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Articles

Publications E. Trifonov

PUBLICATIONS OF 1966-1975

(Russian period)

Trifonov, E. N., Lazurkin, Y. S., Frank-Kamenetskii, M. D., Kinetics of denaturation of DNA under action of formaldehyde. In: "Structure, Properties and Genetic Function of DNA",.Conference of Department of Radiobiology of the Kurchatov Institute of Atomic Energy, Moscow, 1966, pp. 83-110. (Russian, abstr. English)

Kosaganov, Y. N., Trifonov, E. N., Hydrodynamical methods. In: "Physical Methods of Investigation of Proteins and Nucleic Acids", Nauka, Moscow, 1967, pp. 222-288 (Russian)

Trifonov, E. N., Lazurkin, Y. S., Frank-Kamenetskii, M. D., Formaldehyde-induced uncoiling of DNA. Molecular Biology 1, 142-151 (1967)

Trifonov, E. N., Shafranovskaya, N. N., Frank-Kamenetskii, M. D., Lazurkin, Y. S., Kinetic method for determining the concentration of defects of the secondary structure of DNA. Molecular Biology 2, 698-705 (1968)

Trifonov, E. N., Frank-Kamenetskii, M. D., Lazurkin, Y. S., The formaldehyde kinetic method: its physical basis and applications to investigation of DNA structure. In: "Structure and Genetical Functions of Biopolymers", Second Conference of Department of Radiobiology of Kurchatov Institute of Atomic Energy, Moscow, 1969, pp. 305-322 (Russian, abstr. English)

Bannikov, Y. A., Trifonov, E. N., Application of the formaldehyde kinetic method to DNA with single strand breaks. As above, pp. 323-336

Berestetskaya, I. V., Kosaganov, Y. N., Lazurkin, Y. S., Trifonov, E. N., Frank-Kamenetskii, M. D., Melting of DNA with defects in its secondary structure (thermodynamic method for determination of concentration of defects). As above, pp. 355-370

Berestetskaya, I. V., Kosaganov, Y. N., Lazurkin, Y. S., Trifonov, E. N., Frank-Kamenetskii, M. D., Melting of DNA with secondary structure defects. Molecular Biology 4, 106-110 (1970)

Bannikov, Y. A., Trifonov, E. N., Investigation of defects in the secondary structure of DNA with single-strand breaks. Molecular Biology 4, 597-603 (1970)

Bogatyreva, S. A., Trifonov, E. N., Spirin, A. S., Dependence of poly-U directed cell-free system on ratios of divalent and monovalent cations. Doklady Biochemistry 195, 315-318 (1970)

Lazurkin, Y. S., Frank-Kamenetskii, M. D., Trifonov, E. N., Melting of DNA: its study and application as a research method. Biopolymers 9, 1253-1307 (1970)

Trifonov, E. N., Kinetics of unwinding of DNA under action of formaldehyde. Ph. D. thesis, Moscow Physico-Technical Institute, 1970 (Russian)

Lyubchenko, Y. L., Trifonov, E. N., Lazurkin, Y. S., Frank-Kamenetskii, M. D., Detection of low-melting sites in the phage T2 DNA molecule. Molecular Biology 5, 618-623 (1971)

Shafranovskaya, N. N., Trifonov, E. N., Lazurkin, Y. S., Frank-Kamenetskii, M. D., Long range migration of electron excitation energy through a DNA molecule. JETP Letters 15, 285-287 (1972)

Baev, A. S., Lyubchenko, Y. L., Lazurkin, Y. S., Trifonov, E. N., Frank-Kamenetskii, M. D., Study of low-melting segments in T2 phage DNA by electron microscopy and the kinetic formaldehyde method. Molecular Biology 6, 612-617 (1972)

Spirin, A. S., Bogatyreva, S. A., Trifonov, E. N., Dependence of Poly-U directed cell-free system on ratios of divalent and monovalent cations. In: "Molecular Evolution, Prebiological and Biological", eds D. Rohlfing and A. Oparin, Plenum Press, NY, 1972, pp. 291-296 (same as No. 10)

Komolova, G. S., Trifonov, E. N., Egorov, I. A., Investigation of DNA subjected to gamma irradiation in vitro by a kinetic formaldehyde method. Doklady Biochemistry 207, 443-445 (1972)

Shafranovskaya, N. N., Trifonov, E. N., Lazurkin, Y. S., Frank-Kamenetskii, M. D., Clustering of thymine dimers in ultraviolet irradiated DNA and the long-range transfer of electronic excitation along the molecule. Nature New Biology 241, 58-60 (1973)

Lyubchenko, Y. L., Trifonov, E. N., Baev, A. S., Lazurkin, Y. S., Frank- Kamenetskii, M. D., A study of early stages of thermal denaturation of T2 DNA. In: "Conformational Changes of Biopolymers in Solutions", Nauka, Moscow, 1973, pp. 15-22 (Russian)

Komolova, G. S., Trifonov, E. N., Egorov, I. A., Damage to DNA structure in tissues of gamma-irradiated animals. Doklady Biochemistry 208, 7-9 (1973)

Sukhoviya, M. I., Koval'chuk, A. V., Trifonov, E. N., Effect of ionizing electromagnetic radiation on DNA in solution and on white blood cells. Doklady Biophysics 225, 191-194 (1975)

Trifonov, E. N., Lyubchenko, Y. L., An electron microscopic study of low-melting sites in bacteriophage T7. In: "Conformational Changes of Biopolymers in Solutions", Tbilisi 1975, pp. 71-78 (Russian)

1976, 1977 - no publications (unemployed, immigration to Israel)

PUBLICATIONS SINCE 1978 (Israeli period)

1978

Sussman, J. L., Trifonov, E. N., Possibility of non-kinked packing of DNA in chromatin. Proc. Natl. Acad. Sci. USA 75, 103-107 (1978)

Trifonov, E., The helical model of the nucleosome core. Nucl. Acids Res. 5, 1371-1380 (1978)

1979

Trifonov, E. N., Bettecken, T., Noninteger pitch and nuclease sensitivity of chromatin DNA. Biochemistry 18, 454-456 (1979)

Trifonov, E. N., Sussman, J. L., Smooth bending of DNA in chromatin. In: "Molecular Mechanisms of Biological Recognition" (Ed. M. Balaban), Elsevier/North Holland Biomed. Press, 1979, pp. 227-232

Trifonov, E. N., Bettecken, T., On the orientational nature of sensitivity of nucleosomal DNA to nuclease digestion. As above, pp. 233-234

1980

Nussinov, R., Sussman, J. L., Trifonov, E. N., MS2 RNA has a potential to form an unusually large number of stable hairpins. J. Theor. Biol. 85, 481-486 (1980)

Trifonov, E. N., Sussman, J. L., The pitch of chromatin DNA is reflected in its nucleotide sequence. Proc. Natl. Acad. Sci. USA 77, 3816-3820 (1980)

Trifonov, E. N., Sequence-dependent deformational anisotropy of chromatin DNA. Nucl. Acids Res. 8, 4041-4053 (1980)

 1981

Trifonov, E. N., Deformational anisotropy of DNA molecule. In: "Structural Aspects of Recognition and Assembly in Biological Macromolecules", (Eds. M. Balaban, J. Sussman, W. Traub and A. Yonath), Balaban ISS, Rehovot-Philadelphia, 1981, pp. 525-536

Trifonov, E. N., Topological paradox of minichromosomes? As above, pp. 711-720

Trifonov, E. N., Structure of DNA in chromatin. In: "International Cell Biology 1980-1981" (Ed. H. Schweiger), Springer-Verlag, Berlin, 1981, pp. 128-138. Abstract in European Journal of Cell Biology 22, 74-74, 1980.

1982

Kabsch, W., Sander, C., Trifonov, E. N., The ten helical twist angles of B-DNA. Nucl. Acids Res. 10, 1097-1104 (1982)

1983  

Trifonov, E. N., Sequence-dependent variations of B-DNA structure and protein-DNA recognition. Cold Spring Harbor Symp. Quant. Biol. 47, 271-278 (1983)

Trifonov, E. N., Nucleosomal DNA structure. In: "Nucleic Acids: the vectors of life" (Eds. B. Pullman and J. Jortner), D. Reidel Publ. Company, Dordrecht-Boston-Lancaster, 1983, pp. 373-385

Mengeritsky, G., Trifonov, E. N., Nucleotide sequence-directed mapping of the nucleosomes. Nucl. Acids Res. 11, 3833-3851 (1983)

Trifonov, E. N., Bolshoi, G., Open and closed 5S rRNA - the only two universal structures encoded in the nucleotide sequences. J. Molec. Biol. 169, 1-13 (1983)   

Ulanovsky, L. E., Trifonov, E. N., Superhelicity of nucleosomal DNA changes its double-helical repeat. Cell Biophysics 5, 281-283 (1983)

Trifonov, E. N., Principles of Modern Genetics, 2nd Edition - Gershenson, SM. Nature 306, 815-815 (1983) (book review)

1984  

Mengeritsky, G., Trifonov, E. N., Nucleotide sequence-directed mapping of the nucleosomes of SV40 chromatin. Cell Biophysics 6, 1-9 (1984)

Brendel, V., Trifonov, E. N., A computer algorithm for testing potential prokaryotic terminators. Nucl. Acids Res. 12, 4411-4427 (1984)

Wartenfeld, R., Mengeritsky, G., Trifonov, E. N., Periodicity in nucleosomal DNA sequences. CODATA Bull., 56, 14-16 (1984).

Also reprinted in:

"The Role of Data in Scientific Progress", (Ed. P. S. Glaeser), North Holland, Amsterdam, 1985, pp. 111-113

Brendel, V., Trifonov, E. N., Computer-aided mapping of DNA-protein interaction sites. As above, pp. 17-20 and 115-118, respectively

Trifonov, E. N., Construction of an algorithm for locating splicing junctions. As above, pp. 21-26 and 119-124, respectively

Trifonov, E. N., Mengeritsky, G., Simian virus 40 replication pause sites map with the nucleosomes. J. Virol., 52, 1011-1012 (1984)

1985 

Trifonov, E. N., Curved DNA. CRC Crit. Rev. Biochemistry 19, 89-106 (1985)

Trifonov, E. N., Konopka, A. K., Jovin, T. M., Unusual frequencies of certain alternating purine-pyrimidine runs in natural DNA sequences. Relation to Z-DNA. FEBS Let. 185, 197-202 (1985)

Trifonov, E. N., Imperfect complementarity and RNA structure. J. Biosci. 8, Suppl., 781-790 (1985)

1986 

Ulanovsky, L., Bodner, M., Trifonov, E. N., Choder, M., Curved DNA: design, synthesis and circularization. Proc. Natl. Acad. Sci. USA 83, 862-866 (1986)

Brendel, V., Hamm, G. H., Trifonov, E. N., Terminators of transcription with RNA polymerase from Escherichia coli: what they look like and how to find them. J. Biomolec. Str. and Dynamics 3, 705-723 (1986)

Ulanovsky, L. E., Trifonov, E. N., A different view point on the chromatin higher order structure: steric exclusion effects. In: "Biomolecular Stereodynamics III", (Eds. R. H. Sarma and M. H. Sarma), Adenine Press, 1986, pp. 35-44

Trifonov, E. N., Brendel, V., Gnomic - a dictionary of genetic codes (BOOK). Balaban Publishers, Rehovot-Philadelphia, 1986. Reprint: Verlag Chemie, 1987

Brendel, V., Beckmann, J. S., Trifonov, E. N., Linguistics of nucleotide sequences: morphology and comparison of vocabularies. J. Biomolec. Str. and Dynamics 4, 11-21 (1986)

Beckmann, J. S., Brendel, V., Trifonov, E. N., Intervening sequences exhibit distinct vocabulary. J. Biomolec. Str. and Dynamics 4, 391-400 (1986)

Bucher, P., Trifonov, E. N., Compilation and analysis of eukaryotic Pol II promoter sequences. Nucl. Acids Res. 14, 10009-10026 (1986)

1987

Trifonov, E. N., Translation framing code and frame-monitoring mechanism as suggested by the analysis of mRNA and 16S rRNA nucleotide sequences. J. Molec. Biol. 194, 643-652 (1987)

 Bucher, P., Trifonov, E. N., On Nussinov's compilation of eukaryotic transcription initiation sites. J. Theor. Biol. 126, 373-375 (1987)

 Ulanovsky, L. E., Trifonov, E. N., Estimation of wedge components in curved DNA. Nature 326, 720-722 (1987)

1988

Trifonov, E. N., Mengeritsky, G., Bent DNA in chromatin versus free curved DNA. In: "Structure and Expression. Volume 3: DNA Bending and Curvature", (Eds. W. K. Olson, M. H. Sarma, R. H. Sarma and M. Sundaralingam), Adenine Press, 1988, pp 159-167

Trifonov, E. N., Tan, R. K.-Z., Harvey, S. C., Static persistence length of DNA. As above, pp. 243-253

Trifonov, E. N., Ulanovsky, L. E., Inherently curved DNA and its structural elements. In: "Unusual DNA Structures", (Eds. R. D. Wells and S. C. Harvey), Springer Verlag, New York, 1988, pp. 173-187

Trifonov, E. N., Codes of nucleotide sequences. Math. Biosci. 90, 507-517 (1988).

Also reprinted in: "Nonlinearity in Biology and Medicine", (Eds. A. S. Perelson, B. Goldstein, M. Dembo and J. A. Jacques), Elsevier Science Publ. Co., Inc., 1988, pp. 507-517

Trifonov, E. N., Nucleotide sequences as a language: morphological classes of words. In: "Classification and Related Methods of Data Analysis", (Ed. H. H. Bock), Elsevier Science Publ. B. V. (North Holland), 1988, pp. 57-64

Bucher, P., Trifonov, E. N., CCAAT box revisited - bidirectionality, location and context. J. Biomolec. Str. and Dynamics 5, 1231-1236 (1988)

1989 

Trifonov, E. N., Searching for codes in the sequences. In: "Biomolecular Data: A Resource in Transition", (Ed. R. R. Colwell), Oxford University Press, 1989, pp. 199-210

Trifonov, E. N., The multiple codes of nucleotide sequences. Bull. Math. Biol. 51, 417-432 (1989)

1990

Trifonov, E. N., Making sense of the human genome. In: "Structure and Methods, vol. 1, Human Genome Initiative and DNA Recombination", (Eds. R. H. Sarma and M. H. Sarma), Adenine Press, New York, 1990, pp. 69-77

Pietrokovski, S., Hirshon, J., Trifonov, E. N., Linguistic measure of taxonomic and functional relatedness of nucleotide sequences. J. Biomolec. Str. and Dynamics 7, 1251-1268 (1990)

McNamara, P. T., Bolshoy, A., Trifonov, E. N., Harrington, R. E., Sequence-dependent kinks induced in curved DNA. J. Biomolec. Str. and Dynamics 8, 529-538 (1990)

1991

Trifonov, E. N., DNA as chromatin organizer. In: "Theoretical Biochemistry and Molecular Biophysics, v. 1: DNA" (Eds. D. L. Beveridge and R. Lavery), Adenine. Press, New York, 1991, pp. 377-388

Bolshoy, A., McNamara, P., Harrington, R. E., Trifonov, E. N., Curved DNA without AA: experimental estimation of all 16 wedge angles. Proc. Natl. Acad. Sci. USA 88, 2312-2316 (1991)

Beckmann, J. S., Trifonov, E. N., Splice junctions follow a 205-base ladder. Proc. Natl. Acad. Sci. USA 88, 2380-2383 (1991)

Trifonov, E. N., DNA in profile. Trends Biochem. Sc. 16, 467-470 (1991)

Trifonov, E. N., Informational structure of genetic sequences and nature of gene splicing. In "Advances in Biomolecular Simulations. AIP Conference Proceedings 239" (Eds. R. Lavery, J.-L. Rivail and J. Smith), AIP press, New York, 1991, pp. 329-338

1992

Trifonov, E. N., Genetic sequences as a language. Rev. Brasileira de Genetica 15, Suppl. 1, 180-186 (1992)

Ioshikhes, I., Bolshoy, A., Trifonov, E. N., Preferred positions of AA and TT dinucleotides in aligned nucleosomal DNA sequences. J. Biomolec. Str. and Dynamics 9, 1111-1117 (1992)

Trifonov, E. N., Recognition of correct reading frame by the ribosome. Biochimie 74, 357-362 (1992)

Pietrokovski, S., Trifonov, E. N., Imported sequences in yeast mitochondrial genome identified by nucleotide linguistics. Gene 122, 129-137 (1992)

Lagunez-Otero, J., Trifonov, E. N., Translation framing pattern in mRNA - compensation effects. In "Modelling and Computer Methods in Molecular Biology and Genetics", (Eds. V. A. Ratner and N. A. Kolchanov), Nova Science Publishers, New York, 1992, pp. 451-460.

Lagunez-Otero, J., Trifonov, E. N., mRNA periodical infrastructure complementary to the proof-reading site in the ribosome. J. Biomolec. Str. and Dynamics 10, 455-464 (1992)

1993

Trifonov, E. N., Gene splicing: spatial separation of overlapping messages. Computers Chem. 17, 27-31 (1993)

Shpigelman, E. S., Trifonov, E. N., Bolshoy, A., CURVATURE: software for the analysis of curved DNA. CABIOS 9, 435-440 (1993)

Ioshikhes, I., Trifonov, E. N., Nucleosomal DNA sequence database. Nucl. Acids Res. 21, 4857-4859 (1993)

Trifonov, E. N., DNA as a language. In "The Second International Conference on Bioinformatics, Supercomputing and Complex Genome Analysis" (Eds. H. A. Lim, J. W. Fickett, C. R. Cantor and R. J. Robbins), World Scientific, Singapore, 1993, pp. 103-110

1994

Berman, A. L., Kolker, E, Trifonov, E. N., Underlying order in protein sequence organization. Proc. Natl. Acad. Sci. USA 91, 4044-4047 (1994)

Trifonov, E. N., On the recombinational origin of protein-sequence-subunit structure. J. Molec. Evol. 38, 543-546 (1994)

1995  

Kolker, E., Trifonov, E. N., Periodic recurrence of methionines: Fossil of gene fusion? Proc. Natl. Acad. Sci. USA 92, 557-560 (1995)

Trifonov, E. N., Segmented structure of protein sequences and early evolution of genome by combinatorial fusion of DNA elements. J. Molec. Evol. 40, 337-342 (1995)

Kolker, E., Trifonov, E. N., Sequence markers of segmented protein structure. In: "Modelling of biomolecular atructures and mechanisms", (Eds. A. Pullman, J. Jortner and B. Pullman), Kluwer Academic Publishers, Dordrecht, 1995, pp. 461-471

Trifonov, E. N., Hidden segmentation of protein sequences: structural connection with DNA. As above, pp. 473-479

Kolker, E., Trifonov, E. N., Sequence sizes of eukaryotic enzymes. In: "Pacific Symposium on Biocomputing'96", (Eds. L. Hunter and T. E. Klein), World Scientific, London, 1995, pp. 461-471

1996

Popov, O., Segal, D. M., Trifonov, E. N., Linguistic complexity of protein sequences as compared to texts of human languages. BioSystems 38, 65-74 (1996)

Kolker, E., Trifonov, E. N., Segments, folds and overall protein structure. In: "Biological Structure and Dynamics", (Eds. R. H. Sarma and M. H. Sarma), Adenine Press, New York, 1996, pp. 257-266

Ioshikhes, I., Bolshoy, A., Derenshteyn, K., Borodovsky, M., Trifonov, E. N., Nucleosome DNA sequence pattern revealed by multiple alignment of experimentally mapped sequences. J. Molec. Biol. 262, 129-139 (1996)

Bolshoy, A., Ioshikhes, I., Trifonov, E. N., Applicability of the multiple alignment algorithm for detection of weak patterns: Periodically distributed DNA pattern as a study case. CABIOS 12, 383-389 (1996)

Trifonov, E. N., Interfering contexts of regulatory sequence elements. CABIOS 12, 423-429 (1996)

1997

Trifonov, E. N., Segmented structure of mobile and separate DNA and RNA elements as suggested by their size distributions. J. Biomolec. Str. and Dynamics 14, 449-457 (1997)

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

Guimaraes, R. C., Trifonov, E. N., Lagunez-Otero, J., Taxonomy of 5S ribosomal RNA by the linguistic technique: probing with mitochondrial and mammalian sequences. J. Molec. Evol. 45, 271-277 (1997)

Trifonov, E. N., Genetic sequences as product of compression by inclusive superposition of many codes. Molecular Biology 31, 759-767 (1997)

Trifonov, E. N., Bettecken, T., Sequence fossils, triplet expansion, and reconstruction of earliest codons. Gene 205, 1-6 (1997)

Denisov, D. A., Shpigelman, E. S., Trifonov, E. N., Protective nucleosome centering at splice sites as suggested by sequence-directed mapping of the nucleosomes. Gene 205, 145-149 (1997)

1998 

Herzel, H., Trifonov, E. N., Weiss, O., Grosse, I., Interpreting correlations in biosequences. Physica A 249, 449-459 (1998)

Trifonov, E. N., 3-, 10.5-, 200- and 400-base periodicities in genome sequences. Physica A 249, 511-516 (1998)

Jurka, J., Klonowski, P., Trifonov, E. N., Mammalian retroposons integrate at sequence-dependent DNA kinks. J. Biomolec. Str. Dyn. 15, 717-721 (1998)

Trifonov, E. N., How basics of protein evolution could help the gene finding. Proceedings of the First International Conference on Bioinformatics of Genome Regulation and Structure BGRS'98, Novosibirsk - Altai Mountains, August 24-31, 1998, ICG, Novosibirsk, 1998, v.2. Bioinformatics of Genome Structure, pp. 266-268

Herzel, H., Weiss, O., Trifonov, E. N., Sequence periodicity in complete genomes of Archaea suggests positive supercoiling. J. Biomol. Str. Dyn. 16, 341-345 (1998)

Trifonov, E. N., Denisov, D. A., Makhoul, C., Interacting sequence patterns. Math. Modelling and Sci. Computing 9, 24-29 (1998)

1999 

Wada-Kiyama, Y., Kuwabara, K., Sakuma, Y., Onishi, Y., Trifonov, E. N., Kiyama, R., Localization of curved DNA and its association with nucleosome phasing in the promoter region of the human estrogen receptor  gene. FEBS Letters 444, 117-124 (1999)

Ioshikhes, I., Trifonov, E. N., Zhang, M. Q., Periodical distribution of transcription factor sites in promoter regions and connection with chromatin structure. Proc. Natl. Acad. Sci. USA 96, 2891-2895 (1999)

Ozoline, O. N., Deev, A. A., Trifonov, E. N., DNA bendability - a novel feature in E. coli promoter recognition. J. Biomol. Str. Dyn. 16, 825-831 (1999)

Trifonov, E. N., Glycine clock: Eubacteria first, Archaea next, Protoctista, Fungi, Planta and Animalia at last. Gene Therapy and Molecular Biology, Proceedings of the International Conference, Redwood City, April 1999, Gene Therapy Press, Palo Alto, pp. 275-279

Herzel, H., Weiss, O., Trifonov, E. N., 10-11 bp periodicities in complete genomes reflect protein structure and DNA folding. Bioinformatics 15, 187-193 (1999)

Trifonov, E. N., Elucidating sequence codes: three codes for evolution. Annals NY Acad. Sci. 870, 330-338 (1999). (Title of the volume: Molecular Strategies in Biological Evolution, Ed. L. Caporale).

Trifonov, E. N., Direct repeats. In: "Encyclopedia of Molecular Biology", T. E. Creighton, Ed., John Wiley & Sons, Inc., New York, 1999, p. 683

Trifonov, E. N., Downstream. In: "Encyclopedia of Molecular Biology", T. E. Creighton, Ed., John Wiley & Sons, Inc., New York, 1999, p. 766-767

Trifonov, E. N., Inverted repeats. In: "Encyclopedia of Molecular Biology", T. E. Creighton, Ed., John Wiley & Sons, Inc., New York, 1999, p. 1310

Trifonov, E. N., Palindrome. In: "Encyclopedia of Molecular Biology", T. E. Creighton, Ed., John Wiley & Sons, Inc., New York, 1999, p. 1759-1760

Trifonov, E. N., Sequence codes. In: "Encyclopedia of Molecular Biology", T. E. Creighton, Ed., John Wiley & Sons, Inc., New York, 1999, p. 2324-2326

Trifonov, E. N., Tandem repeats. In: "Encyclopedia of Molecular Biology", T. E. Creighton, Ed., John Wiley & Sons, Inc., New York, 1999, p. 2513-2514

Trifonov, E. N., Upstream. In: "Encyclopedia of Molecular Biology", T. E. Creighton, Ed., John Wiley & Sons, Inc., New York, 1999, p. 2726-2727

Trifonov, E. N., Glycine clock: Eubacteria first, Archaea next, Protoctista, Fungi, Planta and Animalia at last. Gene Therapy and Molecular Biology 4, 313-322 (1999). www.gtmb.org

2000

Berezovsky, I. N., Grosberg, A. Y., Trifonov, E. N., Closed loops of nearly standard size: common basic element of protein structure. FEBS Letters 466, 283-286 (2000)

Trifonov, E. N., Leap Into Life's Beginnings. Tracking the chronology of amino acids. Science Spectra 20, 62-71 (2000).

Trifonov, E. N., Earliest pages of bioinformatics. Bioinformatics 16, 5-9 (2000)

Trifonov, E. N., Molecular evolution, over three billion years back. Biophysics 45, 551-553 (2000) [Biofizika 45, 565-568 (2000)]

Trifonov, E. N., Consensus temporal order of amino acids and evolution of the triplet code. Gene 261, 139-151 (2000)

2001

Fajkus, J., Trifonov, E. N., Columnar packing of telomeric nucleosomes. Bioch. Bioph. Res. Com. 280, 961-963 (2001)

Razin, S. V., Ioudinkova, E. S., Trifonov, E. N., Scherrer, K., Non-clonability correlates with genomic instability: a case study of a unique DNA region. J. Mol. Biol. 307, 481-486 (2001)

Berezovsky, I. N., Trifonov, E. N., Evolutionary aspects of protein structure and folding. Molecular Biology 35, 233-239 (English), 278-284 (Russian) (2001)

Berezovsky, I. N., Trifonov, E. N. Van der Waals locks: loop-n-lock structure of globular proteins. J. Mol. Biol. 307, 1419-1426 (2001)

Berezovsky, I. N., Trifonov, E. N., Loop fold nature of globular proteins. Protein Engineering 14, 403-407 (2001)

Trifonov, E. N., Kirzhner, A., Kirzhner, V. M., Berezovsky, I. N., Distinct stages of protein evolution as suggested by protein sequence analysis. J. Mol. Evol. 53, 394-401 (2001)

Bellgard, M., Schibeci, D., Trifonov, E. N., Gojobori, T., Early detection of G+C differences in bacterial species inferred from the comparative analysis of the two completely sequenced Helicobacter pylori strains. J. Mol. Evol. 53, 465-468 (2001)

Berezovsky, I. N., Kirzhner, V. M., Kirzhner, A, Trifonov, E. N., Protein folding: looping from hydrophobic nuclei. Proteins: Structure, Function and Genetics 45, 346-350 (2001)

Berezovsky, I. N., Trifonov, E. N., Protein structure and folding: a new start. J. Biomolec. Str. Dyn. 19, 397-403 (2001)

Yudinkova E. S., Trifonov, E. N., Scherrer, K., Razin, S. V., Characteristics of an "unclonable" DNA sequence located in the intergenic spacer between the pi- and alpha D-globin genes of the chicken. Dokl Biochem Biophys 378, 160-161 (2001)

2002

Kolker, E., Tjaden, B. C., Hubley, R., Trifonov, E. N., Siegel, A. F., Spectral analysis of distributions: finding periodic components in eukaryotic enzyme length data, OMICS: A Journal of Integrative Biology 6, 123-130 (2002)

Trifonov, E. N., Berezovsky, I. N., Proteomic code, Molecular Biology 36, 239-243 (in Russian original pp 315-319) (2002)

Kiyama, R., Trifonov, E. N., What positiones nucleosomes? - A model, FEBS Let. 523, 7-11 (2002)

Trifonov, E. N., Segmented genome: elementary units of genome  structure, Russian J. of Genetics 38, 659-663 (2002)

Berezovsky, I. N., Trifonov, E. N., Loop fold structure of proteins: Resolution of Levinthal's paradox, J. Biomolec. Str. Dyn. 20, 5-6 (2002)

Peleg, O., Brunak, S., Trifonov, E. N., Nevo, E., and Bolshoy, A., RNA

secondary structure and sequence conservation in C1 region of human

immunodeficiency virus type 1 env gene, AIDs Res. and Human Retroviruses 18, 867-878 (2002)

Trifonov, E. N., Berezovsky, I. N., Molecular evolution from abiotic scratch, FEBS Letters 527, 1-4 (2002)

Berezovsky, I. N., Trifonov, E. N., Back to units of protein folding, J. Biomolec. Str. Dyn. 20, 315-316 (2002)

Makhoul, C. H., Trifonov, E. N., Distribution of rare triplets along mRNA and their relation to protein folding, J Biomolec Str Dyn 20, 413-420 (2002)

Berezovsky, I. N., Trifonov, E. N., Flowering buds of globular proteins: transpiring simplicity of protein organization, Comp Funct Genom 3, 525-534 (2002)

Trifonov, E. N., Evolution of the code and the earliest proteins. Reconstruction from present-day sequences. Biophysics 47, 581-586 (2002)

Berezovsky, I. N., Kirzhner, V. M., Kirzhner, A., Rosenfeld, V. R., Trifonov, E. N., Closed loops: persistence of the protein chain returns, Prot. Eng. 15, 955-957 (2002)

2003

Trifonov, E. N., Kirzhner, A., Kirzhner, V.M., Berezovsky, I. N., An eye-opener to protein structure, ComPlexUs 1, 29-37 (2003)   www.karger.com/cpu

Trifonov, E. N., Berezovsky, I. N., Evolutionary aspects of protein structure and folding, Curr. Opinion Struct. Biol. 13, 110-114 (2003)

Kato, M., Onishi, Y., Wada-Kiyama, Y., Abe, T., Ikemura, T., Kogan, S., Bolshoy, A., Trifonov, E. N., KiyamaR., Dinucleosome DNA of human K562 cells: experimental and computational characterizations. J. Molec. Biol. 332, 111-125 (2003)

Berezovsky, I. N., Kirzhner, V. M., Kirzhner, A., Rosenfeld, V. R., Trifonov, E. N., Protein sequences yield a proteomic code, J. Biomol. Struct. Dyn. 21, 317-325 (2003)

Berezovsky, I. N., Kirzhner, A., Kirzhner, V. M., Trifonov, E. N., Spelling protein structure, J. Biomol. Struct. Dyn. 21, 327-339 (2003)

Peleg, O., Trifonov, E. N., Bolshoy, A., Hidden messages in the nef gene of human immunodeficiency virus Type 1 suggest a novel RNA secondary structure. Nucl. Acids Res. 31, 4192-4200 (2003)

Bellgard, M., Gamble, T., Reynolds, M., Hunter, A., Trifonov, E., Taplin, R., Gap Mapping: A paradigm for aligning two sequences. Applied Bioinformatics 2, Suppl. 3, 1-5 (2003)

Berezovsky I. N., Trifonov, E. N., Protein structure: marriage with polymer physics, In "Protein structures. Kaleidoscope of Structural Properties and Functions", v. 1, Uversky V. N., Editor, Transworld Research Network, Trivandrum, India, pp 1-15 (2003)

Trifonov, E. N., Genetic code: evolution. In Cooper D (Ed.), "Encyclopedia of the Human Genome", Nature Publishing Group, London, pp 735-738 (V. 2) (2003).

On line: Trifonov, Edward N., "Genetic Code: Evolution", in Encyclopedia of Life Sciences. Chichester, UK: John Wiley & Sons, Ltd. DOI: 10.1038/npg.els.0005073 (2003)

2004

Trifonov, E. N., The tuning function of the tandemly repeating sequences: molecular device for fast adaptation. In: Evolutionary Theory and Processes: Modern Horizons, Wasser, S. P. (Ed.), Kluwer Academic Publishers, pp 115-138 (2004)

Trifonov, E. N. The triplet code from first principles. J Biomolec Str Dyn 22, 1-11 (2004)

Hosid, S., Trifonov, E. N., Bolshoy, A., Sequence periodicity of Escherichia coli genome is concentrated in intergenic regions. BMC Molecular Biology 5:14 (2004). http://www.biomedcentral.com/bmcmolbiol/

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

2005

Aharonovsky, E., Trifonov, E. N.Sequence structure of van der Waals  

locks in proteins. J Biomol Str Dyn 22, 545-554 (2005)

Frenkel Z., Trifonov, E. N., Closed loops of TIM barrel protein fold, J Biomol Str Dyn 22, 643-656 (2005)

Cohanim, A. B., Kashi, Y., Trifonov, E. N., Yeast nucleosome DNA pattern: deconvolution from genome sequences of S. cerevisiae. J Biomol Str Dyn 22, 687-694 (2005)

Kogan, S., Trifonov, E. N., Gene splice sites correlate with nucleosome positions, Gene 352, 57-62 (2005)

Aharonovsky, E., Trifonov, E. N., Protein sequence modules. J Biomol Str Dyn 23, 237-242 (2005)

Sobolevsky, Y., Trifonov, E. N., Conserved sequences of prokaryotic proteomes and their compositional age. J Mol Evol 61, 591-596 (2005)

2006

Trifonov, E. N. Theory of early molecular evolution: Predictions and confirmations. In: Discovering Biomolecular Mechanisms with Computational Biology (Ed. F. Eisenhaber), Landes Bioscience, Georgetown, pp 107-116      (2006)

King, D. G., Trifonov, E. N., Kashi, Y., Tuning knobs in the genome: evolution of simple sequence repeats by indirect selection. In "The Implicit Genome" (Ed. L. H. Caporale), Oxford University Press, New York, pp 77-90 (2006)

Cohanim, A. B., Kashi, Y., Trifonov, E. N., Three sequence rules for chromatin, J Biomol Str Dyn 23, 559-566 (2006)

Gershenzon, N. I., Trifonov, E. N., Ioshikhes, I. P., The features of Drosophila core promoters revealed by statistical analysis. BMC Genomics 7:161 (2006)

Kogan, S. B., Kato, M., Kiyama, R., Trifonov, E. N., Sequence structure of human nucleosome DNA. J Biomol Str Dyn 24, 43-48 (2006)

Gabdank, I., Barash, D., Trifonov, E. N., Tracing ancient mRNA hairpins. J Biomol Str Dyn 24, 163-170 (2006)

Sobolevsky, Y., Trifonov, E. N., Protein modules conserved since LUCA. J Mol Evol 63, 622-634 (2006)

Trifonov, E. N., Kogan, S., Cohanim, A. B. Latest on the nucleosome positioning sequence patterns. In "DNA Structure, Chromatin and Gene Expression" (Eds. R. Kiyama, M. Shimizu), Transworld Research Network, Trivandrum (India), pp 43-54 (2006)

Trifonov, E. N., Gabdank, I., Barash, D, Sobolevsky, Y., Primordia vita. Deconvolution from modern sequences, Origin Life Evol Biosph 36, 559-565 (2006)

Trifonov, E. N., Self-inflicted fear of evolution, Origin Life Evol Biosph 36, 557-558 (2006)

Cohanim, A. B., Trifonov, E. N., Kashi, Y., Specific selection pressure on the third codon positions: contribution to 10 - 11 base periodicity in prokaryotic genomes. J. Molec. Evol. 63, 393-400 (2006)

Trifonov, E. N., Early molecular evolution, Isr. J. Ecol. Evol. 52, 375-387 (2006)

2007

Frenkel, Z. M., Trifonov, E. N., Walking through protein sequence space. J Theor Biol 244, 77-80 (2007)

Frenkel, Z. M., Trifonov, E. N. Walking through the protein sequence space: Towards new generation of the homology modeling. Proteins Str Function Bioinf 67, 271-284 (2007) 

Salih, F., Salih, B., Trifonov, E. N. Sequence-directed mapping of nucleosome positions. J Biomolec Str Dyn 24, 489-493 (2007)

Frenkel, Z. M., Trifonov, E. N., Evolutionary networks in the formatted protein sequence space, J Comput Biol 14, 1044-1057 (2007)

Sobolevsky, Y, Frenkel, ZM, Trifonov EN. Combinations of ancestral modules in proteins, J Molec Evol 65, 640-650 (2007)

2008     

Trifonov, E. N., Codes of biosequences. In: The Codes of Life. The Rules of Macroevolution. Barbieri, M. (ed.). Springer. New York, pp 3-14, 2008

Frenkel, Z. M., Trifonov, E. N. From protein sequence space to elementary protein modules, Gene 408, 64-71 (2008)

Rapoport, A. E., Trifonov, E. N. Excessive clustering of third codon position pyrimidines in prokaryotes. J Biomolec Str Dyn 25, 647-653 (2008)

Trifonov, E. N., Tracing Life back to elements, Physics of Life Reviews 5, 121-132 (2008)

Salih, F., Salih, B., Kogan, S., Trifonov, E. N. Epigenetic nucleosomes: Alu sequences and CG as nucleosome positioning element. J Biomolec Str Dyn 26, 9-16 (2008)

Trifonov, E. N., Genetic Code: Evolution, Encyclopedia of Life Sciences, John   

Wiley & Sons, Ltd, Chichester, UK, 2008, on line. http://www.els.net/ [DOI:  

10.1002/9780470015902.a0005073.pub2]

Also (the same text):  

Trifonov, E. N., Genetic code: evolution, In Handbook of Human Molecular Evolution edited by David N. Cooper and Hildegard Kehrer-Sawatzki, Wiley & Sons, in press (august 2008)

Salih, F., Salih, B., Trifonov, E. N., Sequence structure of hidden 10.4-base repeat in the nucleosomes of C. elegans . J. Biomol. Str. Dyn 26, 273-282 (2008) 

Frenkel, Z. M., Trifonov, E. N., Structural relatedness via sequence space of protein modules. In "Protein Conformation: New Research" (Ed. L. B. Roswell), 2008. Nova Science Publishers, Inc., Hauppauge, NY, USA, pp. 239-250

2009

Gabdank,I., Barash, D., Trifonov,E. N., Nucleosome DNA bendability matrix (C. elegans). J. Biomol. Str. Dyn 26, 403-412 (2009).

Trifonov, E. N., Frenkel, Z. M., Evolution of protein modularity, Curr Opinion Struct Biol 19, 335-340 (2009)

Trifonov, E. N., Earthly and Heavenly: Abiogenesis and the Invasion of Life,
J. Cosmology 1, 84-85 (2009)

Trifonov, E. N., Origin of the genetic code and of the earliest oligopeptides,   Res. Microbiol. 160, 481-486 (2009)

Bettecken, T., Trifonov E. N., Repertoires of the nucleosome-positioning dinucleotides. PLoS ONE 4, e7654 (2009)

Frenkel, Z. M., Frenkel, Z. M., Trifonov, E. N., Snir, S., Structural Relatedness via Flow Networks in Protein Sequence Space, J Theor Biol 260, 438-444 (2009)

2010

Trifonov, E. N. Base pair stacking in nucleosome DNA and bendability sequence pattern. J Theor Biol 263, 337-339 (2010)

Trifonov, E. N. Nucleosome positioning by sequence, state of the art and apparent finale. J Biomol Str Dyn 27, 741-746 (2010)

Gabdank, I., Barash, D., Trifonov E. N. FineSTR : a web server for single-base-resolution nucleosome positioning. Bioinformatics 26, 845-846 (2010)

Gabdank, I., Barash, D., Trifonov, E. N. Single-base resolution nucleosome mapping on DNA sequences. J Biomol Str Dyn 28, 107-121 (2010)

 2011

Rapoport, A. E., Frenkel, Z. M., Trifonov, E. N. Nucleosome positioning pattern derived from oligonucleotide compositions of genomic sequences. J Biomol Struct Dyn 28, 567-574 (2011)

Trifonov, E. N. Cracking the chromatin code: precise rule of nucleosome positioning. Physics of Life Reviews 8, 39-50 (2011)

Trifonov, E. N. Nucleosome positioning rules: soft and hard disagreements. Physics of Life Reviews 8, 69-72 (2011)

Koren, Z., Trifonov, E. N. Role of everlasting triplet expansions in protein evolution. J Mol Evol 72, 232-239 (2011)

Frenkel, Z. M., Bettecken T.,Trifonov E. N. Nucleosome DNA sequence structure of isochores. BMC Genomics 12:203 (2011)

Trifonov, E. N. Thirty years of multiple sequence codes. Genomics Proteomics Bioinformatics 9, 1-6 (2011)

Pino, S., Trifonov, E. N., Di Mauro E. On the Observable Transition to Living Matter. Genomics Proteomics Bioinformatics 9, 7-14 (2011)

Bettecken, T., Frenkel, Z. M., Trifonov, E. N. Human nucleosomes: special role of CG dinucleotides and Alu-nucleosomes. BMC Genomics 12:273 (2011)

Trifonov, E. N., Zhurkin, V. B., Jond Widom, the Scientist. J Biomol Str Dyn 29, 257-258 (2011)

Trifonov, E. N. Vocabulary of definitions of life suggests a definition, J Biomolec Str Dyn 29, 259-266 (2011)

Rapoport, A. E., Trifonov, E. N.  "Anticipated" nucleosome positioning pattern in prokaryotes, Gene 488, 41-45 (2011)

Hapala, J., Trifonov, E. N. High resolution positioning of intron ends on the nucleosomes, Gene 489, 6-10 (2011)  

Frenkel, Z. M., Trifonov, E. N., Volkovich, Z., Bettecken, T. Nucleosome positioning patterns derived from human apoptotic nucleosomes. J Biomolec Str Dyn 29, 577-583 (2011)

2012

Trifonov, E. N. Definition of Life: Navigation through Uncertainties. JBiomol Str Dyn 29, 647-650 (2012)  

Trifonov E. N. What is life. The Scientist. Feb. 16, (2012) 

Di Mauro, E., A. K. Dunker, E. N. Trifonov, Disorder to order, non-life to life. In the beginning there was ...a mistake. GENESIS - In The Beginning. Precursors of Life, Chemical Models and Early Biological Evolution, Series: Cellular Origin, Life in Extreme Habitats and Astrobiology, Vol. 22, Part 3, 415-435, (Joseph Seckbach and Richard Gordon editors), Springer (2012)

Frenkel Z. M., Trifonov E. N.  Origin and evolution of genes and genomes. Crucial role of triplet expansions. J Biomol Str Dyn 30, 201-210 (2012)   

Bettecken T., Frenkel, Z. M., Altmüller, J., Nürnberg, P., Trifonov, E. N. Apoptotic Cleavage of DNA in Human Lymphocyte Chromatin Shows high Sequence Specificity. J Biomol Str Dyn 30, 211-216 (2012)

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