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1073 results

Full text 2026

Defining neurovascular ecosystem states with single-cell multi-omics and machine learning: insights into cerebrovascular remodeling in the tumor context

Kong D, Chen Y, Wang W, et al.

<h4>Objective</h4>To define neurovascular ecosystem states within the tumor microenvironment and elucidate the regulatory basis of cerebrovascular remodeling through single-cell multi-omics and interpretable machine learning.<h4>Methods</h4>An orthotopic murine brain tumor model was established. Single-cell RNA sequencing (scRNA-seq), …

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Epigenetics Single-Cell Transcriptomics

Full text 2026

Detailed single-cell mapping of the transcriptional response to a virus infection driven by copy-back viral genomes

Yang Y, Achouri E, Tambo M, et al.

The antiviral response to several clinically significant viruses, including respiratory syncytial virus and parainfluenza virus, is driven by copy-back viral genomes (cbVGs) generated during virus replication. However, the broader impact of cbVGs on the functional …

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Single-Cell Transcriptomics

Full text 2026

Study on the Potential Molecular Mechanism of Keloid Disease Associated With Single Cell Combined Mendelian Randomization

Wu HH, Meng YX, Liu JH, et al.

<h4>Background</h4>Keloids are pathological scars with incompletely understood pathogenesis. This study aims to identify the key genes and regulatory networks potentially involved in keloid formation by integrating single-cell transcriptomics (scRNA-seq), protein quantitative trait loci (pQTL), Mendelian …

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Single-Cell Transcriptomics

Full text 2026

Single-cell profiling reveals epithelial and immune responses in BK polyomavirus-infected human kidney biopsies

Marvin T, Sealfon R, McCown PJ, et al.

INTRODUCTIONBK polyomavirus (BKV) infection is associated with injury and subsequent graft loss due to the extent of injury or rejection. However, the molecular mechanisms driving injury and subsequent adverse outcomes remain poorly understood.METHODSIn a cross-sectional …

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Single-Cell Transcriptomics

Full text 2026

scMILD: Single-cell multiple instance learning for sample classification and associated subpopulation discovery

Jeong K, Choi J, Kim K.

Linking cellular states to clinical phenotypes is a major challenge in single-cell analysis. Here, we present single-cell multiple instance learning for sample classification and associated subpopulation discovery (scMILD), a weakly supervised multiple instance learning framework …

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Bioinformatics Single-Cell Transcriptomics

Full text 2026

Estimating time since influenza virus exposure using single-cell proteomic data

Rizzo Nervo K, Hajiakhoond Bidoki N, Chen H, et al.

<h4>Introduction</h4>Determining when the onset of a respiratory infection occurred is important for effective clinical management and can aid in mapping transmission events. However, current diagnostic assays report only pathogen detection status and do not provide …

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Metagenomics Single-Cell

Full text 2025

Pattern Learning and Knowledge Distillation for Single-Cell Data Annotation

Zhang M, Ren B, Li X.

Transferring cell type annotations from reference dataset to query dataset is a fundamental problem in AI-based single-cell data analysis. However, single-cell measurement techniques lead to domain gaps between multiple batches or datasets. The existing deep …

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Single-Cell

Full text 2026

A unified framework for selecting and evaluating cell-type-specific gene co-expressions in single-cell data

Shan X, Lin Y, Zhao H.

Cell-type-specific gene co-expression networks are widely used to characterize gene relationships. Although many methods have been developed to infer such co-expression networks from single-cell data, the lack of consideration of false positive control in many …

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Single-Cell

Full text 2026

Single-cell landscape of immune cells in multiple autoimmune diseases

Zhu L, Sun W, Chen K, et al.

Autoimmune pathologies arise from dysregulated immune activation, yet conserved molecular programs across autoimmune contexts remain incompletely characterized. Here, we analyzed integrative single-cell RNA sequencing data of over 1.3 million cells from 239 samples spanning six …

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Bioinformatics Single-Cell Transcriptomics

Full text 2025

Single-cell RNA-seq data normalization: A benchmarking study

Ge Q, Sheng Y, Lu J, et al.

This study examines the noise and biases introduced by technical factors in single-cell RNA sequencing (scRNA-seq) data, presenting a thorough benchmarking analysis of six widely utilized normalization methods. The evaluation of these methods is conducted …

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Single-Cell Transcriptomics

Full text 2026

Single-cell Raman insights into microbial strategies for sustainable phosphorus mining and recycling

Sun P, Pan H, Cheng D, et al.

Phosphorus (P) management faces a dual crisis of resource depletion and eutrophication, underscoring the need for a sustainable P cycling model. This review systematically elaborates on the microorganism-driven "Mobilization, Retention and Buffering" (MRB) strategy to …

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Metagenomics Single-Cell

Full text 2026

Ion-Channel-Mediated Drug Repurposing Opportunities Validated by Single-Cell Perturbation in Colorectal Cancer

Dong Z, Meng X, Wang L.

Colorectal cancer (CRC) remains a leading cause of cancer mortality, yet no systematic effort has linked druggable CRC driver genes to downstream ion channel effectors. We integrated differential expression analysis, weighted gene co-expression network analysis …

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Single-Cell

Full text 2026

Molecular insights into CRIP1 as an immunometabolic regulator revealed by CRIP1 knockout and single-cell transcriptomics

Kim D, Woo BH, Kim SH, et al.

Cysteine-rich intestinal protein 1 (CRIP1) was first identified as a metabolism-related gene nearly four decades ago, yet its precise biological function remains poorly defined. More recently, CRIP1 has been implicated in several cancers, including hepatocellular …

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Single-Cell Transcriptomics

Full text 2026

Single-cell-based identification of drug synergy with immunotherapy via tumor microenvironment remodeling

Wang Z, Hu J, Liu K, et al.

<h4>Background</h4>Identifying effective therapeutic drugs in the intricate tumor microenvironment (TME) is challenging, further complicated by the lack of a systematic framework for analyzing TME perturbations in response to therapeutic interventions.<h4>Methods</h4>To address this, we established the …

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Bioinformatics Single-Cell Transcriptomics

Full text 2026

Long COVID: Deep single-cell immunophenotyping and machine learning reveal a general signature for fatigue

Sommen SL, Segtnan S, Selvakumar J, et al.

BACKGROUND: The post COVID-19 condition, commonly referred to as “Long COVID” (LC), is a constellation of long-lasting and debilitating symptoms following acute SARS-CoV-2 infection, which closely resembles other post-infective fatigue states. The underlying immunological disturbances …

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Single-Cell

Full text 2026

Single-cell insights into cisplatin resistance mechanisms in bladder cancer tumor microenvironment

Xu L, Lin Y, Shi G, et al.

This study integrates single-cell RNA sequencing with in vitro experimental validation to elucidate the molecular mechanisms underlying cisplatin resistance in bladder cancer (BC) and to characterize cellular heterogeneity within the tumor microenvironment. By analyzing integrated …

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Single-Cell Transcriptomics

Full text 2026

singIST: An integrative method for comparative single-cell transcriptomics between disease models and humans

Moruno-Cuenca A, Picart-Armada S, Bogle R, et al.

<h4>Motivation</h4>Disease models are fundamental tools in drug discovery and early-stage drug development, but they only approximate human disease, and selecting a suitable model is challenging. Quantitative computational methods exist to assess molecular resemblance to human …

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Bioinformatics Single-Cell Transcriptomics

Full text 2026

Identification of Smmhc-expressing mesenchymal cells in orofacial bone at single-cell resolution

Fan Y, Wei Y, Wu Z, et al.

No abstract available.

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Single-Cell

Full text 2026

Integrate single-cell and transcriptome analyses to explore the prognostic genes related to TRPM4 in bladder cancer

Zhao Q, Qin Z, Liu R, et al.

Bladder cancer (BLCA) is a common malignancy of the urinary system, yet the therapeutic relevance of transient receptor potential cation channel subfamily M member 4 (TRPM4) remains unclear. By integrating single-cell and whole-genome transcriptomic data, …

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Single-Cell Transcriptomics

Full text 2026

sCellST predicts single-cell gene expression from H& E images

Chadoutaud L, Lerousseau M, Herrero-Saboya D, et al.

Understanding the spatial organization of individual cell types within tissue and how this organization is disrupted in disease, is a central question in biology and medicine. Hematoxylin and eosin-stained slides are widely available and provide …

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Single-Cell