Advancing Single-Cell RNA Sequencing through Deep Learning: Methodologies and Applications

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Submission deadlines

  1. Manuscript Summary Submission Deadline 25 August 2025 | Manuscript Submission Deadline 13 December 2025

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Background

The integration of deep learning (DL) with single-cell RNA sequencing (scRNA-seq) represents a major advancement in genomic research. This research topic explores the technical aspects and applications of DL in scRNA-seq, addressing the challenges and innovations in this interdisciplinary area.

scRNA-seq reveals cellular heterogeneity through detailed transcriptomic profiles, but its high-dimensional, sparse data is analytically challenging. DL's capability to process large, complex datasets makes it a valuable tool in overcoming these challenges.

Current methodologies:

1. Clustering and Dimensionality Reduction:

DL techniques could offer advanced capabilities in managing high-dimensional data complexities. Additionally, clustering may be further refined by specifically training DL models for this task, potentially enhancing the precision and effectiveness of data categorization.

2. Normalization:

Normalization in scRNA-seq involves adjusting data to correct for batch effects, integrate multiple datasets, and account for cell cycle variations. Techniques like convolutional neural networks (CNNs) and generative adversarial networks (GANs) are increasingly used for normalization.

3. Data Enrichment and Imputation:

DL algorithms could potentially address the sparsity in scRNA-seq data by imputing missing values, potentially leading to more complete datasets for analysis. Furthermore, DL might be capable of exploring connections between differentially expressed genes and biological pathways, possibly uncovering complex patterns and associations beyond the capabilities of standard feature selection methods.
4. Comparison

DL methods, while powerful, are not always superior to standard approaches. Comparing these methods is crucial to identify scenarios where DL is more effective and where traditional methods might yield better results.

Applications:

1. Personalized Therapy:

DL is effective in identifying cell populations specific to certain diseases. They analyze scRNA-seq data to differentiate between healthy and diseased cells, aiding in precise disease diagnosis and subtyping.

2. Drug Discovery:

DL effectively identifies complex and indirect relationships between gene expressions and drug treatments in scRNA-seq data. This approach uncovers subtle correlations, crucial for pinpointing nuanced drug targets beyond direct gene-drug interactions.

Challenges and Future Directions:

Model Interpretability: Despite their effectiveness, DL models often lack transparency in their decision-making processes.

Integration with Other Omics Data: Combining scRNA-seq data with other omics data types using DL is a promising but challenging frontier.

Moving from Association to Causation: A future direction is to shift from identifying associations to understanding causal mechanisms. DL models need to evolve to not only predict outcomes but also to unravel the underlying biological processes.

Conclusion:

This Research Topic aims to highlight the synergistic potential of DL and scRNA-seq, providing a comprehensive overview of current methodologies, applications, and challenges. The integration of DL with scRNA-seq offers tremendous potential, it brings forth challenges that require multidisciplinary efforts to ensure accurate, ethical, and impactful advancements in genomic research.

Article types :

This Research Topic invites the following article types: Brief Research Article, Mini Review, Original Research, Code, Methods, General Commentary

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This Research Topic accepts the following article types, unless otherwise specified in the Research Topic description:

  • Brief Research Report
  • Editorial
  • General Commentary
  • Hypothesis and Theory
  • Methods
  • Mini Review
  • Opinion
  • Original Research
  • Perspective

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Article types

This Research Topic accepts the following article types, unless otherwise specified in the Research Topic description:

  • Brief Research Report
  • Editorial
  • General Commentary
  • Hypothesis and Theory
  • Methods
  • Mini Review
  • Opinion
  • Original Research
  • Perspective
  • Review
  • Technology and Code

Keywords: Deep Learning in Genomics, Single-Cell RNA Sequencing Analysis, Computational Biology, scRNAseq, data analysis, imputation, gene ontology, disease diagnosis, drug discovery, clustering, normalization

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