List of Publications

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. Bolshoy, 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 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 Research and Human 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 Biotheoretica, 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. Bioinform, 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., Peleg O., Anamthawat-Jonsson K., Bolshoy A. and Schulman A. (2003) “LARD retroelements: Major, non-autonomous, components of barley and related genomes” Genetics, in press

23. Kirzhner V.M., Korol A.B., Bolshoy A. and Nevo E. “Large-scale DNA organization: extensive sets of words distinguish genomes across life” – submitted

24. Hosid S. and Bolshoy A. “New elements of the termination of transcription in prokaryotes” – submitted

25. Peleg O., Kirzhner V., Trifonov E.N. and Bolshoy A. “Overlapping messages and survivability” – submitted

26. Hosid S., Trifonov E.N. and Bolshoy A. “Sequence periodicity in intergenic regions of Escherichia coli” – submitted

27. Kozubay-Avraham L., Hosid S. and Bolshoy A. “Curvature distribution in prokaryotic genomes” - submitted

List of manuscripts in preparation

1. Bolshoy A., Peleg O. and Trifonov E.N. “Overlapping messages in human immunodeficiency virus type 1”

2. Bolshoy A., Tatusov R., Wolf Y. and Koonin E. “Environment implies average gene length: comparative analysis of complete genomes”

3. Hosid S., Trifonov E.N. and Bolshoy A. “Dinucleotide periodicity in genomic vs. random texts”

4. Peleg O., Trifonov E.N. and Bolshoy A. “The Rabbit Ears of V3”