Single-Cell and Spatial Epigenomics: Methods and Applications

Dear Colleagues,

The advent of single-cell and spatial transcriptomics has transformed our ability to investigate cellular heterogeneity and tissue organization in health and disease. Unlike bulk approaches, these technologies provide unprecedented resolution, enabling the study of the molecular landscape of individual cells within their native microenvironments, revealing dynamic interactions between the host, the microbiome, and disease states. With applications ranging from cancer biology to neuroscience and infectious disease, the integration of these methods is reshaping biomedical research. However, the rapid accumulation of high-dimensional multi-omics datasets, which now frequently include epigenetic and epitranscriptomic layers, poses significant computational challenges. There is a pressing need for innovative bioinformatics tools that offer robust data analysis, visualization, and biological interpretation. This Special Issue will focus on methodological innovations and applications in single-cell and spatial transcriptomics, emphasizing the development of tools bridging computational approaches and biological insights. We welcome contributions that introduce new algorithms, pipelines, and platforms, specifically those that combine transcriptomic data with epigenetic and/or epitranscriptomic markers or that apply these multi-omics technologies to unravel disease mechanisms. By showcasing research combining experimental advances with computational ingenuity, this Special Issue will highlight the transformative role of bioinformatics in harnessing single-cell and spatial multi-omics data to advance precision medicine.

Dr. Sankarasubramanian Jagadesan
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 250 words) can be sent to the Editorial Office for assessment.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Epigenomes is an international peer-reviewed open access quarterly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.