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    Wyświetlanie 1-9 z 9
    Tytuł:
    On the border between biology, mathematics and computer science
    Autorzy:
    Formanowicz, P.
    Powiązania:
    https://bibliotekanauki.pl/articles/80778.pdf
    Data publikacji:
    2011
    Wydawca:
    Polska Akademia Nauk. Czytelnia Czasopism PAN
    Tematy:
    mathematics
    computer science
    biology
    computational biology
    bioinformatics
    algorithm
    biological process
    biological structure
    biological discovery
    genetic code
    genome
    protein 3D structure
    genetic information
    Źródło:
    BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology; 2011, 92, 3
    0860-7796
    Pojawia się w:
    BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    An overall view of the process of the regulation of human iron metabolism
    Autorzy:
    Formanowicz, D.
    Formanowicz, P.
    Powiązania:
    https://bibliotekanauki.pl/articles/79993.pdf
    Data publikacji:
    2011
    Wydawca:
    Polska Akademia Nauk. Czytelnia Czasopism PAN
    Tematy:
    absorption
    gastrointestinal tract
    enterocyte
    erythropoietin
    ferroportin
    ferrous ion
    hepcidin
    homeostasis
    iron
    iron metabolism
    oxygen radical
    stomach
    transferrin
    transportation
    Źródło:
    BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology; 2011, 92, 2
    0860-7796
    Pojawia się w:
    BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    The Fan-Raspaud conjecture: A randomized algorithmic approach and application to the pair assignment problem in cubic networks
    Autorzy:
    Formanowicz, P.
    Tanaś, K.
    Powiązania:
    https://bibliotekanauki.pl/articles/331003.pdf
    Data publikacji:
    2012
    Wydawca:
    Uniwersytet Zielonogórski. Oficyna Wydawnicza
    Tematy:
    graf sześcienny
    kolorowanie krawędzi
    skojarzenie doskonałe
    algorytm zrandomizowany
    sieć komputerowa
    cubic graph
    edge colouring
    perfect matching
    randomized algorithms
    computer networks
    Opis:
    It was conjectured by Fan and Raspaud (1994) that every bridgeless cubic graph contains three perfect matchings such that every edge belongs to at most two of them. We show a randomized algorithmic way of finding Fan-Raspaud colorings of a given cubic graph and, analyzing the computer results, we try to find and describe the Fan-Raspaud colorings for some selected classes of cubic graphs. The presented algorithms can then be applied to the pair assignment problem in cubic computer networks. Another possible application of the algorithms is that of being a tool for mathematicians working in the field of cubic graph theory, for discovering edge colorings with certain mathematical properties and formulating new conjectures related to the Fan-Raspaud conjecture.
    Źródło:
    International Journal of Applied Mathematics and Computer Science; 2012, 22, 3; 765-778
    1641-876X
    2083-8492
    Pojawia się w:
    International Journal of Applied Mathematics and Computer Science
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    A greedy algorithm for the DNA sequencing by hybridization with positive and negative errors and information about repetitions
    Autorzy:
    Kwarciak, K.
    Formanowicz, P.
    Powiązania:
    https://bibliotekanauki.pl/articles/202322.pdf
    Data publikacji:
    2011
    Wydawca:
    Polska Akademia Nauk. Czytelnia Czasopism PAN
    Tematy:
    DNA sequencing
    l-mer multiplicity
    greedy algorithm
    combinatorial problems
    Opis:
    In this paper a greedy algorithm for some variants of the sequencing by hybridization method is presented. In the standard version of the method information about repetitions is not available. In the paper it is assumed that a partial information of this type is a part of the problem instance. Here two simple but realistic models of this information are taken into consideration. The first one assumes it is known if a given element of a spectrum appears in the target sequence once or more than once. The second model uses the knowledge is a given element of a spectrum occurs in the analyzed sequence once, twice or at least three times. The proposed greedy algorithm solves the variant of the problem with positive and negative errors. Results of a computational experiment are reported which, among others, confirm that the additional information leads to the improvement of the obtained solutions. They also show that the more precise model of information increases the quality of reconstructed sequences.
    Źródło:
    Bulletin of the Polish Academy of Sciences. Technical Sciences; 2011, 59, 1; 111-115
    0239-7528
    Pojawia się w:
    Bulletin of the Polish Academy of Sciences. Technical Sciences
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    The study of the influence of micro-environmental signals on macrophage differentiation using a quantitative Petri net based model
    Autorzy:
    Rżosińska, K.
    Formanowicz, D.
    Formanowicz, P.
    Powiązania:
    https://bibliotekanauki.pl/articles/229319.pdf
    Data publikacji:
    2017
    Wydawca:
    Polska Akademia Nauk. Czytelnia Czasopism PAN
    Tematy:
    Petri nets
    atherosclerosis
    macrophages
    t-invariants
    Opis:
    The complexity of many biological processes, which, thanks to the development of many fields of science, becomes for us more and more obvious, makes these processes extremely interesting for further analysis. In this paper a quantitative model of the process of macrophage differentiation, which is essential for many phenomena occurring in the human body, is proposed and analyzed. The model is expressed in the language of Petri net theory on the basis of one of the three hypotheses concerning macrophage differentiation existing in the literature. The performed analysis allowed to find an importance of individual factors in the studied phenomenon.
    Źródło:
    Archives of Control Sciences; 2017, 27, 2; 331-349
    1230-2384
    Pojawia się w:
    Archives of Control Sciences
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Some remarks on evaluating the quality of the multiple sequence alignment based on the BAliBASE benchmark
    Autorzy:
    Błażewicz, J.
    Formanowicz, P.
    Wojciechowski, P.
    Powiązania:
    https://bibliotekanauki.pl/articles/930013.pdf
    Data publikacji:
    2009
    Wydawca:
    Uniwersytet Zielonogórski. Oficyna Wydawnicza
    Tematy:
    dostosowanie odniesienia
    dokładność ustawienia
    multiple sequence alignment
    reference alignment
    alignment accuracy
    Opis:
    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.
    Źródło:
    International Journal of Applied Mathematics and Computer Science; 2009, 19, 4; 675-678
    1641-876X
    2083-8492
    Pojawia się w:
    International Journal of Applied Mathematics and Computer Science
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Some aspects of modeling and analysis of complex biological systems using time Petri nets
    Autorzy:
    Olszak, J.
    Radom, M.
    Formanowicz, P.
    Powiązania:
    https://bibliotekanauki.pl/articles/199770.pdf
    Data publikacji:
    2018
    Wydawca:
    Polska Akademia Nauk. Czytelnia Czasopism PAN
    Tematy:
    time Petri nets
    t-invariants
    biological system
    system biologiczny
    czasowe sieci Petriego
    inwariant
    Opis:
    Models of complex biological systems can be built using different types of Petri nets. Qualitative nets, for example, can be successfully used to obtain a model of such a system and on its basis a structure-based analysis can be performed. Time is an important factor influencing a whole biological system behaviour and in many cases it should be considered during building a model of such a system. In this paper various types of time Petri nets have been described and methods for studying corresponding models have been discussed. In particular, an algorithm using time parameters to enhance t-invariants based analysis is proposed. This algorithm allows for calculation of the minimal and maximal numbers of tokens (respectively, for an optimistic and pessimistic case) in particular places necessary to assure that all transitions from a given t-invariant support will be able to fire. Additionally, to address the problem of the proper assignment of time values to transitions, the known methods for calculation and evaluation of such time parameters based on the net structure have also been discussed.
    Źródło:
    Bulletin of the Polish Academy of Sciences. Technical Sciences; 2018, 66, 1; 67-78
    0239-7528
    Pojawia się w:
    Bulletin of the Polish Academy of Sciences. Technical Sciences
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Selected aspects of endothelial dysfunction and their influence on the atherosclerosis process modeled and analyzed by Petri net based approach
    Autorzy:
    Formanowicz, D.
    Kozak, A.
    Formanowicz, P.
    Powiązania:
    https://bibliotekanauki.pl/articles/80683.pdf
    Data publikacji:
    2011
    Wydawca:
    Polska Akademia Nauk. Czytelnia Czasopism PAN
    Tematy:
    endothelial dysfunction
    biological system
    modelling
    atherosclerosis
    Petri net based model
    immunological response
    vasodilation
    smooth muscle cell
    oxidative stress
    hypercholesterolemia
    Źródło:
    BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology; 2011, 92, 4
    0860-7796
    Pojawia się w:
    BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    The effect of cigarette smoking on endothelial damage and atherosclerosis development – modeled and analyzed using Petri nets
    Autorzy:
    Chmielewska, K.
    Formanowicz, D.
    Formanowicz, P.
    Powiązania:
    https://bibliotekanauki.pl/articles/229838.pdf
    Data publikacji:
    2017
    Wydawca:
    Polska Akademia Nauk. Czytelnia Czasopism PAN
    Tematy:
    atherosclerosis
    endothelial dysfunction
    cigarette smoking
    modeling
    Petri nets
    t-invariants
    Opis:
    Atherosclerosis as one of the crucial causes of cardiovascular diseases (CVD) is the leading reason of death worldwide. One of the contributing factors to this phenomenon is endothelial dysfunction, which is associated with the impact of various agents and their interactions. Tobacco smoke is one of the well known factors here. For better understanding of its significance a model of its impact on atherosclerotic plaque formation has been proposed. The model contains selected aspects of the influence of tobacco smoke, dual function of nitric oxide (NO) (influence of various mechanisms on NO bioavailability), oxidative stress which promotes low density lipoproteins oxidation, macrophages significance and other mechanisms leading to an aggravation of the endothelial disturbances. The model has been built using Petri nets theory and the analysis has been based on t-invariants. This approach allowed to confirm the important role of inflammation and oxidative stress in atherosclerosis development and moreover it has shown the considerable influence of the cigarette smoke.
    Źródło:
    Archives of Control Sciences; 2017, 27, 2; 211-228
    1230-2384
    Pojawia się w:
    Archives of Control Sciences
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
      Wyświetlanie 1-9 z 9

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