CURRICULUM VITAE ET STUDIORUM Duccio Cavalieri First …...1 CURRICULUM VITAE ET STUDIORUM Duccio...

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1 CURRICULUM VITAE ET STUDIORUM Duccio Cavalieri First name / Surname: Duccio Cavalieri Address: Via Madonna del Piano 6, 50019 Sesto Fiorentino, Firenze, Italy E-mail: [email protected] website: www.duccioknights.org, Gender: Male, Nationality: Italian Date of birth: 30.12.1966 Place of birth: Florence, Italy Current Position: Associate Professor (SSD BIO/19 General Microbiology) Department of Biology, University of Florence. ResearcherID: T-3097-2017 Scopus Author ID 7004993603 ORCID id : http://orcid.org/0000-0001-6426-5719 Education and training 1994: Laurea in Scienze Biologiche-MSC in Biological Sciences (110/110 lode). University of Florence. 1994-1998: PhD in Genetics and Molecular Biology. PhD School of Genetics University of Pavia Italy, Master thesis Advisor Prof. Alessandro Galizzi (Pavia), Prof. Mario Polsinelli (Firenze), Prof R.K.Mortimer (Berkeley). 1998 -1999: Postdoctoral Fellow, Consorzio Catania Ricerche, Università degli studi di Catania, Catania, it. Advisor Prof. Antonino Catara. 1999 -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. Past Academic Positions 2001-2004: Harvard Genomics Fellow, Principal Investigator, Group Leader Yeast Comparative Genomics Group, The Bauer Laboratories, Molecular and Cellular Biology Department (Harvard University USA). 2003-2011: Assistant Professor (Ricercatore SSD BIO/19-Microbiology) Faculty of Parmacy, Department of preclinical and clinical Pharmacology M.Aiazzi Mancini. 2011-2015: Head of the Department of Computational Biology, omparative Genomics Unit Group Leader, First Researcher (Coordinatore del Dipartimento di Biologia Computazionale, Primo Ricercatore, Capo dell’Unità di Genomica Comparativa) Fondazione Edmund Mach, Research and Innovation Centre, S. Michele all’Adige (TN), Italy. Areas of Research: Microbiology, Bioinformatics, Computational Metagenomics, Strain-level Fungal Metagenomics, System immunology of Host Microbe Interactions, Personalized Nutrition, Personalized Microbial Therapy, Molecular Ecology, Evolutionary Biology, Functional and Structural Fungal Genomics. Cavalieri’s main recent achievement are: Elucidating the ecology and evolutionary genomics of the ascomycete S.cerevisiae and its wild sanctuaries, including social insects; Trained Immunity: the cross talk between the mycobiome, immune function and the SNC, the effect of diet globalization on gut microbiota, plant miRNAs as anti-inflammatory agents. Bioinformatic tools for pathway analysis of omics data. Duccio Cavalieri, has a proven track record in yeast and bacterial ecological genomics, metagenomics and bioinformatics. In 2000 he was the first to apply DNA microarrays to study evolutionary ecology of wine yeasts. Since 2010 he has applied Next Generation Sequencing and pathway and network analysis to study metagenomics, host- microbe interaction at the systems level. From 2011 to 2016 as director of the computational biology department at Fondazione Edmund Mach, he led a team of biologists, biotechnologist and bioinformatics researchers in analyzing, assembling and interpreting large phenomics, genomics and metagenomics datasets and contributing substantially to building databases and computational resources. He is currently well recognized in the field of evolutionary metagenomics, having published seminal work on the role of globalization and westernization on microbiotas and on the importance of preserving traditional fermented foods and their immunomodulatory potential. His lab is also active on elucidating the role of the microbiome and mycobiome in the Autism spectrum, Inflammatory Bowel Diseases, and

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Page 1: CURRICULUM VITAE ET STUDIORUM Duccio Cavalieri First …...1 CURRICULUM VITAE ET STUDIORUM Duccio Cavalieri First name / Surname: Duccio Cavalieri Address: Via Madonna del Piano 6,

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CURRICULUM VITAE ET STUDIORUM

Duccio Cavalieri

First name / Surname: Duccio Cavalieri Address: Via Madonna del Piano 6, 50019 Sesto Fiorentino, Firenze, Italy E-mail: [email protected] website: www.duccioknights.org, Gender: Male, Nationality: Italian Date of birth: 30.12.1966 Place of birth: Florence, Italy Current Position: Associate Professor (SSD BIO/19 General Microbiology) Department of Biology, University of Florence. ResearcherID: T-3097-2017 Scopus Author ID 7004993603 ORCID id : http://orcid.org/0000-0001-6426-5719 Education and training

1994: Laurea in Scienze Biologiche-MSC in Biological Sciences (110/110 lode). University of Florence. 1994-1998: PhD in Genetics and Molecular Biology. PhD School of Genetics University of Pavia Italy, Master thesis Advisor Prof. Alessandro Galizzi (Pavia), Prof. Mario Polsinelli (Firenze), Prof R.K.Mortimer (Berkeley). 1998 -1999: Postdoctoral Fellow, Consorzio Catania Ricerche, Università degli studi di Catania, Catania, it. Advisor Prof. Antonino Catara. 1999 -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. Past Academic Positions 2001-2004: Harvard Genomics Fellow, Principal Investigator, Group Leader Yeast Comparative Genomics Group, The Bauer Laboratories, Molecular and Cellular Biology Department (Harvard University USA). 2003-2011: Assistant Professor (Ricercatore SSD BIO/19-Microbiology) Faculty of Parmacy, Department of preclinical and clinical Pharmacology M.Aiazzi Mancini. 2011-2015: Head of the Department of Computational Biology, omparative Genomics Unit Group Leader, First Researcher (Coordinatore del Dipartimento di Biologia Computazionale, Primo Ricercatore, Capo dell’Unità di Genomica Comparativa) Fondazione Edmund Mach, Research and Innovation Centre, S. Michele all’Adige (TN), Italy. Areas of Research: Microbiology, Bioinformatics, Computational Metagenomics, Strain-level Fungal Metagenomics, System immunology of Host Microbe Interactions, Personalized Nutrition, Personalized Microbial Therapy, Molecular Ecology, Evolutionary Biology, Functional and Structural Fungal Genomics. Cavalieri’s main recent achievement are: Elucidating the ecology and evolutionary genomics of the ascomycete S.cerevisiae and its wild sanctuaries, including social insects; Trained Immunity: the cross talk between the mycobiome, immune function and the SNC, the effect of diet globalization on gut microbiota, plant miRNAs as anti-inflammatory agents. Bioinformatic tools for pathway analysis of omics data. Duccio Cavalieri, has a proven track record in yeast and bacterial ecological genomics, metagenomics and bioinformatics. In 2000 he was the first to apply DNA microarrays to study evolutionary ecology of wine yeasts. Since 2010 he has applied Next Generation Sequencing and pathway and network analysis to study metagenomics, host-microbe interaction at the systems level. From 2011 to 2016 as director of the computational biology department at Fondazione Edmund Mach, he led a team of biologists, biotechnologist and bioinformatics researchers in analyzing, assembling and interpreting large phenomics, genomics and metagenomics datasets and contributing substantially to building databases and computational resources. He is currently well recognized in the field of evolutionary metagenomics, having published seminal work on the role of globalization and westernization on microbiotas and on the importance of preserving traditional fermented foods and their immunomodulatory potential. His lab is also active on elucidating the role of the microbiome and mycobiome in the Autism spectrum, Inflammatory Bowel Diseases, and

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RETT syndrome. Cavalieri has international collaborations with Birgitte Regenberg (KU-DK) Curtis Huttenower (Harvard MA), Hans Hofmann (UT-Austin), Daniel Hartl (Harvard OEB), Andrew Murray (Harvard, MCB), Mihai Nethea (Rabound University-NL), Omry Koren (Israel), Carmen Collado (Spain), Neil Gow (Aberdeen), Jens Nielsen (DTU-DK and Gotheborg University, Sweden). Cavalieri’s work has a global impact of over 7630 citations, with and H index of 39 with 215 publications according to Google Scholar and 5044 citations with an H index of 32 and 121 publications according to SCOPUS (http://orcid.org/0000-0001-6426-5719). Cavalieri is also Co-Inventor (45%) of the Patent (PCT 16042015-2014) "Plant sRNA extract for use as an immunosuppressive agent."

Publications

International peer-reviewed (ISI-JCR) 135

Book Chapters, Popular Press, Patents 16

Other with SSID 68

Of which, in n the last 5 years (2013-2018) 65

Total 220

Cavalieri is member of the editorial board of BMC Bioinformatics, Frontiers Microbiology, Molecular Cell, and served as project and center evaluator for the CNR, the University of Padua, the French Agency for research Evaluation AERES, the British agency of research (BBSRC), the Research Agency of Luxemburg, the Israeli Ministry of Science and Technology, the Croucher Foundation of Hong Kong.

Twenty Selected Relevant Signs of Recognition.

1. 2001-2004, Bauer Genomics Fellow, Harvard Society of Fellows. 2. 2007-2011, Member of the Governing Council of DC-Thera (Dendritic Cells for Novel Immunotherapies)

Network of Excellence. 3. 2010-2013, Member of the Directive council board of the SIGMBM, (Società Italiana di Microbiologia e

Genetica dei Microorganismi) Italian branch of FEMS. 4. November 2015- Delegate for the University of Florence and Coordinator of the Computational Metagenomics

section for the Italian JRU-ELIXIR (ESFRI). 5. Head of the Italian JRU and Deputy Coordinator, JPI EMPADASI-EU-2015-2016. 6. Since 2016-Italian delegate to the Finance and Policy Committee of the International society for yeast genetics

and molecular biology. 7. Invited Lecture “Of yeast and men: dissecting the interaction between fungi and immune response”, Wellcome

Trust Advanced Courses and Scientific Conferences, Hinxton Cambridge. June 22-23, 2010. 8. Invited Lecture, Pathogenic fungi and the human immune system “Proceedings of the 11th International

Conference on Systems Biology, (ICSB) Edinburgh 12-16 October 2010. 9. 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.

10. Invited Lecture, “The impact of diet on gut microbiota of children from Europe and rural africa” American Society of Microbiology General Meeting, New Orleans 19-23 May 2011.

11. 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.

12. 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.

13. 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.

14. Convenor and Organizer of ICGYMB 2015, 27th International Conference on Yeast Genetics and Molecular Biology, Levico terme 6th-12th September 2015, www.yeast2015.eu.

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15. I-Biok Plenary Invited Lecturer to the 14th international congress on yeasts, ICY2016, 11-15/09 2016, Awaji Island, Japan.

16. Inivited Speaker Italy-Japan Joint Symposium:New Trends in Enzyme and Microbial Science in the Translational Biology Era: IBB Neaples, October, 18-20, 2017

17. 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 ), broadcasted on The Economist and the major newspapers and TVs, 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 1170 citations ) and has been invited for presentation at the TEDx Roncade on Biodiversity 2014, http://www.youtube.com/watch?v=dEy18XH4lPY.

18. 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", cited 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), Wine Spectator Online (http://www.winespectator.com/webfeature/show/id/47188), 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).

19. The Paper I Stefanini, Dapporto L, Berna L, Polsinelli M., Turillazzi S , Cavalieri D. Social wasps are a Saccharomyces mating nest. Proc Natl Acad Sci US A. 2016 Feb 23;113(8):2247-51. doi: 10.1073/pnas.1516453113. Epub 2016 Jan 19., has been higlighted with an interview to Duccio Cavalieri in Science (http://www.sciencemag.org/news/2016/01/brewer-s-yeasts-mate-inside-guts-hibernating-wasps), The Scientist, il Corriere della Sera, Science Videos and 40 other web sites.

20. Listed amongst the Top Italian Scientists (TIS) -VIA Academy and of the 12 Italian Scientists Awarded the Abilitazione a Professore Ordinario; (Full Professorship) in microbiology and Genetics, in the first round of national evaluation in 2014 and in the current re-evaluation (2018).

Peer reviewed Publications

1. Bradamante S., Rivero D., Barenghi L., Balsamo M., Minardi S.P, Vitali F., Cavalieri D., SCD – Stem Cell Differentiation Toward Osteoblast Onboard the International Space Station. Microgravity Science and Techonology., https://doi.org/10.1007/s12217-018-9653-2.

2. Butera A, Di Paola M, Pavarini L, Strati F, Pindo M, Sanchez M, Cavalieri D, Boirivant M, De Filippo C. Nod2 Deficiency in mice is Associated with Microbiota Variation Favouring the Expansion of mucosal CD4+ LAP+ Regulatory Cells. Sci Rep. 2018 Sep 24;8(1):14241.

3. Ramazzotti M, Stefanini I, Di Paola M, De Filippo C, Rizzetto L, Berná L, Dapporto L, Rivero D, Tocci N, Weil T, Lenucci MS, Lionetti P, Cavalieri D. Population genomics reveals evolution and variation of Saccharomyces cerevisiae in the human and insects gut. Environ Microbiol. 2018 Sep 24. doi: 10.1111/1462-2920.14422.

4. Brunella P, Cavalieri D. Innovative metagenomic approaches for detection of microbial communities involved in biodeteriorattion of cultural heritage, IOP Conference Series: Materials Science and Engineering. 2018, 364(1),012074.

5. Stefanini I, Cavalieri D. Metagenomic Approaches to Investigate the Contribution of the Vineyard Environment to the Quality of Wine Fermentation: Potentials and Difficulties. Front Microbiol. 2018 May 16;9:991.

6. Vitali F, Lombardo R, Rivero D, Mattivi F, Franceschi P, Bordoni A, Trimigno A, Capozzi F, Felici G, Taglino F, Miglietta F, De Cock N, Lachat C, De Baets B, De Tré G, Pinart M, Nimptsch K, Pischon T, Bouwman J, Cavalieri D; ENPADASI consortium. ONS: an ontology for a standardized description of interventions and observational studies in nutrition. Genes Nutr. 2018 Apr 30;13:12.

7. Strati F, Calabrò A, Donati C, De Felice C, Hayek J, Jousson O, Leoncini S, Renzi D, Rizzetto L, De Filippo C, Cavalieri D. Intestinal Candida parapsilosis isolates from Rett syndrome subjects bear potential virulent traits and capacity to persist within the host. BMC Gastroenterol. 2018 May 2;18(1):57.

8. Stefanini I, Rizzetto L, Rivero D, Carbonell S, Gut M, Heath S, Gut IG, Trabocchi A, Guarna A, Ben Ghazzi N, Bowyer P, Kapushesky M, Cavalieri D. Deciphering the mechanism of action of 089, a compound impairing the fungal cell cycle. Sci Rep. 2018 Apr 13;8(1):5964.

9. Cavalieri D., Di Paola M., Rizzetto L., Tocci N., De Filippo C., Lionetti P., Ardizzoni A., Colombari B., Paulone S., Gut I.G., Berna L., Gut M., Blanc J., Kapushesky M., Blasi E., Peppoloni S. Genomic and

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phenotypic variation in morphogenetic networks of two Candida albicans isolates subtends their different pathogenic potential. Front. Immunol. 2018 Jan 19;8:1997.

10. Carmona-Gutierrez D, Bauer MA, Zimmermann A, Aguilera A, Austriaco N, Ayscough K, Balzan R, Bar-Nun S, Barrientos A, Belenky P, Blondel M, Braun RJ, Breitenbach M, Burhans WC, Büttner S, Cavalieri D, Chang M, Cooper KF, Côrte-Real M, Costa V, Cullin C, Dawes I, Dengjel J, Dickman MB, Eisenberg T, Fahrenkrog B, Fasel N, Fröhlich KU, Gargouri A, Giannattasio S, Goffrini P, Gourlay CW, Grant CM, Greenwood MT, Guaragnella N, Heger T, Heinisch J, Herker E, Herrmann JM, Hofer S, Jiménez-Ruiz A, Jungwirth H, Kainz K, Kontoyiannis DP, Ludovico P, Manon S, Martegani E, Mazzoni C, Megeney LA, Meisinger C, Nielsen J, Nyström T, Osiewacz HD, Outeiro TF, Park HO, Pendl T, Petranovic D, Picot S, Polčic P, Powers T, Ramsdale M, Rinnerthaler M, Rockenfeller P, Ruckenstuhl C, Schaffrath R, Segovia M, Severin FF, Sharon A, Sigrist SJ, Sommer-Ruck C, Sousa MJ, Thevelein JM, Thevissen K, Titorenko V, Toledano MB, Tuite M, Vögtle FN, Westermann B, Winderickx J, Wissing S, Wölfl S, Zhang ZJ, Zhao RY, Zhou B, Galluzzi L, Kroemer G, Madeo F. Guidelines and recommendations on yeast cell death nomenclature. Microb Cell. 2018 Jan 1;5(1):4-31.

11. Milan M, Carraro L, Fariselli P, Martino ME, Cavalieri D, Vitali F, Boffo L, Patarnello T, Bargelloni L, Cardazzo B. Microbiota and environmental stress: how pollution affects microbial communities in Manila clams. Aquat Toxicol. 2017 Nov 27;194:195-207.

12. Tocci N., Weil T., Perenzoni D., Narduzzi L., Mãdrinan S., Crockett S., Nürk M.N., Cavalieri D., Mattivi F. Phenolic profile, chemical relationship and antifungal activity of Andean Hypericum species. Industrial Crops and Products, in press February 2018, 112: 32–37.

13. Stefanini I., Albanese A., Sordo M., Legras J-L., De Filippo C., Cavalieri D., Donati C. (2017) SaccharomycesIDentifier, SID: strain-level analysis of Saccharomyces cerevisiae populations by using microsatellite meta-patterns, Sci Rep. 2017 Nov 10;7(1):15343.

14. Modesto M., Michelini S., Sansosti M.S., De Filippo C., Cavalieri D., Qvirist L., Andlid T., Spiezio C., Sandri C., Pascarelli S., Sgorbati B., Mattarelli P. Bifidobacterium callitrichidarum sp. nov. from the faeces of the emperor tamarin (Saguinus imperator). Int J Syst Evol Microbiol. 2017 Nov 8.

15. De Filippo C, Di Paola M, Ramazzotti M, Albanese D, Pieraccini G, Banci E, Miglietta F, Cavalieri D, Lionetti P. Diet, Environments, and Gut Microbiota. A Preliminary Investigation in Children Living in Rural and Urban Burkina Faso and Italy. Front Microbiol. 2017 Oct 13;8:1979.

16. Lenci E., Stefanini I., Guarna A., Menchi G., Cavalieri D., Trabocchi A. Diversity-Oriented Synthesis and Chemical Genetics of Peptidomimetics to Address Lead Discovery of Anti-Infective Agents. Proceedings 2017, 1, 678; doi:10.3390/proceedings1060678.

17. Di Paola M, Sani C, Clemente AM, Iossa A, Perissi E, Castronovo G, Tanturli M, Rivero D, Cozzolino F, Cavalieri D, Carozzi F, De Filippo C, Torcia MG. Characterization of cervico-vaginal microbiota in women developing persistent high-risk Human Papillomavirus infection. Sci Rep. 2017 Aug 31;7(1):10200. doi: 10.1038/s41598-017-09842-6.

18. Weil T, Santamaría R, Lee W, Rung J, Tocci N, Abbey D, Bezerra AR, Carreto L, Moura GR, Bayés M, Gut IG, Csikasz-Nagy A, Cavalieri D, Berman J, Santos MAS. Adaptive Mistranslation Accelerates the Evolution of Fluconazole Resistance and Induces Major Genomic and Gene Expression Alterations in Candida albicans. mSphere. 2017 Aug 9;2(4). pii: e00167-17. doi: 10.1128/mSphere.00167-17. eCollection 2017 Jul-Aug.

19. Buschow S.I., Ramazzotti M., Reinieren-Beeren I M.J., Heinzerling L.M, Westdorp H., Stefanini I., Beltrame L., Hato S.V., Ellebæk E., Gross S., Nguyen V.A., Weinlich G, Ragoussis J., Baban D., Schuler-Thurner B., Svane I.M., Romani N., Austyn9 J.M., De Vries I.J.M, Schuler G., Cavalieri D., Figdor C.G. Survival of metastatic melanoma patients after dendritic cell vaccination correlates with expression of leukocyte phosphatidylethanolamine-binding protein 1 / Raf Kinase inhibitory protein. Oncotarget, online 29/06/2017, doi: 10.18632/oncotarget.18698.

20. Brilli M, Trabocchi A, Weil T, Cavalieri D, Stefanini I. Relations between Effects and Structure of Small Bicyclic Molecules on the Complex Model System Saccharomyces cerevisiae. Front Pharmacol. 2017 Mar 30;8:170. doi: 10.3389/fphar.2017.00170. eCollection 2017.

21. Stefanini I, Carlin S, Tocci N, Albanese D, Donati C, Franceschi P, Paris M, Zenato A, Tempesta S, Bronzato A, Vrhovsek U, Mattivi F, Cavalieri D. Core Microbiota and Metabolome of Vitis vinifera L. cv. Corvina Grapes and Musts. Front Microbiol. 2017 Mar 21;8:457.

22. Weil T, De Filippo C, Albanese D, Donati C, Pindo M, Pavarini L, Carotenuto F, Pasqui M, Poto L, Gabrieli J, Barbante C, Sattler B, Cavalieri D, Miglietta F. Legal immigrants: invasion of alien microbial communities during winter occurring desert dust storms. Microbiome. 2017 Mar 10;5(1):32.

23. Strati F, Cavalieri D, Albanese D, De Felice C, Donati C, Hayek J, Jousson O, Leoncini S, Renzi D, Calabrò A, De Filippo C. New evidences on the altered gut microbiota in Autism specturm syndrome. Microbiome. 2017 Feb 22;5(1):24.

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24. Bianco L, Riccadonna S, Lavezzo E, Falda M, Formentin E, Cavalieri D, Toppo S, Fontana P. Pathway Inspector: a pathway based web application for RNAseq analysis of model and non-model organisms. Bioinformatics. 2017 Feb 1;33(3):453-455.

25. Ceni E, Mello T, Polvani S, Vasseur-Cognet M, Tarocchi M, Tempesti S, Cavalieri D, Beltrame L, Giada M, Pinzani M, Milani S, Galli A The orphan nuclear receptor COUP-TFII coordinates hypoxia-independent proangiogenic responses in hepatic stellate cells. J Hepatol. 2016 Nov 17. pii: S0168-8278(16)30650-X. doi: 10.1016/j.jhep.2016.11.003. (IF 10.590)

26. Bianco L, Riccadonna S, Lavezzo E, Falda M, Formentin E, Cavalieri D, Toppo S, Fontana P. Pathway Inspector: a pathway based web application for RNAseq analysis of model and non-model organisms. Bioinformatics. 2016 Oct 6. pii: btw636 (IF 5.323).

27. Di Paola M., Cavalieri D., Albanese D., Donati C., Sordo M., Pindo M., Pagnini I., Giani T., Simonini G., Paladini A., Lionetti P., De Filippo C., Cimaz R. Alteration of fecal microbiota profiles in juvenile idiopathic arthritis. Associations with HLA-B27 allele and disease status. Front. Microbiol. 2016 Oct 26;7:1703. (I.F 4.61).

28. Qvirist L.A., De Filippo C., Strati F., Stefanini I., Sordo M., Andlid T., Felis G.E., Mattarelli P., Cavalieri D. Isolation, identification and characterization of yeasts from fermented goat milk of the Yaghnob Valley in Tajikistan. Front. Microbiol. 2016 Nov 3;7:1690. (I.F 4.61).

29. Strati F, Cavalieri D, Albanese D, De Felice C, Donati C, Hayek J, Jousson O, Leoncini S, Pindo M, Renzi D, Rizzetto L, Stefanini I, Calabrò A, De Filippo C. Altered gut microbiota in Rett syndrome. Microbiome. 2016 Jul 30;4(1):41 (I.F 9.00).

30. Francesco Strati, Monica Di Paola, Irene Stefanini, Davide Albanese, Lisa Rizzetto, Paolo Lionetti, Antonio Calabrò, Olivier Jousson, Claudio Donati, Duccio Cavalieri* and Carlotta De Filippo Age and gender affect the composition of fungal population of the human gastrointestinal tract. Front. Microbiol. 7:1227. doi: 10.3389/fmicb.2016.01227. (I.F 4.61).

31. Cavalieri D, Rizzetto L, Tocci N, Rivero D, Asquini E, Si-Ammour A, Bonechi E, Ballerini C, Viola R. Plant microRNAs as novel immunomodulatory agents. Sci Rep. 2016 May 11;6:25761. doi: 10.1038/srep25761.

32. Claudio Donati, Moreno Zolfo, Davide Albanese, Duy Tin Truong, Francesco Asnicar, Valerio Iebba, Duccio Cavalieri, Olivier Jousson, Carlotta De Filippo, Curtis Huttenhower & Nicola Segata. Uncovering oral Neisseria tropism and persistence using metagenomic sequencing. Nat Microbiol. 2016 May 27;1(7):16070.

33. Dapporto L, Stefanini I, Rivero D, Polsinelli M, Capretti P, De Marchi P, Viola R, Turillazzi S, Cavalieri D. Social Wasp intestines host the local phenotypic variability of Saccharomyces cerevisiae strains. Yeast. 2016 Jul;33(7):277-87. (I.F 2.259).

34. Rizzetto L, Ifrim DC, Moretti S, Tocci N, Cheng SC, Quintin J, Renga G, Oikonomou V, De Filippo C, Weil T, Blok BA, Lenucci MS, Santos MA, Romani L, Netea MG, Cavalieri D. Fungal chitin induces trained immunity in human monocytes during cross-talk of the host with Saccharomyces cerevisiae. J Biol Chem. 2016 Feb 17. pii: jbc.M115.699645. [Epub ahead of print] (IF 4.573)

35. Stefanini I., Dapporto L., Berna L., Polsinelli M., Turillazzi S., Cavalieri D. Social wasps are a Saccharomyces mating nest. Proc Natl Acad Sci US A. 2016 Feb 23;113(8):2247-51. doi: 10.1073/pnas.1516453113. (IF: 9.681).

36. Hoyer S, 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. J Immunol Res. 2015;2015:952184. doi: 10.1155/2015/952184. Epub 2015 Dec 28.

37. Stefanini I., Albanese D., Donati C., Franciosi E., Cavazza A., De Filippo C., Cavalieri D. Dynamic changes in microbiota and mycobiota during spontaneous "Vino Santo Trentino" fermentation. Microbial Biotechnology, 2016 Jan 18. doi: 10.1111/1751-7915.12337. (IF 3.02).

38. Ramazzotti M., Berna L., Donati C., Cavalieri D. 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.).

39. Barelli C., Albanese D., Donati C., Pindo M., Dallago C., Rovero F., Cavalieri D, Tuohy K.M., Hauffe H. C., De Filippo C. 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).

40. 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.).

41. 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).

42. 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).

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43. 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)

44. 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)

45. Goremykin VV, Nikiforova SV, Cavalieri D, Pindo M, Lockhart P. The root of flowering plants and total evidence. Syst Biol. 2015 Sep;64(5):879-91. doi: 10.1093/sysbio/syv028. Epub 2015 May 20. (IF 11.532).

46. 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)

47. 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)

48. Sonego P, 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).

49. 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)

50. 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.

51. 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)

52. 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)

53. 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)

54. 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)

55. 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).

56. 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).

57. 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)

58. 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)

59. 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)

60. 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)

61. 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).

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62. 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).

63. 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)

64. 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).

65. 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).

66. 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).

67. 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).

68. 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;

69. 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).

70. 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).

71. 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)

72. 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)

73. 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).

74. 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)

75. 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).

76. 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).

77. 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).

78. 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).

79. 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).

80. 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).

81. 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

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Oncol. 2011 Mar;12(3):273-85. Epub 2011 Feb 21. (IF:17.64) 82. 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).

83. 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)

84. 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).

85. 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).

86. 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.

87. 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 .

88. 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)

89. 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

90. 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.

91. 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.

92. 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.

93. 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.

94. 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

95. 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.

96. 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).

97. 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.

98. 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.

99. 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)

100. 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)

101. 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).

102. Salathia N, Lee HN, Sangster TA, Morneau K, Landry CR, Schellenberg K, Behere AS, Gunderson KL,

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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).

103. 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.

104. 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).

105. Sardi I, Cavalieri D, Massimino M. Emerging treatments and gene expression profiling in high-risk medulloblastoma. Paediatr Drugs. 2007;9(2):81-96. Review.

106. 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).

107. 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).

108. 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).

109. 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)

110. 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).

111. 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).

112. 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)

113. Leung, JF., Cavalieri D., Fundamentals of Microarray Data Analysis, (2003). Trends in Genetics, 19 (11):649-659. (IF.9.95).

114. 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)

115. 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).

116. 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)

117. 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).

118. 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).

119. 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

120. 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).

121. 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).

122. 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).

123. 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).

124. Barberio C, Pagliai L, Cavalieri D, Fani R. Biodiversity and horizontal gene transfer in culturable bacteria

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isolated from activated sludge enriched in nonylphenol ethoxylates. Res Microbiol. 2001 Jan-Feb;152(1):105-12. (IF=2.06).

125. 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).

126. 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).

127. 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).

128. 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).

129. 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).

130. 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).

131. 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).

132. 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).

133. 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).

134. 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).

135. 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.

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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.

FUNDING: Young Investigator Startup Grant, University of Florence 2001-2002. PI-Bauer Fellow Startup Package, Harvard Genomics Fellow Program Grant-NIH 2000 Center Grant-Harvard University USA (2001-2004). Co-PI-NSF-National Science Foundation Arabidopsis 2010 grant 0313473 (2004-2005). NUGO-EU FP6- Project ID 506360 Network of Excellence-(NOE) Duccio Cavalieri CoPi-WP leader-2003-2009(NUGO-EU 6th FP Network of Excellence-(NOE) Partecipant-WP leader-2003-2009.( http://cordis.europa.eu/project/rcn/74154_en.html). DC-THERA (Dendritic Cells for Novel Immunotherapies) EU FP6 NOE- Project ID: 512074-Duccio Cavalieri PI, WP leader-Governing Council Member-2007-2011 (http://cordis.europa.eu/result/rcn/51825_en.html). APBRIA-“Use of algae for biofuel production- Unit coordinator, Italian Ministry of Agriculture-2009-2012. SYBARIS-EU 7th FP-Project ID: 242220-Deputy Coordinator-WP leader 2009-2013 (http://cordis.europa.eu/result/rcn/140847_en.html). PRIN-MIUR. Min. of University & Science-2007-2009, Unit coordinator. Istituto Toscano Tumori ITT Research grant-Unit Coordinator-2008. Fondazione Tomasello Research grant-Yeast as a Model in Mitochondrial Diseases 2009. Research Contract-University of Erlangen-Research Contract Bioinformatics-2010-2011. Research Contract-University of Njmegen-Research Contract Bioinformatics-2010-2013. Research Contract-TNO-Bioinformatics-2010. Research Contract-University of Oxford-2010. Research Contract –Keiser, ASI-ESA-Dama Mission 2011. Cassa di Risparmio di Firenze (CRF) Research grant-2011-2012. 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. Metafoodlabs Provincia Autonoma di Trento. (PAT) (2012-2014) Fondazione Edmund Mach Startup Grant, Computational Biology Department 2011-2014. JPI EMPADASI-EU-2015-2016. JPI-Transmic EU-2018-2020. VESPATER- POR-FESR FSE Regione Toscana, 2018-2020. 21/08/2018