Cinzia Pizzi's Research


Research Publications ABCLab Software Teaching Contacts


Welcome! I am an associate professor at the department of Information Engineering of the University of Padova. My research is focused on: Design of efficient algorithms and data structures for sequence analysis; Alignment-free techniques; Design of effective sequence encodings for machine/deep learning based approaches for clustering and classification; Explainable AI.
I am interested in both methodological and theo\ retical aspects related to the efficiency of the proposed algorithms and data structures, and software de\ velopment for the application to real data analysis.
During my carrier I have worked on different computational problems in bioinformatics, starting with motif discovery during my PhD, and then moving to phylogeny and metagenomics. Recently I have been working on phenotype prediction and variant calling within a collaboration with the Comparative Biomedicine and Food Science department (BCA) on a PNNR Project first and now on the European project EUAqua.
Moreover, results on general aspects of pattern matching can be applied also in contexts other than bioinformatics. This led in the past to collaboration with collegues working on different fields, for example text processing and temporal data analysis for smart cities.


Research Projects

Project "COmuNità VEneta per il Calcolo Scientifico - CONVECS", coordinated by UNIPD together with INFN (LNL+Padova), UNIVR, UNIVE Ca' Foscari e IUAV. Participant. Active from: 1/3/25

European Project EUAqua, in collaboration with the department of Comparative Biomedicine and Food Science (BCA). Participant (PI Prof. L. Bargelloni). Active from 1/1/25

- Activity 3, spoke 2, NBFC - National Biodiversity Future Center, PNRR. Active from 1/9/2022 ; participant, computational aspects;

- Department Project (SID): ''Algorithms for Networks Analysis and Bioinformatics Applications''; participant (PI F.Vandin), from 2017 to 2019;

- Project of National Interest (PRIN): ''Compositional approaches for the characterization and mining of omics data'', Role: Principal Investigator; from 2014 to 2017; 391929 euro Project web site

- University of Padova Project: ''Pattern discovery and computational problems for whole genomes comparison'', participant, 2012-2013

- University of Padova Project: ''Computational Assessment of Protein–Protein Interaction Networks and Validation as a Guide for Modern System Biology'', Role:participant, 2008–2010

- CARIPARO projects of excellence: ''Systems Biology approaches to infer gene and protein time-series expression data'', participant; from 01-07-2008 to 31-12-2011

- European project HuBi - Hungarian Bioinformatics MTKD-CT-2006-042794 with a Marie Curie Host Fellowships for Transfer of Knowledge, 2010

- FIRB Projects (Fundings on fundational research) ''Pattern Discovery in Discrete Structures, with Applications to Bioinformatics'', participant; from 01-07-2006 to 30-06-2010

- EU Project ''Regulatory Genomics'' 2004-2008, University of Helsinki, Finland, participant;
from 15-09-2005 to 30-11-2006



 - Project of National Interest (PRIN): ''Metodologie di data mining per le applicazioni di e-business'', Role; participant; from 2005 to 2006

- EU Marie Curie Early Stage Fellowship at European Bioinformatics Institute (EBI), 2005


Short bio

I had my Ph.D. from the Department of Information Engineering, University of Padova, Italy in 2005 under the supervision of Prof. Alberto Apostolico. For my postdoc I joined the From Data to Knowledge Center of Excellence under the supervision of Prof. Esko Ukkonen in Helsinki (Finland). Then I moved for a year to the Bobab Team of Marie-France Sagot in Lyon, before returning to University of Padova (Italy) where I became an Assistant Professor first, and then an Associate Professor. During my early carrier (and before having my beautiful son) I had the chance to be a visiting researcher at several prestigious Universities and Research Centers (University of Purdue, GeorgiaTech, Hungarian Academy of Science). I also had the great opportunity to work at the European Bioinformatics Institute thanks to an early stage Marie-Curie fellowship in the Computational Genomics group of Christos Ouzounis.

Awards:
- "Avere Trent'anni" research award from the University of Padova, assigned by a commission with both academic and industrial representatives among young researchers of the whole University, 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 was also a member of the Ethic Committee of the Center in 2014-2017.


Scientific Community

Main topic editor for the Research Topic "From one genome to many genomes: the evolution of computational approaches for pangenomics and metagenomics analysis" in Frontiers in Bioinfomatics

Co-editor of Recomb-Seq 2021 special issue in the international journal iScience

Reviewer for International Journals:
Reviewer for many international journals in Computer Science and Bioinformatics, amongh which: Nature - Scientific Reports, Plos Computational Biology, BMC Bioinformatics, Bioinformatics, Frontiers in Bioinformatics, Theoretical Computer Science, BMC Algorithms for Molecular Biology, IEEE Transaction in Computational Biology and Bioinformatics, Knowledge and Information Systems, iScience, International Journal of Bioinformatics Research and Applications, Journal of Discrete Algorithms.

Conferences Organization

- CIBB 2026: Organizing committee
- BITS 2026: Organizing committee
- RECOMB 2021:Organizing committee
- RECOMB 2021: Satellites Local Chair
- RECOMB 2020: Organizing committee
- RECOMB 2020: Satellites Local Chair
- BITS 2020: Conference of the Bioinformatics Italian Society. Expected role: co-Chair. The conference did not take place due to the pandemic
- Workshop on algorithms and tools for the analysis of big omics data, co-located with BITS 2019. General co-Chair together with Simona E. Rombo and Fabio Fassetti
- Genome Compression Day, Main Organizer, Padova, 10th September 2018
- AxA Workshop: Advanced Algorithms on strings: Organizing Committee co-Chair
- RECOMB 2006: Organizing Committee Member
- Dialogues 2004: joint event including: Symposium on String Processing and Information Retrieval (SPIRE), Discovery Science (DS), and Algorithmic Learning Theory (ALT): Organizing committee member.
- ESSIR2000: European Summer School in Information Retrieval. Student volunteer.


Program Committees

RECOMB-Seq (co-chair) 2021

Participation to the PC of several edition of conferences in bioinformatics and string processing, among which:
RECOMB, WABI, CPM, SPIRE, CIBB, ICTCS, EPIA, ITBAM, Global Health, CiE, BIGPMED...



Research Publications ABCLab Software Teaching Contacts