I currently work for IIT (Italian Institute of Technology), SEMM division, at the IIT-IFOM-IEO campus.
I am involved in the R&D of several bioinformatics projects (see below).
Besides, I am constantly engaged in supporting/analyzing experimental data of several biological labs.
- 2012-2016 responsible for the bioinformatics analysis of several pathogen Genome Wide siRNA screens performed in Switzerland (UZH, ETH, Novartis Biozentrum), in the context of SystemsX (http://www.systemsx.ch/)
- 2010-2015 responsible (R&D) for the STRING protein-protein interaction database: http://www.string-db.org (Swiss Institute of Bioinformatics).
- 2008-2010 bioinformatician at the SIB (Swiss Institute of Bioinformatics).
- 2007-2008 java software developer at REPLY s.p.a.
In order to tackle the increasing needs of our high-throughput facilities we designed and started to develop (July 2019) a new “sample management” application.
Differently from existing LIMS applications, Sample-Manager entails a more general data model that fits with any type of sample (not just NGS) and any facility (e.g. molecular pathology unit, imaging unit, proteomics unit, genomics unit).
With sequencing data corresponding to hundreds of samples, the ability to monitor the flow of NGS data from their generation to preliminary and higher-level analyses becomes critical. We developed HTS-flow (High-Throughput Sequencing flow) framework to deal with these issue, providing the NGS-users with a system for data management and analysis for NGS data.
Htsflow is a web application that serves our bioinformaticians with the latest bioinformatics tools, ready to be used “out of the box”.
Analysis are divided in “primary analysis” (i.e. alignments to the genome) and “secondary analysis” (i.e. follow up analysis). The results of both these analysis types can be conveniently searched and visualized in suitable tables, and are stored in Htsflow database for subsequent retrieval.
The tool currently offers the following features:
- Alignments to the genome of DNA and transcript fragments.
- Merge and downsample data.
- Chip-Seq data analyis (peak calling and saturation analysis)
- RNA-Seq data analysis (differential gene/exons expression)
- Methylation analysis
- DNA Seq - Variant calling pipeline for both somatic and germinal analysis.
- DNA Seq - CNV pipeline (Copy Number Variation) for both somatic and germinal analysis
- export data to the UCSC genome browser
SVD-phy: Improved prediction of protein functional associations through singular value decomposition of phylogenetic profilesBioinformatics, vol. 32, (no. 7), pp. 1085-1087
The SIB Swiss Institute of bioinformatics' resources: Focus on curated databasesNucleic Acids Research, vol. 44, (no. D1), pp. D27-D37
STRING v10: Protein-protein interaction networks, integrated over the tree of lifeNucleic Acids Research, vol. 43, (no. D1), pp. D447-D452
Genome-wide small interfering RNA screens reveal VAMP3 as a novel host factor required for uukuniemi virus late penetrationJournal of Virology, vol. 88, (no. 15), pp. 8565-8578
Specific inhibition of diverse pathogens in human cells by synthetic microRNA-like oligonucleotides inferred from RNAi screensProceedings of the National Academy of Sciences of the United States of America, vol. 111, (no. 12), pp. 4548-4553
STRING v9.1: Protein-protein interaction networks, with increased coverage and integrationNucleic Acids Research, vol. 41, (no. D1)
STITCH 3: Zooming in on protein-chemical interactionsNucleic Acids Research, vol. 40, (no. D1)
The STRING database in 2011: Functional interaction networks of proteins, globally integrated and scoredNucleic Acids Research, vol. 39, (no. SUPPL. 1)
STITCH 2: An interaction network database for small molecules and proteinsNucleic Acids Research, vol. 38, (no. SUPPL.1)
Statistical analysis of genomic protein family and domain controlled annotations for functional investigation of classified gene listsBMC Bioinformatics, vol. 8, (no. SUPPL. 1)
Genomic functional investigation through statistical analysis of protein families and domains.AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium