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Florence Computational Biology Group

Ricerca LaboratoriComBoSelected publications

Selected publications

2023
  • Alonso-Vásquez T, Fondi M, Perrin E. Understanding Antimicrobial Resistance Using Genome-Scale Metabolic Modeling. Antibiotics (Basel). 2023 May 11;12(5):896. doi: 10.3390/antibiotics12050896. PMID: 37237798; PMCID: PMC10215601.
  • Riccardi C, Koper P, Innocenti G, diCenzo GC, Fondi M, Mengoni A, Perrin E. Independent origins and evolution of the secondary replicons of the class Gammaproteobacteria. Microb Genom. 2023 May;9(5). doi: 10.1099/mgen.0.001025. PMID: 37185344.
  • Calvanese M, Balestra C, Colarusso A, Lauro C, Riccardi C, Fondi M, Parrilli E, Tutino ML. Development of high-copy number plasmids in Pseudoalteromonas haloplanktis TAC125. Appl Microbiol Biotechnol. 2023 Apr;107(7-8):2469-2481. doi: 10.1007/s00253-023-12448-w. Epub 2023 Mar 13. PMID: 36912903; PMCID: PMC10033558.
  • Riccardi C, Calvanese M, Ghini V, Alonso-Vásquez T, Perrin E, Turano P, Giurato G, Weisz A, Parrilli E, Tutino ML, Fondi M. Metabolic Robustness to Growth Temperature of a Cold- Adapted Marine Bacterium. mSystems. 2023 Apr 27;8(2):e0112422. doi: 10.1128/msystems.01124-22. Epub 2023 Feb 27. PMID: 36847563; PMCID: PMC10134870.
2022
  • Daly G, Ghini V, Adessi A, Fondi M, Buchan A, Viti C. Towards a mechanistic understanding of microalgae-bacteria interactions: integration of metabolomic analysis and computational models. FEMS Microbiol Rev. 2022 Sep 2;46(5):fuac020. doi: 10.1093/femsre/fuac020. PMID: 35568502.
  • Riccardi C, Innocenti G, Fondi M, Bacci G. Fast, Ungapped Reads Mapping Using Squid. Int J Environ Res Public Health. 2022 Apr 29;19(9):5442. doi: 10.3390/ijerph19095442. PMID: 35564837; PMCID: PMC9103773.
  • Riccardi C, D'Angelo C, Calvanese M, Ricciardelli A, Tutino ML, Parrilli E, Fondi M. Genome analysis of a new biosurfactants source: The Antarctic bacterium Psychrobacter sp. TAE2020. Mar Genomics. 2022 Feb;61:100922. doi: 10.1016/j.margen.2021.100922. Epub 2022 Jan 3. PMID: 35058036.
2021
  • Scaling down the microbial loop: data-driven modelling of growth interactions in a diatom-bacterium co-culture, Giulia Daly, Elena Perrin, Carlo Viti, Marco Fondi, Alessandra Adessi. Environmental Microbiology Reports, http://doi.org/10.1111/1758-2229.13010  
  • Fondi M, Gonzi S, Dziurzynski M, Turano P, Ghini V, Calvanese M, Colarusso A, Lauro C, Parrilli E, Tutino ML. Modelling hCDKL5 Heterologous Expression in Bacteria. Metabolites. 2021 Jul 28;11(8):491. doi: 10.3390/metabo11080491. PMID: 34436432; PMCID: PMC8401935. https://www.mdpi.com/2218-1989/11/8/491
  • diCenzo GC, Galardini M, Fondi M. Tn-Core: Functionally Interpreting Transposon-Sequencing Data with Metabolic Network Analysis. Methods Mol Biol. 2021;2189:199-215. doi: 10.1007/978-1-0716-0822-7_15. PMID: 33180303.
2020

 

  • Elena Perrin, Veronica Ghini, Michele Giovannini, Francesca Di Patti, Barbara Cardazzo, Lisa Carraro, Camilla Fagorzi, Paola Turano, Renato Fani, Marco Fondi. Diauxie and co-utilization of carbon sources can coexist during bacterial growth in nutritionally complex environments. Nature Communications. 2020;11(1):3135. Published 2020 Jun 19. doi:10.1038/s41467-020-16872-8

 

  • George C diCenzo, Michelangelo Tesi, Thomas Pfau, Alessio Mengoni, andMarco Fondi. Genome-scale metabolic reconstruction of the symbiosis between a leguminous plant and a nitrogen-fixing bacterium. Nature Communications. 2020;11(1):3135. Published 2020 Jun 19. doi:10.1038/s41467-020-16872-8.

 

2019

 

  • Romaniuk K, Styczynski M, Decewicz P, Buraczewska O, Uhrynowski W, Fondi M, Wolosiewicz M, Szuplewska M, Dziewit L. Diversity and Horizontal Transfer of Antarctic Pseudomonas spp. Plasmids. Genes (Basel). 2019 Oct 28;10(11):850. doi: 10.3390/genes10110850. PMID: 31661808; PMCID: PMC6896180.

 

  • Lenzini L, Di Patti F, Livi R, Fondi M, Fani R, Mengoni A. A Method for the Structure-Based, Genome-Wide Analysis of Bacterial Intergenic Sequences Identifies Shared Compositional and Functional Features. Genes (Basel). 2019 Oct 22;10(10):834. doi: 10.3390/genes10100834. PMID: 31652625; PMCID: PMC6826451.

 

  • Lind AL, Lai YYY, Mostovoy Y, Holloway AK, Iannucci A, Mak ACY, Fondi M, Orlandini V, Eckalbar WL, Milan M, Rovatsos M, Kichigin IG, Makunin AI, Johnson Pokorná M, Altmanová M, Trifonov VA, Schijlen E, Kratochvíl L, Fani R, Velenský P, Rehák I, Patarnello T, Jessop TS, Hicks JW, Ryder OA, Mendelson JR 3rd, Ciofi C, Kwok PY, Pollard KS, Bruneau BG. Genome of the Komodo dragon reveals adaptations in the cardiovascular and chemosensory systems of monitor lizards. Nat Ecol Evol. 2019 Aug;3(8):1241-1252. doi: 10.1038/s41559-019-0945-8. Epub 2019 Jul 29. PMID: 31358948; PMCID: PMC6668926.

 

  • Parrilli E, Tedesco P, Fondi M, Tutino ML, Lo Giudice A, de Pascale D, Fani R. The art of adapting to extreme environments: The model system Pseudoalteromonas. Phys Life Rev. 2019 Apr 4:S1571-0645(19)30066-1. doi: 10.1016/j.plrev.2019.04.003. Epub ahead of print. PMID: 31072789.

 

  • Zoledowska S, Presta L, Fondi M, Decorosi F, Giovannetti L, Mengoni A, Lojkowska E. Metabolic Modeling of Pectobacterium parmentieri SCC3193 Provides Insights into Metabolic Pathways of Plant Pathogenic Bacteria. Microorganisms. 2019 Apr 5;7(4):101. doi: 10.3390/microorganisms7040101. PMID: 30959803; PMCID: PMC6518042.

 

  • diCenzo GC, Mengoni A, Fondi M. Tn-Core: A Toolbox for Integrating Tn-seq Gene Essentiality Data and Constraint-Based Metabolic Modeling. ACS Synth Biol. 2019 Jan 18;8(1):158-169. doi: 10.1021/acssynbio.8b00432. Epub 2018 Dec 27. PMID: 30525460.

 

  • diCenzo GC, Zamani M, Checcucci A, Fondi M, Griffitts JS, Finan TM, Mengoni A. Multidisciplinary approaches for studying rhizobium-legume symbioses. Can J Microbiol. 2019 Jan;65(1):1-33. doi: 10.1139/cjm-2018-0377. Epub 2018 Sep 11. PMID: 30205015.

 

2018

 

  • diCenzo GC, Mengoni A, Fondi M. Tn-Core: A Toolbox for Integrating Tn-seq Gene Essentiality Data and Constraint-Based Metabolic Modeling. ACS Synth Biol. 2019 Jan 18;8(1):158-169. doi: 10.1021/acssynbio.8b00432. Epub 2018 Dec 27. PMID: 30525460.

 

  • Checcucci A, diCenzo GC, Ghini V, Bazzicalupo M, Becker A, Decorosi F, Döhlemann J, Fagorzi C, Finan TM, Fondi M, Luchinat C, Turano P, Vignolini T, Viti C, Mengoni A. Creation and Characterization of a Genomically Hybrid Strain in the Nitrogen-Fixing Symbiotic Bacterium Sinorhizobium meliloti. ACS Synth Biol. 2018 Oct 19;7(10):2365-2378. doi: 10.1021/acssynbio.8b00158. Epub 2018 Oct 3. PMID: 30223644.

 

  • Maggini V, Miceli E, Fagorzi C, Maida I, Fondi M, Perrin E, Mengoni A, Bogani P, Chiellini C, Mocali S, Fabiani A, Decorosi F, Giovannetti L, Firenzuoli F, Fani R. Antagonism and antibiotic resistance drive a species-specific plant microbiota differentiation in Echinacea spp. FEMS Microbiol Ecol. 2018 Aug 1;94(8). doi: 10.1093/femsec/fiy118. PMID: 29912319.

 

  • diCenzo GC, Benedict AB, Fondi M, Walker GC, Finan TM, Mengoni A, Griffitts JS. Robustness encoded across essential and accessory replicons of the ecologically versatile bacterium Sinorhizobium meliloti. PLoS Genet. 2018 Apr 19;14(4):e1007357. doi: 10.1371/journal.pgen.1007357. PMID: 29672509; PMCID: PMC5929573.

 

  • Di Salvo M, Pinatel E, Talà A, Fondi M, Peano C, Alifano P. G4PromFinder: an algorithm for predicting transcription promoters in GC-rich bacterial genomes based on AT-rich elements and G-quadruplex motifs. BMC Bioinformatics. 2018 Feb 6;19(1):36. doi: 10.1186/s12859-018-2049-x. PMID: 29409441; PMCID: PMC5801747.

 

  • Fondi M. Modelling the Kinetic Response to Nutrient Fluctuations. Trends Microbiol. 2018 Jan;26(1):4-5. doi: 10.1016/j.tim.2017.11.009. Epub 2017 Nov 24. PMID: 29239769.

 

  • Vignolini T, Mengoni A, Fondi M. Template-Assisted Metabolic Reconstruction and Assembly of Hybrid Bacterial Models. Methods Mol Biol. 2018;1716:177-196. doi: 10.1007/978-1-4939-7528-0_8. PMID: 29222754.

 

 

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