Curriculum Vitae and Publications

Duccio Cavalieri phD.
Researcher and Associate Professor of Microbiology.

Department of Biology
University of Florence
Via Madonna del Piano, 6
50019 Sesto Fiorentino

+39 055 2758322

duccio.cavalieri[at]unifi.it

www.duccioknights.org

Download Duccio Cavalieri’s CV here

See Duccio Cavalieri publications in Pubmed here

Research Interests

The principal research interest of Duccio Cavalieri is Microbial Systems Biology. As a consequence Cavalieri’s research combines both wet lab projects and “in silico” bioinformatics projects. The Cavalieri’s laboratory is currently an interdisciplinary effort of 8 researchers, 3 biologists (one phD student and two undergraduates) and 5 bioinformaticians (3 postdoctoral fellows, one IT person and one database curator), and interacts actively with a company of 2 professional programmers, Inspect. It.
Dr. Cavalieri’s recent research has focused mainly on the following subjects.

1-Evolutionary and environmental comparative genomics. We are investigating how genetic diversity is generated and maintained, and how it affects the populations in laboratory and natural settings with particular attention to how sensing of environmental stimuli affects cell signalling and metabolic shifts.
The interest in studies on population genetics of yeast has grown since 1993, when these studies were initiated during his undergraduate work with Mario Dr. Polsinelli, in collaboration with Dr. Robert Mortimer (UC Berkeley), recipient of the 2003 Beadle Medal of Genetics for his revolutionary work in yeast genetics. These studies have progressed substantially with subsequent application of microarray-based whole genome technologies pioneered by Cavalieri since his arrival in Dr. Daniel Hartl’s laboratory in 1999. The results achieved by our group in this field have been seminal to the application of array based technologies in population genetics.
Cavalieri’s research has shown extensive heterozygotic variation within a single wild strain, between wild strains, and between wild and lab strains in different and ecologically relevant environmental conditions. The genetic determinants underlying this variation have been mapped to regulators of mitochondrial metabolism, and sensors of extracellular aminoacids.
These studies are now integrating expression modules and metabolic networks with fitness at different temperatures and in different environments, in quest for new master regulators of cellular metabolism.
Our studies applying systems biology approach to the study of life at zero degrees, in collaboration with Alfred Goldberg, Harvard Medical School, have indicated novel mechanisms of the adaptation of yeast cells to life at extreme temperatures, underlying the importance of temperature in yeast ecology and evolution.
Upon expanding his research from population genetics to ecological-genomics, Dr. Cavalieri has recently obtained promising results in studies investigating yeast’s ability to adapt to stresses found in its natural environment, such as fatty acids, acetic acid and ethanol and the role of resveratrol in the modulation of the response to high levels of these compounds.
In particular we are proposing that the observation that resveratrol extends life span mimicking caloric restriction is due to a mechanism of physiologic adaptation to mild oxidative stress.

2-Yeast as a model in Nutritional Systems Biology. We propose yeast as a model in comparative Nutrigenomics and Toxicogenomics. In particular we are addressing the connection between diet, balance between respiration and fermentation and reactive oxygen species levels. We are convinced that understanding mechanisms evolved in wine yeasts to adapt to and resist resveratrol and other phitoalexins, high fat levels, osmotic shock, and ethanol and acetic acid stress will likely prove important in understanding strategies that mammalian cells use to cope with ROS overload.

3-Dendritic cells -yeast interaction and pathways. Our research aims at using a systems biology and comparative genomics approach to dissect the specificity of response of dendritic cells to microrganisms. trying to detect genes expressed specifically in response to pathogens. To this aim we propose experiments to investigate the response of dendritic cells to pathogenic and non pathogenic yeasts on a whole genome scale, and development of algorithms and software for the integration of the expression data with protein protein interaction networks, existing biological information and interpretation of the results in the context of the evolution of the host-pathogen interaction in the different systems analyzed.
Our group is also working at establishing the methodological bases and developing the computational infrastructures to investigate the networks of molecular interactions characterizing specific DC differentiation programs. The methodological aim of the project is to develop a repository of pathways and genomics datasets regarding DC’s and algorithms for the integrative analysis of high-throughput molecular data in the light of the structural and functional organization of the genome. These computational methods will contribute fulfilling gaps in the bioinformatics analysis of genomic data where the integration of different types of information still represent a major, and partially unresolved, computational issue. The analytical results will support the reconstruction of regulatory networks and the molecular signatures of DC maturation. Strategically, the project has the objective to create an interdisciplinary research group integrating biological, bioinformatics and statistical expertise which will guarantee the development of a systemic approach to decipher the complex biological system behind DC maturation and the immune response.

4-Systems Biology approaches to the development of new antifungals-Fungal infections are increasing significantly in general and can have serious consequences in immunocompromised patients, in patients heavily treated with antibiotics. Currently only a limited number of antifungal drugs are available all targeted to the cell wall. We are working in collaboration with organic chemists and biochemists to testing new antifungal agents, such as peptides, esculentin, or agents improving the recognition of the fungal pathogen by the immune system. Our approaches are based on the modelling of yeast cell wall and small molecule transport networks, integrating data from competition experiments using the yeast deletion collection, functional assays based on DNA microarrays and proteomics.

5-Bioinformatics: Since 2000 Cavalieri’s group has had a special focus in comparative parallel analysis of large datasets in particular gene expression microarray data. His research proposes novel approaches to the understanding of genomics data.
Given the statistical limitations for assessment of significance at the gene level in microarray data, Cavalieri’s group has pioneered the application of group testing methods and methods for pathway based analysis and module reconstruction.
Regulation of gene expression and protein activity is central to the function of molecular and cellular systems. High throughput methods provide various partial views of the participating genes, RNAs and proteins, and their interactions.
Genes never act alone in a biological system, but participate in a cascade of networks. Pathways represent the biologist’s way of describing the nature of biological interactions and control networks.
Integration of “omics” data in the context of the biological and cellular pathways is particularly relevant for the detection of subtle but co-ordinated changes (Cavalieri D and De Filippo C., Bioinformatic Methods for Integrating Whole-Genome Expression Results into Cellular Networks. may 2005 Drug Discovery Today). A major direction of Dr. Cavalieri’s lab is bioinformatics and systems biology. In extracting the crucial data from microarray experiments, we have not only studied and used the most significant of currently available genomic tools. We have also developed additional innovative Bioinformatic methods (Pathway Processor and EuGene) to analyse expression data according to a pathway-based logic, which in addition indicates the statistical significance of the conclusions and provides user-friendly graphics to map the expression variability of metabolic pathways. Dr. Cavalieri is currently trying to predict the output of metabolic fluxes in these conditions and measure enzyme activities and metabolite levels in order to tackle variation on the level of systems biology.
The integration of pathway information with network reconstruction is studied in the cellular context, integrating the feedback loops of metabolites on the transcriptional regulators on the binding of transcription factors or their possibility to switch function, from activators, to repressors, binding to a metabolite-small molecule.
Cavalieri’s group is leading an initiative named i-Atlas, a curated database of Immunology signalling pathways in particular for the dendritic cell (DC-Base), the initiative is funded by the EU in the 7th framework programme.
Cavalieri’s group has been and is currently involved in the reconstruction of Colon Cancer modules to develop predictive markers of outcome at the pathway level, project funded by the Istituto Toscano Tumori Led by Lucio Luzzatto.
Cavalieri’s group is also involved in the construction of thematic microarray databases for nutrition (NUGO EU in the 6th framework programme), immunology(DC Thera EU in the 6th framework programme), and paediatric tumours (Cassa di Risparmio e associazione Noi Per Voi Meyer’s Hospital), and in the development of tools to interrogate these databases.

Previous Interests

During his previous research, Dr. Cavalieri has acquired fundamental knowledge in yeast genetics, molecular biology and ecology. His undergraduate research applied RAPD and RFLp to the study of genetic diversity in vineyard yeasts, and his graduate research from 1994 to 1998 has focused mainly on the interaction between amino acid and energy metabolism through molecular and genetic characterization of yeast’s resistance to 5,5,5 trifluoroleucine (TflR) as well as evolutionary analysis of the paralog gene families of histidine, leucine, and lysine biosynthesis. The genes conferring TflR resistance have also been used as dominant markers for the construction of plasmid vectors. From 1997 to 1999, Dr. Cavalieri has also contributed to the first European project using reverse genetic and phenotypic analysis of six new genes of S. cerevisiae chromosome IV (EU project EUROFAN). These studies have provided Dr. Cavalieri with a broad knowledge of central metabolism that is now fundamental for interpretation of genomic data.
In 1999 Cavalieri’s research addressed cloning and expression of ß-glucosidase gene from Debariomyces hansenii to enrich of wine with pharmacologically active resveratrol.

Areas of scholarly contributions to the science

Duccio Cavalieri (DC – http://www.duccioknights.org/) started his 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. In 2000 he applied for the first time DNA microarrays to study gene expression variation in wine strains of Saccharomyces cerevisiae. From 2001 to 2004 he was group leader and principal investigator of the Yeast comparative functional genomics unit at the Harvard Center for Systems Biology, where he pioneered the application of functional genomics to yeast population genetics. His work on pathway analysis in 2002 was seminal to the application of bioinformatics to the interpretation of large “omics” datasets. In 2004 DC became group leader, researcher and “professore aggregato” at Florence University, in these years he applied genomics and bioinformatics to the analysis of symbioses between humans, insects, plants and their microbiota, to study the boundaries between commensalism and pathogenicity. Since April 2012 as coordinator of the computational biology department at FEM, he has taken up a novel challenge, apply next generation sequencing and pathway analysis to study host microbe interaction at the systems level, with a special focus on interaction between fungi and immune function.
DC has been active in NUGO, DC-THERA, SYBARIS and other EU funded initiatives in nutrigenomics, metagenomics and immunogenomics, his lab is currently funded by a Computational Biology Centre grant from Provincia Autonoma di Trento (PAT).
The main interests of Duccio Cavalieri range from comparative, ecological and evolutionary genomics of fungi and plants, to metagenomics, host microbe interaction and immune systems biology.
The common theme between all these fields is development and application of bioinformatic tools, based on pathway and network analysis to genomics.

Publication Records – 1989-2010

Type Number
Papers in international peer-reviewed journals (ISI-JCR) 85
Other reviewed publications 10
Papers in Workshop/Congress proceedings 133
Book chapters 11

As of November 2013, the 85 papers published on JCR Journals (ISI-Web of Science) have been cited 2577 times. The most cited paper as main author has currently 449 citations in 36 months, Cavalieri’s H-index is currently equal to 25 (see here).

Cavalieri’s work has been widely presented on the international press, below a selection of the websites presenting his work.

American Museum of Natural History
NPR National Public Radio
New York Times
Wine Spectator
La Gazzetta Italiana
CellarVie Wines

Studies and Academic record

Record Year/Period
Maturità Scientifica, Liceo N.Rodolico, Firenze 1984
Graduated cum Laude in Biological Sciences, Università di Firenze 1994
PhD in Genetics and Molecular Biology University of Pavia, Italy 1998
Post-graduate fellowship Consorzio Catania Ricerche, Catania 1998-99
Post-graduate fellowship OEB-FAS, Harvard University, USA 1999-2000
Harvard Fellow-Group Leader, PI FAS, Harvard University, USA 2001-2004
Research Scientist-Group leader, University of Florence, Firenze 2003-2012
Adjunct Professor of Microbiology, University of Florence, Firenze 2004-2012
Head-Department of Computational Biology, FMach 2012-2015

Membership and major commitments (international level)

Role Year/Period
Harvard Genomics Fellow – Bauer Center of Genomics Research-Harvard Society of Fellows 2001-2004
Master Lecturer and Lecturer of the PhD School of Nutrigenomics, training initiative of the Wageningen University, NUGO, EU 7th framework NOE 2005-2010
Member and advisor of EMDS (European Macrophage and Dendritic Cells Society) 2010-2013
Member of the Governing Council of DC-Thera (Dendritic Cells for Novel Immunotherapies) NOE 2007-2010
Member of the Directive council board of the Italian branch of FEMS (Società Italiana di Microbiologia e Genetica dei Microorganismi) 2010-2013

Top ten most impacting publications (Impact factor-citations-social media)

  1. 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.
  2. Leung, JF, Cavalieri D, Fundamentals of Microarray Data Analysis, (2003). *Trends in Genetics*, 19 (11):649-659. IF 9.95. 300 citations
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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.

Twenty selected last author publications (ISI records) in the past 10 years.

  1. Rizzetto L., Giovannini G., Bromley M, Bowyer P., Romani L., Cavalieri D., Strain dependent variation of immune responses to A. fumigatus: definition of pathogenic species. PLoS One. 2013;8(2):e5665. IF: 4.41.
  2. Rizzetto L, De Filippo C, Rivero D, Riccadonna S, Beltrame L, Cavalieri D. Systems biology of host-mycobiota interactions: Dissecting Dectin-1 and Dectin-2 signalling in immune cells with DC-ATLAS. Immunobiology. 2013 Nov;218(11):1428-37. Epub 2013 Jul 13. IF 3.46.
  3. De Filippo C., Ramazzotti M., Fontana P., Cavalieri D. Bioinformatic approaches for functional annotation and pathway inference in metagenomics data. Briefings in Bioinformatics 2012 Nov;13(6):696-710. IF 9.283.
  4. Stefanini I, Dapporto L, Legras JL, Calabretta A, Di Paola M, De Filippo C, Viola R, Capretti P, Polsinelli M, Turillazzi S, Cavalieri D. Role of social wasps in Saccharomyces cerevisiae ecology and evolution. Proc Natl Acad Sci U S A. 2012 Aug 14;109(33):13398-403. IF 9.737
  5. 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. Nucleic Acids Res. 2012 May;40(9):3834-48. IF 8.728
  6. Rizzetto L, Buschow SI, Beltrame L, Figdor CG, Schierer S, Schuler G, Cavalieri D. The modular nature of dendritic cell responses to commensal and pathogenic fungi. PLoS One. 2012;7(8):e42430. Epub 2012 Aug 3. PMID: 22879980 IF: 4.41.
  7. Tierney L, Kuchler K, Rizzetto L, Cavalieri D. Systems Biology of Host-Fungus Interactions: Turning Complexity into Simplicity. Curr Opin Microbiol. 2012 Aug;15(4):440-6. Epub 2012 Jun 19. IF: 8.25.
  8. Rizzetto L, Cavalieri D. Friend or foe: using systems biology to elucidate interactions between fungi and their hosts. Trends Microbiol. 2011 Oct;19(10):509-15. [Epub 2011 Aug 24] IF: 8.
  9. Beltrame L, Calura E, Popovici RR, Rizzetto L, Guedez DR, Donato M, Romualdi C, Draghici S, Cavalieri D. The Biological Connection Markup Language: a SBGN-compliant format for visualization, filtering and analysis of biological pathways. Bioinformatics. 2011 Aug 1;27(15):2127-33. Epub 2011 Jun 7 (IF 6.325).
  10. Stefanini I, Trabocchi A, Marchi E, Guarna A, Cavalieri D. A systems biology approach to dissection of the effects of small bicyclic peptidomimetics on a panel of Saccharomyces cerevisiae mutants. J Biol Chem. 2010 May 25. IF=5.52
  11. 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. Epub 2010 Mar 12. IF=6.0.
  12. Buschow SI, Lasonder E, van Deutekom HW, Oud MM, Beltrame L, Huynen MA, de Vries IJ, Figdor CG, Cavalieri D. Dominant Processes during Human Dendritic Cell Maturation Revealed by Integration of Proteome and Transcriptome at the Pathway Level. J Proteome Res. 2010 Apr 5;9(4):1727-37. IF=5.68.
  13. Cavalieri D. Evolution of transcriptional regulatory networks in yeast populations 2010. Wiley Interdiscip Rev Syst Biol Med. 2010 May;2(3):324-35. IF 3.726.
  14. Rizzetto L. and Cavalieri D., A systems biology approach to the mutual interaction between yeast and the immune system. Immunobiology. 2010 Sep-Oct;215(9-10):762-9. Epub 2010 Jun 9. IF 3.46.
  15. Beltrame L, Rizzetto L, Paola R, Rocca-Serra P, Gambineri L, Battaglia C, Cavalieri D. Using pathway signatures as means of identifying similarities among microarray experiments. PLoS One. 2009;4(1):e4128. IF 4.41.
  16. Marchi E, Cavalieri D. Yeast as a model to investigate the mitochondrial role in adaptation to dietary fat and calorie surplus. Genes Nutr. 2008 Dec;3(3-4):159-66. IF 3.05.
  17. Brown K.M., Landry C.R., Hartl D.L. and Cavalieri D. Cascading transcriptional effects of a naturally occurring frameshift mutation in Saccharomyces cerevisiae. Mol Ecol. 2008 Jun;17(12):2985-97. IF 6.275.
  18. 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. IF. 6.275.
  19. Landry CR, Oh J, Hartl DL, Cavalieri D. Genome-wide scan reveals that genetic variation for transcriptional plasticity in yeast is biased towards multi-copy and dispensable genes. Gene. 2006 Feb 1;366(2):343-51. IF 2.371.
  20. Leung, JF., Cavalieri D., Fundamentals of Microarray Data Analysis, (2003). Trends in Genetics, 19 (11):649-659. IF.9.95.

Funding ID

Project awarded Role Year
PROJECTS IN EUROPE
VI° FP- NUGO Project Participant 2003-2009
VI° FP –2003-LIFESCIHEALTH-DC-Thera Co-PI Participant 2003-2009
VII° FP –HEALTH Sybaris Co-PI Participant 2009-2013
University of Erlangen Research Contract-Bioinformatics Contractor 2010-2011
TNO-Research contract-Bioinformatics analysis Contractor 2010
University of Oxford Contractor 2010
University of Njmegen Contractor 2011-2013
ASI -ESA
DAMA Mission (Keyser) Participant 2011
PROJECTS OUTSIDE EUROPE
CGR Genomics Fellows Program Startup Grant NIH 2000 Center Grant, Harvard-USA Co-Proponent-recipient 2000-2004
National Science Foundation Arabidopsis 2010 grant 0313473,Harvard-USA Co-Proponent-recipient 2006-
NATIONAL PROJECTS
University of Firenze Young Investigator Grant Proponent 2001-2002
Istituto Toscano Tumori ITT Starting grant Participant 2005
PRIN-MIUR. Min. of University & Science Participant 2007-2009
Istituto Toscano Tumori ITT Research grant Participant 2008
APBRIA-“Use of algae for biofuel production- Min. of Agriculture Participant 2009-2012
Fondazione Tomasello Research grant Participant 2009
Cassa di Risparmio di Firenze Research grant Proponent 2011-2012
PATT-FEM Computational Biology infrastructure grant-ADP Recipient 2012-2013
PATT-FEM Research Programme”Metafoodbook” Proponent 2012-2013
RESEARCH NETWORKS
NUGO-Nutrigenomics Organization Participant 2003-2011
DC-Thera Participant 2003-2009

Selection of 20 invited presentations in internationally established conferences and courses since since 2003.

  1. D.Cavalieri. “Evolution of regulatory networks in natural populations of S.cerevisiae” Symposium on The Evolution of Gene Regulation, IGERT, Eugene Oregon, “Evolutionary and environmental genomics of yeast”, 13/03/2004
  2. Duccio Cavalieri. Everything you always wanted to know about wine yeasts but were afraid to ask. XXII International Conference on Yeast Genetics and Molecular Biology, Bratislava, 22/08/05.
  3. Duccio Cavalieri, Evolution of transcriptional regulatory networks in yeast populations  International Meeting “Microarray and Gene Expression Data Society”, Riva del Garda, Italy 1-4/09/08.
  4. Duccio Cavalieri, “An ecological perspective to the investigation of the Evolution and Variation of the yeast transcriptome”. EMBO Workshop on Evolutionary and Environmental Genomics of Yeasts, EMBL Heidelberg, 1-5 October 2008.
  5. DC-ATLAS: Dissecting signal transduction in the Dendritic cell With a System Biology Approach, Istituto Humanitas, Milano, PhD training course, 19/4/2009.
  6. Duccio Cavalieri: A systems biology approach to dissect genomic responses of dendritic cells to fungi. 23rd annual meeting of the European Macrophage and Dendritic Cells Society, EMDS. Regensburg, Germany, 24-26 September 2009.
  7. Duccio Cavalieri: “Role of transposable elements in shaping the wine yeast Transcriptome”, GDRE “Comparative Genomics” Amphiteatre du CNRS,Universite Lyon 1 La Doua, 16/10/09.
  8. Duccio Cavalieri: “Evolution of transcriptional Regulatory Networks in Yeast Populations”. European Society of Evolutionary Biology, “ESEB” Meeting, 26-28/08/2009 Torino.
  9. Duccio Cavalieri, Invited Speaker “Of yeast and men: dissecting the interaction between fungi and immune response”, Advanced Functional Genomics Course. Wellcome Trust Advanced Courses and Scientific Conferences. June 22-23, 2010
  10. Duccio Cavalieri, University of Florence, Italy – The mutual interaction between yeast and immune cells as a tool to study /S.cerevisiae/ evolution: Experimental approaches to evolution and ecology using yeast, EMBO Conference Series, Heildeberg 29/09-3/10-2010 (1st).
  11. Duccio Cavalieri, Workshop 9 Systems Biology of Infectious Disease and Immunity, Pathogenic fungi and the human immune system “Yeast Proceedings of the 11th International Conference on Systems Biology, (ICSB) Edinburgh 12-16 October 2010.
  12. Duccio Cavalieri “A Systems Biology approach to the dissection of the pathways regulating immune discrimination of fungi.“ Gordon Research Conference 2011 – Immunology of Fungal Infections (16-21 January 2011, Galveston Island, Texas)
  13. Duccio Cavalieri, “The impact of diet on gut microbiota of children from Europe and rural africa” ASM General Meeting, New Orleans 19-23 May 2011.
  14. Duccio Cavalieri, “Friend or Foe: Systems Biology Approaches to elucidate the interaction between fungi and their hosts. In Candida Infection Biology-Fungal Armoury, battlefields and host defences”. FINSysB Marie Curie Initial Training network Conference, 10-14 ottobre 2011, Acquafredda di Maratea.
  15. Duccio Cavalieri: “Friend or Foe, strain and species specific variation in immune responses of dendritic cells”. Conference on Systems biology of innate immunity and infectious fungal disease, Sybaris Conference, Centre d’Immunologie, Marseille, Parc Scientifique De Lumini, Marseille (CNRS).
  16. Duccio Cavalieri: “Systems Biology Approaches to Improve Dendritic Cells Based Immunotherapy” The 7th International Cancer Vaccine Symposium, September 9-11, 2012, Convitto Della Calza Firenze, Italy.
  17. Duccio Cavalieri: Complexity and dynamics of host-fungal interactions. British Society of Medical Micology Annual Meeting, (BSMM) Newcastle Upon Thyne, April 14th – 16th, 2013.
  18. Duccio Cavalieri: “Nutrigenomics meets metagenomics: bioinformatics approaches to interpret heterogeneous high throughput data”. 3rd International Conference on FoodOmics, 22-24 may 2013, Cesena Italy.
  19. Duccio Cavalieri: Systems Biology of Host Fungal Interactions. Fifth FEBS Advanced Lecture Course Human Fungal Pathogens, May 25-31 2013, La Colle Sur Loup, Nice.
  20. Duccio Cavalieri: Systems Biology Approaches to DC-based Melanoma Immunotherapy. Cancer Bio-Immunotherapy in Siena-XI NIBIT Meeting, Siena (Italy) October 17th-19th 2013.

Selection of Conferences organized since 2002

  1. Duccio Cavalieri, Chair-Session Phenotypic Analysis of Eukaryotes: Florence Conference on Phenotype Microarray Analysis of Microorganisms, The environment, Agriculture and Human Health, Firenze, Italy, 19-21 2008.
  2. Duccio Cavalieri Pathway analysis, an overview, and Chair Parallel Workshop, Bioinformatics and Genomics, FISV 2008 X annual congress 24-25 Sept. 2008.
  3. Chair and member of the sceintific committee, Convegno AGI, SIBV, SIGA, Assisi Mercoledì 21 sept 2011, Session V – Systems biology.
  4. Chair and member of the organizing committee 29th meeting SIMGBM Pisa 21-23 sept 2011.
  5. Chair and member of the organizing committee, XI congresso FISV, 24-27 sept 2012, Chair sessione Synthetic and Systems Biology.
  6. Symbiomes-Systems Biology of Host Microbe Interaction, Trento, 11-13 March 2013 International Workshop and Winter School, Sponsored by Sybaris, 7th framework EU program.
  7. British Society of Medical Micology Annual Meeting, (BSMM) Newcastle Upon Thyne, April 14th – 16th, 2013. Chair of the Session 7-Host Fungal Interactions.

Prizes and recognition of research activity.

September 2001-2004, recipient of the Harvard Genomics Fellow Startup Grant, NIH center Grant to the Bauer Center for Genomics Research-Harvard University.
September 2013-Premio G. Magni best scientific paper published by an Italian Research in the field of microbial genetics in 2012, attributed to the work: I. Stefanini, L. Dapporto, JL. Legras, A. Calabretta, M. Di Paola, C. De Filippo, R. Viola, P. Capretti, M. Polsinelli, S. Turillazzi, D. Cavalieri (2012). Role of social wasps in Saccharomyces cerevisiae ecology and evolution. PNAS, vol. 109 (33), p. 13398-13403, ISSN: 1091-6490.
Member of the Directive council board of the Italian branch of FEMS, (Società Italiana di Microbiologia Generale e Biotecnologie Microbiche-(SIMGBM), 2010-2013.
Member of the Italian Genetics Society (AGI), 2009-2013.
Member of EMDS (European Macrophage and Dendritic Cells Society), 2009-2013.
Member of the NUGO Nutrigenomcs Organization, 2009-2011.

Other awards/outreach

The work titled “Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa” (De Filippo C et al., PNAS. 2010, 107(33):14691-6) had a great impact both on the scientific community and on society in general. The Natural History Museum of New York created a short movie describing the results of the work, the movie was screened during the month of September 2010, in the rooms of Human Evolution(see here, Have Humans Adapted to the Western Diet?), the paper was in the list of the most downloaded papers of PNAS for 4 months.
This highly cited PNAS paper was largely cited by Science Now, The new Scientist, The Economist, El Mundo, La Repubblica and a number of blogs and web sites around the world and resulted in 2013 in one long interview on “Il Venerdi di Repubblica”, on the role of microorganisms on human health (Quei piccolissimi complici, download it here).

A more recent work from our team, Stefanini I, Dapporto L, Legras JL, Calabretta A, Di Paola M, De Filippo C, Viola R, Capretti P, Polsinelli M, Turillazzi S, Cavalieri D. Role of social wasps in Saccharomyces cerevisiae ecology and evolution. Proc Natl Acad Sci U S A. 2012 Aug 14;109(33):13398-403, is also having a significant impact on ecology and wine biotechnology, Duccio Cavalieri has been interviewed by National Public Radio (NPR, listen here) and The Wine Spectator Online (listen here), by Radio televisione Italiana, RAI, Leonardo, and A come Alpi RRTR. The implications of this research have been profoundly discussed in the news, including a one page article on the scientific section of the New York Times, Sunday edition of the 06/08/2012 (see here).

Peer reviewed Publications in International Journals

1. Aldinucci A, Turco A, Biagioli T, Toma FM, Bani D, Guasti D, Manuelli C, Rizzetto L, Cavalieri D, Massacesi L, Mello T, Scaini D, Bianco A, Ballerini L, Prato M, Ballerini C. Carbon nanotube scaffolds instruct human dendritic cells: modulating immune responses by contacts at the nanoscale. Nano Lett. 2013 Nov 13. [Epub ahead of print] (IF 13.025)
2. Ferrarini M, Moretto M, Ward JA, Urbanovski N, Stevanovi V, Giongo L, Viola R, Cavalieri D, Velasco R, Cestaro A, Sargent DJ. An evaluation of the PacBio RS platform for sequencing and de novo assembly of a chloroplast genome. BMC Genomics. 2013 Oct 1;14(1):670. (IF 4.40)
3. Baur AS, Lutz MB, Schierer S, Beltrame L, Theiner G, Zinser E, Ostalecki C, Heidkamp G, Haendle I, Erdmann M, Wiesinger M, Leisgang W, Gross S, Pommer AJ, Kämpgen E, Dudziak D, Steinkasserer A, Cavalieri D, Schuler-Thurner B, Schuler G. Denileukin diftitox (ONTAK) induces a tolerogenic phenotype in dendritic cells and stimulates survival of resting Treg. Blood. 2013 Sep 26;122(13):2185-94. doi: 10.1182/blood-2012-09-456988. Epub 2013 Aug 19. (IF 9.60)
4. Rizzetto L, De Filippo C, Rivero D, Riccadonna S, Beltrame L, Cavalieri D. Systems biology of host-mycobiota interactions: Dissecting Dectin-1 and Dectin-2 signalling in immune cells with DC-ATLAS. Immunobiology. 2013 Nov;218(11):1428-37. Epub 2013 Jul 13. (IF 3.46).
5. Bezerra AR, Simões J, Lee W, Rung J, Weil T, Gut IG, Gut M, Bayés M, Rizzetto L, Cavalieri D, Giovannini G, Bozza S, Romani L, Kapushesky M, Moura GR, Santos MA. Reversion of a fungal genetic code alteration links proteome instability with genomic and phenotypic diversification. Proc Natl Acad Sci U S A. 2013 Jun 17 (IF: 9.681).
6. Calura E, Fruscio R, Paracchini L, Bignotti E, Ravaggi A, Martini P, Sales G, Beltrame L, Clivio L, Ceppi L, Di Marino M, Fuso Nerini I, Zanotti L, Cavalieri D, Cattoretti G, Perego P, Milani R, Katsaros D, Tognon G, Sartori E, Pecorelli S, Mangioni C, D’Incalci M, Romualdi C, Marchini S. miRNA landscape in Stage I Epithelial Ovarian Cancer defines the histotype specificities. Clin Cancer Res. 2013 Jun 13. (IF 7.837)
7. Beltrame L, Bianco L, Fontana P, Cavalieri D. Pathway Processor 2.0: a web resource for pathway-based analysis of high-throughput data. Bioinformatics. 2013 Jun 8. (IF 5.323)
8. Nikiforova SV, Cavalieri D, Velasco R, Goremykin V. Phylogenetic analysis of 47 chloroplast genomes clarifies the contribution of wild species to the domesticated apple maternal line. Mol Biol Evol. 2013 May 14. (IF 10.353)
9. Beltrame L, Bianco L, Fontana P, Cavalieri D. Pathway-based analysis of microarray and RNAseq data using Pathway Processor 2.0. Curr Protoc Bioinformatics. 2013 Mar;Chapter 7:Unit 7.6. (IF 2.1)
10. Ometto L, Cestaro A, Ramasamy S, Grassi A, Revadi S, Siozios S, Moretto M, Fontana P, Varotto C, Pisani D, Dekker T, Wrobel N, Viola R, Pertot I, Cavalieri D, Blaxter M, Anfora G, Rota-Stabelli O. Linking genomics and ecology to investigate the complex evolution of an invasive Drosophila pest. Genome Biol Evol. 2013;5(4):745-57. (IF 4.759).
11. Rizzetto L., Giovannini G., Bromley M, Bowyer P., Romani L., Cavalieri D., Strain dependent variation of immune responses to A. fumigatus: definition of pathogenic species. PLoS One. 2013;8(2):e5665. IF: 4.41.
12. De Filippo C., Ramazzotti M., Fontana P., Cavalieri D. Bioinformatic approaches for functional annotation and pathway inference in metagenomics data. Briefings in Bioinformatics 2012 Nov;13(6):696-710. IF 9.283
13. Marchini S, Fruscio R, Clivio L, Beltrame L, Porcu L, Nerini IF, Cavalieri D, Chiorino G, Cattoretti G, Mangioni C, Milani R, Torri V, Romualdi C, Zambelli A, Romano M, Signorelli M, Giandomenico SD, D’Incalci M. Resistance to platinum-based chemotherapy is associated with epithelial to mesenchymal transition in epithelial ovarian cancer. Eur J Cancer. 2013 Jan;49(2):520-30. PMID: 22897840 IF: 5.536
14. Rizzetto L, Buschow SI, Beltrame L, Figdor CG, Schierer S, Schuler G, Cavalieri D. The modular nature of dendritic cell responses to commensal and pathogenic fungi. PLoS One. 2012;7(8):e42430. Epub 2012 Aug 3. PMID: 22879980 IF: 4.41.
15. Stefanini I, Dapporto L, Legras JL, Calabretta A, Di Paola M, De Filippo C, Viola R, Capretti P, Polsinelli M, Turillazzi S, Cavalieri D. Role of social wasps in Saccharomyces cerevisiae ecology and evolution. Proc Natl Acad Sci U S A. 2012 Aug 14;109(33):13398-403. Epub 2012 Jul 30. IF: 9.681
16. Tierney L, Kuchler K, Rizzetto L, Cavalieri D. Systems Biology of Host-Fungus Interactions: Turning Complexity into Simplicity. Curr Opin Microbiol. 2012 Aug;15(4):440-6. Epub 2012 Jun 19. IF: 8.25.
17. Vukich M., Ganga P.L., Cavalieri D., Rizzetto, L., Rivero D., Pollastri S., Mugnai S., Mancuso S., Pastorelli S., Lambreva M,, Antonacci A., Margonelli A., Bertalan I., Johanningmeier U., Giardi M.T., Rea G., Pugliese M., Quarto M., Roca V., Zanini A., Borla O., Rebecchi L., Altiero T., Guidetti R., Cesari M., Marchioro T., Bertolani R., Pace E., De Sio A., Casarosa M., Tozzetti L., Branciamore S., Gallori E., Scarigella M., Bruzzi M., Bucciolini M., Talamonti C., Donati A., Zolesi V. BIOKIS: A Model Payload for Multidisciplinary Experiments in Microgravity, Microgravity Sci. Technol., 24 (6):397-409;
18. Uboldi S, Calura E, Beltrame L, Fuso Nerini I, Marchini S, Cavalieri D, Erba E, Chiorino G, Ostano P, D’Angelo D, D’Incalci M, Romualdi C. A systems biology approach to characterize the regulatory networks leading to trabectedin resistance in an in vitro model of myxoid liposarcoma. PLoS One. 2012;7(4):e35423. Epub 2012 Apr 16 (I.F.4.41).
19. Santarlasci V, Maggi L, Capone M, Querci V, Beltrame L, Cavalieri D, D’Aiuto E, Cimaz R, Nebbioso A, Liotta F, De Palma R, Maggi E, Cosmi L, Romagnani S, Annunziato F. Rarity of human T helper 17 cells is due to retinoic acid orphan receptor-dependent mechanisms that limit their expansion. Immunity. 2012 Feb 24;36(2):201-14. Epub 2012 Feb 9. IF: 22.13.
20. Sales G, Calura E, Cavalieri D, Romualdi C. graphite – a Bioconductor package to convert pathway topology to gene network. BMC Bioinformatics. 2012 Jan 31;13(1):20. [Epub ahead of print] (IF 3.3)
21. 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. Nucleic Acids Res. 2012 May;40(9):3834-48. [Epub ahead of print] (IF 7.83)
22. Fekete T, Szabo A, Beltrame L, Vivar N, Pivarcsi A, Lanyi A, Cavalieri D, Rajnavölgyi E, Rethi B. Constraints for monocyte derived dendritic cell functions under inflammatory conditions. Eur J Immunol. Eur J Immunol. 2012 Feb;42(2):458-69.
23. Splendiani A, Gündel M, Austyn JM, Cavalieri D, Scognamiglio C, Brandizi M. Knowledge sharing and collaboration in translational research, and the DC-THERA Directory. Brief Bioinform. 2011 Nov;12(6):562-75. Epub 2011 Oct 3. (IF 9.283)
24. Santamaría R, Rizzetto L, Bromley M, Zelante T, Lee W, Cavalieri D, Romani L, Miller B, Gut I, Santos M, Pierre P, Bowyer P, Kapushesky M. Systems biology of infectious diseases: a focus on fungal infections. Immunobiology. 2011;216(11):1212-27. (IF 3.46).
25. Sanseverino, C. Purificato, L. Conti, Varano, B.; Beltrame, L.; D. Cavalieri, M. C. Gauzzi, S. Gessani Manipulating human dendritic cells by STAT3 silencing to implement their use in cancer immunotherapy-Cytokine 01/2011; 56(1):14-14. (IF 3.21).
26. Rizzetto L, Cavalieri D. Friend or foe: using systems biology to elucidate interactions between fungi and their hosts. Trends Microbiol. 2011 Oct;19(10):509-15. [Epub 2011 Aug 24] (IF 8).
27. Beltrame L, Calura E, Popovici RR, Rizzetto L, Guedez DR, Donato M, Romualdi C, Draghici S, Cavalieri D. The Biological Connection Markup Language: a SBGN-compliant format for visualization, filtering and analysis of biological pathways. Bioinformatics. 2011 Aug 1;27(15):2127-33. Epub 2011 Jun 7 (IF 6.325).
28. Trabocchi A., Cavalieri D., Guarna A. Chemical genetics approach to drug discovery by Diversity-Oriented Synthesis (DOS) of peptidomimetics, Pure and Applied Chemistry, 2011, Vol. 83, Issue 3, pp. 687-698. (IF 2.128).
29. Cheng SC, van de Veerdonk FL, Lenardon M, Stoffels M, Plantinga T, Smeekens S, Rizzetto L, Mukaremera L, Preechasuth K, Cavalieri D, Kanneganti TD, van der Meer JW, Kullberg BJ, Joosten LA, Gow NA, Netea MG. The dectin-1/inflammasome pathway is responsible for the induction of protective T-helper 17 responses that discriminate between yeasts and hyphae of Candida albicans. J Leukoc Biol. 2011 Aug;90(2):357-66. Epub 2011 Apr 29. (IF 4.18).
30. 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. Lancet Oncol. 2011 Mar;12(3):273-85. Epub 2011 Feb 21. (IF:17.64)
31. Cavalieri D, Rivero D, Beltrame L, Buschow SI, Calura E, Rizzetto L, Gessani S, Gauzzi MC, Reith W, Baur A, Bonaiuti R, Brandizi M, De Filippo C, D’Oro U, Draghici S, Dunand-Sauthier I, Gatti E, Granucci F, Gündel M, Kramer M, Kuka M, Lanyi A, Melief CJ, van Montfoort N, Ostuni R, Pierre P, Popovici R, Rajnavolgyi E, Schierer S, Schuler G, Soumelis V, Splendiani A, Stefanini I, Torcia MG, Zanoni I, Zollinger R, Figdor CG, Austyn JM. DC-ATLAS: a systems biology resource to dissect receptor specific signal transduction in dendritic cells. Immunome Res. 2010 Nov 19;6:10. (IF 5.33).
32. Trabocchi A., Stefanini I, Morvillo M.m, Ciofi L., Cavalieri D., Guarna A . Biochemical genetics approach to identify new small molecule modulators of cell growth by phenotypic screening of Saccharomyces cerevisiae strains with a library of morpholine-derived compounds. Org Biomol Chem. 2010 Dec 21;8(24):5552-7. Epub 2010 Oct 15. (IF=3.55)
33. Aldinucci A, Rizzetto L., Pieri L., Nosi D., Romagnoli P., Biagioli T., Mazzanti B., Saccardi, R., Beltrame L., Massacesi L., Cavalieri D. and Clara Ballerini. Inhibition of active immune synapse formation trough altered dendritic cell (DC) actin distribution: A new pathway of immune regulation by mesenchimal stem cells (MSCs), J Immunol. 2010 Nov 1;185(9):5102-10. (IF 6.00).
34. De Filippo C., Cavalieri D., Di Paola M., Ramazzotti M., Poullet J.B., 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=9.43).
35. Rizzetto L. and Cavalieri D., A systems biology approach to the mutual interaction between yeast and the immune system. Immunobiology. 2010 Sep-Oct;215(9-10):762-9. Epub 2010 Jun 9. IF 3.46.
36. Stefanini I, Trabocchi A, Marchi E, Guarna A, Cavalieri D. A systems biology approach to dissection of the effects of small bicyclic peptidomimetics on a panel of Saccharomyces cerevisiae mutants. J Biol Chem. 2010 May 25. IF=5.52 .
37. Cavalieri D. Evolution of transcriptional regulatory networks in yeast populations 2010. Wiley Interdiscip Rev Syst Biol Med. 2010 May;2(3):324-35. (IF TBA)
38. Tonini G., Baccini M., Cavalieri D. and Mini E., and Dolara P., Biggeri, A. (2010) Using regularization patterns from penalized regression in microarray experiments. Biomedical statistics and clinical epidemiology , 4 (1). pp. 35-46. ISSN 1973-2430
39. De Filippo C, Pini-Prato A, Mattioli G, Avanzini S, Rapuzzi G, Cavalieri D, Di Paola M, Stefanini I, Ceccherini I, Mavilio D, Lionetti P, Jasonni V. Genomics approach to the analysis of bacterial communities dynamics in Hirschsprung’s disease-associated enterocolitis: a pilot study. Pediatr Surg Int. 2010 Mar 20. IF 1.
40. 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. Epub 2010 Mar 12. IF=6.0.
41. Buschow SI, Lasonder E, van Deutekom HW, Oud MM, Beltrame L, Huynen MA, de Vries IJ, Figdor CG, Cavalieri D. Dominant Processes during Human Dendritic Cell Maturation Revealed by Integration of Proteome and Transcriptome at the Pathway Level. J Proteome Res. 2010 Apr 5;9(4):1727-37. IF=5.68.
42. Cavalieri D, Calura E, Romualdi C, Marchi E, Radonjic M, Van Ommen B, Müller M. Filling gaps in PPAR-alpha signaling through comparative nutrigenomics analysis. BMC Genomics. 2009 Dec 11;10:596. IF=3.93.
43. Gamberi T, Magherini F, Borro M, Gentile G, Cavalieri D, Marchi E, Modesti A. Novel insights into phenotype and mitochondrial proteome of yeast mutants lacking proteins Sco1p or Sco2p. Mitochondrion. 2009 Apr;9(2):103-14. IF=4.26
44. Beltrame L, Rizzetto L, Paola R, Rocca-Serra P, Gambineri L, Battaglia C, Cavalieri D. Using pathway signatures as means of identifying similarities among microarray experiments. PLoS One. 2009;4(1):e4128. IF 4.41.
45. Marchi E, Cavalieri D. Yeast as a model to investigate the mitochondrial role in adaptation to dietary fat and calorie surplus. Genes Nutr. 2008 Dec;3(3-4):159-66. (IF 3.05).
46. Cavalieri D, Dolara P, Mini E, Luceri C, Castagnini C, Toti S, Maciag K, De Filippo C, Nobili S, Morganti M, Napoli C, Tonini G, Baccini M, Biggeri A, Tonelli F, Valanzano R, Orlando C, Gelmini S, Cianchi F, Messerini L, Luzzatto L. Analysis of gene expression profiles reveals novel correlations with the clinical course of colorectal cancer. Oncol Res. 2007;16(11):535-48. IF 1.45.
47. Brown K.M., Landry C.R., Hartl D.L. and Cavalieri D. Cascading transcriptional effects of a naturally occurring frameshift mutation in Saccharomyces cerevisiae. Mol Ecol. 2008 Jun;17(12):2985-97. IF 5.33.
48. van Ommen B, Cavalieri D, Roche HM, Klein UI, Daniel H. The challenges for molecular nutrition research 4: the “nutritional systems biology level”. Genes Nutr. 2008 Dec;3(3-4):107-13. Epub 2008 Sep 30. (IF 3.05)
49. Lotito L, Russo A, Chillemi G, Bueno S, Cavalieri D, Capranico G. J. Global transcription regulation by DNA topoisomerase I in exponentially growing Saccharomyces cerevisiae cells: activation of telomere-proximal genes by TOP1 deletion J. Mol Biol. 2008 Mar 21;377(2):311-22. (IF=4.14.)
50. Biggeri A, Dreassi E, Lagazio C, Toti S, De Filippo C, Cavalieri D (2008) Hierarchical Bayesian Modelling of Multiple Arrays Experiments, BioMedical Statistics and Clinical Epidemiology, 2, 1, 47-55 (IF TBA).
51. Salathia N, Lee HN, Sangster TA, Morneau K, Landry CR, Schellenberg K, Behere AS, Gunderson KL, Cavalieri D, Jander G, Queitsch C. Indel arrays: an affordable alternative for genotyping. Plant J. 2007 Aug;51(4):727-37. Epub 2007 Jul 20. (IF=6.49).
52. 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. IF=4.33.
53. Gamberi T, Cavalieri D, Magherini F, Mangoni ML, De Filippo C, Borro M, Gentile G, Simmaco M, Modesti A. An integrated analysis of the effects of Esculentin 1-21 on Saccharomyces cerevisiae. Biochim Biophys Acta. 2007 Jun;1774(6):688-700. (IF 2.2).
54. Sardi I, Cavalieri D, Massimino M. Emerging treatments and gene expression profiling in high-risk medulloblastoma. Paediatr Drugs. 2007;9(2):81-96. Review.
55. 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. (IF. 5.33).
56. Landry CR, Oh J, Hartl DL, Cavalieri D. Genome-wide scan reveals that genetic variation for transcriptional plasticity in yeast is biased towards multi-copy and dispensable genes. Gene. 2006 Feb 1;366(2):343-51. (IF 2.58).
57. Cavalieri D., De Filippo C., Bioinformatic methods for integrating whole-genome expression results into cellular networks. Drug Disc Today 2005, 10:727-734. (IF 6.62).
58. Giuntini E, Mengoni A, De Filippo C, Cavalieri D, Aubin-Horth N, Landry CR, Becker A, Bazzicalupo M Large-scale genetic variation of the symbiosis-required megaplasmid pSymA revealed by comparative genomic analysis of Sinorhizobium meliloti natural strains. BMC Genomics. 2005 Nov 10;6:158.(IF 3.93).
59. Luceri C, De Filippo C, Giovannelli L, Blangiardo M, Cavalieri D, Aglietti F, Pampaloni M, Andreuccetti D, Pieri L, Bambi F, Biggeri A, Dolara P. Extremely low-frequency electromagnetic fields do not affect DNA damage and gene expression profiles of yeast and human lymphocytes. Radiat Res. 2005 Sep;164(3):277-85. (IF 3.04).
60. 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. Mol Cell. 2004 Mar 26;13(6):771-81. (IF 14.44).
61. Cavalieri D, Grosu P. Integrating whole-genome expression results into metabolic networks with Pathway Processor. Curr Protoc Bioinformatics. 2004 May;Chapter 7:Unit 7.6. (IF TBA)
62. Leung, JF., Cavalieri D., Fundamentals of Microarray Data Analysis, (2003). Trends in Genetics, 19 (11):649-659. (IF.9.95).
63. Cavalieri D, McGovern PE, Hartl DL, Mortimer R, Polsinelli M. Evidence for S. cerevisiae fermentation in ancient wine. J Mol Evol. 2003;57 Suppl 1:S226-32. (IF 2.76)
64. Townsend JP, Cavalieri D, Hartl DL. Population genetic variation in genome-wide gene expression. Mol Biol Evol. 2003 Jun;20(6):955-63. (IF 7.3).
65. 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; Microarray Gene Expression Data. The underlying principles of scientific publication. Bioinformatics. 2002 Nov;18(11):1409. Review. 6.325
66. 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; Microarray Gene Expression Data (MGED) Society. Standards for microarray data. Science. 2002 Oct 18;298(5593):539. IF= 30.028.
67. 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; Microarray Gene Expression Data (MGED) Society. A guide to microarray experiments-an open letter to the scientific journals. The Lancet, Volume 360, Issue 9338, Page 1019, 28 September 2002. (IF=33.633).
68. 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
69. Sebastiani F, Barberio C, Casalone E, Cavalieri D, Polsinelli M. Crosses between Saccharomyces cerevisiae and Saccharomyces bayanus generate fertile hybrids. Res Microbiol. 2002 Jan-Feb;153(1):53-8. IF=2.65.
70. Cavalieri D, De Filippo C, Grosu P, and Biggeri A. (2002) Making sense of whole genome expression data: microarray databases and tools for integrating whole-genome expression results into cellular networks. Minerva Biotech, 14:291-304. IF=TBA
71. Roselli G., Petruccelli R, Polsinelli L., Cavalieri D., (2002) Genetic Variability in Olea Europea sp. Journal of Genetics and Breeding Vol 56. IF=TBA
72. Schaus SE, Cavalieri D, Myers AG. Gene transcription analysis of Saccharomyces cerevisiae exposed to neocarzinostatin protein-chromophore complex reveals evidence of DNA damage, a potential mechanism of resistance, and consequences of prolonged exposure. Proc Natl Acad Sci U S A. 2001 Sep 25;98(20):11075-80. IF=9.43.
73. Barberio C, Pagliai L, Cavalieri D, Fani R. Biodiversity and horizontal gene transfer in culturable bacteria isolated from activated sludge enriched in nonylphenol ethoxylates. Res Microbiol. 2001 Jan-Feb;152(1):105-12. IF=2.06.
74. De Filippo C and Cavalieri D., (2001) Yeast in the post genomic era: Use of DNA microarrays to study stress response, response to drugs and alkylating agents in S.cerevisiae. Minerva Biotech. v. 13(#4) pp. 249-254. IF=TBA
75. 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=9.43.
76. Casalone E, Barberio C, Cavalieri D, Polsinelli M. Identification by functional analysis of the gene encoding alpha-isopropylmalate synthase II (LEU9) in Saccharomyces cerevisiae. Yeast. 2000 Apr;16(6):539-45. IF=2.62
77. Casalone E, Barberio C, Cavalieri D, Ceccarelli I, Riparbelli M, Ugolini S, Polsinelli M. Disruption and phenotypic analysis of six novel genes from chromosome IV of Saccharomyces cerevisiae reveal YDL060w as an essential gene for vegetative growth. Yeast. 1999 Nov;15(15):1691-701. IF=2.62
78. Bendoni B, Cavalieri D, Casalone E, Polsinelli M, Barberio C. Trifluoroleucine resistance as a dminant molecular marker in transformation of strains of Saccharomyces cerevisiae isolated from wine. FEMS Microbiol Lett. 1999 Nov 15;180(2):229-33. IF=2.02
79. Cavalieri D, Casalone E, Bendoni B, Fia G, Polsinelli M, Barberio C. Trifluoroleucine resistance and regulation of alpha-isopropyl malate synthase in Saccharomyces cerevisiae. Mol Gen Genet. 1999 Feb;261(1):152-60. IF=2.84.
80. Cavalieri D., C. Barberio ,E. Casalone, F. Pinzauti, F. Sebastiani, R.K. Mortimer, M. Polsinelli. (1998) Genetic and molecular Diversity in S. cerevisiae natural populations. Food Technol. Biotechnol., 36 (1) 45-50. IF=1.23
81. Casalone E, Fia G, Barberio C, Cavalieri D, Turbanti L, Polsinelli M. Genetic and biochemical characterization of Saccharomyces cerevisiae mutants resistant to trifluoroleucine. Res Microbiol. 1997 Sep-Oct;148(7):613-23. IF=2.06.
82. R., Fani, E.Tamburini, E., Mori, A., Lazcano, P., Liò, C., Barberio, E., Casalone, D.Cavalieri, B., Perito and M., Polsinelli (1997). Paralogous histidine biosynthetic genes: evolutionary analysis of the Saccharomyces HIS6 and HIS7 genes. Gene, 197, 9-17. IF=2.58
83. Paffetti D, Barberio C, Casalone E, Cavalieri D, Fani R, Fia G, Mori E, Polsinelli M. DNA fingerprinting by random amplified polymorphic DNA and restriction fragment length polymorphism is useful for yeast typing. Res Microbiol. 1995 Sep;146(7):587-94. IF= 2.65.
84. Bogani P., Cavalieri D., Petruccelli R., Polsinelli L., Roselli G. (1994), Identification of olive tree cultivars by using Random Amplified Polymorphic DNA. Acta Hort., 356, 98-101.

Book Chapters

1.Cavalieri D., De Filippo C., Lebboroni M., Rustioni M., Tuoni G., Ciofi D., Oliva G., Gargini A. e De Filippo G.B. (1997), Il fiume Pesa, la Fitodepurazione. Analisi integrata del Territorio. Comune di Tavarnelle Val di Pesa, pp1-158, Firenze, Settembre 1997.
2. Mario Polsinelli, Claudia Barberio, Enrico Casalone, Duccio Cavalieri. (1998) Le tecnologie biomolecolari nello studio della biodiversità dei lieviti. I Georgofili, Quaderni 1998-VII, 37-64.
3. Duccio Cavalieri, (1998) tesi di Dottorato di Ricerca in Scienze Genetiche (Genetica e Biologia Molecolare) X ciclo, “Isolamento e caratterizzazione genetico-molecolare di mutanti di Saccharomyces cerevisiae resistenti alla 5,5,5-trifluoro-DL leucina e identificazione del gene codificante l’-isopropil-malato sintetasi II” febbraio 1998. Biblioteca del dipartimento di Genetica di Pavia, Biblioteca del dipartimento di Biologia Animale e Genetica di Firenze, Biblioteca Nazionale Centrale di Roma e Firenze.
4. Duccio Cavalieri (2000) La Variabilità in popolazioni naturali di lieviti da vino. (Variability in natural populations of wine yeasts) In “I nostri Lieviti dalla vite al vino”, pag 50-62, Aida edizioni, luglio 2000.
5. Jeffrey Townsend and Duccio Cavalieri Cover Page Image, and paragraph 13.8 page 578-580 Functional Genomics in Chapter 13 Genetic Ingeneering and Genomics, in Genetics-Analysis of Genes and Genomes from DL Hartl and EW Jones, 2001, Jones and Bartlett Publishers Sudbury MA.
6. Hartl, D.L., C.D. Meiklejohn, C.I. Castillo-Davis, D. Cavalieri, J.M. Ranz, and J.P. Townsend, (2003). Expression Profiling in Evolutionary Genetics. In The Evolution of Population Biology: Modern Synthesis, pp74-93 Eds. R. K. Singh and M. K. Uyenoyama. Cambridge University Press, Cambridge.
7. Cavalieri D., Grosu P. (2004) Pathway Processor a tool to integrate whole genome information into metabolic networks. Current Protocols in Bioinformatics Wiley and sons Inc., March 2004.
8. Biggeri A, Cavalieri D, Dreassi E, Lagazio C, Toti S (2004) Hierarchical Bayesian Modelling of Multiple Arrays Experiments, Note di ricerca del Dipartimento di Statistica dell’Università di Udine, 11.04.
9. Duccio Cavalieri e Carlotta De Filippo, Metodi di analisi con microarrays, in Benedetti A., Mocali S., Miclaus N.(Ed.): Manuale di metodi innovativi per lo studio dei microrganismi del suolo. Collana SISS sui Metodi di Analisi del Suolo, Franco Angeli editore, Milano. 2007.
10. Carlotta De Filippo, Duccio Cavalieri, Paolo Lionetti. The Effect of Diet on Gut Microbiota in Humans Living in Different Environments: A Metagenomic Approach. 279-297. In Genomics Applications for the Developing World, Springer. ISBN 978-1-4614-2181-8-DOI 10.1007/978-1-4614-2182-5-2012.
11. Irene Stefanini, Carlotta De Filippo, Duccio Cavalieri. Yeast as a model in High Throughput Screening of Small Molecule Libraries. In Diversity Oriented Synthesis, Wiley, ISBN 978-1-118-14565. 4QD262.D58 2013. Pag. 455-482.