1-1.jpg

    Alexander Bolshoy Ph.D.

    bolshoy

     

    Professor Emeritus
    Office: Multi-Purpose Building, Room 216 | Phone: 972-4-8240-382 | Fax: 972-4-8288-235
    Email: This email address is being protected from spambots. You need JavaScript enabled to view it.

     

    Subject: Comparative genomics, molecular evolution, computational virology, machine-learning algorithms for sequence analysis
    Contact | Photo album | Publications | CV

    Focus: Genome structure and evolution.

    Subject: Comparative genomics, molecular evolution, computational virology, machine-learning algorithms for sequence analysis

    Research Interests

     Molecular Evolution

    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

    DNA Information

    o DNA linguistics.

    o How to measure information contained in DNA texts.

    o Sequence complexity measures


    Alumni:

    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

     

    Selected Publications

    • 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. Over 70 citations.
    • 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. Over 500 citations.
    • Shpigelman E., Trifonov E.N. and Bolshoy A. (1993) “CURVATURE: software for the analysis of curved DNA.” Computer Applications in Biosciences, 9, 435 – 440. Over 200 citations.
    • 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. (J. Dubochet is a Nobel Prize Winner)
    • Bolshoy A. (1995) “CC dinucleotides contribute to the bending of DNA in chromatin.” Nature Structural Biology., 2, 446-448. Over 40 citations.
    • 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. Over 200 citations.
    • Bolshoy A. and Nevo E. (2000) “Ecological genomics of DNA: Upstream bending in prokaryotic promoters” Genome Research 10, 1185-1193. Over 60 citations.
    • 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. Over 90 citations.
    • 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. Over 20 citations.
    • Bolshoy A. (2003) “DNA Sequence Analysis Linguistic Tools. Review” Over 20 citations.
    • Bolshoy A. and Tatarinova T. (2012) "Revealing factors affecting gene length using methods of combinatorial optimization" Bioinformatics and Biology Insights, 6, 317-327 Over 10 citations.
    • Carmi G. and Bolshoy A. (2016) "Prokaryotic gene-family size correlations”, Life, 6(3), 30
    • Bolshoy A. (2018) Towards an Encyclopedia of Sequence Biology, Linguistic Frontiers

     

    Book

    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)

    1.      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. Over 70 citations.

    2.      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. Over 500 citations.

    3.      Shpigelman E., Trifonov E.N. and Bolshoy A. (1993) “CURVATURE: software for the analysis of curved DNA.” Computer Applications in Biosciences, 9, 435 – 440. Over 200 citations.

    4.      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. (J. Dubochet is a Nobel Prize Winner)

    5.      Bolshoy A. (1995) “CC dinucleotides contribute to the bending of DNA in chromatin.” Nature Structural Biology., 2, 446-448. Over 40 citations.

    6.      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. Over 200 citations.

    7.      Bolshoy A. and Nevo E. (2000) “Ecological genomics of DNA: Upstream bending in prokaryotic promoters” Genome Research 10, 1185-1193. Over 60 citations.

    8.      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. Over 90 citations.

    9.      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. Over 20 citations.

    10.   Bolshoy A. (2003) “DNA Sequence Analysis Linguistic Tools. ReviewOver 20 citations.

    11.   Bolshoy A. and Tatarinova T. (2012) "Revealing factors affecting gene length using methods of combinatorial optimization" Bioinformatics and Biology Insights, 6, 317-327 Over 10 citations.

    12.   Carmi G. and Bolshoy A. (2016) "Prokaryotic gene-family size correlations”, Life, 6(3), 30

    13.   Bolshoy A. (2018) Towards an Encyclopedia of Sequence Biology, Linguistic Frontiers

    © 2019 The University of Haifa. All Rights Reserved. Designed By IOE Team