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 space logic, bigraphs, and observational equivalences. We work on the design of specific algorithms for exact or approximate verification of specification properties on the models. Some of such algorithms are currently at the core of tools such as pyHybridAnalysis, SAHA-Tool, Sapo.

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. A model denoted 5 @ (5 amino acid atoms) was developed along with its potential statistical energy. Ad-hoc constraints have been studied and implemented within a constraint solver that is produced and maintained by the group (see also CLPLab). 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.

News & Events

CMSB 2019 aims is to bring together researchers from across biological, mathematical, computational, and physical sciences who are interested in the study, modelling, simulation, advanced analysis, and design of biological systems.

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HSB centres on dynamical models in biology, with an emphasis on both hybrid systems (in the classical sense, i.e., mixed continuous/discrete/stochastic systems) and hybrid approaches that combine modelling, analysis, algorithmic and experimental techniques from different areas.

Hybrid systems and approaches are essential to the understanding of complex living systems, which are characterized by stochasticity and heterogeneous spatiotemporal scales. These methods are crucial also for the design and analysis of artificial biochemical systems (e.g., engineered bacteria or molecular machines) and of medical cyber-physical systems such as pacemakers and infusion pumps. The complexity of such models makes their formal analysis challenging, and even their simulations are often impractical, calling for appropriate model abstractions and scalable analysis methods.

HSB aims at bringing together researchers from different disciplines interested in applying these methods to the study of structure, dynamics, and control mechanisms of living systems.

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The Workshop and School on Cancer Development and Complexity seeks to convene researchers from various related disciplines to explore multiple facets of the challenges posed by cancer a “disease of the systems.” The workshop will provide opportunities for the researchers to exchange new ideas and viewpoints, forge new collaborations and train the next generation of young scientists.

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The conference will to bring together researchers from across biological, mathematical, computational, and physical sciences who are interested in the study, modelling, simulation, advanced analysis, and design of biological systems.

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The workshop aims at exchanging ideas between researchers and collecting, if possible, new problems to be faced in the next future by our community.

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Projects

ENCASE

Efforts in the uNderstanding of Complex interActing SystEms.

Software & Apps

This is a list of software developed at the laboratory.

  • 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

  • Sapo

    Reachability Computation and Parameter Synthesis for Polynomial Systems

  • pyHybridAnalysis

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

Recent Publications

More Publications

. Persistent stochastic non-interference. Electronic Proceedings in Theoretical Computer Science, EPTCS, 2018.

. String attractors: Verification and optimization. Leibniz International Proceedings in Informatics, LIPIcs, 2018.

. LZ77 Computation Based on the Run-Length Encoded BWT. Algorithmica, 2018.

. Lumping-based equivalences in Markovian automata: Algorithms and applications to product-form analyses. Information and Computation, 2018.

. Parallel answer set programming. Handbook of Parallel Constraint Reasoning, 2018.

. Guest editors' foreword. Journal of Logical and Algebraic Methods in Programming, 2018.

. 2D object reconstruction with ASP. CEUR Workshop Proceedings, 2018.

. Encoding sets as real numbers. CEUR Workshop Proceedings, 2018.

. Extending logic programming with labelled variables: Model and semantics. Fundamenta Informaticae, 2018.

. Information Flow Security for Stochastic Processes. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2018.

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