on artesaanileipuri! Niissä piireissä tiedetään, että ruoalla on paitsi terveys-, myös mielenterveysvaikutuksia.

And it is (finally) accepted to be published in Microbiology Spectrum.

On Wednesday the student got to whole genome sequence their isolates on the exploratory laboratory course (studies.helsinki.fi/courses/cour...). Next weeks we will analyse the data and try to assemble as many complete genomes as possible. Thanks @nanoporetech.com for the support.

Turun kaupunki juhlii vuosisataista historiaansa vuonna 2029. Turun yliopiston arkeologit ja historioitsijat julkaisevat tässä blogissa lyhyitä kirjoituksia Turun menneisyydestä, ihmiskohtaloista ja tarinoista, niin arjen kuin juhlankin hetkistä. blogit.utu.fi/turku800/

Another great edition of Environmental #Metagenomics is wrapping up! Huge thanks to @oskolkov.bsky.social , @aroneys.bsky.social and all the amazing participants who joined us this week. 🙌 We wish you all the best with your research projects!

Well done Shafaq Aftab. When a reviewer stole her work and published it under his own name, she fought for a YEAR to get the journal to retract the paper. Just wondering why it took Wiley a YEAR to do this. 🧪 #academicsky retractionwatch.com/2025/10/03/w...

Massive undertaking with @teppo-h.bsky.social and others out. We studied 4 years (!!!) of synthetic 23 microbial species community evolution with/without antibiotic. Resistance mutations occurring over years led to stepwise restructuring and ultimately recovery of undisturbed community composition.

Evolution induced state shifts in a long-term microbial community experiment www.biorxiv.org/content/10.1...

Why not visit Helsinki next winter? There might be snow. Abstract submission is open for the Nordic AMR Research Centre Conference 2026. www.helsinki.fi/en/conferenc...

🌍 Applications now open for our first Bioconductor course in West Africa! 📅 17–21 Nov 2025 | 📍 Abomey-Calavi, Benin Free, in-person training on R, RStudio & RNA-seq workflows. Apply by 15 Oct 👉 forms.gle/d32F6xJJbsFa... More info 🔗 training.bioconductor.org/workshops/20... #Bioconductor #RStats

The perfect location for writing an application to the Water4All call.

You have 50 files. Same header. You want to merge them. Here’s how to do it without going insane. 🧵 👇

🚨 Join us for the Environmental Metagenomics course (Oct 13–17, online) with @oskolkov.bsky.social & @aroneys.bsky.social ! 🔬 Hands-on training on read-based & assembly-based methods, MAGs, and integrating short & long-read @nanoporetech.com data. shorturl.at/HOm6X

Tämä ei ole hyvän mielen postaus, mutta ehkä syksyn tärkein postaukseni. Suosittelen kaikille tutkijoille ja tutkimusryhmille: käsitelkää törkyriskejä ja suunnitelkaa toimenpiteitä etukäteen yhdessä. Lähiaikoina on tiettävästi odotettavissa törkyä tiedeyhteisöä kohtaan. Ketjusta muutama pikavinkki.

Tärkeä ketju tutkijoille, heidän esihenkilöilleen ja tutkimusorganisaatioiden johdolle! Lisäisin vielä yhden toiveen: Älä ryhdy vaihtamaan tai peittelemään tutkimuksesi aihetta häirinnän pelossa. Esihenkilö, sinun tehtäväsi on huolehtia tutkimuksen vapauden toteutumisesta omassa yksikössäsi.

Professor (full) or Associate Professor (tenure track) in Microbial Genetics of Health (U. Turku Finland). Competitive starting package included! Please share. duunitori.fi/tyopaikat/ty...

Happy to share that the paper describing Autocycler is now 100% up: doi.org/10.1093/bioi... (1/3)

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

nice. you know what would be even more equitable? publishing this in a society journal that actually serves the scientific public.

Wow! I am very much against this. The deep value of GenBank is in it being a public domain database with 0 limitations on use. The norm that when we publish, we share the sequencing data supporting its claims *with 0 limitations on use* is so important for open science. I hope it doesn't change!

Kiinnostaako suomalainen tutkimus ihan oikeasti. Tässä ketjussa neljä erinomaista palvelua, joiden kautta siihen voi tutustua. 1/

New blog post! metaMDBG (@gaetanbenoit.bsky.social) and Myloasm (@jimshaw.bsky.social) have had recent releases, so I updated the benchmarks from the Autocycler paper: rrwick.github.io/2025/09/23/a... Both tools improved considerably! Time to update your conda environments 😄

🥗 Diet shifts cut impacts in Sweden A new study shows Swedish diets designed for future food scenarios reduce environmental impacts by ~30% while improving health. Cutting food waste boosts gains further. 🔗 www.nature.com/articles/s43... #SciComm 🧪

📢 PLEASE RT! ❄️ M2 Masters Internship: Metagenomic analysis of microbial cold adaptation in the cryosphere 🧬 Compile & curate ice nucleation & cold-adaptation protein database 🖥️ Build HMM profiles 🦠 Analyze existing metagenomic data using HMMs ☀️ Marseille, France Apply by 15 Oct

📅 UNIX and Shell Scripting for Bioinformatics 🗓️ 12–16 Jan | 💻 Online Learn essential UNIX skills to process NGS data and automate bioinformatics tasks. No prior experience needed www.physalia-courses.org/courses-work...

Join the Physalia online course on Metabolomics with R/Bioconductor from Nov 11-14, 9:30 AM - 1:30 PM Berlin time. Learn data analysis workflows and statistical methods. More info: https://www.physalia-courses.org/courses-workshops/course55/ #course

🚨 Postdoc opportunities! 🚨 We’re looking for postdocs in 🌿 biodiversity science, 🧬 genetic indicator assessment, and 📊 ecological statistics. Join us in unraveling the drivers & consequences of global change on biodiversity — and be part of a supportive & collaborative environment! DL 24 September

Kaikki liittovaltion tiederahoitus alistetaan poliittiseen ohjaukseen. Valkoinen talo määrää, että jatkossa varta vasten nimetyt viranomaiset suuntaavat rahoituksen ”hyödylliseen” tutkimukseen. Kuulostaako tutulta? Me Akatemiassa tiedämme, että suurin hyöty syntyy tieteen vapaudesta.

The latest update of VS Code broke the SSH connection to our HPC cluster, so looking for a good alternative. I might give Warp a try. If you would also like try it, click the link (not a paid ad, but I might get stickers if you do). app.warp.dev/referral/R49LWY Other suggestions are also welcome.

Antimicrobial resistance #AMR is a major #globalhealth threat. How does it vary between genders? We analyzed 14,641 open human gut #metagenomes from 32 countries to investigate gender differences in #antibioticResistance genes (ARGs). www.nature.com/articles/s41...

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/...

Tieteen vapaus on yksi demokraattisen yhteiskunnan kulmakivistä. Viime vuosien kehitys, jossa tutkimuksen vapautta ja tutkitun tiedon tärkeyttä on vähätelty, herättää aiheellista huolta tiedeyhteisössä, toteaa Tieteentekijöiden liittokokous julkilausumassaan. #TieteenVapaus buff.ly/1JjWkEC

I guess I won’t be doing reviews for SpringerNature anymore. Not the first time they send an email days before the review deadline that my report is no longer needed. This time 10 days before the DL. What if I already started? (Of course I didn’t, because the deadline was end of the month).

"opetusmäärän kattamiseksi onkin työnantajalle houkuttelevaa repiä lisää opetustunteja nykyisestä henkilöstöstä. Tällöin on pyrittävä asettamaan rajat sille, kuinka paljon opettajan 1 612 tunnin kokonaistyöajasta voi olla opetusta ja ohjausta" #neuvotellen #MeOlemmeYliopisto yll.fi/2025/05/ala-...

Erinomainen kirjoitus yliopiston opettajien työnkuvasta. #yliopisto #opetus #tutkimus

Autocycler: long-read consensus assembly for bacterial genomes www.biorxiv.org/content/10.1... 🧬🖥️🧪 github.com/rrwick/Autoc...

PhD opportunity in St Andrews on plasmids, antibiotics and defence systems, in collaboration with Helen Alexander in Edinburgh. Funding via BBSRC EastBio, please share & pass on to anyone interested! #microsky🦠🧫🧬 www.findaphd.com/phds/project...

Hope to see lots of interesting Ralstonia research in Wageningen next year!

#EBAME 10 Microbial Ecogenomics Workshop! Brest🇫🇷, Oct 11-25, 2025. A two-week workshop of lectures & tutorials to learn about omics data analysis for microbial ecology and evolution, all in the beautiful Brest Bay! Apply here until June 1: maignienlab.gitlab.io/ebame

Are you interested in the distribution of microbes, viruses, and #phages throughout the Microverse? Come and do a #bioinformatics PhD with us @microverse.bsky.social @uni-jena.de: jobs.uni-jena.de/jobposting/b...

We are looking for PhD students! Fully funded studentships available to work on a range of topics, from small proteins to developing computational tools to study the global microbiome