bioinformatics

Every few minutes, a living cell does something quietly extraordinary: it sheds tiny membrane bubbles into the fluid around it. These extracellular vesicles carry molecular cargo (proteins, lipids, fragments of RNA) and cells have been doing this for so long that biologists spent decades trying to understand what the bubbles were for. A team at the Technical University of Munich has now turned th…

Run an AI model across a human chromosome and what you get back looks like a seismograph readout: peaks and troughs, quiet stretches interrupted by jagged eruptions of ancient time. The quiet zones are where evolution swept through recently, pushing all the variants in a population toward a single common ancestor. The peaks are where something else happened, something older and stranger, where co…

Scientific Data, Published online: 05 May 2026; doi:10.1038/s41597-026-07392-z A reliable and verified dataset of functional miRNA-mRNA target interactions for gene regulation studies

The five-year Virtual Biology Initiative brings together the Broad Institute , Allen Institute, Arc Institute, Wellcome Sanger Institute, Human Cell Atlas, Human Protein Atlas, NVIDIA , and Renaissance Philanthropy in a coordinated global effort to generate the data needed for predictive models of the human cell. Biohub has committed $500 million to the Virtual Biology Initiative, a global effort…

Insertion/deletion (indel) polymorphisms in the bovine PRNP gene promoter region (23 bp) and intron 1 (12 bp) influence gene expression and susceptibility to bovine spongiform encephalopathy (BSE). Conventional detection methods based on DNA sequencing are cumbersome and time-consuming. This study developed a visual detection method for these two polymorphic loci using multienzyme isothermal rapi…

Nature, Published online: 04 May 2026; doi:10.1038/d41586-026-01410-1 By accelerating the identification of DNA sequences that control gene expression, assays are revealing the hidden grammar of the regulatory genome — and giving scientists the means to rewrite it

Scientific Data, Published online: 04 May 2026; doi:10.1038/s41597-026-07354-5 A compendium of horizontal gene transfers in Metazoa

A simple adjustment to water filtration methods can dramatically improve the detection of marine animal DNA when using advanced, PCR-free sequencing. The post A Simple Filter Swap Could Advance Marine eDNA Biomonitoring first appeared on Blog .

A blood cancer-protective inherited variant in the homeotic lncRNA HOTSCRAMBL alters HOXA9 splicing, fine-tuning hematopoietic stem cell self-renewal while constraining HOXA-driven blood cancers.

KMRI is chunk-based MRI compression format for .nii files (Python + Zstd and C++). Got strong compression on synthetic MRI-like volumes, especially smooth data (up to ~900× in best case scenarios due to zero-block skipping). Check it out at https://github.com/Kiamehr5/KMRI and let me know what you think 💻

Nature Microbiology, Published online: 01 May 2026; doi:10.1038/s41564-026-02333-3 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 standardization going forwards.

Congratulations to Dr. Debojyoti Panda and Dr. Max Jiang on successfully defending their PhD dissertations! April 13, 2026 We are excited to announce that Debojyoti Panda has successfully defended his doctoral dissertation. His defense talk was titled “Understanding Bacterial Persistence using Single-Cell Transcriptomics“. His defense committee members were Profs. David Weitz and Davi…

Nature Communications, Published online: 30 April 2026; doi:10.1038/s41467-026-72380-1 Gene co-expression networks reveal co-regulatory and co-functional gene relationships. Here, the authors introduce an ensemble method that combines unsupervised data partitioning with multi-metric co-expression scoring and demonstrates superior performance across public RNA-seq datasets of multiple species.

Synonymous codon usage defines functional gene families Ghanegolmohammadi, Farzan; Ohnuki, Shinsuke; Byrne, Shane; Raman, Rahul; Begley, Thomas J; Dedon, Peter C The degeneracy of the genetic code is increasingly recognized for roles in regulating translation rate, protein folding, and cell response. However, the functional genomics of codon usage patterns remains poorly defined. We previously sh…

Scientific Reports, Published online: 30 April 2026; doi:10.1038/s41598-026-51117-6 Genome-wide cross-trait analysis reveals shared genetic architecture between inflammatory bowel disease and ankylosing spondylitis

BackgroundThe research on human microbiota-associated (HMA) animal models is an important tool for studying the human microbiome and holds great potential for elucidating disease mechanisms and microbe-based therapeutic interactions. However, a systematic bibliometric assessment of this field has been limited.MethodsThis study employed bibliometric methods, retrieving relevant publications publis…