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Functional annotation and pathway analysis

Guest Editor:
Giuseppe Agapito, PhD, Department of Law, Economics and Social Sciences, University "Magna Græcia" of Catanzaro, Italy


BMC Bioinformatics called for submissions to our Collection on functional annotation and pathway analysis.

This Collection welcomed submissions on novel algorithms, computational methods and tools for pathway analysis and the functional annotation of genes and proteins. This includes, but is not limited to, new databases for annotated sequences and pathways, computational solutions to standardization challenges, improvements on automated annotation procedures, and tools and platforms for the visualization of annotation and pathway analysis results.

Meet the Guest Editor

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Giuseppe Agapito: Department of Law, Economics and Social Sciences, University "Magna Græcia" of Catanzaro, Italy

Dr Giuseppe Agapito is presently an Associate Professor at the "Magna Græcia" University in Catanzaro, Italy, where he earned his PhD from in 2013. His research interests are focused on bioinformatics, parallel and distributed computing, machine learning, and biological network analysis. He has written or co-written more than 100 academic papers on bioinformatics and machine learning. Dr Agapito is also a member of the editorial board and guest editor for various international journals, such as BMC Bioinformatics, Frontiers in Bioinformatics, and PeerJ Computer Science.


About the Collection

BMC Bioinformatics is calling for submissions to our Collection on functional annotation and pathway analysis.

Functional annotation is a fundamental step in omics data analysis. The annotation of genes and proteins describes their complete biological identities, including biological functions, pathways they are involved in and localization.

Pathway analysis, also called functional enrichment analysis, is used to identify particularly abundant pathways in a set of genes, thus reducing the amount of data to a more manageable size.

Combined, these techniques enable the analysis of increasingly emerging high-throughput data and shed light into the biological role of molecular mechanisms in disease and pathogenicity.

This Collection welcomes submissions on novel algorithms, computational methods and tools for pathway analysis and the functional annotation of genes and proteins. This includes, but is not limited to, new databases for annotated sequences and pathways, computational solutions to standardization challenges, improvements on automated annotation procedures, and tools and platforms for the visualization of annotation and pathway analysis results.

Image credit: Tartila / stock.adobe.com

  1. Understanding the impact of gene expression in pathological processes, such as carcinogenesis, is crucial for understanding the biology of cancer and advancing personalised medicine. Yet, current methods lack ...

    Authors: Carlos Uziel Pérez Malla, Jessica Kalla, Andreas Tiefenbacher, Gabriel Wasinger, Kilian Kluge, Gerda Egger and Raheleh Sheibani-Tezerji
    Citation: BMC Bioinformatics 2025 26:97
    Content type: Research Published on:

  2. Alterations of metabolism, including changes in mitochondrial metabolism as well as glutathione (GSH) metabolism are a well appreciated hallmark of many cancers. Mitochondrial GSH (mGSH) transport is a poorly ...

    Authors: Luke Kennedy, Jagdeep K. Sandhu, Mary-Ellen Harper and Miroslava Cuperlovic-Culf
    Citation: BMC Bioinformatics 2025 26:48
    Content type: Research Published on:

  3. Advances in transcriptional profiling methods have enabled the discovery of molecular subtypes within and across traditional tissue-based cancer classifications. Such molecular subgroups hold potential for imp...

    Authors: Aideen McCabe, Gerard P. Quinn, Suneil Jain, Micheál Ó Dálaigh, Kellie Dean, Ross G. Murphy and Simon S. McDade
    Citation: BMC Bioinformatics 2024 25:362
    Content type: Software Published on:

  4. The rewiring of molecular interactions in various conditions leads to distinct phenotypic outcomes. Differential network analysis (DINA) is dedicated to exploring these rewirings within gene and protein netwo...

    Authors: Pietro Hiram Guzzi, Arkaprava Roy, Marianna Milano and Pierangelo Veltri
    Citation: BMC Bioinformatics 2024 25:359
    Content type: Research Published on:

  6. Cancer is one of the leading causes of deaths worldwide. Survival analysis and prediction of cancer patients is of great significance for their precision medicine. The robustness and interpretability of the su...

    Authors: Shuo Wang, Yuanning Liu, Hao Zhang and Zhen Liu
    Citation: BMC Bioinformatics 2024 25:133
    Content type: Research Published on:

Submission Guidelines

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This Collection welcomes submission of original Research Articles. Should you wish to submit a different article type, please read our submission guidelines to confirm that type is accepted by the journal. Articles for this Collection should be submitted via our submission system, Snapp. During the submission process you will be asked whether you are submitting to a Collection, please select "Functional annotation and pathway analysis" from the dropdown menu.

Articles will undergo the journal’s standard peer-review process and are subject to all of the journal’s standard policies. Articles will be added to the Collection as they are published.

The Editors have no competing interests with the submissions which they handle through the peer review process. The peer review of any submissions for which the Editors have competing interests is handled by another Editorial Board Member who has no competing interests.