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Preprocessing and analyzing genetic data with complex networks: An application to Obstructive Nephropathy
1. | Faculdade de Ciências e Tecnologia, Departamento de Engenharia Electrotécnica, Universidade Nova de Lisboa, Centre for Biomedical Technology, Technical University of Madrid, Pozuelo de Alarcón, 28223 Madrid, Spain |
2. | Faculty of Computer Science, Technical University of Madrid, Pozuelo de Alarcón, 28223 Madrid, Spain |
3. | Departamento de Engenharia Electrotcnica, Faculdade de Ciencias e, Tecnologia Universidade Nova de Lisboa, Quinta da Torre, 2825 - 182 Caparica, Portugal |
4. | Centre for Biomedical Technology, Technical University of Madrid, Pozuelo de Alarcón, 28223 Madrid, Spain |
References:
[1] |
D. J. Lockhart and E. A. Winzeler, Genomics, gene expression and DNA array, Nature, 405 (2000), 827-836.
doi: 10.1038/35015701. |
[2] |
K. I. Goh, et al., The human disease network, Proc. Natl. Acad. Sci. USA, 104 (2007), 8685-8690.
doi: 10.1073/pnas.0701361104. |
[3] |
T. R. Golub, et al., Molecular classification of cancer: Class discovery and class prediction by gene expression monitoring, Science, 286 (1999), 531-537.
doi: 10.1126/science.286.5439.531. |
[4] |
L. J. van 't Veer, et al., Gene expression profiling predicts clinical outcome of breast cancer, Nature, 415 (2002), 530-536.
doi: 10.1038/415530a. |
[5] |
R. Jaenisch and A. Bird, Epigenetic regulation of gene expression: How the genome integrates intrinsic and environmental signals, Nature Genetics, 33 (2003), 245-254.
doi: 10.1038/ng1089. |
[6] |
A. L. Barabási and Z. N. Oltvai, Network biology: Understanding the cell's functional organization, Nature Reviews Genetics, 5 (2004), 101-113. |
[7] |
S. Boccaletti, V. Latora, Y. Moreno, M. Chavez and D. U. Hwang, Complex networks: Structure and dynamics, Physics Reports, 424 (2006), 175-308.
doi: 10.1016/j.physrep.2005.10.009. |
[8] |
M. E. J. Newman, The structure and function of complex networks, SIAM Review, 45 (2003), 167-256.
doi: 10.1137/S003614450342480. |
[9] |
P. W. Anderson, More is different, Science, 177 (1972), 393-397.
doi: 10.1126/science.177.4047.393. |
[10] |
L. da F. Costa, O. N. Oliveira Jr., G. Travieso, F. A. Rodrigues, P. R. Villas Boas, L. Antiqueira, M. P. Viana and L. E. C. da Rocha, Analyzing and modeling real-world phenomena with complex networks: A survey of applications,, preprint, ().
|
[11] |
B. Zhang and S. Horvath, A general framework for weighted gene co-expression network analysis, Statistical Applications in Genetics and Molecular Biology, 4 (2005) 45 pp.. |
[12] |
M. Zanin and S. Boccaletti, Complex networks analysis of Obstructive Nephropathy data, Chaos, 21 (2011), 033103.
doi: 10.1063/1.3608126. |
[13] |
I. Guyon and A. Elisseeff, An introduction to variable and feature selection, The Journal of Machine Learning Research, 3 (2003), 1-48. |
[14] |
I. Guyon, S. Gunn, M. Nikravesh and L. A. Zadeh, "Feature Extraction-Foundations and Applications," 1st edition, Springer-Verlag, Berlin, 2006. |
[15] |
R. L. Chevalier, Molecular and cellular pathophysiology of Obstructive Nephropathy, Pediatric Nephrology, 13 (1999), 612-619.
doi: 10.1007/s004670050756. |
[16] |
J. G. Wen, J. Frokiaer, T. M. Jorgensen and J. C. Djurhuus, Obstructive Nephropathy: An update of the experimental research, Urology Research, 27 (1999), 29-39.
doi: 10.1007/s002400050086. |
[17] |
D. P. Bartel, MicroRNAs: Genomics, biogenesis, mechanism, and function, Cell, 116 (2009), 281-297.
doi: 10.1016/S0092-8674(04)00045-5. |
[18] |
D. P. Bartel, MicroRNAs: Target recognition and regulatory functions, Cell, 136 (2009), 215-233.
doi: 10.1016/j.cell.2009.01.002. |
[19] |
V. Latora and M. Marchiori, Is the Boston subway a small-world network?, Physica A, 314 (2002), 109-113.
doi: 10.1016/S0378-4371(02)01089-0. |
[20] |
T. H. Cormen, C. E. Leiserson, R. L. Rivest and C. Stein, "Introduction to Algorithms," 3rd edition, MIT Press, New York, 2009. |
[21] |
R. G. D. Steel and J. H. Torrie, "Principles and Procedures of Statistics," 1st edition, McGraw-Hill, New York, 1960. |
[22] |
Karmeshu, "Entropy Measures, Maximum Entropy Principle and Emerging Applications," 1st edition, Springer, Berlin, 2003. |
show all references
References:
[1] |
D. J. Lockhart and E. A. Winzeler, Genomics, gene expression and DNA array, Nature, 405 (2000), 827-836.
doi: 10.1038/35015701. |
[2] |
K. I. Goh, et al., The human disease network, Proc. Natl. Acad. Sci. USA, 104 (2007), 8685-8690.
doi: 10.1073/pnas.0701361104. |
[3] |
T. R. Golub, et al., Molecular classification of cancer: Class discovery and class prediction by gene expression monitoring, Science, 286 (1999), 531-537.
doi: 10.1126/science.286.5439.531. |
[4] |
L. J. van 't Veer, et al., Gene expression profiling predicts clinical outcome of breast cancer, Nature, 415 (2002), 530-536.
doi: 10.1038/415530a. |
[5] |
R. Jaenisch and A. Bird, Epigenetic regulation of gene expression: How the genome integrates intrinsic and environmental signals, Nature Genetics, 33 (2003), 245-254.
doi: 10.1038/ng1089. |
[6] |
A. L. Barabási and Z. N. Oltvai, Network biology: Understanding the cell's functional organization, Nature Reviews Genetics, 5 (2004), 101-113. |
[7] |
S. Boccaletti, V. Latora, Y. Moreno, M. Chavez and D. U. Hwang, Complex networks: Structure and dynamics, Physics Reports, 424 (2006), 175-308.
doi: 10.1016/j.physrep.2005.10.009. |
[8] |
M. E. J. Newman, The structure and function of complex networks, SIAM Review, 45 (2003), 167-256.
doi: 10.1137/S003614450342480. |
[9] |
P. W. Anderson, More is different, Science, 177 (1972), 393-397.
doi: 10.1126/science.177.4047.393. |
[10] |
L. da F. Costa, O. N. Oliveira Jr., G. Travieso, F. A. Rodrigues, P. R. Villas Boas, L. Antiqueira, M. P. Viana and L. E. C. da Rocha, Analyzing and modeling real-world phenomena with complex networks: A survey of applications,, preprint, ().
|
[11] |
B. Zhang and S. Horvath, A general framework for weighted gene co-expression network analysis, Statistical Applications in Genetics and Molecular Biology, 4 (2005) 45 pp.. |
[12] |
M. Zanin and S. Boccaletti, Complex networks analysis of Obstructive Nephropathy data, Chaos, 21 (2011), 033103.
doi: 10.1063/1.3608126. |
[13] |
I. Guyon and A. Elisseeff, An introduction to variable and feature selection, The Journal of Machine Learning Research, 3 (2003), 1-48. |
[14] |
I. Guyon, S. Gunn, M. Nikravesh and L. A. Zadeh, "Feature Extraction-Foundations and Applications," 1st edition, Springer-Verlag, Berlin, 2006. |
[15] |
R. L. Chevalier, Molecular and cellular pathophysiology of Obstructive Nephropathy, Pediatric Nephrology, 13 (1999), 612-619.
doi: 10.1007/s004670050756. |
[16] |
J. G. Wen, J. Frokiaer, T. M. Jorgensen and J. C. Djurhuus, Obstructive Nephropathy: An update of the experimental research, Urology Research, 27 (1999), 29-39.
doi: 10.1007/s002400050086. |
[17] |
D. P. Bartel, MicroRNAs: Genomics, biogenesis, mechanism, and function, Cell, 116 (2009), 281-297.
doi: 10.1016/S0092-8674(04)00045-5. |
[18] |
D. P. Bartel, MicroRNAs: Target recognition and regulatory functions, Cell, 136 (2009), 215-233.
doi: 10.1016/j.cell.2009.01.002. |
[19] |
V. Latora and M. Marchiori, Is the Boston subway a small-world network?, Physica A, 314 (2002), 109-113.
doi: 10.1016/S0378-4371(02)01089-0. |
[20] |
T. H. Cormen, C. E. Leiserson, R. L. Rivest and C. Stein, "Introduction to Algorithms," 3rd edition, MIT Press, New York, 2009. |
[21] |
R. G. D. Steel and J. H. Torrie, "Principles and Procedures of Statistics," 1st edition, McGraw-Hill, New York, 1960. |
[22] |
Karmeshu, "Entropy Measures, Maximum Entropy Principle and Emerging Applications," 1st edition, Springer, Berlin, 2003. |
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