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Computational Biology Papers


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 he Antarctic bacterium Pseudoalteromonas haloplanktis TAC125. Environ Microbiol. 014 May 28. doi: 10.1111/1462-2920.12513. [Epub ahead of print] PubMed PMID: 4889559.

Bacci G, Bazzicalupo M, Benedetti A, Mengoni A. StreamingTrim 1.0: a Java oftware for dynamic trimming of 16S rRNA sequence data from metagenetic studies. Mol Ecol Resour. 2014 Mar;14(2):426-34. doi: 10.1111/1755-0998.12187. Epub 2013 ov 16. PubMed PMID: 24128146.

Maida I, Fondi M, Orlandini V, Emiliani G, Papaleo MC, Perrin E, Fani R. Origin, duplication and reshuffling of plasmid genes: Insights from Burkholderia vietnamiensis G4 genome. Genomics. 2014 Feb-Mar;103(2-3):229-38. doi: 10.1016/j.ygeno.2014.02.004. Epub 2014 Feb 24. PubMed PMID: 24576463.

Scoffone VC, Spadaro F, Udine C, Makarov V, Fondi M, Fani R, De Rossi E, Riccardi G, Buroni S. Mechanism of resistance to an antitubercular 2-thiopyridine derivative that is also active against Burkholderia cenocepacia. Antimicrob Agents Chemother. 2014 Apr;58(4):2415-7. doi: 10.1128/AAC.02438-13. Epub 2014 Jan . PubMed PMID: 24395233; PubMed Central PMCID: PMC4023784.

Orlandini V, Maida I, Fondi M, Perrin E, Papaleo MC, Bosi E, de Pascale D, Tutino ML, Michaud L, Lo Giudice A, Fani R. Genomic analysis of three sponge-associated Arthrobacter Antarctic strains, inhibiting the growth of Burkholderia cepacia complex bacteria by synthesizing volatile organic compounds. Microbiol Res. 2014 Jul-Aug;169(7-8):593-601. doi: 10.1016/j.micres.2013.09.018.  epub 2013 Oct 20. PubMed PMID: 24231161

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: 4401162.


Galardini M, Mengoni A, Biondi EG, Semeraro R, Florio A, Bazzicalupo M, Benedetti A, Mocali S. DuctApe: a suite for the analysis and correlation of Genomic and OmniLogTM Phenotype Microarray data. Genomics. 2014 Jan;103(1):1-10. doi: 10.1016/j.ygeno.2013.11.005. Epub 2013 Dec 4. PubMed PMID: 24316132. 

Galardini M, Bazzicalupo M, Biondi E, Brambilla E, Brilli M, Bruce D, Chain P,Chen A, Daligault H, Davenport KW, Deshpande S, Detter JC, Goodwin LA, Han C, HanJ, Huntemann M, Ivanova N, Klenk HP, Kyrpides NC, Markowitz V, Mavrommatis K, Mocali S, Nolan M, Pagani I, Pati A, Pini F, Pitluck S, Spini G, Szeto E, Teshima H, Woyke T, Mengoni A. Permanent draft genome sequences of the symbiotic nitrogen fixing Ensifer meliloti strains BO21CC and AK58. Stand Genomic Sci. 2013 Dec 15;9(2):325-33. doi: 10.4056/sigs.3797438. eCollection 2013 Dec 20. PubMed PMID: 24976889.

Fondi M et al. The genome sequence of the hydrocarbon degrading Acinetobacter venetianus VE-C3, Research in Microbiology, in press.

Fondi M et al. Draft genome sequence of the volatile organic compound-producing Antarctic bacterium Arthrobacter sp. strain TB23, able to inhibit cystic fibrosis pathogens belonging to the Burkholderia cepacia complex. J Bacteriol. 2012

Fondi M et al. Draft genome sequence of the hydrocarbon-degrading and
emulsan-producing strain Acinetobacter venetianus RAG-1T. J Bacteriol. 2012

Santopolo, Luisa, et al. Draft Genome Sequence of Chromate-Resistant and Biofilm-Producing Strain Pseudomonas alcaliphila 34. Genome Announcements 1.1 (2013).  

Galardini M., Pini F., Bazzicalupo M., Biondi E.G., Mengoni A. (2013) Replicon-dependent bacterial genome evolution: the case of Sinorhizobium meliloti. Genome Biology and Evolution (in press) 


Peleg, Anton Y., et al. The Success of Acinetobacter Species; Genetic, Metabolic and Virulence Attributes. PloS one 7.10 (2012): e46984.

Ye M., et al. (2012) Contrasting patterns of genetic divergence in two sympatric pseudo-metallophytes: Rumex acetosa L. and Commelina communis L. BMC Evolutionary Biology 12:84

Trabelsi D., et al. (2012) Appraisal of the crop-rotation effect of rhizobial inoculation on potato cropping systems in relation to soil bacterial communities. Soil Biology & Biochemistry 54:1-6.

Pini F., et al. (2012) Exploring the plant-associated bacterial communities in Medicago sativa L. BMC Microbiology 12:78 


Tamminen M, Virta M, Fani R, Fondi M. Large scale analysis of plasmids relationships through gene sharing networks, Mol Biol Evol 2011. [In Press] 

Pini F., Galardini M., Bazzicalupo M., Mengoni A. (2011) Plant-bacteria association and symbiosis: are there common genomic traits in Alphaproteobacteria? Genes 2: 1017-1032 doi:10.3390/genes2041017 

Bosi E, Fani R, Fondi M. The mosaicism of plasmids revealed by atypical genes  detection and analysis. BMC Genomics. 2011 Aug 8;12(1):403. [Epub ahead of print] PubMed PMID: 21824433.

Galardini M, Biondi EG, Bazzicalupo M, Mengoni A. CONTIGuator: a bacterial genomes finishing tool for structural insights on draft genomes. Source Code Biol Med. 2011 Jun 21;6:11. PMID: 21693004

Galardini M, Mengoni A, Brilli M, Pini F, Fioravanti A, Lucas S, Lapidus A, Cheng JF, Goodwin L, Pitluck S, Land M, Hauser L, Woyke T, Mikhailova N, Ivanova N, Daligault H, Bruce D, Detter C, Tapia R, Han C, Teshima H, Mocali S, Bazzicalupo M, Biondi EG. Exploring the symbiotic pangenome of the nitrogen-fixing bacterium Sinorhizobium meliloti. BMC Genomics. 2011 May 12;12:235. PMID: 21569405


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.

Perrin E, Fondi M, Papaleo MC, Maida I, Buroni S, Pasca MR, Riccardi G, Fani R. Exploring the HME and HAE1 efflux systems in the genus Burkholderia. BMC Evol Biol. 2010 Jun 3;10:164. PubMed PMID: 20525265; PubMed Central PMCID: PMC2891726.

Brilli M, Fondi M, Fani R, Mengoni A, Ferri L, Bazzicalupo M, Biondi EG. The diversity and evolution of cell cycle regulation in alpha-proteobacteria: a comparative genomic analysis. BMC Syst Biol. 2010 Apr 28;4:52. PubMed PMID: 20426835; PubMed Central PMCID: PMC2877005.

Fondi M, Bacci G, Brilli M, Papaleo MC, Mengoni A, Vaneechoutte M, Dijkshoorn  L, Fani R. Exploring the evolutionary dynamics of plasmids: the Acinetobacter pan-plasmidome. BMC Evol Biol. 2010 Feb 24;10:59. PubMed PMID: 20181243; PubMed Central PMCID: PMC2848654.


Fondi M, Emiliani G, Liò P, Gribaldo S, Fani R. The evolution of histidinebiosynthesis in archaea: insights into the his genes structure and organization in LUCA. J Mol Evol. 2009 Nov;69(5):512-26. Epub 2009 Nov 3. PubMed PMID: 19888544.

Papaleo MC, Russo E, Fondi M, Emiliani G, Frandi A, Brilli M, Pastorelli R, Fani R. Structural, evolutionary and genetic analysis of the histidine biosynthetic "core" in the genus Burkholderia. Gene. 2009 Dec 1;448(1):16-28. Epub 2009 Aug 13. PubMed PMID: 19683039.

Fondi M, Emiliani G, Fani R. Origin and evolution of operons and metabolic pathways. Res Microbiol. 2009 Sep;160(7):502-12. Epub 2009 May 22. Review. PubMed PMID: 19465116.

Emiliani G, Fondi M, Fani R, Gribaldo S. A horizontal gene transfer at the origin of phenylpropanoid metabolism: a key adaptation of plants to land. Biol Direct. 2009 Feb 16;4:7. PubMed PMID: 19220881; PubMed Central PMCID: PMC2657906.

5: Fani R, Fondi M. Origin and evolution of metabolic pathways. Phys Life Rev. 2009 Jan 8. [Epub ahead of print] PubMed PMID: 20416849.


Brilli M, Mengoni A, Fondi M, Bazzicalupo M, Liò P, Fani R. Analysis of plasmid genes by phylogenetic profiling and visualization of homology relationships using Blast2Network. BMC Bioinformatics. 2008 Dec 21;9:551. PubMed PMID: 19099604; PubMed Central PMCID: PMC2640388.


Fani R, Brilli M, Fondi M, Lió P. The role of gene fusions in the evolution of metabolic pathways: the histidine biosynthesis case. BMC Evol Biol. 2007 Aug 16;7 Suppl 2:S4. PubMed PMID: 17767732; PubMed Central PMCID: PMC1963479.

Fondi M, Brilli M, Emiliani G, Paffetti D, Fani R. The primordial metabolism: an ancestral interconnection between leucine, arginine, and lysine biosynthesis. BMC Evol Biol. 2007 Aug 16;7 Suppl 2:S3. PubMed PMID: 17767731; PubMed Central PMCID: PMC1963480.

Fondi M, Brilli M, Fani R. On the origin and evolution of biosynthetic pathways: integrating microarray data with structure and organization of the Common Pathway genes. BMC Bioinformatics. 2007 Mar 8;8 Suppl 1:S12. PubMed PMID: 17430556; PubMed Central PMCID: PMC1885841.


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