scRNA-seq

Single-Cell Proteo-Transcriptomic Profiling Uncovers Post-Translational Regulatory Layers in Human Hematopoiesis

This paper uses single-cell proteo-transcriptomic profiling to reveal post-translational regulatory mechanisms in human hematopoiesis, showing that protein-RNA correlations and transcription factor dynamics provide insights into lineage commitment and fate decisions.

Malignant and stromal partial EMT programmes and cetuximab outcome in head and neck cancer

The paper identifies malignant and stromal partial EMT programs in head and neck cancer and shows that malignant measures correlate with better cetuximab outcomes.

Microbial Invasion and Immunosuppression Drives Adenoma Progression in Early Colorectal Cancer Development

The paper shows bacterial invasion and neutrophil immunosuppression drive adenoma progression in a porcine FAP model using single-cell RNA sequencing and spatial transcriptomics.

Coordinated Enhancement of Molecular and Spatial Fidelity for Biological Inference in Spatial Transcriptomics

FOCUS improves spatial transcriptomics by coordinating molecular and spatial fidelity across multiple tasks and datasets, revealing clearer biological patterns in immunology, development, and oncology.

Engineered regulatory states resolve context-dependent genetics in macular degeneration

The paper uses CRISPR activation to engineer regulatory states in RPE-1 cells, revealing hidden genetic effects in AMD by analyzing chromatin accessibility and transcriptional interactions.

Human single-neuron correlates of somatosensation

The paper investigates the neural correlates of conscious tactile perception by analyzing single-neuron activity in PPC and S1 during vibrotactile stimulation.

Concurrent de novo inference of cell types and gene regulatory networks with NetMap

NetMap jointly infers cell-level gene regulatory networks and clusters cells based on shared regulatory programs, outperforming existing methods on synthetic data and reliably detecting regulons on real data.

A perturbation atlas of mouse neural organoids resolves macroglial reactivity and nominates drivers of degeneration

This study creates a perturbation atlas of mouse neural organoids to understand macroglial reactivity and identify drivers of degeneration.

A Unified Comparison of 10X Genomics and Parse Biosciences scRNA-seq Technologies

This study compares 10X Genomics and Parse Biosciences scRNA-seq technologies, finding platform-specific biases in gene counts and composition, with Parse showing GC-content bias and potential nuclear RNA enrichment.

DAP12-deficient microglia adopt a TREM2-independent antigen-presenting state with a glial-to-neuronal cascade in Nasu-Hakola disease

The paper profiles NHD microglia and shows they adopt an antigen-presenting state without TREM2 dependence, triggering glial-to-neuronal changes.

Cellular and molecular census of the pleiotropic disease locus Negr1 in zebrafish

The paper identifies cell types expressing Negr1 in zebrafish and links its expression to diverse traits, suggesting broad gene action.

Cause-excluded Effect Evaluation: a framework for the faithful assessment of genetic perturbation target identification

The paper introduces CEE, a framework to assess genetic perturbation target identification by eliminating evaluation artefacts, and finds simple methods outperform complex models.

Restoration of deficient IL-15 signaling enhances innate lymphoid cell immunity in brain metastasis

This study shows that restoring IL-15 signaling enhances group 1 ILCs' anti-tumor activity in brain metastasis, reducing tumor burden through improved cytotoxicity and tissue residency.

Cell cycle exit is required for differentiation and cell fate diversification but not neoblast specialisation in planarians

This study shows cell cycle exit is necessary for terminal differentiation but not neoblast specialization in planarians, with lineage commitment occurring in cycling neoblasts.

Human Th17 state classification reveals a selective vulnerability in acylcarnitine metabolism in type 2 diabetes

The paper classifies human Th17 cells into non-pathogenic and pathogenic states and identifies acylcarnitine metabolism as a vulnerability in type 2 diabetes.

Multi-omic spatial mapping of the human habenula defines the molecular and anatomical organization of medial and lateral subregions

This study maps the spatiomolecular organization of the human habenula using multi-omic approaches, identifying molecular signatures and spatial domains linked to psychiatric disorders.

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.

Point-Process Modelling of Cell-Type Interaction Structure in CosMx Glioma Data for Hypothesis-Driven Tumor Inference from scRNA-seq

The paper develops a spatial-statistical framework to model cell-type interactions in glioblastoma using CosMx data, revealing patient-specific spatial patterns and their molecular correlates.

scPRIME-seq uncovers synchronized multimodal molecular collapse facilitated by pre-neoplastic epigenetic burden in prostate cancer

The paper introduces scPRIME-seq, a multimodal single-cell platform, and finds pre-neoplastic epigenetic changes drive tumor progression in prostate cancer.

Perturbation of the replication stress-ATR axis accelerates human erythroid differentiation but blocks terminal maturation

The paper shows that replication stress from chemotherapy accelerates erythroid differentiation but blocks terminal maturation, leading to impaired red cell output.

Systematic evaluation of integration methods and parameters on single-cell RNA-sequencing biological insights: a case study on cattle embryos.

The paper evaluates integration methods and parameters on cattle embryos to assess their impact on biological insights, finding that parameter choices affect cell type classification and functional interpretation.

The dark transcriptome mouse organogenesis cell atlas

The paper presents a single-cell atlas of noncoding RNAs during mouse organogenesis, revealing their cell-type-specific and lineage-regulated expression patterns.

STEER-seq: a recombinase based platform for pooled multimodal single-cell perturbation screening

STEER-seq enables pooled single-cell perturbation screening in hiPSCs by using defined genomic integration and barcode tracking to study transcription factor effects on cell identity.

Tumour-stroma signaling drives a reversible program with neural-like features in cancer-associated fibroblasts

The paper identifies tumor-derived signals that induce a reversible neural-like program in cancer-associated fibroblasts and shows it is regulated by growth factors and MAPK/ERK signaling.

Ligand-specific endothelial Notch signaling coordinates brain pericyte specification and expansion

This study identifies ligand-specific endothelial Notch signaling as a mechanism coordinating brain pericyte specification and expansion in zebrafish.

High-throughput identification of chromatin-opening transcription factors

The paper identifies chromatin-opening transcription factors in mouse embryonic stem cells using CRISPRa screens, revealing autonomous, opportunistic, and hierarchical mechanisms.

Spatiotemporal Mapping of Glomerular Endothelial Regeneration Identifies Apold1 as an Intrinsic Regulator of Repair

This study identifies Apold1 as a key regulator of glomerular endothelial regeneration using single-cell RNA sequencing and spatial transcriptomics in a mouse model.

Neutrophils orchestrate pre-metastatic immunosuppressive bone marrow remodeling during prostate cancer metastasis

This study identifies IGF1R-dependent neutrophil reprogramming in the bone marrow microenvironment during prostate cancer metastasis and shows its therapeutic targeting potential.

Paired single-nucleus and spatial transcriptomics of the lung adenocarcinoma invasion sequence reveal niche domains and candidate reversal compounds

This study uses paired single-nucleus and spatial transcriptomics to analyze lung adenocarcinoma progression and identifies potential reversal compounds.

Multi-Omic and Spatial Profiling Defines Outcome-Associated Tumor States in Head and Neck Adenoid Cystic Carcinoma

The paper integrates multi-omic and spatial data from HNACC tumors to identify outcome-associated tumor states, finding that aggressive tumors adopt a MYC/E2F-driven luminal state and develop a four-gene classifier for survival prediction.