UMR CNRS 5558 Laboratoire de Biométrie et Biologie Évolutive

• Activités

  I studied Biological Sciences in Florence, where I also obtained my Master degree in 2002 with a thesis concerning bioinformatics approaches for the study of different aspects of metabolic pathways evolution. You may want to give a look to the following (1, 2, 3) and this (4) for a review. After the MS degree I continued to work in the same Laboratory, and started a PhD in Genetics, with a project devoted to developing and using bioinformatics tools for genomics analysis in general and the study of metabolic pathways in detail (5, 6, 7 and 8).

  During the PhD we started to collaborate with Dr. Pietro Lio’ (Senior Lecturer in Bioinformatics at the University of Cambridge). We published together several methodological and applicative papers (see below). Now we are collaborating (slowly..) on a small program to build gene neighborhood networks from the comparison of multiple genomes. In brief, we are developing a program called the ’pan-profiler’ to build phylogenetic profiles of the pan-genome for a number of species. Orthologous identification is made at the moment using Blast and bidirectional best hit (BBH), but probably in the future we will adopt some clustering of all-against-all blast searches. At the moment we prefer the BBH because it is a well defined way to define orthologs operationally. We refer to this program as the ’pan-profiler’ because the profiles are built for all proteins in a predefined number of genomes, and not only for proteins of a reference genome. Once the matrix of phylogenetic profiles is ready, we will use it to build the gene neighborhood networks, i.e. graphs where genes are connected by edges whose value reflect the evolutionary conservation of gene proximity. In this way we will provide a tool to explore genome regions whose synteny is conserved during a given evolutionary time. Conserved gene neighborhoods will form in this network motifs of functional associations. We will also implement a way to change the granularity of the gene neighborhood network, so that it will be possible to select ’motifs’ at different taxonomic levels. With Pietro, after the publication concerning the prediction of VirR regulated genes in Clostridium perfringens, we are also thinking of starting to work together on a ODE model of the corresponding gene regulatory network, which controls toxin expression in this highly pathogen bacterium. The interest here is that the system includes transcriptional regulation but also regulations mediated by small non-coding RNA. Moreover, the idea is to build a model for each of the strains that we analysed in the BMC Microbiology paper so as to provide a sort of comparative systems biology of this regulatory system in these species.

  Another collaboration was set up with Luigi Michaud and Angela Lo Giudice of the University of Messina (Italy) that are interested in Bacteria isolated from Antarctica. Working with them I made phylogenetic analyses 9, but we also developed a way to analyze antagonistic relationships between bacterial samples using network theory (see pictures here Fig Lo Giudice et ql., 2007 and Fig mangano et al., 2009) : 10 and 11 based on the work of PhD student Santina Mangano. Santina spent some week in Florence in 2006 and she perfectly integrated the lab life. After that she went to Trieste for some months to work with Prof. XXX and now she is back in Messina to end her PhD.

  After my PhD (end date December 2006) I’ve got another contract in the same Department as a Post-Doc, where I continued to work in bioinformatics under the supervision of Prof. Marco Bazzicalupo on a project headed by Dr. Emanuele Biondi. The project concerns a comparative analysis of cell cycle regulation in alpha-proteobacteria, starting from the accumulated knowledge on Caulobacter crescentus and see at least the following :Laub biblio . The paper has been recently accepted on BMC Systems Biology, it will appear in a few days. The work has been also presented as an oral contribution at the FISV meeting and at Integrative Post-Genomics 2008 see the presentation in Lyon.

  During the collaboration with Emanuele Biondi, I was asked to participate in a project he was preparing, concerning the genome sequencing of two environmental strains of Sinorhizobium meliloti, by thinking about the necessary bioinformatics follow-up of sequencing. The project has been accepted at the Department of Energy (USA). A recent survey of the project has been published on the official journal of the JGI, see pag. 4 link. A new update concerning the project’s status indicates that 454 and Illumina runs have been performed on the strains, and the Pair End 454 will be obtained soon. The DOE will do the preliminary annotations that then will be refined.

  With researcher Alessio Mengoni PhD student Antonio Frandi, both from Florence, we performed a comparative analysis of the genes controlled by the VirR/VirS two-component system in Clostridium perfringens, that regulates several virulence factors, both on chromosomes and plasmids. Preliminary results obtained by Antonio indicate that the targets identified by Okumura et al., 2008 are generally conserved in different C. perfringens strains, except for some encoding regulatory RNAs. This may imply differences in the response of those strains to signals eliciting the activation of the VirR/VirS system. The paper has been accepted (at end, submission made in August, BMC microbiology was extremely lazy). We are now seeking collaborators to proceed in two ways : from one side we are looking for experimentalists working with C. perfringens to test some of the predicted targets, especially in str. JGS1987 that seems to have experienced an expansion of the VirR regulon (10 specific targets). On the other side we are also planning to develop a mathematical model taking into account both transcriptional regulation mediated by VirR and the activity of regulatory RNAs Scheme with the aim to assess the importance of the differences in the presence of sRNAs on the dynamics of gene expression 12, highly accessed !.

  Collaborators/Friends

  Pietro Liò

  DBLAGE

  Marco Fondi

  Alessio Mengoni

  Emanuele Biondi

  Francesco Pini

  Enrico Calzavarini

  Duccio Cavalieri

  Misc

  Caffé Scienza (Firenze)

  Bar des Sciences (Lyon)

  Wired Science

• Publications

  Peer reviewed Journals

  Published/Accepted

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

  HIGHLY ACCESSED Brilli M, Fondi, M, Ferri, L, Fani R, Bazzicalupo M, Mengoni, A, Biondi EG. The diversity of cell cycle regulation in alpha proteobacteria : a comparative genomic analysis . BMC Systems Biology

  HIGHLY ACCESSED Frandi A, Mengoni A, Brilli M. Comparative genomics of VirR regulons in Clostridium perfringens strains. BMC Microbiology 2010, 10:65

  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 Evolutionary Biology 2010, 10:59

  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 Aug 13

  HIGHLY ACCESSED Brilli M, Mengoni A, Fondi M, Bazzicalupo M, Liò P, Fani R.Analysis of plasmid genes by phylogenetic profiling and visualization of homologous relationships using Blast2Network. BMC Bioinformatics Dec 2008

  Mangano S, Michaud L, Caruso C, Brilli M, Bruni V, Fani R, Lo Giudice A. Antagonistic interactions between psychrotrophic cultivable bacteria isolated from Antarctic sponges : a preliminary analysis. Res Microbiol. 2008 Oct 25.

  Brilli M, Fani R, Liò P. Current trends in the bioinformatic sequence analysis of metabolic pathways in prokaryotes. Brief Bioinform. 2008 Jan ;9(1):34-45.

  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.

  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.

  Lo Giudice A, Brilli M, Bruni V, De Domenico M, Fani R, Michaud L. Bacterium-bacterium inhibitory interactions among psychrotrophic bacteria isolated from Antarctic seawater (Terra Nova Bay, Ross Sea). FEMS Microbiol Ecol. 2007 Jun ;60(3):383-96.

  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.

  Brilli M, Fani R, Lió P. MotifScorer : using a compendium of microarrays to identify regulatory motifs. Bioinformatics. 2007 Feb 15 ;23(4):493-5.

  Ramazzotti M, Brilli M, Fani R, Manao G, Degl’innocenti D. The CAI Analyser Package : inferring gene expressivity from raw genomic data. In Silico Biol. 2007 ;7(4-5):507-26.

  Fani R, Brilli M, Liò P. Inference from proteobacterial operons shows piecewise organization : a reply to Price et al. J Mol Evol. 2006 Oct ;63(4):577-80.

  Fani R, Brilli M, Liò P. The origin and evolution of operons : the piecewise building of the proteobacterial histidine operon. J Mol Evol. 2005 Mar ;60(3):378-90.

  Brilli M, Fani R. The origin and evolution of eucaryal HIS7 genes : from metabolon to bifunctional proteins ? Gene. 2004 Sep 15 ;339:149-60.

  Brilli M, Fani R. Molecular evolution of hisB genes. J Mol Evol. 2004 Feb ;58(2):225-37.

  Michaud L, Di Cello F, Brilli M, Fani R, Lo Giudice A, Bruni V. Biodiversity of cultivable psychrotrophic marine bacteria isolated from Terra Nova Bay (Ross Sea, Antarctica). FEMS Microbiol Lett. 2004 Jan 15 ;230(1):63-71.

  Book Chapters

  Lio’ P, Brilli M, Fani R. Phylogenetics and computational biology of multigene families. In : Structural approaches to sequence evolution:Molecules, networks, populations. U. Bastolla et al., eds. SpringerSeries `Biological and Medical Physics/Biomedical Engineering’,Springer, Berlin, Heidelberg, 2006

  Brilli M, Fani R. Origin and Evolution of metabolic pathways. In : Life in the Universe. J. Seckbach et al., eds. Kluwer Academic Publishers.The Netherlands, 2004

  Lio’ P, Brilli M and Fani R. Topological Metrics in Blast Data Mining : Plasmid and Nitrogen-Fixing Proteins Case Studies. In : M. Elloumi et al. (Eds.) : BIRD 2008, CCIS 13, pp. 207–220, 2008.Springer-Verlag Berlin Heidelberg 2008

  NEW Brilli M, Calistri E, Lio’ P.Transcription factors and gene regulatory networks. In : Networks in cell biology. Edited by M. Buchanan, G. Caldarelli, P. De Los Rios, F. Rao and M. Vendruscolo (2009)

  NEW Brilli M, Lio’ P. The structural and dynamical properties of biological systems. In : Handbook on biological networks. World Scientific Lecture Notes in Complex Systems - Vol. 10. Edited by Boccaletti S, Latora V and Moreno Y (2009) - in press

• My work at LBBE

+Publications -Publications