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   Articles with "cell multiomics" as a keyword



Efficient Generation of Paired Single-Cell Multiomics Profiles by Deep Learning.

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recommendations! Published in 2023 at "Advanced science"

DOI: 10.1002/advs.202301169

Abstract: Recent advances in single-cell sequencing technology have made it possible to measure multiple paired omics simultaneously in a single cell such as cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) and single-nucleus chromatin accessibility… read more here.

Keywords: cell multiomics; cell; efficient generation; single cell ... See more keywords

Narrowing Down Key Players in Autoimmunity via Single‐Cell Multiomics

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recommendations! Published in 2025 at "European Journal of Immunology"

DOI: 10.1002/eji.202451233

Abstract: Autoimmune diseases encompass a range of conditions in which our own immune system reacts against molecules encoded by our own genome. This phenomenon is mediated by the action of antigen receptors expressed by T and… read more here.

Keywords: key players; single cell; narrowing key; players autoimmunity ... See more keywords

scMDCL: A Deep Collaborative Contrastive Learning Framework for Matched Single-Cell Multiomics Data Clustering

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recommendations! Published in 2025 at "Journal of chemical information and modeling"

DOI: 10.1021/acs.jcim.4c02114

Abstract: Single-cell multiomics clustering integrates multiple omics data to analyze cellular heterogeneity and is crucial for uncovering complex biological processes and disease mechanisms. However, existing matched single-cell multiomics clustering methods often neglect the full utilization of… read more here.

Keywords: framework; single cell; cell multiomics; cell ... See more keywords

Interpretable and integrative analysis of single-cell multiomics with scMKL

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recommendations! Published in 2025 at "Communications Biology"

DOI: 10.1038/s42003-025-08533-7

Abstract: The rapid advancement of single-cell technologies has led to the development of various analysis methods, each with trade-offs between predictive power and interpretability particularly for multimodal data integration. Complex machine learning models achieve high accuracy,… read more here.

Keywords: cancer; single cell; analysis; biology ... See more keywords

Resolving leukemic stem cell heterogeneity and plasticity with single-cell multiomics.

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recommendations! Published in 2025 at "Seminars in hematology"

DOI: 10.1053/j.seminhematol.2025.07.001

Abstract: Acute myeloid leukemia (AML) is an aggressive blood cancer in which disease initiation and relapse are driven by leukemic cells with stem-like properties, known as leukemic stem cells (LSCs). The LSC compartment is highly heterogenous… read more here.

Keywords: single cell; plasticity; cell multiomics; cell ... See more keywords

JSNMF enables effective and accurate integrative analysis of single-cell multiomics data

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recommendations! Published in 2022 at "Briefings in bioinformatics"

DOI: 10.1093/bib/bbac105

Abstract: The single-cell multiomics technologies provide an unprecedented opportunity to study the cellular heterogeneity from different layers of transcriptional regulation. However, the datasets generated from these technologies tend to have high levels of noise, making data… read more here.

Keywords: cell multiomics; jsnmf; cell; multiomics data ... See more keywords

scME: a dual-modality factor model for single-cell multiomics embedding

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recommendations! Published in 2023 at "Bioinformatics"

DOI: 10.1093/bioinformatics/btad337

Abstract: Abstract Motivation Single-cell multiomics technologies are emerging to characterize different molecular features of cells. This gives rise to an issue of combining various kinds of molecular features to dissect cell heterogeneity. Most single-cell multiomics integration… read more here.

Keywords: cell multiomics; dual modality; cell; factor ... See more keywords

TFcomb identifies transcription factor combinations for cellular reprogramming based on single-cell multiomics data

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recommendations! Published in 2025 at "Genome Research"

DOI: 10.1101/gr.279955.124

Abstract: Reprogramming cell state transitions provides the potential for cell engineering and regenerative therapy. Finding the reprogramming transcription factors (TFs) and their combinations that can direct the desired state transition is crucial for the task. Computational… read more here.

Keywords: single cell; reprogramming tfs; cell multiomics; cell ... See more keywords
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DIRECT-NET: An efficient method to discover cis-regulatory elements and construct regulatory networks from single-cell multiomics data

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recommendations! Published in 2022 at "Science Advances"

DOI: 10.1126/sciadv.abl7393

Abstract: The emergence of single-cell multiomics data provides unprecedented opportunities to scrutinize the transcriptional regulatory mechanisms controlling cell identity. However, how to use those datasets to dissect the cis-regulatory element (CRE)–to–gene relationships at a single-cell level… read more here.

Keywords: cell multiomics; multiomics data; cell; direct net ... See more keywords

Single-cell multiomics identifies clinically relevant mesenchymal stem-like cells and key regulators for MPNST malignancy

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recommendations! Published in 2022 at "Science Advances"

DOI: 10.1126/sciadv.abo5442

Abstract: Malignant peripheral nerve sheath tumor (MPNST), a highly aggressive Schwann cell (SC)–derived soft tissue sarcoma, arises from benign neurofibroma (NF); however, the identity, heterogeneity and origins of tumor populations remain elusive. Nestin+ cells have been… read more here.

Keywords: cell multiomics; cell; stem like; mesenchymal stem ... See more keywords

scMaui: a widely applicable deep learning framework for single-cell multiomics integration in the presence of batch effects and missing data

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recommendations! Published in 2024 at "BMC Bioinformatics"

DOI: 10.1186/s12859-024-05880-w

Abstract: The recent advances in high-throughput single-cell sequencing have created an urgent demand for computational models which can address the high complexity of single-cell multiomics data. Meticulous single-cell multiomics integration models are required to avoid biases… read more here.

Keywords: single cell; cell multiomics; cell; batch ... See more keywords