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Computational Methods for Integrative Cancer Data Analysis

A special issue of Cancers (ISSN 2072-6694). This special issue belongs to the section "Cancer Informatics and Big Data".

Deadline for manuscript submissions: 10 July 2026 | Viewed by 598

Special Issue Editor

Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
Interests: computational medicine; bioinformatics; data analysis; cancer

Special Issue Information

Dear Colleagues,

This Special Issue focuses on computational and bioinformatics advances that enable a deeper understanding of cancer biology and improved clinical decision-making. With the rapid growth of high-dimensional data from genomics, transcriptomics, proteomics, spatial profiling, and digital pathology, there is an urgent need for robust analytical frameworks that integrate multimodal data and translate molecular patterns into biological and clinical insights. We welcome contributions that develop or apply novel bioinformatic methods for cancer detection, classification, prognosis, therapeutic response prediction, and biomarker discovery. Topics of interest include, but are not limited to, machine learning and deep learning approaches, multi-task and multi-omics integration, advanced mass spectrometry data analysis, spatial and single-cell analytics, and interpretable models for clinical translation. By highlighting innovative computational methodologies and real-world cancer applications, this Special Issue aims to bridge methodological development and translational oncology research.

Dr. Kai Li
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 communications are invited. For planned papers, a title and short abstract (about 250 words) can be sent to the Editorial Office for assessment.

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Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2900 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

  • cancer bioinformatics
  • multi-omics integration
  • machine learning
  • translational oncology

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Published Papers (1 paper)

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Research

27 pages, 6337 KB  
Article
Integrated Characterization of AP-2δ Reveals Distinct Regulatory Architecture in Lung Adenocarcinoma and Lung Squamous Cell Carcinoma
by Damian Kołat, Weronika Kruczkowska, Żaneta Kałuzińska-Kołat, Cromwel Tepap Zemnou, Mateusz Kciuk, Lin-Yong Zhao, Renata Kontek and Elżbieta Płuciennik
Cancers 2026, 18(8), 1278; https://doi.org/10.3390/cancers18081278 - 17 Apr 2026
Viewed by 322
Abstract
Background/Objectives: AP-2δ, encoded by TFAP2D, is one of the least characterized members of the AP-2 transcription factor family, although available evidence suggests biologically relevant roles in lung cancer that have not yet been thoroughly examined. The aim of the present study [...] Read more.
Background/Objectives: AP-2δ, encoded by TFAP2D, is one of the least characterized members of the AP-2 transcription factor family, although available evidence suggests biologically relevant roles in lung cancer that have not yet been thoroughly examined. The aim of the present study was to provide an integrated characterization of AP-2δ/TFAP2D in lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC). Methods: LUAD and LUSC data were obtained from The Cancer Genome Atlas. The analysis comprised the expression profiling of AP-2δ target genes, survival-guided TFAP2D stratification, clinical profiling, differential expression and intersection analyses, methylation-derived chromatin compartment profiling, TFAP2D-associated cofactor rewiring, and genome-wide enrichment of AP-2δ targets. In parallel, pocket prioritization was performed using an AlphaFold model of AP-2δ with cross-tool consensus mapping. Results: TFAP2D stratification delineated biologically-distinct states in both histological subtypes (LUAD and LUSC). AP-2δ target genes showed subtype-specific expression patterns and functional organization. The consistent survival association was observed for progression-free interval rather than uniformly across all endpoints. Clinical profiling was more closely associated with molecular subtype composition than broad clinicopathological differences. Differential expression analyses identified both shared and histology-dependent programs associated with TFAP2D. In the chromatin-compartment analysis, LUSC showed a broader and more coherent footprint, whereas LUAD displayed more selective cofactor rewiring. Structure-based analysis prioritized a small set of reproducible candidate pockets concentrated within ordered regions of the TF_AP-2 domain. Conclusions: AP-2δ marks biologically meaningful but histologically non-uniform regulatory states in lung cancer. These findings provide an integrated framework for understanding TFAP2D-dependent regulation in LUAD and LUSC, highlighting AP-2δ as a candidate for future mechanistic and translational investigation. Full article
(This article belongs to the Special Issue Computational Methods for Integrative Cancer Data Analysis)
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