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Computer Analysis for Molecular Pathological 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 October 2025 | Viewed by 1477

Special Issue Editor


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Guest Editor
Smilow Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA
Interests: machine learning; neural network; artificial intelligence; immuno-oncology; immuno-informatics; cancer neo antigens discovery; computational cancer genomics; molecular dynamics; AI digital pathology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The advancements in computing technologies and the rapid development of increasingly sophisticated AI applications have highlighted the growing need for artificial intelligence in the molecule medical and biological fields. Recent literature is increasingly enriched with applications aimed at processing and analyzing big data derived from molecule pathological biospecimens. Once perceived as a field with limited innovation, molecule pathology is now experiencing an intense period of insights, discoveries, and improvements in diagnostic accuracy thanks to machine learning and the collaboration of scientists from exact sciences who are increasingly focusing on applying AI algorithms in molecule pathology.

With this in mind, I am pleased to introduce this particular issue that is dedicated to those who wish to contribute to developing computer analysis in molecule pathology. This special issue will cover multiple areas of interest, ranging from biomedical image recognition and classification by convolutional neural networks to foundation models and multimodal learning for integrating pathology data with genomic and proteomic sequencing data and identifying new biomarkers, both for diagnosis and as therapeutic targets.

I warmly invite you to participate in this unique Special Issue, which has the potential to shape the future of molecule pathology significantly.

Sincerely,  

Dr. Luca Zammataro
Guest Editor

Manuscript Submission Information

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Keywords

  • machine learning
  • artifical intelligence
  • large language models
  • pathology
  • digital pathology
  • multimodal learning

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Published Papers (1 paper)

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Research

15 pages, 3372 KiB  
Article
Identification of Endometriosis Pathophysiologic-Related Genes Based on Meta-Analysis and Bayesian Approach
by Jieun Kang, Kwangjin Ahn, Jiyeon Oh, Taesic Lee, Sangwon Hwang, Young Uh and Seong Jin Choi
Int. J. Mol. Sci. 2025, 26(1), 424; https://doi.org/10.3390/ijms26010424 - 6 Jan 2025
Viewed by 1255
Abstract
Endometriosis is a complex disease with diverse etiologies, including hormonal, immunological, and environmental factors; however, its exact pathogenesis remains unknown. While surgical approaches are the diagnostic and therapeutic gold standard, identifying endometriosis-associated genes is a crucial first step. Five endometriosis-related gene expression studies [...] Read more.
Endometriosis is a complex disease with diverse etiologies, including hormonal, immunological, and environmental factors; however, its exact pathogenesis remains unknown. While surgical approaches are the diagnostic and therapeutic gold standard, identifying endometriosis-associated genes is a crucial first step. Five endometriosis-related gene expression studies were selected from the available datasets. Approximately, 14,167 genes common to these 5 datasets were analyzed for differential expression. Meta-analyses utilized fold-change values and standard errors obtained from each analysis, with the binomial and continuous datasets contributing to endometriosis presence and endometriosis severity meta-analysis, respectively. Approximately 160 genes showed significant results in both meta-analyses. For Bayesian analysis, endometriosis-related single nucleotide polymorphisms (SNPs), the human transcription factor catalog, uterine SNP-related gene expression, disease–gene databases, and interactome databases were utilized. Twenty-four genes, present in at least three or more databases, were identified. Network analysis based on Pearson’s correlation coefficients revealed the HLA-DQB1 gene with both a high score in the Bayesian analysis and a central position in the network. Although ZNF24 had a lower score, it occupied a central position in the network, followed by other ZNF family members. Bayesian analysis identified genes with high confidence that could support discovering key diagnostic biomarkers and therapeutic targets for endometriosis. Full article
(This article belongs to the Special Issue Computer Analysis for Molecular Pathological Research)
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