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Francesco Gandolfi



Name Francesco Gandolfi

Address Via Gandhi 23


Telephone (+39)3333272598

Nationality Italy

Date of birth June, 10th, 1981


Dates (from) April 2015 – present

Position Postdoctoral fellow

Istitution Biocomputing group at department of Physics, Sapienza Universita' di Roma, Piazzale Aldo Moro 5, 00185 Rome – Italy

Main activities Study and application of computational methods for the analysis of high-throughput functional genomic data from Next Generation Sequencing experiments

Development of integrative computational approaches to identify and characterize chromatin patterns in multiple epigenetic datasets (ChIP-seq and DNase-seq data)

Computational analysis of functional genomic data to characterize the GadX-dependent circuit in the control of the gene expression and its role in the maintenance of the acid-resistance in E.Coli



Dates(from/to) September 2012 – December 2014

Position Postdoctoral fellow

Istitution Genethon, Rue de l'Internationale 1/bis, Evry - France

Main Activities Development of computational pipelines for genome-wide analysis of integration sites of HIV-based therapy vectors in human hematopoietic stem cells

NGS-data analyses for the identification of small non-coding RNAs as putative biomarkers in the Duchenne Muscular Dystrophy

Dates(from/to) January 2009 – August 2012

Position PhD student

Istitution Department of Life Science, Universita' di Modena and Reggio Emilia, Italy

Main Activities Development of 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)

Dates (from/to) June 2008 – September 2008

Position Trainee

Istitution Institute of Molecular Oncology – FIRC (Fondazione Italiana per la Ricerca sul Cancro) Via Adamello 16, 20139 Milano - Italy

Main Activities Computational analysis of microRNA-targets involved in colon cancer (miR17-92 cluster) ,

Integration of gene and microRNA expression data in breast cancer datasets: sequence analysis of microRNAs targeting different variants of the 3'UTR region in the BRCA1 gene



Dates (from/to) January 2009 – August 2012

Istitution Universita' di Modena e Reggio Emilia

Title of the

Qualification Ph.D in Bioinfomatics and Neuroscience

Main subjects Computational biology, Genomics, Transcriptomics

Other notes Received the nomination as Expert in Bioinformatics (October 2011)

Dates (from/to) November 2007 – November 2008

Istitution Sapienza Universita' di Roma

Title of the

Qualification Master course (II level) in Bioinformatics: biomedical and pharmaceutical applications

Main subjects Computational biology, Programming languages, molecular biology, genetics

Dates (from/to) October 2000 – November 2006

Istitution Universita' degli Studi di Parma, Department of Biochemistry and Molecular Biology

Title of the

Qualification Master Degree (cum laude) in Biological Science (specialization in Molecular Biology)

Thesis title Molecular analysis of the origin of the uricemia in hominoids

Skills covered Protein sequence analysis, multiple sequence alignments, phylogenetic analyses




tools Genomic databases: UCSC Genome Browser, Ensembl, Integrative Genome Viewer,

MicroRNA-targets prediction databases: miRBase, Target Scan, Pictar, MAGIA, Mirecords

Other genomic tools: GSEA (gene set enrichment analysis), BIOMART, David, TopGO

Tools for NGS-data analysis: Blat, Blast, Star, Bowtie, Bwa, samtools, bedtools, Cufflinks, Cuffdiff, TopHat, RSEM, DEseq, DEXseq, edgeR


Language Bash scripting, R (good knowledge), R-Bioconductor, Perl


Mother tongue Italian

Other languages English (Upper-intermediate); French (Upper-intermediate);


Reproducible data analysis using short and long-read RNA-seq data. 6 April 2016, Center for Genomic Regulation (CRG) , Barcelona (Spain)

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

EuGESMA Bioinformatics School, 11-14 September 2011, Modena ( Italy )

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 )

Informatics course: Python for Computational Science, 29 November-1 December 2010, CINECA, Casalecchio di Reno, Bologna (Italy)

EBI-SLING Roadshow, 7-9 April 2010, Florence ( Italy ) : Ensembl databases, comparative genomics databases, transcriptomic resources

Data Analysis Workshop, An Introductory course to GeneChipExon1.0ST Arrays, 9-11 December 2009, Orbassano (Italy)

Informatics course: Perl for life scientists, 25-27 November 2009, CINECA, Casalecchio di Reno, Bologna (Italy)



Annual Meeting of Epigen 2016, 24-27 May 2016, Ergife Palace, Rome - Italy

Barcelona NGS 2016, International Society of Computational Biology (ISCB) – 4-6 April 2016 Center for Genomic Regulation , Barcelona (Spain)

Annual Meeting of Epigen 2015, 21-24 April 2015, Ergife Palace, Rome - Italy

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

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

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

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

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

Next Generation Sequencing Congress, 16-17 November 2009, Waldorf Hilton Hotel, London, UK



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.

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. Behav Brain Res. 2014 Oct 1;272:121-30. doi: 10.1016/j.bbr.2014.06.040. Epub 2014 Jun 27.

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, Tramontano A. A computational approach for functional classification of the epigenome. Barcelona NGS Conference (ISCB) 2016, 4-6 April 2016, Center for Genomic Regulation, Barcelona, Spain.

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: 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)

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: 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 )

Last Updated ( Tuesday, 31 May 2016 12:54 )