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Molecular Informatics and AI in Cancer Research

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Informatics".

Deadline for manuscript submissions: 20 June 2026 | Viewed by 1249

Special Issue Editors


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Guest Editor
1. Rutgers, The State University of New Jersey, Newark, NJ 07102, USA
2. Phalcon, LLC, Manhasset, NY 11030, USA
Interests: medical informatics; artificial intelligence; personalized medicine; cancer; drug repositioning

E-Mail Website
Guest Editor
Department of Medicine, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ 07103, USA
Interests: cancer biology; drug design; immunology; molecular mechanisms of cancer; signal transduction; therapeutics

Special Issue Information

Dear Colleagues,

The convergence of molecular informatics and artificial intelligence (AI) is catalyzing a revolution in cancer research and care. This synergy enables the translation of vast molecular data into actionable knowledge, driving advancements across the cancer continuum from early detection and personalized medicine to drug discovery and a deeper understanding of cancer biology.

The Evolving Landscape

Cancer's complexity, driven by inter- and intratumoral heterogeneity, demands sophisticated analytical approaches. High-throughput technologies generate vast amounts of molecular data, offering deep insights and posing significant analytical challenges. Understanding molecular aberrations is paramount for effective therapies. To unlock the ultimate potential of molecular data to understand cancer progression and treatment, the context-specific incorporation of vast amounts of patient-specific data from large, curated datasets can be leveraged.

Molecular Informatics in Cancer

In oncology, molecular informatics involves systematically generating, managing, analyzing, and interpreting diverse molecular datasets (such as genomics, epigenomics, and proteomics) to illuminate cancer biology. It bridges raw molecular data and biological understanding, aiming to identify biomarkers, understand disease mechanisms, and inform the development of new therapies.

Artificial Intelligence

AI creates machines for tasks requiring human intelligence, such as reasoning, learning, and decision-making. Key capabilities include advanced data analysis, pattern recognition, automation, prediction, image analysis (e.g., medical imaging), and natural language processing (NLP) for unstructured data, including clinical notes.

The Synergistic Imperative

Molecular informatics provides structured molecular data; AI offers tools to extract knowledge from it. AI can combine this knowledge with patient-specific data to generate unique patient and cancer scenarios that identify highly accurate prognostic and treatment options for clinical applications. This synergy transforms oncology from discovery to personalized treatment. AI's capacity to analyze vast amounts of data is indispensable for navigating the molecular complexity of cancer.

Highlights

Future progress hinges on addressing challenges, including data quality, algorithmic bias, interpretability, clinical integration, and the ethical, legal, and social implications. Ultimately, this fusion heralds a new era of predictive, personalized, and equitable oncology, requiring sustained multidisciplinary collaboration and robust ethical frameworks to translate technological innovations into meaningful improvements in patient outcomes globally.

This Special Issue is supervised by Prof. Dr. Nabil Adam, Prof. Dr. Robert Wieder, and assisted by Dr. Tarek Adam.

Prof. Dr. Nabil Adam
Prof. Dr. Robert Wieder
Guest Editors

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Keywords

  • molecular informatics
  • artificial intelligence (AI)
  • cancer research
  • personalized medicine
  • high-throughput data
  • biomarkers
  • clinical applications
  • longitudinal data

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Published Papers (2 papers)

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Research

19 pages, 6525 KB  
Article
A Cytokine-Related Gene Signature for Pan-Cancer Prognostic Stratification and Malignant Phenotype Characterization
by Shih-Chieh Chen, Kai-Fu Chang, Chien-Cheng Chao, Chung-Hsien Lin, Chih-Hsuan Chang, Ching-Chung Ko, Hui-Ru Lin, Chi-Jen Wu, Chien-Han Yuan, Sachin Kumar, Dahlak Daniel Solomon, Do Thi Minh Xuan, Neethu Palekkode, Ayman Fathima, Junanda Waikhom, Chih-Yang Wang, Yung-Kuo Lee and Hui-Pu Liu
Int. J. Mol. Sci. 2026, 27(6), 2830; https://doi.org/10.3390/ijms27062830 - 20 Mar 2026
Viewed by 386
Abstract
Cytokines are central regulators of inflammation and immune responses within the tumor microenvironment and have been implicated in cancer progression and prognosis. However, the prognostic value of coordinated cytokine-related transcriptional programs across cancer types has not been systematically explored. Pan-cancer transcriptomic and clinical [...] Read more.
Cytokines are central regulators of inflammation and immune responses within the tumor microenvironment and have been implicated in cancer progression and prognosis. However, the prognostic value of coordinated cytokine-related transcriptional programs across cancer types has not been systematically explored. Pan-cancer transcriptomic and clinical data were analyzed to construct a cytokine-related prognostic signature using least absolute shrinkage and selection operator (LASSO) Cox regression. Patients were stratified into high-risk and low-risk groups based on the derived risk score. Prognostic performance was evaluated in training and test cohorts, and biological relevance was assessed through survival analyses and pathway-level investigations. A 16-gene cytokine-related signature was established that consistently stratified patients into distinct prognostic groups across multiple cancer types. High cytokine-related risk scores were significantly associated with unfavorable survival outcomes and were linked to enhanced cell cycle activity, epithelial-mesenchymal transition, and extracellular matrix remodeling. Integration of the risk score with clinical variables improved individualized survival prediction. Immunohistochemical analyses further confirmed increased protein expression of representative risk-associated genes, including pannexin 1 (PANX1) and FERM domain containing 8 (FRMD8), in multiple tumor tissues compared with corresponding normal tissues. The cytokine-related prognostic signature captures key inflammatory and immune-related programs underlying tumor aggressiveness and provides a robust tool for pan-cancer risk stratification with potential clinical utility. Full article
(This article belongs to the Special Issue Molecular Informatics and AI in Cancer Research)
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18 pages, 7668 KB  
Article
AI/ML-Assisted Detection of HMGA2 RNA Isoforms in Prostate Cancer Patient Tissue
by Bor-Jang Hwang, Oluwatunmise Akinniyi, Sharon Harrison, Denise Gibbs, Charles Waihenya, Andrew Gachii, Precious E. Dike, Bethtrice Elliott, Fahmi Khalifa, Camille Ragin and Valerie Odero-Marah
Int. J. Mol. Sci. 2026, 27(1), 196; https://doi.org/10.3390/ijms27010196 - 24 Dec 2025
Viewed by 530
Abstract
RNA In Situ Hybridization (RISH) is a powerful tool for spatial gene expression analysis, yet its quantitative use remains limited by the high cost and inaccessibility of commercial software, particularly in under-resourced settings. This study developed an Artificial Intelligence/Machine Learning (AI/ML)-assisted RISH quantification [...] Read more.
RNA In Situ Hybridization (RISH) is a powerful tool for spatial gene expression analysis, yet its quantitative use remains limited by the high cost and inaccessibility of commercial software, particularly in under-resourced settings. This study developed an Artificial Intelligence/Machine Learning (AI/ML)-assisted RISH quantification pipeline to evaluate expression patterns of High Mobility Group AT Hook-2 (HMGA2) in prostate cancer (PCa), focusing on racial disparities. We created a machine learning model capable of analyzing RISH images. Expressions of full-length (wild-type) and truncated HMGA2 isoforms were assessed in tissues from 85 men of African descent, European American, and Asian descent. A training dataset was generated for supervised learning analysis of the full cohort. RISH findings revealed that the wild-type HMGA2 isoform was significantly more abundant in tumors from men of African descent and positively correlated with increasing Gleason grade. The truncated isoform was less abundant and did not display a consistent expression pattern across racial groups. These results demonstrate the feasibility of AI/ML-based RISH quantification and suggest that elevated wild-type HMGA2 expression may represent a biomarker linked to prostate cancer aggressiveness and racial disparities. These findings highlight the importance of interdisciplinary collaboration and equitable computational tools in advancing biomarker discovery and addressing cancer health inequities. Full article
(This article belongs to the Special Issue Molecular Informatics and AI in Cancer Research)
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