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Edward Trifonov

Summary

Edward Nikolayevich Trifonov (Hebrew: אדוארד טריפונוב, Russian: Эдуapд Тpифoнoв; b. March 31, 1937) is a Russian-born Israeli molecular biophysicist and a founder of Israeli bioinformatics. In his research, he specializes in the recognition of weak signal patterns in biological sequences and is known for his unorthodox scientific methods.

Edward Nikolayevich Trifonov
BornMarch 31, 1937 (1937-03-31) (age 87)
Leningrad, USSR
NationalityIsraeli
Alma materMoscow Institute of Physics and Technology
Known forDNA periodicity, DNA curvature, nucleosome positioning, protein structure, molecular evolution
Scientific career
FieldsBioinformatics, genomics, molecular biophysics, proteomics
InstitutionsMoscow Institute of Physics and Technology
I. V. Kurchatov Institute of Atomic Energy
Weizmann Institute of Science
University of Haifa
Doctoral advisorYuri Semenovich Lazurkin
Doctoral studentsJaime Lagunez
שָׁלוֹם
This section contains Hebrew text. Without proper rendering support, you may see question marks, boxes, or other symbols instead of Hebrew letters.

He discovered the 3-bp and 10-bp periodicity in the DNA sequences, as well as the rules determining the curvature of DNA molecules and their bending within nucleosomes. Trifonov unveiled multiple novel codes in biological sequences and the modular structure of proteins. He proposed an abiogenic theory of the origin of life, and molecular evolution from single nucleotides and amino acids to present-day DNA and protein sequences.

Biography edit

Trifonov was born in Leningrad (now Saint Petersburg), USSR in 1937. He was raised by his mother, Riva, and his step-father, Nikolay Nikolayevich Trifonov. In his school years, he became interested in medicine and physics.[1] As a result, he went to study biophysics in Moscow. He started his scientific career in the USSR. In 1976, he made aliyah (immigrated as a Jew) to Israel.[2] His role model is Gregor Mendel.[1][3]

Education and scientific career edit

 
With refuseniks and Andrei Sakharov before 1976

Trifonov graduated[4] in biophysics from the Moscow Institute of Physics and Technology in 1961 and earned his PhD degree in molecular biophysics there in 1970. He worked as a researcher at the Moscow Physico-Technical Institute from 1961 to 1964. Then he moved to the Biological Department at the I. V. Kurchatov Institute of Atomic Energy in Moscow, staying there until 1975. After his immigration to Israel, he joined the Department of Polymer Research at The Weizmann Institute of Science as an associate professor. He worked there from 1976 to 1991 before moving to the Department of Structural Biology as a full professor in 1992. He was appointed professor emeritus in 2003. During that time, he was also a head of the Center for Genome Structure and Evolution at the Institute of Molecular Sciences in Palo Alto, California (1992–1995).

Trifonov has been a head of the Genome Diversity Center at the Institute of Evolution at the University of Haifa in Israel since 2002, and a professor at Masaryk University in Brno, Czech Republic since 2007.

Membership of learned societies

  • USSR Biochemical Society (1970)
  • The Israel National Committee for CODATA (1987)
  • International Society of Molecular Evolution (1993)
  • International Society of Gene Therapy and Molecular Biology (1997)

Editorial and advisory Boards

  • Editor, microbiology and biochemistry sections of Russian "Biological Abstracts" (1970–1975)
  • Editor, Journal of Biomolecular Structure and Dynamics (1988–1995)
  • Editorial board and associate editor, Journal of Molecular Evolution (1993–2004)
  • Academic Council of the College of Judea and Samaria (Kedumim–Ariel, West Bank) (1994–1999)
  • Editorial board of Gene Therapy and Molecular Biology (since 1997)
  • Editorial board of OMICS, Journal of Integrative Biology (since 2006)
  • Editorial advisory board, Biomolecular Structure and Dynamics (since 2010)

Research edit

At the beginning of his scientific career, Trifonov studied characteristics of the DNA with biophysical methods. After his relocation to Israel in 1976, he switched over to bioinformatics, and established the first research group for that discipline in the country.[2] He is known for his innovative insights into the world of biological sequences.[5]

Research areas edit

Periodicity in biological sequences edit

Trifonov pioneered the application of digital signal processing techniques to biological sequences. In 1980, he and Joel Sussman used autocorrelation to analyse chromatin DNA sequences.[6] They were the first to discover two periodical patterns in the DNA sequences, namely 3 bp and 10-11bp (10.4) periodicity.[7]

Chromatin structure edit

Since the beginning of his Israeli scientific period Trifonov has been studying the chromatin structure,[8] investigating how certain segments of the DNA are packed inside the cells in protein-DNA complexes called nucleosomes. In a nucleosome, the DNA winds around the histone protein component. The principle of this winding (and thus the rules determining nucleosome positions), was not known at the beginning of the 1980s, although multiple models had been suggested.[9] These included

  • The "hinge" model: the DNA molecule was assumed to be a rigid rod-like structure interrupted by sharp kinks (up to 90°), with the straight segments being a multiple of 10 bp long.
  • The "isotropic" model: the DNA molecule is bent smoothly along its length, with the same angle between every two base pairs.
  • The "mini-kinks" model: Similar to the hinge model, but with smoother kinks every 5 bp.

Trifonov supported the concept of smooth bending of the DNA.[10] However, he proposed that angles between the base pairs are not equal, but their size depends on the particular neighboring base pairs thus introducing an "anisotropic" or "wedge" model.

This model was based on the work of Trifonov and Joel Sussman who had shown[11] in 1980 that some of the dinucleotides (nucleotide dimers) are frequently placed in regular (periodical) distances from each other in the chromatin DNA. This was a breakthrough discovery[11] initiating a search for sequence patterns in the chromatin DNA. They had also pointed out that those dinucleotides repeated with the same period as the estimated pitch (the length of one DNA helix repeat) of the chromatin DNA (10.4 bp).

Thus in his wedge model, Trifonov supposed that each combination of neighboring base pairs form a certain angle (specific for these base pairs). He called this feature curvature.[12] Moreover, he suggested that in addition to curvature, each base pairs step could be deformed to different extent being bound to the histone octamer and he called it bending.[13] These two features of DNA present in the nucleosomes – curvature and bending have been now considered major factors playing a role in the nucleosome positioning.[14]: 41  Periodicity of other dinucleotides were confirmed later by Alexander Bolshoy and co-workers.[15] Finally, an ideal sequence of the nucleosomal DNA was derived in 2009 by Gabdank, Barash and Trifonov.[16] The proposed sequence CGRAAATTTYCG (R standing for a purine: A or G, Y for a pyrimidine: C or T) expresses the preferential order of the dinucleotides in the sequence of the nucleosomal DNA. However, these inferences are disputed by some scientists.[17]

Another question closely related to the chromatin structure which Trifonov pursued to answer was the length of the DNA helical repeat (turn) within nucleosomes.[14]: 42  It is known that in free DNA (i.e. DNA which is not part of a nucleosome), the DNA helix twists 360° per approximately 10.5 bp. In 1979, Trifonov and Thomas Bettecken estimated[18] the length of a nucleosomal DNA repeat to be 10.33–10.4 bp. This value was finally confirmed and refined to 10.4 bp with crystallographic analysis in 2006.[19]

Multiple genetic codes edit

Trifonov advocates[20]: 4  the notion that biological sequences bear many codes contrary to the generally recognized one genetic code (coding amino acids order). He was also the first to demonstrate[21] that there are multiple codes present in the DNA. He points out that even so called non-coding DNA has a function, i.e. contains codes, although different from the triplet code.

Trifonov recognizes[20]: 5–10  specific codes in the DNA, RNA and proteins:

  1. in DNA sequences
    chromatin code (Trifonov 1980)
    is a set of rules responsible for positioning of the nucleosomes.
  2. in RNA sequences
    RNA-to-protein translation code (triplet code)
    Every triplet in the RNA sequence corresponds (is translated) to a specific amino acid.
    splicing code
    is a code responsible for RNA splicing; still poorly identified.
    framing code (Trifonov 1987)
    The consensus sequence of the mRNA is (GCU)n which is complementary to (xxC)n in the ribosomes.
    It maintains the correct reading frame during mRNA translation.
    translation pausing code (Makhoul & Trifonov 2002)
    Clusters of rare codons are placed in the distance of 150 bp from each other.
    The translation time of these codons is longer than of their synonymous counterparts which slows down the translation process and thus provides time for the fresh-synthesized segment of a protein to fold properly.
  3. in protein sequences
    protein folding code (Berezovsky, Grosberg & Trifonov 2000)
    Proteins are composed of modules.
    The newly synthesized protein is folded a module by module, not as a whole.
  4. fast adaptation codes (Trifonov 1989)
  5. codes of evolutionary past
    binary code (Trifonov 2006)
    The first ancient codons were GGC and GCC from which the other codons have been derived by series of point mutations. Nowadays, we can see it in modern genes as "mini-genes" containing a purine at the middle position in the codons alternating with segments having a pyrimidine in the middle nucleotides.
    genome segmentation code (Kolker & Trifonov 1995)
    Methionines tend to occur every 400 bps in the modern DNA sequences as a result of fusion of ancient independent sequences.

The codes can overlap[20]: 10  each other so that up to 4 different codes can be identified in one DNA sequence (specifically a sequence involved in a nucleosome). According to Trifonov, other codes are yet to be discovered.

Modular structure of proteins edit

Trifonov's concept of protein modules tries to address the questions of proteins evolution and protein folding. In 2000, Trifonov with Berezovsky and Grosberg studied[22] protein sequences and tried to identify simple sequential elements in proteins. They postulated that structurally diverse closed loops of 25–30 amino acid residues are universal building blocks of protein folds.

They speculated that at the beginning of the evolution, there were short polypeptide chains which later formed these closed loops. They supposed[23] that the loops structure provided more stability to the sequence and thus was favored in the evolution. Modern proteins are probably a group of closed loops fused together.

To trace the evolution of sequences, Trifonov and Zakharia Frenkel introduced[24][25] a concept of protein sequence space based on the protein modules. It is a network arrangement of sequence fragments of the length of 20 amino acids obtained from a collection of fully sequenced genomes. Each fragment is represented as a node. Two fragments with certain level of similarity to each other are connected with an edge. This approach should make it possible to determine function of uncharacterized proteins.

Protein modularity could also give an answer to the Levinthal's paradox, i.e. the question how a protein sequence can fold in a very short time.[26]

Molecular evolution and the origin of life edit

In 1996 Thomas Bettecken, a German geneticist noticed[27]: 108  that most of the triplet expansion diseases can be attributed only to two triplets: GCU and GCC, the rest being their permutations or complementary counterparts. He discussed this finding with Trifonov, his friend and colleague. Trifonov had earlier discovered (GCU)n to be a hidden mRNA consensus sequence. Thus the combination of these two facts led them to the idea that the (GCU)n could reflect a pattern of ancient mRNA sequences.

The first triplets

Since GCU and GCC appeared to be the most expandable (or the most "aggressive") triplets, Trifonov and Bettecken inferred that they could be the first two codons. Their ability to expand rapidly comparing to other triplets would provide them with evolutionary advantage.[28]: 123  Single point mutations of these two would give rise to 14 other triplets.

Consensus temporal order of amino acids

Having the suspected first two triplets, they pondered which amino acids appeared the first, or more generally in which order all the proteinogenic amino acids emerged. To address this question, they resorted[27]: 108  to three, according to them the most natural, hypotheses:

  1. The earliest amino acids were chemically the simplest.
  2. They would be present among the products of the Miller–Urey experiment.
  3. They would be associated with the older one of the two known classes of aminoacyl-tRNA synthetases.

Later on, Trifonov collected even 101 criteria[20]: 123  for the amino acids order. Each criterion could be represented as a vector of length 20 (for 20 basic amino acids). Trifonov averaged over them and got the proposed temporal order of the amino acids emergence, glycine and alanine being the first two ones.

Results and predictions

Trifonov elaborated these concepts further and proposed[27]: 110–115  these notions:

  • Evolutionary table of the triplet code.
  • Glycine-content of a protein can be used as a measure of the respective protein age (Glycine clock).[29]
  • Proteins are composed of short oligopeptides derived from ancient sequences being either oligoalanines or oligoglycines (thus two "alphabets").
  • These two alphabets distinguished by the type of nucleotide in the middle positions within triplets (purines or pyrimidines) provide us with a "binary code" which can be used for more accurate analyses of proteins relatedness.

Definition of life

A part of Trifonov's work on the molecular evolution is his aim to find a concise definition of life. He collected[30] 123 definitions by other authors. Instead of dealing with logical or philosophical arguments, he analyzed the vocabulary of the present definitions. By an approach close to the Principal component analysis, he derived a consensus definition: "Life is self-reproduction with variations". This work gained multiple critical comments.[31]

Research techniques and approaches edit

Linguistic sequence complexity edit

Linguistic sequence complexity[32] (LC) is a measure introduced by Trifonov in 1990. It is used for analyses and characterization of biological sequences. LC of a sequence is defined as "richness" of its vocabulary, i.e. how many different substrings of certain length are present in the sequence.

Terminology edit

DNA curvature vs. DNA bending edit

Trifonov strictly differentiates[14]: 47  between two notions:

curvature
a property of free DNA which has curvilinear shape due to slight differences in the angles between neighboring base pairs
bending
a deformation of DNA as a result of binding to proteins (e.g. to the histone octamer)

Both of these features are directed by the particular DNA sequence.

(Multiple) Genetic codes edit

While the scientific community recognize one genetic code,[20]: 4  Trifonov promotes the idea of multiple genetic codes. He adverts to recurring events of a discovery of yet another "the second" genetic code.

Honors edit

  • Kurchatov Prize for Young Scientists (1969)
  • Kurchatov Prize for Basic Research (1971)
  • Kleeman Professor of Molecular Biophysics (1982–2002)
  • Adjunct Professor of Lomonosov Moscow State University (1999)
  • The Stanislaw Ulam Memorial Lecture at the 2003 RECOMB meeting, Berlin (2003)
  • Mendel Lecture, Brno, Abbey of St. Thomas, (2004)
  • Distinguished Membership Award of ISBCB[33](2008)
  • Distinguished Citizen Fellow Indiana University South Bend, South Bend, Indiana, USA (2009)

Citations edit

  1. ^ a b Czech TV 2011.
  2. ^ a b Interface Magazine 1999.
  3. ^ IL GSGM 2010.
  4. ^ Trifonov: CV.
  5. ^ ISBCB Distinguished Membership Award.
  6. ^ Trifonov & Sussman 1980.
  7. ^ Vaidyanathan & Yoon 2004 and Poptsova 2014, p. 128
  8. ^ Trifonov: Publications.
  9. ^ Zhurkin, Lysov & Ivanov 1979, p. 1081.
  10. ^ Trifonov 1980, p. 4041.
  11. ^ a b Trifonov & Sussman 1980 cited in Cui & Zhurkin 2010, p. 822
  12. ^ Trifonov & Sussman 1980 and Trifonov 1980 cited in Cui & Zhurkin 2010, p. 822 and Trifonov 2011b, p. 41
  13. ^ Ohyama 2001, p. 708.
  14. ^ a b c Trifonov 2011b.
  15. ^ Bolshoy et al. 1991 cited in Pérez-Martín, Rojo & de Lorenzo 1994, p. 268
  16. ^ Gabdank, Barash & Trifonov 2009 cited in Trifonov 2011b, p. 46
  17. ^ Travers 2011, p. 54.
  18. ^ Trifonov & Bettecken 1979 cited in Trifonov 2011b, p. 42
  19. ^ Cohanim, Trifonov & Kashi 2006 cited in Trifonov 2011b, p. 42
  20. ^ a b c d e Trifonov 2008a.
  21. ^ Trifonov 1980 cited in Trifonov 2008a, p. 4
  22. ^ Berezovsky, Grosberg & Trifonov 2000.
  23. ^ Trifonov & Berezovsky 2003.
  24. ^ Frenkel & Trifonov 2007.
  25. ^ Frenkel & Trifonov 2008.
  26. ^ Berezovsky & Trifonov 2002.
  27. ^ a b c Trifonov 2006.
  28. ^ Trifonov 2008b.
  29. ^ Trifonov 1999.
  30. ^ Trifonov 2011a.
  31. ^ Zimmer 2012
    Szostak 2012
    Di Mauro 2012
    Koonin 2012
    Mittal 2012
    Sarma 2012
  32. ^ Trifonov 1990 cited in Troyanskaya et al. 2002, p. 680
  33. ^ ISBCB Distinguished Membership Award
    ISBCB 11th Symposium report
    ISBCB homepage

References edit

Books edit

  • Trifonov, Edward N. (2006). "Theory of early molecular evolution: predictions and confirmations". In Eisenhaber, Frank (ed.). Discovering biomolecular mechanisms with computational biology. Springer. ISBN 978-0-387-34527-7. Retrieved 22 March 2012.
  • Trifonov, Edward N. (2008a). "Codes of biosequences". In Barbieri, Marcello (ed.). The Codes of Life. Biosemiotics. Vol. 1. Springer (published 2008). pp. 3–14. doi:10.1007/978-1-4020-6340-4_1. ISBN 978-1-4020-6339-8.
  • Poptsova, Maria S. (2014). Poptsova, Maria S. (ed.). Genome analysis : current procedures and applications. Norfolk: Caister Academic Press. ISBN 9781908230294.

Scientific papers edit

  • Cui, Feng; Zhurkin, Victor B. (2010). "Structure-based Analysis of DNA Sequence Patterns Guiding Nucleosome Positioning in vitro". Journal of Biomolecular Structure & Dynamics. 27 (6): 821–841. doi:10.1080/073911010010524947. ISSN 0739-1102. PMC 2993692. PMID 20232936.
  • Di Mauro, Ernesto (2012). "Comment Trifonov's Meta-Definition of Life" (PDF). Journal of Biomolecular Structure & Dynamics. 29 (4): 601–602. doi:10.1080/073911012010524999. ISSN 0739-1102. PMID 22208252.
  • Koonin, Eugene V. (2012). "Comment Defining Life: An Exercise in Semantics or A Route to Biological Insights?" (PDF). Journal of Biomolecular Structure & Dynamics. 29 (4): 603–605. doi:10.1080/073911012010525000. ISSN 0739-1102. PMID 22208253. S2CID 1732987.
  • Mittal, Aditya (2012). "Comment Self-Generated and Reproducible Dynamics in "Gene Years" Represent Life". Journal of Biomolecular Structure & Dynamics. 29 (4): 609–611. doi:10.1080/073911012010525002. ISSN 0739-1102. PMID 22208255.
  • Ohyama, Takashi (2001). "Intrinsic DNA bends: an organizer of local chromatin structure for transcription". BioEssays. 23 (8): 708–715. doi:10.1002/bies.1100. ISSN 0265-9247. PMID 11494319. S2CID 32669357.
  • Pérez-Martín, José; Rojo, Fernando; de Lorenzo, Víctor (1994). "Promoters Responsive to DNA Bending – A Common Theme in Prokaryotic Gene-Expression". Microbiological Reviews. 58 (2): 268–290. doi:10.1128/MMBR.58.2.268-290.1994. ISSN 0146-0749. PMC 372964. PMID 8078436.
  • Sarma, Ramaswamy H. (2012). "A Conversation on Definition of Life" (PDF). Journal of Biomolecular Structure & Dynamics. 29 (4): 597–598. doi:10.1080/073911012010524997. ISSN 0739-1102. PMID 22208249. S2CID 22483508.
  • Segal, Eran; Widom, Jonathan (2009). "What controls nucleosome positions?" (PDF). Trends in Genetics. 25 (8): 335–343. doi:10.1016/j.tig.2009.06.002. ISSN 0168-9525. PMC 2810357. PMID 19596482.
  • Szostak, Jack W. (2012). "Comment Attempts to Define Life Do Not Help to Understand the Origin of Life" (PDF). Journal of Biomolecular Structure & Dynamics. 29 (4): 599–600. doi:10.1080/073911012010524998. ISSN 0739-1102. PMC 4208307. PMID 22208251.
  • Travers, Andrew (2011). "The nature of DNA sequence preferences for nucleosome positioning. Comment on 'Cracking the chromatin code: Precise rule of nucleosome positioning' by Trifonov". Physics of Life Reviews. 8 (1): 53–55. Bibcode:2011PhLRv...8...53T. doi:10.1016/j.plrev.2011.01.010. ISSN 1571-0645. PMID 21292572.
  • Trifonov, Edward N. (2011b). "Cracking the chromatin code: Precise rule of nucleosome positioning". Physics of Life Reviews. 8 (1): 39–50. Bibcode:2011PhLRv...8...39T. doi:10.1016/j.plrev.2011.01.004. ISSN 1571-0645. PMID 21295529.
  • Troyanskaya, Olga G.; Arbell, Ora; Koren, Yehuda; Landau, Gad M.; Bolshoy, Alexander (2002). "Sequence complexity profiles of prokaryotic genomic sequences: A fast algorithm for calculating linguistic complexity". Bioinformatics. 18 (5): 679–688. doi:10.1093/bioinformatics/18.5.679. ISSN 1367-4803. PMID 12050064.
  • Vaidyanathan, P.P.; Yoon, Byung-Jun (2004). "The role of signal-processing concepts in genomics and proteomics". Journal of the Franklin Institute. 341 (1–2): 111–135. CiteSeerX 10.1.1.72.6984. doi:10.1016/j.jfranklin.2003.12.001.
  • Zhurkin, Victor B. (2011). "The first thirty years of nucleosome positioning – Comment on "Cracking the chromatin code: Precise rule of nucleosome positioning" by Trifonov". Physics of Life Reviews. 8 (1): 64–66. Bibcode:2011PhLRv...8...64Z. doi:10.1016/j.plrev.2011.02.001. ISSN 1571-0645. PMID 21330223.
  • Zhurkin, Victor B.; Lysov, Yury P.; Ivanov, Valery I. (1979). "Anisotropic flexibility of DNA and the nucleosomal structure". Nucleic Acids Research. 6 (3): 1081–1096. doi:10.1093/nar/6.3.1081. PMC 327755. PMID 440969.

Scientific papers – primary sources edit

  • Trifonov, Edward N.; Bettecken, Thomas (1979). "Noninteger pitch and nuclease sensitivity of chromatin DNA". Biochemistry. 18 (3): 454–456. doi:10.1021/bi00570a011. ISSN 0006-2960. PMID 420792.
  • Trifonov, Edward N.; Sussman, Joel L. (1980). "The pitch of chromatin DNA is reflected in its nucleotide sequence". Proceedings of the National Academy of Sciences. 77 (7): 3816–3820. Bibcode:1980PNAS...77.3816T. doi:10.1073/pnas.77.7.3816. PMC 349717. PMID 6933438.
  • Trifonov, Edward N. (1980). "Sequence-dependent deformational anisotropy of chromatin DNA". Nucleic Acids Research. 8 (17): 4041–4054. doi:10.1093/nar/8.17.4041. ISSN 0305-1048. PMC 324213. PMID 7443521.
  • Trifonov, Edward N. (1987). "Translation framing code and frame-monitoring mechanism as suggested by the analysis of mRNA and 16 S rRNA nucleotide sequences". Journal of Molecular Biology. 194 (4): 643–652. doi:10.1016/0022-2836(87)90241-5. ISSN 0022-2836. PMID 2443708.
  • Trifonov, Edward N. (1989). "The multiple codes of nucleotide sequences". Bulletin of Mathematical Biology. 51 (4): 417–432. doi:10.1007/BF02460081. ISSN 0092-8240. PMID 2673451. S2CID 189884626.
  • Trifonov, Edward N. (1990). "Making sense of the human genome". Structure and Methods, Vol. 1. Human Genome Initiative and DNA Recombination; Proceedings of the Sixth Conversation in the Discipline Biomolecular Stereodynamics. Albany, New York, USA: Adenine Press. pp. 69–78. ISBN 0-940030-29-2.
  • Bolshoy, Alexander; McNamara, Peter; Harrington, Robert E.; Trifonov, Edward N. (1991). "Curved DNA without A-A: experimental estimation of all 16 DNA wedge angles". Proceedings of the National Academy of Sciences of the United States of America. 88 (6): 2312–6. Bibcode:1991PNAS...88.2312B. doi:10.1073/pnas.88.6.2312. ISSN 0027-8424. PMC 51221. PMID 2006170.
  • Kolker, Eugene; Trifonov, Edward N. (1995). "Periodic Recurrence of Methionines: Fossil of Gene Fusion?". Proceedings of the National Academy of Sciences. 92 (2): 557–560. Bibcode:1995PNAS...92..557K. doi:10.1073/pnas.92.2.557. ISSN 0027-8424. PMC 42780. PMID 7831328.
  • Trifonov, Edward N. (1999). "Glycine clock: eubacteria first, archaea next, protoctista, fungi, planta and animalia at last". Gene Therapy and Molecular Biology. 4: 313–322.
  • Berezovsky, Igor N.; Grosberg, Alexander Y.; Trifonov, Edward N. (2000). "Closed loops of nearly standard size: common basic element of protein structure". FEBS Letters. 466 (2–3): 283–286. doi:10.1016/S0014-5793(00)01091-7. ISSN 0014-5793. PMID 10682844.
  • Berezovsky, Igor N.; Trifonov, Edward N. (2002). "Loop fold structure of proteins: Resolution of Levinthal's paradox" (PDF). Journal of Biomolecular Structure & Dynamics. 20 (1): 5–6. doi:10.1080/07391102.2002.10506817. ISSN 0739-1102. PMID 12144347. S2CID 33174198. Archived from the original (PDF) on 2005-02-12.
  • Makhoul, Cameel H.; Trifonov, Edward N. (2002). "Distribution of rare triplets along mRNA and their relation to protein folding". Journal of Biomolecular Structure & Dynamics. 20 (3): 413–420. doi:10.1080/07391102.2002.10506859. ISSN 0739-1102. PMID 12437379. S2CID 21978672.
  • Trifonov, Edward N.; Berezovsky, Igor N. (2003). "Evolutionary aspects of protein structure and folding". Current Opinion in Structural Biology. 13 (1): 110–114. doi:10.1016/S0959-440X(03)00005-8. ISSN 0959-440X. PMID 12581667. ISI:000181133300015.
  • Cohanim, Amir B.; Trifonov, Edward N.; Kashi, Yechezkel (2006). "Specific Selection Pressure at the Third Codon Positions: Contribution to 10- to 11-Base Periodicity in Prokaryotic Genomes". Journal of Molecular Evolution. 63 (3): 393–400. Bibcode:2006JMolE..63..393C. doi:10.1007/s00239-005-0258-1. ISSN 0022-2844. PMID 16897261. S2CID 32737768.
  • Frenkel, Zakharia M.; Trifonov, Edward N. (2007). "Walking through the protein sequence space: Towards new generation of the homology modeling". Proteins: Structure, Function, and Bioinformatics. 67 (2): 271–284. doi:10.1002/prot.21325. ISSN 0887-3585. PMID 17286283. S2CID 23415265.
  • Frenkel, Zakharia M.; Trifonov, Edward N. (2008). "From protein sequence space to elementary protein modules". Gene. 408 (1–2): 64–71. doi:10.1016/j.gene.2007.10.024. ISSN 0378-1119. PMID 18022768.
  • Trifonov, Edward N. (2008b). "Tracing Life back to elements". Physics of Life Reviews. 5 (2): 121–132. Bibcode:2008PhLRv...5..121T. doi:10.1016/j.plrev.2008.03.001. ISSN 1571-0645.
  • Gabdank, Idan; Barash, Danny; Trifonov, Edward N. (2009). "Nucleosome DNA Bendability Matrix (C-elegans)". Journal of Biomolecular Structure & Dynamics. 26 (4): 403–411. doi:10.1080/07391102.2009.10507255. ISSN 0739-1102. PMID 19108579.
  • Trifonov, Edward N. (2011a). "Vocabulary of Definitions of Life Suggests a Definition" (PDF). Journal of Biomolecular Structure & Dynamics. 29 (2): 259–266. doi:10.1080/073911011010524992. ISSN 0739-1102. PMID 21875147. S2CID 38476092.

Journals edit

  • "The First Genetic Word". Interface Magazine. Spring–Summer 1999. Archived from the original on 15 June 2022. Retrieved 10 May 2012.
  • Trifonov, Edward N. (April 2010). "Magic lead" (PDF). Informační Listy (36): 2–3. Archived from the original (PDF) on 5 January 2011.

Media edit

  • Vědci začali mapovat rostlinné DNA v trojrozměrném měřítku [The scientists started to map plant DNA in three dimensions] (in Czech). Brno, Czech Republic: Czech Television. 2011. Retrieved 22 March 2012.

Websites edit

  • "ISBCB presents this Distinguished Membership Award to Professor Edward Trifonov" (PDF). The Israeli Society for Bioinformatics and Computational Biology. 2008. Archived from the original (PDF) on 10 January 2012. Retrieved 20 March 2012.
  • "Report about the 11th Israeli Bioinformatics Symposium, April 2008". The Israeli Society for Bioinformatics and Computational Biology. 2008. Archived from the original on 20 March 2012. Retrieved 20 March 2012.
  • "Welcome to the home page of the Israeli Society for Bioinformatics and Computational Biology". The Israeli Society for Bioinformatics and Computational Biology. 2008. Archived from the original on 2009-05-10. Retrieved 20 March 2012.
  • Trifonov, Edward N. "Edward N. Trifonov Ph.D." The Institute of Evolution, University of Haifa. Archived from the original on 20 February 2012. Retrieved 20 March 2012.
  • Trifonov, Edward N. "(Curriculum Vitae)". The Institute of Evolution, University of Haifa. Archived from the original on 28 September 2013. Retrieved 20 March 2012.
  • Trifonov, Edward N. "(list of publications by Edward N. Trifonov)". The Institute of Evolution, University of Haifa. Archived from the original on 28 September 2013. Retrieved 20 March 2012.
  • Zimmer, Carl. "Can Science Define Life In Three Words?". Science 2.0. Archived from the original on 16 March 2012. Retrieved 22 March 2012.

External links edit

  • Trifonov, Edward N. (lecturer) (2010). Second, third, fourth... genetic codes - One spectacular case of code crowding. Prague, Czech Republic. Archived from the original (mp3) on 2010-10-10. Retrieved 26 March 2012.

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