scRNA-seq

Keratinocyte FABP5 mediates saturated fat-induced MAPK/CCL20 signaling in psoriatic inflammation

Early-life human lymphopoiesis generates a distinct B-cell lineage

The paper identifies a distinct B-cell lineage generated during early human lymphopoiesis that shapes antibody specificity before birth.

scIRES-seq reveals multimodal molecular heterogeneity in CTCs from small cell cervical cancer

This study introduces scIRES-seq to analyze CTCs from cervical cancer, revealing multimodal molecular heterogeneity through integrated genetic, epigenomic, and transcriptomic profiling.

Revealing pan-cancer clonal niches of T cells from single-cell RNA sequencing using contrastive learning

CloneTrast uses contrastive learning to infer T-cell clonal niches from single-cell RNA-seq, identifying NK-like niches linked to poor immunotherapy response across cancers.

A multimodal precision oncology platform integrating genomics,single-cell transcriptomics, and functional drug screening expandstherapeutic options in pediatric brain tumors

A constitutively active cortical nitrate-uptake cell state underlies nitrogen-use efficiency in perennial ryegrass

The paper identifies a constitutively active cortical nitrate-uptake cell state in perennial ryegrass linked to nitrogen-use efficiency, showing differences in transporter expression between high- and low-NUE genotypes.

Trp53 heterozygosity defines novel states impacting tumor plasticity and progression in Kras-initiated non-small cell lung cancer

This study shows that TP53 heterozygosity in Kras-mutant lung cancer affects tumor plasticity and progression, with distinct genomic and survival outcomes compared to complete TP53 loss.

cit_gsa: gene set analysis for scRNA-seq with covariate adjustment

cit_gsa is a single-cell RNA-seq gene set analysis method that allows covariate adjustment and handles multiple conditions, showing improved performance in complex scenarios.

FLASH X-rays preserve neutrophil chromatin to boost antitumor immunity

This study shows FLASH X-rays preserve neutrophil chromatin, reducing NET formation and enhancing antitumor immunity when combined with anti-PD-1 therapy.

Deep-learning-driven tumor microenvironment profiling improves immunotherapy response prediction

EcoNet improves immunotherapy response prediction by modeling tumor microenvironment signaling networks, outperforming existing methods in AUC and stratifying ccRCC patients by clinical outcome.

Direct 3D isolation in gelatin methacryloyl microbeads versus conventional 2D isolation and culture: a trade-off between mesenchymal stromal cell purity and niche-associated transcriptional profiles

This study compares 3D GelMA microbeads with 2D culture for MSC isolation, finding 2D yields purer MSCs while 3D retains niche-associated transcriptional profiles.

PIEZO1 marks a low neuroendocrine state and supports cisplatin tolerance in small cell lung cancer

This study identifies PIEZO1 as a marker of low neuroendocrine state and a contributor to cisplatin tolerance in SCLC through mechanistic and multi-omics analyses.

A split-control criterion for few-shot adaptation in single-cell perturbation prediction

This paper introduces SafeDelta, a split-control criterion for few-shot adaptation in single-cell perturbation prediction, showing it improves reproducibility and identifies biological programs.

RNA evidence supports clinical stage antibody drug targets in oncology

The paper evaluates whether single-cell RNA-seq improves the prioritization of antibody-based oncology targets by combining tumor specificity, normal safety, and blood sink features.

A versatile set of computational tools for inference of genetic ancestry from human molecular data

The paper introduces RAIDS, a toolset for inferring genetic ancestry from various sequence data, including cancer and low-coverage scenarios.

BioMod: Biological Module Tokenization for Single-Cell Foundation Modeling

BioMod introduces biological modules as intermediate units for single-cell foundation modeling, achieving state-of-the-art performance in cell-type annotation and drug-response prediction.

Autonomous Dampening of Wnt Signaling Selects Zebrafish Spinal Cord Progenitors for an Oligodendrocyte Fate

The paper identifies pre-OPCs in zebrafish spinal cord and shows that Wnt signaling modulation influences oligodendrocyte fate through gene expression and chromatin accessibility.

BCR repertoire analysis and cloning of antibody candidates targeting native and Asp7-isomerized β-amyloid

The paper demonstrates a repertoire-guided workflow to prioritize antibody candidates targeting β-amyloid and its isoAsp7 proteoform, identifying potential heavy-light chain combinations through computational and experimental methods.

Single-cell variant landscape of the human mitochondrial genome reveals cell type-specific functions and disease mechanisms

The paper presents scMOCHA, a tool to analyze mtDNA heteroplasmy from scRNA-seq data, revealing cell type-specific mtDNA variants and disease mechanisms in hematopoietic cells.

Single-Cell Multimodal Profiling Reveals Maternal Diabetes-Nkx2-5 Interaction in Congenital Heart Disease in a Genetic Model Recapitulating Human Embryopathies

The paper shows that maternal diabetes and Nkx2-5 haploinsufficiency together cause severe cardiac defects in mice, with single-cell multiomic data revealing transcriptional and chromatin changes.

Preoptic transcriptomes during courtship reveal the molecular basis of behavioral coordination in a highly social cichlid

The paper examines transcriptome synchronization in the preoptic area of male-female cichlid pairs during courtship, revealing sex-specific gene expression patterns linked to reproductive behavior.

The Human Gut Cell Atlas v1.0: A Unified, Community-Built Reference of Cellular Diversity Across the Gut

The paper presents the Human Gut Cell Atlas v1.0, a unified reference of gut cell diversity, revealing how tissue structure influences cellular composition and enabling disease and organoid analysis.

scGSCA: gene-set differential co-expression analysis for single-cell RNA sequencing data

scGSCA analyzes single-cell RNA sequencing data to detect differential gene-set co-expression across phenotypes, identifying pathway changes missed by bulk methods.

AnnZarro: scalable, interactive exploration of cell-by-cell and gene-by-gene relationships in single-cell data

AnnZarro enables interactive exploration of cell-by-cell and gene-by-gene relationships in single-cell data through a browser-based viewer linked to AnnData objects.

An integrated multi-omic atlas of the choroid plexus highlights conserved molecular programs of epithelial function

This study integrates multi-omic data from mouse and human choroid plexus to identify conserved molecular programs of epithelial function across species.

Intersectional genetic targeting of molecularly distinct melanin-concentrating hormone neuron subpopulations reveals distinct and overlapping subcircuit architecture

The paper identifies two molecularly distinct MCH neuron subpopulations in the LHA and characterizes their unique and overlapping anatomical projections using genetic and imaging approaches.

Beyond the Final Layer: Evaluating Single-Cell Foundation Model Representations for Molecular Prediction

This paper evaluates the performance of intermediate layers in single-cell foundation models for cell-type and perturbation prediction, finding that some layers perform as well as final layers.

Benchmarking single-cell foundation models reveals an advantage in the low-data regime for cell-type and disease-state prediction

The paper benchmarks single-cell foundation models for cell-type and disease-state prediction, finding they outperform baselines in low-data regimes.

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.

Optimizing copy number profiles for tumor cell phylogeny inference from low-coverage single-cell sequencing data

This study shows that selecting optimal bin sizes improves tumor cell phylogeny inference from low-coverage single-cell sequencing data.