The AI Scientist paper is out in Nature today. Runs the full ML research pipeline: idea generation, literature search, coding experiments, running them via agentic tree search, writing the paper in LaTeX, automated review. Towards end-to-end automation of AI research www.nature.com/articles/s41...

Super cool!

🎉 Our first paper this year is out! We show that treated wastewater microbiomes reflect operational changes in WWTPs, using 16S rRNA (DNA & cDNA) and FISH. 24-h composite sampling gives highly representative profiles. 🧬 #Microbiome #NGS #Wastewater www.nature.com/articles/s41...

💾 mlst 2.25.0 has been released! Fixed a bug that missed alleles in increasingly larger schemes like senterica (thanks @microbiologikat.bsky.social) and updated the databases. #bioinformatiocs #microbiology #genomics github.com/tseemann/mls...

💾 Shovill 1.4.1 has been released! The best way to de novo assemble microbial genomes from Illumina FASTQ. Major fixes to the SKESA module, plasmid mode for the Spades module, and more error checking. #bioinformatiocs #genomics #microbiology github.com/tseemann/sho...

Efficient near telomere-to-telomere assembly of Nanopore Simplex reads doi.org/10.1101/2025... Cookbook for Plant Genome Sequences www.preprints.org/manuscript/2...

Join us at this exciting Workshop on #LongReads with keynotes from @aphillippy.bsky.social @mydennis.bsky.social co-organized by @christinebeck.bsky.social and Mark Adams @jacksonlab.bsky.social Register www.jax.org/longread #RNA #genomics #bioinformatics #cancer #medicine #evolution #neuroscience

Easy and interactive taxonomic profiling with Metabuli App. It integrates database curation, read QC, taxonomic profiling, and visualization right on your desktop. No command line, server, or internet required. Now published in Bioinformatics! 🧵1/5 doi.org/10.1093/bioi... github.com/steineggerla...

Quite interesting pipeline for bacterial isolate QC including de novo assembly and contamination detection. github.com/B-UMMI/INNUca

Today in @nature.com , we highlight how a cousin of CRISPR-Cas10, mCpol, establishes an evolutionary trap in anti-phage immune systems. Check out @erinedoherty.bsky.social and my work from @doudna-lab.bsky.social lab here: www.nature.com/articles/s41...

Precisely calling mutations across hundreds of bacterial isolates has been hard, requiring manual filtering and expertise. Until now, using AccuSNV. Herui Liao trained an ML model based on our previous meticulously called SNVs. www.biorxiv.org/content/10.1...

Nauka i badania, w kraju, który jest 20-tą gospodarką świata, powinny być priorytetem ponad podziałami. Apelujemy do wszystkich, którzy rozumieją potrzebę prowadzenia badań naukowych w Polsce o zapoznanie się z treścią listu i poparcie Apelu. www.petycjeonline.com/list_otwarty...

Our paper is out! We report the first genome-wide essential gene map of Streptococcus anginosus 980/01, a human commensal & opportunistic pathogen. Using TnSeq, we found 348 essential genes, incl. 40 unique ones, shedding light on its biology & pathogenic potential. www.nature.com/articles/s41...

Microbiome sequencing has come so far in 2 decades. In my PhD— I used TRFLP…. am now doing long read sequencing of entire soil metagenomes! This review was great fun- thanks Gitta Szabó @emileyeloe-fadrosh.bsky.social Tanja Woyke of @jgi.doe.gov www.nature.com/articles/s41...

GenMasterTable: a user-friendly desktop application for filtering, summarising, and visualising large-scale annotated genetic variants. #GeneticVariants #VariantExploration #DataVisualization #GUI #BMCbioinformatics 🧬 🖥️ bmcbioinformatics.biomedcentral.com/articles/10....

Our high-precision metagenomic strain caller, PHLAME, is now published in Cell Reports!! www.cell.com/cell-reports... PHLAME works on tough sample types -- including those with coexisting strains of a species and low depth.

I'm offering a new workshop that's part instruction, part group coaching. This program will focus on the design principles we should consider when generating visuals. There won't be any coding so don't let that hold you back shop.riffomonas.org/products/tra...

The software updates on NovaSeq X Series really do improve performance, quality and output. It's all documented in the #illumina blog- sapac.illumina.com/science/geno...

NEW publication: Super happy to see the ClipKIT web application now published in Nucleic Acids Research @narjournal.bsky.social!! Trim your alignments for FREE on us :D Application: clipkit.genomelybio.com#/ Manuscript: academic.oup.com/nar/article/... #phylogenetics #evolution #bioinformatics

Our paper is out!🦠 The S. aureus phage ASZ22RN can infect or lyse all tested strains and efficiently transfer plasmids—even in strains with phage defenses. Its unique ability to bypass intracellular barriers makes it a valuable tool for genetic delivery into clinical isolates.

Delighted to share a new preprint from the lab! We identified essential genes in S. anginosus, a bloodstream isolate, under optimal laboratory conditions using a transposon mutagenesis combined with Transposon-Directed Insertion Site Sequencing (TraDIS). www.biorxiv.org/content/10.1...

Explore microbial evolution with AutoMLST2, a web server for automated phylogenetic analysis for bacterial & archaeal genomes. PMID:40357641, Nucleic Acids Res 2025, @NAR_Open https://doi.org/10.1093/nar/gkaf397 #Medsky #Pharmsky #RNA #ASHG #ESHG 🧪

Excited to share our latest work on comparing and visualizing multiple genome assemblies to identify conservation and structural variation in pangenomes with Mumemto! Check out poster 250 at #bog25 if you are here. New preprint coming very soon 👀

🌐Our @nature.com paper is out! Researchers from IIMCB and other Polish institutions show how TENT5A boosts mRNA vaccine efficacy by stabilizing therapeutic mRNAs and enhancing antigen production. A step toward better therapies for cancer and beyond! 🧬 👉Read the story: bit.ly/3XYvQkI #Nature #mRNA

The best food choices for healthy aging! Huge cohort - 105,000 people tracked over 30 years. Eat fruit and vegetables and avoid red meat. Wine is quite good. www.nature.com/articles/s41...

Our first paper this year is out! We studied the occurrence and diversity of fungi on the skin of Atopic dermatitis patients and healthy volunteers by using a two-pronged strategy (culture-dependent and NGS-based). onlinelibrary.wiley.com/doi/10.1111/...

Has anyone of you know how to speed up docker compose? I run the Phastest phage identification pipeline in docker and it is really slow due to running on single thread. Interestingly first sample in my batch is runing faster on multiple cores. Any hints?

A link between yogurt intake and reduce risk of colon cancer, from cohort of over 130,00 participants, with inverse relationship to Bifidobacterium in gut microbiome www.tandfonline.com/doi/full/10.... open-access

Highly multiplexed spatial transcriptomics in bacteria https://www.science.org/doi/10.1126/science.adr0932

In 2014 Dutch scientists left a hamster wheel outside, to see if wild animals would use it like their domesticated counterparts. The answer: hell yes! 734 visits from wild mice - plus rats, shrews, slugs ("running" being subjective here) & even frogs and snails. The apparent reason: fun. Just fun.

After shuttting down 454 in 2013, Roche is trying to get back into the sequencing market with its soon-to-be-released sequencer.

I have one open PhD position. Maybe one of the last PhD positions in the lab as I'm planning changes in what we do and how we will do it some five years from now. I'm offering freedom (pun intended), respect, an interesting project, and a good full time contract w. health insurance.

getphylo is finally official! Build phylogenetic trees directly from genbank files - at breakneck speed! I'd like to thank everyone who provided feedback and encourage you to continue. Improving getphylo doesn't stop now the paper is out! 1/5 🧪 bmcbioinformatics.biomedcentral.com/articles/10....

Our paper is out! We have sequenced the plastid genomes of 13 Prototheca strains and reconstructed a comprehensive phylogeny that reveals evolutionary patterns within the genus and among its closest relatives. bmcbiol.biomedcentral.com/articles/10....

What are your favourite tools for visualizing Metaphlan or kraken2 results? I just found this one: github.com/acvill/brack... There is even shiny app: acvill.shinyapps.io/bracken_plot/

Today I had opportunity to see the newest @illumina MiSeq i100 Plus. The doors were opened:

Is it Bad to leave Twitter? No. Here are 7+ years of insights from my lab’s research that explain why. Featuring work w/ @williambrady.bsky.social @killianmcloughlin.bsky.social 🧵

EasyPubPlot - Easy and Publishable Plotting pharmaco-omicslab.shinyapps.io/EasyPubPlot/

Check this out👇 Another bacterial genome comparison tool. It even works on Windows!

Archaeome - the dark matter of the microbiome. asm.org/articles/202...

I was looking for alternative 16S database to SILVA and found MIMt. Has anyone tested it yet? environmentalmicrobiome.biomedcentral.com/articles/10....

Gene regulation involves thousands of proteins that bind DNA, yet comprehensively mapping these is challenging. Our paper in Nature Genetics describes ChIP-DIP, a method for genome-wide mapping of hundreds of DNA-protein interactions in a single experiment. www.nature.com/articles/s41...

NEW Publication!😄 Here, we show how #PhyKIT — a broadly applicable toolkit for #phylogenomics — can be used to construct phylogenomic data matrices (& quantify biases therein), detect anomalies in predicted orthology, calculate gene-gene coevolution, & more! 🔗: tinyurl.com/yc5ja4xz

Another great comparative genomics tool: art-egorov.github.io/lovis4u/

Get ready to dance, our paper – Phage DisCo: targeted discovery of bacteriophages by co-culture – has been pre-printed! 🪩 This has been a really fun project to work on with @sianowen.bsky.social, @baym.lol, @nquinoneso.bsky.social, and our two talented undergrads Kesther and Carmen!

It looks like our gut microbiome is socially dependent. Amazing work.

@stepelka.bsky.social check this out!

(1st post @BlueSky) Preprint alert🚨a long thread. Cautions in the use of @nanopore sequencing to map DNA modifications: officially reported “accuracy” ≠ reliable mapping in real applications. We performed a critical assessment of nanopore sequencing (across different versions of models) for the 1/n

1/ Our review on sequencing-based #microbiome analysis is in the Dec 24 issue of Nature Reviews Genetics. We explore DNA/RNA-sequencing approaches for studying microbiome structure and function, highlighting the biological insights sequencing-based microbiome research offers. go.nature.com/3XFqonu

🦠🧬💻 Bakta v1.10 - largest update so far: Highlights: - user-provided HMMs: --hmms - output file recovery from JSON files: bakta_io - export of inference metrics: inference.tsv - bypass overlap filters: --skip-filter - improved genome plots github.com/oschwengers/... 👇 (1/11)