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   Articles with "cell data" as a keyword



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Gene Regulatory Networks from Single Cell Data for Exploring Cell Fate Decisions.

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recommendations! Published in 2019 at "Methods in molecular biology"

DOI: 10.1007/978-1-4939-9224-9_10

Abstract: Single cell experimental techniques now allow us to quantify gene expression in up to thousands of individual cells. These data reveal the changes in transcriptional state that occur as cells progress through development and adopt… read more here.

Keywords: single cell; gene regulatory; cell data; regulatory networks ... See more keywords
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Cell type prioritization in single-cell data

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recommendations! Published in 2020 at "Nature biotechnology"

DOI: 10.1038/s41587-020-0605-1

Abstract: We present Augur, a method to prioritize the cell types most responsive to biological perturbations in single-cell data. Augur employs a machine-learning framework to quantify the separability of perturbed and unperturbed cells within a high-dimensional… read more here.

Keywords: single cell; prioritization single; type prioritization; cell data ... See more keywords

Disentanglement of single-cell data with biolord

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recommendations! Published in 2024 at "Nature Biotechnology"

DOI: 10.1038/s41587-023-02079-x

Abstract: Biolord is a deep generative method for disentangling single-cell multi-omic data to known and unknown attributes, including spatial, temporal and disease states, used to reveal the decoupled biological signatures over diverse single-cell modalities and biological… read more here.

Keywords: single cell; data biolord; biolord; disentanglement single ... See more keywords

Integrating single-cell data with biological variables

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recommendations! Published in 2025 at "Proceedings of the National Academy of Sciences of the United States of America"

DOI: 10.1073/pnas.2416516122

Abstract: Significance Data integration of multiple single-cell batches from various biological variables, such as tissues, diseases, and developmental stages, presents a significant challenge due to the confounding of biological effects with batch effects. Current integration strategies… read more here.

Keywords: single cell; data biological; integrating single; biological variables ... See more keywords

Identification of gene regulation models from single-cell data.

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recommendations! Published in 2018 at "Physical biology"

DOI: 10.1088/1478-3975/aabc31

Abstract: In quantitative analyses of biological processes, one may use many different scales of models (e.g. spatial or non-spatial, deterministic or stochastic, time-varying or at steady-state) or many different approaches to match models to experimental data… read more here.

Keywords: gene regulation; single cell; cell data; model ... See more keywords

A review and performance evaluation of clustering frameworks for single-cell Hi-C data

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recommendations! Published in 2022 at "Briefings in bioinformatics"

DOI: 10.1093/bib/bbac385

Abstract: The three-dimensional genome structure plays a key role in cellular function and gene regulation. Single-cell Hi-C (high-resolution chromosome conformation capture) technology can capture genome structure information at the cell level, which provides the opportunity to… read more here.

Keywords: cell; evaluation; clustering frameworks; cell data ... See more keywords

PIPET: predicting relevant subpopulations in single-cell data using phenotypic information from bulk data

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recommendations! Published in 2024 at "Briefings in Bioinformatics"

DOI: 10.1093/bib/bbae260

Abstract: Abstract Single-cell RNA sequencing has revealed cellular heterogeneity in complex tissues, notably benefiting research on diseases such as cancer. However, the integration of single-cell data from small samples with extensive clinical features in bulk data… read more here.

Keywords: single cell; subpopulations single; cell; bulk data ... See more keywords

scHiClassifier: a deep learning framework for cell type prediction by fusing multiple feature sets from single-cell Hi-C data

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recommendations! Published in 2024 at "Briefings in Bioinformatics"

DOI: 10.1093/bib/bbaf009

Abstract: Abstract Single-cell high-throughput chromosome conformation capture (Hi-C) technology enables capturing chromosomal spatial structure information at the cellular level. However, to effectively investigate changes in chromosomal structure across different cell types, there is a requisite for… read more here.

Keywords: framework; single cell; feature sets; cell ... See more keywords

Multi-omics single-cell data alignment and integration with enhanced contrastive learning and differential attention mechanism

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recommendations! Published in 2025 at "Bioinformatics"

DOI: 10.1093/bioinformatics/btaf443

Abstract: Abstract Motivation Identifying cell types that constitute complex tissue components using single-cell sequencing data is a critical issue in the field of biology. With the continuous advancement of sequencing technologies, the recognition of cell types… read more here.

Keywords: multi omics; single cell; cell; omics single ... See more keywords

Reconstructing physical cell interaction networks from single-cell data using Neighbor-seq

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recommendations! Published in 2022 at "Nucleic Acids Research"

DOI: 10.1093/nar/gkac333

Abstract: Cell-cell interactions are the fundamental building blocks of tissue organization and multicellular life. We developed Neighbor-seq, a method to identify and annotate the architecture of direct cell-cell interactions and relevant ligand-receptor signaling from the undissociated… read more here.

Keywords: cell; cell data; single cell; neighbor seq ... See more keywords

Integrated analysis of multimodal single-cell data with structural similarity

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recommendations! Published in 2022 at "Nucleic Acids Research"

DOI: 10.1093/nar/gkac781

Abstract: Abstract Multimodal single-cell sequencing technologies provide unprecedented information on cellular heterogeneity from multiple layers of genomic readouts. However, joint analysis of two modalities without properly handling the noise often leads to overfitting of one modality… read more here.

Keywords: cell; cell data; multimodal single; analysis ... See more keywords