Search Results - "Single-Cell Gene Expression Analysis"

Active learning framework leveraging transcriptomics identifies modulators of disease phenotypes.

Authors: DeMeo B Nesbitt C Miller SA et al.

Source: Science (New York, N.Y.) [Science] 2025 Nov 27; Vol. 390 (6776), pp. eadi8577. Date of Electronic Publication: 2025 Nov 27.

Publication Type: Journal Article

Journal Info: Publisher: American Association for the Advancement of Science Country of Publication: United States NLM ID: 0404511 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1095-9203 (Electronic) Linking ISSN: 00368075 NLM ISO Abbreviation: Science Subsets: MEDLINE

MeSH Terms: Deep Learning* , Drug Discovery*/methods , Single-Cell Gene Expression Analysis*, Humans ; Algorithms ; Drug Evaluation, Preclinical/methods ; Phenotype

Unraveling Diabetes Mechanisms: A Computational scRNA-Seq Approach to Inflammation and Diabetes.

Authors: Kondaki K Lazaros K Vrahatis AG

Source: Advances in experimental medicine and biology [Adv Exp Med Biol] 2026; Vol. 1487, pp. 551-557.

Publication Type: Journal Article

Journal Info: Publisher: Kluwer Academic/Plenum Publishers Country of Publication: United States NLM ID: 0121103 Publication Model: Print Cited Medium: Print ISSN: 0065-2598 (Print) Linking ISSN: 00652598 NLM ISO Abbreviation: Adv Exp Med Biol Subsets: MEDLINE

MeSH Terms: Diabetes Mellitus*/genetics , Diabetes Mellitus*/metabolism , Inflammation*/genetics , Inflammation*/metabolism , RNA-Seq*/methods , Single-Cell Gene Expression Analysis*/methods, Humans ; Computational Biology/methods ; Gene Expression Profiling ; Gene Expression Regulation ; Insulin Resistance/genetics ; Transcriptome

Dissecting microbial communities with single-cell transcriptome analysis.

Authors: Pountain AW Yanai I

Source: Science (New York, N.Y.) [Science] 2025 Sep 04; Vol. 389 (6764), pp. eadp6252. Date of Electronic Publication: 2025 Sep 04.

Publication Type: Journal Article; Review

Journal Info: Publisher: American Association for the Advancement of Science Country of Publication: United States NLM ID: 0404511 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1095-9203 (Electronic) Linking ISSN: 00368075 NLM ISO Abbreviation: Science Subsets: MEDLINE

MeSH Terms: Bacteria*/drug effects , Bacteria*/genetics , Gastrointestinal Microbiome*/drug effects , Gastrointestinal Microbiome*/genetics , Single-Cell Gene Expression Analysis* , Transcriptome*, Humans ; Anti-Bacterial Agents/pharmacology ; Interspersed Repetitive Sequences

Single-cell transcriptomics reveals predominantly inflammatory endothelial cell responses and suppressed vascular repair in silicosis.

Authors: Cao D Cui H Chen Z et al.

Source: Frontiers in immunology [Front Immunol] 2025 Sep 03; Vol. 16, pp. 1629226. Date of Electronic Publication: 2025 Sep 03 (Print Publication: 2025).

Publication Type: Journal Article

Journal Info: Publisher: Frontiers Research Foundation] Country of Publication: Switzerland NLM ID: 101560960 Publication Model: eCollection Cited Medium: Internet ISSN: 1664-3224 (Electronic) Linking ISSN: 16643224 NLM ISO Abbreviation: Front Immunol Subsets: MEDLINE

MeSH Terms: Single-Cell Gene Expression Analysis* , Silicosis*/genetics , Silicosis*/immunology , Endothelial Cells*/immunology , Lung*/immunology , Lung*/pathology, Animals ; Mice ; Inflammation ; Disease Models, Animal ; Male ; Mice, Inbred C57BL

A single-cell, spatial transcriptomic atlas of the Arabidopsis life cycle.

Authors: Lee TA Illouz-Eliaz N Nobori T et al.

Source: Nature plants [Nat Plants] 2025 Sep; Vol. 11 (9), pp. 1960-1975. Date of Electronic Publication: 2025 Aug 19.

Publication Type: Journal Article

Journal Info: Publisher: Nature Publishing Group, a division of Macmillan Publishers Limited Country of Publication: England NLM ID: 101651677 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 2055-0278 (Electronic) Linking ISSN: 20550278 NLM ISO Abbreviation: Nat Plants Subsets: MEDLINE

MeSH Terms: Single-Cell Gene Expression Analysis* , Arabidopsis*/cytology , Arabidopsis*/growth & development , Arabidopsis*/metabolism , Gene Expression Regulation, Plant* , Transcriptome*

A hybrid adversarial autoencoder-graph network model with dynamic fusion for robust scRNA-seq clustering.

Authors: Tang B Feng Y Gao X

Source: BMC genomics [BMC Genomics] 2025 Aug 18; Vol. 26 (1), pp. 749. Date of Electronic Publication: 2025 Aug 18.

Publication Type: Journal Article

Journal Info: Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2164 (Electronic) Linking ISSN: 14712164 NLM ISO Abbreviation: BMC Genomics Subsets: MEDLINE

MeSH Terms: Autoencoder* , RNA-Seq*/methods , Single-Cell Gene Expression Analysis*/methods, Humans ; Cluster Analysis

SCAN-ACT: adoptive T cell therapy target discovery through single-cell transcriptomics.

Authors: Testa S Pal A Subramanian A et al.

Source: Genome medicine [Genome Med] 2025 Aug 14; Vol. 17 (1), pp. 89. Date of Electronic Publication: 2025 Aug 14.

Publication Type: Journal Article

Journal Info: Publisher: BioMed Central Country of Publication: England NLM ID: 101475844 Publication Model: Electronic Cited Medium: Internet ISSN: 1756-994X (Electronic) Linking ISSN: 1756994X NLM ISO Abbreviation: Genome Med Subsets: MEDLINE

MeSH Terms: Immunotherapy, Adoptive* , Single-Cell Gene Expression Analysis* , Computational Biology*/methods, Receptors, Chimeric Antigen ; T-Lymphocytes ; Humans ; Sarcoma/therapy ; Internet ; User-Computer Interface ; Molecular Targeted Therapy

Using R, Seurat, and CellChat to Analyze a Single-Cell Transcriptomics Dataset of Mouse Skin Wound Healing.

Authors: Keiser S Botello N Cruz E et al.

Source: Journal of visualized experiments : JoVE [J Vis Exp] 2025 Aug 01 (222). Date of Electronic Publication: 2025 Aug 01.

Publication Type: Journal Article

Journal Info: Publisher: MYJoVE Corporation Country of Publication: United States NLM ID: 101313252 Publication Model: Electronic Cited Medium: Internet ISSN: 1940-087X (Electronic) Linking ISSN: 1940087X NLM ISO Abbreviation: J Vis Exp Subsets: MEDLINE

MeSH Terms: Single-Cell Gene Expression Analysis* , Skin*/metabolism , Software* , Wound Healing* , Computational Biology*/methods, Animals ; Mice ; Algorithms ; Datasets as Topic ; Transcriptome

CYCLONE: recycle contrastive learning for integrating single-cell gene expression data.

Authors: Ji H He X Li H

Source: BMC bioinformatics [BMC Bioinformatics] 2025 Jul 30; Vol. 26 (1), pp. 202. Date of Electronic Publication: 2025 Jul 30.

Publication Type: Journal Article

Journal Info: Publisher: BioMed Central Country of Publication: England NLM ID: 100965194 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2105 (Electronic) Linking ISSN: 14712105 NLM ISO Abbreviation: BMC Bioinformatics Subsets: MEDLINE

MeSH Terms: Single-Cell Gene Expression Analysis*/methods , Machine Learning*, Autoencoder ; Datasets as Topic ; Computer Simulation ; Humans ; Animals ; Mice

MuST: multiple-modality structure transformation for single-cell spatial transcriptomics.

Authors: Zang Z Li L Xu Y et al.

Source: Briefings in bioinformatics [Brief Bioinform] 2025 Jul 02; Vol. 26 (4).

Publication Type: Journal Article

Journal Info: Publisher: Oxford University Press Country of Publication: England NLM ID: 100912837 Publication Model: Print Cited Medium: Internet ISSN: 1477-4054 (Electronic) Linking ISSN: 14675463 NLM ISO Abbreviation: Brief Bioinform Subsets: MEDLINE

MeSH Terms: Single-Cell Gene Expression Analysis*/methods , Deep Learning* , Brain*/metabolism, Sequence Analysis, RNA ; Animals ; Mice ; Bias ; Olfactory Bulb/metabolism ; Hippocampus/metabolism ; Dorsolateral Prefrontal Cortex/metabolism ; Humans ; Gene Expression

Single-cell transcriptome reveals the reprogramming of immune microenvironment during the transition from MASH to HCC.

Authors: Huang Y Xie Y Zhang Y et al.

Source: Molecular cancer [Mol Cancer] 2025 Jun 11; Vol. 24 (1), pp. 177. Date of Electronic Publication: 2025 Jun 11.

Publication Type: Journal Article

Journal Info: Publisher: BioMed Central Country of Publication: England NLM ID: 101147698 Publication Model: Electronic Cited Medium: Internet ISSN: 1476-4598 (Electronic) Linking ISSN: 14764598 NLM ISO Abbreviation: Mol Cancer Subsets: MEDLINE

MeSH Terms: Transcriptome* , Single-Cell Gene Expression Analysis* , Fatty Liver*/complications , Fatty Liver*/genetics , Fatty Liver*/immunology , Fatty Liver*/metabolism , Liver Neoplasms*/genetics , Liver Neoplasms*/immunology , Liver Neoplasms*/metabolism , Liver Neoplasms*/pathology , Carcinoma, Hepatocellular*/genetics , Carcinoma, Hepatocellular*/immunology , Carcinoma, Hepatocellular*/metabolism, Male ; Animals ; Mice ; Mice, Inbred C57BL ; Cellular Reprogramming ; T-Lymphocytes/immunology ; B-Lymphocytes/immunology ; Cell Differentiation ; Cell Lineage ; Apolipoproteins E/metabolism

Single-cell RNA sequencing and spatial transcriptomics reveal unique subpopulations of infiltrating macrophages and dendritic cells following AKI.

Authors: Melkonian AL Cheung MD Erman EN et al.

Source: American journal of physiology. Renal physiology [Am J Physiol Renal Physiol] 2025 Jun 01; Vol. 328 (6), pp. F907-F920. Date of Electronic Publication: 2025 May 07.

Publication Type: Journal Article

Journal Info: Publisher: American Physiological Society Country of Publication: United States NLM ID: 100901990 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1522-1466 (Electronic) Linking ISSN: 15221466 NLM ISO Abbreviation: Am J Physiol Renal Physiol Subsets: MEDLINE

MeSH Terms: Single-Cell Gene Expression Analysis* , Gene Expression Profiling* , Macrophages*/immunology , Dendritic Cells*/immunology , Acute Kidney Injury*/immunology, Male ; Animals ; Mice ; Mice, Inbred C57BL ; Reperfusion Injury ; Biomarkers

Single-Cell Profiling of Mononuclear Cells Identifies Transcriptomics Signatures Differentiating Prostate Cancer From Benign Prostatic Hyperplasia.

Authors: Enikeeva K Korobeynikov V Sharifyanova Y et al.

Source: Genes, chromosomes & cancer [Genes Chromosomes Cancer] 2025 May; Vol. 64 (5), pp. e70051.

Publication Type: Journal Article

Journal Info: Publisher: Wiley-Liss Country of Publication: United States NLM ID: 9007329 Publication Model: Print Cited Medium: Internet ISSN: 1098-2264 (Electronic) Linking ISSN: 10452257 NLM ISO Abbreviation: Genes Chromosomes Cancer Subsets: MEDLINE

MeSH Terms: Single-Cell Gene Expression Analysis* , Prostatic Neoplasms*/diagnosis , Prostatic Neoplasms*/genetics , Prostatic Neoplasms*/immunology , Prostatic Neoplasms*/pathology, Humans ; Male ; Leukocytes, Mononuclear/pathology ; Cell Communication ; Tumor Microenvironment

Mapping Organism-wide Single Cell mRNA Expression Linked to Extracellular Vesicle Biogenesis, Secretion, and Cargo.

Authors: LaRocca TJ Lark DS

Source: Function (Oxford, England) [Function (Oxf)] 2025 Mar 24; Vol. 6 (2).

Publication Type: Journal Article

Journal Info: Publisher: Oxford University Press Country of Publication: England NLM ID: 101770668 Publication Model: Print Cited Medium: Internet ISSN: 2633-8823 (Electronic) Linking ISSN: 26338823 NLM ISO Abbreviation: Function (Oxf) Subsets: MEDLINE

MeSH Terms: Extracellular Vesicles* , Organelle Biogenesis* , Single-Cell Gene Expression Analysis*, RNA, Messenger ; Animals ; Mice

Development of a MVI associated HCC prognostic model through single cell transcriptomic analysis and 101 machine learning algorithms.

Authors: Zhang J Zhang Z Yang C et al.

Source: Scientific reports [Sci Rep] 2025 Mar 07; Vol. 15 (1), pp. 7977. Date of Electronic Publication: 2025 Mar 07.

Publication Type: Evaluation Study; Journal Article; Validation Study

Journal Info: Publisher: Nature Publishing Group Country of Publication: England NLM ID: 101563288 Publication Model: Electronic Cited Medium: Internet ISSN: 2045-2322 (Electronic) Linking ISSN: 20452322 NLM ISO Abbreviation: Sci Rep Subsets: MEDLINE

MeSH Terms: Carcinoma, Hepatocellular*/genetics , Carcinoma, Hepatocellular*/mortality , Carcinoma, Hepatocellular*/pathology , Carcinoma, Hepatocellular*/therapy , Liver Neoplasms*/genetics , Liver Neoplasms*/mortality , Liver Neoplasms*/pathology , Liver Neoplasms*/therapy , Machine Learning* , Precision Medicine*/methods , Single-Cell Gene Expression Analysis*/methods, Microvessels/pathology ; Neoplasm Invasiveness/genetics ; Neoplasm Invasiveness/pathology ; Prognosis ; Meta-Analysis as Topic ; Humans ; Mutation ; Gene Expression Regulation, Neoplastic/immunology ; Immunotherapy/methods ; Treatment Outcome ; Clinical Decision-Making/methods ; Datasets as Topic ; Liver/blood supply ; Liver/pathology ; Biomarkers, Tumor/genetics ; Biomarkers, Tumor/immunology ; Immune Checkpoint Proteins/genetics ; Immune Checkpoint Proteins/immunology ; Kaplan-Meier Estimate ; Risk Assessment/methods

Single-cell transcriptomics of clinical grade adipose-derived regenerative cells reveals consistency between donors independent of gender and BMI.

Authors: Bjerre FA Nielsen JV Burton M et al.

Source: Stem cell research & therapy [Stem Cell Res Ther] 2025 Mar 05; Vol. 16 (1), pp. 109. Date of Electronic Publication: 2025 Mar 05.

Publication Type: Comparative Study; Journal Article

Journal Info: Publisher: BioMed Central Country of Publication: England NLM ID: 101527581 Publication Model: Electronic Cited Medium: Internet ISSN: 1757-6512 (Electronic) Linking ISSN: 17576512 NLM ISO Abbreviation: Stem Cell Res Ther Subsets: MEDLINE

MeSH Terms: Single-Cell Gene Expression Analysis* , Stromal Vascular Fraction*/genetics , Stromal Vascular Fraction*/transplantation , Donor Selection*/methods, Body Mass Index ; Sex Factors ; Clinical Decision-Making ; Living Donors ; Humans ; Male ; Female

Analysis of multi-condition single-cell data with latent embedding multivariate regression.

Authors: Ahlmann-Eltze C Huber W

Source: Nature genetics [Nat Genet] 2025 Mar; Vol. 57 (3), pp. 659-667. Date of Electronic Publication: 2025 Jan 03.

Publication Type: Journal Article

Journal Info: Publisher: Nature Pub. Co Country of Publication: United States NLM ID: 9216904 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1546-1718 (Electronic) Linking ISSN: 10614036 NLM ISO Abbreviation: Nat Genet Subsets: MEDLINE

MeSH Terms: Multivariate Analysis* , Single-Cell Gene Expression Analysis*/methods, Cluster Analysis ; Gene Expression ; Humans ; Animals ; Zebrafish ; Neoplasms/genetics ; Gene Expression Regulation, Neoplastic ; Gene Expression Regulation, Developmental

Single-cell RNA sequencing reveals the dysfunctional characteristics of PBMCs in patients with type 2 diabetes mellitus.

Authors: Zhao J Fang Z

Source: Frontiers in immunology [Front Immunol] 2025 Jan 23; Vol. 15, pp. 1501660. Date of Electronic Publication: 2025 Jan 23 (Print Publication: 2024).

Publication Type: Clinical Trial; Journal Article

Journal Info: Publisher: Frontiers Research Foundation] Country of Publication: Switzerland NLM ID: 101560960 Publication Model: eCollection Cited Medium: Internet ISSN: 1664-3224 (Electronic) Linking ISSN: 16643224 NLM ISO Abbreviation: Front Immunol Subsets: MEDLINE

MeSH Terms: Diabetes Mellitus, Type 2*/immunology , Diabetes Mellitus, Type 2*/genetics , Diabetes Mellitus, Type 2*/blood , Leukocytes, Mononuclear*/immunology , Leukocytes, Mononuclear*/metabolism , Single-Cell Gene Expression Analysis*, Adult ; Female ; Humans ; Male ; Middle Aged ; Biomarkers ; Blood Glucose ; Gene Expression Profiling ; Glycated Hemoglobin ; RNA-Seq ; Prospective Studies

Utilizing sc-linker to integrate single-cell RNA sequencing and human genetics to identify cell types and driver genes associated with non-small cell lung cancer.

Authors: Zhou Y Zhao L Cai M et al.

Source: BMC cancer [BMC Cancer] 2025 Jan 23; Vol. 25 (1), pp. 130. Date of Electronic Publication: 2025 Jan 23.

Publication Type: Dataset; Journal Article

Journal Info: Publisher: BioMed Central Country of Publication: England NLM ID: 100967800 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2407 (Electronic) Linking ISSN: 14712407 NLM ISO Abbreviation: BMC Cancer Subsets: MEDLINE

MeSH Terms: Carcinoma, Non-Small-Cell Lung*/genetics , Lung Neoplasms*/genetics , Single-Cell Gene Expression Analysis*/methods, Cancer-Associated Fibroblasts/metabolism ; Disease Progression ; Genome-Wide Association Study ; Humans

Mapping the spatial atlas of the human bone tissue integrating spatial and single-cell transcriptomics.

Authors: Lin W Li Y Qiu C et al.

Source: Nucleic acids research [Nucleic Acids Res] 2025 Jan 11; Vol. 53 (2).

Publication Type: Journal Article

Journal Info: Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN: 1362-4962 (Electronic) Linking ISSN: 03051048 NLM ISO Abbreviation: Nucleic Acids Res Subsets: MEDLINE

MeSH Terms: Femur*/metabolism , Femur*/pathology , Single-Cell Gene Expression Analysis*/methods , Bone Marrow Cells*/cytology , Bone Marrow Cells*/metabolism, Adult ; Humans ; Male ; Cell Communication ; Cell Lineage ; Fibroblasts/cytology ; Fibroblasts/metabolism ; Gene Expression Profiling/methods ; Gene Expression Regulation ; Gene Regulatory Networks ; Osteoarthritis/genetics ; Osteoarthritis/metabolism ; Osteoarthritis/pathology ; Osteoblasts/cytology ; Osteoblasts/metabolism ; Signal Transduction