-
1
-
-
0036898577
-
Microarray data normalization and transformation
-
J. Quackenbush, "Microarray data normalization and transformation," Nat. Genet., vol. 32, pp. 496-501, Dec. 2002. (Pubitemid 35435152)
-
(2002)
Nature Genetics
, vol.32
, Issue.5 SUPPL. DEC.
, pp. 496-501
-
-
Quackenbush, J.1
-
2
-
-
0036184629
-
Probabilistic Boolean networks: A rule-based uncertainty model for gene regulatory networks
-
I. Shmulevich, E. R. Dougherty, S. Kim, and W. Zhang, "Probabilistic Boolean networks: A rule-based uncertainty model for gene regulatory networks," Bioinformatics, vol. 18, no. 2, p. 261, 2002.
-
(2002)
Bioinformatics
, vol.18
, Issue.2
, pp. 261
-
-
Shmulevich, I.1
Dougherty, E.R.2
Kim, S.3
Zhang, W.4
-
3
-
-
45849093636
-
Boolean network model predicts cell cycle sequence of fission yeast
-
M. I. Davidich and S. Bornholdt, "Boolean network model predicts cell cycle sequence of fission yeast," PLoS One, vol. 3, no. 2, p. e1672, 2008.
-
(2008)
PLoS One
, vol.3
, Issue.2
-
-
Davidich, M.I.1
Bornholdt, S.2
-
4
-
-
0032616683
-
Identification of genetic networks from a small number of gene expression patterns under the Boolean network model
-
T. Akutsu, S. Miyano, and S. Kuhara, "Identification of genetic networks from a small number of gene expression patterns under the Boolean network model," in Proc. Pacific Symp. Biocomput., vol. 4. 1999, pp. 17-28.
-
(1999)
Proc. Pacific Symp. Biocomput
, vol.4
, pp. 17-28
-
-
Akutsu, T.1
Miyano, S.2
Kuhara, S.3
-
5
-
-
33749825955
-
Comparative evaluation of reverse engineering gene regulatory networks with relevance networks, graphical Gaussian models and Bayesian networks
-
A. V. Werhli, M. Grzegorczyk, and D. Husmeier, "Comparative evaluation of reverse engineering gene regulatory networks with relevance networks, graphical Gaussian models and Bayesian networks," Bioinformatics, vol. 22, no. 20, p. 2523, 2006.
-
(2006)
Bioinformatics
, vol.22
, Issue.20
, pp. 2523
-
-
Werhli, A.V.1
Grzegorczyk, M.2
Husmeier, D.3
-
6
-
-
0033707946
-
Using Bayesian networks to analyze expression data
-
N. Friedman, M. Linial, I. Nachman, and D. Pe'er, "Using Bayesian networks to analyze expression data," J. Computat. Biol., vol. 7, nos. 3-4, pp. 601-620, 2000.
-
(2000)
J. Computat. Biol
, vol.7
, Issue.3-4
, pp. 601-620
-
-
Friedman, N.1
Linial, M.2
Nachman, I.3
Pe'Er, D.4
-
8
-
-
16344385431
-
Evolutionary optimization with data collocation for reverse engineering of biological networks
-
K. Y. Tsai and F. S. Wang, "Evolutionary optimization with data collocation for reverse engineering of biological networks," Bioinformatics, vol. 21, no. 7, p. 1180, 2005.
-
(2005)
Bioinformatics
, vol.21
, Issue.7
, pp. 1180
-
-
Tsai, K.Y.1
Wang, F.S.2
-
9
-
-
40249090398
-
Accelerating differential evolution using an adaptive local search
-
DOI 10.1109/TEVC.2007.895272
-
N. Noman and H. Iba, "Accelerating differential evolution using an adaptive local search," IEEE Trans. Evol. Computat., vol. 12, no. 1, pp. 107-125, Feb. 2008. (Pubitemid 351330335)
-
(2008)
IEEE Transactions on Evolutionary Computation
, vol.12
, Issue.1
, pp. 107-125
-
-
Noman, N.1
Iba, H.2
-
10
-
-
41949109225
-
Inference of biochemical network models in S-system using multiobjective optimization approach
-
P. K. Liu and F. S. Wang, "Inference of biochemical network models in S-system using multiobjective optimization approach," Bioinformatics, vol. 24, no. 8, p. 1085, 2008.
-
(2008)
Bioinformatics
, vol.24
, Issue.8
, pp. 1085
-
-
Liu, P.K.1
Wang, F.S.2
-
11
-
-
75149166629
-
Reverse engineering gene regulatory network from microarray data using linear time-variant model
-
Jan
-
M. Kabir, N. Noman, and H. Iba, "Reverse engineering gene regulatory network from microarray data using linear time-variant model," BMC Bioinform., vol. 11, Suppl. 1, p. S56, Jan. 2010.
-
(2010)
BMC Bioinform
, vol.11
, Issue.SUPPL. 1
-
-
Kabir, M.1
Noman, N.2
Iba, H.3
-
12
-
-
69249164121
-
A survey of particle swarm optimization applications in electric power systems
-
Apr
-
M. Al-Rashidi and M. El-Hawary, "A survey of particle swarm optimization applications in electric power systems," IEEE Trans. Evol. Computat., vol. 13, no. 4, pp. 913-918, Apr. 2009.
-
(2009)
IEEE Trans. Evol. Computat
, vol.13
, Issue.4
, pp. 913-918
-
-
Al-Rashidi, M.1
El-Hawary, M.2
-
13
-
-
4344682502
-
Recent advances in particle swarm
-
R. Eberhart, "Recent advances in particle swarm," in Proc. Congr. Evol. Computat., 2004, pp. 90-97.
-
(2004)
Proc. Congr. Evol. Computat
, pp. 90-97
-
-
Eberhart, R.1
-
14
-
-
44349195551
-
Analysis of the publications on the applications of particle swarm optimisation
-
R. Poli, "Analysis of the publications on the applications of particle swarm optimisation," J. Artif. Evol. Applicat., vol. 2008, no. 2, pp. 1-10, 2008.
-
(2008)
J. Artif. Evol. Applicat
, vol.2008
, Issue.2
, pp. 1-10
-
-
Poli, R.1
-
15
-
-
36248944068
-
Inference of genetic regulatory networks with recurrent neural network models using particle swarm optimization
-
DOI 10.1109/TCBB.2007.1057
-
R. Xu, I. I. D. Wunsch, and R. Frank, "Inference of genetic regulatory networks with recurrent neural network models using particle swarm optimization," IEEE/ACM Trans. Computat. Biol. Bioinform., vol. 4, no. 4, pp. 681-692, Oct.-Dec. 2007. (Pubitemid 350125889)
-
(2007)
IEEE/ACM Transactions on Computational Biology and Bioinformatics
, vol.4
, Issue.4
, pp. 681-692
-
-
Xu, R.1
Wunsch II, D.C.2
Frank, R.L.3
-
16
-
-
84897548593
-
Dissipative particle swarm optimization
-
X. F. Xie, W. J. Zhang, and Z. L. Yang, "Dissipative particle swarm optimization," in Proc. CEC, vol. 2. 2002, pp. 1456-1461.
-
(2002)
Proc. CEC
, vol.2
, pp. 1456-1461
-
-
Xie, X.F.1
Zhang, W.J.2
Yang, Z.L.3
-
17
-
-
4344714817
-
A comparative study of differential evolution, particle swarm optimization, and evolutionary algorithms on numerical benchmark problems
-
Jun
-
J. Vesterstrom and R. Thomsen, "A comparative study of differential evolution, particle swarm optimization, and evolutionary algorithms on numerical benchmark problems," Evol. Computat., vol. 2, pp. 1980-1987, Jun. 2004.
-
(2004)
Evol. Computat
, vol.2
, pp. 1980-1987
-
-
Vesterstrom, J.1
Thomsen, R.2
-
18
-
-
0014649230
-
Biochemical systems analysis: I. Some mathematical properties of the rate law for the component enzymatic reactions
-
M. A. Savageau, "Biochemical systems analysis: I. Some mathematical properties of the rate law for the component enzymatic reactions," J. Theoretic. Biol., vol. 25, no. 3, pp. 365-369, 1969.
-
(1969)
J. Theoretic. Biol
, vol.25
, Issue.3
, pp. 365-369
-
-
Savageau, M.A.1
-
19
-
-
0014658880
-
Biochemical systems analysis: II. The steady-state solutions for an n-pool system using a power-law approximation
-
M. A. Savageau, "Biochemical systems analysis: II. The steady-state solutions for an n-pool system using a power-law approximation," J. Theoretic. Biol., vol. 25, no. 3, pp. 370-379, 1969.
-
(1969)
J. Theoretic. Biol
, vol.25
, Issue.3
, pp. 370-379
-
-
Savageau, M.A.1
-
20
-
-
0014733809
-
Biochemical systems analysis: III. Dynamic solutions using a power-law approximation
-
M. A. Savageau, "Biochemical systems analysis: III. Dynamic solutions using a power-law approximation," J. Theoretic. Biol., vol. 26, no. 2, pp. 215-226, 1970.
-
(1970)
J. Theoretic. Biol
, vol.26
, Issue.2
, pp. 215-226
-
-
Savageau, M.A.1
-
21
-
-
0000000513
-
Efficient numerical optimization algorithm based on genetic algorithm for inverse problem
-
D. Tominaga, N. Koga, and M. Okamoto, "Efficient numerical optimization algorithm based on genetic algorithm for inverse problem," in Proc. Genet. Evol. Computat. Conf., vol. 251. 2000, p. 258.
-
(2000)
Proc. Genet. Evol. Computat. Conf
, vol.251
, pp. 258
-
-
Tominaga, D.1
Koga, N.2
Okamoto, M.3
-
22
-
-
32444432616
-
Inference of gene regulatory networks using S-system and differential evolution
-
N. Noman and H. Iba, "Inference of gene regulatory networks using S-system and differential evolution," in Proc. Conf. Genet. Evol. Computat., 2005, p. 439.
-
(2005)
Proc. Conf. Genet. Evol. Computat
, pp. 439
-
-
Noman, N.1
Iba, H.2
-
23
-
-
33847314052
-
Parameter estimation using simulated annealing for S-system models of biochemical networks
-
DOI 10.1093/bioinformatics/btl522
-
O. R. Gonzalez, C. Küper, K. Jung, P. C. Naval, and E. Mendoza, "Parameter estimation using simulated annealing for S-system models of biochemical networks," Bioinformatics, vol. 23, no. 4, pp. 480-486, Feb. 2007. (Pubitemid 46323129)
-
(2007)
Bioinformatics
, vol.23
, Issue.4
, pp. 480-486
-
-
Gonzalez, O.R.1
Kuper, C.2
Jung, K.3
Naval Jr., P.C.4
Mendoza, E.5
-
24
-
-
9744243208
-
Feature selection, L1 vs. L2 regularization, and rotational invariance
-
A. Y. Ng, "Feature selection, L1 vs. L2 regularization, and rotational invariance," in Proc. 21st ICML, 2004, pp. 78-86.
-
(2004)
Proc. 21st ICML
, pp. 78-86
-
-
Ng, A.Y.1
-
25
-
-
80053041567
-
4W1H and particle swarm optimization for human activity recognition
-
L. Palafox and H. Hashimoto, "4W1H and particle swarm optimization for human activity recognition," J. Adv. Computat. Intell. Intell. Inform., vol. 15, no. 7, pp. 793-799, 2011.
-
(2011)
J. Adv. Computat. Intell. Intell. Inform
, vol.15
, Issue.7
, pp. 793-799
-
-
Palafox, L.1
Hashimoto, H.2
-
26
-
-
0037475094
-
The particle swarm optimization algorithm: Convergence analysis and parameter selection
-
I. C. Trelea, "The particle swarm optimization algorithm: Convergence analysis and parameter selection," Inform. Process. Lett., vol. 85, no. 6, pp. 317-325, 2003.
-
(2003)
Inform. Process. Lett
, vol.85
, Issue.6
, pp. 317-325
-
-
Trelea, I.C.1
-
27
-
-
20144387371
-
Inference of S-system models of genetic networks using a cooperative coevolutionary algorithm
-
S. Kimura, K. Ide, A. Kashihara, M. Kano, M. Hatakeyama, R. Masui, N. Nakagawa, S. Yokoyama, S. Kuramitsu, and A. Konagaya, "Inference of S-system models of genetic networks using a cooperative coevolutionary algorithm," Bioinformatics, vol. 21, no. 7, p. 1154, 2005.
-
(2005)
Bioinformatics
, vol.21
, Issue.7
, pp. 1154
-
-
Kimura, S.1
Ide, K.2
Kashihara, A.3
Kano, M.4
Hatakeyama, M.5
Masui, R.6
Nakagawa, N.7
Yokoyama, S.8
Kuramitsu, S.9
Konagaya, A.10
-
28
-
-
0037461033
-
Dynamic modeling of genetic networks using genetic algorithm and S-system
-
S. Kikuchi, D. Tominaga, M. Arita, K. Takahashi, and M. Tomita, "Dynamic modeling of genetic networks using genetic algorithm and S-system," Bioinformatics, vol. 19, no. 5, p. 643, 2003.
-
(2003)
Bioinformatics
, vol.19
, Issue.5
, pp. 643
-
-
Kikuchi, S.1
Tominaga, D.2
Arita, M.3
Takahashi, K.4
Tomita, M.5
-
29
-
-
33748530630
-
Reverse engineering genetic networks using evolutionary computation
-
Jan
-
N. Noman and H. Iba, "Reverse engineering genetic networks using evolutionary computation," Genome Inform., vol. 16, no. 2, pp. 205-214, Jan. 2005.
-
(2005)
Genome Inform
, vol.16
, Issue.2
, pp. 205-214
-
-
Noman, N.1
Iba, H.2
-
30
-
-
36248948496
-
Inferring gene regulatory networks using differential evolution with local search heuristics
-
DOI 10.1109/TCBB.2007.1058
-
N. Noman and H. Iba, "Inferring gene regulatory networks using differential evolution with local search heuristics," IEEE/ACM Trans. Computat. Biol. Bioinform., vol. 4, no. 4, pp. 634-647, Oct.-Dec. 2007. (Pubitemid 350125886)
-
(2007)
IEEE/ACM Transactions on Computational Biology and Bioinformatics
, vol.4
, Issue.4
, pp. 634-647
-
-
Noman, N.1
Iba, H.2
-
31
-
-
34547356594
-
On the reconstruction of gene regulatory networks from noisy expression profiles
-
1688625, 2006 IEEE Congress on Evolutionary Computation, CEC 2006
-
N. Noman and H. Iba, "On the reconstruction of gene regulatory networks from noisy expression profiles," in Proc. IEEE Int. Conf. Evol. Computat., no. 1. Sep. 2006, pp. 2543-2550. (Pubitemid 47130814)
-
(2006)
2006 IEEE Congress on Evolutionary Computation, CEC 2006
, pp. 2543-2550
-
-
Noman, N.1
Iba, H.2
-
32
-
-
84896721435
-
Empirical study of particle swarm optimization
-
Y. Shi and R. C. Eberhart, "Empirical study of particle swarm optimization," in Proc. CEC, 1999, pp. 1945-1950.
-
(1999)
Proc. CEC
, pp. 1945-1950
-
-
Shi, Y.1
Eberhart, R.C.2
-
33
-
-
77951547999
-
A prior knowledge based approach to infer gene regulatory networks
-
M. M. Hasan, N. Noman, and H. Iba, "A prior knowledge based approach to infer gene regulatory networks," in Proc. ISB, 2010, p. 1.
-
(2010)
Proc. ISB
, pp. 1
-
-
Hasan, M.M.1
Noman, N.2
Iba, H.3
-
34
-
-
0036678794
-
Assigning numbers to the arrows: Parameterizing a gene regulation network by using accurate expression kinetics
-
M. Ronen, R. Rosenberg, B. I. Shraiman, and U. Alon, "Assigning numbers to the arrows: Parameterizing a gene regulation network by using accurate expression kinetics," Proc. Nat. Acad. Sci., vol. 99, no. 16, p. 10555, 2002.
-
(2002)
Proc. Nat. Acad. Sci
, vol.99
, Issue.16
, pp. 10555
-
-
Ronen, M.1
Rosenberg, R.2
Shraiman, B.I.3
Alon, U.4
-
36
-
-
0037899231
-
Multicriteria optimization of biochemical systems by linear programming: Application to production of ethanol by Saccharomyces cerevisiae
-
DOI 10.1002/bit.10676
-
J. Vera, P. De Atauri, M. Cascante, and N. V. Torres, "Multicriteria optimization of biochemical systems by linear programming: Application to production of ethanol by Saccharomyces cerevisiae," Biotechnol. Bioeng., vol. 83, no. 3, pp. 335-343, 2003. (Pubitemid 36818434)
-
(2003)
Biotechnology and Bioengineering
, vol.83
, Issue.3
, pp. 335-343
-
-
Vera, J.1
De Atauri, P.2
Cascante, M.3
Torres, N.V.4
-
37
-
-
0028052437
-
Ethanol production in baker's yeast: Application of experimental perturbation techniques for model development and resultant changes in flux control analysis
-
P. M. Schlosser, G. Riedyf, and J. E. Bailey, "Ethanol production in bakers yeast: Application of experimental perturbation techniques for model development and resultant changes in flux control analysis," Biotechnol. Progress, vol. 10, no. 2, pp. 141-154, Mar.-Apr. 1994. (Pubitemid 2069679)
-
(1994)
Biotechnology Progress
, vol.10
, Issue.2
, pp. 141-154
-
-
Schlosser, P.M.1
Riedy, G.2
Bailey, J.E.3
-
38
-
-
33745616528
-
Identification of biochemical networks by S-tree based genetic programming
-
DOI 10.1093/bioinformatics/btl122
-
D.-Y. Cho, K.-H. Cho, and B.-T. Zhang, "Identification of biochemical networks by S-tree based genetic programming," Bioinformatics, vol. 22, no. 13, pp. 1631-1640, 2006. (Pubitemid 43985297)
-
(2006)
Bioinformatics
, vol.22
, Issue.13
, pp. 1631-1640
-
-
Cho, D.-Y.1
Cho, K.-H.2
Zhang, B.-T.3
-
39
-
-
4143058645
-
Gene networks inference using dynamic Bayesian networks
-
DOI 10.1093/bioinformatics/btg1071
-
B.-E. Perrin, L. Ralaivola, A. Mazurie, S. Bottani, J. Mallet, and F. D'Alche-Buc, "Gene networks inference using dynamic Bayesian networks," Bioinformatics, vol. 19, Suppl. 2, pp. ii138-ii148, Oct. 2003. (Pubitemid 41296650)
-
(2003)
Bioinformatics
, vol.19
, Issue.SUPPL. 2
-
-
Perrin, B.-E.1
Ralaivola, L.2
Mazurie, A.3
Bottani, S.4
Mallet, J.5
D'Alche-Buc, F.6
-
40
-
-
39849091950
-
Function approximation approach to the inference of reduced NGnet models of genetic networks
-
Jan
-
S. Kimura, K. Sonoda, S. Yamane, H. Maeda, K. Matsumura, and M. Hatakeyama, "Function approximation approach to the inference of reduced NGnet models of genetic networks," BMC Bioinform., vol. 9, p. 23, Jan. 2008.
-
(2008)
BMC Bioinform
, vol.9
, pp. 23
-
-
Kimura, S.1
Sonoda, K.2
Yamane, S.3
Maeda, H.4
Matsumura, K.5
Hatakeyama, M.6
|