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

  • 113

    Total views and downloads

Participate in this topic

Submit your idea

You will be redirected to our submission process.

Submit your manuscript summarySubmit your manuscript

About this Research Topic

Submission deadlines

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

  2. This Research Topic is still accepting articles.

    1. Check author guidelines

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

Article types and fees

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

Articles that are accepted for publication by our external editors following rigorous peer review incur a publishing fee charged to Authors, institutions, or funders.

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

Important note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.

Topic editors

Topic coordinators

Frequently asked questions

  • Frontiers' Research Topics are collaborative hubs built around an emerging theme.Defined, managed, and led by renowned researchers, they bring communities together around a shared area of interest to stimulate collaboration and innovation.

    Unlike section journals, which serve established specialty communities, Research Topics are pioneer hubs, responding to the evolving scientific landscape and catering to new communities.

  • The goal of Frontiers' publishing program is to empower research communities to actively steer the course of scientific publishing. Our program was implemented as a three-part unit with fixed field journals, flexible specialty sections, and dynamically emerging Research Topics, connecting communities of different sizes and maturity.

    Research Topics originate from the scientific community. Many of our Research Topics are suggested by existing editorial board members who have identified critical challenges or areas of interest in their field.

  • As an editor, Research Topics will help you build your journal, as well as your community, around emerging, cutting-edge research. As research trailblazers, Research Topics attract high-quality submissions from leading experts all over the world.

    A thriving Research Topic can potentially evolve into a new specialty section if there is sustained interest and a growing community around it.

  • Each Research Topic must be approved by the specialty chief editor, and it falls under the editorial oversight of our editorial boards, supported by our in-house research integrity team. The same standards and rigorous peer review processes apply to articles published as part of a Research Topic as for any other article we publish.

    In 2023, 80% of the Research Topics we published were edited or co-edited by our editorial board members, who are already familiar with their journal's scope, ethos, and publishing model. All other topics are guest edited by leaders in their field, each vetted and formally approved by the specialty chief editor.

  • Publishing your article within a Research Topic with other related articles increases its discoverability and visibility, which can lead to more views, downloads, and citations. Research Topics grow dynamically as more published articles are added, causing frequent revisiting, and further visibility.

    As Research Topics are multidisciplinary, they are cross-listed in several fields and section journals – increasing your reach even more and giving you the chance to expand your network and collaborate with researchers in different fields, all focusing on expanding knowledge around the same important topic.

    Our larger Research Topics are also converted into ebooks and receive social media promotion from our digital marketing team.

     

  • Frontiers offers multiple article types, but it will depend on the field and section journals in which the Research Topic will be featured. The available article types for a Research Topic will appear in the drop-down menu during the submission process.

    Check available article types here 

  • Yes, we would love to hear your ideas for a topic. Most of our Research Topics are community-led and suggested by researchers in the field. Our in-house editorial team will contact you to talk about your idea and whether you’d like to edit the topic. If you’re an early-stage researcher, we will offer you the opportunity to coordinate your topic, with the support of a senior researcher as the topic editor. 

    Suggest your topic here 

  • A team of guest editors (called topic editors) lead their Research Topic. This editorial team oversees the entire process, from the initial topic proposal to calls for participation, the peer review, and final publications.

    The team may also include topic coordinators, who help the topic editors send calls for participation, liaise with topic editors on abstracts, and support contributing authors. In some cases, they can also be assigned as reviewers.

  • As a topic editor (TE), you will take the lead on all editorial decisions for the Research Topic, starting with defining its scope. This allows you to curate research around a topic that interests you, bring together different perspectives from leading researchers across different fields and shape the future of your field. 

     

    You will choose your team of co-editors, curate a list of potential authors, send calls for participation and oversee the peer review process, accepting or recommending rejection for each manuscript submitted.

  • As a topic editor, you're supported at every stage by our in-house team. You will be assigned a single point of contact to help you on both editorial and technical matters. Your topic is managed through our user-friendly online platform, and the peer review process is supported by our industry-first AI review assistant (AIRA).

  • If you’re an early-stage researcher, we will offer you the opportunity to coordinate your topic, with the support of a senior researcher as the topic editor. This provides you with valuable editorial experience, improving your ability to critically evaluate research articles and enhancing your understanding of the quality standards and requirements for scientific publishing, as well as the opportunity to discover new research in your field, and expand your professional network.

  • Yes, certificates can be issued on request. We are happy to provide a certificate for your contribution to editing a successful Research Topic.

  • Research Topics thrive on collaboration and their multi-disciplinary approach around emerging, cutting-edge themes, attract leading researchers from all over the world.

  • As a topic editor, you can set the timeline for your Research Topic, and we will work with you at your pace. Typically, Research Topics are online and open for submissions within a few weeks and remain open for participation for 6 – 12 months. Individual articles within a Research Topic are published as soon as they are ready.

    Find out more about our Research Topics

  • Our fee support program ensures that all articles that pass peer review, including those published in Research Topics, can benefit from open access – regardless of the author's field or funding situation.

    Authors and institutions with insufficient funding can apply for a discount on their publishing fees. A fee support application form is available on our website.

  • In line with our mission to promote healthy lives on a healthy planet, we do not provide printed materials. All our articles and ebooks are available under a CC-BY license, so you can share and print copies.

     

Manuscripts can be submitted to this Research Topic via the main journal or any other participating journal.

Submit your idea

You will be redirected to our submission process.

Submit your manuscript summarySubmit your manuscript

Impact

  • 113Topic views
View impact