scRNA-seq Search Results PubMed https://pubmed.ncbi.nlm.nih.gov/?term=%28single+cell+RNA-seq%5BTitle%2FAbstract%5D+OR+scRNA-seq%5BTitle%2FAbstract%5D+OR+RNA+sequencing%5BTitle%2FAbstract%5D+OR+single+cell+sequencing%5BTitle%2FAbstract%5D+OR+single+cell+transcriptomics%5BTitle%2FAbstract%5D%29+AND+%28algorithm%5BTitle%2FAbstract%5D+OR+computational+method%5BTitle%2FAbstract%5D+OR+analysis+tool%5BTitle%2FAbstract%5D+OR+pipeline%5BTitle%2FAbstract%5D+OR+software%5BTitle%2FAbstract%5D+OR+model%5BTitle%2FAbstract%5D+OR+framework%5BTitle%2FAbstract%5D%29+AND+%28Nature+Methods%5BJournal%5D+OR+Genome+Biology%5BJournal%5D+OR+Cell%5BJournal%5D+OR+Nature+Biotechnology%5BJournal%5D+OR+Genome+Research%5BJournal%5D+OR+Nucleic+Acids+Research%5BJournal%5D%29+AND+%28alignment%5BTitle%2FAbstract%5D+OR+clustering%5BTitle%2FAbstract%5D+OR+dimensionality+reduction%5BTitle%2FAbstract%5D+OR+visualization%5BTitle%2FAbstract%5D+OR+differential+expression%5BTitle%2FAbstract%5D+OR+trajectory+inference%5BTitle%2FAbstract%5D%29+AND+%28%222021%2F01%2F01%22%5BPDAT%5D+%3A+%223000%2F12%2F31%22%5BPDAT%5D%29 Tue, 10 Mar 2026 14:55:07 -0400 Rss Everything 360 c73acba5f147d5ed026edb9a576fa70c Mon, 02 Mar 2026 15:03:16 -0500 Single-cell protein activity analysis identifies recurrence-associated renal tumor macrophages https://pubmed.ncbi.nlm.nih.gov/34019793/ Cell. 2021 May 27;184(11):2988-3005.e16. doi: 10.1016/j.cell.2021.04.038. Epub 2021 May 20. To assemble a comprehensive ccRCC tumor microenvironment (TME) atlas, we performed single-cell RNA sequencing (scRNA-seq) of hematopoietic and non-hematopoietic subpopulations from tumor and tumor-adjacent tissue of treatment-naive ccRCC resections. We …

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]]> 696fa562a6774b197d200e33afbdba34 Mon, 02 Mar 2026 15:03:15 -0500 A single-embryo, single-cell time-resolved model for mouse gastrulation https://pubmed.ncbi.nlm.nih.gov/33932341/ Cell. 2021 May 27;184(11):2825-2842.e22. doi: 10.1016/j.cell.2021.04.004. Epub 2021 Apr 30. Here, we introduce a temporal model for mouse gastrulation, consisting of data from 153 individually sampled embryos spanning 36 h of molecular diversification. ...Our study rejects the notion of differentiation being governed by a series of binary choices, providing an al …

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]]> 173736cd0192789bef51771332aba105 Mon, 02 Mar 2026 15:03:06 -0500 Method of moments framework for differential expression analysis of single-cell RNA sequencing data https://pubmed.ncbi.nlm.nih.gov/39454576/ Cell. 2024 Oct 31;187(22):6393-6410.e16. doi: 10.1016/j.cell.2024.09.044. Epub 2024 Oct 24. Differential expression analysis of single-cell RNA sequencing (scRNA-seq) data is central for characterizing how experimental factors affect the distribution of gene expression. ...We introduce Memento, a tool for robust and efficient di …

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]]> b38c482052878346a71e2ac35a7696f7 Mon, 02 Mar 2026 15:03:01 -0500 CellNEST reveals cell-cell relay networks using attention mechanisms on spatial transcriptomics https://pubmed.ncbi.nlm.nih.gov/40481363/ Nat Methods. 2025 Jul;22(7):1505-1519. doi: 10.1038/s41592-025-02721-3. Epub 2025 Jun 6. Dysregulation of communication between cells mediates complex diseases such as cancer and diabetes; however, detecting cell-cell communication at scale remains one of the greatest challenges in transcriptomics. Most current single-cell RNA sequencing and spatial tra …

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]]> 587fbec0f68cb3a0bf53c5dd314ed61b Mon, 02 Mar 2026 15:02:58 -0500 A visual-omics foundation model to bridge histopathology with spatial transcriptomics https://pubmed.ncbi.nlm.nih.gov/40442373/ Nat Methods. 2025 Jul;22(7):1568-1582. doi: 10.1038/s41592-025-02707-1. Epub 2025 May 29. Recent developments in omics technologies, including single-cell RNA sequencing and spatial transcriptomics, provide detailed genomic data alongside tissue histology. ...Building on OmiCLIP, our Loki platform offers five key functions: tissue alignment, annot …

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]]> 4076209d8e5871769edf807bc47d152f Mon, 02 Mar 2026 15:02:49 -0500 Significance analysis for clustering with single-cell RNA-sequencing data https://pubmed.ncbi.nlm.nih.gov/37429993/ Nat Methods. 2023 Aug;20(8):1196-1202. doi: 10.1038/s41592-023-01933-9. Epub 2023 Jul 10. Unsupervised clustering of single-cell RNA-sequencing data enables the identification of distinct cell populations. ...Here we extend a previous method, significance of hierarchical clustering, to propose a model-based hypothesis testing approac …

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]]> 6ab6df38e52a70224f170ee0424d059c Mon, 02 Mar 2026 15:02:42 -0500 CellRank 2: unified fate mapping in multiview single-cell data https://pubmed.ncbi.nlm.nih.gov/38871986/ Nat Methods. 2024 Jul;21(7):1196-1205. doi: 10.1038/s41592-024-02303-9. Epub 2024 Jun 13. Single-cell RNA sequencing allows us to model cellular state dynamics and fate decisions using expression similarity or RNA velocity to reconstruct state-change trajectories; however, trajectory inference does not incorporate valuable time point …

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]]> b8ecc872cdc944a6c885d338e5cde43d Mon, 02 Mar 2026 15:02:37 -0500 Joint representation and visualization of derailed cell states with Decipher https://pubmed.ncbi.nlm.nih.gov/40702544/ Genome Biol. 2025 Jul 23;26(1):219. doi: 10.1186/s13059-025-03682-8. Here, we present Decipher, a deep generative model that characterizes derailed cell-state trajectories. Decipher jointly models and visualizes gene expression and cell state from normal and perturbed single-cell RNA-seq data, revealing shared an …

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]]> 653fd9c3075119db02f50120bab4e890 Mon, 02 Mar 2026 15:02:30 -0500 Integrated analysis of multimodal single-cell data with structural similarity https://pubmed.ncbi.nlm.nih.gov/36130281/ Nucleic Acids Res. 2022 Nov 28;50(21):e121. doi: 10.1093/nar/gkac781. Multimodal single-cell sequencing technologies provide unprecedented information on cellular heterogeneity from multiple layers of genomic readouts. ...In this work, we propose a deep learning framework, named SAILERX, for efficient, robust, and flexib …

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]]> 1afbe183382e498adc165b173535bf01 Mon, 02 Mar 2026 15:02:28 -0500 SingmiR: a single-cell miRNA alignment and analysis tool https://pubmed.ncbi.nlm.nih.gov/38572750/ Nucleic Acids Res. 2024 Jul 5;52(W1):W374-W380. doi: 10.1093/nar/gkae225. Single-cell RNA sequencing (RNA-seq) has revolutionized our understanding of cell biology, developmental and pathophysiological molecular processes, paving the way toward novel diagnostic and therapeutic approaches. ...Numerous standard and advanced analyses …

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