A new study has mapped the distinct molecular “fingerprints” that 59 diseases leave in blood protein – which would enable blood tests to discern troubling signs from those that are more common #research supported by Knut and Alice Wallenberg Foundation @proteinatlas.bsky.social tinyurl.com/5x8wfurm

Nature Reviews Genetics: Forensic genetics in the omics era www.nature.com/articles/s41... free: rdcu.be/eKbQn) 🧬🖥️🧪

Within-host genetic diversity of pneumococcal serotype 3 during one-year prolonged carriage in a healthy adult www.nature.com/articles/s41...

Dear community, Bakta needs your help! To further improve the functional annotation of "hypothetical" CDS, me and @gbouras13.bsky.social, we are looking for the worst Bakta-annotated bacterial genomes ;-) (1/2)

A genomic view of the bacterial family Endozoicomonadaceae in marine symbioses www.nature.com/articles/s42...

What is the benefit of a T2T reference instead of GRCh38 for population-scale sequencing projects? Read all about it in our latest paper. Special thanks to Daniel Schmitz for leading this work, which involved reanalysis of 1000 samples! genome.cshlp.org/content/earl...

🚀 Seqera AI in Platform: Develop, debug, and execute in one unified experience We’re thrilled to announce that Seqera AI, the bioinformatics agent for the R&D lifecycle, now has read and write access to Seqera Platform. 🧵 📚 Learn more: hubs.ly/Q03JL7wB0

Elucidating the role of group A Streptococcus genomics and pharyngeal microbiota in acute paediatric pharyngitis www.nature.com/articles/s41...

Combined genomic and phenomic analyses reveals multifunctionality of Paenibacillus polymyxa K16 for plant’s nutrition, growth and health www.nature.com/articles/s41...

"Illumina is ideal for broad microbial surveys, whereas ONT excels in species-level resolution and real-time applications" Comparative analysis of illumina and oxford nanopore sequencing platforms for 16S rRNA profiling of respiratory microbial communities www.nature.com/articles/s41...

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

Has anyone already done the work-kitchen sponge microbiome project?

In another Perspective, Spakowicz, Ma and colleagues explore the debate surrounding the role of the tumor microbiota and discuss strategies that might help answer these questions. www.nature.com/articles/s41...

A comprehensive benchmarking of adaptive sampling tools for nanopore sequencing. #Nanopore #Sequencing #AdaptiveSampling #Benchmarking #GenomeBiology #Bioinformatics #Genomics @nanoporetech.com 🧬 🖥️ genomebiology.biomedcentral.com/articles/10....

Delighted to finally announce a preprint describing the Q100 project! “A complete diploid human genome benchmark for personalized genomics” For which we finished HG002 to near-perfect accuracy: www.biorxiv.org/content/10.1... 🧵[1/14]

Check out the latest blog post by Nextflow Ambassador Jeferyd Yepes on MAGFlow/BIgMAG: The Batman & Robin of the Metagenomics Field🧵 hubs.la/Q03KvrS20

Automated, almost-error-free consensus #assemblies with Autocycler Impressive benchmarks in Fig 2B (below): ≤10 median errors PER genome Once again, incredible, landmark work from @rrwick.bsky.social doi.org/10.1093/bioi... Tool here: github.com/rrwick/Autoc... #bioinformatics #genomics

📘 Just out in Bioinformatics Advances: "Competencies for bioinformatics core facility scientists: Extension of the ISCB competency framework for bioinformatics" Explore the full study: https://doi.org/10.1093/bioadv/vbaf206 Authors include: @downingtim.bsky.social

An NGS-assisted diagnostic workflow for culture-independent detection of bloodstream pathogens and prediction of antimicrobial resistances in sepsis www.frontiersin.org/journals/cel...

Trust but verify? #mlsky #scientificpublishing #sciencejournals @science.org www.science.org/content/arti...

On this #InternationalMicroorganismDay let’s celebrate Leeuwenhoek’s first report of microorganisms 352 years ago — but he never called them “animalcules”: in Dutch he wrote dierken/diertgens/diertjes (“small animals”); “animalcule” came from Henry Oldenburg’s English translations.

Generative genomics predicts future and impossible experiments! Read the new preprint from Synthesize Bio: www.biorxiv.org/content/10.1... and anyone can try our models on the cloud or in R/Python! product.synthesize.bio

Paper2Agent converts research papers into AI agents, enabling researchers to apply complex methodologies without extensive expertise. This innovation promises to transform scientific dissemination, accelerating discoveries across fields. https://arxiv.org/abs/2509.06917

People seem to spend longer on the toilet if they use a smartphone while sitting there – and all that scrolling may be boosting their likelihood of getting haemorrhoids

Our second paper with @tcostalab.bsky.social and GoogleDeepMind reports our experience with Google’s co-scientist: remarkably, the AI independently recapitulated our experimental discovery on cf-PICIs, showcasing AI’s potential to accelerate biology. www.cell.com/cell/fulltex...

Heads up: ignore samtools dot org, similarly minimap2 dot com and likely others. It's owned by a known phishing site and while the binaries they offer look valid currently (but note they may be serving us different binaries to others), that could change. Ie: it's not us (Samtools team)! Be warned

Highlights on Roche SBX Duplex Data webinar albertvilella.substack.com/p/roche-sbx-...

New blog post – A quick look at Roche's SBX lh3.github.io/2025/09/11/a...

AmpliconTyper – a tool for analysing ONT multiplex PCR data from environmental and other complex samples - go.shr.lc/4nsr1KF

Gut bacteria in early pregnancy—especially Clostridium innocuum—may raise the risk of preterm birth. It breaks down estradiol, a key hormone for maintaining pregnancy, and worsens genetic risk. www.sciencedirect.com/science/arti...

🚀 Nextflow Training Week is back on Sep 22-26! 💻 This self-paced online training features on-demand walkthrough videos and support via office hours and the community forum! 🔗 Register now: hubs.la/Q03HWK4L0

Sometimes you meet absolutely incredible bioinfo-magicians. It was a huge privilege when @shenwei356.bsky.social joined our group for a year on an @embl.org sabbatical. While here, he developed a new way of aligning to millions of bacteria, called LexicMap 1/n www.nature.com/articles/s41...

Next Generation Sequencing Improves Diagnostic 16S rRNA Amplicon‐Based Microbiota Analyses of Clinical Samples Compared to Sanger Sequencing - Aftab - 2025 - APMIS - Wiley Online Library onlinelibrary.wiley.com/doi/10.1111/...

"At the same sequencing read depth, FL-16S sequencing analysis with Emu yields comparable alpha & taxonomic diversity metrics, while providing superior species-level resolution compared to V3–V4 amplicon sequencing [using QIIME2] of tracheal aspirates." journals.asm.org/doi/10.1128/...

Preprint out for myloasm, our new nanopore / HiFi metagenome assembler! Nanopore's getting accurate, but 1. Can this lead to better metagenome assemblies? 2. How, algorithmically, to leverage them? with co-author Max Marin @mgmarin.bsky.social, supervised by Heng Li @lh3lh3.bsky.social 1 / N

Accurate and reproducible whole-genome genotyping for bacterial genomic surveillance with @nanoporetech.com sequencing data | Journal of Clinical Microbiology journals.asm.org/doi/10.1128/...

Finding microbes in cancer sequencing data has been controversial. Are we seeing real biology… or just contamination + batch effects?

We're still not finding any good evidence for a microbiome in any cancer type: see our new paper in @ScienceTM led by PhD student Yuchen (Peter) Ge www.science.org/doi/10.1126/... and the accompanying news piece, www.science.org/content/arti...

New blog post! I added a new feature to @gbouras13.bsky.social's Pypolca: homopolymer-only polishing. Potentially useful for cross-sample polishing - early test on Cryptosporidium looks promising. Check it out here: rrwick.github.io/2025/09/04/h...

Just published! 🧬 My student Valentina & I contributed to an FLI-led study on assembling ONT from pathogenic bacteria. 6.5% of ONT errors were methylation-related and could be reduced with the use of the right models. Thanks for the great collaboration, Jena folk! 🔗 doi.org/10.1186/s128...

🌎👩‍🔬 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...

What was antibiotic resistance like before we ever used antibiotics? How did we change what antibiotic resistance genes looked like over 100 years? Our paper looking at resistance genes from a century of NCTC historical isolates now out in mGen: www.microbiologyresearch.org/content/jour...

Determination of the prevalence of hypervirulent Klebsiella pneumoniae strains in Northeast Iran, Mashhad www.nature.com/articles/s41...

Amycolatopsis cyclosori sp. nov., isolated from the rhizosphere soil of Cyclosorus parasiticus www.nature.com/articles/s41...

Bringing the uncultivated microbial majority of freshwater ecosystems into culture www.nature.com/articles/s41...

Ecophysiology and global dispersal of the freshwater SAR11-IIIb genus Fontibacterium www.nature.com/articles/s41...

Ecological connectivity of genomic markers of antimicrobial resistance in Escherichia coli in Hong Kong www.nature.com/articles/s41...

🚀 Excited to see this work on "Empowering bioinformatics communities with Nextflow and @nf-co.re" is now published, showcasing the incredible growth and impact of the community. link.springer.com/article/10.1...

⚡️Thrilled that #VirtualLab is published in @nature.com! www.nature.com/articles/s41... We created a team of AI agents to mirror my Stanford lab 🤖. Led by a PI agent, the AI scientists ran their own group meetings and discovered effective binders to new CoVID variants that we validated.

Identifying reproducible biomarkers for microbiome association studies requires sample sizes of thousands www.sciencedirect.com/science/arti...