Vincenzo Belcastro - Graduate Student

From Dibernardo

Short biography

I was born in a little village in the south of the Italian peninsula in the green “National park of Cilento” where numerous species, vegetal and animal, can be found. Since I was young I have always been in tight contact with nature. Understanding some of its secrets is one of the goals I try to reach during my life.

I started studying Computer Science in the University of Naples; when I started it was an increasing area of interests. Unfortunately no bioinformatics courses were taught in my own university, so I decided to spend some study time as foreign student in Denmark having the possibility to attend two Bioinformatics courses and one of Machine Learning. This gave me the opportunity to learn some biology that fascinating me deeply so I decided to move a little bit my study following biology. As I was back in Naples, soon I got the possibility to join a research group. Thanks to a presentation I have heard whom speaker was Dott. Diego di Bernardo. I contacted him and we started a long collaboration that brought me here, in the beautiful and interesting world of the research.

I started working on transcriptional gene network inference. I posed my attention in the union between Information technology and biological research. Nowadays most of the information we scientist try to observe from Microarray experiment (like gene influence) is already present as information stored in databases placed all around the web. It sounds difficult to merge different sources of information using them as unique source of information for the purpose of gene network reconstruction. Sometimes higher is difficult to solve a problem greater is the interest we pone on it.

In the last decade or even more, Computer Science and biology research walked together. Computers help researcher to store and easily retrieve those information coming from experiment. Computer tools are applied to analyze massive biological data (data mining) for scientific discovery purpose. Vice versa computer scientists need to be putted side by side with biologists to understand result. I would like to work in a group as data analyst joined with biologists trying to carry out from data those information common hidden in huge amount of data.

Education Degree: Master of Science (5 years university program) Subject: Computer Science Awarding Body: University of Naples “Federico II”, Naples, Italy Date of award: May 2007 Grade: 108/110 Dates attended: November 1999 – May 2007

Position: Exchange student (European ERASMUS project). Subject: Computer Science Institute: University of Aarhus, Aarhus, Denmark Dates attended: August 2004 – January 2005 Courses attended in Aarhus: Data mining; Machine learning and scientific discovery; Algorithms in bioinformatics: trees and structure; Algorithm in bioinformatics: sequence analysis; Aspect of object oriented programming.

Computer Skills Programming Language : C, C++, Java, MATLAB, R Web Applications : Java Servlets, JSP, HTML, XML, JDOM Database : ORACLE, MySQL, Postgres

Academic Projects Position: M.Sc. Project Site: Università di Napoli “Federico II”, Naples, Italy Duration: June-2006 to May-2007 Summary: Design and development of a reverse-engineering approach to infer gene regulatory networks. In collaboration with Diego di Bernardo and Mukesh Bansal of respectively head and Ph.D. student of the TIGEM’s system biology group, I developed a new algorithm to solve the problem of gene regulatory networks inference. The approach has never been used until now. The algorithm is able to merge different sources of information like: Microarray data and literature information using the latter as a Bayesian Approach Prior. This work has been done as Thesis work.

Position: Internship Site: TIGEM (Telethon Institute of Genetics and Medicine), Naples, Italy. Duration: January-2007 to August-2007 Summary: I worked in collaboration with the System Biology research group headed by Diego di Bernardo at the Tigem Institute. The aim of my work was the generation of simulated data: nets to simulate transcriptional gene networks; expressions to simulate expression profiles readable from microarray; noisy expressions to simulate the common measurement noise from microarray data. I simulated steady state expression sand time-series expressions. Using these data we compared some algorithms based on different statistical and mathematical models. Generated data, comparison results together with an explanation of the models the various algorithms implement have been submitted and published in Bansal,M. Belcastro,V. et al. (Molecular System Biology 2007).

Publications

Peer Journal Publications:

1) A Parallel Implementation of the Network Identification by Multiple Regression (NIR) Algorithm to Reverse-Engineer Regulatory Gene Networks. F. Gregoretti, V. Belcastro, D. di Bernardo, G. Oliva. PLoS ONE 5(4): e10179. doi:10.1371/journal.pone.0010179

2) A Yeast Sintetic Network for In Vivo Assessment of Reverse-Engineering and Modeling Approaches. I. Cantone, L. Marucci, F. Iorio, M.A. Ricci, V. Belcastro, M. Bansal, S. Santini, M. di Bernardo, D. di Bernardo, M.P. Cosma. Cell. 2009:137(1)pp.172-181

3) How to infer gene networks from gene expression profiles. M. Bansal*, V. Belcastro*, A. Ambesi-Impiombato, D. di Bernardo. Molecular Systems Biology; 3:78; 2007. Epub 2007 Feb 13. Erratum in: Mol Syst Biol. 2007;3:122.* These authors contributed equally to this work.

Conferences:

1) Networking Genes: Inference and analysis of the gene regulatory network in mammals from Large-scale Experimental Data. Integrative Biology Workshop - Wednesday, 20 January - University of Birmingham.

2) CENTRO: A CoExpression NeTwoRk Omnibus for gene function and pathway discovery. Vicenzo Belcastro, Velia Siciliano, Francesco Gregoretti, Francesco Iorio, Gennaro Oliva, Diego di Bernardo. RECOMB, MIT Boston, December, 2009, Poster Presentation.

3) Untangling biological complexity: inference and analysis of a global network of gene-gene regulation in human cells. V. Belcastro, V. Siciliano, L. Cutillo, F. Gregoretti, G. Oliva and D. di Bernardo, NetSci09 (International Workshop on Network Science), Venice, June-July 2009. Oral Presentation.

4) Inference of the human and mouse Interactome from massive dataset using a parallel-computing inference algorithm. V. Belcastro, L. Cutillo, F. Gregoretti, G. Oliva, D. di Bernardo. RECOMB, MIT Boston, Oct-Nov, 2008, Poster Presentation

5) The human interactome: inference of a comprehensive gene network in human cells. V. Belcastro, L. Cutillo, F. Gregoretti, G. Oliva, D. di Bernardo. European Conference on Computational Biology, Cagliari, Italy, Sept 2008. Poster Presentation

6) The human interactome: inference of a comprehensive gene network in human cells. V. Belcastro, L. Cutillo, D. di Bernardo. TIGEM (Telethon Institute of Genetics and Medicine), Retreat, Città di Castello (PG), May 2008. Oral presentation

7) The human interactome: inference of a comprehensive gene network in human cells. V. Belcastro, L. Cutillo, D. di Bernardo. ENFIN, CNIO Madrid, April 2008. Poster presentation

8) An integrative reverse engineering algorithm to infer gene networks from multiple sources of data. V. Belcastro, M. Bansal, D. di Bernardo. ICSB (International conference on system biology), Long Beach California, October 2007. Poster presentation

9) Gene network reverse engineering: comparison of algorithms. V. Belcastro, M. Bansal, A. Ambesi-Impiombato, D. di Bernardo. Bioinformatics ITalian Society (BiTS) April 2007 Annual Meeting, Naples, Italy. Poster presentation

10) Gene network reverse engineering: comparison of algorithms. V. Belcastro, M. Bansal, A. Ambesi-Impiombato, D. di Bernardo. TIGEM (Telethon Institute of Genetics and Medicine), Retreat, Perugia, Italy, September 2006. Poster presentation

Training Programme

1) Embo Practical course on “Network in Biology: analysis, modeling and reverse engineering”. 22-25 September 2009, Bologna, Italy.

2) Summer school on Bayesian modeling and computation – St John’s College, University of British Columbia, Vancouver, Canada, July 14-18 2008.

3) ABS08 – 2008 Applied Bayesian Statistics School on Bayesian Decision Problems in Biostatistics and Clinical Trials, organized by DEPMQ – University of Pavia and CNR IMATI – Milano, Trento (Italy), June 9-13, 2008.

4) Graduate courses:

• Bioinformatics • Functional Genomics • Proteomics and Structural Biology • Animal models • Mammalian Physiopathology • Molecular basis of Genetics Diseases and Diagnostics • Gene and Cell Therapy • Genomics and Proteomics for the study of Genetic Diseases • Animal Models of Genetics Diseases • Team Management / Grant writing

Other Scientific activities

1) Acted as Project reviewer for the FCT (The Portuguese Foundation for Science and Technology).

2) Acted as a reviewer of scientific journals: Bioinformatics, PlosOne, IEEE/ACM Transactions on Computational Biology and Bioinformatics - ScholarOne.

3) Member of FANTOM Consortium: A consortium funded by Japanese Government to comprehensively annotate the mammalian genome and to identify transcriptional network.

Honors, Scholarships, Prices and Awards

2000 Scholarship offered by E.D.I.S.U. to deserving year student.

2004 Scholarship offered by ERASMUS to cover fees and accommodation to foreign students.

February 2007 Honor offered by TIGEM to cover payments during research collaboration period.

June 2007 Monthly salary covered by TIGEM for research association. Referees