scRNA-seq Search Results PubMed

Single-cell protein activity analysis identifies recurrence-associated renal tumor macrophages

Fri, 09 Oct 2026 07:54:16 +0000

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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A single-embryo, single-cell time-resolved model for mouse gastrulation

Fri, 09 Oct 2026 07:54:09 +0000

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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A visual-omics foundation model to bridge histopathology with spatial transcriptomics

Fri, 09 Oct 2026 07:54:05 +0000

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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Iterative single-cell multi-omic integration using online learning

Fri, 09 Oct 2026 07:53:45 +0000

Nat Biotechnol. 2021 Aug;39(8):1000-1007. doi: 10.1038/s41587-021-00867-x. Epub 2021 Apr 19. Here we describe online integrative non-negative matrix factorization (iNMF), an algorithm for integrating large, diverse and continually arriving single-cell datasets. ...Comparisons with previous methods indicate that the improvements in efficiency do not sacrifice datas …

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Joint representation and visualization of derailed cell states with Decipher

Mon, 12 Oct 2026 09:25:42 +0000

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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PseudoGA: cell pseudotime reconstruction based on genetic algorithm

Fri, 09 Oct 2026 07:53:29 +0000

Nucleic Acids Res. 2021 Aug 20;49(14):7909-7924. doi: 10.1093/nar/gkab457. Bulk RNA-seq analysis can only detect average change in expression levels and is unable to identify this dynamics. Single cell RNA-seq presents an unprecedented opportunity that helps in placing the cells on a hypothetical time trajectory that reflects …

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Identifying cell state-associated alternative splicing events and their coregulation

Mon, 12 Oct 2026 09:25:37 +0000

Genome Res. 2022 Jul 27;32(7):1385-1397. doi: 10.1101/gr.276109.121. Alternative splicing shapes the transcriptome and contributes to each cell's unique identity, but single-cell RNA sequencing (scRNA-seq) has struggled to capture the impact of alternative splicing. ...Here, we present a method, Psix, to confidently ide …

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Integrated analysis of multimodal single-cell data with structural similarity

Mon, 12 Oct 2026 09:25:28 +0000

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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Fast and accurate out-of-core PCA framework for large scale biobank data

Mon, 12 Oct 2026 09:25:24 +0000

Genome Res. 2023 Sep;33(9):1599-1608. doi: 10.1101/gr.277525.122. Epub 2023 Aug 24. Principal component analysis (PCA) is widely used in statistics, machine learning, and genomics for dimensionality reduction and uncovering low-dimensional latent structure. To address the challenges posed by ever-growing data size, fast and memory-efficient PCA met …

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MultiMAP: dimensionality reduction and integration of multimodal data

Mon, 12 Oct 2026 09:25:17 +0000

Genome Biol. 2021 Dec 20;22(1):346. doi: 10.1186/s13059-021-02565-y. Multimodal data is rapidly growing in many fields of science and engineering, including single-cell biology. We introduce MultiMAP, a novel algorithm for dimensionality reduction and integration. MultiMAP can integrate any number of datasets, leverages featur …

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