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Computational Genomics and Bioinformatics in Microbiology

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 January 2026 | Viewed by 993

Special Issue Editor


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Guest Editor
School of Science, Constructor University, Campus Ring 6, 28759 Bremen, Germany
Interests: genomic data analysis; computational biology; infectiology and epidemiology; synthetic biology

Special Issue Information

Dear Colleagues,

Through continued advancements in high-throughput technology, the raw experimental data extracted from genomes of microorganisms continue to grow at an increasing rate. As viruses, archaea, bacteria, fungi and unicellular protozoa together are the main contributors to the Earth’s total biomass, its climate, and the known spectrum of human, animal and plant diseases, we must rise to this data challenge through scalable computational methods that help to uncover the intrinsic and contextual meaning of their genomes. At the same time, these data allow us to explore microbial genomes at unprecedented resolutions and precisions in terms of evolutionary time, structural organisation and their functional elements. Many of these data are already in public repositories waiting to be (re-)analysed with novel computational and bioinformatics methods.

With this preamble, this Special Issue invites research contributions in comparative, structural, and functional genomics that, from fine-grained details to large-scale organization, use computational methods to microbial genomics data.

Topics of interest include, but are not limited to, computational and bioinformatics approaches to comparative genomics in the context of emerging infectious diseases, genomic and genetic signatures of cross-species and cross-domain interactions between macro- and microorganisms (e.g., host-pathogen genomics), and large-scale organisational principles of microbial genomes in data-driven structural genomics.

Dr. Andreas Martin Lisewski
Guest Editor

Manuscript Submission Information

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Keywords

  • computational microbial genomics
  • comparative genomics
  • structural genomics
  • functional genomics
  • genomic data bioinformatics

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Published Papers (1 paper)

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Research

13 pages, 1935 KB  
Article
Enteroflow: Automated Pipeline for In Silico Characterization of Enterococcus faecium/faecalis Isolates from Short Reads
by Daniele Smedile, Elena L. Diaconu, Matteo Grelloni, Barbara Middei, Virginia Carfora, Antonio Battisti, Patricia Alba and Alessia Franco
Int. J. Mol. Sci. 2025, 26(19), 9441; https://doi.org/10.3390/ijms26199441 - 26 Sep 2025
Viewed by 439
Abstract
Antimicrobial resistance (AMR) is a critical global health challenge that affects both human and animal populations. In accordance with the One Health paradigm, AMR has been monitored in Italy since 2014 in major zoonotic pathogens and opportunistic commensal bacteria from animal productions, in [...] Read more.
Antimicrobial resistance (AMR) is a critical global health challenge that affects both human and animal populations. In accordance with the One Health paradigm, AMR has been monitored in Italy since 2014 in major zoonotic pathogens and opportunistic commensal bacteria from animal productions, in the frame of the EU Harmonized Monitoring Program for AMR (according to EU Decision 2013/652, repealed by EU Decision 2020/1729), conducted by the Italian National Reference Center (CRN-AR) and National Reference Laboratory (NRL-AR) for antimicrobial resistance at the “Istituto Zooprofilattico Sperimentale del Lazio e della Toscana (IZSLT)” (on behalf of the Italian Ministry of Health). Among all monitored bacterial species, the commensal Enterococcus (E.) faecium and E. faecalis have emerged as opportunistic human pathogens with increasing AMR profiles. To address this challenge, the CRN-AR and NRL-AR have developed a custom bioinformatic pipeline, named Enteroflow, which enables the efficient analysis of high-throughput sequencing (HTS) data for the genomic characterization of E. faecium/faecalis isolates. A pivotal feature in this tool is the integration of Nextflow’s workflow manager and Domain Specific Language (DSL), ensuring the reproducibility and scalability of genomic analyses while allowing the monitoring of processes and computational performances. The list of tools included in the workflow spans from short read assemblers to genomic characterization tools for AMR and virulence gene detection and plasmid replicon typing, with results also being combined in structured and usable reports. These developments represent a major step forward in supporting the surveillance efforts and mitigation strategies for AMR in zoonotic and commensal bacteria. Full article
(This article belongs to the Special Issue Computational Genomics and Bioinformatics in Microbiology)
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