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Riccardi, Christopher; Koper, Piotr; Innocenti, Gabriel; diCenzo, George C.; Fondi, Marco; Mengoni, Alessio; Perrin, Elena

Independent origins and evolution of the secondary replicons of the class Gammaproteobacteria

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Microbiology Society, 2023

Published in: Microbial Genomics
Riccardi, Christopher; Passeri, Iacopo; Cangioli, Lisa; Fagorzi, Camilla; Fondi, Marco; Mengoni, Alessio

Crossing Bacterial Genomic Features and Methylation Patterns with MeStudio: An Epigenomic Analysis Tool

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MDPI AG, 2022

Published in: International Journal of Molecular Sciences
Daly, Giulia; Ghini, Veronica; Adessi, Alessandra; Fondi, Marco; Buchan, Alison; Viti, Carlo

Towards a mechanistic understanding of microalgae–bacteria interactions: integration of metabolomic analysis and computational models

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Oxford University Press (OUP), 2022

Published in: FEMS Microbiology Reviews
diCenzo, George C.; Tesi, Michelangelo; Pfau, Thomas; Mengoni, Alessio; Fondi, Marco

Genome-scale metabolic reconstruction of the symbiosis between a leguminous plant and a nitrogen-fixing bacterium

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Springer Science and Business Media LLC, 2020

Published in: Nature Communications
Zoledowska, Sabina; Presta, Luana; Fondi, Marco; Decorosi, Francesca; Giovannetti, Luciana; Mengoni, Alessio; Lojkowska, Ewa

Metabolic Modeling of Pectobacterium parmentieri SCC3193 Provides Insights into Metabolic Pathways of Plant Pathogenic Bacteria

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MDPI AG, 2019

Published in: Microorganisms
Lenzini, Leonardo; Di Patti, Francesca; Livi, Roberto; Fondi, Marco; Fani, Renato; Mengoni, Alessio

A Method for the Structure-Based, Genome-Wide Analysis of Bacterial Intergenic Sequences Identifies Shared Compositional and Functional Features

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MDPI AG, 2019

Published in: Genes
Presta, Luana; Bosi, Emanuele; Mansouri, Leila; Dijkshoorn, Lenie; Fani, Renato; Fondi, Marco

Constraint-based modeling identifies new putative targets to fight colistin-resistant A. baumannii infections

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Springer Science and Business Media LLC, 2017

Published in: Scientific Reports
Maida, Isabel; Chiellini, Carolina; Mengoni, Alessio; Bosi, Emanuele; Firenzuoli, Fabio; Fondi, Marco; Fani, Renato

Antagonistic interactions between endophytic cultivable bacterial communities isolated from the medicinal plant Echinacea purpurea

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Wiley, 2016

Published in: Environmental Microbiology
Bosi, Emanuele; Monk, Jonathan M.; Aziz, Ramy K.; Fondi, Marco; Nizet, Victor; Palsson, Bernhard Ø.

Comparative genome-scale modelling of Staphylococcus aureus strains identifies strain-specific metabolic capabilities linked to pathogenicity

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Proceedings of the National Academy of Sciences, 2016

Published in: Proceedings of the National Academy of Sciences
Bosi, Emanuele; Monk, Jonathan M.; Aziz, Ramy K.; Fondi, Marco; Nizet, Victor; Palsson, Bernhard Ø.

Comparative genome-scale modelling of Staphylococcus aureus strains identifies strain-specific metabolic capabilities linked to pathogenicity

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National Academy of Sciences, 2016

Published in: Proceedings of the National Academy of Sciences of the United States of America
Papaleo, Maria Cristiana; Fondi, Marco; Maida, Isabel; Perrin, Elena; Bevivino, Annamaria; Dalmastri, Claudia; Fani, Renato

Analysis of a Pool of Small Plasmids from Soil Heterotrophic Cultivable Bacterial Communities

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Bentham Science Publishers Ltd., 2015

Published in: The Open Microbiology Journal
Orlandini, Valerio; Emiliani, Giovanni; Fondi, Marco; Maida, Isabel; Perrin, Elena; Fani, Renato

Network Analysis of Plasmidomes: The Azospirillum brasilense Sp245 Case

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Hindawi Limited, 2014

Published in: International Journal of Evolutionary Biology
Maida, Isabel; Fondi, Marco; Orlandini, Valerio; Emiliani, Giovanni; Papaleo, Maria Cristiana; Perrin, Elena; Fani, Renato

Origin, duplication and reshuffling of plasmid genes: Insights from Burkholderia vietnamiensis G4 genome

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Elsevier BV, 2014

Published in: Genomics
Maida, Isabel; Fondi, Marco; Papaleo, Maria Cristiana; Perrin, Elena; Fani, Renato

The Gene Flow between Plasmids and Chromosomes: Insights from Bioinformatics Analyses

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Bentham Science Publishers Ltd., 2011

Published in: The Open Applied Informatics Journal
Franchi, Alessandro; Palomba, Annarita; Fondi, Cristina; Miligi, Lucia; Paglierani, Milena; Pepi, Monica; Santucci, Marco

Immunohistochemical investigation of tumorigenic pathways in sinonasal intestinal-type adenocarcinoma. A tissue microarray analysis of 62 cases : Tumorigenic pathways in sinonasal intestinal type adenocarcinoma : Tumorigenic pathways in sinonasal intestinal type adenocarcinoma

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Wiley, 2011

Published in: Histopathology
Papaleo, Maria Cristiana; Perrin, Elena; Maida, Isabel; Fondi, Marco; Fani, Renato; Vandamme, Peter

Identification of species of the Burkholderia cepacia complex by sequence analysis of the hisA gene

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Microbiology Society, 2010

Published in: Journal of Medical Microbiology
Franchi, Alessandro; Fondi, Cristina; Paglierani, Milena; Pepi, Monica; Gallo, Oreste; Santucci, Marco

Epidermal growth factor receptor expression and gene copy number in sinonasal intestinal type adenocarcinoma

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Elsevier BV, 2009

Published in: Oral Oncology
Bosi, Emanuele; Donati, Beatrice; Galardini, Marco; Brunetti, Sara; Sagot, Marie-France; Lió, Pietro; Crescenzi, Pierluigi; Fani, Renato; Fondi, Marco

MeDuSa: a multi-draft based scaffolder

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Oxford University Press (OUP), 2015

Published in: Bioinformatics
Calvanese, Marzia; Balestra, Cecilia; Colarusso, Andrea; Lauro, Concetta; Riccardi, Christopher; Fondi, Marco; Parrilli, Ermenegilda; Tutino, Maria Luisa

Development of high-copy number plasmids in Pseudoalteromonas haloplanktis TAC125

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Springer Science and Business Media LLC, 2023

Published in: Applied Microbiology and Biotechnology
Romaniuk, Krzysztof; Styczynski, Michal; Decewicz, Przemyslaw; Buraczewska, Oliwia; Uhrynowski, Witold; Fondi, Marco; Wolosiewicz, Marcin; Szuplewska, Magdalena; Dziewit, Lukasz

Diversity and Horizontal Transfer of Antarctic Pseudomonas spp. Plasmids

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MDPI AG, 2019

Published in: Genes

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