Wyniki wyszukiwania - Biblioteka Nauki

1

System wspomagania wytwarzania i analiz szczepionek genetycznych

100%

Błażewicz J. , Łukasiak P.

Kosmos

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2009

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tom 58

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nr 1-2

113-125

EN

Genetic vaccines and especially recombinant viral vectors and virus-like particles are considered the most promising vehicles for delivery of antigens in prophylactic and therapeutic vaccines against infectious diseases and cancer. Several potential vaccine design systems exist but their cost-effective development cruelly lacks a standardized evaluation system. Solving the problem Genetic Vaccine Decision Support system (GeVaDSs, http://www.compuvac.org) has been implemented as a part of CompuVac project realized within 6th Framework Program of European Commission. Using GeVaDSs we have successfully developed and standardized methods for evaluation of the efficacy and safety of individual vaccine vectors, in a manner that allows comparison between different vaccine designs, tested in different laboratories, at different time points. With these methods, the efficacy of a unique set of vaccines has been analyzed and compared with an intelligent database. GeVaDSs has allowed to make significant comparisons between different types of vaccines and to initiate novel vaccine design and vaccination regimens. Besides monitoring of T- and B-cell immune responses, GeVaDSs is also aimed at monitoring vaccine "efficacy" and "safety" profiles by analyzing relevant molecular signatures obtained from transcriptomes studies. The "efficacy" and the "safety profile" have been validated, based on analyzing molecular signatures from whole liver and spleen after injection of vaccine vectors. The results of these experiments will drive the development of HCV vaccines. The first HCV vectors generated in single immunization regimen were tested, and interesting results obtained suggest the great potential for the association of our two classes of vectors, viral and VLP derived.

2

Some remarks on evaluating the quality of the multiple sequence alignment based on the BALiBASE benchmark

80%

Błażewicz J. , Formanowicz P. , Wojciechowski P.

International Journal of Applied Mathematics and Computer Science

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2009

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tom 19

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nr 4

675-678

EN

BAliBASE is one of the most widely used benchmarks for multiple sequence alignment programs. The accuracy of alignment methods is measured by bali score-an application provided together with the database. The standard accuracy measures are the Sum of Pairs (SP) and the Total Column (TC). We have found that, for non-core block columns, results calculated by bali score are different from those obtained on the basis of the formal definitions of the measures. We do not claim that one of these measures is better than the other, but they are definitely different. Such a situation can be the source of confusion when alignments obtained using various methods are compared. Therefore, we propose a new nomenclature for the measures of the quality of multiple sequence alignments to distinguish which one was actually calculated. Moreover, we have found that the occurrence of a gap in some column in the first sequence of the reference alignment causes column discarding.

3

Zastosowanie sieci petriego do modelowania procesów biologicznych

80%

Błażewicz J. , Formanowicz D. , Formanowicz P.

Kosmos

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2009

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tom 58

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nr 1-2

79-88

EN

Rapid growth of the amount of available biological data made it clear that an analysis of complex biological processes can be made only with the support of mathematics and computer sciences. It is especially important nowadays when the systems biology approach is becoming more and more widely used in biological science. This new way of investigation of biological phenomena allows, at least in principle, to observe complex relationships between different parts of the analyzed system. These interactions may be crucial for the system's nature and behavior, so observing them may lead to important biological discoveries. Probably the most important part of this process consists in building of a formal model of the biological process. One of the promising methods of such an analysis is based on the theory of Petri nets. Models expressed in the language of this theory are very precise on the one hand, and on the other, they are intuitive, which makes their analysis easier in comparison, for example, to models based on ordinary differential equations. In this paper, a brief introduction to the theory of Petri nets is given and its applications for modeling of some exemplary biological processes are shortly discussed. Moreover, some extensions of the classical Petri nets and their biological applications are also presented.

4

Internet shopping optimization problem

70%

Błażewicz J. , Kovalyov M. , Musiał J. , Urbański A. , Wojciechowski A.

International Journal of Applied Mathematics and Computer Science

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2010

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tom 20

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nr 2

385-390

EN

A high number of Internet shops makes it difficult for a customer to review manually all the available offers and select optimal outlets for shopping. A partial solution to the problem is brought by price comparators which produce price rankings from collected offers. However, their possibilities are limited to a comparison of offers for a single product requested by the customer. The issue we investigate in this paper is a multiple-item multiple-shop optimization problem, in which total expenses of a customer to buy a given set of items should be minimized over all available offers. In this paper, the Internet Shopping Optimization Problem (ISOP) is defined in a formal way and a proof of its strong NP-hardness is provided. We also describe polynomial time algorithms for special cases of the problem.

5

New machine learning methods for prediction of protein secondary structures

60%

Błażewicz J. , Łukasik P. , Wilk S.

Control and Cybernetics

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2007

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tom 36

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nr 1

183-201

6

Assembling the SARS-CoV genome - new method based on graph theoretical approach.

51%

Błażewicz J. , Figlerowicz M. , Formanowicz P. , Kasprzak M. , Nowierski B. , Styszyński R. , Szajkowski Ł. , Widera P. , Wiktorczyk M.

Acta Biochimica Polonica

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2004

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tom 51

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nr 4

983-993

EN

Nowadays, scientists may learn a lot about the organisms studied just by analyzing their genetic material. This requires the development of methods of reading genomes with high accuracy. It has become clear that the knowledge of the changes occuring within a viral genome is indispensable for effective fighting of the pathogen. A good example is SARS-CoV, which was a cause of death of many people and frightened the entire world with its fast and hard to prevent propagation. Rapid development of sequencing methods, like shotgun sequencing or sequencing by hybridization (SBH), gives scientists a good tool for reading genomes. However, since sequencing methods can read fragments of up to 1000 bp only, methods for sequence assembling are required in order to read whole genomes. In this paper a new assembling method, based on graph theoretical approach, is presented. The method was tested on SARS-CoV and the results were compared to the outcome of other widely known methods.