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TaxoFormer: Hierarchical Transformer for Predicting the Full Taxonomic Lineage of Protein Sequences
Predicting labels in massive, hierarchically structured output spaces is a core challenge in machine learning. In this work, we use the problem of predicting the full taxonomic lineage of a protein from its sequence as a case study for this challenge. We introduce TaxoFormer, an architecture whose primary contribution is a structured tokenization scheme that losslessly represents the entire NCBI phylogenetic tree, a graph with over 1.3 million nodes using a compact vocabulary of just 15,000...
Antimicrobial activity of polymyxin A, and characterisation of the cognate biosynthetic gene cluster within the genome of the producing Paenibacillus polymyxa.
We report the isolation and identification of a Paenibacillus polymyxa strain from the citizen science project; Swab and Send. Through whole genome sequencing we are able to describe the biosynthetic gene cluster of polymyxin A produced by P. polymyxa 1G (NCBI accession no. JBVPZV000000000), compare the pmxA, pmxB and pmxE genes to five other polymyxin genes encoding known polymyxin variants, and provide mass spectrometry data that supports the production of polymyxin A1 (1157 m/z) and A2...
A cross-domain tropical species dataset with Chinese vernacular names and CITES source links
Announce Type: new Abstract: We describe a versioned cross-domain dataset of 410,499 active tropical species (working snapshot 2026-04-20) spanning three applied subdomains -- tropical_plants, tropical_aquatic, and tropical_pets -- that share a commercial and regulatory life cycle but are distributed across kingdom-organised biodiversity infrastructures. The resource joins taxonomic identifiers from GBIF, Plants of the World Online, iNaturalist, NCBI Taxonomy, the Catalogue of Life and the...
Cohort-HMM marker recruitment with per-OG orthology QC for phylogenomic supermatrices
OrthoFinder's all-vs-all DIAMOND step systematically misses single-copy orthogroups (SC OGs) at deep taxonomic divergence: a marker recovered cleanly within a tightly defined cohort is dropped when the same marker is searched against phylum-broad metagenome-assembled genome (MAG) sets, because pairwise sequence similarity falls below DIAMOND's detection threshold even when the underlying ortholog is present. The result is biased dropout - supermatrices that retain genomes near the cohort but...
Gene ancestries reveal diverse microbial associations during eukaryogenesis
Abstract The origin of eukaryotes remains a central enigma in biology1. Continuing debates agree on the pivotal role of a symbiosis between an alphaproteobacterium and an Asgard archaeon2,3. However, the nature, timing and contributions of other potential bacterial partners4,5,6 and the role of interactions with viruses7,8,9 remain contentious.
Data gaps of international databases on HPAI H5 in wildlife in the Americas: implications for surveillance, research, and conservation
Global efforts to prevent and mitigate the impacts of high pathogenicity avian influenza (HPAI) H5 on domestic animals, humans, and wildlife rely on timely and transparent information that is both accurate and interpretable across countries and sectors. International epidemiological and genomic databases, such as the World Animal Health Information System (WAHIS), the Global Animal Disease Information System (EMPRES-i+), the Global Initiative on Sharing All Influenza Data (GISAID), and the...
Mutation-dependent responses to sleep and exercise in clonal haematopoiesis
Abstract Clonal haematopoiesis (CH) activates inflammation and increases the risk of atherosclerosis1,2. Whether lifestyle alters CH clone expansion or the phenotypic programming of CH mutant cells, thereby affecting atherosclerosis, is unknown. Here, in humans and mice and across mutations in Jak2, Tet2, Trp53 and Dnmt3a, we demonstrate mutation-dependent responses to sleep and exercise in CH and show that mutant cells are uniquely sensitive to lifestyle.
Weight loss jab users warned not to ignore 1 symptom affecting the eyes
Weight loss jab users warned not to ignore 1 symptom affecting the eyes Health officials have issued a warning to weight loss jab users after a rare eye condition was linked to a popular medication used by thousands Millions of people use weight loss and diabetes jabs every year, but health officials are warning patients to be alert to one potentially serious symptom that could affect their eyesight. The alert concerns medicines containing semaglutide, including Wegovy, Ozempic and Rybelsus....
Transcriptomic and proteomic responses to gas vesicle collapse in native and engineered bacterial systems
Gas vesicles (GVs) are air-filled protein nanostructures produced by microbes to regulate buoyancy and have emerged as powerful tools in biomedical imaging, particularly as acoustic reporter genes. Their mechanically robust shells enclose a stable air compartment, which collapses irreversibly when subjected to sufficient hydrostatic or acoustic pressure, leaving behind large protein sheets. This collapse phenomenon underlies key applications such as differential imaging and controlled...
Sprinkling 1 simple ingredient over chicken before cooking makes it taste better
Sprinkling 1 simple ingredient over chicken before cooking makes it taste better A simple kitchen cupboard ingredient can transform bland chicken into a flavourful dish Chicken ranks among Britain's most beloved dinner options, yet drawing out the very best flavour from it can sometimes prove trickier than expected. The good news is that food experts say one simple ingredient found in many kitchen cupboards could make a remarkable difference. According to spice experts at Spices Inc,...