-
1
-
-
33750374139
-
Linking data to models: Data regression
-
DOI 10.1038/nrm2030, PII NRM2030
-
Jaqaman K, Danuser G (2006) Linking data to models: data regression. Nat Rev Mol Cell Biol 7:813-819 (Pubitemid 44627474)
-
(2006)
Nature Reviews Molecular Cell Biology
, vol.7
, Issue.11
, pp. 813-819
-
-
Jaqaman, K.1
Danuser, G.2
-
2
-
-
41849104688
-
Hybrid optimization method with general switching strategy for parameter estimation
-
DOI 10.1186/1752-0509-2-26
-
Balsa-Canto E, Peifer M, Banga JR, Timmer J, Fleck C (2008) Hybrid optimization method with general switching strategy for parameter estimation. BMC Syst Biol 2:26 (Pubitemid 351494149)
-
(2008)
BMC Systems Biology
, vol.2
, pp. 26
-
-
Balsa-Canto, E.1
Peifer, M.2
Banga, J.R.3
Timmer, J.4
Fleck, C.5
-
3
-
-
46349105936
-
Optimization in computational systems biology
-
DOI 10.1186/1752-0509-2-47
-
Banga JR (2008) Optimization in computational systems biology. BMC Syst Biol 2:47 (Pubitemid 351917285)
-
(2008)
BMC Systems Biology
, vol.2
, pp. 47
-
-
Banga, J.R.1
-
4
-
-
0032406131
-
Non-linear optimization of biochemical pathways: Applications to metabolic engineering and parameter estimation
-
DOI 10.1093/bioinformatics/14.10.869
-
Mendes P, Kell D (1998) Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation. Bioinformatics 14:869-883 (Pubitemid 29041543)
-
(1998)
Bioinformatics
, vol.14
, Issue.10
, pp. 869-883
-
-
Mendes, P.1
Kell, D.B.2
-
5
-
-
79956222191
-
An integrative and practical evolutionary optimization for a complex, dynamic model of biological networks
-
10.1007/s00449-010-0486-7 1:CAS:528:DC%2BC3MXksFehtbw%3D
-
Maeda K, Fukano Y, Yamamichi S, Nitta D, Kurata H (2011) An integrative and practical evolutionary optimization for a complex, dynamic model of biological networks. Bioprocess Biosyst Eng 34:433-446
-
(2011)
Bioprocess Biosyst Eng
, vol.34
, pp. 433-446
-
-
Maeda, K.1
Fukano, Y.2
Yamamichi, S.3
Nitta, D.4
Kurata, H.5
-
6
-
-
78650784246
-
Quasi-multiparameter sensitivity measure for robustness analysis of complex biochemical networks
-
10.1016/j.jtbi.2010.12.012
-
Maeda K, Kurata H (2011) Quasi-multiparameter sensitivity measure for robustness analysis of complex biochemical networks. J Theor Biol 272:174-186
-
(2011)
J Theor Biol
, vol.272
, pp. 174-186
-
-
Maeda, K.1
Kurata, H.2
-
7
-
-
77951099999
-
Two-phase search (TPS) method: Nonbiased and high-speed parameter search for dynamic models of biochemical networks
-
10.2197/ipsjtbio.2.2
-
Maeda K, Kurata H (2009) Two-phase search (TPS) method: nonbiased and high-speed parameter search for dynamic models of biochemical networks. IPSJ Trans Bioinforma 2:2-14
-
(2009)
IPSJ Trans Bioinforma
, vol.2
, pp. 2-14
-
-
Maeda, K.1
Kurata, H.2
-
8
-
-
42549157090
-
Mathematical identification of critical reactions in the interlocked feedback model
-
DOI 10.1371/journal.pone.0001103
-
Kurata H, Tanaka T, Ohnishi F (2007) Mathematical identification of critical reactions in the interlocked feedback model. PLoS One 2:e1103 (Pubitemid 351586217)
-
(2007)
PLoS ONE
, vol.2
, Issue.10
-
-
Kurata, H.1
Tanaka, T.2
Ohnishi, F.3
-
9
-
-
84857405878
-
A symmetric dual feedback system provides a robust and entrainable oscillator
-
10.1371/journal.pone.0030489 1:CAS:528:DC%2BC38Xjt1KrsLo%3D
-
Maeda K, Kurata H (2012) A symmetric dual feedback system provides a robust and entrainable oscillator. PLoS One 7:e30489
-
(2012)
PLoS One
, vol.7
, pp. 30489
-
-
Maeda, K.1
Kurata, H.2
-
10
-
-
20144387371
-
Inference of S-system models of genetic networks using a cooperative coevolutionary algorithm
-
DOI 10.1093/bioinformatics/bti071
-
Kimura S, Ide K, Kashihara A, Kano M, Hatakeyama M, Masui R, Nakagawa N, Yokoyama S, Kuramitsu S, Konagaya A (2005) Inference of S-system models of genetic networks using a cooperative coevolutionary algorithm. Bioinformatics 21:1154-1163 (Pubitemid 40467940)
-
(2005)
Bioinformatics
, vol.21
, Issue.7
, pp. 1154-1163
-
-
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
-
11
-
-
33747876155
-
A decompositional approach to parameter estimation in pathway modeling: A case study of the Akt and MAPK pathways and their crosstalk
-
DOI 10.1093/bioinformatics/btl264
-
Koh G, Teong HF, Clement MV, Hsu D, Thiagarajan PS (2006) A decompositional approach to parameter estimation in pathway modeling: a case study of the Akt and MAPK pathways and their crosstalk. Bioinformatics 22:e271-e280 (Pubitemid 44288296)
-
(2006)
Bioinformatics
, vol.22
, Issue.14
-
-
Koh, G.1
Teong, H.F.C.2
Clement, M.-V.3
Hsu, D.4
Thiagarajan, P.S.5
-
12
-
-
33845410054
-
Dynamic modelling and analysis of biochemical networks: Mechanism-based models and model-based experiments
-
DOI 10.1093/bib/bbl040
-
van Riel NA (2006) Dynamic modelling and analysis of biochemical networks: mechanism-based models and model-based experiments. Brief Bioinforma 7:364-374 (Pubitemid 44896739)
-
(2006)
Briefings in Bioinformatics
, vol.7
, Issue.4
, pp. 364-374
-
-
Van Riel, N.A.W.1
-
13
-
-
33746604865
-
Parameter estimation in models combining signal transduction and metabolic pathways: The dependent input approach
-
DOI 10.1049/ip-syb:20050076
-
van Riel NA, Sontag ED (2006) Parameter estimation in models combining signal transduction and metabolic pathways: the dependent input approach. Syst Biol 153:263-274 (Pubitemid 44151486)
-
(2006)
IEE Proceedings: Systems Biology
, vol.153
, Issue.4
, pp. 263-274
-
-
Van Riel, N.A.W.1
Sontag, E.D.2
-
14
-
-
4444351989
-
Decoupling dynamical systems for pathway identification from metabolic profiles
-
DOI 10.1093/bioinformatics/bth140
-
Voit EO, Almeida J (2004) Decoupling dynamical systems for pathway identification from metabolic profiles. Bioinformatics 20:1670-1681 (Pubitemid 39172057)
-
(2004)
Bioinformatics
, vol.20
, Issue.11
, pp. 1670-1681
-
-
Voit, E.O.1
Almeida, J.2
-
15
-
-
33746639260
-
Module-based analysis of robustness tradeoffs in the heat shock response system
-
DOI 10.1371/journal.pcbi.0020059
-
Kurata H, El-Samad H, Iwasaki R, Ohtake H, Doyle JC, Grigorova I, Gross CA, Khammash M (2006) Module-based analysis of robustness tradeoffs in the heat shock response system. PLoS Comput Biol 2:e59 (Pubitemid 44147378)
-
(2006)
PLoS Computational Biology
, vol.2
, Issue.7
, pp. 0663-0675
-
-
Kurata, H.1
El-Samad, H.2
Iwasaki, R.3
Ohtake, H.4
Doyle, J.C.5
Grigorova, I.6
Gross, C.A.7
Khammash, M.8
-
16
-
-
84455183878
-
Biological design principles of complex feedback modules in the E. coli ammonia assimilation system
-
10.1162/artl-a-00049
-
Masaki K, Maeda K, Kurata H (2012) Biological design principles of complex feedback modules in the E. coli ammonia assimilation system. Artif Life 18:53-90
-
(2012)
Artif Life
, vol.18
, pp. 53-90
-
-
Masaki, K.1
Maeda, K.2
Kurata, H.3
-
17
-
-
38349066180
-
Computer-aided rational design of the phosphotransferase system for enhanced glucose uptake in Escherichia coli
-
10.1038/msb4100201
-
Nishio Y, Usuda Y, Matsui K, Kurata H (2008) Computer-aided rational design of the phosphotransferase system for enhanced glucose uptake in Escherichia coli. Mol Syst Biol 4:160
-
(2008)
Mol Syst Biol
, vol.4
, pp. 160
-
-
Nishio, Y.1
Usuda, Y.2
Matsui, K.3
Kurata, H.4
-
18
-
-
17844397967
-
CADLIVE dynamic simulator: Direct link of biochemical networks to dynamic models
-
DOI 10.1101/gr.3463705
-
Kurata H, Masaki K, Sumida Y, Iwasaki R (2005) CADLIVE dynamic simulator: direct link of biochemical networks to dynamic models. Genome Res 15:590-600 (Pubitemid 41057822)
-
(2005)
Genome Research
, vol.15
, Issue.4
, pp. 590-600
-
-
Kurata, H.1
Masaki, K.2
Sumida, Y.3
Iwasaki, R.4
-
19
-
-
0034575517
-
Two-phase partition method for simulating a biological system at an extremely high speed
-
1:CAS:528:DC%2BD3MXjsVWiu7s%3D
-
Kurata H, Taira K (2000) Two-phase partition method for simulating a biological system at an extremely high speed. Genome Inform Ser Workshop Genome Inform 11:185-195
-
(2000)
Genome Inform ser Workshop Genome Inform
, vol.11
, pp. 185-195
-
-
Kurata, H.1
Taira, K.2
-
20
-
-
0242574982
-
Parameter estimation in biochemical pathways: A comparison of global optimization methods
-
DOI 10.1101/gr.1262503
-
Moles CG, Mendes P, Banga JR (2003) Parameter estimation in biochemical pathways: a comparison of global optimization methods. Genome Res 13:2467-2474 (Pubitemid 37428271)
-
(2003)
Genome Research
, vol.13
, Issue.11
, pp. 2467-2474
-
-
Moles, C.G.1
Mendes, P.2
Banga, J.R.3
-
21
-
-
81455142792
-
Parameter estimation using metaheuristics in systems biology: A comprehensive review
-
Sun J, Garibaldi JM, Hodgman C (2012) Parameter estimation using metaheuristics in systems biology: a comprehensive review. IEEE/ACM Trans Comput Biol Bioinforma 9:185-202
-
(2012)
IEEE/ACM Trans Comput Biol Bioinforma
, vol.9
, pp. 185-202
-
-
Sun, J.1
Garibaldi, J.M.2
Hodgman, C.3
-
24
-
-
36749043657
-
Extended CADLIVE: A novel graphical notation for design of biochemical network maps and computational pathway analysis
-
DOI 10.1093/nar/gkm769
-
Kurata H, Inoue K, Maeda K, Masaki K, Shimokawa Y, Zhao Q (2007) Extended CADLIVE: a novel graphical notation for design of biochemical network maps and computational pathway analysis. Nucleic Acids Res 35:e134 (Pubitemid 350201824)
-
(2007)
Nucleic Acids Research
, vol.35
, Issue.20
-
-
Kurata, H.1
Inoue, K.2
Maeda, K.3
Masaki, K.4
Shimokawa, Y.5
Zhao, Q.6
-
25
-
-
0242380634
-
CADLIVE for constructing a large-scale biochemical network based on a simulation-directed notation and its application to yeast cell cycle
-
DOI 10.1093/nar/gkg461
-
Kurata H, Matoba N, Shimizu N (2003) CADLIVE for constructing a large-scale biochemical network based on a simulation-directed notation and its application to yeast cell cycle. Nucleic Acids Res 31:4071-4084 (Pubitemid 37442287)
-
(2003)
Nucleic Acids Research
, vol.31
, Issue.14
, pp. 4071-4084
-
-
Kurata, H.1
Matoba, N.2
Shimizu, N.3
-
26
-
-
0033655445
-
Integration of antagonistic signals in the regulation of nitrogen assimilation in Escherichia coli
-
10.1016/S0070-2137(01)80002-9 1:CAS:528:DC%2BD3cXivVehtb0%3D
-
Ninfa AJ, Jiang P, Atkinson MR, Peliska JA (2000) Integration of antagonistic signals in the regulation of nitrogen assimilation in Escherichia coli. Curr Top Cell Regul 36:31-75
-
(2000)
Curr Top Cell Regul
, vol.36
, pp. 31-75
-
-
Ninfa, A.J.1
Jiang, P.2
Atkinson, M.R.3
Peliska, J.A.4
|