Computational Biology and Bioinformatics

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

About

Our Research Group is mainly focused on the definition of models and query languages for the representation and study of biological systems. In particular, for modeling systems we consider formalisms such as hybrid automata, stochastic automata, process algebra, parametric dynamical systems, while as property specification languages we refer to temporal and spatial logic, bigraphs, and observational equivalences. We work on the design of specific algorithms for exact or approximate verification of specification properties on the models.

The group is involved in the study of the problem of predicting the tertiary structure of proteins using logic programming techniques. The methods proposed by our group combine both the use of publicly available data bases and constraint solvers. In the implementation, the parallelization of programmable graphics cards (GPGPU) was also used.

The group has developed algorithms for assembling and analyzing new generation sequencing data. In particular, algorithms for global assembly (full genomes) and for local assembly (regions included in the paired-end of a single sequence) have been developed. In addition, the problem of combining different assemblies known for the same organism / species has been studied. Finally, methods for aligning sequences on compressed indexes that do not require decompression of text have been studied.

The group is involved in the organization of international conferences, workshops and schools on systems of biology and bioinformatics including BITS, HSB, WCB, MecBIC, BCI, FMMB, CMSB. Group members have been guest editors and editors of international journals in the area. They have participated in national and international projects and have established international collaborations with NYU Bioinformatics Group, NMSU Center for Bioinformatics and Computational Biology, Institut de Biologie Paris Seine.

People

Members

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Carla Piazza

Associate Professor of Computer Science

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Alberto Policriti

Full Professor of Computer Science

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Agostino Dovier

Full Professor of Computer Science

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Marino Miculan

Associate Professor of Computer Science

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Nicola Gigante

Postdoctoral Researcher

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Nicola Vitacolonna

Assistant Professor of Computer Science

External Members

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Tommaso Dreossi

Applied Scientist

Projects

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ENCASE

ENCASE

Efforts in the uNderstanding of Complex interActing SystEms.

Software & Apps

This is a list of software developed at the laboratory:

.js-id-Protein-folding

Cimice

CIMICE-R: (Markov) Chain Method to Infer Cancer Evolution

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

Reachability Computation and Parameter Synthesis for Polynomial Systems.

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