2017-now Associate Karolinska Institute, Division of Chemical Chemistry
2016-now Associate CNR IAC Rome
2015-now Systems Biology Coordinator at Personal Genomics spin-off University of Bologna and Verona, Italy;
2008-2014. Principal Investigator and Full Professor at Max Planck Institute- Chinese Academy of Science - Partner Institute for Computational Biology CAS-MPG PICB, Shanghai, China.
2007 Collaborator at the Telethon Institute for Genetics and Medicine (TIGEM) in Naples, Project on gene-network reverse-engineering.
2006- 2007. Research Assistant at the Department of Electronic Informatics and Systems (DEIS) at the University of Bologna. Research on complex diseases (Funded by PRIN 2004, Italian National Grant); Research on synthetic biology (Genetic Schmitt Trigger in E. coli, Funded by SYNBIOCOM, European Grant).
2005 Visiting Researcher at The Center for Translational Medical Systems at University of California San Diego (UCSD, USA), with Michael D. Kuo, MD, development of Radiogenomics.
2003-2004 – Visiting researcher at the Computer Science Department at Stanford University (CA, USA), with Prof Giovanni de Micheli. Development of data mining approaches applied to microarrays for gene expression analyses.
1999 - 2002. Field Engineer in the Cardiac Rhythm Management Division at Medtronic S.p.A. Assistance during implant and follow-up of patients with implantable devices for brady/tachy arrhythmias. Education activity on brady/tachy arrhythmias and cardiac stimulation for nurses and medical doctors in hospitals in Emilia Romagna and Marche (Italy).
Italian: mother tongue;
German: intermediate level;
Chinese: beginner-intermediate (spoken).
2002-2006 PhD in Electronics and Informatics at the University of Bologna. Thesis Title: “Statistical-Computational Techniques for Extraction of Functional Genomic Units from Microarray Experiments”.
1999 National Habilitation to Engineers Professional Activity.
1998 a.a EE Master Degree in Electrical Engineering – Biomedical specialization at the University of Bologna (90/100). Thesis title: “Identification of non-linear dynamics through space and time dependent neural networks”.
1992 – BS Degree at Istituto N. Copernico in Bologna (60/60).
My main interest is in the discovery, analysis and control of the regenerative and healing mechanisms that can be triggered to control autoimmune, chronic and degenerative diseases.
I am expert in the development, application and integration of methods from high-throughput data mining and network modeling to biological hypotheses validation on animal models and to the design of human clinical studies to take maximum advantage from the systems biology pipeline “from desk-to bench-to bed “.
To date I have focused on rheumatoid arthritis as a notable model disease with special attention to the variations occurring in blood and in the gut intestinal microbiome
Specialties: Translational Research; High throughput biological data mining; multi-omic data integration. Computational biology, biostatistics.
February 23rd 2016, lecturer Winter School of Bologna on Biomarkers for Precision Medicine, “Biomarkers for Nanobiochips”.
2015 Lecturer for Advanced teaching at the International Master of Bioinformatics at the University of Bologna. Course title: “Omics & Multi-omics”
February 2015, lecturer Bologna Winter School on Bioinformatics and New Molecular Scenarios, “Are clustering and association rules enough for inferring causation”
February 2014, lecturer Bologna Winter School on complexity in Biology, “The added complexity of the gut intestinal microbiome”
2012 Lecturer for a module of the “Bioinformatics Algorithms” 1st year PICB course
2011 Lecturer for a module of the “Bioinformatics Algorithms” 1st year PICB course.
2011 Lecturer for the school Advanced Computational Biology
2009 Lecturer for a module of the “Bioinformatics Algorithms” 1st year PICB course.
2006 –Faculty for the refresher course ‘Integrating Cancer Genomics and Radiological Imaging: Practical Answers to Complex Problems (How-to Workshop)’, Conference RSNA Radiological Society of North America,
2007-2008 – Lecturer for the course ‘Biosensors’ at the University of Bologna for the Bioinformatics Degree in the Faculty of Mathematics Physics and Natural Sciences.
2006-2007 – Lecturer for the course ‘Biosensors’ at the University of Bologna for the Bioinformatics Degree in the Faculty of Mathematics Physics and Natural Sciences.
A method for automated pathogenic content estimation with application to rheumatoid arthritis
BMC SYSTEMS BIOLOGY 2016;:107-
Correlation enhanced modularity-based belief propagation method for community detection in networks
JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT 2016;:-
Systemic Wound Healing Associated with local sub-Cutaneous Mechanical Stimulation
SCIENTIFIC REPORTS 2016;:39043-
Editorial: Multi-omic data integration
Frontiers in cell and developmental biology 2015;3():46-
Mechanotransduction map: simulation model, molecular pathway, gene set
i-Needle: Detecting the biological mechanisms of acupuncture
Multi-omic landscape of rheumatoid arthritis: re-evaluation of drug adverse effects
Frontiers in cell and developmental biology 2014;2():59-
From desk to bed: Computational simulations provide indication for rheumatoid arthritis clinical trials
BMC SYSTEMS BIOLOGY 2013;:10-
MIMO: an efficient tool for molecular interaction maps overlap
BMC BIOINFORMATICS 2013;:159-
Multilevel omic data integration in cancer cell lines: advanced annotation and emergent properties
BMC SYSTEMS BIOLOGY 2013;:14-
Signalling pathway database usability: lessons learned
MOLECULAR BIOSYSTEMS 2013;9(10):2401-7
SPNConverter: a new link between static and dynamic complex network analysis
Understanding human diseases with high-throughput quantitative measurement and analysis of molecular signatures
SCIENCE CHINA-LIFE SCIENCES 2013;56(3):213-9
An S-System Parameter Estimation Method (SPEM) for Biological Networks
JOURNAL OF COMPUTATIONAL BIOLOGY 2012;19(2):175-87
Brain cancer prognosis: independent validation of a clinical bioinformatics approach
Journal of clinical bioinformatics 2012;2():2-
Inference of gene networks-application to Bifidobacterium
LEARNING OVERLAPPING COMMUNITIES IN COMPLEX NETWORKS VIA NON-NEGATIVE MATRIX FACTORIZATION
INTERNATIONAL JOURNAL OF MODERN PHYSICS C 2011;22(10):1173-1190
Partitioning networks into communities by message passing
PHYSICAL REVIEW E 2011;83(1):016115-
A Comprehensive Molecular Interaction Map for Rheumatoid Arthritis
PLOS ONE 2010;5(4):e10137-
Adapting functional genomic tools to metagenomic analyses: investigating the role of gut bacteria in relation to obesity
BRIEFINGS IN FUNCTIONAL GENOMICS 2010;9(5-6):355-61
Enhanced modularity-based community detection by random walk network preprocessing
PHYSICAL REVIEW E 2010;81(6):066118-
Extracting weights from edge directions to find communities in directed networks
JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT 2010;:-
Finding communities in directed networks by PageRank random walk induced network embedding
PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS 2010;389(12):2443-2454
MANIA: A GENE NETWORK REVERSE ALGORITHM FOR COMPOUNDS MODE-OF-ACTION AND GENES INTERACTIONS INFERENCE
ADVANCES IN COMPLEX SYSTEMS 2010;13(1):83-94
High Parallelism, Portability, and Broad Accessibility: Technologies for Genomics
ACM JOURNAL ON EMERGING TECHNOLOGIES IN COMPUTING SYSTEMS 2008;4(1):-
Identification of noninvasive imaging surrogates for brain tumor gene-expression modules
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 2008;105(13):5213-8
TOM: enhancement and extension of a tool suite for in silico approaches to multigenic hereditary disorders
TOM: a web-based integrated approach for identification of candidate disease genes
NUCLEIC ACIDS RESEARCH 2006;:W285-92
Discovering coherent biclusters from gene expression data using zero-suppressed binary decision diagrams
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2005;2(4):339-54