scRNA-seq

Dynamic Tumor Immune Microenvironment Remodeling Predicts Response of Checkpoint Inhibitor Therapy

The paper maps treatment-associated changes in the tumor immune microenvironment using single-cell RNA sequencing and identifies transition patterns that predict response to checkpoint inhibitor therapy.

Clear cell renal cell carcinoma consensus transcriptomic programs reveal converging trajectories towards aggressive disease

The paper identifies 17 consensus transcriptomic programs in ccRCC using NMF and links them to cellular sources and clinical outcomes, revealing converging trajectories toward aggressive disease.

Distal-less homeobox 5 gives rise to myofibroblastic carcinoma-associated fibroblasts to promote collective breast cancer invasion

This study identifies DLX5 as a key driver of myofibroblastic carcinoma-associated fibroblasts (myCAFs) in breast cancer, showing its role in promoting tumor invasion through TGF-β signaling.

Endocrine Neural Interactions Regulate Antral CCK2R+ Stem Cells in Gastric Inflammation and Preneoplasia

The paper shows that gastrin loss activates a vagal reflex that promotes CCK2R+ stem cell expansion and preneoplasia in gastric inflammation.

Predicting cellular responses to perturbation across diverse contexts with STATE

State, a set-based transformer trained on over 100 million perturbed cells, predicts perturbation responses in new cellular contexts better than mean, linear and deep learning baselines.

The insect brain is specified by a conserved transcriptional program distinct from the segmental CNS

The paper identifies brain-specific transcription factors in insect neuroblasts, revealing a distinct regulatory program for the insect brain compared to the posterior CNS.

Metastatic founder cell candidates resemble preimplantation embryonic blastomeres

The paper identifies metastatic founder cell candidates in bone marrow that resemble preimplantation embryonic blastomeres, linking cancer metastasis to early embryonic development mechanisms.

Single-Cell Inference of Structural States Of Ribosomes

SCISSOR infers global translation activity in single cells using ribosomal RNA protection signatures, revealing cell cycle and differentiation-related translation variations in human and murine cells.

Lineage-specific X chromosome inactivation escape and skew underlie sex-biased immune gene dosage and deleterious variant exposure

This paper introduces scDaisyChain to analyze X chromosome inactivation escape and skew in immune cells, revealing lineage-specific effects on gene dosage and variant exposure in healthy and autoimmune disease contexts.

Transcriptomic characteristics along the longitudinal axis of the hippocampus and medial entorhinal cortex across species

The paper uses spatial transcriptomics and single-nucleus RNA sequencing to analyze dorsoventral molecular organization in hippocampus and medial entorhinal cortex across five species, identifying conserved and species-specific patterns.

In vivo multimodal lineage tracing of mammalian development by DeepTrack barcoding

The paper introduces DeepTrack, a lineage tracing model that combines cellular barcoding with single-cell multi-omics to study cell fate transitions and molecular changes during mammalian development.

Enhancer buffering protects dosage-sensitive housekeeping genes during vulnerable developmental transitions

TCOF1 dosage is limiting for transitional human neural crest cells; its enhancers buffer promoter output against MYC fluctuations rather than amplifying it, a pattern seen across 14 dosage-sensitive promoters.

seqproc: An efficient, flexible, and concise tool for sequence geometry description and transformation

seqproc is a tool that efficiently compiles sequence-geometry descriptions into execution graphs, outperforming existing tools in speed and memory usage for single-cell RNA-sequencing protocols.

mmVelo: A deep generative model for estimating cell state-dependent dynamics across multiple modalities

mmVelo estimates cell state-dependent dynamics across multiple modalities using deep generative modeling, validated on mouse and human data.

COBRA: Cell-type-specific Orthogonal Batch effect Removal Algorithm in single cell RNA-sequencing data

COBRA removes cell-type-specific batch effects in scRNA-seq data, preserving biological differences and improving integration across datasets.

Closing the fusion-detection gap in single-cell RNA-seq with a scalable, probe-based workflow

The paper introduces a probe-based workflow to detect oncogenic gene fusions in single-cell RNA-seq, validated in cancer cell lines and pediatric B-ALL cohorts.

Decoding Radiation-Induced Transcriptomic Signatures of Human Leukocytes using Long-Read RNA-Seq: Clinical and Biodosimetric Implications

Nanopore long-read RNA-seq of leukocytes from 4 Gy X-irradiated blood (three donors, 6 h) recovers p53 signaling and reveals isoform-level regulation plus candidate unannotated FBXO22/PHPT1 isoforms.

Decoding the Transcriptome Dark Matter: Construction of Single-Cell Whole-Transcriptome Regulatory Atlas by dropTotal

The paper introduces dropTotal, a method for single-cell total RNA-seq that detects both coding and non-coding transcripts, and applies it to human glioma nuclei to uncover ncRNA-driven regulatory landscapes.

fastCNV: Fast and accurate copy number variation prediction from High-Definition Spatial Transcriptomics and scRNA-Seq Data

fastCNV predicts copy number variations from spatial transcriptomics and scRNA-seq data, showing high accuracy and speed improvements over existing methods.

SALRR: Scalable Analysis of Long-Read RNA-Seq Enables Comprehensive Transcriptome Profiling in Human Brain

SALRR provides a scalable platform for long-read RNA-seq analysis, identifying novel splice variants in human brain tissue.

Genome-scale perturb-seq in primary human CD4+ T cells maps context-specific regulators of T cell programs and human immune traits

Genome-scale CRISPRi perturb-seq in 22 million primary human CD4+ T cells maps stimulation-specific regulators and links perturbation signatures to T cell states and autoimmune genetics.

Cross-chemistry single-nucleus RNA-seq identifies gene length and CpG-island promoters as determinants of transcriptional noise.

The paper compares two scRNA-seq platforms to quantify transcriptional noise and identifies gene length and CpG-island promoters as factors influencing noise levels.

scLANTERN: High-Throughput Retrospective Lineage Tracing via Full-Length Single-Cell Transcriptomics and Expressed Repeat Variation

This paper introduces scLANTERN, a method using full-length single-cell transcriptomics and expressed repeat variation to enable high-throughput retrospective lineage tracing in cancer.

Multi-compartment immune and tumor cell reprogramming by IFNa2 overcomes colon cancer immunotherapy resistance

This paper shows that delivering IFN2 via LNPs reprograms tumor and immune cells in ICI-resistant CRC, enhancing PD-1 blockade efficacy and reducing metastasis.

scProtoTransformer: Scalable Reference Mapping Across Molecules, Cells and Donors

scProtoTransformer provides a scalable reference mapping framework across molecular, cellular, and donor levels using a prototype-based Transformer model with improved interpretability and performance.

CD1b-specific T cells are transcriptionally closer to conventional CD4 T cells than to innate-like NKT and MAIT cells

The paper compares the transcriptional profiles of CD1b-specific T cells with conventional and innate-like T cells, finding CD1b-specific cells are more similar to conventional T cells.

Disrupting Myeloid Persistence and Replenishment Enables Sustained Control of Esophageal Squamous Cell Carcinoma

The paper shows that combining CSF1R inhibition with low-dose decitabine suppresses both myeloid persistence and replenishment, leading to sustained control of ESCC in multiple models.

G2T: Tissue Reconstruction from Gene Expression via Embedding-Distance Flow Matching

G2T reconstructs tissue geometry from gene expression data using a generative deep learning model, outperforming existing methods on spatial reconstruction benchmarks.

Generation of effector CD4+ T cells from Human iPSC

This paper generates functional CD4+ T cells from human iPSC by modulating Notch signaling, showing cytokine diversity and transcriptional similarity to blood CD4+ T cells.

The Neural Impact Score benchmarks drugs in Multi-Region Brain Organoids

The paper introduces the Neural Impact Score (NIS) to evaluate drug effects on brain organoids across multiple biological categories, demonstrating its utility in cross-species drug benchmarking.