My overall research area includes microbial pan-genomics, microbial evolution, metabolic modelling. My research activity is mainly devoted to the exploitation of computational biology for the understanding of the basic processes underlying the behaviour of biological systems, including the evolutionary dynamics that are responsible for the shaping of their genomes. Also the design and the implementation of algorithms for the analysis of massive sequence data (see  and  is a central theme in my research. Furthermore, the possibility to integrate different sources of biological information to unravel the behaviour of major biological systems/processes also occupies a central position in my present research area. By integrating "-omics" data with methodologies for modelling biological systems, I aim to developing and implementing computational and statistical models to elucidate the biosynthetic circuits responsible for the production of biological/biotechnological key molecules (including antibiotics, bacterial toxins, secondary metabolites in general). In this context, the use of constraint-based metabolic modelling techniques has gained a fundamental position in my present and future research activity. 

Personal information

Name and Surname: Marco Fondi
Born in Pistoia, Italy, 9 Settembre 1980

Current Affiliation :
Florence Computational Biology Group (ComBo)
Department of Biology, University of Florence, Via Madonna del Piano 6, 50143 Sesto F.no, Firenze Italy
Present position: Researcher
Mobile: +39-328-9573014
E-mail: marco.fondi at unifi.it – mrcfnd at gmail.com

Education and positions:

October 2017 - present, Tenure track researcher at the Dep. Of Biology, University of Florence, Italy

April 2014 – September 2017, Post-doc at the Dep. Of Biology, University of Florence, Italy

June 2012 – January 2014, FEMS research fellow, Computer Lab Cambridge University, UK (Supervisor: Prof. Pietro Liò).

January 2012 – June 2012, Visiting post-doc at the Bioinformatics and Moecular Evolution Unit, Department of Biology, National University of Ireland Maynooth, Ireland (Supervisor: Prof. James McInerney).

January 2011 – December 2011, Research Fellow (supported by Fondazione Adriano Buzzati Traverso), Dep. Of Biology, University of Florence, Italy

March 2010-December 2010, Post-doc at the Dep. Of Biology, University of Florence, Italy

2007-2009, PhD student at at the Dep. Of Biology, University of Florence, Italy. Area of the PhD program: Genetics, Microbiology and Bioinformatics

2006-20017: Research Fellow (supported by PNRA, Piano Nazionale di Ricerca in Antartide), Dep. Of Biology, University of Florence, Italy

2000-2005, Master degree ib Biology, University of Florence

Research activity

Most relevant Publications (2007-present)

• Emanuele Bosi, Jonathan Monk, Ramy Aziz, Marco Fondi, Victor Nizet,and Bernhard O. Palsson. Comparative genome-scale modelling of S. aureus strains identifies strain-specific metabolic capabilities linked to pathogenicity. PNAS, accepted for publication (Manuscript ID: 2015-23199R)
• diCenzo GC, Checcucci A, Bazzicalupo M, Mengoni A, Viti C, Dziewit L, Finan TM, Galardini M, Fondi M. Metabolic modelling reveals the specialization of secondary replicons for niche adaptation in Sinorhizobium meliloti. Nat Commun. 2016 Jul 22;7:12219. doi: 10.1038/ncomms12219. PubMed PMID: 27447951; PubMed Central PMCID: PMC4961836.
• M Fondi, A Karkman, M Tamminen, E Bosi, M Virta, R Fani, E Alm, and JO McInerney, Every gene is everywhere but the environment selects: Global geo-localization of gene sharing in environmental samples through network analysisGenome Biol Evol first published online April 29, 2016doi:10.1093/gbe/evw077
• Fondi M, Maida I, Perrin E, Orlandini V, La Torre L, Bosi E, Negroni A, Zanaroli G, Fava F, Decorosi F, Giovannetti L, Viti C, Vaneechoutte M, Dijkshoorn L, Fani R. Genomic and phenotypic characterization of the species Acinetobacter venetianus. Sci Rep. 2016 Feb 23;6:21985. doi: 10.1038/srep21985. PubMed PMID: 26902269; PubMed Central PMCID: PMC4763211.
• Bosi E, Donati B, Galardini M, Brunetti S, Sagot MF, Lió P, Crescenzi P, Fani R, Fondi M. MeDuSa: a multi-draft based scaffolder. Bioinformatics. 2015 Aug1;31(15):2443-51. doi: 10.1093/bioinformatics/btv171. Epub 2015 Mar 25. PubMed PMID: 25810435.
• 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. 2015 Mar;17(3):751-66. doi: 10.1111/1462-2920.12513. Epub 2014 Jun 30. PubMed PMID: 24889559.
• Fondi M, Liò P. Multi -omics and metabolic modelling pipelines: challenges and tools for systems microbiology. Microbiol Res. 2015 Feb;171:52-64. doi: 10.1016/j.micres.2015.01.003. Epub 2015 Jan 7. Review. PubMed PMID: 25644953.
• Fondi M, Liò P. Genome-scale metabolic network reconstruction. Methods Mol Biol. 2015;1231:233-56. doi: 10.1007/978-1-4939-1720-4_15. PubMed PMID: 25343869.
• Tamminen M, Virta M, Fani R, Fondi M. Large-scale analysis of plasmid relationships through gene-sharing networks. Mol Biol Evol. 2012 Apr;29(4):1225-40. doi: 10.1093/molbev/msr292. Epub 2011 Nov 29. PubMed PMID: 22130968.
• Fondi M, Fani R. The horizontal flow of the plasmid resistome: clues from inter-generic similarity networks. Environ Microbiol. 2010 Dec;12(12):3228-42. doi: 10.1111/j.1462-2920.2010.02295.x. PubMed PMID: 20636373.

Full list at: https://scholar.google.com/citations?user=R7cSmlIAAAAJ&hl=en

Fellowships and Grants

2012 - FEMS Advanced Research Fellowship 2012, on Genome-scale functional modelling of Antarctic bacteria: biotechnological potentials of extreme environment adapted metabolism. Supervisor: Prof. Pietro Liò, Computer Lab, University of Cambridge UK.

2012 - Short Term Travel Fellowship, Science Foundation of Ireland Incoming STTF Programme, in collaboration with the Bioinformatics and Molecular Evolution Unit, Department of Biology, National University of Ireland Maynooth, Ireland.

2013 – PNRA project call 2013. Project tile: Exploiting Antarctica biotechnological potential: metabolic modelling for optimization of bioactive molecules biosynthesis from Antarctic bacteria. Financing Istitution: Ministero dell’Istruzione, dell'Università e della Ricerca, Programma Nazionale di Ricerche in Antartide, Call 2013. Budget: 90.000 €

Visiting scientist periods

1. November 22 2008 – December 22 2008: Visiting student ar BMGE, Institut Pasteur (Paris, France). Supervisor: Dr. Simonetta Gribaldo.

2. April 6-13 2010–: Visiting student at ITB-CNR Milan, Italy. Supervisor: Dr. Gianluca De Bellis

3. October 31- November 5 2010–: Visiting researcher at University of Helsinki, Department of Applied Chemistry and Microbiology, Division of Microbiology. Supervisor: Prof Marko Virta.

4. January 2012 – June 2012. Visiting post-doc at the Bioinformatics and Molecular Evolution Unit, Department of Biology, National University of Ireland Maynooth, Ireland (Supervisor: Prof. James McInerney).

Awards

1. SIMGBM- Franco Tatò Prize 2010 for the best PhD thesis in General Microbiology.

2. Young Scientist Grant (sponsored by FEMS and ESCMID) for Acinetobacter 2010, 8th International Symposium on the Biology of Acinetobacter Rome 1 – 3 Settembre 2010

3. Firenze University Press 2010 prize, for the best PhD thesis in the Scientific Area

5. Young Scientist Grant (sponsored by FEMS and ESCMID) per Marine Microbiology & Biotechnology:Biodiscovery, Biodiversity and Bioremediation 2012 , Cork (Ireland) 14-17 Novembre 2012

6. Young Scientist Grant (sponsored by FEMS) per partecipazione a FEMS2013, Liepzig (Germany) 21-25 Luglio 2013.
Abstracts for national and international conferences
See complete list at http://www.dblemm.unifi.it/CMpro-v-p-208.html