Computational Biology and Bioinformatics

Research group at the Department of Mathematics, Computer Science and Physics
University of Udine

About

Our Research Group is focused on the definition of models and query languages for the representation and study of biological systems.

We are involved in the development of algorithms for assembling and analyzing new generation sequencing data.

The group has investigated on the problem of predicting the tertiary structure of proteins using logic programming techniques.

Open Positions

Publication Highlights

Roberto Pagliarini, Fabio Marroni, Carla Piazza, Giovanni Gabelli, Gabriele Magris, Gabriele Di Gaspero, Michele Morgante, Alberto Policriti

Last updated on Sep 14, 2024

Towards a Computational Approach to Quantification of Allele Specific Expression at Population Level

Alberto Casagrande, F. Fabris, R. Girometti

Last updated on Dec 2, 2023

An information-oriented paradigm in evaluating accuracy and agreement in radiology

A. Colautti, N. Rossi, Carla Piazza, G. Comi, L. Iacumin

Last updated on Dec 2, 2023

Draft genome sequences of 14 Lacticaseibacillus spp. strains, representatives of a collection of 200 strains

Nicolò Rossi, Nicola Gigante, Nicola Vitacolonna, Carla Piazza

Last updated on Dec 2, 2023

Inferring Markov Chains to Describe Convergent Tumor Evolution With CIMICE

M. Coan, M. Toso, L. Cesaratto, I. Rigo, S. Borgna, A. Dalla Pieta, L. Zandona, L. Iuri, A. Zucchetto, Carla Piazza, G. Baldassarre, R. Spizzo, M. S. Nicoloso

Last updated on Dec 2, 2023

LINC01605 Is a Novel Target of Mutant p53 in Breast and Ovarian Cancer Cell Lines

Maria Elena Steidl, Elisa A Nigro, Anne Kallehauge Nielsen, Roberto Pagliarini, Laura Cassina, Matteo Lampis, Christine Podrini, Marco Chiaravalli, Valeria Mannella, Gianfranco Distefano, Ming Yang, Mariam Aslanyan, Giovanna Musco, Ronald Roepman, Christian Frezza, Alessandra Boletta

Last updated on Dec 2, 2023

Primary cilia sense glutamine availability and respond via asparagine synthetase

A. Dal Palu, Agostino Dovier, A. Formisano, E. Pontelli

Last updated on Dec 2, 2023

Prolog Meets Biology

F. Fogolari, R. Borelli, Agostino Dovier, G. Esposito

Last updated on Dec 2, 2023

The kth nearest neighbor method for estimation of entropy changes from molecular ensembles

Alberto Casagrande, F. Fabris, R. Girometti

Last updated on Dec 2, 2023

Fifty years of Shannon information theory in assessing the accuracy and agreement of diagnostic tests

Alberto Casagrande, R. Gentilini, Carla Piazza, Alberto Policriti

Last updated on Dec 2, 2023

Hybrid automata in systems biology

A. Brunello, M. Civilini, S. De Martin, A. Felice, M. Franchi, L. Iacumin, N. Saccomanno, Nicola Vitacolonna

Last updated on Dec 2, 2023

Machine learning-assisted environmental surveillance of Legionella: A retrospective observational study in Friuli-Venezia Giulia region of Italy in the period 2002–2019

Alberto Casagrande, Francesco Quintavalle, Enrico Lena, Francesco Fabris, Umberto Lucangelo

Last updated on Dec 2, 2023

Pressure-flow breath representation eases asynchrony identification in mechanically ventilated patients

N. Rossi, A. Colautti, L. Iacumin, Carla Piazza

Last updated on Dec 2, 2023

WGA-LP: A pipeline for whole genome assembly of contaminated reads

Projects

NBFC

National Biodiversity Future Center.

ENCASE

Efforts in the uNderstanding of Complex interActing SystEms.

Software

This is a list of software developed at the laboratory:

Cimice

CIMICE-R: A Bioconductor package implementing a (Markov) Chain Method to Infer Cancer Evolution. Also available as Java APP.

COLA

A COnstraint solver on LAttices.

DYNAMIC

A succint and compressed dynamic data structures library.

ERNE

Extended Randomized Numerical alignEr.

FIASCO

Fragment-based Interactive Assembly for protein Structure prediction with COnstraints.

GAM-NGS

Genome Assemblies Merger for Next Generation Sequencing.

ProPesca

A simple Java application for the analysis and identification of gene expression networks.

pyHybridAnalysis

A Python Package for the epsilon-Semantics Analysis of Hybrid Systems.

Sapo

A library for Reachability Computation and Parameter Synthesis of Polynomial Systems. Also available as a Web APP.

WGA-LP

WGA-LP: a pipeline for whole genome assembly of contaminated reads.

Recent Publications

D. Castelnovo, F. Gadducci, Marino Miculan (2024). A simple criterion for M,N-adhesivity. THEORETICAL COMPUTER SCIENCE.

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D. Ressi, R. Romanello, Carla Piazza, S. Rossi (2024). AI-enhanced blockchain technology: A review of advancements and opportunities. JOURNAL OF NETWORK AND COMPUTER APPLICATIONS.

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M. Pasqua, Marino Miculan (2024). Behavioral equivalences for AbU: Verifying security and safety in distributed IoT systems. THEORETICAL COMPUTER SCIENCE.

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G. D'Agostino, L. Geatti, D. Martincigh, Alberto Policriti (2024). Cascade products and Wheeler automata. THEORETICAL COMPUTER SCIENCE.

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D. Ressi, R. Romanello, S. Rossi, Carla Piazza (2024). Compressing neural networks via formal methods. NEURAL NETWORKS.

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Members

UniUD Members

Carla Piazza

Full Professor of Computer Science

Alberto Policriti

Full Professor of Computer Science

Agostino Dovier

Full Professor of Computer Science

Marino Miculan

Associate Professor of Computer Science

Alberto Casagrande

Assistant Professor of Computer Science

Nicola Vitacolonna

Assistant Professor of Computer Science

Roberto Pagliarini

Assistant Professor of Computer Science

External Members

Nicolò Rossi

PhD Student

Tommaso Dreossi

Applied Scientist

Nicola Gigante

Researcher

Contact

carla.piazza@uniud.it
+39 0432 558497
via delle Scienze 206, Udine, 33100