THE INTERNET IS THINKING
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 ↗1328 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
Gene-level evolutionary conservation and human constraint decline at comparable rates across the age of onset of Mendelian disease ↗
Background: Gene-level constraint and conservation scores are widely used to prioritise disease genes and to benchmark genomic language models. Purifying selection acts weakly on phenotypes manifesting after reproduction, so these scores are expected to carry less information about late-onset disease. An onset-dependent gradient has been demonstrated for human allele frequencies but not for the gene-level scores used in practice. Results We built an age-of-onset axis for 2,885 Mendelian diseases from Orphanet and fitted cross-species conservation (241-way phyloP) and human-population constrain
- Europe PMC · Published · First archived
Compatible Comma-Free Codes and the Origin of the Genetic Code ↗
The genetic code is the rule that (apart from minor modifications) is used by all contemporary life on Earth to translate genes into proteins. It is summarized by a 4x4x4 table which maps the 64 possible triplet RNA codons to the 20 canonical amino acids ("AAs"). Understanding the origin of this code is a fundamental open problem in biology. We review the idea of a comma-free code, and put forward a general reason to suspect the primordial code was comma-free (even though the modern code is not). We explain why this primordial code should then persist as a comma-free subcode within the modern
- Europe PMC · Published · First archived
The porin MspA is a phage-specific determinant of mycobacteriophage infection ↗
Mycobacteriophages are being developed as therapeutics for mycobacterial infections, but their highly variable host ranges limit this application and the bacterial factors that determine whether infection succeeds remain poorly defined. The determinants characterized so far are dominated by cell envelope lipids and glycolipids. Here, we performed a genome-wide CRISPRi screen in Mycobacterium smegmatis to identify host functions associated with susceptibility to BPsΔ33HTH HRM10. After prolonged phage challenge, the outer membrane porin genes mspA and mspC were among the most strongly enriched h
- Europe PMC · Published · First archived
A modular DNA toolkit for single-molecule biophysics ↗
Long, customizable DNA molecules are an essential tool for in vitro single-molecule biophysics. Most studies still rely on the λ-phage genome, which has a fixed sequence, a non-uniform GC distribution, and limited options for modification. To overcome these limitations, we developed a modular DNA (ModDNA) toolkit that integrates in silico sequence design with cloning, to create long (up to 100 kb) DNA molecules with entirely user-defined sequences. We used a computational workflow with curated databases to design a motif-depleted sequence backbone, into which any desired sequence can be insert
- Europe PMC · Published · First archived
Winnow-tax: sensitive and precise taxonomic profiling of low-coverage organisms in shotgun metagenomes ↗
Accurate species-level profiling of shotgun metagenomes becomes difficult when an organism is represented by only sparse sequence coverage. Per-read k-mer classifiers can retain sensitivity under these conditions, but short reads from conserved or shared genomic regions can generate false-positive calls among closely related references. More conservative marker-gene and genome-containment approaches generally provide stronger species-level specificity but may lose sensitivity as genomic sampling becomes sparse. We present winnow-tax, a two-stage taxonomic profiling pipeline that separates sens
- Europe PMC · Published · First archived
RiboFlow v2: a configurable ribosome profiling pipeline reveals measurements sensitive to read-mapping methodology ↗
Ribosome profiling experiments capture a snapshot of translation by sequencing ribosome-protected fragments (RPFs). Alignment to a well-curated transcriptome captures most RPF signal, but can miss ribosome activity when expressed exons are absent from the reference. Genome alignment of RPFs expands the detectable sequence space, but can expose ambiguity between homologous loci. Existing workflows often couple reference choice with the handling of ambiguously mapped reads, making it difficult to isolate the effects of either decision on downstream analyses. Here, we developed RiboFlow v2 by add
- Europe PMC · Published · First archived
The genome sequence of the Lined Click Beetle, Agriotes lineatus (Linnaeus, 1767) (Coleoptera: Elateridae) ↗
Abstract We present a genome assembly from an individual Agriotes lineatus (Lined Click Beetle; Arthropoda; Insecta; Coleoptera; Elateridae). The assembly contains two haplotypes with total lengths of 2,590.71 megabases and 2,557.49 megabases. Most of the haplotype 1 assembly (87.5%) was scaffolded into 10 chromosomal pseudomolecules. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 16.27 kilobases. This assembly was generated as part of the Darwin Tree of Life project, which produces genomes for eukaryotic species found in Britain
- Europe PMC · Published · First archived
The genome sequence of the yellow-flowered strawberry, Potentilla indica (Andrews Th.Wolf, 1904) (Rosales: Rosaceae) ↗
We present a genome assembly of Potentilla indica (Yellow-flowered Strawberry; Streptophyta; Magnoliopsida; Rosales; Rosaceae). The assembly consists of two haplotypes with total lengths of 1,525.10 megabases and 1,436.58 megabases. Most of the haplotype 1 assembly (99.54%) was scaffolded into 42 chromosomal pseudomolecules. Haplotype 2 was assembled to scaffold level. The mitochondrial genome assembly has a length of 435.44 kilobases and the plastid genome assembly has a length of 156.08 kilobases. Gene annotation of this assembly by Ensembl identified 122,091 protein-coding genes. This assem
- Europe PMC · Published · First archived
The genome sequence of the Smooth Newt, Lissotriton vulgaris (Linnaeus, 1758) (Caudata: Salamandridae) ↗
We present a genome assembly from an individual female Lissotriton vulgaris (Smooth Newt; Chordata; Amphibia; Caudata; Salamandridae). The genome sequence has a total length of 24,225.52 megabases. Most of the assembly (87.93%) is scaffolded into 16 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 16.37 kilobases. This assembly was generated as part of the Darwin Tree of Life project, which produces genomes for eukaryotic species found in Britain and Ireland.
- Europe PMC · Published · First archived
The genome sequence of the Common Sedge, Carex nigra (L.) Reichard (Poales: Cyperaceae) ↗
We present a genome assembly of Carex nigra (Common Sedge; Streptophyta; Magnoliopsida; Poales; Cyperaceae). The assembly consists of two haplotypes with total lengths of 417.60 megabases and 412.78 megabases. Most of the haplotype 1 assembly (99.88%) was scaffolded into 43 chromosomal pseudomolecules, including the B 1 supernumerary chromosome. Haplotype 2 was assembled to scaffold level. The mitochondrial genome assembly has a length of 1469.56 kilobases and the plastid genome assembly has a length of 206.44 kilobases. This assembly was generated as part of the Darwin Tree of Life project, w
Live window recorded . This is the ingestion observation time, not the publication or discovery date of each source.
How to assess evidence about Science
Check each original source for its methods, release status, limitations, and supporting data. A repository announcement, a preprint, and a published study provide different kinds of evidence. SYMTRI’s subject classification helps discovery; it does not independently validate the source’s claims.
See the collection and counting methodology ↗ · Read the weekly synthesis ↗
Follow a thread
Explore related regions
These navigation suggestions are part of the map’s editorial structure, rather than measured evidence of a connection.