Research

Research Publications ABCLab Software Teaching Contacts


Research Interests:

Resolution of combinatorial problems mainly emerging from biological data analysis. The results cover both theoretical aspects related to the efficiency of the proposed algorithms and data structures, and software development for the application to real data analysis.
In particular, I am interested in the design and development of compact model for representing, searching and discovery biological signals as complex structures: patterns with variability in unknown positions (iid and Markov distribution), co-occurrences, position weight matrices, and dynamic networks. Results on general aspects of pattern matching can be applied in contexts other than bioinformatics such as, for example text processing and temporal data analysis.

Current research topics include: compositional alignment free methods, metagenomics, phylogenomics, temporal data mining .

Research Projects

Current Reserch Project

PRIN 2012: Compositional approches for the characterization and mining of omics data. Principal Investigator (Responsabile Scientifico Nazionale) 2014-2017
Project web site

Past Research Project
Previously, my research activity has been partially supported by European Union (EU project HuBi - Hungarian Bioinformatics MTKD-CT-2006-042794 with a Marie Curie Host Fellowships for Transfer of Knowledge; EU research project Regulatory Genomics, EU Marie Curie Early Stage Fellowship at European Bioinformatics Institute (EBI), Academy of Finland; past national projects PRIN (Research Projects of National Interest) and FIRB (National Funding for Foundational Research), Past University of Padova Research Programs.

Short bio

Appointments:
- Assistant Professor at the Department of Information Engineering (DEI) of the University of Padova, since 2011 - Senior Research Fellow, DEI, University of Padova, 2008-2011
- PostDoctoral Researcher, Baobab Team (with M.-F. Sagot), University of Lyon I (INRIA fellowship), 2007
- PostDoctoral Researcher, dept. Computer Science, University of Helsinki and From Data to Knowledge Center of Excellence (with E.Ukkonen), 2005-2006
- Marie-Curie Early Stage Fellowship at European Bionformatics Institute, Hinxton, Cambridge, UK, 2005

Visiting Scientist at: Renyi Institute of Mathematics of the Hungarian Academy of Science (2010), GeorgiaTech (2009), and Purdue University (2004).

Education:
- Ph.D. at the Department of Information Engineering, University of Padova, Italy, 2005. Advisor: Prof. Alberto Apostolico
- Laurea Degree (5 years, Summa cum laude) in Computer Engineering, University of Padova, Italy, 2001. Advisor Prof.ssa Maristella Agosti

Awards:
- "Avere Trent'anni" research award from the University of Padova, assigned by a commission with both academic and industrial representatives, 2008
- Outstanding Young Researcher, Department of Information Engineering, University of Padova, 2010

I am a member of the inter-departments Research Center HIT (Human Inspired Technology) of the University of Padova since its fundation in 2013. I am also a member of the Ethic Committee of the Center.

In 2006 I was in the Organizing Committe of one of the leading conferences in Computational Biology: RECOMB.

I regularly serve as reviewer for several International Journals among which Theoretical Computer Science, Plos Computational Biology, Journal of Discrete Algorithms, BMC Bioinformatics, Bioinformatics, ACM/IEEE Transaction in Computational Biology, BMC Algorithms for Molecular Biology, Knowledge and Information Systems, International Journal of Bioinformatics Research and Applications;

I have been in the Program Committee of several International Conferences, among which SPIRE, WABI, ITBAM, Global Health, EPIA - Artificial Intelligence in Medicine track; or served as external reviewer (e.g. RECOMB, CPM, WABI, BIMB, SPIRE, ICALP, IEEE-WCCI).



Research Publications ABCLab Software Teaching Contacts



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