Metabolomics-based and functional validation to explore the effect of the gut microbe-associated metabolite guanidinoacetic acid on rectal adenocarcinoma www.nature.com/articles/s41...

NovaSeq 6000's two-color chemistry introduces a recurrent T>G substitution artifact that doesn't show up on HiSeq X10's four-color chemistry.

Germline and high-VAF somatic calls are fine. Low-VAF mosaicism calls are not.

Blog post on "The AI Rewrite Dilemma": lh3.github.io/2026/04/17/t...

A microbiome catalog of Chinese traditional artisanal cheeses provides insights into functional and microbial diversity www.nature.com/articles/s41...

Targeted long-read RNA sequencing for rare disease diagnosis and variant interpretation www.science.org/doi/10.1126/...

Global genomic and molecular epidemiology of carbapenem-resistant Enterobacter hormaechei www.nature.com/articles/s42...

🌐 Participate in the 15th ISCB Student Wikipedia Competition! Improve or create Wikipedia articles in #computationalbiology and #bioinformatics until Friday, May 1, 2026.

For details and to get started with your entry, visit www.iscb.org/iscb-awards/wikipedia-wi...

Pesticides may wreak havoc on the gut microbiome Disruption of intestinal ecosystem could contribute to diabetes and other health issues, scientists say

Pesticides may wreak havoc on the gut microbiome | Science | AAAS www.science.org/content/arti...

An ancient genome of Streptococcus pyogenes from a pre-Columbian Bolivian mummy www.nature.com/articles/s41...

Congratulations @wshuai.bsky.social and co-authors!

We’re excited to introduce MODIFI, our new scalable method for detecting DNA modifications in PacBio metagenomic data and estimating ECE-host linkage.
Check out the preprint: www.biorxiv.org/content/10.6...

Umi-pipeline-nf: A modular and scalable workflow for UMI-tagged nanopore amplicon analysis with real time sequencing integration and GPU-acceleration AbstractMotivation. Unique Molecular Identifiers (UMIs) enable efficient error correction in amplicon sequencing but UMI-aware analysis workflows for long-

Umi-pipeline-nf: A modular and scalable workflow for UMI-tagged @nanoporetech.com amplicon analysis with real time sequencing integration and GPU-acceleration academic.oup.com/bioinformati...

Can we really detect multiple diseases via a cell-free DNA methylation blood test at low cost? www.pnas.org/doi/10.1073/...

Welcome to RustQC Fast quality control tools for sequencing data, written in Rust.

Super excited to be launching two things today: #RustQC 🦀🧬 and rewrites.bio 🚀

I used AI to rewrite 15 RNA-seq QC tools into a single Rust binary (I've never written any Rust). It ended up being over 60x faster. Here's the story 🧵

seqeralabs.github.io/RustQC/

Evolution of pandemic cholera at its global source - Nature The seventh cholera pandemic, driven by El Tor Vibrio cholerae, evolved separately in Bangladesh and India, with the Ganges Basin acting as the global source, and its evolution has been shaped by...

Evolution of pandemic cholera at its global source www.nature.com/articles/s41...

GitHub - fulcrumgenomics/fgumi: High-performance UMI tools for NGS data analysis High-performance UMI tools for NGS data analysis. Contribute to fulcrumgenomics/fgumi development by creating an account on GitHub.

We built fgbio years ago to support UMI-aware sequencing.

As datasets grew, the single-threaded design started to show its limits.

fgumi is the next iteration: same expected outputs, rewritten for performance and scale.

github.com/fulcrumgenom...

Blog post details below👇

Whole-body molecular and cellular mapping of the laboratory mouse A scalable experimental and computational platform for mapping all organs and cell types in the mouse body, enabling comprehensive analysis of tissue organization and disease responses.

Now online! Whole-body molecular and cellular mapping of the laboratory mouse

Generate Presentation Images Using Google Gemini Reproducibly generate slide images using Google Gemini. Define your images in a YAML configuration file with support for reference images and style defaults, eliminating the need to copy and paste pro...

New (mostly vibe coded) package to generate slide images using Gemini in a (mostly) reproducible way: hadley.github.io/bananarama/ I made this to scratch a personal itch; please let me know if you also find it useful #rstats

SNP calling, haplotype phasing and allele-specific analysis with long RNA-seq reads Nature Methods - In this study, long-read RNA sequencing achieves accurate single-nucleotide polymorphism calling, haplotype phasing and allele-specific expression analysis.

LongcallR for competitive SNP calling and haplotype phasing, and simplified allele-specific analysis with long RNA-seq reads. Found ~100 junctions affected by SNPs per sample with most junctions novel.

Developed by Neng Huang. Published in @natmethods.nature.com. Read at rdcu.be/faKhL

We are happy to announce that “The AI Scientist: Towards Fully Automated AI Research” has been published in Nature!

We shared a vision of an agent executing the entire machine learning research lifecycle.

Nature: www.nature.com/articles/s41... Blog: sakana.ai/ai-scientist...

Thread 🧵

Long reads carry multiple small vars and SVs and their phasing. LongcallD is the only caller that tightly integrates germline/mosaic small/structural vars/MEIs and their phasing in a single C program. One command line to get competitive small variant calls and better SVs. Led by Yan Gao.

Generalist biological artificial intelligence in modeling the language of life - Nature Biotechnology This Review discusses the promises and pitfalls of biological AI algorithms and presents a vision for generalist biological artificial intelligence, in which models can perform diverse tasks across bi...

AI to understand the language of life.
Our review just published
nature.com/articles/s41...
Free access rdcu.be/e89lQ

But they haven't done the work, have they? They WILL create the Trillion Gene Atlas using PacBio etc. in my understanding.

Roseburia inulinivorans increases muscle strength Background Gut bacteria have been implicated in a wide range of health conditions, yet their potential role in preventing and treating muscle-wasting disorders remains largely unexplored. Objective W...

Cool, a gut bacterium that makes you strong! Roseburia inulinivorans increases muscle strength gut.bmj.com/content/earl...

Complete genome sequence of Sphingomonas sp. gentR, a high-level gentamicin-resistant bacterium www.nature.com/articles/s41...

Integrating ANI and phylogenies for re-evaluation of Fusobacterium taxonomy and disease associations www.nature.com/articles/s41...

Acinetobacter baumannii’s lifestyle includes soil-dwelling colonization of decaying plant material and airborne spread - Nature Communications Little is known about the ecology and evolution of the nosocomial pathogen Acinetobacter baumannii outside the hospital. Here, Wilharm et al. show that the lifestyle of A. baumannii includes soil-dwel...

Acinetobacter baumannii’s lifestyle includes soil-dwelling colonization of decaying plant material and airborne spread www.nature.com/articles/s41...

Oxford Nanopore enhanced accuracy of long-read amplicons applied to microbial whole-genome sequencing | Microbiology Spectrum Recent advances in genome sequencing have greatly improved our ability to study microbes and detect infections. One such technology, Oxford Nanopore Technologies (ONT), can read long stretches of nucleic acids. ONT is also portable and can sequence in real time, making it useful in clinical settings. However, ONT accuracy is known to be lower than traditional short-read methods, limiting its widespread use. Fortunately, many strategies have emerged to overcome this limitation: better ONT chemistry, better basecaller, and hybrid approaches combining ONT with highly accurate short reads. Another promising method uses molecular barcodes or “Unique Molecular Identifiers” (UMIs) to make long reads at high accuracy, reaching accuracy levels similar to the existing short-read technologies. In our study, we optimized this UMI-based method and successfully applied it to human blood samples spiked with common infection-causing bacteria. The results showed a significant drop in ONT error rate, suggesting that this approach could make ONT a reliable tool for diagnosing infections and analyzing microbial DNA in clinical samples.

Happy to share our paper is now online! Building on the UMI-based @nanoporetech.com strategy of Karst et al. 2021, we optimized it for microbial WGS and blood-culture samples, reducing error from 3.36% to 0.097%, and to 0.040% with V14+SUP doi.org/10.1128/spec...

Now published in Microbial Genomics www.microbiologyresearch.org/content/jour...

Eubiota: Modular Agentic AI for Autonomous Discovery in the Gut Microbiome www.biorxiv.org/content/10.64898/2026.02...