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Genome characterization through dichotomic classes: An analysis of the whole chromosome 1 of A. thaliana
1. | Dipartimento di Scienze Statistiche, Università di Bologna, Via delle Belle Arti 41, 40126, Bologna, Italy, Italy |
2. | CNR-IMM, UOS di Bologna, Via Gobetti 101, 40129 Bologna, Italy |
3. | Dipartimento di Scienze Statistiche, Università di Bologna, Via delle Belle Arti 41, 40126 Bologna, Italy |
References:
[1] |
B. Efron, "Large-Scale Inference: Empirical Bayes Methods for Estimation, Testing, and Prediction," Cambridge University Press, Cambridge, 2010. |
[2] |
G. Elgar and T. Vavouri, Tuning in to the signals: Noncoding sequence conservation in vertebrate genomes, Trends in genetics, 24 (2008), 344-352. |
[3] |
A. Elzanowski and J. Ostell, The genetic codes, National Center for Biotechnology Information (NCBI), (2008-04-07). Retrieved 2010-03-10. |
[4] |
D. L. Gonzalez, Can the genetic code be mathematically described?, Medical Science Monitor, 10 (2004), 11-17. |
[5] |
D. L. Gonzalez, Error detection and correction codes, in "The Codes of Life: the Rules of Macroevolution, volume 1 of Biosemiotics. Chapter 17" (eds. M. Barbieri and J. Hoffmeyers), Springer Netherlands, (2008), 379-394. |
[6] |
D. L. Gonzalez, The mathematical structure of the genetic code, in "The Codes of Life: the Rules of Macroevolution, volume 1 of Biosemiotics. Chapter 8" (eds. M. Barbieri and J. Hoffmeyers), Springer Netherlands, (2008), 111-152. |
[7] |
D. L. Gonzalez, S. Giannerini and R. Rosa, Detecting structures in parity binary sequences: Error correction and detection in DNA, IEEE Engineering in Medicine and Biology Magazine, 25 (2006), 69-81. |
[8] |
D. L. Gonzalez, S. Giannerini and R. Rosa, Strong short-range correlations and dichotomic codon classes in coding DNA sequences, Physical review E, 78 (2008), 051918. |
[9] |
D. L. Gonzalez, S. Giannerini and R. Rosa, The mathematical structure of the genetic code: a tool for inquiring on the origin of life, Statistica, LXIX (2009), 143-157. |
[10] |
D. L. Gonzalez, S. Giannerini and R. Rosa, Circular codes revisited: A statistical approach, Journal of Theoretical Biology, 275 (2011), 21-28. |
[11] |
S. Giannerini, D. L. Gonzalez and R. Rosa, DNA, frame synchronization and dichotomic classes: a quasicrystal framework, Philosophical Transactions of the Royal Society. Series A, 370 (2012), 2987-3006. |
[12] |
D. L. Gonzalez and M. Zanna, Una nuova descrizione matematica del codice genetico, Systema Naturae, Annali di Biologia Teorica, 5 (2003), 219-236. |
[13] |
International Human Genome Sequencing Consortium, Initial sequencing and analysis of the human genome, Nature, 409 (2001), 860-921. |
[14] |
A. G. Jegga and B. J. Aronow, Evolutionary conserved noncoding DNA, in "Encyclopedia of Life Sciences," John Wiley & sons, (2006). |
[15] |
S. Ohno, So much "junk" DNA in our genome, Brookhaven Symposia in Biology, 23 (1972), 366-370. |
[16] |
H. Pearson, Genetics: What is a gene?, Nature, 441 (2006), 398-401.
doi: 10.1038/441398a. |
[17] |
E. Pennisi, Genomics. DNA study forces rethink of what it means to be a gene., Science (New York, N. Y.), 316 (2007), 1556-1-557. |
[18] |
E. Properzi, "Genome Characterization Through the Mathematical Structure of the Genetic Code: An Analysis of the Whole Chromosome 1 of A. Thaliana," PhD Thesis, University of Bologna. |
[19] |
M. Quimbaya, K. Vandepoele, E. Rasp, M. Matthijs, S. Dhondt, G. T. Beemster, G. Berx and L. De Veylder, Identification of putative cancer genes through data integration and comparative genomics between plants and humans, Cell. Mol. Life Sci., 69 (2012), 2041-2055.
doi: 10.1007/s00018-011-0909-x. |
[20] |
R Development Core Team, R: A language and environment for statistical computing, R Foundation for Statistical Computing, Vienna, Austria, (2012), http://www.R-project.org/. |
[21] |
The Arabidopsis Genome Initiative, Analysis of the genome sequence of the flowering plant Arabidopsis thaliana, Nature, 408 (2000), 796-815.
doi: 10.1038/35048692. |
[22] |
TAIR, Genome Annotation, http://www.arabidopsis.org/ |
[23] |
O. Trapp, K. Seeliger and H. Puchta, Homologs of breast cancer genes in plants, Front. Plant Sci., 2 (2011). |
[24] |
J. C. Venter et al., The sequence of the human genome, Science, 291 (2001), 1304-1351. |
[25] |
K. Watanabe and T. Suzuki, "Genetic Code and its Variants," in "Encyclopedia of Life Sciences," John Wiley & sons, 2006. |
show all references
References:
[1] |
B. Efron, "Large-Scale Inference: Empirical Bayes Methods for Estimation, Testing, and Prediction," Cambridge University Press, Cambridge, 2010. |
[2] |
G. Elgar and T. Vavouri, Tuning in to the signals: Noncoding sequence conservation in vertebrate genomes, Trends in genetics, 24 (2008), 344-352. |
[3] |
A. Elzanowski and J. Ostell, The genetic codes, National Center for Biotechnology Information (NCBI), (2008-04-07). Retrieved 2010-03-10. |
[4] |
D. L. Gonzalez, Can the genetic code be mathematically described?, Medical Science Monitor, 10 (2004), 11-17. |
[5] |
D. L. Gonzalez, Error detection and correction codes, in "The Codes of Life: the Rules of Macroevolution, volume 1 of Biosemiotics. Chapter 17" (eds. M. Barbieri and J. Hoffmeyers), Springer Netherlands, (2008), 379-394. |
[6] |
D. L. Gonzalez, The mathematical structure of the genetic code, in "The Codes of Life: the Rules of Macroevolution, volume 1 of Biosemiotics. Chapter 8" (eds. M. Barbieri and J. Hoffmeyers), Springer Netherlands, (2008), 111-152. |
[7] |
D. L. Gonzalez, S. Giannerini and R. Rosa, Detecting structures in parity binary sequences: Error correction and detection in DNA, IEEE Engineering in Medicine and Biology Magazine, 25 (2006), 69-81. |
[8] |
D. L. Gonzalez, S. Giannerini and R. Rosa, Strong short-range correlations and dichotomic codon classes in coding DNA sequences, Physical review E, 78 (2008), 051918. |
[9] |
D. L. Gonzalez, S. Giannerini and R. Rosa, The mathematical structure of the genetic code: a tool for inquiring on the origin of life, Statistica, LXIX (2009), 143-157. |
[10] |
D. L. Gonzalez, S. Giannerini and R. Rosa, Circular codes revisited: A statistical approach, Journal of Theoretical Biology, 275 (2011), 21-28. |
[11] |
S. Giannerini, D. L. Gonzalez and R. Rosa, DNA, frame synchronization and dichotomic classes: a quasicrystal framework, Philosophical Transactions of the Royal Society. Series A, 370 (2012), 2987-3006. |
[12] |
D. L. Gonzalez and M. Zanna, Una nuova descrizione matematica del codice genetico, Systema Naturae, Annali di Biologia Teorica, 5 (2003), 219-236. |
[13] |
International Human Genome Sequencing Consortium, Initial sequencing and analysis of the human genome, Nature, 409 (2001), 860-921. |
[14] |
A. G. Jegga and B. J. Aronow, Evolutionary conserved noncoding DNA, in "Encyclopedia of Life Sciences," John Wiley & sons, (2006). |
[15] |
S. Ohno, So much "junk" DNA in our genome, Brookhaven Symposia in Biology, 23 (1972), 366-370. |
[16] |
H. Pearson, Genetics: What is a gene?, Nature, 441 (2006), 398-401.
doi: 10.1038/441398a. |
[17] |
E. Pennisi, Genomics. DNA study forces rethink of what it means to be a gene., Science (New York, N. Y.), 316 (2007), 1556-1-557. |
[18] |
E. Properzi, "Genome Characterization Through the Mathematical Structure of the Genetic Code: An Analysis of the Whole Chromosome 1 of A. Thaliana," PhD Thesis, University of Bologna. |
[19] |
M. Quimbaya, K. Vandepoele, E. Rasp, M. Matthijs, S. Dhondt, G. T. Beemster, G. Berx and L. De Veylder, Identification of putative cancer genes through data integration and comparative genomics between plants and humans, Cell. Mol. Life Sci., 69 (2012), 2041-2055.
doi: 10.1007/s00018-011-0909-x. |
[20] |
R Development Core Team, R: A language and environment for statistical computing, R Foundation for Statistical Computing, Vienna, Austria, (2012), http://www.R-project.org/. |
[21] |
The Arabidopsis Genome Initiative, Analysis of the genome sequence of the flowering plant Arabidopsis thaliana, Nature, 408 (2000), 796-815.
doi: 10.1038/35048692. |
[22] |
TAIR, Genome Annotation, http://www.arabidopsis.org/ |
[23] |
O. Trapp, K. Seeliger and H. Puchta, Homologs of breast cancer genes in plants, Front. Plant Sci., 2 (2011). |
[24] |
J. C. Venter et al., The sequence of the human genome, Science, 291 (2001), 1304-1351. |
[25] |
K. Watanabe and T. Suzuki, "Genetic Code and its Variants," in "Encyclopedia of Life Sciences," John Wiley & sons, 2006. |
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