scRNA-seq

De novo lipogenesis controls antigen presentation and metastatic immune escape in triple-negative breast cancer.

FASN-driven lipogenesis sustains EGFR palmitoylation and PI3K-AKT-mTOR signaling, suppressing tumor MHC-I antigen presentation; blocking it curbs TNBC metastasis in mice via CD8 T cell recognition.

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.

Multi-omics analysis reveals chromatin and transcriptomic remodeling in hippocampal CA1 following adolescent social isolation

Two weeks of post-weaning isolation in male mice altered expression of 106 CA1 genes, enriched for myelination, while chromatin accessibility shifted only at nominal significance and tracked expression weakly.

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.

The epidermal growth factor (EGF) receptor family network in cardiac hypertrophy and heart failure

EGFR-family ligand mRNAs shift in failing human hearts; NRG1 and EGF drive distinct, differently ERBB2-dependent transcriptional programmes in rat cardiomyocytes; afatinib blunts mouse angiotensin II hypertrophy but worsens fibrosis.

Gut microbial interaction networks control autoimmunity to neuroretina

Akkermansia expansion reduces short-chain fatty acid-producing Firmicutes in human-flora uveitis mice, raising Th1 responses and disease; a Verrucomicrobia/Firmicutes ratio is elevated in uveitis, MS and Crohn's patients.

Prenatal immune priming to Plasmodium falciparum is characterized by multi-lineage T-cell responses that are influenced by maternal microchimerism and predict malaria outcomes

Maternal microchimerism in Malian cord blood is associated with fewer Pf-responsive ZBTB16+ CD4 and Vγ9Vδ2 T cells, and with infant malaria outcomes.

Gene Regulatory Network Inference reveals tcf4 as a key a player in neuroblastoma gene expression circuitry

Mechanistic stochastic gene regulatory network inference on neuroblastoma tumoroid scRNA-seq predicts TCF4 as a hub whose loss slows chromaffin-to-sympathoblast progression, supported by JQ1 treatment ex vivo.

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.

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.

PIE: Generalizing perturbation effects across unseen perturbations, contexts and datasets

Predicting differentially expressed genes and expression shifts per condition from database embeddings plus per-gene evidence, PIE reaches 1.2–3.2 times the best baseline's AUPRC on unseen contexts, perturbations and datasets.

Cysteine reactivity profiling links metabolic rewiring to the dysfunctional human T cell proteome.

In chronically stimulated human T cells, suppressed oxidative metabolism and nucleotide loss accompany MAP2K4 activation. Inhibiting MAP2K4 (with the MKK4/7 inhibitor BSJ-04-122) restored tumor-cell killing in vitro.

replicateFest: An R Package and Shiny App for Analysis of T Cell Receptor Repertoire Data from the Functional Expansion

replicateFest uses negative binomial models for replicated and Fisher's exact tests for unreplicated FEST TCR-seq to call antigen-expanded clonotypes, recovering all nine published HIV-1 responders.

Dataset structure outweighs method choice in single-cell cell-type annotation

In a 63-tool benchmark, dataset identity explained ≈84% of Cohen's κ variance on synthetic data versus ≈4% for tool identity, and k-nearest-neighbor (kNN) purity predicted accuracy near-linearly (R² = 0.85–0.99).

Transcriptionally distinct atypical B cell populations contribute to insulin autoreactivity and show differential activation, isotype switching, and somatic hypermutation in early-stage type 1 diabetes individuals

B cells from 24 early-stage type 1 diabetes individuals include four atypical clusters differing in switching and mutation; Cluster 10 had the highest insulin-binding antibody rate (5/16).

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.

Tfh dysfunction is associated with poor responses to HBV vaccination

HBV vaccine-draining lymph node biopsies tie low antibody titers to reduced, interferon-skewed GNG4+ germinal center T follicular helper cells; public B cell clonotypes did not track response.

CycloCross: Adversarial single-cell RNA-seq data translation across species

Translating cells between mouse, macaque and human scRNA-seq with a CycleGAN, without ortholog mapping, preserved developmental time structure, imputed missing states and produced more realistic synthetic cells than scGAN.

TxCyto: A machine learning framework for estimating cytokine activity from whole transcriptome

A fully connected neural network trained on 9491 TCGA bulk tumor transcriptomes estimates activity of 645 cytokines and secreted proteins, checked against perturbation and protein data.

AnnoAudit: a marker-based protocol for auditing single-cell atlas annotations reveals systematic, state-dependent annotation failure in a widely used traumatic brain injury resource

A marker audit finds 97.9% of CEREBRI's 45,051 official 'glutamatergic neuron' cells are not glutamatergic (four-check composite 82.6%), creating false ion-channel and OXPHOS signals; true neurons show acute KCNC3 up-regulation.

sfate: Schur-free, target-conditioned absorption probabilities for scalable single-cell fate analysis

sfate computes annotation-targeted absorption probabilities by column-wise GMRES on a latent kNN graph, skipping Schur decomposition; a 74,984-cell mouse microglia analysis peaked at 1.76 GiB.

Galectin and Myc enable cochlear progenitor expansion in vitro and in vivo

Single-cell profiling of mouse greater epithelial ridge (GER) organoids points to galectin-1 and Myc as drivers of cochlear progenitor expansion. Myc overexpression also yields organoids from post-hearing-onset cochlear epithelium.

Senescence-directed nanotherapy ameliorates fibrosis and overcomes immune exclusion in cancer

P-selectin-targeted fucoidan nanoparticles carrying Navitoclax or dBET6 deplete a senescent-like, lipid-associated macrophage subset, reverse mouse liver and lung fibrosis with less toxicity, and restore checkpoint therapy response in fibrotic tumors.

STAR Suite: Transcriptomics processing in a single binary through AI-assisted development

Open-source STAR binary for five transcriptomic assays runs 3.9- to 6.2-fold faster than Cell Ranger 9.0.1 for scRNA-seq and Perturb-seq, 17- to 41-fold for Flex, with closely concordant counts.

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.

The Unreasonable Effectiveness of Cell Types in Describing Neuronal Physiological Features

On 495 human Patch-seq neurons, cell type means predicted electrophysiology better than neural networks on scGPT embeddings or gene panels; fusing scGPT embeddings with cell type labels predicted best.

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.

Chemotherapy-Induced Oral Mucosal Injury Is Defined by p53 Activation, Cell Cycle Arrest and Diverse Epithelial Progenitor Dynamics

In 5-FU-treated mice, oral and intestinal epithelial atrophy stems from p53-linked cell cycle arrest, not apoptosis, while a chemoresistant AP-1/p53 basal cluster expands in tongue.

FlashDeconv reveals resolution horizons in atlas-scale spatial transcriptomics

Leverage-weighted sketching plus sparse spatial regularization deconvolves 1.6 million Visium HD bins in 153 seconds on commodity hardware, revealing tissue-specific resolution limits where cell-type co-localization can reverse sign.

SPP1+ Microglia Are Associated with Neuroimmune Rewiring and Glutamatergic Neuronal Injury in ART-Suppressed People Living with HIV

In ART-suppressed human brain, an SPP1+ activated microglial subset holds most detected HIV RNA and shows chronic interferon-I and MHC-I signatures, alongside complement signaling and neuronal loss.