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Homepage of Christian Michel THEORETICAL
BIOINFORMATICS Responsable Prof. Christian MICHEL
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Bioinformatique Théorique CSTB, ICube Université de Strasbourg, CNRS 300 Boulevard Sébastien Brant 67400 Illkirch, France Site: https://dpt-info.di.unistra.fr/~c.michel/ Site équipe: http://icube-cstb.unistra.fr/fr/index.php/Accueil |
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THEORETICAL BIOINFORMATICS
RESEARCH CIRCULAR CODE AND GENETIC CODE |
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SURPRISING DISCOVERY OF
A NEW GALAXY ! OF STARS ? OF GENOMES ? An answer in the article of Michel and Sereni (2023)
[PDF].
CURRENT INTERNATIONAL COLLABORATIONS Prof. Elena Fimmel, Hochschule Mannheim, Institut
für Angewandte Mathematik, Mannheim, Allemagne Prof. Lutz Strüngmann, Hochschule Mannheim, Institut
für Angewandte Mathematik, Mannheim, Allemagne THEORETICAL
BIOINFORMATICS RESEARCH The
objectives of the Theoretical Bioinformatics group are placed on the level of
fundamental and theoretical knowledge with the identification of rules and
properties in genes (more than 200 theorems, lemmas, propositions). Review: Article A38 Identification of statistical signals in genes: Articles
[A1,3-8,11,14,16] Identification of circular codes in genes: Articles
[A19,21,22,30,33,61,67,74,83,85,89] Identification of circular code motifs: Articles
[A53,59,65,72,73,77,79,80,82,84,87,88] Properties of circular codes in genes: Articles
[A36,41,46,49,63,64,66,92] Combinatorics of circular codes: Articles
[A27,39,40,47,50,52,54,55,57,58,60,70,71,75,76,78,81,86, 90,91,93] Computer models of gene evolution: Articles
[A8-10,12,20] Probabilistic models of gene evolution by substitution: Articles
[A13,15,17,23,24,31,32,34,35,37,42, 43,45,51] Probabilistic models of gene evolution by substitution, insertion and deletion: Articles [A48,56,62, 65,68] Phylogenetic distances and inference methods: Articles
[A35,37,44] Research software in bioinformatics: Articles
[A9,28,45,65,68] CIRCULAR
CODE AND GENETIC CODE
Figure
1. Main research fields of the theory of circular code in genes. The circular code theory proposes that a circular code has preceded
the genetic code. The circular code X identified in genes of bacteria, archaea,
eukaryotes, plasmids and viruses (Michel, 2017, Life 7, 20, 1-16, doi:10.3390/life7020020; Michel,
2015, J. Theor. Biol. 380, 156-177, doi:10.1016/j.jtbi.2015.04.009;
Arquès and Michel, 1996, J. Theor. Biol. 182, 45-58,
doi:10.1006/jtbi.1996.0142) is based on the 20 following trinucleotides:
Precisely, X is a maximal
C3 self-complementary trinucleotide circular code and has
three major properties: (i) to retrieve, maintain and synchronize the reading (correct) frame
at any position in a gene; (ii) to code 12 amino acids (according to the standard amino acid
code):
(iii) to generate X circular
code motifs in genes (Michel, Nguefack Ngoune, Poch, Ripp
and Thompson, 2017, Life 7, 52, 1-20,
doi:10.3390/life7040052) which can pair with the X circular
code motifs in tRNAs and rRNAs, in particular in the ribosome decoding center
(Michel, 2012, Comput. Biol. Chem. 37, 24-37,
doi:10.1016/j.compbiolchem.2011.10.002; El Soufi and Michel, 2014, Comput.
Biol. Chem. 52, 9-17, doi:10.1016/j.compbiolchem.2014.08.001). The
universally conserved nucleotides A1492 and A1493 and the conserved nucleotide
G530 are included in X circular code motifs. Reviews
in english [PDF] and [PDF] Review
in french [PDF] Fimmel
et Strüngmann, review article in Biosystems
(2018, vol. 164, 186-198):
MOTIFS OF THE CIRCULAR CODE X (X MOTIFS) IN THE RIBOSOME
DECODING CENTER
Motifs
of the circular code X in the ribosome decoding center: X
motifs of mRNA in green, X motif containing the universally conserved
A1492 and A1492 of rRNA in purple, X motif containing the universally
converved G530 of rRNA in fuchsia and X motifs of tRNAs in dark blue
(anticodon in black) (Michel, 2012; El Soufi and Michel, 2014).
Graphical representation here with the 16s rRNA of Thermus thermophilus (PDB
3I8G). Models
of gene evolution by substitution of genetic motifs (Benard, Michel) [PDF] Models
of gene evolution by substitution, insertion and deletion of nucleotides
(Lèbre, Michel) [PDF] Models
of gene evolution by substitution, insertion and deletion of genetic motifs
(Benard, Lèbre, Michel) [PDF] GETEC (Genome
Evolution by Transformation, Expansion and Contraction) (Benard E., Lèbre S.,
Michel C.J., 2015; [PDF])
to determine evolutionary analytical solutions of genetic motifs based on
substitution, insertion and deletion as a function of time or sequence
length, as well as in direct time direction (past-present) or in inverse time
direction (present-past) THEORETICAL
BIOINFORMATICS ARTICLES IN INTERNATIONAL JOURNALS 2025 [A98] Michel C.J., Sereni J.-S.
2025. Genome galaxy identified by
the circular code theory. Bulletin of Mathematical Biology 87:5, 1-35 [PDF] 2024 [A97] Michel C.J. 2024. Circular code identified by
the codon usage. Biosystems 244, 105308,
1-12. [PDF] [A96] Fimmel E., Michel C.J., Strüngmann L. 2024.
Circular cut codes in genetic information. Biosystems 243,
105263, 1-10. [PDF] [A95] Michel C.J. 2024. Circular code in introns. Biosystems
239, 105215, 1-9. [PDF] 2023 [A94] Fimmel E., Michel C.J., Strüngmann L. 2023.
Circular mixed sets. Biosystems 229,
104906, 1-11. [PDF] [A93] Fimmel E., Michel C.J., Pirot F., Sereni J.-S.,
Strüngmann L. 2023. Diletter and
triletter comma-free codes over finite alphabets. The
Australasian Journal of Combinatorics 86(2),
233-270. [PDF] [A92] Michel C.J., Sereni J.-S.
2023. Reading frame retrieval of
genes: a new parameter of codon usage based on the circular code theory. Bulletin
of Mathematical Biology 85:24, 1-21. [PDF] 2022 [A91] Michel C.J., Sereni J.-S.
2022. Trinucleotide k-circular
codes II: Biology. Biosystems 217, 104668, 1-18. [PDF]. [A90] Michel C.J., Mouillon B., Sereni
J.-S. 2022. Trinucleotide k-circular codes I:
Theory. Biosystems 217, 104667, 1-11. [PDF]. 2021 [A89] Michel C.J. 2021. Genes on the
circular code alphabet. Biosystems 206, 104431,
1-12. [PDF]. [A88] Thompson J.D., Ripp R., Mayer
C., Poch O., Michel C.J. 2021. Potential role of the X circular code in the regulation of
gene expression. Biosystems 203, 104368,
1-15. [PDF]. 2020 [A87] Michel C.J., Mayer
C., Poch O., Thompson J.D. 2020. Characterization of accessory
genes in coronavirus genomes. Virology Journal 17:131, 1-13.
[PDF]. [A86] Fimmel E., Michel C.J., Pirot F., Sereni J.-S.,
Starman M., Strüngmann L. 2020. The
relation between k-circularity and circularity of codes. Bulletin
of Mathematical Biology 82:105, 1-34. [PDF] [A85] Michel C.J. 2020. The maximality of circular
codes in genes statistically verified. Biosystems
197, 104201, 1-7. [PDF] [A84] Dila G., Michel C.J., Thompson J.D. 2020.
Optimality of circular codes versus the genetic code after frameshift errors. Biosystems
195, 104134, 1-11. [PDF] [A83] Michel C.J., Thompson J.D. 2020.
Identification of a circular code periodicity in the bacterial ribosome:
origin of codon periodicity in genes? RNA
Biology 17, 571-583. [PDF] 2019 [A82] Dila G., Ripp R., Mayer
C., Poch O., Michel C.J., Thompson J.D. 2019. Circular code
motifs in the ribosome: a missing link in the evolution of translation? RNA
25, 1714-1730. [PDF] [PDF Suppl. Mat.] [A81] Fimmel E., Michel C.J., Pirot F., Sereni J.-S.,
Strüngmann L. 2019. Mixed circular
codes. Mathematical Biosciences 317, 108231,
1-14. [PDF] [A80] Michel C.J. 2019. Single-frame, multiple-frame
and framing motifs in genes. Life 9, 18, 1-22. [PDF] [A79] Dila G., Michel C.J., Poch O., Ripp R.,
Thompson J.D. 2019. Evolutionary conservation and functional implications of
circular code motifs in eukaryotic genomes. Biosystems 175, 57-74. [PDF] 2018 [A78] Fimmel E., Michel C.J., Starman M., Strüngmann
L. 2018. Self-complementary circular
codes in coding theory. Theory in
Biosciences 137, 51-65. [PDF] 2017 [A77] Michel C.J., Nguefack Ngoune V., Poch O., Ripp
R., Thompson J.D. 2017. Enrichment of circular code motifs in the genes of
the yeast Saccharomyces cerevisiae.
Life 7, 52, 1-20. [PDF] [A76] Fimmel E., Michel C.J., Strüngmann L. 2017. Diletter circular codes over finite
alphabets. Mathematical Biosciences 294, 120-129. [PDF] [A75] Fimmel E., Michel C.J., Strüngmann L. 2017. Strong comma-free codes in genetic
information. Bulletin of Mathematical Biology 79,
1796-1819. [PDF] [A74] Michel C.J. 2017. The maximal C3
self-complementary trinucleotide circular code X in genes of bacteria,
archaea, eukaryotes, plasmids and viruses. Life 7, 20, 1-16. [PDF] [A73] El Soufi K., Michel C.J. 2017. Unitary
circular code motifs in genomes of eukaryotes. Biosystems 153, 45-62.
[PDF] 2016 [A72] El Soufi K., Michel C.J. 2016. Circular
code motifs in genomes of eukaryotes. Journal of Theoretical Biology
408, 198-212. [PDF] [A71] Fimmel E., Michel C.J., Strüngmann L. 2016. n-Nucleotide
circular codes in graph theory. Philosophical Transactions of the Royal
Society A: Mathematical, Physical and
Engineering Sciences 374, 20150058, 1-19. [PDF] [A70] Michel C.J., Pellegrini M., Pirillo G. 2016. Maximal
dinucleotide and trinucleotide circular codes. Journal of Theoretical
Biology 389, 40-46. [PDF] 2015 [A69] El Soufi K., Michel C.J. 2015. Circular
code motifs near the ribosome decoding center. Computational Biology and
Chemistry 59, 158-176. [PDF] [A68] Benard E., Lèbre S., Michel C.J. 2015. Genome
evolution by transformation, expansion and contraction GETEC. Biosystems
135, 15-34. [PDF] [A67] Michel C.J. 2015. The maximal C3
self-complementary trinucleotide circular code X in genes of bacteria,
eukaryotes, plasmids and viruses. Journal of Theoretical Biology 380,
156-177. [PDF] [A66] Michel C.J. 2015. An extended genetic scale of
reading frame coding. Journal of Theoretical Biology 365, 164-174. [PDF] 2014 [A65] El Soufi K., Michel C.J. 2014. Circular
code motifs in the ribosome decoding center. Computational Biology and
Chemistry 52, 9-17. [PDF] [A64] Michel C.J. 2014. A genetic scale of reading
frame coding. Journal of Theoretical Biology 355, 83-94. [PDF] [A63] Michel C.J., Seligmann H. 2014. Bijective
transformation circular codes and nucleotide exchanging RNA transcription. Biosystems
118, 39-50. [PDF] 2013 [A62] Lèbre S., Michel C.J. 2013. A
new molecular evolution model for limited insertion independent of
substitution. Mathematical Biosciences 245, 137-147. [PDF] [A61] Herrmann M., Michel C.J., Zugmeyer B. 2013. A necklace
algorithm to determine the growth function of trinucleotide circular codes. Journal
of Applied Mathematics and Bioinformatics 3, 1-40. [PDF] [A60] Benard E., Michel C.J. 2013. Transition and
transversion on the common trinucleotide circular code. Computational
Biology Journal 2013, Article ID 795418, 1-10. [PDF] [A59] Michel C.J. 2013. Circular code motifs in
transfer RNAs. Computational Biology and Chemistry 45, 17-29. [PDF] [A58] Michel C.J., Pirillo G. 2013. Dinucleotide
circular codes. ISRN Biomathematics 2013, Article ID 538631, 1-8. [PDF] [A57] Michel C.J., Pirillo G. 2013. A permuted set
of a trinucleotide circular code coding the 20 amino acids in variant nuclear
codes. Journal of Theoretical Biology 319, 116-121. [PDF] 2012 [A56] Lèbre S., Michel C.J. 2012. An evolution model
for sequence length based on residue insertion-deletion independent of
substitution: an application to the GC content in bacterial genomes. Bulletin
of Mathematical Biology 74, 1764-1788. [PDF] [A55] Michel C.J., Pirillo G., Pirillo M.A. 2012. A
classification of 20-trinucleotide circular codes. Information and
Computation 212, 55-63. [PDF] [A54] Bussoli L., Michel C.J., Pirillo G. 2012. On
conjugation partitions of sets of trinucleotides. Applied Mathematics
3, 107-112. [PDF] [A53] Michel C.J. 2012. Circular code motifs in
transfer and 16S ribosomal RNAs: a possible translation code in genes. Computational
Biology and Chemistry 37, 24-37. [PDF] 2011 [A52] Bussoli L., Michel C.J., Pirillo G. 2011. On
some forbidden configurations for self-complementary trinucleotide circular
codes. Journal for Algebra and Number Theory Academia 2, 223-232. [PDF] [A51] Benard E., Michel C.J. 2011. A generalization
of substitution evolution models of nucleotides to genetic motifs. Journal
of Theoretical Biology 288, 73-83. [PDF] [A50] Michel C.J., Pirillo G. 2011. Strong
trinucleotide circular codes. International Journal of Combinatorics
2011, Article ID 659567, 1-14. [PDF] [A49] Ahmed A., Michel C.J. 2011. Circular code
signal in frameshift genes. Journal of
Computer Science and Systems Biology 4,
7-15. [PDF] 2010 [A48] Lèbre S., Michel C.J. 2010. A
stochastic evolution model for residue insertion-deletion independent from
substitution. Computational Biology and Chemistry 34, 259-267. [PDF] [A47] Michel C.J., Pirillo G. 2010. Identification
of all trinucleotide circular codes. Computational Biology and Chemistry
34, 122-125. [PDF] [A46] Ahmed A., Frey G., Michel C.J. 2010. Essential
molecular functions associated with the circular code evolution. Journal
of Theoretical Biology 264, 613-622. [PDF] 2009 [A45] Benard E., Michel C.J. 2009.
Computation of direct and inverse mutations with the SEGM web server
Stochastic Evolution of Genetic Motifs: an application to splice sites of
human genome introns. Computational Biology and Chemistry 33,
245-252. [PDF] [A44] Criscuolo A., Michel C.J. 2009. Phylogenetic
inference with weighted codon evolutionary distances. Journal
of Molecular Evolution 68, 377-392. [PDF] [A43] Bahi J.M., Michel C.J. 2009. A stochastic
model of gene evolution with time dependent pseudochaotic mutations. Bulletin
of Mathematical Biology 71, 681-700. [PDF] 2008 [A42] Bahi J.M., Michel C.J. 2008. A stochastic
model of gene evolution with chaotic mutations. Journal of Theoretical
Biology 255, 53-63. [PDF] [A41] Ahmed A., Michel C.J. 2008. Plant microRNA
detection using the circular code information. Computational Biology and
Chemistry 32, 400-405. [PDF] [A40] Michel C.J., Pirillo G., Pirillo M.A. 2008. A
relation between trinucleotide comma-free codes and trinucleotide circular
codes. Theoretical Computer Science
401, 17-26. [PDF] [A39] Michel C.J., Pirillo G., Pirillo M.A. 2008. Varieties
of comma free codes. Computer and Mathematics with Applications 55,
989-996. [PDF] [A38] Michel C.J. 2008. A 2006 review of circular
codes in genes. Computer and Mathematics with Applications 55,
984-988. [PDF] 2007 [A37] Michel C.J. 2007. Evolution probabilities and
phylogenetic distance of dinucleotides. Journal of Theoretical Biology
249, 271-277. [PDF] [A36] Ahmed A., Frey G., Michel C.J. 2007.
Frameshift signals in genes associated with the circular code. In
Silico Biology 7, 155-168. [PDF] [A35] Michel C.J. 2007. Codon phylogenetic distance.
Computational Biology and Chemistry 31, 36-43. [PDF] [A34] Michel C.J. 2007. An analytical model of gene
evolution with 9 mutation parameters: an application to the amino acids coded
by the common circular code. Bulletin of Mathematical Biology 69,
677-698. [PDF] 2006 [A33] Frey G., Michel C.J. 2006. Identification of
circular codes in bacterial genomes and their use in a factorization method
for retrieving the reading frames of genes. Computational Biology and
Chemistry 30, 87-101. [PDF] [A32] Frey G., Michel C.J. 2006. An analytical model
of gene evolution with 6 mutation parameters: an application to archaeal
circular codes. Computational Biology and Chemistry 30, 1-11. [PDF] 2004 [A31] Bahi J.M., Michel C.J. 2004. A
stochastic gene evolution model with time dependent mutations. Bulletin of
Mathematical Biology 66, 763-778. [PDF] 2003 [A30] Frey G., Michel C.J. 2003. Circular codes in
archaeal genomes. Journal of Theoretical Biology 223, 413-431. [PDF] [A29] Michel C.J. 2003. A computer method for
identifying patterns in the electroencephalogram signals. Journal
of Medical Engineering and Technology 27,
267-275. [PDF] 2002 [A28] Arquès D.G., Lacan J., Michel C.J. 2002. Identification
of protein coding genes in genomes with statistical functions based on the
circular code. Biosystems 66, 73-92. [PDF] 2001 [A27] Lacan J., Michel C.J. 2001. Analysis
of a circular code model. Journal of Theoretical Biology 213, 159-170.
[PDF] 2000 [A26] Bahi J.M., Michel C.J. 2000. Convergence
of discrete asynchronous iterations. International Journal of Computer
Mathematics 74, 113-125. [PDF] 1999 [A25] Bahi J.M., Michel C.J. 1999. Simulations
of asynchronous evolution of discrete systems. Simulation Practice and
Theory 7, 309-324. [PDF] [A24] Arquès D.G., Fallot J.-P., Marsan L., Michel
C.J. 1999. An evolutionary analytical model of a complementary circular code.
Biosystems 49, 83-103. [PDF] 1998 [A23] Arquès D.G., Fallot J.-P., Michel C.J. 1998.
An evolutionary analytical model of a complementary circular code simulating
the protein coding genes, the 5' and 3' regions. Bulletin of Mathematical
Biology 60, 163-194. [PDF] 1997 [A22] Arquès D.G., Michel C.J. 1997. A
circular code in the protein coding genes of mitochondria. Journal of
Theoretical Biology 189, 273-290. [PDF] [A21] Arquès D.G., Michel C.J. 1997. A
code in the protein coding genes. Biosystems 44, 107-134. [PDF] [A20] Arquès D.G., Fallot J.-P., Michel C.J. 1997.
An evolutionary model of a complementary circular code. Journal of
Theoretical Biology 185, 241-253. [PDF] 1996 [A19] Arquès D.G., Michel C.J. 1996. A
complementary circular code in the protein coding genes. Journal of
Theoretical Biology 182, 45-58. [PDF] [A18] Arquès D.G., Fallot J.-P., Michel C.J. 1996.
Identification of several types of periodicities in the collagens and their
simulation. International Journal of Biological Macromolecules 19,
131-138. [PDF] 1995 [A17] Arquès D.G., Michel C.J. 1995. Analytical
solutions of the dinucleotide probability after and before random mutations. Journal
of Theoretical Biology 175, 533-544. [PDF] [A16] Arquès D.G., Lapayre J.-C., Michel C.J. 1995. Identification
and simulation of shifted periodicities common to protein coding genes of
eukaryotes, prokaryotes and viruses. Journal of Theoretical Biology
172, 279-291. [PDF] 1994 [A15] Arquès D.G., Michel C.J. 1994. Analytical
expression of the purine/pyrimidine autocorrelation function after and before
random mutations. Mathematical Biosciences 123, 103-125. [PDF] 1993 [A14] Arquès D.G., Michel C.J. 1993. Identification
and simulation of new non-random statistical properties common to different
eukaryotic gene subpopulations. Biochimie 75, 399-407. [PDF] [A13] Arquès D.G., Michel C.J. 1993. Analytical
expression of the purine/pyrimidine codon probability after and before random
mutations. Bulletin of Mathematical Biology 55, 1025-1038. [PDF] [A12] Arquès D.G., Michel C.J. 1993. A
model of gene evolution based on recognizable languages and on insertion and
deletion operations. International Journal of Modelling
and Simulation 13, 110-113. [PDF] [A11] Arquès D.G., Michel C.J., Orieux K. 1993. Identification
and simulation of new non-random statistical properties common to different
populations of eukaryotic non-coding genes. Journal of Theoretical Biology
161, 329-342. [PDF] 1992 [A10] Arquès D.G., Michel C.J. 1992. A
simulation of the genetic periodicities modulo 2 and 3 with processes of
nucleotide insertions and deletions. Journal of Theoretical Biology
156, 113-127. [PDF] [A9] Arquès D.G., Michel C.J., Orieux K. 1992. Analysis
of Gene Evolution: the software AGE. Bioinformatics 8, 5-14. [PDF] 1990 [A8] Arquès D.G., Michel C.J. 1990. A
model of DNA sequence evolution. Part 1: Statistical features and
classification of gene populations, 743-753. Part 2: Simulation model,
753-766. Part 3: Return of the model to the reality, 766-770. Bulletin of
Mathematical Biology 52, 741-772. [PDF] [A7] Arquès D.G., Michel C.J. 1990. Periodicities
in coding and noncoding regions of the genes. Journal of Theoretical
Biology 143, 307-318. [PDF] 1989 [A6] Michel C.J. 1989. A study of the
purine/pyrimidine codon occurrence with a reduced centered variable and an
evaluation compared to the frequency statistic. Mathematical Biosciences
97, 161-177. [PDF] 1987 [A5] Arquès D.G., Michel C.J. 1987. Periodicities
in introns. Nucleic Acids Research 15, 7581-7592. [PDF] [A4] Arquès D.G., Michel C.J. 1987. A purine-pyrimidine
motif verifying an identical presence in almost all gene taxonomic groups. Journal
of Theoretical Biology 128, 457-461. [PDF] [A3] Arquès D.G., Michel C.J. 1987. Study
of a perturbation in the coding periodicity. Mathematical Biosciences
86, 1-14. [PDF] 1986 [A2] Michel C.J., Jacq B., Arquès D.G., Bickle T.A.
1986. A remarkable amino acid sequence homology between a
phage T4 tail fibre protein and ORF314 of phage lambda located in the tail
operon. Gene 44, 147-150. [PDF] [A1] Michel C.J. 1986. New statistical approach to discriminate between protein coding and non-coding regions in DNA sequences and its evaluation. Journal of Theoretical Biology 120, 223-236. [PDF] |
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