Duccio Cavalieri (DC, www.duccioknights.org) started his scientific career in 1995 applying molecular biology to ecological and evolutionary genomics of microorganisms. After obtaining his PhD in Genetics from the University of Pavia in 1998, DC moved to Harvard as a postdoc with professor Daniel Hartl. From 2001 to 2004 he was Harvard Fellow, Group Leader and Principal Investigator at the Harvard Center for Systems Biology, where he pioneered the application of functional genomics to yeast population genetics. In 2004 DC became group leader, and assistant professor at the Faculty of Biotechnology of the University of Florence.
Since April 2012 as coordinator of the computational biology department at Fondazione E. Mach (CRI), he has undertaken the ambitious challenge to lead the application of computational biology to complex agricultural systems and to the connection between nutrition, the microbiome, and human health (see here).
Cavalieri’s Comparative Genomics research unit main scientific focus is investigating the evolutionary biology of the “holobiome”, the complex network of symbiotic interactions linking the microbiome and the host, including immune system regulation.
The Cavalieri’s led Computational Biology Department (DBC) integrates biological, bioinformatics and statistical expertise necessary for the development of systemic approaches, integrating information from DNA-Microarrays, Next Generation Sequencing, Metagenomics, Proteomics and Metabolomics. 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. This challenge can be successfully undertaken only creating a dynamic community with multidisciplinary competences focusing both on biology, informatics, systems level biological modeling and technology development, as the one created in DBC.
DC has been active in NUGO, DC-THERA, SYBARIS and other EU and nationally funded collaborative research initiative of excellence (PRIN-ADP). DC published 105 publications, 85 of which on JCR journals, cited 2577 times. His H-index is currently equal to 25 (see Google Scholar records here).
Top ten publications
- De Filippo C, Cavalieri D, Di Paola M, Ramazzotti M, Poullet JB, Massart S, Pieraccini, G, Collini S, and Lionetti P. “Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa”. *Proc Natl Acad Sci U S A*. 2010 Aug 17;107(33):14691-6. Epub 2010 Aug 2. IF=9.737. 449 citations.
Widely cited on the press by ScienceNow, New Scientist, Science News, The Economist, Telegraph, Reuters, CNN International, DieWelt, El Mundo
- Leung, JF, Cavalieri D, Fundamentals of Microarray Data Analysis, (2003). *Trends in Genetics*, 19 (11):649-659. IF 9.95. 300 citations
The first extensive review of microarray analysis tools.
- Ball CA, Sherlock G, Parkinson H, Rocca-Sera P, Brooksbank C,Causton HC, Cavalieri D, Gaasterland T, Hingamp P, Holstege F, RingwaldM, Spellman P, Stoeckert CJ Jr, Stewart JE, Taylor R, Brazma A, QuackenbushJ; Microarray Gene Expression Data (MGED) Society. Standards for microarray data. *Science*. 2002 Oct 18;298(5593):539. IF= 30.028. 164 citations.
Widely featured on the scientific press as “keystone” in Omics
- 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. IF=9.737. 162 citations.
This paper pioneered theapplication of DNA microarrays to population genetics.
- Kandror O, Bretschneider N, Kreydin E, Cavalieri D, Goldberg AL. Yeast adapt to near-freezing temperatures by STRE/Msn2,4-dependent induction of trehalose synthesis and certain molecular chaperones. *MolCell*. 2004 Mar 26;13(6):771-81. IF 14.44. 119 citations.
Seminal discovery on life at zero degrees
- Grosu P, Townsend JP, Hartl DL, Cavalieri D. Pathway Processor: a tool for integrating whole-genome expression results into metabolic networks. *Genome Res*. 2002 Jul;12(7):1121-6. IF= 10.176. 113 citations.
The first pathway analysis tool for the interpretation of functional genomics data.
- Marchini S & Cavalieri D, Fruscio R, et al. Association between miR-200c and the survival of patients with stage I epithelial ovarian cancer: a retrospective study of two independent tumour tissue collections. *LancetOncol.* 2011 Mar;12(3):273-85. IF 17.64. 50 citations.
Keynote discovery onthe role of micro RNA and cancer.
- Rizzetto L, Kuka M, De Filippo C, Cambi A, Netea MG, Beltrame L,Napolitani G, Torcia MG, D’Oro U, Cavalieri D. Differential IL-17 Production and Mannan Recognition Contribute to Fungal Pathogenicity and Commensalism. J Immunol. 2010 Apr 15;184(8):4258-68. IF=6.0. 21 citations.
Widely featured in the community as the demonstration of how to understand commensalism is key to elucidate pathogenicity.
- Stefanini I, Dapporto L, Legras JL, Calabretta A, Di Paola M, DeFilippo C, Viola R, Capretti P, Polsinelli M, Turillazzi S, CavalieriD. Role of social wasps in Saccharomyces cerevisiae ecology andevolution. *ProcNatl Acad Sci U S A. *2012 Aug 14;109(33):13398-403. IF: 9.737 8 citations.
The article has been featured on NPR radio-USA and two TV interviews (Leonardo, A come Alpi), 6 newspaper articles (i.e.The NYT).
- Ramazzotti M, Berná L, Stefanini I, Cavalieri D. A computational pipeline to discover highly phylogenetically informative genes in sequenced genomes: application to Saccharomyces cerevisiae natural strains. *NucleicAcids Res*. 2012 May;40(9):3834-48. IF 8.728-1 citation.
Paradigm change in evolutionary genomics.
Top ten citations of Cavalieri’s research on the www
NPR National Public Radio
New York Times
British Society of Paediatric Gastroenterology Hepatology and Nutrition