Multi-Omics Data Integration in Complex Diseases (2nd Edition)

A special issue of Biology (ISSN 2079-7737). This special issue belongs to the section "Bioinformatics".

Deadline for manuscript submissions: 31 January 2027 | Viewed by 1867

Special Issue Editors

School of Science, Technology, and Engineering, University of the Sunshine Coast, Maroochydore, QSL 4558, Australia
Interests: bioinformatics; disease genomics; big data integration
Special Issues, Collections and Topics in MDPI journals

E-Mail Website
Guest Editor
Institute for Biomedical Technologies-National Research Council (ITB-CNR), Via Fratelli Cervi 93, 20090 Segrate, MI, Italy
Interests: proteomics; liquid chromatography; mass-spectrometry; computational biology methods; biomarker discovery; systems biology; protein–protein interaction network; co-expression networks
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Genetic and multifactorial diseases kill millions of people worldwide. These include diabetes, cardiovascular disease, respiratory disease, Parkinson's disease, Alzheimer's disease, and many forms of cancer.

The molecular causes of these diseases can have multilevel effects, ranging from gene expression to protein and metabolic alterations.

To shed light on these mechanisms, genomic, transcriptomic, proteomic, and metabolomic technologies provide essential support, as do increasingly robust and comprehensive molecular network models.

Although integrating and interpreting the complexity of different molecular levels remains a challenge, these strategies represent a promising starting point for unravelling the influence molecular interactions underlying complex diseases. In addition to providing a holistic description of emerging mechanisms, they can identify target molecules whose discovery could improve and accelerate the development of increasingly precise and accurate drugs.

Furthermore, in this scenario, the roles of innovative omics technologies, such as single-cell or imaging technologies, as well as computational strategies based on artificial intelligence, are increasingly impactful.

Based on these premises, this Special Issue will collect manuscripts that provide valuable information for the clinical, basic, and applied drug development research communities.

Specifically, we invite submissions on the following:

(1) Molecular insights through the integration of multiomics data and molecular networks;

(2) Novel computational frameworks for the integration and interpretation of large amounts of omics data;

(3) Diagnostic strategies based on omics and computational methods such as artificial intelligence;

(4) Identification of molecular targets for the development of new drugs.

We accept a varied types of manuscripts, including original research articles and meta-analyses, timely reviews, and short communications.

Dr. Min Zhao
Dr. Dario Di Silvestre
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. Biology is an international peer-reviewed open access semimonthly 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 2700 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.

Keywords

  • omics
  • data integration
  • computational biology
  • network analysis
  • artificial intelligence

Benefits of Publishing in a Special Issue

  • Ease of navigation: Grouping papers by topic helps scholars navigate broad scope journals more efficiently.
  • Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
  • Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
  • External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
  • Reprint: MDPI Books provides the opportunity to republish successful Special Issues in book format, both online and in print.

Further information on MDPI's Special Issue policies can be found here.

Related Special Issue

Published Papers (2 papers)

Order results
Result details
Select all
Export citation of selected articles as:

Research

20 pages, 3116 KB  
Article
Exploring the Prognostic, Mutational and Therapeutic Potential of ANXA2 in Ovarian Cancer via Multi-Omics and In Silico Approach
by Prithvi Singh, Joyeeta Talukdar, Hajed Obaid A. Alharbi, Wanian M. Alwanian, Indrakant Kumar Singh and Arshad Husain Rahmani
Biology 2026, 15(7), 523; https://doi.org/10.3390/biology15070523 - 25 Mar 2026
Viewed by 675
Abstract
Background: Among gynecological malignancies, ovarian cancer (OC) remains a leading cause of mortality worldwide, often characterized by the highest fatality-to-case ratio due to its asymptomatic progression and late-stage detection. Despite substantial investigation, the root cause of disease development and pathology remains unknown. Early [...] Read more.
Background: Among gynecological malignancies, ovarian cancer (OC) remains a leading cause of mortality worldwide, often characterized by the highest fatality-to-case ratio due to its asymptomatic progression and late-stage detection. Despite substantial investigation, the root cause of disease development and pathology remains unknown. Early detection is critical for improving OC prognosis. Unfortunately, because of the lack of identifiable symptoms in the early stages, the disease is frequently detected late. As a result, regular check-ups, being aware of risk factors, and paying attention to unusual symptoms can all help discover OC early. Apolipoproteins (APOs) and Annexins (ANXs) have recently been linked to OC. Aim: We conducted a cutting-edge bioinformatics investigation to find novel therapeutic targets and precise biomarkers linked to OC against APO and ANX. Methods: We started by compiling the ANX and APO families via HUGO Gene Nomenclature Committee (HGNC) homepage. Next, we accessed GEPIA2 to compare the relative messenger RNA (mRNA) expression levels of all ANX and APO family members across the cancer genome atlas (TCGA)-OC cohort and matched normal and GTEx data. Prognostic analysis of all significantly expressed ANXs and APOs was performed via Kaplan–Meier (KM) plotter. cBioPortal was used for mutational analysis of prognostic ANXs and APOs. Finally, we ran functional enrichment, molecular docking, and molecular dynamics (MD) simulation analyses. Results: Overall, the results suggest that ANXA2 and its related genetic changes represent potential focal points for precision oncology, offering a computational rationale for the development of target-driven therapeutic interventions in OC. Conclusions: Molecular docking and MD simulation analyses identified curcumin as a potential inhibitor of ANXA2, demonstrating stable binding affinity and structural conservation throughout the simulation period. These computational findings characterize curcumin as a promising candidate for targeting ANXA2 in OC, warranting further experimental validation to confirm its therapeutic efficacy. Full article
(This article belongs to the Special Issue Multi-Omics Data Integration in Complex Diseases (2nd Edition))
Show Figures

Figure 1

26 pages, 3644 KB  
Article
EZH2 Inhibition Restores Tumor Suppressor SFRP1 Activity by Reprogramming Extrachromosomal Circular DNA Dynamics in Ovarian Cancer
by Tao Han, Qingya Yan, Yaqi Zhang, Yu Gan, Kaifan Li, Liping Guan, Changqin Jing, Ciqing Yang, Pengfei Li, Bo Gao, Xiang Zhou and Qian Hao
Biology 2026, 15(4), 340; https://doi.org/10.3390/biology15040340 - 15 Feb 2026
Viewed by 792
Abstract
Extrachromosomal circular DNA (eccDNA) has emerged as a pivotal contributor to cancer progression, facilitating oncogene amplification, dysregulated gene expression, and tumor heterogeneity. Despite its significance in cancer, the interplay between eccDNA and key epigenetic regulators such as EZH2 remains largely unexplored. In this [...] Read more.
Extrachromosomal circular DNA (eccDNA) has emerged as a pivotal contributor to cancer progression, facilitating oncogene amplification, dysregulated gene expression, and tumor heterogeneity. Despite its significance in cancer, the interplay between eccDNA and key epigenetic regulators such as EZH2 remains largely unexplored. In this study, we systematically investigate the correlation between Tazemetostat, a highly selective EZH2 inhibitor, and alterations in the eccDNA landscape and transcriptional programs in ovarian cancer. Through integrated profiling using Circle-seq and RNA sequencing, we demonstrate that EZH2 inhibition is associated with markedly reprogrammed eccDNA dynamics. Furthermore, multi-omics integration identified that 67 genes exhibited concordant changes in both eccDNA abundance and transcript expression. Subsequent analyses also pinpointed 11 genes as putative effectors of drug response. Notably, spatial single-cell transcriptomics identified SFRP1 as the most consistently reactivated tumor suppressor across eccDNA, bulk expression, and spatial datasets, based on predefined statistical and biological criteria, by Tazemetostat. Moreover, SFRP1 was one of the genes that varied the most within cancer-associated fibroblast populations, exhibiting distinct spatial expression patterns. Taken together, this study establishes the first potential evidence that EZH2 inhibition may reprogram eccDNA dynamics to potentially restore SFRP1 tumor suppressor expression in ovarian cancer. By integrating multi-omics and spatial single-cell transcriptomics, we uncovered a novel epigenetic–eccDNA axis that may contribute to oncogenic plasticity and therapeutic resistance. This could result in a paradigm shift in targeting eccDNA-driven malignancies. Full article
(This article belongs to the Special Issue Multi-Omics Data Integration in Complex Diseases (2nd Edition))
Show Figures

Figure 1

Back to TopTop