Duccio Cavalieri

Duccio Cavalieri

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Duccio Cavalieri

Publications by authors named "Duccio Cavalieri"

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Propolis hosts a diversemicrobial community.

World J Microbiol Biotechnol 2020 Mar 10;36(3):50. Epub 2020 Mar 10.

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

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http://dx.doi.org/10.1007/s11274-020-02827-0DOI Listing
March 2020

Environmental pollution effects on plant microbiota: the case study of poplar bacterial-fungal response to silver nanoparticles.

Appl Microbiol Biotechnol 2019 Oct 11;103(19):8215-8227. Epub 2019 Aug 11.

Department of Agriculture, Food, Environment and Forestry, University of Florence, 50145, Florence, Italy.

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http://dx.doi.org/10.1007/s00253-019-10071-2DOI Listing
October 2019

Gut Microbiota Profiles Differ among Individuals Depending on Their Region of Origin: An Italian Pilot Study.

Int J Environ Res Public Health 2019 10 23;16(21). Epub 2019 Oct 23.

Division of Gastroenterology, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, Italy.

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http://dx.doi.org/10.3390/ijerph16214065DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6862301PMC
October 2019

Longitudinal Survey of Fungi in the Human Gut: ITS Profiling, Phenotyping, and Colonization.

Front Microbiol 2019 10;10:1575. Epub 2019 Jul 10.

Department of Surgery, Medicine, Dentistry and Morphological Sciences with Interest in Transplant, Oncology and Regenerative Medicine, University of Modena and Reggio Emilia, Modena, Italy.

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http://dx.doi.org/10.3389/fmicb.2019.01575DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6636193PMC
July 2019

Bifidobacterium callitrichidarum sp. nov. from the faeces of the emperor tamarin (Saguinus imperator).

Int J Syst Evol Microbiol 2018 Jan 8;68(1):141-148. Epub 2017 Nov 8.

Department of Agricultural Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy.

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http://dx.doi.org/10.1099/ijsem.0.002472DOI Listing
January 2018

Guidelines and recommendations on yeast cell death nomenclature.

Microb Cell 2018 Jan 1;5(1):4-31. Epub 2018 Jan 1.

Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria.

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http://dx.doi.org/10.15698/mic2018.01.607DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5772036PMC
January 2018

SaccharomycesIDentifier, SID: strain-level analysis of Saccharomyces cerevisiae populations by using microsatellite meta-patterns.

Sci Rep 2017 11 10;7(1):15343. Epub 2017 Nov 10.

Computational Biology Unit, Fondazione Edmund Mach, via E. Mach 1, 38010 San Michele all'Adige, Trento, Italy.

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http://dx.doi.org/10.1038/s41598-017-15729-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5681646PMC
November 2017

Diet, Environments, and Gut Microbiota. A Preliminary Investigation in Children Living in Rural and Urban Burkina Faso and Italy.

Front Microbiol 2017 13;8:1979. Epub 2017 Oct 13.

Department of Neuroscience, Psychology, Drug Research and Child Health, University of Florence, Meyer Children Hospital, Florence, Italy.

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http://dx.doi.org/10.3389/fmicb.2017.01979DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5645538PMC
October 2017

Non-invasive real time monitoring of yeast volatilome by PTR-ToF-MS.

Metabolomics 2017 31;13(10):118. Epub 2017 Aug 31.

Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, San Michele all'Adige, TN Italy.

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http://link.springer.com/10.1007/s11306-017-1259-y
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http://dx.doi.org/10.1007/s11306-017-1259-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5579147PMC
August 2017

The orphan nuclear receptor COUP-TFII coordinates hypoxia-independent proangiogenic responses in hepatic stellate cells.

J Hepatol 2017 04 17;66(4):754-764. Epub 2016 Nov 17.

Gastroenterology Research Unit, Department of Experimental and Clinical Biochemical Sciences, University of Florence, Florence, Italy; Center of Excellence for Research, Transfer and High Education, DENOthe, University of Florence, Italy; FiorGen Foundation, Florence, Italy. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S01688278163065
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http://dx.doi.org/10.1016/j.jhep.2016.11.003DOI Listing
April 2017

Relations between Effects and Structure of Small Bicyclic Molecules on the Complex Model System .

Front Pharmacol 2017 30;8:170. Epub 2017 Mar 30.

Division of Biomedical Cell Biology, Warwick Medical School, University of WarwickCoventry, UK.

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http://dx.doi.org/10.3389/fphar.2017.00170DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5371657PMC
March 2017

New evidences on the altered gut microbiota in autism spectrum disorders.

Microbiome 2017 02 22;5(1):24. Epub 2017 Feb 22.

Institute of Agriculture Biology and Biotechnology, National Research Council (CNR), Via Moruzzi 1, 56124, Pisa, Italy.

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http://dx.doi.org/10.1186/s40168-017-0242-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5320696PMC
February 2017

Alteration of Fecal Microbiota Profiles in Juvenile Idiopathic Arthritis. Associations with HLA-B27 Allele and Disease Status.

Front Microbiol 2016 26;7:1703. Epub 2016 Oct 26.

Department of Neuroscience, Psychology, Drug Research and Child Health, Meyer Children's Hospital, University of FlorenceFlorence, Italy; Rheumatology Unit, Anna Meyer Children's Hospital, University of FlorenceFlorence, Italy.

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http://dx.doi.org/10.3389/fmicb.2016.01703DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5080347PMC
October 2016

Social wasp intestines host the local phenotypic variability of Saccharomyces cerevisiae strains.

Yeast 2016 07;33(7):277-87

Department of Computational Biology, Centre for Research and Innovation, Fondazione Edmund Mach, San Michele all'Adige, Trento, Italy.

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http://dx.doi.org/10.1002/yea.3173DOI Listing
July 2016

Altered gut microbiota in Rett syndrome.

Microbiome 2016 07 30;4(1):41. Epub 2016 Jul 30.

Institute of Biometeorology (IBIMET), National Research Council (CNR), Via Giovanni Caproni 8, I-50145, Florence, Italy.

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http://dx.doi.org/10.1186/s40168-016-0185-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4967335PMC
July 2016

Plant microRNAs as novel immunomodulatory agents.

Sci Rep 2016 05 11;6:25761. Epub 2016 May 11.

Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38010 San Michele all'Adige (TN), Italy.

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http://dx.doi.org/10.1038/srep25761DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4863160PMC
May 2016

Uncovering oral Neisseria tropism and persistence using metagenomic sequencing.

Nat Microbiol 2016 05 27;1(7):16070. Epub 2016 May 27.

Centre for Integrative Biology, University of Trento, Via Sommarive 9, 38123 Trento, Italy.

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http://dx.doi.org/10.1038/nmicrobiol.2016.70DOI Listing
May 2016

Fungal Chitin Induces Trained Immunity in Human Monocytes during Cross-talk of the Host with Saccharomyces cerevisiae.

J Biol Chem 2016 Apr 17;291(15):7961-72. Epub 2016 Feb 17.

From the Research and Innovation Centre, Fondazione Edmund Mach, 38010 San Michele all'Adige TN, Italy, the Institute of Biometeorology, National Research Council, 50145 Florence, Italy, the Department of Biology, University of Florence, 50019 Sesto Fiorentino FI, Italy

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http://dx.doi.org/10.1074/jbc.M115.699645DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4825003PMC
April 2016

Dynamic changes in microbiota and mycobiota during spontaneous 'Vino Santo Trentino' fermentation.

Microb Biotechnol 2016 Mar 18;9(2):195-208. Epub 2016 Jan 18.

Department of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige, Italy.

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http://dx.doi.org/10.1111/1751-7915.12337DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4767281PMC
March 2016

Social wasps are a Saccharomyces mating nest.

Proc Natl Acad Sci U S A 2016 Feb 19;113(8):2247-51. Epub 2016 Jan 19.

Centre for Research and Innovation, Fondazione Edmund Mach, 38010 Trento, Italy; Department of Biology, University of Florence, 50019 Florence, Italy;

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http://dx.doi.org/10.1073/pnas.1516453113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4776513PMC
February 2016

riboFrame: An Improved Method for Microbial Taxonomy Profiling from Non-Targeted Metagenomics.

Front Genet 2015 17;6:329. Epub 2015 Nov 17.

Centre for Research and Innovation, Fondazione Edmund Mach San Michele all'Adige, Italy.

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http://dx.doi.org/10.3389/fgene.2015.00329DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4646959PMC
December 2015

Habitat fragmentation is associated to gut microbiota diversity of an endangered primate: implications for conservation.

Sci Rep 2015 Oct 7;5:14862. Epub 2015 Oct 7.

Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S. Michele all'Adige, Trento, Italy.

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http://www.nature.com/articles/srep14862
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http://dx.doi.org/10.1038/srep14862DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4595646PMC
October 2015

Hsp12p and PAU genes are involved in ecological interactions between natural yeast strains.

Environ Microbiol 2015 Aug 30;17(8):3069-81. Epub 2015 Jul 30.

Department of Neurosciences, Psychology, Drug Research and Child Health, University of Florence, Florence, Italy.

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http://dx.doi.org/10.1111/1462-2920.12950DOI Listing
August 2015

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. Epub 2015 Aug 21.

Research and Innovation Center, Fondazione E. Mach, via E. Mach 1, San Michele all'Adige (TN) 38010, Italy.

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http://www.mdpi.com/2076-0817/4/3/639
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http://dx.doi.org/10.3390/pathogens4030639DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4584279PMC
August 2015

MICCA: a complete and accurate software for taxonomic profiling of metagenomic data.

Sci Rep 2015 May 19;5:9743. Epub 2015 May 19.

Fondazione Edmund Mach, Research and Innovation Centre, Computational Biology Department, Via E. Mach 1, 38010 - S. Michele all'Adige (TN), Italy.

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http://www.nature.com/articles/srep09743
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http://dx.doi.org/10.1038/srep09743DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4649890PMC
May 2015

Explaining diversity in metagenomic datasets by phylogenetic-based feature weighting.

PLoS Comput Biol 2015 Mar 27;11(3):e1004186. Epub 2015 Mar 27.

Department of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy.

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http://dx.doi.org/10.1371/journal.pcbi.1004186DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4376673PMC
March 2015

Richness and diversity of mammalian fungal communities shape innate and adaptive immunity in health and disease.

Eur J Immunol 2014 Nov 30;44(11):3166-81. Epub 2014 Oct 30.

Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, TN, Italy.

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http://dx.doi.org/10.1002/eji.201344403DOI Listing
November 2014

Systems biology of host-mycobiota interactions: dissecting Dectin-1 and Dectin-2 signalling in immune cells with DC-ATLAS.

Immunobiology 2013 Nov 13;218(11):1428-37. Epub 2013 Jul 13.

Fondazione Edmund Mach, Research and Innovation Centre, San Michele all'Adige (TN), Italy.

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http://dx.doi.org/10.1016/j.imbio.2013.07.002DOI Listing
November 2013

Strain dependent variation of immune responses to A. fumigatus: definition of pathogenic species.

PLoS One 2013 18;8(2):e56651. Epub 2013 Feb 18.

Department of Neuroscience, Pharmacology and Child's Health (NEUROFARBA), University of Florence, Florence, Italy.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0056651PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3575482PMC
August 2013

Phylogenetic analysis of 47 chloroplast genomes clarifies the contribution of wild species to the domesticated apple maternal line.

Mol Biol Evol 2013 Aug 14;30(8):1751-60. Epub 2013 May 14.

Research and Innovation Centre, Fondazione E. Mach, San Michele all'Adige (TN), Italy.

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https://academic.oup.com/mbe/article-lookup/doi/10.1093/molb
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http://dx.doi.org/10.1093/molbev/mst092DOI Listing
August 2013

Pathway Processor 2.0: a web resource for pathway-based analysis of high-throughput data.

Bioinformatics 2013 Jul 5;29(14):1825-6. Epub 2013 Jun 5.

Translational Genomics Unit, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via La Masa 19, 20159 Milano, Italy.

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http://dx.doi.org/10.1093/bioinformatics/btt292DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3702260PMC
July 2013

Reversion of a fungal genetic code alteration links proteome instability with genomic and phenotypic diversification.

Proc Natl Acad Sci U S A 2013 Jul 17;110(27):11079-84. Epub 2013 Jun 17.

RNA Biology Laboratory, Department of Biology and Centre for Environmental and Marine Studies, University of Aveiro, 3810-193 Aveiro, Portugal.

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http://dx.doi.org/10.1073/pnas.1302094110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3704024PMC
July 2013

Pathway-based analysis of microarray and RNAseq data using Pathway Processor 2.0.

Curr Protoc Bioinformatics 2013 Mar;Chapter 7:Unit 7.6

Translational Genomics Unit, Department of Oncology, Mario Negri Research Institute, Milan, Italy.

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http://dx.doi.org/10.1002/0471250953.bi0706s41DOI Listing
March 2013

Systems biology of host-fungus interactions: turning complexity into simplicity.

Curr Opin Microbiol 2012 Aug 19;15(4):440-6. Epub 2012 Jun 19.

Medical University of Vienna, Christian Doppler Laboratory Infection Biology, Max F. Perutz Laboratories, A-1030 Vienna, Austria.

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http://dx.doi.org/10.1016/j.mib.2012.05.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3501689PMC
August 2012

A computational pipeline to discover highly phylogenetically informative genes in sequenced genomes: application to Saccharomyces cerevisiae natural strains.

Nucleic Acids Res 2012 May 20;40(9):3834-48. Epub 2012 Jan 20.

Department of Preclinical and Clinical Pharmacology, University of Florence, Viale G. Pieraccini 6, 50139 Firenze, Italy.

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http://dx.doi.org/10.1093/nar/gks005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3351171PMC
May 2012

Constraints for monocyte-derived dendritic cell functions under inflammatory conditions.

Eur J Immunol 2012 Feb 14;42(2):458-69. Epub 2011 Dec 14.

Department of Immunology, University of Debrecen, Debrecen, Hungary.

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http://dx.doi.org/10.1002/eji.201141924DOI Listing
February 2012

graphite - a Bioconductor package to convert pathway topology to gene network.

BMC Bioinformatics 2012 Jan 31;13:20. Epub 2012 Jan 31.

Department of Biology, University of Padova, via U, Bassi 58/B, Padova, Italy.

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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
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http://dx.doi.org/10.1186/1471-2105-13-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3296647PMC
January 2012

Friend or foe: using systems biology to elucidate interactions between fungi and their hosts.

Trends Microbiol 2011 Oct 24;19(10):509-15. Epub 2011 Aug 24.

Department of Preclinical and Clinical Pharmacology, University of Florence, viale Pieraccini 6, 50139 Firenze, Italy.

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http://dx.doi.org/10.1016/j.tim.2011.07.007DOI Listing
October 2011

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.

Department of Clinic and Preclinic Pharmacology, University of Firenze, Firenze, Italy.

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http://dx.doi.org/10.1016/j.imbio.2010.05.009DOI Listing
March 2011

Evolution of transcriptional regulatory networks in yeast populations.

Authors:
Duccio Cavalieri

Wiley Interdiscip Rev Syst Biol Med 2010 May-Jun;2(3):324-335

Department of Pharmacology, University of Florence, Florence, Italy.

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http://doi.wiley.com/10.1002/wsbm.68
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http://dx.doi.org/10.1002/wsbm.68DOI Listing
January 2011

Chemical 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 15;8(24):5552-7. Epub 2010 Oct 15.

Department of Chemistry Ugo Schiff, University of Florence, Polo Scientifico e Tecnologico, Via della Lastruccia 13, I-50019, Sesto F.no, Florence, Italy.

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http://xlink.rsc.org/?DOI=c0ob00357c
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http://dx.doi.org/10.1039/c0ob00357cDOI Listing
December 2010

Dominant processes during human dendritic cell maturation revealed by integration of proteome and transcriptome at the pathway level.

J Proteome Res 2010 Apr;9(4):1727-37

Department of Tumor Immunology and CMBI at the Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1021/pr9008546DOI Listing
April 2010

Differential IL-17 production and mannan recognition contribute to fungal pathogenicity and commensalism.

J Immunol 2010 Apr 12;184(8):4258-68. Epub 2010 Mar 12.

Department of Preclinic and Clinic Pharmacology, University of Firenze, Firenze, Italy.

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http://dx.doi.org/10.4049/jimmunol.0902972DOI Listing
April 2010

Filling gaps in PPAR-alpha signaling through comparative nutrigenomics analysis.

BMC Genomics 2009 Dec 11;10:596. Epub 2009 Dec 11.

Department of Pharmacology, University of Firenze, Firenze, Italy.

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http://dx.doi.org/10.1186/1471-2164-10-596DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2801700PMC
December 2009

Novel insights into phenotype and mitochondrial proteome of yeast mutants lacking proteins Sco1p or Sco2p.

Mitochondrion 2009 Apr 17;9(2):103-14. Epub 2009 Jan 17.

Dipartimento di Scienze Biochimiche, Università degli Studi di Firenze, Viale G. Morgagni, 50, I-50134 Firenze, Italy.

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http://dx.doi.org/10.1016/j.mito.2009.01.002DOI Listing
April 2009

Cascading transcriptional effects of a naturally occurring frameshift mutation in Saccharomyces cerevisiae.

Mol Ecol 2008 Jun 18;17(12):2985-97. Epub 2008 Apr 18.

Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA.

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http://dx.doi.org/10.1111/j.1365-294X.2008.03765.xDOI Listing
June 2008

Eu.Gene Analyzer a tool for integrating gene expression data with pathway databases.

Bioinformatics 2007 Oct 28;23(19):2631-2. Epub 2007 Jun 28.

Department of Preclinical and Clinical Pharmacology, Department of Statistics, University of Florence, Florence, Italy.

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http://dx.doi.org/10.1093/bioinformatics/btm333DOI Listing
October 2007

Indel arrays: an affordable alternative for genotyping.

Plant J 2007 Aug 20;51(4):727-37. Epub 2007 Jul 20.

FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA.

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http://dx.doi.org/10.1111/j.1365-313X.2007.03194.xDOI Listing
August 2007

Emerging treatments and gene expression profiling in high-risk medulloblastoma.

Paediatr Drugs 2007 ;9(2):81-96

Department of Pediatrics, Onco-hematology and Neuro-surgery Units, University of Florence Medical School, A. Meyer Children's Hospital, Florence, Italy.

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http://dx.doi.org/10.2165/00148581-200709020-00002DOI Listing
June 2007

An integrated analysis of the effects of Esculentin 1-21 on Saccharomyces cerevisiae.

Biochim Biophys Acta 2007 Jun 21;1774(6):688-700. Epub 2007 Apr 21.

Dipartimento di Scienze Biochimiche, Università degli Studi di Firenze, Viale G. Morgagni, 50 I-50134 Firenze, Italy.

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http://dx.doi.org/10.1016/j.bbapap.2007.04.006DOI Listing
June 2007

Ecological and evolutionary genomics of Saccharomyces cerevisiae.

Mol Ecol 2006 Mar;15(3):575-91

Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.

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http://dx.doi.org/10.1111/j.1365-294X.2006.02778.xDOI Listing
March 2006

Genome-wide scan reveals that genetic variation for transcriptional plasticity in yeast is biased towards multi-copy and dispensable genes.

Gene 2006 Feb 20;366(2):343-51. Epub 2006 Jan 20.

Department of Organismic and Evolutionary Biology, Harvard University, Cambridge MA, USA.

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http://linkinghub.elsevier.com/retrieve/pii/S037811190500657
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http://dx.doi.org/10.1016/j.gene.2005.10.042DOI Listing
February 2006

Bioinformatic methods for integrating whole-genome expression results into cellular networks.

Drug Discov Today 2005 May;10(10):727-34

Department of Pharmacology, University of Florence, Viale Pieraccini 6, 50139 Florence, Italy.

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http://linkinghub.elsevier.com/retrieve/pii/S135964460503433
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http://dx.doi.org/10.1016/S1359-6446(05)03433-1DOI Listing
May 2005

Integrating whole-genome expression results into metabolic networks with Pathway Processor.

Curr Protoc Bioinformatics 2004 May;Chapter 7:Unit 7.6

Bauer Center for Genomics Research, Harvard University, Cambridge, Massachusetts, USA.

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http://doi.wiley.com/10.1002/0471250953.bi0706s05
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http://dx.doi.org/10.1002/0471250953.bi0706s05DOI Listing
May 2004