multiome

A surviving beta cell subpopulation enriched in patients with T1D

Regulon-based clustering of islet scRNA-seq finds an IRF1-high, cytokine-driven beta cell state with reduced identity and autoantigen genes, enriched in type 1 diabetes donors.

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.

Layer-to-cell-class correspondence is gene-specific for pyroptosis-related transcription in human skin

Epidermal NLRP1, PYCARD and CASP4 versus dermal GSDMD polarity in systemic sclerosis skin is reproduced by same-donor cell-class pseudobulk for PYCARD and GSDMD, but rarely NLRP1.

Mammalian spermatogenesis at single-cell resolution downstream of genetic perturbations in meiotic double-strand break repair

Single-nucleus RNA+ATAC profiling of 32 mice shows asymmetric PRDM9 binding drives asynapsis, pachytene cell loss, aneuploidy and multi-megabase crossover redistribution, tuned by a chromosome 15 locus.

A novel RRM activity orchestrates ribosome homeostasis

40S subunit binding to a previously unrecognised RRM in LARP1 activates its TOP-binding HEAT repeats, licensing repression of ribosomal protein mRNA translation in human cells.

SCALE: Scalable Conditional Atlas-Level Endpoint transport for virtual cell perturbation prediction

A set-aware latent transport model predicts treated cell populations from unpaired controls, keeps perturbation-specific signal in CRISPR, drug and cytokine data, and guided a cytokine choice tested in three donors.

Extracellular matrix regulates lineage plasticity in prostate cancer through YAP/TEAD

Loss of extracellular matrix-integrin signaling switches off YAP/TEAD and lets prostate adenocarcinoma organoids turn neuroendocrine; LATS inhibition reverses it, and combined YAP, NOTCH and AR inhibition fully reprograms them.

Short RNA chaperones promote aggregation-resistant TDP-43 conformers to mitigate neurodegeneration

Short UG-rich RNAs bind and stabilize TDP-43 RNA-recognition motifs to allosterically destabilize its prion-like domain helical region, preventing aggregation and mitigating neurodegeneration in cells and mice.

Biodistribution of mRNA vaccines in rats: Enrichment in injection site and lymph tissues and rapid clearance without tissue persistence

Three mRNA-LNP products sharing one lipid matrix show rat intramuscular biodistribution (injection site, lymph nodes, spleen) and rapid clearance, with no Spike accumulation after repeat dosing.

An integrated single cell and spatial omics atlas of human prenatal development

Human Developmental Cell Atlas integrates ~4.6 million cells/nuclei from 4-22 post-conception weeks into 454 refined cell types and maps 114 spatial niches across 6PCW whole-embryo sections.

Oncogenic and tumor-suppressive forces converge on a progenitor niche at the benign-to-malignant transition

In mouse pancreatic cancer models, p53, CDKN2A and SMAD4 programs converge on a rare Kras-mutant progenitor-like state whose niche KRAS inhibition collapses and p53 loss expands.

HIF1α gates tendon response to overload and drives tendinopathy independently of vascular recruitment

Mechanical overload activates hypoxia-inducible factor 1-alpha (HIF1a) in tenocytes to drive tendinopathy independently of VEGFA-mediated vascular ingrowth, and tenocyte Hif1a deletion prevents overload-induced tendon degeneration in mice.

Alveolar epithelial cell plasticity and injury memory in human pulmonary fibrosis

Single-nucleus multiomic and ex vivo lung slice profiling of human idiopathic pulmonary fibrosis identifies Alveolar Intermediate cells bridging alveolar and Aberrant Basaloid states and reveals AP-1 chromatin injury memory.

Biomni: A General-Purpose Biomedical AI Agent

An LLM agent with a literature-mined environment of 150 tools, 105 packages and 59 databases plans in code, matching reported human accuracy on database and sequence question answering.

Mapping cells through time and space with moscot

moscot unifies optimal transport for temporal, spatial and spatiotemporal single-cell mapping, using multimodal cost spaces and low-rank solvers to scale to 1.7 million mouse embryo cells.

Dictionary learning for integrative, multimodal, and scalable single-cell analysis

Dictionary learning enables assumption-free cross-modality single-cell mapping via multi-omic bridge datasets and scales single-modality integration to millions of cells in under an hour via atomic sketching.

Decoding gene regulation in the mouse embryo using single-cell multi-omics

A mouse embryo multiome atlas (E7.5 to E8.75) and an unsupervised transcription factor binding predictor; a Brachyury knockout supports its network predictions in neuromesodermal progenitors.

Single-cell chromatin state analysis with Signac

Signac extends Seurat with a ChromatinAssay for single-cell chromatin and multimodal analysis, adds modified TF-IDF weighting, peak-gene linkage and mitochondrial-variant clonotyping, and scales to 733,526 cells.

Integrated analysis of multimodal single-cell data

Weighted-nearest neighbor (WNN) analysis in Seurat v4 learns per-cell modality weights to define cell states, enabling a 228-antibody human PBMC CITE-seq reference for RNA-only query mapping.

ArchR: An integrative and scalable software package for single-cell chromatin accessibility analysis

ArchR, an HDF5-backed R suite for end-to-end scATAC-seq analysis, outpaces SnapATAC and Signac and processes over 1.2 million simulated cells within 8 h on a laptop.