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1

Factors Influencing Essential Hypertension and Cardiovascular Disease Modeled and Analyzed using Stochastic Petri Nets

Formanowicz D., Rybarczyk A., Formanowicz P.

Fundamenta Informaticae

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2018

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Vol. 160, nr 1/2

143--165

EN

Essential hypertension is the world’s most prevalent cardiovascular disorder, however, its etiology remains poorly understood, making it difficult to study. The evidence suggests that inflammation can lead to the development of hypertension and that oxidative stress and endothelial dysfunction are involved in the inflammatory cascade. In this work, to investigate the influence of these factors on the essential hypertension development, a stochastic Petri net model has been built and then analyzed. To obtain appropriate initial marking and kinetic rate constants for the model, a simple heuristic has been developed. The application of this variant of Petri nets allowed for taking into account some important dependencies present in the modeled system what would be impossible in the case of qualitative models. This has enabled for an in-depth analysis of the studied phenomenon and a validation of biological conclusions previously obtained on the basis of a qualitative model.

2

Computational Aspects of DNA Sequencing by Hybridization : a Survey

Kwarciak K., Radom M., Formanowicz P.

Computational Methods in Science and Technology

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2018

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Vol. 24, No. 4

259--271

EN

Sequencing by hybridization (SBH) is a method of reading DNA sequence from its smaller fragments. Such a method has been proposed in late 1980s and until the emergence of the new generation sequencing it has been widely used and improved. Since the initial, classical approach to SBH, many modifications and enhancements was proposed, aimed at improving the preciseness and the length of sequences which can be unambiguously read. Even now, for some DNA sequences sequencing by hybridization can still be used effectively and at a low cost. In this paper many different approaches to the SBH will be described, mainly from the points of view of algorithms and computational complexity.

3

Some aspects of modeling and analysis of complex biological systems using time Petri nets

Olszak J., Radom M., Formanowicz P.

Bulletin of the Polish Academy of Sciences. Technical Sciences

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2018

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Vol. 66, nr 1

67--78

EN

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.

4

The study of the influence of micro-environmental signals on macrophage differentiation using a quantitative Petri net based model

Rżosińska K., Formanowicz D., Formanowicz P.

Archives of Control Sciences

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2017

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Vol. 27, no. 2

331--349

EN

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.

5

The effect of cigarette smoking on endothelial damage and atherosclerosis development – modeled and analyzed using Petri nets

Chmielewska K., Formanowicz D., Formanowicz P.

Archives of Control Sciences

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2017

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Vol. 27, no. 2

211--228

EN

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.

6

The Fan-Raspaud conjecture: A randomized algorithmic approach and application to the pair assignment problem in cubic networks

Formanowicz P., Tanaś K.

International Journal of Applied Mathematics and Computer Science

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2012

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Vol. 22, no. 3

765-778

EN

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.

7

A survey of graph coloring : its types, methods and applications

Formanowicz P., Tanaś K.

Foundations of Computing and Decision Sciences

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2012

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Vol. 37, No. 3

223--238

EN

Graph coloring is one of the best known, popular and extensively researched subject in the field of graph theory, having many applications and conjectures, which are still open and studied by various mathematicians and computer scientists along the world. In this paper we present a survey of graph coloring as an important subfield of graph theory, describing various methods of the coloring, and a list of problems and conjectures associated with them. Lastly, we turn our attention to cubic graphs, a class of graphs, which has been found to be very interesting to study and color. A brief review of graph coloring methods (in Polish) was given by Kubale and a more detailed one in a book by the same author. We extend this review and explore the field of graph coloring further, describing various results obtained by other authors and show some interesting applications of this field of graph theory.

8

A Petri net based model of oxidative stress in atherosclerosis

Formanowicz D., Kozak A., Formanowicz P.

Foundations of Computing and Decision Sciences

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2012

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Vol. 37, No. 2

59--78

EN

In this paper a Petri net based model of the process of oxidative stress in atherosclerosis is presented and analyzed. Model expressed in the language of Petri net theory have, on one hand, an intuitive graphical representation, and on the other hand their formal properties can be analyzed using rigorous mathematical methods. Moreover, the behavior of a net can be simulated what supports the process of model development and an interpretation of the results of the analysis. Both the analysis and the simulation can be supported by many freely available software tools. In the case of biological systems an analysis the t-invariants is especially important since they correspond to some elementary biological subprocesses. In this paper the results of such an analysis are presented. In particular, minimal t-invariants, MCT-sets and t-clusters are calculated, their biological meaning is determined and some biological conclusions are drawn.

9

A greedy algorithm for the DNA sequencing by hybridization with positive and negative errors and information about repetitions

Kwarciak K., Formanowicz P.

Bulletin of the Polish Academy of Sciences. Technical Sciences

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2011

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Vol. 59, nr 1

111-115

EN

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.

10

Algorytmy dla problemów sekwencjonowania przez hybrydyzację opartych o nieklasyczne chipy DNA

Radom M., Formanowicz P.

Przegląd Elektrotechniczny

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2010

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R. 86, nr 9

97-100

PL

W niniejszym artykule przedstawione zostaną algorytmy dla problemów sekwencjonowania przez hybrydyzację opartych o dwa nieklasyczne chipy DNA. Opisane zostaną zasady kontrukcji rozpatrywanych chipów oraz sposób działania algorytmów rozwiązujących problem SBH z ich pomocą. Przedstawione zostaną także wyniki eksperymentów obliczeniowych, w których testowane będą omawiane algorytmy oraz algorytm klasyczny.

EN

In this paper algorithms for sequencing by hybridization problems based on two non-classical DNA chips are presented. The idea of these chips is briefly described and the algorithms are presented and analyzed in detail. Also the results of an extensive experiment are showed and commented.

11

Cerberus: A New Information Retrieval Tool for Marine Metagenomics

Radom M., Kottmann R., Rybarczyk A., Formanowicz P., Szachniuk M., Glöckner F. O., Błażewicz J.

Foundations of Computing and Decision Sciences

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2010

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Vol. 35, No. 2

107-126

EN

The number of papers published every year in scientific journals is growing tremendously, especially in biological sciences. Keeping the track of a given branch of science is therefore a difficult task. This was one of the reasons for developing the classification tool we called Cerberus. The classification categories may correspond to some areas of research defined by the user. We have used the tool to classify papers as containing marine metagenomic, terrestrial metagenomic or non-metagenomic information. Cerberus is based on special filters using weighted domain vocabularies. Depending on the number of occurrences of the keywords from the vocabularies in the paper, the program classifies the paper to a predefined category. This classification can precede the information extraction since it can reduce the number of papers to be analyzed. Classification of papers using the method we propose results in an accurate and precise result set of articles that are relevant to the scientist. This can reduce the resources needed to find the data required in ones field of studies.

12

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

Błażewicz J., Formanowicz P., Wojciechowski P.

International Journal of Applied Mathematics and Computer Science

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2009

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Vol. 19, no 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.

13

Sekwencjonowanie DNA z błędami negatywnymi oraz informacją o powtórzeniach

Kwarciak K., Radom M., Formanowicz P.

Zeszyty Naukowe. Automatyka / Politechnika Śląska

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2008

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z. 151

215-222

PL

W pracy przedstawiony jest algorytm typu podziału i ograniczeń dla problemu sekwencjonowania przez hybrydyzację z błędami negatywnymi oraz częściową informacją o powtórzeniach. Uwzględnienie tego rodzaju informacji możliwe jest ze względu na rozwój technologii stosowanej w eksperymencie hybrydyzacyjnym. Prowadzi ono do rozszerzenia standardowej wersji metody sekwencjonowania przez hybrydyzację oraz do polepszenia jakości uzyskiwanych rozwiązań.

EN

In this paper a branch and bound algorithm for sequencing by hybridization problem with negative errors and partial information about repetitions is presented. Taking into account information of this type is possible because of the development of the technology used in the hybridization experiment. It leads to an extension of the standard sequencing by hybridization method and to an improvement of the quality of the obtained results.

14

Grafy bazowo-etykietowalne jako jednolita reprezentacja grafów sprzężonych

Kozak A., Głowacki T., Formanowicz P.

Zeszyty Naukowe. Automatyka / Politechnika Śląska

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2008

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z. 151

209-214

PL

Praca stanowi wprowadzenie do klasy grafów (α, κ, σ) -bazowo-etykietowalnych, które przedstawiają ujednoliconą reprezentację matematyczną grafów (α, κ)-etykietowalnych oraz (α, κ)- dowolnie-etykietowalnych (które są równoważne klasie grafów sprzężonych [1]). Omówione są podstawowe zależności między tymi klasami, zależności między parametrami κ i σ oraz znaczenie tych klas dla kombinatoryki wraz z praktycznymi przykładami zastosowań w bio-informatyce.

EN

This work introduces a class of (α, κ, σ) -base-labeled graphs that presents unified mathematical representation of (α, κ)-labeled and (α, κ) free-labeled graphs (that are equivalent to adjoints [1]). It describes basic relationships between these classes, relationship between parameters κ and σ - and the meaning of these classes for computing science. There are also some practical examples of application in bioinformatics.

15

Asemblacja długich łańcuchów peptydowych przy wykorzystaniu metaheurystyki GRASP

Głowacki T., Kozak A., Formanowicz P.

Zeszyty Naukowe. Automatyka / Politechnika Śląska

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2008

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z. 151

203-208

PL

Ustalenie kolejności aminokwasów w cząsteczce białka nosi nazwę sekwencjonowania. Brak bezpośrednich metod sekwencjonowania długich peptydów powoduje, że potrzebne są dedykowane metody asemblacyjne, które odpowiednio poskładają krótkie łańcuchy w jeden długi łańcuch aminokwasów. W pracy tej został zaproponowany algorytm asemblacyjny typu GRASP. Przedstawiony algorytm został zaimplementowany i przetestowany dla zbioru rzeczywistych peptydów, a uzyskane rozwiązanie zostało przedyskutowane.

EN

Determining an order of amino acids in peptide structure is called sequencing method. Lack of direct sequencing methods for long peptides causes that assembling methods to combine many short peptides into one long structure are necessary. In this paper assembling algorithm based on GRASP method was proposed. The algorithm was implemented and tested on real peptides set and the obtained results was discussed.

16

Problemy izotermicznego sekwencjonowania przez hybrydyzację z informacją o powtórzeniach

Formanowicz P.

Przegląd Elektrotechniczny

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2008

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R. 84, nr 9

103-107

PL

W pracy przedstawiono formalne definicje różnych wariantów problemu izotermicznego sekwencjonowania przez hybrydyzację z dodatkową informacją o powtórzeniach. W większośći przypadków podano złożoność obliczeniową oraz sformuowano odpowiedniki grafowe rozważanych problemów.

EN

In the paper formal definitions of many variants of the isotherimc sequencing by hybridization problem with additional information about repetitions are presented. For most of the problems their computational complexity is determined and graph theoretical counterparts are also formulated.

17

On graph theoretical models for peptide sequence assembly

Błażewicz J., Borowski M., Formanowicz P., Głowacki T.

Foundations of Computing and Decision Sciences

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2005

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Vol. 30, No. 3

183-191

EN

The amino acid sequences of proteins determine their structure and functionality, hence methods for reading such sequences are crucial for many areas of biological sciences. Obviously, the genetic information encoding proteins is written in DNA however, knowing gene sequences is not always sufficient for determining the corresponding amino acid sequences. Since direct methods for reading amino acid seqeunces allow for determination of only very short fragments, some methods for assembly of these fragments are required. In this paper, we show and analyze some graph theoretic models of the peptide sequence assembly process.

18

DNA sequencing by hybridization with additional information available

Formanowicz P.

Computational Methods in Science and Technology

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2005

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Vol. 11, nr 1

21-29

EN

In classical DNA sequencing by hybridization it is assumed that the information obtained in the biochemical stage of the method is a set of the l-tuples composing the target sequence. It means that the information concerning the number of the repeated l-tuples is not available. Such an assumption was justified by the DNA chip technology constraints. However, nowadays some approximate information about l-tuple multiplicities can be obtained in the experiments, where DNA chips are used. It was a motivation for formulating combinatorial problems which arise when such additional information is taken into account. The goal of this paper is to formulate and classify these problems, what should establish a good starting point for further research concerning algorithmic methods solving DNA sequencing problems with multiplicity information. Moreover, the computational complexity of the new problems is determined, which in most cases is analogous to the complexity of their classical counterparts.

19

DNA computing

Formanowicz P.

Computational Methods in Science and Technology

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2005

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Vol. 11, nr 1

11-20

EN

DNA computing is an alternative method of performing computations. It is based on the observation that in general it is possible to design a series of biochemical experiments involving DNA molecules which is equivalent to processing information encoded in these molecules. In classical computing devices electronic logic gates are elements which allow for storing and transforming information. Designing of an appropriate sequence or a net of “store” and “transform” operations (in a sense of building a device or writing a program) is equivalent to preparing some computations. In DNA computing the situation is analogous. The main difference is the type of computing devices, since in this new method of computing instead of electronic gates DNA molecules are used for storing and transforming information. From this follows that the set of basic operations is different in comparison to electronic devices but the results of using them may be similar. Moreover, the inherent massive parallelism of DNA computing may lead to methods solving some intractable computational problems. In this paper basic principles of DNA computing are described and examples of DNA based algorithms solving some combinatorial problems are presented.

20

Computational methods in diagnostics of chronic hepatitis C

Kędziora P., Figlerowicz M., Formanowicz P., Alejska M., Jackowiak P., Malinowska N., Frątczak A., Błażewicz J.

Bulletin of the Polish Academy of Sciences. Technical Sciences

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2005

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Vol. 53, nr 3

273-281

EN

Despite the considerable progress that has recently been made in medicine, the treatment of viral infections is still a problem remaining to be solved. This especially concerns infections caused by newly emerging patogenes such as: human immunodeficiency virus, hepatitis C virus or SARS-coronavirus. There are several lines of evidence that the unusual genetic polymorphism of these viruses is responsible for the observed therapeutic difficulties. In order to determine whether some parameters describing a very complex and variable viral population can be used as prognostic factors during antiviral treatment computational methods were applied. To this end, the structure of the viral population and virus evolution in the organisms of two patients suffering from chronic hepatitis C were analyzed. Here we demonstrated that phylogenetic trees and Hamming distances best reflect the differences between virus populations present in the organisms of patients who responded positively and negatively to the applied therapy. Interestingly, the obtained results suggest that based on the elaborated method df virus population analysis one can predict the final outcome of the treatment even before it has started.