Long-read sequencing facilitates observation of contiguous DNA molecules, providing access to variants previously ignored. In this Primer, Zheng et al. discuss the computational foundations of long-re...

The use of whole-genome sequencing for classification and surveillance of the pathogen Chlamydia trachomatis is limited due to the lack of standardized typing frameworks. Here, the authors present a c...

Nature Biomedical Engineering, Published online: 04 August 2026; doi:10.1038/s41551-026-01769-6XunZi is an AI biologist capable of synergizing logical reasoning and multimodal data fusion to generate de novo therapeutic target hypotheses. XunZi was used to discover two therapeutic targets in Parkinson’s disease that were subsequently verified.

In this study, the authors demonstrate that trimeric autotransporter adhesins drive bacterial chain-like adhesion, expanding the surface colonization strategies of Shiga toxin-producing Escherichia co...

The web is increasingly accessed by AI agents rather than humans. Every agent needs knowledge, especially in the life-sciences, where agentic pipelines are growing fast. Access to the literature is a ...

AI agents can now plan, execute, and refine multi-step genomic analyses from natural-language instructions. Corpas and colleagues define this emerging paradigm, “agentic genomics,” and argue that it m...

Complete sequencing of more than 2,000 centromeres from diverse humans reveals structures and elevated mutation rates that shape the evolution of these critically important regions.

This Perspective highlights key research areas within mass spectrometry-based proteomics where AI is poised to drive significant advances.

a short-read polishing tool for long-read assemblies - rrwick/Polypolish

Plague, caused by the pathogen Yersinia pestis, has affected human societies for millennia. Here, the authors screened 1,400 ancient human remains from eastern Eurasia and recovered three prehistoric ...

a blog for miscellaneous bioinformatics stuff

Nature Methods - EviAnn surpasses existing genome annotation methods by leveraging gene expression and protein sequence homology evidence to achieve higher accuracy and efficiency.

a blog for miscellaneous bioinformatics stuff

Bacteria of the genus Gardnerella are associated with bacterial vaginosis. Here, the authors compile and analyse a reference set of high-quality Gardnerella genomes, revealing previously hidden specie...

a blog for miscellaneous bioinformatics stuff

Purine bias is critical for gene expression in bacteria, preventing premature transcription in species that exhibit runaway transcription.

a blog for miscellaneous bioinformatics stuff

“Wikipedia for Researchers: Building reliable knowledge through citations” is a new free course on WikiLearn! Co-developed by Kath Burton, Carlos Areia, and Asaf Bartov, it brings toget…

Nature Protocols, Published online: 08 June 2026; doi:10.1038/s41596-026-01362-wSniffles2 is an open-source software for reliable detection of structural variants (50 bp and upward) from long-read sequencing. Sniffles2 is able to call variants over a wide variant allele fraction (5–100%) and across multiple samples (population).

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A conversation with Helen Pearson on her new book BEYOND BELIEF

Scientific Data - High-Quality Genome Assembly, Metabolome, Pangenome, and Metabolic Models of Megasphaera hexanoica KCCM 43214T

Antibiotics have been used to treat tuberculosis for over 80 years. Here, Chen et al. analyze over 18,000 Mycobacterium tuberculosis genomes to reconstruct the temporal and spatial evolution of drug r...

London Calling 2025 Technology Update

Coppens & Ledesma-Amaro present a transformer-based computational model trained on 9 million bacterial sequences from over 3,000 species, which enables automated identification of diverse promoter...

Nectar bacteria turn floral sugar into a weapon: Acinetobacter converts glucose to gluconic acid, acidifies nectar, and triggers pollen tube burst, revealing a nectar-adapted strategy coupling glucose...

Abstract. Ultra-processed foods (UPFs) have increasingly displaced traditional diets globally and have become a significant public health concern, particul

It all started with a discussion in 1998

Bacterial genomes often include extrachromosomal replicons, ranging from small plasmids to chromosome-scale replicons. Here, Czarnecki et al. analyse more than 40,000 complete bacterial genomes and sh...

This Review summarizes recent advances in bacterial single-cell transcriptomics approaches, while also discussing technological and computational challenges remaining to be met and the need for standa...

Nature Communications - Long-read sequencing enables comprehensive transcriptome characterization but remains challenging to benchmark due to sequencing errors, sample variability, and the limited...

Scientific Reports - Metabolomics-based and functional validation to explore the effect of the gut microbe-associated metabolite guanidinoacetic acid on rectal adenocarcinoma

While cheese is enjoyed globally, most of the known physiochemical and microbial characteristics are from western cheeses. Here, the authors expand the global catalogue of cheeses by investigating 235...