CV

CURRENT POSITION

Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR), Rome, IT
Scientific Researcher, 2017-Present
ELIXIR-IIB (http://elixir-italy.org)
ELIXIR Italy Training Coordinator, 2014-Present
University of Bologna, Master in Bioinformatics, Bologna, IT
Adjunct professor, 2016-Present

NATIONAL SCIENTIFIC QUALIFICATION

Molecular Biology (05/E2 - SSD BIO/11) - Associate Professor
Applied Physics (02/B3 - SSD FIS/07) - Associate Professor
Biochemistry (05/E1 – SSD BIO/10) - Associate Professor

EDUCATION

Università di “Tor Vergata”, Roma, IT
PhD, Cellular and Molecular Biology, 2003
Dissertation: “Protein structural study for the optimization and analysis of sequence functional motifs”
Supervisor: Prof. Manuela Helmer-Citterich
Sapienza Università, Roma, IT
Master Degree, Physics, 1997
Dissertation: “Analytical study of the Sherrington and Kirkpatrick spin-glass model”
Supervisor: Prof. Giorgio Parisi
Université Paris Diderot – Paris 7, Paris, FR
Erasmus programme, Dept. of Mathematics, 1994-1995

ATTENDANCE TO TRAINING COURSES

EMBL-EBI, Hinxton, UK
GOBLET/ELIXIR “Metagenomics Hackathon”, April 2016
CSC, Espoo, Helsinki, FI
ELIXIR-EXCELERATE workshop “Using clouds and VMs in bioinformatics training”, May 2016
University of Lausanne, Lausanne, CH
Software and Data Carpentry course on “Instructor Training”, January 2016
Wellcome Trust Sanger Institute, Hinxton, UK
BioMalPar (FP6 Malaria Initiative) course on “Introduction to Plasmodium Bioinformatics”, August 2005
Università di Bologna, Bologna, IT
4th Bologna Winter School “Hot Topics in Structural Genomics”, February 2003
**Institute for Scientific Interchange foundation, Villa Gualino, Torino, IT **
Euroconference on “Protein folding and structure prediction”, June 1998

RESEARCH EXPERIENCE

- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council (CNR), Bari, IT

Research Associate, 2016
Topics:
- Design, organisation and delivery of bioinformatics training courses
- Train the Trainer activities
- Learning theories and how they can be translated into teaching practices
- Cognitive science/Educational psychology
Sapienza Università, Roma, IT
Research Associate (RTD), 2009-2015
Topics:
- Therapeutic targets and their inhibitors, host-pathogen interactions using state-of-the art tools in computational biology.
- Modelling of biological systems. Development of bioinformatics resources. Building pipelines.
Sapienza Università, Department of Biochemical Sciences, Roma, IT
Postdoctoral fellow, 2007-2009
Topics:
- Protein structure, function and disease using state-of-the art tools in computational biology
- Development of bioinformatics methodologies and resources. Building pipelines.
Università di Bologna, Department of Experimental Biology of Evolution, Bologna, IT
Postdoctoral fellow, 2006-2007
Topics:
- Protein structure and function; Protein phosphorylation; Linear motifs.
- Development of bioinformatics methodologies and resources; Neural networks.
*Università di “Tor Vergata”, Department of Biology, Roma, IT **
*Postdoctoral fellow, 2003-2006
Topics:
- Protein structure and function; PTM, modular domains and signalling; functional motifs.
- Development of bioinformatics methodologies and resources.

GRANTS AND AWARDS

Sapienza Università research grant for the “Characterisation of Plasmodium falciparum antigens triggering autoimmune response”, 2013
Sapienza Università research grant for the “Identification of molecular targets in malaria and schistosomiasis and characterisation of their interactions with candidate inhibitors”, 2011
Telethon awards for the work in the project “Multi-centre bioinformatics project for a systematic investigation of gene expressed in human skeletal muscle”, 2005 and 2002
Genes, Protein & Computer VI Conference best poster award, Chester College, Chester, 2000

ACADEMIC TEACHING AND ADVISING EXPERIENCE

Università di Bologna, School of Science, MD in Bioinformatics, Bologna, IT
Head teaching fellow, Module 3 (on Protein Interactions, 20h) in the Laboratory of Bioinformatics 1 course, 2015-2016
Sapienza Università, MD in Engineering of Nanotechnology, Roma, IT
Head teaching fellow, “Macromolecular structures” (6 CFU), 2010-2015
Sapienza Università, MD in Physics of Biosystems, Roma, IT
*Head teaching fellow8, “Biochemistry” (6 CFU), 2011-2012
Università di “Tor Vergata”, MD in Bioinformatics, Roma, IT
Head teaching fellow, “Computational methods for Biology” (6 CFU), 2005-2010
Università di “Tor Vergata”, MDs in Cellular and Molecular Biology, in Human Biology, and in Bioinformatics, Roma, IT
Teaching assistant, “ Molecular Bioinformatics”, 2003-2005
Università di “Tor Vergata”, B.Sc. in Cellular and Molecular Biology & B.Sc. in Human Biology, Roma, IT
Teaching assistant, “Bioinformatics”, 2002-2003

TRAINING EXPERIENCE

ELIXIR-IIB practical course, University of Bari, Bari, Italy
Organiser and instructor, “Python for Life Scientists”, 26-30 September 2016
RDA-CODATA Research Data Science Summer School, ICTP, Trieste, Italy
Lead Instructor, “Software Carpentry module”, 01-04 Aug 2016
ELIXIR-EXCELERATE Train the Trainer course, IGC, Oeiras, Portugal
Organiser and instructor, 10-15 Jul 2016
Scientific School on “Computational modeling for Life Sciences”, Sardinian Scientific and Technological Park, Pula (CA), Italy
Invited speaker and Instructor, 06-10 June 2016
RNA-seq data analysis workshop, University of Naples Federico II in collaboration with ELIXIR-IIB, Naples, Italy
Invited speaker, June 6th-10th, 2016
ELIXIR-IIB practical course, CNR, Napoli, Italy
Organiser and instructor, “NGS for evolutionary biologists: from basic scripting to variant calling”, 2-5 May 2016
EMBO practical course, Budapest, Hungary
Instructor, “Introduction to Linux command line” and “ Structure and interfaces of PPIs “ in the EMBO practical course on “Computational analysis of protein-protein interactions: Sequences, networks and diseases” (http://events.embo.org/16-protein-protein/), 30th May-4th Jun 2016
ELIXIR-IIB practical course, Università di Bologna, Bologna, IT
Organiser and instructor, “Protein networks and systems biology”, 14-18 Dec 2015
ELIXIR-IIB practical course, CINECA Auditorium, Rome, IT
Organiser and instructor, “NGS for evolutionary biologists: from basic scripting to variant calling”, 23-27 Nov 2015
ELIXIR-IIB practical course, CINECA Auditorium, IT
Organiser and instructor, “Gene expression profiling with HTS: RNA-Seq data analysis”, 19-22 Oct 2015
PhD School in Biology and Molecular Medicine Training course, Sapienza Università, Rome, IT
Organiser and instructor, “Next Generation Sequencing data analysis”, 5-7 Oct 2015
EMBO practical course, TGAC, Norwich, UK
Instructor, “Structure of PPIs and interfaces of PPIs, predicting globular 3D structure” in the EMBO Practical Course: Computational Analysis of Protein-Protein Interactions: From Sequences to Networks (http://events.embo.org/15-protein-protein/), 28th Sept- 3rd Oct 2015
2nd level Master in Bioinformatics: Biomedical and Pharmaceutical applications, Sapienza Università, Rome, IT
Instructor, “Programming and algorithms for Bioinformatics” (24h), 2014 and 2015
GTPB practical course, Instituto Gulbenkian de Ciência, Oeiras, PT
Instructor, “Bioinformatics using Python for Biologists” (40h each year), 2010-2016
TGAC practical course, Norwich, UK
Instructor, “Python for Life Scientists” (40h each year), 2013-2015
Institut Pasteur practical course, Tunis, TN
Instructor, “Proteomics and drug design” (20h), April 2012
Università di “Tor Vergata” post-graduate training course, Roma, IT
Instructor, “Bioinformatics applications” (30h), 2000

RELATED PROFESSIONAL EXPERIENCE

ELIXIR-IIB Training Coordinator Coordinates the ELIXIR Italian node training activities. ELIXIR (http://www.elixir-europe.org) is a distributed sustainable European infrastructure for life science information, supporting life science research and its translation to medicine, agriculture, bioindustries and society. ELIXIR-ITA, the Italian node of ELIXIR, is a Joint Research Unit with 17 member institutions (11 Universities, CNR, CRS4, INFN, CINECA, FONDAZIONE EDMUND MACH), 2014-present
ELIXIR-IIB Technical Coordinator for Sapienza Università
Coordinates ELIXIR-ITA research support activities for - Sapienza Univeristà, Rome, 2014-present
ELIXIR-EXCELERATE Train the Trainer subtask leader (WP11, Training platform)
Coordinates the WP11 Train the Trainer subtask activities for the ELIXIR-EXCELERATE EC funded project (2015-2018) Italian representative in the ELIXIR taskforce on “Best practices in software development”.
ELIXIR’s liaison to the EU Project: “EDISON, building the data science profession”, 2016-present.
Secretary of the Global Organisation for Bioinformatics Learning Education and Training (GOBLET, http://www.mygoblet.org), 2012-2013.
Chair of the Bioinformatics Training Network (BTN, http://www.biotnet.org), 2011-2013.
Italian representative in the “Training portal” and “e-learning and training” ELIXIR task forces, 2014-present. Data/Software Carpentry certified Instructor (http://software-carpentry.org), since Jan 2016.
Member of the PC for the following conferences: ECCB (European Conference on Computational Biology); ISMB (International Conference on Intelligent Systems for Molecular Biology); BIRD (International Conference on Bioinformatics Research and Development); BIOINFORMATICS (http://www.bioinformatics.biostec.org); NETTAB (Network Tools and Applications in Biology).
Organisation of practical courses, workshops and conferences:
- Local organiser for the NETTAB 2016 workshop on “Reproducibility, standards and SOP in bioinformatics”, CNR, Rome, IT, 100 participants, October 2016.
- Co-organised the NETTAB 2016 satellite Goblet/ELIXIR-IIB joint tutorial on “Train the Trainer”, CNR, Rome, IT, expected 20 participants, October 2016.
- Co-organised the Education & Training special session of the NETTAB 2016 Workshop, CNR, Rome, IT, October 2016.
- Co-organised the practical course on “Python for Life Scientists”, University of Bari, Bari, IT, expected 24 participants, September 2016.
- Co-organised the practical course on “Exome analysis using Galaxy”, University of Milano-Bicocca, Milano, IT, expected 24 participants, September 2016.
- Co-organised the 2nd ELIXIR-EXCELERATE “Train the Trainer” course, IGC, Oeiras, PT, (limited to) 8 participants, July 2016.
- Co-organised the BITS 2016 satellite workshop on “Effective academic teaching”, University of Salerno, Fisciano (SA), IT, 20 participants, June 2016.
- Co-organised and co-chaired the round table on “Teaching Bioinformatics: state-of-the-art and new ideas” at the BITS 2016 conference, University of Salerno, Fisciano (SA), IT, June 2016.
- Co-organised the 1st ELIXIR-EXCELERATE “Train the Trainer” course, University of Cambridge, Cambridge, UK, (limited to) 10 participants, May 2016.
- Co-organised the ELIXIR-IIB practical course on “NGS for evolutionary biologists: from basic scripting to variant calling”, CNR, Naples, IT, 24 participants, May 2016.
- Co-chaired the ELIXIR-EXCELERATE “Train the Trainer” framework workshop, EBI, Hinxton, UK, January 2016.
- Co-organised the ELIXIR-IIB practical course on “Protein networks and systems biology”. Università di Bologna, Bologna, IT, 24 participants, December 2015.
- Co-organised the ELIXIR-IIB practical course on “NGS for evolutionary biologists: from basic scripting to variant calling”. CINECA Auditorium, Rome, IT, 24 participants, November 2015.
- Organised the ELIXIR-IIB practical course on “Gene expression profiling with HTS: RNA-Seq data analysis”. CINECA Auditorium, Rome, IT, 24 participants, October 2015.
- Co-organised the practical course on “Next Generation Sequencing data analysis”. PhD School in Biology and Molecular Medicine (BeMM), Rome, IT, 40 participants, October 2015.
- Co-organised the practical course on “Python for Life Scientists”. The Genome Analysis Centre, Norwich, UK, 25 participants, 40h, October 2013 and April 2015.
- Co-organised the workshop: “Bioinformatics Training for Life Scientists: Showcases and Challenges from Tutors’ Perspectives”, Basel, CH, 40 participants, September 2012.
- Local organising committee member of ECCB’08 (European Conference on Computational Biology), Cagliari, Sardinia, IT, > 400 participants, September 2008.

LANGUAGES
Italian, native; English, fluent; French, fluent; German, basic

SKILLS and TECHNIQUES

UNIX/Linux and Mac OSX administration
Python programming
Web programming (HTML, CGI, Django)
R scripting for statistical analyses
Pipeline building (NGS data analysis, data retrieval and filtering, etc.)
Bioinformatics tools development and testing
Relational database management systems MySQL and PostgreSQL
Molecular graphics systems: PyMOL, Chimera, SwissPDB viewer
Docking packages (e.g. Autodock)
Most of the state-of-the-art tools for bioinformatics and computational biology analyses (e.g. local Blast+, ClustalW, Modeller, etc.)
VM and Cloud computing

SELECTED INVITED TALKS

“Ten simple rules to make your teaching more effective”, BITS 2016 Conference, University of Salerno, Fisciano (SA), IT, June 2016
“Role of structure-based homology modeling in biomolecular sciences”, Scientific School on “Computational modeling for Life Sciences”, Sardinian Scientific and Technological Park, Pula (CA), IT, June 2016
“Computational approaches to the study of functional sites in biomolecules”, Università di “Tor Vergata”, Roma, IT, 2014
“A computational approach for the study of therapeutic targets and their inhibitors in human pathogens”, TAGC Inserm, Aix-Marseille Université, FR, 2014
“Best practices in programming for biological data management”, The Genome Analysis Centre, Norwich, UK, 2013
“GOBLET”, NextGenBug 31st meeting, ARK Genomics, Roslin, Edinburgh, UK, 2013
“A structural approach to the study of therapeutical targets and their inhibitors in human pathogens”, Bi-national Israel-Italy meeting, Tel Aviv University, Israel, 2012
“Cross-talking between human genome variations and their protein environment: a computational study”, IRB Barcelona, SP, 2009
“Structural bioinformatics: a meeting-place for Biology and Physics”, Università di Bologna, IT, 2008
“High-throughput protein functional annotation based upon local structure similarity”, Genome Annotation: a BioSapiens Network of Excellence Initiative. 5th European Conference on Computational Biology (ECCB), IL, 2006
“Proteins: Structure, Function, Evolution”, IUSS (Istituto Universitario di Studi Superiori), Università di Pavia, Pavia, IT, 2001
“The structure of Proteins”, in the Course of “Problems in Biological Evolution”; Scuola di Genetica di Cortona, Associazione Genetica Italiana (AGI), Cortona, IT, 2001