database / resource

Whole-body single-cell atlas of an adult vertebrate in homeostasis and regeneration

Region-stratified scRNA-seq of 607,370 cells plus 500-gene MERFISH maps adult Danionella cerebrum cell types body-wide, revealing fibroblast Hox and limb-identity programs and telencephalon regeneration dynamics.

OpenAntigens: a structure-aware database for antigen construct design across the human cell-surface and secreted proteome

A static web database proposes 55 305 construct suggestions for 5328 human secreted and cell-surface proteins, using AlphaFold pLDDT and PAE, with ortholog, paralog and BLAST cross-reactivity context.

Zea Lip: An atlas of glycerolipid profiles across leaf development in maize

UHPLC-MS/MS lipidomics of maize leaves (149 species, three genotypes, four growth stages, three leaf zones) shows genotype and leaf number explain most lipid variation.

Impact of Rare and Common Genetic Variation on Cell Type-Specific Gene Expression

Single-cell eQTL mapping in 5.4 million PBMCs from 1,925 individuals with matched WGS finds common-variant eQTLs for 83% and rare-variant signals for 47% of 21,404 genes.

Mixtures of stably coexisting species overyield

In generalized Lotka–Volterra communities, stable coexistence almost always requires overyielding; in four long-term biodiversity experiments, underyielding raised species-loss odds within two observations (pooled odds ratio 2.61).

A clinically annotated proteomic and histological resource of 1,000 colorectal cancers

Deep proteomics of 997 treatment-naïve colorectal cancers defines six subgroups, splitting chromosomally unstable tumors into three and revealing a rare adverse subgroup, with H&E slide benchmarks.

Data mining of global sequence datasets markedly expands known diversity within the Tobamovirus genus

Serratus-guided Snakemake mining, expert curation, clustering and phylogenetic placement identify at least 32 putative novel tobamoviruses in public short-read data, mostly Amazon River metatranscriptomes; a random-forest classifier partly automates curation.

Tracking claim changes from preprint to publication across 72,644 biomedical studies using large language models

In 72,644 matched bioRxiv preprint-publication pairs, LLM-extracted primary abstract claims were unchanged or minorly revised in about 90%; hedging shifted toward caution in 8.4% versus confidence in 4.2%.

gene2fish: a multi-gene spatial expression browser for in situ hybridization data across zebrafish development

gene2fish arranges 53,595 Thisse in situ hybridization images of 8,263 zebrafish genes into a gene-by-stage grid, with anatomy-term search for validating scRNA-seq markers.

MetaDome 2027: a comprehensively updated resource for aggregating missense variant evidence across homologous human protein domains

MetaDome now supports GRCh38 alongside GRCh37, adds coordinate lookup, and identifies 52,463 GRCh38 ClinVar missense variants of uncertain significance with uncontradicted pathogenic evidence at homologous Pfam-domain positions.

The modular nature of long-association pathways in the human brain

Diffusion MRI tractography below 750 µm resolves the dorsal superior longitudinal fasciculus into layered fiber systems of varying length, matching macaque tracing; 1.5 mm tractography misses this.

It runs in the family: New extinct species from charismatic clades are more likely to be published in high-impact journals than those from non-charismatic clades

Among 8,331 new extinct species named in thirteen journals since 2000, avemetatarsalians and mammaliamorphs exceed 50% of species in Nature and Science but are under 15% in paleontology journals.

A Framework for Comparing Mouse Neoantigen Immunogenicity

Experimental pMHC melting-temperature stability ranked in vivo CD8+ T cell responses of 25 mouse neoantigens better than affinity assays or nine in silico predictors.

KRAKEN: A provenance-tracked knowledge graph for multiomic and wellness research

A Biolink-compliant graph (∼15 million nodes, ∼113 million edges) adds RefMet and LIPID MAPS metabolite and lipid classifications, plus polygenic score and clinical data element entities, to Translator content.

Integrative Multi-omics Analysis of the Human Skeletal Muscle Response to Endurance or Resistance Exercise: Findings from the Molecular Transducers of Physical Activity Consortium (MoTrPAC)

In 174 sedentary adults, resistance exercise changed more muscle molecular features than endurance exercise across omes and time points; network analysis nominates MEF2A and NFIC as regulatory hubs.

A DNA Typewriter records the cell lineage history of a mouse, from zygote to late organogenesis

A prime-editing recorder in one mouse embryo yields a dated, zygote-rooted lineage tree of 1.28M cells at E13.5, enabling clonal dominance, sibling-fate and cell-type coupling analyses.

NEK1 autophosphorylation is disrupted by amyotrophic lateral sclerosis-associated missense variants: activity biomarkers and structural insights

Kinase-dead controls, XIC quantification and phosphospecific antibodies establish pSer14, pThr156 and pSer418 as NEK1 autophosphorylation sites; a pThr156 assay shows ALS missense variants differ, with R261C reducing it most.

Recomb-Mix Cloud: a cost-efficient and scalable cloud-friendly pipeline for local ancestry inference

On the All of Us workbench, a Recomb-Mix-based cloud pipeline runs whole-genome local ancestry inference for an estimated $0.01 per sample, versus $0.43 for FLARE and $4.58 for RFMix.

High Quality, Long-Read Genome Assemblies of Two Virulent Field Isolates of Pyricularia oryzae from Portugal

Two Portuguese rice-blast fungus isolates were assembled from PacBio HiFi reads into near-complete genomes; one isolate lacks Avr-Pii, Avr-Pia and Avr-Pik yet remains virulent on two rice cultivars.

The Sorghum Lipid Database (SoLD): population-scale lipidomics linking environmental and genetic variation in the Sorghum Association Panel

SoLD, a leaf lipidomics resource (244 species) for the Sorghum Association Panel across two field trials, reveals low-input sulfoquinovosyldiacylglycerol depletion, triacylglycerol enrichment, and environment-specific GWAS loci.

Accurate ab initio gene prediction in eukaryotes with Tiberius in multiple clades

Extended Tiberius models outscore Helixer and ANNEVO on all 33 genomes from the five clades all three tools cover, and approach BRAKER3 accuracy in four clades without extrinsic evidence.

Comprehensive Lineage Tracing Maps the Landscape of Cell Fate Decisions in Mouse Embryogenesis

Prime-editing lineage trees for 16 mouse embryos (E7.5 to E10.0, >1.4 million cells) quantify fate restriction timing, progenitor numbers and lineage relationships, and are reproducible across replicate embryos.

Predicted Effector Gene Aggregation, Standards and Unified Schema (PEGASUS): A Community Framework for Effector Gene Reporting

PEGASUS defines a community reporting standard for GWAS predicted effector genes: a metadata record, a full locus-by-gene evidence matrix, and a derived author-prioritised gene list.

Multiscale harmonization, semantic integration, and immersive exploration of single-cell data in support of novel biological insights

A free Meta Quest virtual reality app harmonizes CODEX, Visium, Xenium, volumetric immunofluorescence and electron microscopy data from 5 organs into 4 scale levels using the Human Reference Atlas.

Human protein complex interfaces reveal candidate assembly roles for initiator methionine excision

N-terminal positions whose residue 2 permits methionine aminopeptidase cleavage are less often buried at human assembly interfaces (37.5% vs 47.5%), yet 175 such proteins stay engaged after boundary filtering.

Accessing Enzyme Kinetic Data and Prediction Methods at Scale

OpenKinetics Predictor unifies thirteen enzyme kinetic predictors behind one interface and API; on E. coli iML1515, eight kcat predictors correlate pairwise at r 0.08 to 0.67.

An RNA Language Model trained on sequence alone reveals the structural logic of Internal Ribosome Entry Sites

Continued pretraining of an RNA language model on picornaviral 5′ UTRs alone predicts IRES base pairs with median precision 0.80 versus 0.47 for Infernal, and reveals a Type II subclass.

An atlas of eukaryotic centromere architecture reveals recurrent evolutionary dynamics

Across 325 Darwin Tree of Life genomes, satellite-array and transposon-cluster centromeres are phylogenetically scattered, fitting a model of repeated interconversion; satellites share higher-order repeat structure but not sequence.

BOTANIC-1: a series of long-context plant genomic foundation models in the agentic era

Bidirectional Mamba2 plant genomic language models (318M to 3.2B parameters) trained on 320 land-plant genomes top a 22-task frozen-model aggregate; a small variant reaches 131,072 bp context.

Scrub Data: A Framework for Reproducible Data Curation with AI Coding Agents

Scrub Data routes AI-agent data edits through an API-enforced provenance graph of executable Python steps; it curated 89M wildlife GPS points into the 2.6M-point MoveBench benchmark.