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136 results on '"Mackiewicz, Dorota"'

3. The Properties of the Standard Genetic Code and Its Selected Alternatives in Terms of the Optimal Graph Partition

Author

Aloqalaa, Daniyah A., Kowalski, Dariusz R., Błażej, Paweł, Wnȩtrzak, Małgorzata, Mackiewicz, Dorota, Mackiewicz, Paweł, Filipe, Joaquim, Editorial Board Member, Ghosh, Ashish, Editorial Board Member, Kotenko, Igor, Editorial Board Member, Prates, Raquel Oliveira, Editorial Board Member, Zhou, Lizhu, Editorial Board Member, Roque, Ana, editor, Tomczyk, Arkadiusz, editor, De Maria, Elisabetta, editor, Putze, Felix, editor, Moucek, Roman, editor, Fred, Ana, editor, and Gamboa, Hugo, editor

Published
2020
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4. Genome analyses and modelling the relationship between coding density, recombination rate and chromosome length

Author

Mackiewicz, Dorota, Zawierta, Marta, Waga, Wojciech, and Cebrat, Stanislaw

Subjects
Quantitative Biology - Populations and Evolution
Abstract

In the human genomes, recombination frequency between homologous chromosomes during meiosis is highly correlated with their physical length while it differs significantly when their coding density is considered. Furthermore, it has been observed that the recombination events are distributed unevenly along the chromosomes. We have found that many of such recombination properties can be predicted by computer simulations of population evolution based on the Monte Carlo methods. For example, these simulations have shown that the probability of acceptance of the recombination events by selection is higher at the ends of chromosomes and lower in their middle parts. The regions of high coding density are more prone to enter the strategy of haplotype complementation and to form clusters of genes which are "recombination deserts". The phenomenon of switching in-between the purifying selection and haplotype complementation has a phase transition character, and many relations between the effective population size, coding density, chromosome size and recombination frequency are those of the power law type., Comment: 26 pages, 7 figures

Published
2010

5. To Understand Nature - Computer Modelling between Genetics and Evolution

Author

Mackiewicz, Dorota and Cebrat, Stanislaw

Subjects
Quantitative Biology - Genomics, Quantitative Biology - Populations and Evolution
Abstract

We have presented the basic knowledge on the structure of molecules coding the genetic information, mechanisms of transfer of this information from DNA to proteins and phenomena connected with replication of DNA. In particular, we have described the differences of mutational pressure connected with replication of the leading and lagging DNA strands. We have shown how the asymmetric replication of DNA affects the structure of genomes, positions of genes, their function and amino acid composition. Results of Monte Carlo simulations of evolution of protein coding sequences have shown a specific role of genetic code in minimizing the effect of nucleotide substitutions on the amino acid composition of proteins. The results of simulations were compared with the results of analyses of genomic and proteomic data bases. This chapter is considered as an introduction to further chapters where chromosomes with genes represented by nucleotide sequences were replaced by bitstrings with single bits representing genes., Comment: 32 pages, 19 figures

Published
2009

6. Phase Transition in Sexual Reproduction and Biological Evolution

Author

Zawierta, Marta, Waga, Wojciech, Mackiewicz, Dorota, Biecek, Przemyslaw, and Cebrat, Stanislaw

Subjects
Quantitative Biology - Populations and Evolution
Abstract

Using Monte Carlo model of biological evolution we have discovered that populations can switch between two different strategies of their genomes' evolution; Darwinian purifying selection and complementing the haplotypes. The first one is exploited in the large panmictic populations while the second one in the small highly inbred populations. The choice depends on the crossover frequency. There is a power law relation between the critical value of crossover frequency and the size of panmictic population. Under the constant inbreeding this critical value of crossover does not depend on the population size and has a character of phase transition. Close to this value sympatric speciation is observed., Comment: 13 pages, 8 figures

Published
2008
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10. Optimisation of Asymmetric Mutational Pressure and Selection Pressure Around the Universal Genetic Code

Author

Mackiewicz, Paweł, Biecek, Przemysław, Mackiewicz, Dorota, Kiraga, Joanna, Baczkowski, Krystian, Sobczynski, Maciej, Cebrat, Stanisław, Hutchison, editor, Kanade, editor, Kittler, editor, Kleinberg, editor, Mattern, editor, Mitchell, editor, Naor, editor, Nierstrasz, editor, Pandu Rangan, editor, Steffen, editor, Sudan, editor, Terzopoulos, editor, Tygar, editor, Vardi, editor, Weikum, editor, Bubak, Marian, editor, van Albada, Geert Dick, editor, Dongarra, Jack, editor, and Sloot, Peter M. A., editor

Published
2008
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12. Differential Gene Survival under Asymmetric Directional Mutational Pressure

Author

Mackiewicz, Paweł, Dudkiewicz, Małgorzata, Kowalczuk, Maria, Mackiewicz, Dorota, Banaszak, Joanna, Polak, Natalia, Smolarczyk, Kamila, Nowicka, Aleksandra, Dudek, Mirosław R., Cebrat, Stanisław, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Bubak, Marian, editor, van Albada, Geert Dick, editor, Sloot, Peter M. A., editor, and Dongarra, Jack, editor

Published
2004
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13. How Gene Survival Depends on Their Length

Author

Polak, Natalia, Banaszak, Joanna, Mackiewicz, Paweł, Dudkiewicz, Małgorzata, Kowalczuk, Maria, Mackiewicz, Dorota, Smolarczyk, Kamila, Nowicka, Aleksandra, Dudek, Mirosław R., Cebrat, Stanisław, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Bubak, Marian, editor, van Albada, Geert Dick, editor, Sloot, Peter M. A., editor, and Dongarra, Jack, editor

Published
2004
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14. Correlation between Mutation Pressure, Selection Pressure, and Occurrence of Amino Acids

Author

Nowicka, Aleksandra, Mackiewicz, Pawel, Dudkiewicz, Małgorzata, Mackiewicz, Dorota, Kowalczuk, Maria, Cebrat, Stanisław, Dudek, Mirosław R., Goos, G., editor, Hartmanis, J., editor, van Leeuwen, J., editor, Sloot, Peter M. A., editor, Abramson, David, editor, Bogdanov, Alexander V., editor, Gorbachev, Yuriy E., editor, Dongarra, Jack J., editor, and Zomaya, Albert Y., editor

Published
2003
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15. Properties of the Genetic Code under Directional, Asymmetric Mutational Pressure

Author

Dudkiewicz, Małgorzata, Mackiewicz, Pawełl, Nowicka, Aleksandra, Kowalczuk, Maria, Mackiewicz, Dorota, Polak, Natalia, Smolarczyk, Kamila, Dudek, Mirosław R., Cebrat, Stanisław, Goos, G., editor, Hartmanis, J., editor, van Leeuwen, J., editor, Sloot, Peter M. A., editor, Abramson, David, editor, Bogdanov, Alexander V., editor, Dongarra, Jack J., editor, Zomaya, Albert Y., editor, and Gorbachev, Yuriy E., editor

Published
2003
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29. How Gene Survival Depends on Their Length

Author

Polak, Natalia, primary, Banaszak, Joanna, additional, Mackiewicz, Paweł, additional, Dudkiewicz, Małgorzata, additional, Kowalczuk, Maria, additional, Mackiewicz, Dorota, additional, Smolarczyk, Kamila, additional, Nowicka, Aleksandra, additional, Dudek, Mirosław R., additional, and Cebrat, Stanisław, additional

Published
2004
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37. High correlation between the turnover of nucleotides under mutational pressure and the DNA composition

Author

Dudkiewicz Malgorzata, Nowicka Aleksandra, Mackiewicz Dorota, Mackiewicz Pawel, Kowalczuk Maria, Dudek Miroslaw R, and Cebrat Stanislaw

Subjects
Evolution, QH359-425
Abstract

Abstract Background Any DNA sequence is a result of compromise between the selection and mutation pressures exerted on it during evolution. It is difficult to estimate the relative influence of each of these pressures on the rate of accumulation of substitutions. However, it is important to discriminate between the effect of mutations, and the effect of selection, when studying the phylogenic relations between taxa. Results We have tested in computer simulations, and analytically, the available substitution matrices for many genomes, and we have found that DNA strands in equilibrium under mutational pressure have unique feature: the fraction of each type of nucleotide is linearly dependent on the time needed for substitution of half of nucleotides of a given type, with a correlation coefficient close to 1. Substitution matrices found for sequences under selection pressure do not have this property. A substitution matrix for the leading strand of the Borrelia burgdorferi genome, having reached equilibrium in computer simulation, gives a DNA sequence with nucleotide composition and asymmetry corresponding precisely to the third positions in codons of protein coding genes located on the leading strand. Conclusions Parameters of mutational pressure allow us to count DNA composition in equilibrium with this mutational pressure. Comparing any real DNA sequence with the sequence in equilibrium it is possible to estimate the distance between these sequences, which could be used as a measure of the selection pressure. Furthermore, the parameters of the mutational pressure enable direct estimation of the relative mutation rates in any DNA sequence in the studied genome.

Published
2001
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44. Current Topics in Genetics 2005 1 pp. 87-101

Author

Kowalczuk, Maria, Mackiewicz, Dorota, Mackiewicz, Paweł, Polak, Natalia, Smolarczyk, Kamila, Kiraga, Joanna, Dudek, Mirosław R., and Cebrat, Stanisław

Abstract

Paweł Mackiewicz

Published
2005

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