Methods and applications for single-cell and spatial multi-omics

Nature Reviews Genetics, Journal Year: 2023, Volume and Issue: 24(8), P. 494 - 515

Published: March 2, 2023

Language: Английский

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Best practices for single-cell analysis across modalities

Nature Reviews Genetics, Journal Year: 2023, Volume and Issue: 24(8), P. 550 - 572

Published: March 31, 2023

Language: Английский

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The scverse project provides a computational ecosystem for single-cell omics data analysis

Nature Biotechnology, Journal Year: 2023, Volume and Issue: 41(5), P. 604 - 606

Published: April 10, 2023

Language: Английский

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Identifying temporal and spatial patterns of variation from multimodal data using MEFISTO

Nature Methods, Journal Year: 2022, Volume and Issue: 19(2), P. 179 - 186

Published: Jan. 13, 2022

Factor analysis is a widely used method for dimensionality reduction in genome biology, with applications from personalized health to single-cell biology. Existing factor models assume independence of the observed samples, an assumption that fails spatio-temporal profiling studies. Here we present MEFISTO, flexible and versatile toolbox modeling high-dimensional data when spatial or temporal dependencies between samples are known. MEFISTO maintains established benefits multimodal data, but enables performance spatio-temporally informed reduction, interpolation, separation smooth non-smooth patterns variation. Moreover, can integrate multiple related datasets by simultaneously identifying aligning underlying variation data-driven manner. To illustrate apply model different resolution, including evolutionary atlas organ development, longitudinal microbiome study, multi-omics mouse gastrulation spatially resolved transcriptomics.

Language: Английский

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MUON: multimodal omics analysis framework

Genome biology, Journal Year: 2022, Volume and Issue: 23(1)

Published: Feb. 1, 2022

Advances in multi-omics have led to an explosion of multimodal datasets address questions from basic biology translation. While these data provide novel opportunities for discovery, they also pose management and analysis challenges, thus motivating the development tailored computational solutions. Here, we present a standard framework multi-omics, MUON, designed organise, analyse, visualise, exchange data. MUON stores efficient yet flexible interoperable structure. enables versatile range analyses, preprocessing alignment.

Language: Английский

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Integrated single-nucleus and spatial transcriptomics captures transitional states in soybean nodule maturation

Nature Plants, Journal Year: 2023, Volume and Issue: 9(4), P. 515 - 524

Published: April 13, 2023

Language: Английский

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Spatial omics technologies at multimodal and single cell/subcellular level

Genome biology, Journal Year: 2022, Volume and Issue: 23(1)

Published: Dec. 13, 2022

Abstract Spatial omics technologies enable a deeper understanding of cellular organizations and interactions within tissue interest. These assays can identify specific compartments or regions in with differential transcript protein abundance, delineate their interactions, complement other methods defining phenotypes. A variety spatial methodologies are being developed commercialized; however, these techniques differ resolution, multiplexing capability, scale/throughput, coverage. Here, we review the current prospective landscape single cell to subcellular resolution analysis tools provide comprehensive picture for both research clinical applications.

Language: Английский

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The T-cell-directed vaccine BNT162b4 encoding conserved non-spike antigens protects animals from severe SARS-CoV-2 infection

Cell, Journal Year: 2023, Volume and Issue: 186(11), P. 2392 - 2409.e21

Published: April 13, 2023

T cell responses play an important role in protection against beta-coronavirus infections, including SARS-CoV-2, where they associate with decreased COVID-19 disease severity and duration. To enhance immunity across epitopes infrequently altered SARS-CoV-2 variants, we designed BNT162b4, mRNA vaccine component that is intended to be combined BNT162b2, the spike-protein-encoding vaccine. BNT162b4 encodes variant-conserved, immunogenic segments of nucleocapsid, membrane, ORF1ab proteins, targeting diverse HLA alleles. elicits polyfunctional CD4+ CD8+ animal models, alone or when co-administered BNT162b2 while preserving spike-specific immunity. Importantly, demonstrate protects hamsters from severe reduces viral titers following challenge variants. These data suggest a combination could reduce duration caused by circulating future currently being clinically evaluated BA.4/BA.5 Omicron-updated bivalent (NCT05541861).

Language: Английский

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A fast, scalable and versatile tool for analysis of single-cell omics data

Nature Methods, Journal Year: 2024, Volume and Issue: 21(2), P. 217 - 227

Published: Jan. 8, 2024

Abstract Single-cell omics technologies have revolutionized the study of gene regulation in complex tissues. A major computational challenge analyzing these datasets is to project large-scale and high-dimensional data into low-dimensional space while retaining relative relationships between cells. This low dimension embedding necessary decompose cellular heterogeneity reconstruct cell-type-specific regulatory programs. Traditional dimensionality reduction techniques, however, face challenges efficiency comprehensively addressing diversity across varied molecular modalities. Here we introduce a nonlinear algorithm, embodied Python package SnapATAC2, which not only achieves more precise capture single-cell heterogeneities but also ensures efficient runtime memory usage, scaling linearly with number Our algorithm demonstrates exceptional performance, scalability versatility diverse datasets, including assay for transposase-accessible chromatin using sequencing, RNA Hi-C multi-omics underscoring its utility advancing analysis.

Language: Английский

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scPerturb: harmonized single-cell perturbation data

Nature Methods, Journal Year: 2024, Volume and Issue: 21(3), P. 531 - 540

Published: Jan. 26, 2024

Language: Английский

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