Integrative Computational Methods for Second-and Third-Generation Sequencing Data

Dear Colleagues,

The advent of second- and third-generation sequencing technologies has revolutionized our capacity to investigate cellular systems at unprecedented resolutions. While short-read RNA-Seq and single-cell RNA-Seq offer high accuracy and throughput, long-read technologies such as Iso-Seq provide full-length transcript coverage, isoform-level resolution, and direct detection of epigenetic modifications. However, the integration of these heterogeneous data types presents significant algorithmic and computational challenges. This Special Issue is dedicated to highlighting novel algorithms, workflows, and frameworks designed for the integration of multi-platform sequencing data. Interdisciplinary contributions that leverage bioinformatics, machine learning, and systems biology to tackle fundamental challenges in transcriptomics and cellular regulation are especially encouraged. Papers may report on original research, discuss methodological aspects, review the current state of the art, or offer perspectives on future prospects.

Specific methods and fields of applications include, but are not limited to, the following:

• Hybrid modeling of short- and long-read transcriptomic data;
• Machine learning approaches for integrative omics;
• Noise reduction, normalization, and batch effect correction;
• Annotation pipelines leveraging long-read accuracy;
• Reference-based and reference-free cell identification;
• Cell typing in rare or heterogeneous cell populations;
• Isoform quantification and novel transcript discovery;
• Detection of tissue- or disease-specific splicing events;
• Functional implications of splicing diversity;
• Tumor-specific isoform identification and fusion detection;
• Splicing-based biomarkers and therapeutic targets;
• Single-cell multi-omics integration for tumor heterogeneity;
• Integration of gene expression, splicing, and epigenetic data;
• Open-source tools for integrative sequencing analysis;
• Longitudinal and spatial transcriptomics using multi-omics sequencing.

Prof. Dr. Hao Lin
Dr. Guojun Liu
Dr. Alexey Sarapultsev
Guest Editors

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. Computation is an international peer-reviewed open access monthly 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 1800 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.