A new ggCaller version is out! v1.4 includes tweaks to improve efficiency, outputs Panaroo-friendly GFFs, and enables iterative gene calling; if you have already called a gene set, you can now add more genomes either one by one or in batches github.com/bacpop/ggCal...

If you made it this far, thanks for reading. I hope you enjoyed the thread. I am currently looking for my next research adventure. If you have insights on the microbiome/microbial genomics🧬🦠 job market in Europe (academia and industry), or want to chat about this work, please reach out!

MMseqs2-GPU sets new standards in single query search speed, allows near instant search of big databases, scales to multiple GPUs and is fast beyond VRAM. It enables ColabFold MSA generation in seconds and sub-second Foldseek search against AFDB50. 1/n 📄 www.nature.com/articles/s41... 💿 mmseqs.com

We are looking to integrate a fluorescent marker in an E. coli BW strain we built; what's your favorite integration site (and why)? (asking here seemed to have worked quite well for @wvschaik.bsky.social and so I figured why not trying?)

The EMBL PhD programme is open until 13th October (entry ~Sep 2026): www.embl.org/about/info/e... We have three positions in microbial genomics at EMBL-EBI, including one in my group. Please do apply, or if you know anyone that would be interested pass on to them

I'm curious if other mid career PIs have considered completely abandoning the trad publication model. We've been making gradual moves towards that end goal. But it's been difficult to completely jump ship for one main reason for me at least. 1/

My German might still be rusty, but I'm locked in culturally

#Job opportunity The Key Lab @keyfm.bsky.social is looking for a #postdoc in evolutionary genetics - join a young team in the heart of #Berlin to investigate the evolution of ancient microbial pathogens. ⏰ Deadline: October 17 📌 More info and how to apply: www.mpiib-berlin.mpg.de/2193291/job_...

We are looking for a postdoc to study single-cell transcriptional heterogeneity in the human skin microbiome. We have a new protocol mostly developed, but need someone to see it through. Experience with protocol dev or RNAseq appreciated. Funded by a new grant from MIT-HEALS.

No Genetics? Try ASOs – A non-genetic approach to silence genes at the phage-host interface. We use it to study jumbo phage biology and anti-phage defence. @jorg-vogel-lab.bsky.social @helmholtz-hiri.bsky.social @uni-wuerzburg.de @helmholtzhzi.bsky.social published now in @nature.com

Love a good data compression tip!

The LLM built by the Swiss AI initiative (Apertus) has made the tech news but I have seen no benchmark comparisons. The internal benchmarks in their technical report that place Apertus around the level of Llama 3.1, great for a fist attempt and open model github.com/swiss-ai/ape...

We have a position for an Assist Prof in Microbial Genomics in our School of III. Hod Joan Geoghegan will be happy to field questions if you are interested. No specific area of microbial genomics preferred so please do consider it www.jobs.ac.uk/job/DOO184/a...

A common type of ant in Europe breaks a fundamental rule in biology: its queens can produce male offspring that are a whole different species go.nature.com/4mOb5T9

🌎👩‍🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵 Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open. doi.org/10.1101/2024...

Only 10 days left to apply: We are searching for a senior postdoc (3 +3 years) in the field of theoretical ecology and evolution. The position provides the opportunity to closely interact with experimentalists and develop own research projects. Please RT. Details 👇: shorturl.at/iiiOv

Evolution varies the number of teeth in mammals from 0 to more than 100, depending on diet, lifestyle, etc. If we ever set out to alter human genetics, how would we decide if our current number of teeth (which evolved under conditions very unlike how we live now) is optimal?

Microcolony-seq reveals inherited phenotypic diversity directly from infected human samples, revealing that bacteria can retain long-term genetic and nongenetic memory from the host environment @cellcellpress.bsky.social www.cell.com/cell/fulltex...

This work is finally published! 🥳🧬 Plasmids are associated with very variable fitness costs in their different bacterial hosts. But, what is the contribution of each of the plasmid-genes in these host-specific effects? Study led by @jorgesastred.bsky.social, @sanmillan.bsky.social and myself! 1/14

In new study led by @bdadonaite.bsky.social, we measure how spike mutations affect function & antigenicity of spike of KP.3.1.1 strain of SARS-CoV-2. Sheds light on how key neutralizing epitopes are changing & importance of RBD up/down motion. www.biorxiv.org/content/10.1...

My favorite kinds of scientists are 1) Crazy enough to publish a paper where you give ecstasy to octopuses and study their social behavior 2) Detail-oriented enough to specify in the figure that 30 minutes is exactly 1800 seconds www.cell.com/current-biol...

My PhD student @leonielorenz.bsky.social (with Eva Geissen) has made this nice (free) online course to introduce mathematical modelling for biology: www.ebi.ac.uk/training/onl... Including both molecular and epidemiological examples

How diverse are E. coli capsules? How are they linked to ecology and disease? Find out with > 25,000 genomes and MAGs including undersampled environments and hosts from all over the world. Great genomics - glycobiology synergy in Sunagawa and Slack groups at ETH! www.biorxiv.org/content/10.1... 🧪🧫🔬

A simple design framework that will massively improve your slides and your public speaking clauswilke.substack.com/p/slides-tha...

We're very happy to release our new database Metalog metalog.embl.de ! It offers manually curated and harmonised contextual data for 110k metagenomics samples across the globe, incl. precomputed taxonomic profiles, for interactive browsing and for download 🧵 1/7 #microsky

We are also hiring a 4-year postdoc to study the dynamics and evolution of mobile genetic elements in the C-fixing Icelandic host-spring microbiomes Join our exciting multidisciplinary team funded by @ukri.org BBSRC sLoLa www.jobs.manchester.ac.uk/Job/JobDetai...

Wrote a review of ChatGPT 5 for the company newsletter. aboard.com/desperately-...

We’re hiring a Postdoc on Gut Microbiome–Host Interactions @leibniz-hki.de, Jena 🇩🇪 You'll create organ-on-chip models to study how microbes mediate host responses to xenobiotics jobs.hki-jena.de/jobs/Postdoc...

I am excited to announce that the position of a senior postdoc (3 +3 years) in the field of theoretical biology is available in my group. The position provides the opportunity to closely interact with experimentalists and develop own research projects. Please RT. Details 👇: shorturl.at/iiiOv

We are searching for a professor in Biology Didactics (W2) at Osnabrück University. The research focus should be on organismic biology, biodiversity, organismic interactions in ecosystems and human-environment interactions. Link to (German) advertisement 👇 shorturl.at/aKKAB

Two take-aways from a nice talk by John Jumper last week www.johnlees.me/posts/alphaf...

This is fascinating. It is also evidence in favour of taking biological agency seriously, rather than treating it as an "as if" property.

Ready to lead pioneering research that bridges systems-level investigations of biological systems to molecular mechanism? The EMBL Molecular Systems Biology Unit in Heidelberg is hiring a Group Leader!

A 2-year postdoc position in my lab, under the supervision of P-Alex Kaminski, on Z-DNA phages and the benefit given by ZTGC DNA and the replication machinery, with attempt to create a Z based minireplicon research.pasteur.fr/en/job/a-two...

**NEW Doctoral Training Programme just launched!!** This exciting programme on Microbial Genomics for Health Protection is joint between @imibirmingham.bsky.social and UKHSA @ukhsa.bsky.social. 9 brilliant projects available!!

Finally out! A small screen helps understand a little more about how E. coli regulates major transporters, and reveals how caffeine induces phenotypical antibiotic resistance. Huge thanks to collab @andrenmateus.bsky.social (Umeå) and Christian L. Müller (Munich)! journals.plos.org/plosbiology/...

We are on the lookout for postdocs for two different projects at the intersection of ecology, evolution, and the human microbiome. See thread for more information and reach out!

New blog post: Why do we still publish in scientific journals ? What is holding us back from letting go of traditional publishing? No major insight here but I am curious what others think. www.evocellnet.com/2025/07/why-...

Sehr hoher Besuch bei RESIST: Heute war der Bundeskanzler Friedrich Merz zusammen mit dem Ministerpräsidenten Olaf Lies in der MHH zu Besuch bei RESIST! Beide hat die RESIST-Forschung und die Auswirkungen auf die Klinik sehr beeindruckt. 😊 www.resist-cluster.de/deutschland-...

A remake of "Back to the future", but with Rick and Morty. I guess that's just "Rick and Morty", but I'd still watch that

💥 Excited to introduce Bacformer 🦠 - the first foundation model for bacterial genomics. Bacformer represents genomes as sequences of ordered proteins, learning the “grammar” of how genes are arranged, interact and evolve. Preprint 📝: biorxiv.org/content/10.1... 🧵 1/n

Join us at the Perutz, part of the Vienna Biocenter! Opening for a full professorship in Molecular Mechanisms of Disease 👇🏻 @maxperutzlabs.bsky.social @viennabiocenter.bsky.social @univie.ac.at

Spending some time in Germany at my parents' place after moving to Bio2Q / Keio University in Tokyo at the beginning of the year. Feels good to contemplate and find that's it was an awesome move. We have a few open positions at Postdoc level with lots of freedom and resources. DM if interested

Finally online! Our latest research is out @nature.com: We show that non-antibiotic drugs can disrupt colonization resistance, raising the risk of enteric infections. rdcu.be/ewwrG

All those grumpy comments about the conference generated enough negative karma to manifest some very harsh comments on my poster. Ouch

Another grumpy hot take: not allowing for questions in a plenary session at a big conference is NUTS. They could just upload the talk on YouTube and we'd have a better chance to engage in a productive discussion there

Are you looking for a Postdoc or Research Programmer position? Want to work as part of highly collaborative infectious disease programs that have direct relevance to global health? Well, we got you covered! Learn more 👇 andersen-lab.com/about/

It gets worse: anyone that used the conference template for slides is lamenting that the layout changed due to font issues. So it's not just annoying, it's actively disrupting the quality of the talks!

Continuing with these grumpy conference pet peeves: green laser pointers are clearly superior, but they are hardly available. An easy fix!