CV Italiano Breve.

Il/La sottoscritto Duccio Cavalieri, Professore Associato presso il Dipartimento di Biologia dal 1 noembre 2015, Ricercatore Universitario dal 01/01/2004, presso l’Università degli Studi di Firenze, Ricercatore di Prima Fascia e Coordinatore di Dipartimento di Biologia Computazionale del Centro di Ricerca e Innovazione (CRI) della Fondazione Edmund Mach (FEM), San Michele all’Adige, Trento, dal 01/04/2012 al 31/03/2015, essendo entrato in aspettativa senza assegni secondo l’ art. 7 L. 240/30.12.2010. Cavalieri ha mostrato fin da giovane un elevata capacità di reperimento risorse e dinamicità. Ha ottenuto le seguenti borse di studio e contratti di ricerca, dottorato di ricerca in Scienze Genetiche, Università di Pavia: dal 31 ottobre 1994 al 31 ottobre 1997, Post Dottorato, 1997 Dipartimento di Biologia Animale e Genetica “Leo Pardi”, Laboratorio di Mario Polsinelli, Università degli Studi di Firenze. Contratto di Collaborazione Coordinata e Continuativa, Consorzio Catania Ricerche, laboratorio di Patologia Vegetale, Prof, Antonino Catara, dal 8-7-1998 al 9-6-1999. Borsa di Post Dottorato presso l’Organismic and Evolutionary Biology Department, Harvard University, laboratorio di Daniel Hartl, dal 16/10/1999 al 03/09/2001. Cavalieri ha inoltre ricoperto le seguenti posizioni con corrispondenti titoli accademici: Group Leader, capo laboratorio, Harvard Genomics Fellow, Molecular and Cellular Biology Department, Center for Genomics Research, Bauer Labs (Harvard University USA) dal 03/09/2001 al 30/09/2004. Ricercatore nella facoltà di FARMACIA per il SSD BIO/19 dal 29/12/2003 al 30/03/2012. Prof. Aggregato presso l’università degli studi di Firenze dal 01/11/2004 al 10/06/2011.

Nell’ambito della sua attività professionale Cavalieri ha anche avuto esperienza come consulente per le seguenti aziende e istituti di ricerca nel settore delle biotecnologie microbiche e genomica microbica: ArteFir (Barberino V.E., Tuscany, 1996-1998), Bio-SFIR (Bertinoro Emilia, 1997-2001), Consorzio Catania Ricerche (Catania, Sicilia) 1999, e Istituto Tumori di Genova (Genova, Liguria) 2002. Fondazione Edmund Mach (2011-2012), UNIFARM Trento (2013 e 2014).

Altre attività da me svolte sono state attività di valutatore per procedura di valutazione comparativa per la selezione di direttore di dipartimento del CNR, valutazione dell’Unita Sanoublat del centro di eccellenza Genoscope di Parigi per conto dell’AERES (Agenzia di Valutazione della ricerca Francese) e valutazione di progetti scientifici per l’agenzia francese della ricerca, per l’agenzia inglese della ricerca, per l’agenzia di ricerca del lussemburgo e per il ministero dell’università e della ricerca scientifica Italiana.

Cavalieri si è distinto a livello nazionale e internazionale per l’applicazione di metodi di genomica integrata, “Systems Biology”, per lo studio dell'evoluzione dei genomi microbici e delle piante. Il gruppo di cavalieri unisce quindi sia competenze biologiche che bioinformatiche. Cavalieri è stato il primo ad applicare i DNA microarrays allo studio della variabilità in popolazioni di lieviti delle specie Saccharomyces cerevisiae e Saccharomyces bayanus nella risposta allo stress da fonti di azoto e all’esposizione alle basse temperature, l’uso del lievito S. cerevisiae come modello ha consentito la comprensione di meccanismi responsabili dell’evoluzione del genoma di piante e batteri, la scoperta del meccanismo di azione di farmaci antitumorali e di inibitori naturali della crescita, la comprensione delle reti di segnalazione della disponibilità e qualità di nutrienti e del loro ruolo in processi di morfogenesi in procarioti ed eucarioti. Negli anni Cavalieri ha esteso le tecniche bioinformatiche sviluppate e testate nei microorganismi allo studio della regolazione del sistema immune e della genetica e fisiologia del cancro e oggi anche alla genomica evolutiva e funzionale delle piante, raggiungendo risultati fondamentali nello studio della variabilità clonale di Olivo, mappare tratti quantitativi in Arabidopsis e in Melo. Una recente applicazione di marcatori molecolari indirizzati allo studio del DNA mitocondriale e plastidiale, ha consentito di comprendere i processi di domesticazione delle piante da frutto e il loro ruolo nell’evoluzione delle rosacee. Di particolare rilevanza sono stati gli studi sull'interazione fra microorganismi, sistema immunitario e dieta con lo scopo di capire le regole che guidano la tolleranza e la patogenicità di microorganismi. Nell’ambito di questi studi fino dal 2002 Cavalieri ha anche contribuito a sviluppare metodi bioinformatici per analizzare i dati di “omica” nel contesto delle reti metaboliche di trasduzione del segnale, utilizzando bioinformatica e big data screening per la definizione delle loro proprietà bioattive. Recentemente il gruppo di Cavalieri ha avuto l’opportunità di portare contributi fondamentali sull’influenza della dieta sul microbioma, attraverso uno studio in metagenomica di popolazioni africane è ad oggi citato più di 1300 volte. L' attività di ricerca di Cavalieri ha prodotto un totale di 160 pubblicazioni di cui 100 articoli su riviste indicizzate, citate oltre 4300 volte, con un H index rispettivamente di 25 (scopus e ISI) e 31 (Google Scholar).

Pubblicazioni

Peer reviewed Publications

1. Stefanie Hoyer, Kerstin F. Gerer, Isabell A. Pfeiffer, Sabrina Prommersberger, Sandra Höfflin, Tanushree Jaitly, Luca Beltrame, D. Cavalieri, Julio Vera, Gerold Schuler, Niels Schaft and Jan Dörrie Electroporated antigen-encoding mRNA is not a danger signal to human mature monocyte-derived dendritic cells. Journal of Immunology Research. In press 12/2015.
2. Irene Stefanini, Davide Albanese, Claudio Donati, Elena Franciosi, Agostino Cavazza, Carlotta De Filippo, Duccio Cavalieri. Dynamic changes in microbiota and mycobiota during spontaneous "Vino Santo Trentino" fermentation. Microbial Biotechnology, (IF 3.02). In press 12/2015.
3. Matteo Ramazzotti, Luisa Berna, Claudio Donati, Duccio Cavalieri. riboFrame: An Improved Method for Microbial Taxonomy Profiling from Non-Targeted Metagenomics. Frontiers in Genetics, 17 November 2015 doi: 10.3389/fgene.2015.00329. (IF N.A.).
4. Claudia Barelli, Davide Albanese, Claudio Donati, Massimo Pindo, Chiara Dallago, Francesco Rovero, Duccio Cavalieri, Kieran Michael Tuohy, Heidi Christine Hauffe. Carlotta De Filippo.Habitat fragmentation is associated to gut microbiota diversity of an endangered primate: implications for conservation. (Nature) Sci Rep. 2015 Oct 7;5:14862. doi: 10.1038/srep14862. (IF 5.078).
5. Rizzetto L, Weil T, Cavalieri D. Systems Level Dissection of Candida Recognition by Dectins: A Matter of Fungal Morphology and Site of Infection. Pathogens. 2015 Aug 21;4(3):639-61. (IF N.A.).
6. Clemente AM, Rizzetto L, Castronovo G, Perissi E, Tanturli M, Cozzolino F, Cavalieri D, Fusi F, Cialdai F, Vignali L, Torcia MG, Monici M. Effects of near-infrared laser radiation on the survival and inflammatory potential of Candida spp. involved in the pathogenesis of chemotherapy-induced oral mucositis. Eur J Clin Microbiol Infect Dis. 2015 Jul 15. (IF 2.668).
7. Rizzetto L, De Filippo C, Cavalieri D (2015) Mycobiota: Micro-Eukaryotes Inhabiting Our Body as Commensals or Opportunistic Pathogens. Fungal Genom Biol 4:120. doi: 10.4172/2165-8056.1000120. (IF NA).
8. Rivero D, Berná L, Stefanini I, Baruffini E, Bergerat A, Csikász-Nagy A, De Filippo C, Cavalieri D. Hsp12p and PAU genes are involved in ecological interactions between natural yeast strains. Environ Microbiol. 2015 un 16. doi: 10.1111/1462-2920.12950. (IF 6.021)
9. Angeletti S, Spoto S, Fogolari M, Cortigiani M, Fioravanti M, De Florio L, Curcio B, Cavalieri D, Costantino S, Dicuonzo G. Diagnostic and prognostic role of procalcitonin (PCT) and MR-pro-Adrenomedullin (MR-proADM) in bacterial infections. APMIS. 2015 Jun 8. (IF 2.042)
10. Goremykin VV, Nikiforova SV, Cavalieri D, Pindo M, Lockhart P. The root of flowering plants and total evidence. Syst Biol. 2015 May 20. pii: syv028. [Epub ahead of print] (IF 11.532).
11. Albanese D, Fontana P, De Filippo C, Cavalieri D, Donati C. MICCA: a complete and accurate software for taxonomic profiling of metagenomic data. (Nature) Sci Rep. 2015 May 19;5:9743. doi: 10.1038/srep09743. (IF 5.078)
12. Albanese D, De Filippo C, Cavalieri D, Donati C. Explaining diversity in metagenomic datasets by phylogenetic-based feature weighting. PLoS Comput Biol. 2015 Mar 27;11(3):e1004186. (IF 4.87)
13. Sonego P1, Meysman P, Moretto M, Viola R, Laukens K, Cavalieri D, Engelen K. Comparative Analysis of Gene Expression: Uncovering Expression Conservation and Divergence Between Salmonella enterica Serovar Typhimurium Strains LT2 and 14028S. Methods Mol Biol. (2015);1231:125-35. doi: 10.1007/978-1-4939-1720-4_8. (I.F. 1.29).
14. Rizzetto L, De Filippo C, Cavalieri D. Richness and diversity of mammalian fungal communities shape innate and adaptive immunity in health and disease. Eur J Immunol. 2014 Sep 25. doi: 10.1002/eji.201344403. (I.F. 4.5)
15. De Filippo, C., Di Paola, M., Stefanini, I., Rizzetto, L., Berna, L., Ramazzotti, M., Dapporto, L., Rivero, D., Gut, I.G., Gut, M., Bayés, M., Legras, J.L., Viola, R., Massi-Benedetti, C., De Luca, A., Romani, L., Lionetti, P., Cavalieri, D. (2014). Population genomics of Saccharomyces cerevisiae human isolates: passengers, colonizers, invaders. BioX Riv, 2014 doi:101101/001891,2013 – Web Preprint.
16. Santarlasci V, Maggi L, Mazzoni A, Capone M, Querci V, Rossi MC, Beltrame L, Cavalieri D, De Palma R, Liotta F, Cosmi L, Maggi E, Romagnani S, Annunziato F. IL-4-induced gene 1 maintains high Tob1 expression that contributes to TCR unresponsiveness in human T helper 17 cells. Eur J Immunol. 2014 Mar;44 (I.F. 4.5)
17. 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)
18. 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)
19. 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)
20. 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).
21. 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).
22. 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)
23. 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)
24. 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)
25. 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)
26. 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).
27. 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).
28. 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)
29. 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).
30. 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).
31. 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).
32. 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).
33. 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;
34. 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).
35. 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).
36. 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)
37. 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)
38. 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. 2012 Feb;42(2):458-69. (I.F. 4.5).
39. 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)
40. 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).
41. 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).
42. 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).
43. 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).
44. 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).
45. 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).
46. 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)
47. 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).
48. 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)
49. 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).
50. 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).
51. 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.
52. 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 .
53. 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)
54. 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
55. 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.
56. 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.
57. 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.
58. 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.
59. 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
60. 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.
61. 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).
62. 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.
63. 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.
64. 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)
65. 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)
66. 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).
67. 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).
68. 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.
69. 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).
70. Sardi I, Cavalieri D, Massimino M. Emerging treatments and gene expression profiling in high-risk medulloblastoma. Paediatr Drugs. 2007;9(2):81-96. Review.
71. 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).
72. 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).
73. 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).
74. 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)
75. 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).
76. 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).
77. 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)
78. Leung, JF., Cavalieri D., Fundamentals of Microarray Data Analysis, (2003). Trends in Genetics, 19 (11):649-659. (IF.9.95).
79. 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)
80. 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).
81. 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. (IF 6.325)
82. 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).
83. 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).
84. 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
85. 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).
86. 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=0.2).
87. Roselli G., Petruccelli R, Polsinelli L., Cavalieri D., (2002) Genetic Variability in Olea Europea sp. Journal of Genetics and Breeding Vol 56. (IF=0.2).
88. 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).
89. 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).
90. 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=0.2).
91. 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).
92. 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).
93. 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).
94. 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).
95. 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).
96. 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).
97. 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).
98. 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).
99. 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).
100. 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, "Microorganismi cibo e ambiente: un equilibrio da scoprire". Info Intesa Nr 233 Dicembre 2012, www.intesa.unifarm.it.
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. Kieran M. Tuohy, Paola Venuti, Simone Cuva, Cesare Furlanello, Mattia Gasperotti, Andrea Mancini, Florencia Ceppa, Duccio Cavalieri, Carlotta de Filippo, Urska Vrhovsek, Francesca Fava. “ Diet and the gut microbiota – how the gut:brain axis impacts on autism” in “Diet-Microbe Interactions in the Gut”, 2014 Publisher: Elsevier, Editor: Kieran Tuohy & Daniele Del Rio, ISBN: 978-0-12-407825-3
12. 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.
13. Franco Miglietta, Duccio Cavalieri, Alla ricerca dei "vecchi amici" fascicolo: Sapere - numero 2 - marzo/aprile 2014 - pp. 34-38 editore: edizioni Dedalo - Bari – Italia DOI: 10.12919/sapere.2014.02.5.
14. Duccio Cavalieri. Vivere bene col nostro micobiota: candidiasi, dieta e altre infezioni fungine ricorrenti. Info Intesa Nr 265 Agosto 2015, www.intesa.unifarm.it.
15. Patent (PCT 16042015-2014) from Fondazione Mach, Plant sRNA extract for use as an immunosuppressive agent. Roberto Viola, Duccio Cavalieri, Lisa Rizzetto, Azzedine Siammour.

Publications in ISSN journals of International Conference proceedings

1. Brilli M, Tamburini E., Cavalieri D., Burgalassi F., Fani R., (2002). Evolution and Biochemical Correlations Between NiFV and LeuA genes. Origins of life and evolution in the Biosphere. vol. 32, p. 485-486, ISSN: 0169-6149.
2. J.P.Townsend, D.Cavalieri, D.L.Hartl (2001). Population genomics: Gene expression in a vineyard yeast from Tuscany. Biology International, vol. 41, p. 91-98, ISSN: 0253-2069.
3. Moretto, Marco; Moser, Mirko; Romualdi, Chiara; Cavalieri, Duccio; Velasco, Riccardo; Si-Ammour, Azeddine " A hybrid approach to assemble complex transcriptomes, Bioinformatics, (2011) 27,17,2325-2329.
4. Aldinucci, Alessandra; Biagioli, Tiziana; Mazzanti, Benedetta; Pieri, Laura; Romagnoli, Paolo; Saccardi, Riccardo; Cavalieri, Duccio; Massacesi, Luca; Ballerini, Clara; ",MSCS SHIFT DCS FROM IMMUNOGENIC TO TOLEROGENIC THROUGH CONTACT INDUCED CYTOSKELETON MODIFICATIONS,BONE MARROW TRANSPLANTATION,45,,S20-S20, (2010),"NATURE PUBLISHING GROUP MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND"
5. Tonini, Giulia; Baccini, Michela; Cavalieri, Duccio; Mini, Enrico; Dolara, Piero; Biggeri, Annibale; ",Using regularization patterns from penalized regression in microarray experiments,Biomedical statistics and clinical epidemiology,4,1,35-46, (2010),CIC Edizioni internazionali.
6. Cavalieri, D; Grosu, P; De Filippo, C; Townsend, JP; Hartl, DL; ",Pathway Processor: a method for integrating whole-genome expression results into biological networks.,CHEMICAL RESEARCH IN TOXICOLOGY,15,12,1652-1652, (2002) "AMER CHEMICAL SOC 1155 16TH ST, NW, WASHINGTON, DC 20036 USA.
7. Casalone, E; Barberio, C; Cavalieri, D; Ceccarelli, I; Riparbelli, M; Ugolini, S; Polsinelli, M;YEAST FUNCTIONAL ANALYSIS REPORTS-Disruption and Phenotypic Analysis of Six Novel Genes from Chromosome IV of Saccharomyces cerevisiae Reveal YDL060w as an Essential Gene for Vegetative Growth,Yeast-Bognor Regis,15,15,1691-1702, (1999),"Chichester; New York: Wiley, c1985
8. P Bogani, D Cavalieri, R Petruccelli, L Polsinelli, G Roselli, II International Symposium on Olive Growing. (1993) 356, 98-101.

Research awards and fellowships

FUNDED PROJECTS

Metafoodlabs Provincia Autonoma di Trento. PAT (2012-2014) 200.000,00 Eu = 200.000 Eu.

UNIFARM sponsorship of FIRST PhD Fellowship (2012-2015) 50.000 EU-

AdP project (code P1412011I) Provincia Autonoma di Trento. New insights into the biology and ecology of the insects vectors of apple proliferation for the development of sustainable control strategies. WP3: VECTOR – PATHOGEN INTERACTIONS AND SPECIFICITY-150.000 Eu.

ADP project Startup Grant Computational Biology Department 2011-2014: 5.000.000 EU.

JPI EMPADASI EU Network 2014-2015: 150.000 EU.

CURRICULUM VITAE ET STUDIORUM

Duccio Cavalieri, PhD

First name / Surname: Duccio Cavalieri

Address:Via Madonna del Piano 6, 50019 Sesto Fiorentino, Firenze, Italy

E-mail: duccio.cavalieri@unifi.it

website: www.duccioknights.org,

Nationality:   Italian

Date of birth:             30.12.1966

Place of birth: Florence, Italy

Gender: Male

Current Position: Associate Professor (SSD BIO/19 General Microbiology) Department of Biology, University of Florence.

Areas of Research: Microbiology, Molecular Ecology, Evolutionary Biology, Genetics and Molecular Biology, Bioinformatics, Systems Biology, Functional Genomics, Immunology.

Education and training

1994-Laurea in Scienze Biologiche (110/110 lode), MSC in Biological Sciences.University of Florence, Italy, Advisor Mario Polsinelli, Enrico Casalone, Claudai Barberio. Master thesis in Molecular Microbiology and Population Genetics.

15/9/1994 al 15/9/1995-Tirocinante- University of Florence, Italy Abilitiazione all'esercizio della professione di Biologo, Advisor Dott.ssa Claudia Barberio (150/150), Genetics andMicrobiology

31/10/1994-4/05/1998. PhD in Genetics and Molecular Biology. PhD School of Genetics University of Pavia Italy Advisor Prof. Alessandro Galizzi, Prof. Mario Polsinelli, Prof. Robert K. Mortimer, Skills aquired: Functional Genomics and Molecular Biology.

08/07/1998 -09/06/1999: Postdoctoral Fellow, Consorzio Catania Ricerche, Università degli studi di Catania, Catania, it. Advisor Prof. Antonino Catara, skills aquired, Genetics and Molecular Biology,

01/07/1999 al 15/9/1999: Postdoctoral Fellow, University of Florence, Italy, Advisor Prof. Mario Polsinelli and Claudia Barberio, skills acquired,Genetics andMicrobiology.

01/10/1999 -01/09/2001: Postdoctoral Fellow, Harvard University, Faculty of Arts and Sciences, Organismic and Evolutionary Biology Department, Cambridge, Boston, MA, USA Advisors Daniel Hartl, Andrew Murray, Rich Losick. Population Genetics, Evolutionary Biology, Systems Biology, Genomics and Bioinformatics.

Previously held Academic Positions

2001-2004. Principal Investigator, Group Leader Yeast Comparative Genomics Group, Faculty Member, Harvard Genomics Fellow, Molecular and Cellular Biology Department, Center for Genomics Research, Bauer Labs (Harvard University USA) 03/09/2001 al 30/09/2004.

2003-2004. Assistant Professor (Ricercatore non confermato SSD BIO/19-Microbiology) Faculty of Parmacy, Department of preclinical and clinical Pharmacology M.Aiazzi Mancini.) 29/12/2003-01/11/2004. Research project: Yeast as a model to study mitochondrial disease, stress response and dietary modulation.

2002-2011. Teaching Activities and courses held to the Faculty of Biotechnology and Pharmacy as Adjunct Professor of Microbiology (Professore Aggregato), Florence University.

2002-2015. Assistant Professor, (Ricercatore confermato-SSD BIO/19 General Microbiology) Department of Clinical and Preclinical Pharmacology 'M. Aiazzi Mancini'.

2012-2015. Department head Department of Computational Biology, Group Leader, Comparative Genomics Unit. Fondazione Edmund Mach, Research and Innovation Centre, Food Quality Nutrition & Health Department, Via E. Mach 1, 38010 S. Michele all’Adige (TN), Italy.

Scientific Interests

Cavalieri has pioneered the application of genomics to population genetics and ecology, producing the first yeast microarrays on the east coast in 2009 while at Harvard.

Cavalieri’s main scientific focus is investigating the evolutionary biology of the fungal “holobiome”, the complex network of symbiotic interactions linking fungi and the host, including immune system regulation. In this perspective Cavalieri’s team has mastered the application of metagenomics and metabolomics to the analysis of community structure, gene content, and function of complex microbial communities in human populations. Cavalieri’s research interests range from nutrigenomics, metagenomics, computational metagenomics and immunology to the study of the molecular determinants of the interaction of fungi and immune system in health and disease. In order to understand the evolutionary forces driving the adaptation of fungi to the host Cavalieri’s lab is also investigating the evolutionary ecology of the ascomycete S.cerevisiae and its wild sanctuaries, including social insects such as wasps, and the role of the fungal cell wall as immune-modulator. These research lines have also led to the development of novel antifungals and discovery of molecules acting as master regulators of the cross talk between the microbe and its host, including immunostimulants and immunosuppressors.

Cavalieri’s work (orcid.org/0000-0001-6426-5719) has over 4380 citations, with and H index of 31 (Google Scholar) that makes him one of the Top Italian Scientists (TIS) according to VIA Academy. In scopus (Author ID: 7004993603) his work has 2903 citations and an H factor of 25. Cavalieri is also Co-Inventor (45%) of a Patent (PCT 2014) from Fondazione Mach, on the Immunomodulatory potential of plant miRNAs and has pending (25%) a Patent application with Unifi (Bicyclic peptidomimetics for use in the treatment of fungal infections). Cavalieri is also member of the editorial board of BMC Bioinformatics and FEMS Yeast Microbiology, and served as project and center evaluator for the CNR, the University of Padua, the French Agency for research Evauation AERES, the British agency of research (BBSRC), and the Research Agency of Luxemburg.

Twenty Selected Recent Signs of Recognition.

1. 2001-2004, Member of the Harvard Society of Fellows, Bauer Genomics Fellow.
2. 2005-2010, Master Lecturer and Lecturer of the PhD School of Nutrigenomics, training initiative of the Wageningen University, NUGO, EU 7th framework Network of Excellence.
3. 2007-2011, Member of the Governing Council of DC-Thera (Dendritic Cells for Novel Immunotherapies) Network Of Excellence.
4. 2010-2015, Member and advisor of EMDS (European Macrophage and Dendritic Cells Society.
5. Member of the Directive council board of the SIGMBM, (Società Italiana di Microbiologia e Genetica dei Microorganismi) Italian branch of FEMS.
6. Invited Lecture “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.
7. Invited Lecture, Pathogenic fungi and the human immune system “Yeast Proceedings of the 11th International Conference on Systems Biology, (ICSB) Edinburgh 12-16 October 2010.
8. Invited Lecture – 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).
9. Invited Lecture, “The impact of diet on gut microbiota of children from Europe and rural africa” ASM General Meeting, New Orleans 19-23 May 2011.
10. Invited Lecture: Systems Biology of Host Fungal Interactions. Fifth FEBS Advanced Lecture Course Human Fungal Pathogens, May 25-31 2013, La Colle Sur Loup, Nice.

1. Presentation TEDx Roncade on Biodiversity 2014, http://www.youtube.com/watch?v=dEy18XH4lPY.
2. December 2013-Passed three degrees of selection and selected for the oral selection for the ERC Sinergy Grant Proposal-Fluxes, Biophysics and Climatic impact of Biological Aerosols. This has been the only Italian proposal that arrived in the top 20 best at the Sinergy Reviewing Committee-2008-2013 Bruxelles.
3. With the DM 17/10/2013 n 828, (provvedimento 000120), he was nominated Research Director “Dirigente di Ricerca Chiara fama” from the President of the Italian National Research Council (CNR).
4. On January 23/2014 he was habilitated and passed the national selection for Full Professor in Genetics and Microbiology, “abilitazione a professore ordinario di prima fascia nel settore disciplinare Bio5I, Genetica e Microbiologia”.
5. The work "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 huge impact on both on the scientific community and on society in general. The article is the second most cited articles in PNAS since 2010 (over 1000 citations ).
6. The paper " I Stefanini , Dapporto L, Legras JL , Calabretta A, Di Paola M, De Filippo C , Viola R , P Kids , Polsinelli M, Turillazzi S , Cavalieri D. Role of social wasps in Saccharomyces cerevisiae ecology and evolution. Proc Natl Acad Sci US A. 2012 Aug 14; 109 (33) : 13398-403 " appears to have a significant impact on the yeast biotechnology and ecology. Won the Magni Award as best publication from an Italian Scientist in 2013, and has been broadcasted on National Public Radio NPR, http://www.npr.org/blogs/thesalt/2012/08/02/157606554/thank-the-simple-wasp-for-that-complex-glass-of-wine) on Wine Spectator Online (http://www.winespectator.com/webfeature/show/id/47188), on the New York Times, of the 06/08/2012 (http://www.nytimes.com/2012/08/07/science/dont-swat-that-bug-it-may-be-working-on-next-years-vintage.html?_r=0).

1. Invited Lecture. Population Genomics of Saccharomyces cerevisiae human isolates: Passengers, Colonizers, Invaders. ISSY 2014, October 9-12, 2014 Nova Gorica, Slovenia.
2. Invited Lecture British Society of Medical Micology Annual Meeting, (BSMM) Newcastle Upon Thyne, April 14th – 16th, 2013. Chair of the Session 7-Host Fungal Interactions. 1. And speaker: Complexity and dynamics of host-fungal interactions.
3. Organizer speaker and award winner, Symbiomes: Systems Biology of Host Microbe Interactions, ESF-EMBO, 5-10 june 2015, Pultisk Poland, http://symbiomes.esf.org/chairs-speakers.html.
4. Convenor of Yeast2015, 27th International Conference on Yeast Genetics and Molecular Biology, Levico terme 6^th-12^th September 2015, www.yeast2015.eu.

Peer reviewed Publications

1. Stefanie Hoyer, Kerstin F. Gerer, Isabell A. Pfeiffer, Sabrina Prommersberger, Sandra Höfflin, Tanushree Jaitly, Luca Beltrame, D. Cavalieri, Julio Vera, Gerold Schuler, Niels Schaft and Jan Dörrie Electroporated antigen-encoding mRNA is not a danger signal to human mature monocyte-derived dendritic cells. Journal of Immunology Research. In press 12/2015.
2. Irene Stefanini, Davide Albanese, Claudio Donati, Elena Franciosi, Agostino Cavazza, Carlotta De Filippo, Duccio Cavalieri. Dynamic changes in microbiota and mycobiota during spontaneous "Vino Santo Trentino" fermentation. Microbial Biotechnology, (IF 3.02). In press 12/2015.
3. Matteo Ramazzotti, Luisa Berna, Claudio Donati, Duccio Cavalieri. riboFrame: An Improved Method for Microbial Taxonomy Profiling from Non-Targeted Metagenomics. Frontiers in Genetics, 17 November 2015 doi: 10.3389/fgene.2015.00329. (IF N.A.).
4. Claudia Barelli, Davide Albanese, Claudio Donati, Massimo Pindo, Chiara Dallago, Francesco Rovero, Duccio Cavalieri, Kieran Michael Tuohy, Heidi Christine Hauffe. Carlotta De Filippo. Habitat fragmentation is associated to gut microbiota diversity of an endangered primate: implications for conservation. (Nature) Sci Rep. 2015 Oct 7;5:14862. doi: 10.1038/srep14862. (IF 5.078).
5. Rizzetto L, Weil T, Cavalieri D. Systems Level Dissection of Candida Recognition by Dectins: A Matter of Fungal Morphology and Site of Infection. Pathogens. 2015 Aug 21;4(3):639-61. (IF N.A.).
6. Clemente AM, Rizzetto L, Castronovo G, Perissi E, Tanturli M, Cozzolino F, Cavalieri D, Fusi F, Cialdai F, Vignali L, Torcia MG, Monici M. Effects of near-infrared laser radiation on the survival and inflammatory potential of Candida spp. involved in the pathogenesis of chemotherapy-induced oral mucositis. Eur J Clin Microbiol Infect Dis. 2015 Jul 15. (IF 2.668).
7. Rizzetto L, De Filippo C, Cavalieri D (2015) Mycobiota: Micro-Eukaryotes Inhabiting Our Body as Commensals or Opportunistic Pathogens. Fungal Genom Biol 4:120. doi: 10.4172/2165-8056.1000120. (IF NA).
8. Rivero D, Berná L, Stefanini I, Baruffini E, Bergerat A, Csikász-Nagy A, De Filippo C, Cavalieri D. Hsp12p and PAU genes are involved in ecological interactions between natural yeast strains. Environ Microbiol. 2015 un 16. doi: 10.1111/1462-2920.12950. (IF 6.021)
9. Angeletti S, Spoto S, Fogolari M, Cortigiani M, Fioravanti M, De Florio L, Curcio B, Cavalieri D, Costantino S, Dicuonzo G. Diagnostic and prognostic role of procalcitonin (PCT) and MR-pro-Adrenomedullin (MR-proADM) in bacterial infections. APMIS. 2015 Jun 8. (IF 2.042)
10. Goremykin VV, Nikiforova SV, Cavalieri D, Pindo M, Lockhart P. The root of flowering plants and total evidence. Syst Biol. 2015 May 20. pii: syv028. [Epub ahead of print] (IF 11.532).
11. Albanese D, Fontana P, De Filippo C, Cavalieri D, Donati C. MICCA: a complete and accurate software for taxonomic profiling of metagenomic data. (Nature) Sci Rep. 2015 May 19;5:9743. doi: 10.1038/srep09743. (IF 5.078)
12. Albanese D, De Filippo C, Cavalieri D, Donati C. Explaining diversity in metagenomic datasets by phylogenetic-based feature weighting. PLoS Comput Biol. 2015 Mar 27;11(3):e1004186. (IF 4.87)
13. Sonego P1, Meysman P, Moretto M, Viola R, Laukens K, Cavalieri D, Engelen K. Comparative Analysis of Gene Expression: Uncovering Expression Conservation and Divergence Between Salmonella enterica Serovar Typhimurium Strains LT2 and 14028S. Methods Mol Biol. (2015);1231:125-35. doi: 10.1007/978-1-4939-1720-4_8. (I.F. 1.29).
14. Rizzetto L, De Filippo C, Cavalieri D. Richness and diversity of mammalian fungal communities shape innate and adaptive immunity in health and disease. Eur J Immunol. 2014 Sep 25. doi: 10.1002/eji.201344403. (I.F. 4.5)
15. De Filippo, C., Di Paola, M., Stefanini, I., Rizzetto, L., Berna, L., Ramazzotti, M., Dapporto, L., Rivero, D., Gut, I.G., Gut, M., Bayés, M., Legras, J.L., Viola, R., Massi-Benedetti, C., De Luca, A., Romani, L., Lionetti, P., Cavalieri, D. (2014). Population genomics of Saccharomyces cerevisiae human isolates: passengers, colonizers, invaders. BioX Riv, 2014 doi:101101/001891,2013 – Web Preprint.
16. Santarlasci V, Maggi L, Mazzoni A, Capone M, Querci V, Rossi MC, Beltrame L, Cavalieri D, De Palma R, Liotta F, Cosmi L, Maggi E, Romagnani S, Annunziato F. IL-4-induced gene 1 maintains high Tob1 expression that contributes to TCR unresponsiveness in human T helper 17 cells. Eur J Immunol. 2014 Mar;44 (I.F. 4.5)
17. 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)
18. 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)
19. 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)
20. 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).
21. 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).
22. 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)
23. 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)
24. 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)
25. 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)
26. 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).
27. 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).
28. 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)
29. 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).
30. 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).
31. 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).
32. 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).
33. 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;
34. 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).
35. 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).
36. 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)
37. 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)
38. 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. 2012 Feb;42(2):458-69. (I.F. 4.5).
39. 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)
40. 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).
41. 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).
42. 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).
43. 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).
44. 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).
45. 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).
46. 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)
47. 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).
48. 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)
49. 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).
50. 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).
51. 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.
52. 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 .
53. 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)
54. 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
55. 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.
56. 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.
57. 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.
58. 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.
59. 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
60. 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.
61. 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).
62. 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.
63. 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.
64. 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)
65. 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)
66. 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).
67. 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).
68. 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.
69. 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).
70. Sardi I, Cavalieri D, Massimino M. Emerging treatments and gene expression profiling in high-risk medulloblastoma. Paediatr Drugs. 2007;9(2):81-96. Review.
71. 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).
72. 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).
73. 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).
74. 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)
75. 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).
76. 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).
77. 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)
78. Leung, JF., Cavalieri D., Fundamentals of Microarray Data Analysis, (2003). Trends in Genetics, 19 (11):649-659. (IF.9.95).
79. 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)
80. 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).
81. 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. (IF 6.325)
82. 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).
83. 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).
84. 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
85. 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).
86. 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=0.2).
87. Roselli G., Petruccelli R, Polsinelli L., Cavalieri D., (2002) Genetic Variability in Olea Europea sp. Journal of Genetics and Breeding Vol 56. (IF=0.2).
88. 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).
89. 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).
90. 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=0.2).
91. 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).
92. 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).
93. 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).
94. 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).
95. 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).
96. 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).
97. 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).
98. 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).
99. 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).
100. 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,"Microorganismi cibo e ambiente: un equilibrio da scoprire". Info Intesa Nr 233 Dicembre 2012, www.intesa.unifarm.it.
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. Kieran M. Tuohy, Paola Venuti, Simone Cuva, Cesare Furlanello, Mattia Gasperotti, Andrea Mancini, Florencia Ceppa, Duccio Cavalieri, Carlotta de Filippo, Urska Vrhovsek, Francesca Fava. “ Diet and the gut microbiota – how the gut:brain axis impacts on autism” in “Diet-Microbe Interactions in the Gut”, 2014 Publisher: Elsevier, Editor: Kieran Tuohy & Daniele Del Rio, ISBN: 978-0-12-407825-3
12. 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.
13. Franco Miglietta, Duccio Cavalieri, Alla ricerca dei "vecchi amici" fascicolo: Sapere - numero 2 - marzo/aprile 2014 - pp. 34-38 editore: edizioni Dedalo - Bari – Italia DOI: 10.12919/sapere.2014.02.5.
14. Duccio Cavalieri. Vivere bene col nostro micobiota: candidiasi, dieta e altre infezioni fungine ricorrenti. Info Intesa Nr 265 Agosto 2015, www.intesa.unifarm.it.
15. Patent (PCT 16042015-2014) from Fondazione Mach, Plant sRNA extract for use as an immunosuppressive agent. Roberto Viola, Duccio Cavalieri, Lisa Rizzetto, Azzedine Siammour.

Publications in ISSN journals of International Conference proceedings

1. Brilli M, Tamburini E., Cavalieri D., Burgalassi F., Fani R., (2002). Evolution and Biochemical Correlations Between NiFV and LeuA genes. Origins of life and evolution in the Biosphere. vol. 32, p. 485-486, ISSN: 0169-6149.
2. J.P.Townsend, D.Cavalieri, D.L.Hartl (2001). Population genomics: Gene expression in a vineyard yeast from Tuscany. Biology International, vol. 41, p. 91-98, ISSN: 0253-2069.
3. Moretto, Marco; Moser, Mirko; Romualdi, Chiara; Cavalieri, Duccio; Velasco, Riccardo; Si-Ammour, Azeddine " A hybrid approach to assemble complex transcriptomes, Bioinformatics, (2011) 27,17,2325-2329.
4. Aldinucci, Alessandra; Biagioli, Tiziana; Mazzanti, Benedetta; Pieri, Laura; Romagnoli, Paolo; Saccardi, Riccardo; Cavalieri, Duccio; Massacesi, Luca; Ballerini, Clara; ",MSCS SHIFT DCS FROM IMMUNOGENIC TO TOLEROGENIC THROUGH CONTACT INDUCED CYTOSKELETON MODIFICATIONS,BONE MARROW TRANSPLANTATION,45,,S20-S20, (2010),"NATURE PUBLISHING GROUP MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND"
5. Tonini, Giulia; Baccini, Michela; Cavalieri, Duccio; Mini, Enrico; Dolara, Piero; Biggeri, Annibale; ",Using regularization patterns from penalized regression in microarray experiments,Biomedical statistics and clinical epidemiology,4,1,35-46, (2010),CIC Edizioni internazionali.
6. Cavalieri, D; Grosu, P; De Filippo, C; Townsend, JP; Hartl, DL; ",Pathway Processor: a method for integrating whole-genome expression results into biological networks.,CHEMICAL RESEARCH IN TOXICOLOGY,15,12,1652-1652, (2002) "AMER CHEMICAL SOC 1155 16TH ST, NW, WASHINGTON, DC 20036 USA.
7. Casalone, E; Barberio, C; Cavalieri, D; Ceccarelli, I; Riparbelli, M; Ugolini, S; Polsinelli, M;YEAST FUNCTIONAL ANALYSIS REPORTS-Disruption and Phenotypic Analysis of Six Novel Genes from Chromosome IV of Saccharomyces cerevisiae Reveal YDL060w as an Essential Gene for Vegetative Growth,Yeast-Bognor Regis,15,15,1691-1702, (1999),"Chichester; New York: Wiley, c1985
8. P Bogani, D Cavalieri, R Petruccelli, L Polsinelli, G Roselli, II International Symposium on Olive Growing. (1993) 356, 98-101.

Research awards and fellowships

FUNDED PROJECTS

Metafoodlabs Provincia Autonoma di Trento. PAT (2012-2014) 200.000,00 Eu = 200.000 Eu.

UNIFARM sponsorship of FIRST PhD Fellowship (2012-2015) 50.000 EU-

AdP project (code P1412011I) Provincia Autonoma di Trento. New insights into the biology and ecology of the insects vectors of apple proliferation for the development of sustainable control strategies. WP3: VECTOR – PATHOGEN INTERACTIONS AND SPECIFICITY-150.000 Eu.

ADP project Startup Grant Computational Biology Department 2011-2014: 5.000.000 EU.

JPI EMPADASI EU Network 2014-2015: 150.000 EU.