1. Scientific activity - Our last papers: DNA Analysis and Population Dynamics
5. Free time?
| Scientific activity: |
Formerly I worked on genetics of bacterial plasmids, especially I was
interested in some properties of plasmid aggregates.
For the last four years I have been working on stochastic analysis
of DNA coding properties. I am cooperating with Dr Miroslaw R. Dudek from
the Institute of Physics at Zielona Gora Pedagogical University
(mdudek@proton.if.wsp.zgora.pl) , with Agnieszka
Gierlik, Maria Kowalczuk, Pawel Mackiewicz, Ola Nowicka and Dorota Szczepanik-
graduate students in the Department of Genetics and with five other students:
Asia Borkowska, Malgosia Dudkiewicz, Dorota Cieslakiewicz, Ela Stojek,
and Hania Wroblewska. Asia Borkowska and Dorota Cieslakiewicz graduated
in June 1999.
I am also dealing with population dynamics. In this field I am cooperating
with Prof. Dietrich Stauffer from the Institute of Theoretical Physics
in Cologne, Germany and with Prof. Andrzej Pekalski from the Institute
of Theoretical Physics Wroclaw University.
| Our last papers: |
1. S. Cebrat, M.R. Dudek: 1996, Generation of overlapping reading frames. Trends in Genetics, 12, 12.
2. S. Cebrat. M.R. Dudek: 1996, Symmetry in chromosome fractal organization and DNA domain structure. Proceedings of the 8th Joint EPS-APS Int. Conference on Physics Computing ‘96, eds. P. Borchards, M. Bubak, A. Maksymowicz (Academic Computer Center, CYFRONET-KRAKÓW), 371 -374.
3. S. Cebrat, M.R. Dudek, A. Rogowska: 1997, Asymmetry in nucleotide composition of sense and antisense strands as a parameter for discriminating open reading frames as protein coding sequences. J. Appl. Genetics, 38(1), 1 - 9.
4. S. Cebrat, M. R. Dudek, P. Mackiewicz, Maria Kowalczuk, Malgorzata Fita. 1997, Asymmetry of coding versus non-coding strand in coding sequences of different genomes. Microbial & Comparative Genomics. 2/4, 259 - 268.
5. S. Cebrat, M. Dudek, P. Mackiewicz, 1997, Is there any mystery of ORPHANs? J. Appl. Genet., 38(4), 365 - 372.
6. S. Cebrat, M. Dudek, 1998, The effect of DNA phase structure on DNA walks, The European Physical Journal B 3, 271 - 276
7. S. Cebrat, P. Mackiewicz,M. R. Dudek, 1998, The role of the genetic code in generating new coding sequences inside existing genes, Biosystems, 45/2, 165 - 176.
8. S. Cebrat, M. R. Dudek, P. Mackiewicz, 1998, Sequence asymmetry as a parameter indicating coding sequence in Saccharomyces cerevisiae genome.Theory in Biosciences, 117, 78 - 89.
9. S. Cebrat, M. R. Dudek, A. Gierlik, M. Kowalczuk P. Mackiewicz,
1999, Effect of replication on the third base of codons. Physica
A, 265 (1-2),
78 -84.
10. P. Mackiewicz, A.Gierlik, M. Kowalczuk, M. R. Dudek, S. Cebrat, 1999, Asymmetry of nucleotide composition of prokaryotic chromosomes, J. Appl. Genet., 40(1), 1-14.
11. P. Mackiewicz,A.Gierlik, M. Kowalczuk, M. R. Dudek, S. Cebrat, 1999, How does replication-associated mutational pressure influence amino acid composition of proteins?, Genome Research, 9(5), 409-416.
12. M. Kowalczuk, P. Mackiewicz, A. Gierlik, M. R. Dudek, S. Cebrat, 1999, Total Number of Coding Open Reading Frames in the Yeast Genome, YEAST, 15, 1031-1034.
13. P. Mackiewicz, M. Kowalczuk, A. Gierlik, M. R. Dudek, S. Cebrat, 1999, Origin and properties of noncoding ORFs in the yeast genome, Nucleic Acid Research, 27(17), 3503-3509.
14. S. Cebrat. M.R. Dudek: 1999, Periodycznosc w zdolnociach kodujacych DNA; in Symetrie, Systemy, Ewolucja. Wydawnictwo Uniwersytetu Wroclawskiego, ed. A. Nobis, A. Ogorzalek, 69 - 92 (in Polish).
15. S. Cebrat, P. Mackiewicz, M. R. Dudek, 1999, Kodujace
palindromy; Symetrie, Systemy, Ewolucja. Wydawnictwo Uniwersytetu
Wroclawskiego,
ed. A. Nobis, A. Ogorzalek, 93 - 114 (in Polish).
16. P. Mackiewicz, A. Gierlik, M. Kowalczuk, D. Szczepanik, M.R. Dudek, S. Cebrat, 1999, Mechanisms generating correlation in nucleotide composition in Borrelia burgdorferi genome. Physica A, 273, 103 - 115.
17. M. Kowalczuk, A. Gierlik, P. Mackiewicz, S. Cebrat, M.R. Dudek, 1999, Optimization of Gene Sequences under Constant Mutational Pressure and Selection. Physica A, 273, 116 - 131.
18. A. Gierlik, P. Mackiewicz, M. Kowalczuk, M. R. Dudek, S. Cebrat, 1999, Some hints on Open Reading Frame statistics - how ORF length depends on selection , Int. J. Modern Phys. C., 10(4) 635-643 .
19. A. Bartkowiak, S. Cebrat, P. Mackiewicz. 1999, Some statistical problems arising when investigating DNA sequences. Second European Conference on Highly Structured Stochastic Systems. Pavia, Book of Abstracts, 19 - 21.
20. A Gierlik, M Kowalczuk, P Mackiewicz, M R Dudek, S Cebrat,
2000, Is There a Replication-Associated Mutational Pressure in the
Saccharomyces cerevisae Genome? J. Theor. Biol., 202(4),
305-314.
21. P. Mackiewicz, M. Kowalczuk, A. Gierlik, D. Szczepanik, A. Nowicka, M. R. Dudek, S. Cebrat, 2000, No mystery of ORFans in Genomics - Generation of ORFans in the Antisense of Coding Sequences, Proceedings of the Second International Conference on Bioinformatics of Genome Regulation and Structure, Novosybirsk, 2000, vol.2, 38 - 41
22.
22. S. Cebrat, J. Kakol, 1997, The effect of social alliances on wolve population on their survival under hunting, Int. J. Mod. Physics C, 8. 2. 417 - 426.
23. S. Cebrat, 1998, Penna Model From the Perspective of One Geneticist, Physica A, 258, 493 - 498.
24. J. Schneider, S. Cebrat, D. Stauffer; 1998, Why do women live longer than men? A monte Carlo simulation of Penna models with X and Y chromosomes. Int. J. Mod. Physics C, 9. 721 -725.
25. S. Cebrat, A. Pekalski; 1999, Model of population evolution with and without eugenics. Eur. Phys. J. B 11 (1999) 4, 687-690 .
26. Paulo Murilo de Oliveira, Suzana Moss de Oliveira, Dietrich Stauffer and Stanislaw Cebrat, 1999, Penna Ageing Model and Improvement of Medical Care in 20th Century. Physica A, 273, 145 -149.
27. E. Niewczas, A. Kurdziel, S. Cebrat, 2000, Housekeeping Genes and Death Genes in the Penna Ageing Model, Int. J. Modern Phys. C. 11. No. 4. 775-784.
28. E. Niewczas, S. Cebrat, D. Stauffer, 2000, The influence of the Medical Care on the Human Life Expectancy in20th Century and the Penna Ageing Model. Theory in Biosciences, 119, 122-131.
29. J.S. Sa Martins, S. Cebrat, 2000, Random Deaths in a Computational
model for age-structured populations, Theory in Biosciences.119,
156-165.
| Papers in press: |
30. A. Nowicka, M.R. Dudek, S. Cebrat, M. Kowalczuk, P. Mackiewicz, M. Dudkiewicz, D. Szczepanik, 2000 Long Tail Feature of DNA Words Over- and Under-representation in Coding Sequences, Computational Methods in Science and Technology, Vol. 6, 85-92.
31. D. Szczepanik, P. Mackiewicz, M. Kowalczuk, A. Gierlik, A.
Nowicka, M. R. Dudek, S Cebrat, 2001, Evolution rates of genes on leading
and lagging DNA strands, J. Mol. Evol.
Three other manuscripts are wating for editorial decisions.
| Preprint series: |
32. S. Cebrat, M.R. Dudek: 1995, Coding rhythm of DNA strands, preprint of the Institute of Theoretical Physics Wroclaw University
33. M.R. Dudek, S. Cebrat: 1995, Stochastic DNA in the presence of the coding bias, preprint of the Institute of Theoretical Physics Wroclaw University
34. S. Cebrat, M.R. Dudek: 1996, Symmetry in chromosome fractal organization and DNA domain structure. preprint Institute of Theoretical Physics Wroclaw University
Participation in the more prestigious International Conferences during last three years:
1. S. Cebrat, M.R. Dudek: Symmetry in DNA domains of Yeast Chromosomes, Virtual Poster for 8th Joint EPS-APS Int. Conference on Physics Computing 96, Kraków, 1996.
2. S. Cebrat, M.R. Dudek: Symmetry in chromosome fractal organization and DNA domain structure, 8th Joint EPS-APS Int. Conference on Physics Computing ‘96, Kraków,1996.
3. S. Cebrat, M. Dudek; Compensation of coding trends in yeast genome. Middle European Cooperation in Statistical Physics, Szklarska Poreba, April 1997.
4. S. Cebrat, M. Dudek, P. Mackiewicz, The number of coding ORFs in Saccharomyces cerevisiae genome and the mystery of orphans. 18th Int. Conf. Yeast Genetics Mol. Biol. Stellenbosch, South Africa. Yeast, 13. 189. 1997,
5. S. Cebrat, M. R. Dudek, P. Mackiewicz, M. Kowalczuk, M. Fita, 1997„Asymmetry of coding versus noncoding strands of protein coding sequences”, 9th International Genome Sequencing and Analysis Conference, Sept. 13-16 1997 Hilton Head, USA.
6. J. Schneider, S. Cebrat, D. Stauffer; Why do women live longer than men? A monte Carlo simulation of Penna models with X and Y chromosomes. Fifth International Conference Mathematical Population Dynamics, Zakopane, June 1998
7. S. Cebrat, M.R. Dudek, A. Gierlik, M., Kowalczuk, P. Mackiewicz; Effect of replication on the third base of codons. The 11th Marian Smoluchowski Symposium on Statistical Physics, Zakopane, Sept. 1-5, 1998
8. M. Dudkiewicz, P. Mackiewicz, A. Gierlik, M. Kowalczuk, A. Nowicka. M. R. Dudek, S. Cebrat. Logic structure of DNA coding sequences. XIII Max Born Symposium, Wroclaw, May 26-30 1999.
9. P. Mackiewicz, A. Gierlik, M. Kowalczuk, D. Szczepanik, E. Stojek, M.R. Dudek, S. Cebrat. Asymmetry of coding sequences in Borrelia burgdorferi genome. XIII Max Born Symposium, Wroclaw, May 26-30 1999.
10. A. Gierlik, M. Kowalczuk, P. Mackiewicz, D. Szczepanik, M. Dudkiewicz, M.R. Dudek, S. Cebrat. Distribution of coding sequences on the surface of torus. XIII Max Born Symposium, Wroclaw, May 26-30 1999.
11. P. Mackiewicz, A. Gierlik, M. Kowalczuk, D. Cielakiewicz, J. Borkowska, M.R. Dudek, S. Cebrat. Graphic representation of coding sequences - spiders and doughnuts. XIII Max Born Symposium, Wroclaw, May 26-30 1999.
12. P. Mackiewicz, A. Gierlik, M. Kowalczuk, D. Szczepanik, E. Stojek, M.R. Dudek, S. Cebrat. Asymmetry of coding properties of prokaryotic genomes. XIII Max Born Symposium, Wroclaw, May 26-30 1999.
13. A. Gierlik, M. Kowalczuk, P. Mackiewicz, H. Wróblewska, A. Nowicka, M.R. Dudek, S. Cebrat. Correlation in coding sequences in different genomes. XIII Max Born Symposium, Wroclaw, May 26-30 1999.
14. M. Kowalczuk, P. Mackiewicz, A. Gierlik, D. Szczepanik, E. Stojek, M.R. Dudek, S. Cebrat. Asymmetry of nucleotide composition of prokaryotic chromosomes. XIII Max Born Symposium, Wroclaw, May 26-30 1999.
15. Paulo Murilo de Oliveira, Suzana Moss de Oliveira, Dietrich Stauffer and Stanislaw Cebrat. Penna Ageing Model and Improvement of Medical Care in 20th Century. XIII Max Born Symposium, Wroclaw, May 26-30 1999.
16. P. Mackiewicz, A. Gierlik, M. Kowalczuk, M.R. Dudek, S. Cebrat. How were noncoding ORFs generated in the yeast genome? 19th International Conference on Yeast Genetics and Molecular Biology, Rimini, Italy, May 25 - 30, 1999, Current Genetics, 35(3-4), 226.
17. M. Kowalczuk, A. Gierlik, P. Mackiewicz, M.R. Dudek, S. Cebrat. Is there replication-associated mutational pressure in the Saccharomyces cerevisiae genome? 19th International Conference on Yeast Genetics and Molecular Biology, Rimini, Italy, May 25 - 30, 1999, Current Genetics, 35(3-4), 225.
18. A. Bartkowiak, S. Cebrat, P. Mackiewicz. Some statistical problems arising when investigating DNA sequences. Proceedings of Second European Conference on Highly Structured Stochastic Systems. Pavia, Sept. 14 - 18 1999. 19 - 21.
19. S. Cebrat. Geny smierci, starzenie sie i eugenika. (Death genes, ageing and eugenics). Plenary lecture. XVII Conference of Polish Society for Zoology, Slupsk, 1999. Book of abstracts, 25-26.
20. P. Mackiewicz, M. Kowalczuk, A. Gierlik, D. Szczepanik, A. Nowicka, M. R. Dudek, S. Cebrat, 2000, No mystery of ORFans in Genomics - Generation of ORFans in the Antisense of Coding Sequences, Proceedings of the Second International Conference on Bioinformatics of Genome Regulation and Structure, Novosybirsk, 2000, vol.2, 38 - 41.
21. M. Kowalczuk, P. Mackiewicz, A. Gierlik, D. Szczepanik, A. Nowicka, M.R. Dudek, S. Cebrat. Thousands of noncoding ORFs in the yeast genome. 2000 Yeast Genetics and Molecular Biology Meeting, Seattle 2000, Book of Abstracts p 61.
and about 35 communications during the last five years at Polish Conferences. Our students won GRAND PRIX during 5th International Students’ Scientific Conference, Gdansk'97 and a Special Award during the 6th International Students’ Scientific Conference, Gdansk'98.
May 1999 Dr M.R. Dudek from the
Institute of Theoretical Physics, Wroclaw University and me, we organised
XIII Max Born Symposium devoted to DNA analysis and population dynamics.
Proceedings of the Symposium
have been published in the Journal Physica A: Statistical Mechanics
and its Applications, 1999, 273/(1-2)
It has happened that we have reported periodicity in DNA coding capacity
in two papers submitted to Physical Review Letters in 1995 an 1996: Coding
Rhytm of DNA strands and Stochastic
DNA in the presence of the coding bias. After almost one year,
papers have been rejected with very curious PRL Referees' comments.
We have also shown symmetry in the structure of
DNA domains what is the subject of the presentation at the conference Physics
Computing'96 and virtual poster Symmetry in DNA Domains of Yeast
Chromosomes . Our last papers deal with DNA asymmetry and evolution of
DNA sequences. In population dynamics, Prof. A. Pekalski and me we are
trying to prove that some eugenic technologies which have been lately
introduced could be fatal for the human gene pool.
| More natural philosophy? |
I claim that the life is extraterrestrial and in my opinion the panspermy
hypothesis is supported by the properties of genetic code exploited by
terrestrial organisms and by genetic relations between Eubacteria, Archebacteria
and Eukaryota. I presented this hypothesis at the the Conference of
International Society for the Study of the Origin of Life in Prague
1989;
| Free time? |
I am a free man or I think I am a free man. I am doing what I like to do or it seems to me that I am doing what I like to do. The only moments when I am doing what I don't like to do is when I am writing scientific papers.