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Earlier sources: Science
Science investigates the natural world through observation, experiments, and mathematical models. Explore papers and developments in biology, medicine, materials, neuroscience, physics, climate, and mathematics; a reported finding is not necessarily established consensus.
SYMTRI organizes observations from public sources into a living map. Connections reflect shared subject matter; they do not establish causation or endorse a source.
Open in the map ↗1348 classified signals in the fourteen-day window. Recent momentum: steady. These counts include signals awaiting readable evidence.
Earlier sources
Up to ten sources with readable evidence, ordered by their feed timestamp. These archive sources can be older than the live fourteen-day window. This list is a sample, not a measure of total activity. Dates distinguish paper publication, repository creation, model/dataset activity, Hacker News posts, and KEV catalog additions. “First archived” records when SYMTRI first stored the signal.
- Europe PMC · Published · First archived
BoNTax: a curated genome-based framework for taxonomic classification and characterization of Clostridium botulinum Group I and Clostridium sporogenes ↗
Clostridium botulinum Group I and Clostridium sporogenes are closely related genomic lineages for which historical toxin-based nomenclature can obscure species-level relationships. We developed BoNTax, a curated taxonomy-first framework that separates average nucleotide identity (ANI)-based species assignment from botulinum neurotoxin (BoNT) characterization while integrating assembly quality assessment, multilocus sequence typing (MLST), AMRFinderPlus-based detection of bont genes, other virulence-associated genes, and antimicrobial resistance genes into standardized outputs. Analysis of 966
- Europe PMC · Published · First archived
GenDiMug: a generic inclusive multigraph framework to analyze genomic organizations and -omics data at multiple scales ↗
After decades of investigation, analyses of genome organization remain challenging. This is because genome descriptions are very information-rich and usually rendered as a linear map of genomic features corresponding to an ordered list of position intervals on a nucleic acid macromolecular backbone. This formalism, while accurate, is not fully optimized to mathematically analyze all genome structural properties, in particular the relations between genomic features, nor to integrate large amounts of -omics data, such as transcriptomes, epigenomes, proteomes, meltomes or chromatin accessibility
- Europe PMC · Published · First archived
Cromosomal genomes assemblies of twelve sheep breeds ↗
The sheep research community benefits from a genome assembly that has been refined over the last 15 years. However, the rich diversity of sheep breeds suggests that a single individual genome is not enough to represent the species full genomic content. Third-generation sequencing technologies have recently made it possible to generate high quality assemblies that should enable to elucidate unique and/or complex phenotype determinisms depending on genetic structural variations. In the SeqOccin project, twelve breeds were selected to represent (mostly French) sheep genetic diversity: Basco-Bearn
- Europe PMC · Published · First archived
Genome assemblies and annotations of the poneroid ants Platythyrea mocquerysi (Ponerinae) and Stigmatomma oregonense (Amblyoponinae) ↗
We present draft genome assemblies for two poneroid ant species with distinctive life history traits: Platythyrea mocquerysi Emery, 1899 (Ponerinae) and Stigmatomma oregonense Wheeler, 1915 (Amblyoponinae). Platythyrea mocquerysi is a Malagasy ant in which larvae produce secretions from a ventral tubercle that are consumed by adults, representing an unusual form of larva-to-adult trophallaxis. Stigmatomma oregonense, a North American "dracula ant," feeds non-lethally on larval haemolymph. Using PacBio HiFi long-read sequencing, we assembled the P. mocquerysi genome (187 Mb, 307 scaffolds, N50
- Europe PMC · Published · First archived
Structural variants from donor-specific assemblies affect recurrent chromatin contact divergence in humans ↗
Structural variants (SVs) are a major source of human genetic diversity, yet their contribution to three-dimensional (3D) genome organization remains difficult to resolve using a standard reference genome. Here, we integrate haplotype-resolved chromatin interaction maps across 354 human and 12 nonhuman ape haplotypes with matched genome assemblies and long-read transcriptomes to determine how inherited SVs influence chromatin organization. We observe significant improvements in contact mapping, with 13.2% of cis Hi-C contacts showing >25 kbp changes in inferred genomic separation and an additi
- Europe PMC · Published · First archived
Mutation in Ralstonia pseudosolanacearum F1C1 cytochrome p450 homologue impairs virulence through root but not through shoot of tomato plants ↗
Ralstonia pseudosolanacearum causes a lethal bacterial wilt disease in many plants. The pathogen enters through roots and systemically colonizes the xylem tissue, resulting in wilting and eventual death of the host. Using transposon mutagenesis followed by screening in tomato seedlings, we identified a mutant exhibiting virulence deficiency by root inoculation, but not by leaf inoculation. The mutation was recreated in the wild-type genome via natural transformation to prove the linkage of virulence deficiency with the transposon insertion. Whole genome sequencing revealed that the transposon
- Europe PMC · Published · First archived
The Genetic Landscape of Structural Variants in Aspergillus flavus using ONT and PacBio Sequencing ↗
Genetic rearrangement in the absence of selection is poorly understood. Long-read, high-depth sequencing has enabled analysis of the genetic landscape of spontaneous structural variants. We have applied PacBio Revio sequencing to identify the major classes of genetic alterations during long-term vegetative growth in Aspergillus flavus. These classes include a) precise deletions frequently associated with the flanking region of homology, b) clusters of short deletions that are heavily enriched within centromeric and subtelomeric regions that are typically 94% A+T, and c) deletions and expansion
- Europe PMC · Published · First archived
Goat genome assemblies, nine breeds for pangenome contribution ↗
The goat research community benefits from one of the most comprehensive livestock genome assemblies, ARS1. However, the rich diversity of goat breeds suggests that a single individual genome is not enough to represent the species full genomic content. Third-generation sequencing technologies have recently made it possible to generate very high quality assemblies that should enable to elucidate unique and/or complex phenotype determinisms depending on genetic structural variations. In the SeqOccin project, nine goat breeds were selected to represent French goat genetic diversity: Alpine, Boer,
- Europe PMC · Published · First archived
GLARE: Genomic Language model for Automated Repetitive Element classification ↗
Reliable classification of transposable elements (TEs) is important for genome annotation and evolutionary analysis, yet remains challenging: TE families differ widely across taxa, reference databases label them inconsistently, and many TEs are represented only by degraded copies. We introduce GLARE (Genomic Language model for Automated Repetitive Element classification), a TE classifier built by fine-tuning a genomic language model on harmonized PanTEon and Repbase reference data to predict TE superfamily across 32 superfamilies in 11 orders. Among the genomic language models compared, Nucleo
- Europe PMC · Published · First archived
Genome-engineered C. elegans strains with sex-transformed neurons and gut ↗
The sexual identity of specific tissues can be altered through cell-autonomous manipulation of the sex determination pathway in the nematode Caenorhabditis elegans . Previously described sexually mosaic strains carried multicopy transgenic arrays that are potentially subject to transgene silencing or misexpression artefacts. We used here the CRISPR/Cas9 system to engineer strains in which coding sequences for either a masculinizing agent (FEM-3) or a feminizing agent (intracellular domain of TRA-2) are inserted with a trans-splicing system at the 3 end of endogenous genetic loci that are known
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