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...

Releases · tseemann/mlst :id: Scan contig files against PubMLST typing schemes - tseemann/mlst

💾 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...

Releases · tseemann/shovill ⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads - tseemann/shovill

💾 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...

Long-Read Sequencing Workshop The program will involve sessions on Genome Evolution, Genome Regulation, Transcriptomics, Rare Diseases, Common Diseases, and Viral and Microbial Genomes. Committed speakers include Adam Phillipy (NH...

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...

GitHub - B-UMMI/INNUca: INNUENDO quality control of reads, de novo assembly and contigs quality assessment, and possible contamination search INNUENDO quality control of reads, de novo assembly and contigs quality assessment, and possible contamination search - B-UMMI/INNUca

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

A miniature CRISPR–Cas10 enzyme confers immunity by inhibitory signalling - Nature Panoptes, an anti-phage defence system against virus-mediated immune suppression, is revealed.

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...

High-accuracy SNV calling for bacterial isolates using deep learning with AccuSNV Accurate detection of mutations within bacterial species is critical for fundamental studies of microbial evolution, reconstructing transmission events, and identifying antimicrobial resistance mutati...

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...

List otwarty do Prezydenta RP, Marszałka Sejmu RP, Marszałka Senatu RP,  Prezesa Rady Ministrów oraz Wiceprezesów Rady Ministrów w sprawie finansowania nauki, w tym zwłaszcza Narodowego Centrum Nauki Szanowni Państwo, W niniejszej petycji prezentujemy List otwarty, który będzie wysłany do Kancelarii Prezydenta, Marszałków Sejmu i Senatu, Prezesa Rady Ministr&oacut...

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...

Genome-wide identification of essential genes in the invasive Streptococcus anginosus strain - Scientific Reports Scientific Reports - Genome-wide identification of essential genes in the invasive Streptococcus anginosus strain

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...

A genomic view of Earth’s biomes - Nature Reviews Genetics Genome-wide approaches have uncovered the vast microbial and viral diversity across ecosystems. This Review explores advances in metagenomics, single-cell sequencing and functional profiling to elucid...

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.

Please check this on agarose gel and confirm the concentration by densitometry. Typically such high OD is due to the remaining RNA in miniprep.

Transform your data visualizations in 5 weeks - no judgement, no code

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...

NovaSeq X software update 1.3 improves data quality and customer usability The first shipments of the NovaSeq X Series introduced XLEAP-SBS chemistry on Illumina’s next-generation high-throughput platform. With the 25B flow cell, NovaSeq X software update 1.2 enabled up to 1...

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...

ClipKIT in the browser: fast online trimming of multiple sequence alignments for phylogenetics Abstract. Multiple sequence alignment trimming can help improve phylogenetic signal and reduce computational load. ClipKIT trims multiple sequence alignmen

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

Characterization of a novel Phietavirus genus bacteriophage and its potential for efficient transfer of modified shuttle plasmids to Staphylococcus aureus strains of different clonal complexes - PubMe... This study highlights the capacity of a newly isolated staphylococcal <i>Phietavirus</i>, ASZ22RN, to transfer a low-copy-number shuttle <i>Staphylococcus aureus</i>-<i>Escherichia coli</i> plasmid to...

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.

Genome-Wide Identification of Essential Genes in the Invasive Streptococcus anginosus Strain Background: Streptococcus anginosus, part of the Streptococcus anginosus group (SAG), is a human commensal increasingly recognized as an opportunistic pathogen responsible for abscesses formation and ...

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 🧪

Pushing the limits of de novo genome assembly for complex prokaryotic genomes harboring very long, near identical repeats Abstract. Generating a complete, de novo genome assembly for prokaryotes is often considered a solved problem. However, we here show that Pseudomonas koree

There is also briliant paper regarding the complexity in bacterial genomes:
academic.oup.com/nar/article/...

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 👀

IIMCB

🌐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

Optimal dietary patterns for healthy aging - Nature Medicine In two longitudinal cohorts followed for 30 years, the associations of eight different dietary patterns with healthy aging—encompassing cognitive, physical and mental health—were studied, identifying ...

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...

The Skin Mycobiome of Patients With Atopic Dermatitis and Healthy Volunteers: A Case–Control Study Atopic dermatitis (AD) is a common inflammatory skin disease, for which dysbiosis of the skin mycobiome is considered a triggering factor. The aim of this study was to explore the skin mycobiome of A...

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