Alexander Bolshoy Ph.D.
Focus: Genome structure and evolution.
Subject: Comparative genomics, molecular evolution, computational virology, machine-learning algorithms for sequence analysis
o Revealing evolutionary factors affecting gene length in prokaryotes
o Evolutionary factors affecting exon-intron structure
Evolution of RNA viruses
o Overlapping Codes in RNA Viral Genomes
- Usually, the phenomenon of overlapping is explained by the need to store large quantities of information in a small genome. The model that we presented a few years ago is in general accord with previous models associating high mutation rate with message overlapping. However, unlike the previous models, our analysis suggested a direct evolutionary advantage for message overlapping under conditions of high mutation rate.
o Interplay between conservation and variability (in HIV-1):
- How do viruses ensure robustness against genetic and environmental perturbations?
- How do viruses simultaneously achieve sufficient plasticity to adapt to changing environments?
- Objective: to develop a more general evolutionary model of overlapping in retroviruses.
o Population Dynamics of RNA Viruses
o DNA linguistics.
o How to measure information contained in DNA texts.
o Sequence complexity measures
Subject: Possible regulatory mechanisms in viral genomes
PhD students: O. Peleg, V. Rosenfeld (together with Prof. E. N. Trifonov), S. Hosid, L. Kozubay-Avraham, L. Brodskii (together with Prof. E. Nevo and E. N. Trifonov), V. Khailenko (together with Prof. Ivashchenko), A. Kaplunovski
MSc students: T. Nov Klaiman, L. Perlmuter Shoshani
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. (Link)
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. (Link)
Peleg O., Kirzhner V., Trifonov E.N. and Bolshoy A. (2004) "Overlapping messages and survivability" J. Mol. Evol., 59, 520-527. (Link)
Bolshoy A. (1995) "CC dinucleotides contribute to the bending of DNA in chromatin." Nat. Struct. Biol., 2, 446-448. (Link)
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." J. Mol. Biol., 262, 129-139. (Link)
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. (Link)
Shpigelman E., Trifonov E.N. and Bolshoy A. (1993) "CURVATURE: software for the analysis of curved DNA." Computer Applications in Biosciences, 9, 435-440. (Link)
Kozubay-Avraham L., Hosid S., Volkovich Z. and Bolshoy A. (2009) "Prokaryote clustering based on curvature distribution" Discrete Applied Mathematics 157(10), 2378-2387. (Link)
Bolshoy A. and Volkovich Z. (2009) "Whole-genome prokaryotic clustering based on gene lengths" Discrete Applied Mathematics 157(10), 2370-2377. (Link)
Hoischen C., Bolshoy A., GerdesK, and Diekmann S. (2004) "E. coli plasmid R1 centromeric sequence parC is curved" Nucleic Acids Research, 32, 5907-5915. (Link)
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. (Link)
Bolshoy A. (2003) "DNA Sequence Analysis Linguistic Tools. Review" Applied Bioinformatics, 2, 103-112.
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. (Link)
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. (Link)
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. (Link)
Bolshoy A., Z. Volkovich, V. Kirzhner and Z. Barzily: Genome Clustering: from linguistics models to classification of genetic texts, Studies in Computational Intelligence, Springer-Verlag, 2010. (Link)