Understanding the Genomic Mechanisms of Oncology

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

Deadline for manuscript submissions: 30 September 2024 | Viewed by 1082

Special Issue Editors


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Guest Editor
Info-CORE, Bioinformatics Unit of the I-CORE, Faculty of Medicine, The Hebrew University of Jerusalem, P.O. Box 12272, Jerusalem 91120, Israel
Interests: bioinformatics; omics; single-cell analysis; data integration; immunology

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Guest Editor
1. Department of Molecular Biology, Ariel University, Ariel 407000, Israel
2. Adelson School of Medicine, Ariel University, Ariel 407000, Israel
Interests: breast cancer genomics; medulloblastoma diagnostics; RNA epigenetics; machine learning

Special Issue Information

Dear Colleagues,

Coping with cancer requires an understanding of the cellular and molecular processes that enable tumor cells to survive, proliferate, invade and generate metastases. Over the past decade, there have been groundbreaking advancements in DNA sequencing technologies and other high-throughput platforms, leading to a new era in biology and medical sciences known as "omics". These technologies offer a wide range of applications that significantly enhance the diagnosis, prognosis and treatment of cancer. Moreover, they present new opportunities for drug development, facilitating precise and personalized medical treatments tailored to the unique molecular functions and pathways of each patient.

These innovative technologies generate an enormous amount of molecular data, allowing for the exploration of the cellular and tissue landscape of transcripts, proteins, metabolites, genomic functional regions, genome-wide mutation profiling, epigenetic modifications, as well as gene structure and activity within various types of cancers. Nevertheless, to comprehend this vast amount of information, the development of advanced computational algorithms, AI-powered tools and machine learning techniques is essential. Their vital role lies in transforming copious raw data into interpretable and actionable biological and medical knowledge.

This Special Issue in Biology on "Understanding the Genomic Mechanisms of Oncology” will focus on omics and integrated multi-omics studies. It will include both pool-level and single-cell analyses, to elucidate the mechanisms of tumor formation, tumor evasion and to understand the significant role played by the tumor microenvironment in the process of tumorigenesis. It will also highlight advanced computational methods or algorithms aimed at enhancing diagnosis, prognosis and treatment response in the field of oncology. We invite researchers to submit their experimental and/or computational research papers, review articles and short communications relevant to these fields in basic science and clinical studies. We encourage researchers to contribute their valuable work to this issue and become a part of the collective effort to advance the field of oncology genomics.

Dr. Sharona Elgavish
Dr. Mali Salmon-Divon
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 100 words) can be sent to the Editorial Office for announcement on this website.

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 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 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
  • genomics
  • proteomics
  • metabolomics
  • genome-wide mutation profiling
  • epigenetics
  • medical imaging
  • tumor microenvironment
  • machine-learning

Published Papers (1 paper)

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Research

13 pages, 2211 KiB  
Article
A Cyclic Permutation Approach to Removing Spatial Dependency between Clustered Gene Ontology Terms
by Rachel Rapoport, Avraham Greenberg, Zohar Yakhini and Itamar Simon
Biology 2024, 13(3), 175; https://doi.org/10.3390/biology13030175 - 08 Mar 2024
Viewed by 827
Abstract
Traditional gene set enrichment analysis falters when applied to large genomic domains, where neighboring genes often share functions. This spatial dependency creates misleading enrichments, mistaking mere physical proximity for genuine biological connections. Here we present Spatial Adjusted Gene Ontology (SAGO), a novel cyclic [...] Read more.
Traditional gene set enrichment analysis falters when applied to large genomic domains, where neighboring genes often share functions. This spatial dependency creates misleading enrichments, mistaking mere physical proximity for genuine biological connections. Here we present Spatial Adjusted Gene Ontology (SAGO), a novel cyclic permutation-based approach, to tackle this challenge. SAGO separates enrichments due to spatial proximity from genuine biological links by incorporating the genes’ spatial arrangement into the analysis. We applied SAGO to various datasets in which the identified genomic intervals are large, including replication timing domains, large H3K9me3 and H3K27me3 domains, HiC compartments and lamina-associated domains (LADs). Intriguingly, applying SAGO to prostate cancer samples with large copy number alteration (CNA) domains eliminated most of the enriched GO terms, thus helping to accurately identify biologically relevant gene sets linked to oncogenic processes, free from spatial bias. Full article
(This article belongs to the Special Issue Understanding the Genomic Mechanisms of Oncology)
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