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Dott. Marco Fondi (Post-doc)


 My general research area includes microbial genomicsbioinformatics  and metabolic modeling. I'm deeply interested in the understanding of the evolutionary dynamics responsible for the shaping of microbial genomes as well as in the design and the development of bioinformatics tools for the massive analysis of sequence data. Furthermore, the possibility to integrate several sources of biological information to unravel the behavior of major biological systems/processes also occupies a central position in my present research area. I'm involved into several genome(s) sequencing projects (e.g.Acinetobacter venetianus) focused on microorganisms of biotechnological and clinical relevance and their consequent anaysis by means of (constraints-based) metabolic modeling.
I've been a visiting post-doc at the National University of Ireland in Maynooth, in the Bioinformatics and Molecular Evolution unit headed by Prof. James McInerney. I have been a FEMS fellow in a collaboration with the Computer Lab of the University of Cambridge  under the supervision of Pietro Liò 

As on June 2104 I am the coordinator of the multi-unit PNRA project ENABLE (ExploitiNg Antarctica BiotechnologicaL potEntial: metabolic modelling for optimization of bioactive molecules biosynthesis from Antarctic bacteria). The project aims at integrating "-omics" data with in silico metabolic modeling biological systems to elucidate the biosynthetic circuits responsible for the production of bioactive molecules and to gain a complete knowledge on the metabolisms of Antarctic strains for their possible biotechnological use. Read more... 
I am a member of COMBO (florence COmputational BiOlogy group).

Super-recent publications:

Fondi M, Maida I, Perrin E, Mellera A, Mocali S, Parrilli E, Tutino ML, Liò P, Fani R.Genome-scale metabolic reconstruction and constraint-based modelling of the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125. Environ Microbiol. 2014 May 28. doi: 10.1111/1462-2920.12513. [Epub ahead of print] PubMed PMID: 4889559. Link to the paper 

Spagnoletti M, Ceccarelli D, Rieux A, Fondi M, Taviani E, Fani R, Colombo MM, Colwell RR, Balloux F. Acquisition and Evolution of SXT-R391 Integrative Conjugative Elements in the Seventh-Pandemic Vibrio cholerae Lineage. MBio. 2014 Lug 19;5(4). pii: e01356-14. doi: 10.1128/mBio.01356-14. PubMed PMID: 25139901; PubMed Central PMCID: PMC4147863. Link to the paper
Fondi M, Orlandini V, Perrin E, Maida I, Bosi E, Papaleo MC, Michaud L, Lo Giudice A, de Pascale D, Tutino ML, Liò P, Fani R. Draft genomes of three Antarctic Psychrobacter strains producing antimicrobial compounds against Burkholderia cepacia complex, opportunistic human pathogens. Mar Genomics. 2014 Feb;13:37-8. doi: 10.1016/j.margen.2013.12.009. Epub 2014 Jan 5. PubMed PMID: 24401162. Link to the paper 
Fondi M, Orlandini V, Corti G, Severgnini M, Galardini M, Pietrelli A, Fuligni F, Iacono M, Rizzi E, De Bellis G, Fani R. Enly: Improving Draft Genomes through reads Recycling. J Genomics. 2014 Apr 5;2:89-93. doi: 10.7150/jgen.7298. Collection 2014. PPubMed PMID: 25031660; PubMed Central PMCID: PMC4091449. Link to the paper
Fondi M, Rizzi E, Emiliani G, Orlandini V, Berna L, Papaleo MC, Perrin E, Maida I, Corti G, De Bellis G, Baldi F, Dijkshoorn L, Vaneechoutte M, Fani R. The genome sequence of the hydrocarbon-degrading Acinetobacter venetianus VE-C3. Res Microbiol. 2013 Jun;164(5):439-49. doi: 10.1016/j.resmic.2013.03.003. Epub 2013 Mar 23. PubMed PMID: 23528645. Link to the paper

Complete list of contributions to National and International meetings here. 
My PhD thesis (PhD_thesis_marco.pdf

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