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Rational design and standardized evaluation of novel genetic vaccines

Period: 2005-2009

Recombinant viral vectors and virus-like particles are considered the most promising vehicles to deliver antigens in prophylactic and therapeutic vaccines against infectious diseases and cancer. Several potential vaccine designs exist but their cost-effective development cruelly lacks a standardised evaluation system. On these grounds, COMPUVAC is devoted to:
(i) rational development of a novel platform of genetic vaccines
(ii) standardisation of vaccine evaluation.

COMPUVAC assembles a platform of viral vectors and virus-like particles that are among today's most promising vaccine candidates and that are backed up by the consortium's complementary expertise and intellectual property, including SMEs focusing on vaccine development. COMPUVAC recognizes the lack of uniform means for side-by-side qualitative and quantitative vaccine evaluation and will thus standardise the evaluation of vaccine efficacy and safety by using "gold standard" tools, molecular and cellular methods in virology and immunology, and algorithms based on genomic and proteomic information. "Gold standard" algorithms for intelligent interpretation of vaccine efficacy and safety will be built into COMPUVAC's interactive Genetic Vaccine Decision Support System, which should generate:
(i) vector classification according to induced immune response quality, accounting for gender and age
(ii) vector combination counsel for prime-boost immunisations
(iii) vector safety profile according to genomic analysis.

Since one of our "gold standard" antigens is the West Nile virus (WNV) envelope protein, an additional aim of COMPUVAC is to generate a candidate vaccine against WNV. As end products, our vector platform and "gold standard" tools, methods and algorithms will be available to the scientific and industrial communities as a toolbox and interactive database which standardised nature should contribute to cost-effective development of novel vaccines with validated efficacy and safety profile

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Bioinformatics Optimisation Training

Period: 2005-2009

Completion of the sequencing of the entire human genome and other major technological advances in bioinformatics have opened up a huge range of scientific challenges that will need to be addressed in order to maintain Europe's scientific and commercial competitiveness and effectiveness in this emerging area of healthcare. An FP6 Network of Excellence, BIOPATTERN, has been established to integrate leading institutes around Europe to form a virtual institute for the study of individualised healthcare. The overall grand vision of BIOPATTERN is to integrate the analysis of the nano level bioinformatic data with micro level biosignal data and macro level patient information data in a pan-European cooperative research effort to combat major disease classes. Selected members of BIOPATTERN (University of Nottingham, UK (UoN), University of Florence, Italy (UoF), Katholieke Universiteit Leuven, Belgium (KUL), University College of Borås, Sweden (UCB) and Poznan University of Technology, Poland (PUT) ) will form the core of the BIOPTRAIN EST, the aim of which is to establish a complementary wide-ranging training programme of world-class quality in bioinformatic optimisation algorithms. There are two crucial groupsof beneficiaries:
(i) the next generation of European scientists must be trained to take advantage of the latest advances in bioinformatics with an aim of creating a vibrant, future-proof and self-sustaining research effort;
(ii) benefits from bioinformatics advances worldwide must be targeted to the European citizen ? we cannot dependon research communities based in the USA and elsewhere to meet the specific needs of European healthcare.

More information in Fact Sheet.
Environmental - and Meta-Genomics - a bioinformatic system to detect and assign functions to habitat specific gene patterns

Period: 2005-2008

The METAFUNCTIONS project, funded within the European Commission’s FP6 NEST Adventure programme, has pooled expertise in bioinformatics, computer science, geographical information systems and marine sciences and has developed a data-mining system that correlates genetic patterns in marine genomes and metagenomes with contextual environmental data.

This innovative system provides scientists with hints towards the functions of hypothetical genes. Such insight provides a wealth of information pertaining to niche adaptations, as well as substances with potential medical and industrial use.

The project partner, Poznan University of Technology (PUT), has developed an innovative and unique text mining pipeline called Poseidon. Thousands of accessible scientific publications are regularly screened for relevant information. The analysis includes text classification and information retrieval and extraction. A variety of natural language processing algorithms are applied to extract relevant information from texts to collate and store marine metagenomics data in the MetaStorage database.
Sequences and 3D-structures of nucleic acids and proteins - analysis and algorithms

Polish Title: Pierwszorzędowa i przestrzenna struktura kwasów nukleinowych i białek - analiza i algorytmy

Period: 2008-2011
Identifier: N N519 314635

Computational aspects of biomolecule structure analysis

Polish Title: Informatyczne aspekty analizy strukturalnej biomolekuł
Period: 2004-2007
Identifier: 3T11F00227

Algorithms for an analysis of primary and tertiary structure of proteins and nucleic acids

Polish Title: Algorytmy wspomagające analizę liniowej i przestrzennej struktury kwasów nukleinowych i białek

Period: 2001-2003
Identifier: 7T11F02621

Combinatorial aspects of computational biology

Polish Title: Kombinatoryczne aspekty biologii obliczeniowej

Period: 1998-2000
Identifier: 8T11F01815