Dr Carlotta De Filippo, PhD - Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche - Staff Researcher

Dr Carlotta De Filippo

PhD

Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche

Staff Researcher

Pisa | Italy

Main Specialties: Gastroenterology, Medical Microbiology, Pediatric Gastroenterology

ORCID logohttps://orcid.org/0000-0002-2222-6524


Top Author

Dr Carlotta De Filippo, PhD - Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche - Staff Researcher

Dr Carlotta De Filippo

PhD

Introduction

Personal Statement
De Filippo’s research interest is the application of metagenomics and metabolomics to the analysis of community structure, gene content, and function of complex microbial communities in human populations exposed to different diets. Actually De Filippo’s research interests integrated multidisciplinary competences, including functional genomics and toxicology, to the study of the molecular determinants of dietary modulation of gut inflammation and cancer. C. De Filippo applied meta-genomics techniques (Next Generation Sequencing) to the characterization of the intestinal microbiota, studying the interaction between intestinal mucosa, immune system and microorganisms, unravelling the joint role of diet and microorganisms for the intestinal liberation of short chain fatty acids, bioactive molecules important for gut health. C. De Filippo is applying metagenomics and metabolomics to the analysis of community structure, gene content, and function of complex microbial communities in human populations exposed to different diets. The research plan is to couple these techniques to additional experimental techniques such as in vitro cell culture and animal models, to study the metabolic functions of the human gut microbiome, with potential implications for human health and nutrition.

EDUCATION/TRAINING
1995, MSc Molecular Biology, University of Florence, Italy.
1997, Profession of Biologist, University of Florence, Italy.
1995- 1999 Fellowship, Research assistant, Nutrition, Department of Preclinical and Clinical Pharmacology “M. Aiazzi Mancini” University 1999- 2002 PhD student in Pharmacology and Toxicology, Department of Preclinical and Clinical Pharmacology, University of Florence, Italy
1999-2000 PhD student (visiting), Functional Genomics, Department of Cancer Cell Biology, Division of Toxicology "Harvard School of Public Health” (Boston, MA, USA)
2003, PhD in Pharmacology and Toxicology, Department of Preclinical and Clinical Pharmacology, University of Florence, Italy.
POSITIONS
2016-present, Staff Researcher, Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, Pisa, Italy
2015-2016, Researcher, Istituto di Biometeorologia Consiglio Nazionale delle Ricerche, Firenze, Toscana, Italy
2011-2015, Researcher, Nutrition and Nutrigenomics, Fondazione Edmund Mach, Research and Innovation Centre, San Michele all’Adige (TN) Italy.
2002-2011 Professor of Pharmacogenomics University of Florence, Graduate Course in Biotechnology at the University of Florence (Teaching activity)
2006-2011 Research fellow in Nutrigenomics and Toxicogenomics, Department of Preclinical and Clinical Pharmacology, University of Florence, Italy. Research project: Molecular determinants of dietary motulation of gut inflammation and cancer to studies of nutritional genomics and molecular markers of inflammatory bowel diseases in pediatric patients and their association with dysbiosis.
2003-2006 Post doctoral fellow, Department of Preclinical and Clinical Pharmacology, University of Florence, Italy. Research project : Studying molecular mechanisms involved he effect of dietary components on colon carcinogenesis, gastrointestinal diseases and on the genetic control of such processes in particular studying gene expression profiles using functional genomics approach
2002-2003 Visiting Scientist, Functional Genomics, Bauer Center for Genomics Research, Harvard University (Cambridge, MA, USA)
1999- 2002 PhD student in Pharmacology and Toxicology, Department of Preclinical and Clinical Pharmacology, University of Florence, Italy
1999-2000 PhD student (visiting), Functional Genomics, Department of Cancer Cell Biology, Division of Toxicology "Harvard School of Public Health” (Boston, MA, USA)
1995- 1999 Fellowship, Research assistant, Nutrition, Department of Preclinical and Clinical Pharmacology “M. Aiazzi Mancini” University

Primary Affiliation: Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche - Pisa , Italy

Specialties:


View Dr Carlotta De Filippo’s Resume / CV

Education

Oct 1999 - Mar 2003
University of Florence
PhD
Pharmacology
Oct 1989 - Mar 1995
University of Florence
MSc Molecular Biology / Dr
Biomedical Sciences, Experimental and Clinical

Experience

May 2018
HDHL-INTIMIC Call for Joint Transnational Research Proposals on “Interrelation of the Intestinal Microbiome, Diet and Health”
Coordinator
Grant
Dec 2016 - Dec 2016
Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche
Staff Researcher
Istituto di Biologia e Biotecnologia Agraria
Sep 2015 - Dec 2016
Istituto di Biometeorologia Consiglio Nazionale delle Ricerche
Researcher/PhD
Dec 2011 - Sep 2015
Fondazione Edmund Mach
Senior Researcher
Food Quality Nutrition & Health
Oct 2006 - Nov 2011
University of Florence
Researcher
Preclinical and Clinical Pharmacology
Mar 2003 - Sep 2006
University of Florence
Post doctoral fellow
Preclinical and Clinical Pharmacology

Publications

42Publications

368Reads

66Profile Views

Gut microbiota in children and altered profiles in juvenile idiopathic arthritis.

J Autoimmun 2019 Mar 9;98:1-12. Epub 2019 Jan 9.

Rheumatology Unit, Anna Meyer Children's Hospital, University of Florence, Viale G. Pieraccini 24, 50139, Florence, Italy; Department of Neuroscience, Psychology, Drug Research and Child Health, Meyer Children's Hospital, University of Florence, Viale G. Pieraccini 6, 50139, Florence, Italy. Electronic address:

Microbial diversity plays a key role in the maintenance of intestinal homeostasis and in the development of the immune system in the gut mucosa. Maybe one of the most important function of our gut microbiota is the immune system education, in particular the discrimination of friends from foes that occurs during childhood. In addition to bacterial antigens, several metabolites of microbial origin have a crucial role in training of the immune system, such as Short Chain Fatty Acids (SCFAs). There are many evidences on the role of the gut microbiota in rheumatic diseases, in particular modifications of microbiota composition causing dysbiosis that, in turn, can induce gut permeability, and thus immunological imbalance and trigger inflammation. In particular, immune cells can reach extra-intestinal sites, such as joints and trigger local inflammation. Childhood is a crucial period of life for development and evolution of the gut microbiota, especially for the acquisition of fundamental functions such as immunotolerance of commensal microorganisms. For this reason, gut dysbiosis is gaining interest as a potential pathogenetic factor for Juvenile Idiopathic Arthritis (JIA). Here we summarized the studies conducted on JIA patients in which a pro-arthritogenic microbial profiles has been observed; this, together with a depletion of microbial biodiversity, clearly distinguish patients' from healthy subjects' microbiota. Further studies are however needed to better clarify the role of microbiota in JIA pathogenesis.

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http://dx.doi.org/10.1016/j.jaut.2019.01.001DOI Listing
March 2019
5 Reads
8.410 Impact Factor

Host: Microbiome co-metabolic processing of dietary polyphenols - An acute, single blinded, cross-over study with different doses of apple polyphenols in healthy subjects.

Food Res Int 2018 Oct 8;112:108-128. Epub 2018 Jun 8.

Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, Via Mach 1, 38010 San Michele all'Adige, TN, Italy; Center Agriculture Food Environment, University of Trento, San Michele all'Adige, Italy. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S09639969183046
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http://dx.doi.org/10.1016/j.foodres.2018.06.016DOI Listing
October 2018
9 Reads
2.818 Impact Factor

Influence of essential oils in diet and life-stage on gut microbiota and fillet quality of rainbow trout (Oncorhynchus mykiss).

Int J Food Sci Nutr 2018 May 31;69(3):318-333. Epub 2017 Aug 31.

f Department of Agri-Food Production and Environmental Sciences, Section of Animal Sciences , University of Firenze , Firenze , Italy.

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http://dx.doi.org/10.1080/09637486.2017.1370699DOI Listing
May 2018
41 Reads
1.202 Impact Factor

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.

1​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
9 Reads
2.511 Impact Factor

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

Sci Rep 2017 Nov 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
8 Reads
5.078 Impact Factor

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
3 Reads
3.941 Impact Factor

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
8 Reads

DNA copy number alterations, gene expression changes and disease-free survival in patients with colorectal cancer: a 10 year follow-up.

Cell Oncol (Dordr) 2016 Dec 5;39(6):545-558. Epub 2016 Oct 5.

Department of Neuroscience, Psychology, Drug Research and Child Health (NEUROFARBA), University of Florence, Viale Pieraccini 6, 50139, Florence, Italy.

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http://dx.doi.org/10.1007/s13402-016-0299-zDOI Listing
December 2016
5 Reads
3.032 Impact Factor

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
12 Reads
3.941 Impact Factor

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
8 Reads

Evaluation of the effects of intrapartum antibiotic prophylaxis on newborn intestinal microbiota using a sequencing approach targeted to multi hypervariable 16S rDNA regions.

Appl Microbiol Biotechnol 2016 Jun 14;100(12):5537-46. Epub 2016 Mar 14.

Department of Agricultural Sciences, University of Bologna, viale Fanin 42, 40127, Bologna, Italy.

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http://dx.doi.org/10.1007/s00253-016-7410-2DOI Listing
June 2016
11 Reads
3.337 Impact Factor

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
9 Reads

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
20 Reads
4.573 Impact Factor

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
3 Reads

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
Publisher Site
http://dx.doi.org/10.1038/srep14862DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4595646PMC
October 2015
5 Reads
5.078 Impact Factor

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
13 Reads
6.201 Impact Factor

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
7 Reads
5.078 Impact Factor

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
1 Read

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
5 Reads
4.034 Impact Factor

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
8 Reads
3.044 Impact Factor

Role of social wasps in Saccharomyces cerevisiae ecology and evolution.

Proc Natl Acad Sci U S A 2012 Aug 30;109(33):13398-403. Epub 2012 Jul 30.

Dipartimento di Farmacologia, University of Florence, 50139, Florence, Italy.

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http://dx.doi.org/10.1073/pnas.1208362109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3421210PMC
August 2012
8 Reads
9.809 Impact Factor

Prenatal exposure to carbon monoxide delays postnatal cardiac maturation.

Lab Invest 2010 Nov 19;90(11):1582-93. Epub 2010 Jul 19.

Centro Interuniversitario di Medicina Molecolare e Biofisica Applicata (C.I.M.M.B.A.), University of Firenze, Firenze, Italy.

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http://circ.ahajournals.org/content/109/3/419.full.pdf
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http://www.nature.com/doifinder/10.1038/labinvest.2010.122
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http://dx.doi.org/10.1038/labinvest.2010.122DOI Listing
November 2010
3 Reads
3.676 Impact Factor

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 2;107(33):14691-6. Epub 2010 Aug 2.

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

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http://dx.doi.org/10.1073/pnas.1005963107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2930426PMC
August 2010
12 Reads
9.809 Impact Factor

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
4 Reads
4.922 Impact Factor

Smokers and passive smokers gene expression profiles: correlation with the DNA oxidation damage.

Free Radic Biol Med 2007 Aug 29;43(3):415-22. Epub 2007 Apr 29.

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

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http://dx.doi.org/10.1016/j.freeradbiomed.2007.04.018DOI Listing
August 2007
1 Read
5.736 Impact Factor

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
1 Read

Red wine polyphenols influence carcinogenesis, intestinal microflora, oxidative damage and gene expression profiles of colonic mucosa in F344 rats.

Mutat Res 2005 Dec 15;591(1-2):237-46. Epub 2005 Nov 15.

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

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http://dx.doi.org/10.1016/j.mrfmmm.2005.04.022DOI Listing
December 2005
12 Reads
3.680 Impact Factor

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. Epub 2005 Nov 10.

Dipartimento di Biologia Animale e Genetica, Università di Firenze, via Romana 17, I-50125 Firenze, Italy.

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http://dx.doi.org/10.1186/1471-2164-6-158DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1298293PMC
November 2005
6 Reads
3.986 Impact Factor

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

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

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September 2005
3 Reads
2.911 Impact Factor

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
1 Read
6.691 Impact Factor

Defining best practice for microarray analyses in nutrigenomic studies.

Br J Nutr 2005 Apr;93(4):425-32

Institute of Food Research, Norwich Research Park, Norwich NR5 7UA, UK.

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April 2005
1 Read
3.453 Impact Factor

Top co-authors

Carlotta De Filippo
Carlotta De Filippo

Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche

42
Duccio Cavalieri
Duccio Cavalieri

University of Florence

32
Davide Albanese
Davide Albanese

University of Copenhagen

15
Claudio Donati
Claudio Donati

Institute for Genomic Research

12
Lisa Rizzetto
Lisa Rizzetto

University of Florence

10
Irene Stefanini
Irene Stefanini

University of Florence

9
Piero Dolara
Piero Dolara

University of Florence

6
Paolo Lionetti
Paolo Lionetti

University of Florence

6
Cristina Luceri
Cristina Luceri

University of Florence

6