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European
curriculum vitae
format

Personal information
Name / FRANCESCO GANDOLFI
Address
Telephone
E-mail
Nationality / Italian
Date of birth / 10 June 1981
Work experience
• Dates / September 2012 – December 2014
• Name and address of employer / Genethon,1 rue de l’Internationale, 91002 Evry Cedex
• Type of business or sector / Bioinformatics, Genomics, Transcriptomics
• Occupation or position held / Post-doctoral fellows
NGS-data analysis:
Genome targeted sequencing – development of a computational pipeline to study lentiviral integration sites human CD34+ cells.
Computational analysis of the HIV integration pattern in different hematopoietic cell lines from patients affected by WAS (Wiskott-Aldrich Syndrome)
RNA-sequencing – bioinformatic analysis of small non-coding RNAs to identify putative biomarkers in Duchenne Muscular Dystrophy.
• Dates / January 2009 – August 2012
• Name and address of employer / Università degli Studi di Modena e Reggio Emilia
Department of Biomedical Sciences, Center for Genomic Research
Via Campi 287, 41125 Modena - Italy
• Type of business or sector / Bioinformatics, Genomics
• Occupation or position held / PhD Student
• Main activities and responsibilities / Ph.D. project: New computational methods for the analysis of alternative splicing in the Central Nervous System
Computational and statistical analysis of transcriptomic/proteomic data: gene expression microarrays, Exon Arrays, RPPA (Reverse Phase Protein Arrays), Next Generation Sequencing data
Genomic databases: UCSC Genome Browser, Ensembl, Genome Viewer,
MicroRNA-targets prediction databases: miRBase, Target Scan, Pictar, MAGIA, Mirecords
Bioinformatics tools: GSEA (gene set enrichment analysis), BLAST, tools for sequences manipulation, functional annotation analysis ( BIOMART, David )
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• Dates / June 2008 – September 2008
• Name and address of employer / FIRC (Fondazione Italiana per la Ricerca sul Cancro) Institute of Molecular Oncology
Via Adamello 16, 20139 Milano - Italy
Type of business or sector / Molecular Genetics of Cancer
• Occupation or position held / Bioinformatician (Apprentice)
• Main activities and responsibilities / Computational analysis of microRNA-targets involved in colon cancer (miR17-92 cluster) ,
Integration of gene and microRNA expression data in Breast Cancer: sequence analysis of microRNAs targeting different variants of the 3’UTR region in the BRCA1 gene
Education and training
• Dates / January 2009 – August 2012
• Name and type of organization providing education and training / Università degli Studi di Modena e Reggio Emilia
Ph.D. School in Neuroscience
• Principal subjects/occupational
skills covered / Bioinformatics, Genomics, Molecular biology
Received the nomination of ‘Expert in Bioinformatics’ ( October 2011, Università di Modena e Reggio Emilia )
• Dates / November 2007- November 2008
• Name and type of organization providing education and training / Università degli studi La Sapienza, Roma
Master (second level) in Bioinformatics: Biomedical and Pharmaceutical applications
• Principal subjects/occupational / Computational Biology, Molecular Biology, Biochemistry, Genetics, Informatics, Pharmacology
• Dates / October 2000 – November 2006
• Name and type of organization providing education and training / Università degli Studi di Parma
•Title of qualification awarded
• Principal subjects/occupational
skills covered / 9 November 2006: Master Degree in Biological Sciences (110 cum laude)
Thesis Title: “Molecular Analysis of the origin of uricaemia in hominoids”,
Protein sequences analysis, multiple sequence alignment, phylogenetic analysis, visualization of 3D protein structures (PDB, pyMOL)
Personal skills
and competences
Informatics skills
Mother tongue / Programming languages: R, R-Bioconductor, Perl, Bash, Python
Software: NGS-data tools: BLAST, BLAT, Bowtie, BWA, MIRA-assembler, Sam-tools, Bed-tools,
R-pakcages for NGS-data analysis: GenomicRanges, EdgeR, DESeq.
Visualization tools: Integrative Genome Browser, UCSC Genome Browser.
Italian
Other languages: English (B2/B2), French (B1/B1)

AI FINI DELLA PUBBLICAZIONE

scientific publications and abstract / Benatti C, Alboni S, Blom J, Gandolfi F, Mendlewicz J, Brunello N; Tascedda F. Behavioural and transcriptional effects of escitalopram in the chronic escape deficit model of depression. Behavioural Brain Research
Moiani A, Suerth J, Gandolfi F, Rizzi E, Severgnini M, De Bellis G, Schambach A, Mavilio F . Genome-wide analysis of alpha-retroviral, gamma-retroviral and lentiviral vector integration in human hematopoietic stem/progenitor cells. Genes. 2014
Pasquariello M, Barabaschi D, Himmelbach A, Steuernagel B, Ariyadasa R, Stein N, Gandolfi F, Tenedini E, Bernardis I, Tagliafico E, Pecchioni N, Francia E. The barley Frost resistance-H2 locus. Funct Integr Genomics. 2014 Jan 18.
Maciotta S, Meregalli M, Cassinelli L, Parolini D, Farini A, Fraro GD, Gandolfi F, Forcato M, Ferrari S, Gabellini D, Bicciato S, Cossu G, Torrente Y.Hmgb3 is regulated by microRNA-206 during muscle regeneration. PLoS One. 2012;7(8):e43464. doi10.1371/journal.pone.0043464. Epub 2012 Aug 17.
Abstract: Gandolfi F, Moiani A,Vega-Czarny N, Mavilio F, Gyapay G. A computational workflow to study lentiviral integrations in the human genome using a targeted genomic sequencing approach. XI Annual Meeting of the Bioinformatics Italian Society (BITS), 26-28 February 2014, Rome (Italy).
Abstract: E. Crippa, L. Lusa, E. Marchesi, L. De Cecco, J.F. Reid, F. Gandolfi, C.M. Croce, M.A. Pierotti,M. Gariboldi. Integration of gene and miRNA expression data in breast cancer. TRANSFOG Oncogenomics Technology Showcase ( 6-7 November 2008, University Foundation of Brussels, Belgium )
Abstract: F.Gandolfi, C. Valensisi, F. Ferrari, C. Benatti, E. Roncaglia, N.Brunello, F. Tascedda, S. Bicciato. A combined approach for analyzing exon-profiling data from functionally relevant areas of the central nervous system. RECOMB 2010 (Fourteenth International Conference in Computational Molecular Biology. 12-15 August 2010, Lisbon (Portugal)
Abstract: F.Gandolfi, G. Malagoli Tagliazucchi, D. Albanese, M. Chierici, C. Furlanello, S.Bicciato.
A wavelet-based approach for the analysis of exon array data. VIII Annual Meeting of the Bioinformatics Italian Society (BITS), 20-22 June 2011, Pisa (Italy)
CONGRESSES, WORKSHOPS,
OTHER COURSES / Courses, Workshops
Informatics course: Perl for life scientists, 25-27 November 2009, CINECA, Casalecchio di Reno, Bologna (Italy)
Informatics course: Python for Computational Science, 29 November-1 December 2010, CINECA, Casalecchio di Reno, Bologna (Italy)
Data Analysis Workshop, An Introductory course to GeneChipExon1.0ST Arrays, 9-11 December 2009, Orbassano (Italy)
EBI-SLING Roadshow, 7-9 April 2010, Florence ( Italy ) : Ensembl databases, comparative genomics databases, transcriptomic resources
Lipari International Summer School in Bioinformatics: Biological Sequence Analysis and High-troughput Technologies, 2-9 July 2011, Lipari (ME – Italy)
/ NGS Day, 1st Unimore (University of Modena and Reggio Emilia) Workshop on the Next Generation Sequencing, 22 February 2011, Modena ( Italy )
EuGESMA Bioinformatics School, 11-14 September 2011, Modena ( Italy )

Advanced RNA-seq and ChIP-seq Data Analysis Course, 12-15 May 2014, EMBL-EBI, Hinxton UK

Congresses, Meetings

Next Generation Sequencing Congress

16-17 November 2009, Waldorf Hilton Hotel, London, UK

14th International Conference on Research in Computational Molecular Biology (RECOMB 2010), 12-15 August 2010, Lisbon, Portugal

2nd Meeting of the 454 Roche Technology Italian users. 3-4 March 2011, Bari ( Italy )

Regenerative Medicine and Stem Cell Research: A challenge for the present, 3 May 2011, Royal Carlton Hotel, Bologna ( Italy )

VIII Annual Meeting of the Bioinformatics Italian Society (BITS), 20-22 June 2011, Pisa (Italy)

XI Annual Meeting of the Bioinformatics Italian Society (BITS), 26-28 February 2014, Rome (Italy).

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[Francesco Gandolfi ]