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Publications A. Bolshoy

1. Bolshoy A. (1971) "On LR(k) Attribute and Equivalent Transformations of Grammars" (in Russian) in Numerical Methods and Computing (Problems of Computer Science), vol. XVII, pp. 9 - 12, eds. Zhogolev, Kabanov and Trofimov, Moscow State University Press, Moscow.

2. McNamara, P., Bolshoy, A., Trifonov, E.N. and Harrington, R.E. (1990) "Sequence-dependent kinks induced in curved DNA." Journal of Biomolecular Structure and Dynamics, 8, 529 - 538

3. Bolshoy A., McNamara, P., Harrington, R.E. and Trifonov, E.N. (1991) "Curved DNA without AA: experimental estimation of all 16 wedge angles." Proceedings of the National Academy of Sciences of the USA, 88, 2312 - 2316

4. Ioshikhes I., Bolshoy A. and Trifonov E.N. (1992) "Preferred positions of AA and TT dinucleotides in aligned nucleosomal DNA sequences." Journal of Biomolecular Structure and Dynamics, 9, 1111 - 1117

5. Shpigelman E., Trifonov E.N. and Bolshoy A. (1993) "CURVATURE: software for the analysis of curved DNA." Computer Applications in Biosciences, 9, 435 - 440

6. Dubochet J., Bednar J., Furrer P., Stasiak A.Z., Stasiak A. and Bolshoy A. (1994) "Determination of the DNA helical repeat by cryo-electron microscopy." Nature Structural Biology, 1, 361 - 363

 7. A. (1995) "CC dinucleotides contribute to the bending of DNA in chromatin." Nature Structural Biology., 2, 446-448

8. Ioshikhes I., Bolshoy A., Derenshteyn K., Borodovsky M. and Trifonov E.N. (1996) "Nucleosomal DNA Sequence Pattern Revealed by Multiple Alignment of Experimentally Mapped Sequences." Journal of Molecular Biology, 262, 129-139

9. Bolshoy A., Ioshikhes I. and Trifonov E.N. (1996) "Applicability of the multiple alignment algorithm for detection of weak patterns: periodically distributed DNA pattern as a study case." Computer Applications in Biosciences, 12, 383-389

10. Bolshoy A., Shapiro K., Trifonov E.N. and Ioshikhes I. (1997) "Enhancement of the nucleosomal pattern in sequences of lower complexity." Nucleic Acids Research, 25, 3248-3254

11. Ussery D.W., Higgins C.F. and Bolshoy A. (1999) "Environmental influences on DNA curvature." Journal of Biomolecular Structure and Dynamics, 16, 811-823

12. Gabrielian A. and Bolshoy A. (1999) "Sequence complexity and DNA curvature." Computers & Chemistry 23, 263-274

13. Gabrielian A. E., Landsman D., and Bolshoy A. (1999) "Curved DNA in promoter sequences" In Silico Biology 1, 183-196

14. Bolshoy A. and Nevo E. (2000) "Ecological genomics of DNA: Upstream bending in prokaryotic promoters" Genome Research 10, 1185-1193.

15. Troyanskaya O.G., Arbell O., Koren Y., Landau G.M. and Bolshoy A. (2002) "Sequence Complexity Profiles of Prokaryotic Genomic Sequences: A Fast Algorithm for Calculating Linguistic Complexity", Bioinformatics, 18, 679-688

16. Peleg O., Brunak S., Trifonov E.N., Nevo E. and Bolshoy A. (2002) "RNA Secondary Structure and Sequence Conservation in C1 Region of Human Immunodeficiency Virus Type 1 env Gene", AIDS Res. Hum. Retroviruses, 18, 867-878

17. Kirzhner V.M, Korol A.B., Bolshoy A., and Nevo E. (2002) "Compositional spectrum - revealing patterns for genomic sequence characterization and comparison." Physica A, 312,447-458

18. Kirzhner V.M, Korol A.B., Nevo E. and Bolshoy A. (2003) "One promising approach to a large scale comparison of genomic sequences" Acta Biotheor., 51, 73-89

19. Peleg O., Trifonov E.N. and Bolshoy A. (2003) "Hidden Messages with RNA Secondary Structure Feature along the nef Gene of Human Immunodeficiency Virus Type 1" Nucleic Acids Res., 31, 4192-4200

20. Bolshoy A (2003) "DNA Sequence Analysis Linguistic Tools. Review" Appl. Bioinformatics, 2, 103-112

21. Kato M., Onishi Y., Wada-Kiyama Y., Abe T., Ikemura T., Kogan S., Bolshoy A., Trifonov E.N. and Kiyama R. (2003) "Dinucleosome DNA of Human K562 Cells: Experimental and Computational Characterizations" J. Mol. Biol., 332, 111-125

22. Kalendar R., Vicient C.M., Peleg O., Anamthawat-Jonsson K., Bolshoy A., Schulman A.H. (2004) "Large retrotransposon derivatives: abundant, conserved but nonautonomous retroelements of barley and related genomes." Genetics 166, 1437-1450.

23. Peleg O., Kirzhner V., Trifonov E.N. and Bolshoy A. (2004) "Overlapping messages and survivability" - J. Mol. Evol., 59, 520-527

24. Kozubay-Avraham L., Hosid S. and Bolshoy A. (2004) "Curvature distribution in prokaryotic genomes" - In Silico Biol., 4(3), 361-375.

25. Hosid S. and Bolshoy A. (2004) "New elements of the termination of transcription in prokaryotes" - J. Biomol. Str. Dyn., 22, 347-354

26. Hosid S., Trifonov E.N. and Bolshoy A. (2004) "Sequence periodicity in intergenic regions of Escherichia coli" - BMC Mol Biol. 5: 14

27. Hoischen C., Bolshoy A., GerdesK, and Diekmann S. (2004) "E. coli plasmid R1 centromeric sequence parC is curved" - Nucleic Acids Res., 32, 5907-5915

29. Volkovich Z., Kirzhner V., Bolshoy A., Nevo E. and Korol A. (2005) "The method of fuzzy-N-grams in large-scale clustering of the DNA texts" - Pattern Recognition, 38, 1902-1912

30. Khmel I.A., Ovadis M.I., Mayatskaya A.V., Veselovskii A.M., Bass I.A., Lipasova V.A., Bolshoy A., Chet I., and Chernin L.S. (2005) "Cloning of Serratia plymuthica IC1270 gene chiA promoter region and study of its activity in Escherichia coli cells deficient in global regulators of transcription" - J. Basic Microbiol., 45, 426-437.

31. Kozubay-Avraham L., Hosid S. and Bolshoy A. (2006) "Involvement of DNA curvature in intergenic regions of prokaryotes" - Nucleic Acids Res., 34, 2316-2327

32. Kozubay-Avraham L., Bolshoy A. and Volkovich Z. (2006) "On prokaryotes' clustering based on curvature distribution" in M. Last, P. S. Szczepaniak, Z. Volkovich, and A. Kandel (Editors), in "Advances in Web Intelligence and Data Mining", Studies in Computational Intelligence Series, Vol. 23, Springer-Verlag.

33. Bolshoy A. (2008) "Revisiting the relationship between compositional sequence complexity and periodicity" - Comput. Biol. Chem. 32, 17-28.

34. Kozubay-Avraham L., Hosid S., Volkovich Z. and Bolshoy A. (2009) "Prokaryote clustering based on curvature distribution" - Discrete Applied Mathematics 157(10), 2378-2387

35. Bolshoy A. and Volkovich Z. (2009) "Whole-genome prokaryotic clustering based on gene lengths" - Discrete Applied Mathematics 157(10), 2370-2377

36. Kaplunovsky A., Khailenko V, Bolshoy A., Atambayeva Sh. and Ivashchenko A. (2009) "Statistics of Exon Lengths in Animals, Plants, Fungi, and Protists" - Proceedings of World Academy of Science, Engineering and Technology, Volume 40, April 2009ublishing Ltd

37. Yang Z., Zhang T., Bolshoy A., Beharav A. and Nevo E. (2009) "Adaptive microclimatic structural and expressional dehydrin 1 evolution in wild barley, Hordeum spontaneum, at ‘Evolution Canyon', Mount Carmel, Israel", Molecular Ecology 18, 2063-2075 Blackwell P

38. Nov Klaiman T., Hosid S. and Bolshoy A. (2009) "Upstream curved sequences in E. coli are related to the regulation of transcription initiation" Comput. Biol. Chem. 33, 275-282.

39. Kaplunovsky A., Khailenko V, Bolshoy A., Atambayeva Sh. and Ivashchenko A. (2009) "Statistics of Exon Lengths in Animals, Plants, Fungi, and Protists" International Journal of Biological and Life Sciences 1(3), 139-144

40. Kaplunovsky A., Zabrodsky D., Ivashchenko A. , Volkovich Z. and Bolshoy A. (2010) "Statistics of Exon Lengths in Fungi" The Open Bioinformatics Journal 4, 31-40.

41. Kaplunovsky A., Ivashchenko A. and Bolshoy A. (2011) "Statistics of Exon Lengths in Various Eukaryotes", Journal of Open Access Bioinformatics, 3, 1-15.

42. Berillo O., Khailenko V, Ivashchenko A, Perlmuter-Shoshany L. and Bolshoy, A. (2012) "Explaining tropism of human parvovirus B19" Computational Biology and Chemistry, 40, 1-6.

43. Korenblat K., Volkovich Z. and Bolshoy A. (2012) "Robustness of the whole-genome prokaryotic clustering based on gene lengths" Computational Biology and Chemistry, 40, 20-29.

44. Bolshoy A. and Tatarinova T. (2012) "Revealing factors affecting gene length: review of applicable methods of combinatorial optimization" Bioinformatics and Biology Insights, 6, 317-327.

45. Bolshoy A. (2013) "Modeling of DNA curvature. Comment on "Sequence-dependent collective properties of DNAs and their role in biological systems" by Pasquale De Santis and Anita Scipioni" Physics of Life Reviews, 10(1):73-4; DOI: 10.1016/j.plrev.2013.01.010

46. Bolshoy A. and Kirzhner V. (2013) "Algorithms of an optimal integer tree labeling", arXiv:1305.5551

47. Bolshoy A. and Kirzhner V. (2013) "Algorithms of reconstructions of ancestral gene lengths" Biomed Res Int.;2013:472163

48. Salih B., Cohen I., Tatarinova T., and Bolshoy A. (2014) "Ranking of Prokaryotic Genomes Based on Maximization of Sortedness of Gene Lengths" J Data Mining Genomics Proteomics, 5:1 DOI: 10.4172/2153-0602.1000151

49. Tatarinova, T., B. Salih, J. Dien Bard, I. Cohen and A. Bolshoy. 2014. Lengths of orthologous prokaryotic proteins are affected by evolutionary factors. Biomed. Res. Int. 2014:786861.


Book

1. A. Bolshoy, Z. Volkovich, V. Kirzhner and Z. Barzily: Genome Clustering: from linguistics models to classification of genetic texts, Studies in Computational Intelligence, Springer-Verlag, 2010.

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