Genomics and Bioinformatics Tools in Host-Pathogen Interactions

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Systems Microbiology".

Deadline for manuscript submissions: 31 August 2024 | Viewed by 175

Special Issue Editors

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Guest Editor
Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza Università di Roma, Rome, Italy
Interests: bioinformatics; protein interactions; disease-associated variants; host–pathogen interactions; programming; machine learning; science of learning and teaching

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Guest Editor
Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza University of Rome, Piazzale Aldo Moro, 5, 00185 Roma, Italy
Interests: structural bioinformatics; structural biology; protein evolution; protein variants; protein structure and function; protein structure prediction; protein–protein interaction; protein–ligand interaction; genome biology and evolution
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Special Issue Information

Dear Colleagues,

As one of the most significant public health challenges of our era, which include the SARS-CoV-2 pandemic and antibiotic resistance, host–pathogen interactions have garnered unprecedented attention. The study of host–pathogen interactions is crucial in understanding infection dynamics and developing therapeutic strategies. This includes the molecular and cellular dialogues occurring during infection, which involve complex signaling pathways and responses from both the host and pathogen. Computational resources and methodologies increasingly contribute to shaping our understanding of these intricate host–pathogen relationships, as well as deciphering the genomic and proteomic landscape of pathogens and their interactions with their hosts. This informs therapeutic interventions, advancing our broader comprehension of infectious diseases. Key areas of focus include the identification of the pathogen and host proteins involved, structural analyses to unveil the mechanisms of interaction and the role and pathogenicity of new variants, and the study of host immune responses. Next-generation sequencing and proteomic analyses elucidate the genomic and proteomic landscapes of pathogens and their hosts, and functional genomics shed light on the changes in gene expression, while immunoinformatics aids in predicting potential epitopes and vaccine candidates. Pathway and network analyses unravel the complex signaling pathways underlying these interactions, while machine learning applications model novel interactions.

This Special Issue aims to gather up-to-date computational studies of the interactions between pathogens and their hosts and examples of successful applications of bioinformatics tools in studying specific host–pathogen interactions, creating a comprehensive overview of the bioinformatics tools and resources available for studying host–pathogen interactions. It will cover the following topics and approaches:

  • Resources and databases for host–pathogen interaction studies;
  • Genomic and proteomic approaches for studying pathogen genomes and identifying the host and pathogen proteins involved in interactions;
  • Structural bioinformatics for the prediction and analysis of protein structures related to host–pathogen interactions;
  • How pathogen variants affect their interactions with the host;
  • Gene expression analysis in host cells during infection;
  • Pathway and network analysis of host–pathogen molecular interactions;
  • Immunoinformatics for the prediction of antigenic epitopes;
  • Antibiotic resistance;
  • Vaccine design using computational approaches;
  • Evolutionary analyses applied to the phylogenesis of pathogens and/or host–pathogen interactions. The study of the molecular evolution of virulence factors;
  • Machine learning-based predictive modeling for identifying novel host–pathogen interactions, as well as classification and clustering approaches;
  • Integration of multi-omics data: combining genomics, transcriptomics, and proteomics data to elucidate host–pathogen relationships;
  • Systems biology approaches to the study of host–pathogen interactions.

Dr. Allegra Via
Prof. Dr. Stefano Pascarella
Dr. Rino Ragno
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at 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. Microorganisms 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.


  • host–pathogen interactions
  • bioinformatics
  • genomics
  • proteomics
  • structural bioinformatics
  • functional genomics
  • immunoinformatics
  • next-generation sequencing
  • pathway analysis
  • machine learning applications

Published Papers

This special issue is now open for submission.
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