Duccio Cavalieri’s group is involved in the application of genomics approaches to study yeast variation and interaction with the immune system as well as the evolution of transcriptional regulatory networks.
Cavalieri’s team, integrates biological, bioinformatics and statistical expertise necessary for the development of systemic approaches to the analysis of complex biological systems. The group has large experience on DNA-microarrays and multidisciplinary competences focusing both biology and technology development.
The massive accumulation of genomic data holds the promise of a scientific breakthrough in the analysis of complex biological systems. Whole genome approaches created an unprecedented challenge which is how to extract a comprehensive overview from a huge amount of information. With this aim we are developing bioinformatic methods to interpret genomics data in the context of cellular pathways and regulatory networks.
Upon expanding his research from population genetics to ecological-genomics, Cavalieri and collaborators obtained promising results in studies on investigating transcriptional plasticity in yeast’s stress response and genetic variation in environmental sensing. These studies will likely prove important in toxicogenomics, understanding strategies that mammalian cells use to resist to small molecules and chemotherapeutic agents.
The Cavalieri’s group is using yeast as a model organism in nutrigenomics, studying the compartmentalization of fatty acid metabolism in different organism and the response to resveratrol and phenolic compounds present in wine, with the aim to generalize results and technologies developed in yeast to mammals.
One of the new alleys explored by Cavalieri’s group is now the application of Systems approaches to the reconstruction of the maze of intracellular signaling pathways subtending to maturation and activation of Dendritic cells. In particular our interest is focusing on the rules of the immune discrimination of microorganisms as friends or foes, applying genome-wide approaches to elucidate the interaction between the immune system cells and different pathogenic and non pathogenic yeasts. Our most recent technological interest focuses on development of microarray approaches to study yeast in the environment including the fungal component of the gut metagenome.
A Systems Biology approach to the investigation of the interaction between yeasts and mammalian cells holds the promise to understand the differences between harmful and beneficial effects of microorganisms.
- Differential IL-17 Production and Mannan Recognition Contribute to Fungal Pathogenicity and Commensalism.
Rizzetto L, Kuka M, De Filippo C, Cambi A, Netea MG, Beltrame L, Napolitani G, Torcia MG, D’Oro U, Cavalieri D.
J Immunol. 2010 Mar 12. [Epub ahead of print]PMID: 20228201 IF 6.
- Dominant Processes during Human Dendritic Cell Maturation Revealed by Integration of Proteome and Transcriptome at the Pathway Level. Buschow SI, Lasonder E, van Deutekom HW, Oud MM, Beltrame L, Huynen MA, de Vries IJ, Figdor CG, Cavalieri D. J Proteome Res. 2010 Mar 15. [Epub ahead of print]PMID: 20131907 IF 5.7
- Filling gaps in PPAR-alpha signaling through comparative nutrigenomics analysis.
Cavalieri D, Calura E, Romualdi C, Marchi E, Radonjic M, Van Ommen B, Müller M.
BMC Genomics. 2009 Dec 11;10:596.PMID: 20003344 IF 3.9
- Novel insights into phenotype and mitochondrial proteome of yeast mutants lacking proteins Sco1p or Sco2p. Gamberi T, Magherini F, Borro M, Gentile G, Cavalieri D, Marchi E, Modesti A.
Mitochondrion. 2009 Apr;9(2):103-14. Epub 2009 Jan 17.PMID: 19460303 IF 4.3
- Using pathway signatures as means of identifying similarities among microarray experiments. Beltrame L, Rizzetto L, Paola R, Rocca-Serra P, Gambineri L, Battaglia C, Cavalieri D.PLoS One. 2009;4(1):e4128. Epub 2009 Jan 6.PMID: 19125200 IF 1.8
- Yeast as a model to investigate the mitochondrial role in adaptation to dietary fat and calorie surplus.
Marchi E, Cavalieri D. Genes Nutr. 2008 Dec;3(3-4):159-66. Epub 2008 Nov 27.PMID: 19037676 IF.1.8
- Kyle M. Brown, Christian R. Landry, Daniel L. Hartl and Duccio Cavalieri. Cascading transcriptional effects of a naturally occurring frameshift mutation in Saccharomyces cerevisiae. Mol Ecol. 2008 Jun;17(12):2985-97. Epub 2008 Apr 18.
- Cavalieri D., Castagnini C., Toti S., Maciag K., Kelder T., Gambineri P., Angioli S.and Dolara P. Eu.Gene Analyzer a tool for integrating gene expression data with pathway databases. Bioinformatics. 2007 Oct 1;23(19):2631-2.
- Cavalieri D., De Filippo C., Bioinformatic methods for integrating whole-genome expression results into cellular networks. Drug Disc Today 2005, 10:727-734.
- Christian R. Landry, Jeffrey P. Townsend, Daniel L. Hartl and Cavalieri D Ecological and Evolutionary Genomics of Saccharomyces cerevisiae (2006) Mol Ecol. 2006 Mar;15(3):575-91.
- Kandror O., Bretschneider N., Evgenj Kreydin, Cavalieri D., Goldberg A.L. (2004). Production of threalose and certain heat shock proteins occurs as part of a new adaptative response in yeast that enhances viability at 0 centigrades and upon freezing. Molecular Cell, 13, 771-781.
- Leung, JF., Cavalieri D., Fundamentals of Microarray Data Analysis, (2003). Trends in Genetics, 19 (11):649-659. IF=9.950
- Ball CA, Sherlock G, Parkinson H, Rocca-Sera P, Brooksbank C, Causton HC,
- Cavalieri D Gaasterland T, Hingamp P, Holstege F, Ringwald M, Spellman P, Stoeckert CJ Jr, Stewart JE, Taylor R, Brazma A, Quackenbush J. (2002) Standards for microarray data. Science. 298(5593):539. IF= 30.028.
- Cavalieri, D., Townsend, J. P. & Hartl, D. L. (2000) Manifold anomalies in gene expression in a vineyard isolate of Saccharomyces cerevisiae revealed by DNA microarray analysis. Proc Natl Acad Sci USA.; 97:12369-12374