-
1
-
-
33644527950
-
The model organism as a system: Integrating 'omics' data sets
-
Joyce, A.R.; Palsson, B.O. The model organism as a system: integrating 'omics' data sets. Nat. Rev. Mol. Cell. Bio. 2006, 7, 198-210.
-
(2006)
Nat. Rev. Mol. Cell. Bio
, vol.7
, pp. 198-210
-
-
Joyce, A.R.1
Palsson, B.O.2
-
2
-
-
34247276037
-
Integrating scientific cultures
-
Ideker, T.; Bafna, V.; Lemberger, T. Integrating scientific cultures. Mol. Syst. Biol. 2007, 3, 105-106.
-
(2007)
Mol. Syst. Biol
, vol.3
, pp. 105-106
-
-
Ideker, T.1
Bafna, V.2
Lemberger, T.3
-
3
-
-
35348891430
-
Network-based classification of breast cancer metastasis
-
Chuang, H.Y.; Lee, E.; Liu, Y.T.; Lee, D.; Ideker, T. Network-based classification of breast cancer metastasis. Mol. Syst. Biol. 2007, 3, 140-157.
-
(2007)
Mol. Syst. Biol
, vol.3
, pp. 140-157
-
-
Chuang, H.Y.1
Lee, E.2
Liu, Y.T.3
Lee, D.4
Ideker, T.5
-
4
-
-
33747035889
-
Predicting disease genes using protein-protein interactions
-
Oti, M.; Snel, B.; Huynen, M.A.; Brunner, H.G. Predicting disease genes using protein-protein interactions. J. Med. Genet. 2006, 43, 691-698.
-
(2006)
J. Med. Genet
, vol.43
, pp. 691-698
-
-
Oti, M.1
Snel, B.2
Huynen, M.A.3
Brunner, H.G.4
-
5
-
-
10744224197
-
Development of human protein reference database as an initial platform for approaching systems biology in humans
-
Peri, S.; Navarro, J.D.; Amanchy, R.; Kristiansen, T.Z.; Jonnalagadda, C.K.; Surendranath, V.; Niranjan, V.; Muthusamy, B.; Gandhi, T.K.B.; Gronborg, M., et al. Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Res. 2003, 13, 2363-2371.
-
(2003)
Genome Res
, vol.13
, pp. 2363-2371
-
-
Peri, S.1
Navarro, J.D.2
Amanchy, R.3
Kristiansen, T.Z.4
Jonnalagadda, C.K.5
Surendranath, V.6
Niranjan, V.7
Muthusamy, B.8
Gandhi, T.K.B.9
Gronborg, M.10
-
6
-
-
34548407017
-
Discovering functions and revealing mechanisms at molecular level from biological networks
-
Zhang, S.H.; Jin, G.X.; Zhang, X.S.; Chen, L.N. Discovering functions and revealing mechanisms at molecular level from biological networks. Proteomics 2007, 7, 2856-2869.
-
(2007)
Proteomics
, vol.7
, pp. 2856-2869
-
-
Zhang, S.H.1
Jin, G.X.2
Zhang, X.S.3
Chen, L.N.4
-
8
-
-
84863518282
-
On the calculation of signal transduction ability of signaling transduction pathways in intracellular communication: Systematic approach
-
Chen, B.S.; Wu, C.C. On the calculation of signal transduction ability of signaling transduction pathways in intracellular communication: systematic approach. Bioinformatics 2012, 28, 1604-1611.
-
(2012)
Bioinformatics
, vol.28
, pp. 1604-1611
-
-
Chen, B.S.1
Wu, C.C.2
-
9
-
-
1542619848
-
Opinon-Cancer as a robust system: Implications for anticancer therapy
-
Kitano, H. Opinon-Cancer as a robust system: Implications for anticancer therapy. Nat. Rev. Cancer 2004, 4, 227-235.
-
(2004)
Nat. Rev. Cancer
, vol.4
, pp. 227-235
-
-
Kitano, H.1
-
10
-
-
4544346660
-
Robustness of cellular functions
-
Stelling, J.; Sauer, U.; Szallasi, Z.; Doyle, F.J.; Doyle, J. Robustness of cellular functions. Cell 2004, 118, 675-685.
-
(2004)
Cell
, vol.118
, pp. 675-685
-
-
Stelling, J.1
Sauer, U.2
Szallasi, Z.3
Doyle, F.J.4
Doyle, J.5
-
11
-
-
24644519314
-
Significance analysis of time course microarray experiments
-
Storey, J.D.; Xiao, W.Z.; Leek, J.T.; Tompkins, R.G.; Davis, R.W. Significance analysis of time course microarray experiments. Proc. Natl. Acad. Sci. USA 2005, 102, 12837-12842.
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 12837-12842
-
-
Storey, J.D.1
Xiao, W.Z.2
Leek, J.T.3
Tompkins, R.G.4
Davis, R.W.5
-
12
-
-
0031858914
-
SGD, Saccharomyces genome database
-
Cherry, J.M.; Adler, C.; Ball, C.; Chervitz, S.A.; Dwight, S.S.; Hester, E.T.; Jia, Y.K.; Juvik, G.; Roe, T.; Schroeder, M., et al. SGD, Saccharomyces genome database. Nucleic Acids Res. 1998, 26, 73-79.
-
(1998)
Nucleic Acids Res
, vol.26
, pp. 73-79
-
-
Cherry, J.M.1
Adler, C.2
Ball, C.3
Chervitz, S.A.4
Dwight, S.S.5
Hester, E.T.6
Jia, Y.K.7
Juvik, G.8
Roe, T.9
Schroeder, M.10
-
13
-
-
0033637153
-
Genomic expression programs in the response of yeast cells to environmental changes
-
Gasch, A.P.; Spellman, P.T.; Kao, C.M.; Carmel-Harel, O.; Eisen, M.B.; Storz, G.; Botstein, D.; Brown, P.O. Genomic expression programs in the response of yeast cells to environmental changes. Mol. Biol. Cell. 2000, 11, 4241-4257.
-
(2000)
Mol. Biol. Cell
, vol.11
, pp. 4241-4257
-
-
Gasch, A.P.1
Spellman, P.T.2
Kao, C.M.3
Carmel-Harel, O.4
Eisen, M.B.5
Storz, G.6
Botstein, D.7
Brown, P.O.8
-
14
-
-
4544352942
-
Transcriptional regulatory code of a eukaryotic genome
-
Harbison, C.T.; Gordon, D.B.; Lee, T.I.; Rinaldi, N.J.; Macisaac, K.D.; Danford, T.W.; Hannett, N.M.; Tagne, J.B.; Reynolds, D.B.; Yoo, J., et al. Transcriptional regulatory code of a eukaryotic genome. Nature 2004, 431, 99-104.
-
(2004)
Nature
, vol.431
, pp. 99-104
-
-
Harbison, C.T.1
Gordon, D.B.2
Lee, T.I.3
Rinaldi, N.J.4
Macisaac, K.D.5
Danford, T.W.6
Hannett, N.M.7
Tagne, J.B.8
Reynolds, D.B.9
Yoo, J.10
-
15
-
-
33644873683
-
The YEASTRACT database, a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae
-
Teixeira, M.C.; Monteiro, P.; Jain, P.; Tenreiro, S.; Fernandes, A.R.; Mira, N.P.; Alenquer, M.; Freitas, A.T.; Oliveira, A.L.; Sa-Correia, I. The YEASTRACT database, a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae. Nucleic Acids Res. 2006, 34, D446-D451.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Teixeira, M.C.1
Monteiro, P.2
Jain, P.3
Tenreiro, S.4
Fernandes, A.R.5
Mira, N.P.6
Alenquer, M.7
Freitas, A.T.8
Oliveira, A.L.9
Sa-Correia, I.10
-
16
-
-
33644873184
-
BioGRID, a general repository for interaction datasets
-
Stark, C.; Breitkreutz, B.J.; Reguly, T.; Boucher, L.; Breitkreutz, A.; Tyers, M. BioGRID, a general repository for interaction datasets. Nucleic Acids Res. 2006, 34, D535-D539.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Stark, C.1
Breitkreutz, B.J.2
Reguly, T.3
Boucher, L.4
Breitkreutz, A.5
Tyers, M.6
-
17
-
-
0034069495
-
Gene ontology, Tool for the unification of biology. The gene ontology consortium
-
Ashburner, M.; Ball, C.A.; Blake, J.A.; Botstein, D.; Butler, H.; Cherry, J.M.; Davis, A.P.; Dolinski, K.; Dwight, S.S.; Eppig, J.T., et al. Gene ontology, Tool for the unification of biology. The gene ontology consortium. Nat. Genet. 2000, 25, 25-29.
-
(2000)
Nat. Genet
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
Blake, J.A.3
Botstein, D.4
Butler, H.5
Cherry, J.M.6
Davis, A.P.7
Dolinski, K.8
Dwight, S.S.9
Eppig, J.T.10
-
18
-
-
4444339832
-
Quantitative characterization of the transcriptional regulatory network in the yeast cell cycle
-
Chen, H.C.; Lee, H.C.; Lin, T.Y.; Li, W.H.; Chen, B.S. Quantitative characterization of the transcriptional regulatory network in the yeast cell cycle. Bioinformatics 2004, 20, 1914-1927.
-
(2004)
Bioinformatics
, vol.20
, pp. 1914-1927
-
-
Chen, H.C.1
Lee, H.C.2
Lin, T.Y.3
Li, W.H.4
Chen, B.S.5
-
19
-
-
20744452513
-
A new measure of the robustness of biochemical networks
-
Chen, B.S.; Wang, Y.C.; Wu, W.S.; Li, W.H. A new measure of the robustness of biochemical networks. Bioinformatics 2005, 21, 2698-2705.
-
(2005)
Bioinformatics
, vol.21
, pp. 2698-2705
-
-
Chen, B.S.1
Wang, Y.C.2
Wu, W.S.3
Li, W.H.4
-
20
-
-
25444464334
-
Quantitative inference of dynamic regulatory pathways via microarray data
-
Chang, W.C.; Li, C.W.; Chen, B.S. Quantitative inference of dynamic regulatory pathways via microarray data. BMC Bioinf. 2005, 6, 44-62.
-
(2005)
BMC Bioinf
, vol.6
, pp. 44-62
-
-
Chang, W.C.1
Li, C.W.2
Chen, B.S.3
-
21
-
-
27744485351
-
Dynamic modeling of cis-regulatory circuits and gene expression prediction via cross-gene identification
-
Lin, L.H.; Lee, H.C.; Li, W.H.; Chen, B.S. Dynamic modeling of cis-regulatory circuits and gene expression prediction via cross-gene identification. BMC Bioinf. 2005, 6, 258-274.
-
(2005)
BMC Bioinf
, vol.6
, pp. 258-274
-
-
Lin, L.H.1
Lee, H.C.2
Li, W.H.3
Chen, B.S.4
-
22
-
-
33748694308
-
Identification of transcription factor cooperativity via stochastic system model
-
Chang, Y.H.; Wang, Y.C.; Chen, B.S. Identification of transcription factor cooperativity via stochastic system model. Bioinformatics 2006, 22, 2276-2282.
-
(2006)
Bioinformatics
, vol.22
, pp. 2276-2282
-
-
Chang, Y.H.1
Wang, Y.C.2
Chen, B.S.3
-
23
-
-
33751222851
-
Computational reconstruction of transcriptional regulatory modules of the yeast cell cycle
-
Wu, W.S.; Li, W.H.; Chen, B.S. Computational reconstruction of transcriptional regulatory modules of the yeast cell cycle. BMC Bioinf. 2006, 7, 421-435.
-
(2006)
BMC Bioinf
, vol.7
, pp. 421-435
-
-
Wu, W.S.1
Li, W.H.2
Chen, B.S.3
-
24
-
-
34447279700
-
Identifying regulatory targets of cell cycle transcription factors using gene expression and ChIP-chip data
-
Wu, W.S.; Li, W.H.; Chen, B.S. Identifying regulatory targets of cell cycle transcription factors using gene expression and ChIP-chip data. BMC Bioinf. 2007, 8, 188-205.
-
(2007)
BMC Bioinf
, vol.8
, pp. 188-205
-
-
Wu, W.S.1
Li, W.H.2
Chen, B.S.3
-
25
-
-
33645813418
-
On the attenuation and amplification of molecular noise in genetic regulatory networks
-
Chen, B.S.; Wang, Y.C. On the attenuation and amplification of molecular noise in genetic regulatory networks. BMC Bioinf. 2006, 7, 52-65.
-
(2006)
BMC Bioinf
, vol.7
, pp. 52-65
-
-
Chen, B.S.1
Wang, Y.C.2
-
26
-
-
34447545562
-
Analysing microarray data in drug discovery using systems biology
-
Chen, B.-S.; Li, C.-W. Analysing microarray data in drug discovery using systems biology. Expert Opin. Drug Discovery 2007, 2, 755-768.
-
(2007)
Expert Opin. Drug Discovery
, vol.2
, pp. 755-768
-
-
Chen, B.-S.1
Li, C.-W.2
-
27
-
-
36348946191
-
On the Robust Circuit Design Schemes of Biochemical Networks, Steady-State Approach
-
Chen, B.S.; Wu, W.S.; Wang, Y.C.; Li, W.H. On the Robust Circuit Design Schemes of Biochemical Networks, Steady-State Approach. IEEE T Biomed. Circ. S 2007, 1, 91-104.
-
(2007)
IEEE T Biomed. Circ. S
, vol.1
, pp. 91-104
-
-
Chen, B.S.1
Wu, W.S.2
Wang, Y.C.3
Li, W.H.4
-
28
-
-
52249111600
-
Robust Engineered Circuit Design Principles for Stochastic Biochemical Networks With Parameter Uncertainties and Disturbances
-
Chen, B.S.; Chen, P.W. Robust Engineered Circuit Design Principles for Stochastic Biochemical Networks With Parameter Uncertainties and Disturbances. IEEE T Biomed. Circ. S 2008, 2, 114-132.
-
(2008)
IEEE T Biomed. Circ. S
, vol.2
, pp. 114-132
-
-
Chen, B.S.1
Chen, P.W.2
-
29
-
-
84874513506
-
A unifying mathematical framework for genetic robustness, environmental robustness, network robustness and their trade-off on phenotype robustness in biological networks Part I, Gene regulatory networks in systems and evolutionary biology
-
Chen, B.S.; Lin, Y.P. A unifying mathematical framework for genetic robustness, environmental robustness, network robustness and their trade-off on phenotype robustness in biological networks Part I, Gene regulatory networks in systems and evolutionary biology. Evol. Bioinform 2013, 9, 43-68.
-
(2013)
Evol. Bioinform
, vol.9
, pp. 43-68
-
-
Chen, B.S.1
Lin, Y.P.2
-
30
-
-
84874529981
-
A Unifying mathematical framework for genetic robustness, environmental robustness, Network robustness and their tradeoff on phenotype robustness in biological networks Part II, Ecological networks
-
Chen, B.S.; Lin, Y.P. A Unifying mathematical framework for genetic robustness, environmental robustness, Network robustness and their tradeoff on phenotype robustness in biological networks Part II, Ecological networks. Evol. Bioinform 2013, 9, 69-85.
-
(2013)
Evol. Bioinform
, vol.9
, pp. 69-85
-
-
Chen, B.S.1
Lin, Y.P.2
-
31
-
-
84859610969
-
Prediction of phenotype-associated genes via a cellular network approach, a candida albicans infection case study
-
Wang, Y.C.; Huang, S.H.; Lan, C.Y.; Chen, B.S. Prediction of phenotype-associated genes via a cellular network approach, a candida albicans infection case study. PloS One 2012, 7, e35339.
-
(2012)
PloS One
, vol.7
-
-
Wang, Y.C.1
Huang, S.H.2
Lan, C.Y.3
Chen, B.S.4
-
32
-
-
84876120342
-
Identification of infectionand defense-related genes via a dynamic host-pathogen interaction network using a candida albicans -zebrafish infection model
-
Kuo, Z.Y.; Chuang, Y.J.; Chao, C.C.; Liu, F.C.; Lan, C.Y.; Chen, B.S. Identification of infectionand defense-related genes via a dynamic host-pathogen interaction network using a candida albicans -zebrafish infection model. J. Innate Immun. 2013, 5, 137-152.
-
(2013)
J. Innate Immun
, vol.5
, pp. 137-152
-
-
Kuo, Z.Y.1
Chuang, Y.J.2
Chao, C.C.3
Liu, F.C.4
Lan, C.Y.5
Chen, B.S.6
-
33
-
-
84873805440
-
New measurement methods of network robustness and response ability via microarray data
-
Tu, C.T.; Chen, B.S. New measurement methods of network robustness and response ability via microarray data. PloS One 2013, 8, e55230.
-
(2013)
PloS One
, vol.8
-
-
Tu, C.T.1
Chen, B.S.2
-
34
-
-
84882980715
-
On the Increase in Network Robustness and Decrease in Network Response Ability During the Aging Process, A Systems Biology Approach via Microarray Data
-
Tu, C.T.; Chen, B.S. On the Increase in Network Robustness and Decrease in Network Response Ability During the Aging Process, A Systems Biology Approach via Microarray Data. IEEE/ACM Trans. Comput. Biol. Bioinf. 2013, 10, 468-480.
-
(2013)
IEEE/ACM Trans. Comput. Biol. Bioinf
, vol.10
, pp. 468-480
-
-
Tu, C.T.1
Chen, B.S.2
-
35
-
-
0036500834
-
Reverse engineering of biological complexity
-
Csete, M.E.; Doyle, J.C. Reverse engineering of biological complexity. Science 2002, 295, 1664-1669.
-
(2002)
Science
, vol.295
, pp. 1664-1669
-
-
Csete, M.E.1
Doyle, J.C.2
-
36
-
-
36849002434
-
Systems metabolic engineering of Escherichia coli for L-threonine production
-
Lee, K.H.; Park, J.H.; Kim, T.Y.; Kim, H.U.; Lee, S.Y. Systems metabolic engineering of Escherichia coli for L-threonine production. Mol. Syst. Biol. 2007, 3, 149.
-
(2007)
Mol. Syst. Biol
, vol.3
, pp. 149
-
-
Lee, K.H.1
Park, J.H.2
Kim, T.Y.3
Kim, H.U.4
Lee, S.Y.5
-
37
-
-
47249096975
-
Application of systems biology for bioprocess development
-
Park, J.H.; Lee, S.Y.; Kim, T.Y.; Kim, H.U. Application of systems biology for bioprocess development. Trends Biotechnol 2008, 26, 404-412.
-
(2008)
Trends Biotechnol
, vol.26
, pp. 404-412
-
-
Park, J.H.1
Lee, S.Y.2
Kim, T.Y.3
Kim, H.U.4
-
38
-
-
39649116670
-
Robust H infinity-stabilization design in gene networks under stochastic molecular noises, fuzzy-interpolation approach
-
Chen, B.S.; Chang, Y.T.; Wang, Y.C. Robust H infinity-stabilization design in gene networks under stochastic molecular noises, fuzzy-interpolation approach. IEEE Trans. Syst. Man Cybern B Cybern 2008, 38, 25-42.
-
(2008)
IEEE Trans. Syst. Man Cybern B Cybern
, vol.38
, pp. 25-42
-
-
Chen, B.S.1
Chang, Y.T.2
Wang, Y.C.3
-
39
-
-
48549092620
-
Construction of a cancer-perturbed protein-protein interaction network for discovery of apoptosis drug targets
-
Chu, L.H.; Chen, B.S. Construction of a cancer-perturbed protein-protein interaction network for discovery of apoptosis drug targets. BMC Syst. Biol. 2008, 2, 56.
-
(2008)
BMC Syst. Biol
, vol.2
, pp. 56
-
-
Chu, L.H.1
Chen, B.S.2
-
40
-
-
47849111293
-
Robust model matching control of immune systems under environmental disturbances, Dynamic game approach
-
Chen, B.S.; Chang, C.H.; Chuang, Y.J. Robust model matching control of immune systems under environmental disturbances, Dynamic game approach. J. Theor. Biol. 2008, 253, 824-837.
-
(2008)
J. Theor. Biol
, vol.253
, pp. 824-837
-
-
Chen, B.S.1
Chang, C.H.2
Chuang, Y.J.3
-
41
-
-
70349761106
-
A systems biology approach to construct the gene regulatory network of systemic inflammation via microarray and databases mining
-
Chen, B.S.; Yang, S.K.; Lan, C.Y.; Chuang, Y.J. A systems biology approach to construct the gene regulatory network of systemic inflammation via microarray and databases mining. BMC Med. Genomics 2008, 1, 46
-
(2008)
BMC Med. Genomics
, vol.1
, pp. 46
-
-
Chen, B.S.1
Yang, S.K.2
Lan, C.Y.3
Chuang, Y.J.4
-
42
-
-
70450222907
-
On the estimation of robustness and filtering ability of dynamic biochemical networks under process delays, internal parametric perturbations and external disturbances
-
Chen, B.S.; Chen, P.W. On the estimation of robustness and filtering ability of dynamic biochemical networks under process delays, internal parametric perturbations and external disturbances. Math. Biosci. 2009, 222, 92-108.
-
(2009)
Math. Biosci
, vol.222
, pp. 92-108
-
-
Chen, B.S.1
Chen, P.W.2
-
43
-
-
77951192371
-
Global screening of potential Candida albicans biofilm-related transcription factors via network comparison
-
Wang, Y.C.; Lan, C.Y.; Hsieh, W.P.; Murillo, L.A.; Agabian, N.; Chen, B.S. Global screening of potential Candida albicans biofilm-related transcription factors via network comparison. BMC Bioinf. 2010, 11, 53-73.
-
(2010)
BMC Bioinf
, vol.11
, pp. 53-73
-
-
Wang, Y.C.1
Lan, C.Y.2
Hsieh, W.P.3
Murillo, L.A.4
Agabian, N.5
Chen, B.S.6
-
44
-
-
77952510758
-
Identifying Functional Mechanisms of Gene and Protein Regulatory Networks in Response to a Broader Range of Environmental Stresses
-
Li, C.W.; Chen, B.S. Identifying Functional Mechanisms of Gene and Protein Regulatory Networks in Response to a Broader Range of Environmental Stresses. Comp. Funct. Genom. 2010, 2010, 408705.
-
(2010)
Comp. Funct. Genom. 2010
, pp. 408705
-
-
Li, C.W.1
Chen, B.S.2
-
45
-
-
0034688174
-
Construction of a genetic toggle switch in Escherichia coli
-
Gardner, T.S.; Cantor, C.R.; Collins, J.J. Construction of a genetic toggle switch in Escherichia coli. Nature 2000, 403, 339-342.
-
(2000)
Nature
, vol.403
, pp. 339-342
-
-
Gardner, T.S.1
Cantor, C.R.2
Collins, J.J.3
-
46
-
-
0034688173
-
A synthetic oscillatory network of transcriptional regulators
-
Elowitz, M.B.; Leibler, S. A synthetic oscillatory network of transcriptional regulators. Nature 2000, 403, 335-338.
-
(2000)
Nature
, vol.403
, pp. 335-338
-
-
Elowitz, M.B.1
Leibler, S.2
-
47
-
-
0037079012
-
Engineered gene circuits
-
Hasty, J.; McMillen, D.; Collins, J.J. Engineered gene circuits. Nature 2002, 420, 224-230.
-
(2002)
Nature
, vol.420
, pp. 224-230
-
-
Hasty, J.1
McMillen, D.2
Collins, J.J.3
-
48
-
-
23444461901
-
Advances in synthetic biology, on the path from prototypes to applications
-
McDaniel, R.; Weiss, R. Advances in synthetic biology, on the path from prototypes to applications. Curr. Opin. Biotechnol. 2005, 16, 476-483.
-
(2005)
Curr. Opin. Biotechnol
, vol.16
, pp. 476-483
-
-
McDaniel, R.1
Weiss, R.2
-
49
-
-
28544451327
-
Foundations for engineering biology
-
Endy, D. Foundations for engineering biology. Nature 2005, 438, 449-453.
-
(2005)
Nature
, vol.438
, pp. 449-453
-
-
Endy, D.1
-
50
-
-
0033083733
-
It's a noisy business! Genetic regulation at the nanomolar scale
-
McAdams, H.H.; Arkin, A. It's a noisy business! Genetic regulation at the nanomolar scale. Trends Genet. 1999, 15, 65-69.
-
(1999)
Trends Genet
, vol.15
, pp. 65-69
-
-
McAdams, H.H.1
Arkin, A.2
-
51
-
-
34548747486
-
Robustness analysis and tuning of synthetic gene networks
-
Batt, G.; Yordanov, B.; Weiss, R.; Belta, C. Robustness analysis and tuning of synthetic gene networks. Bioinformatics 2007, 23, 2415-2422.
-
(2007)
Bioinformatics
, vol.23
, pp. 2415-2422
-
-
Batt, G.1
Yordanov, B.2
Weiss, R.3
Belta, C.4
-
52
-
-
67649887149
-
Robust synthetic biology design, stochastic game theory approach
-
Chen, B.S.; Chang, C.H.; Lee, H.C. Robust synthetic biology design, stochastic game theory approach. Bioinformatics 2009, 25, 1822-1830.
-
(2009)
Bioinformatics
, vol.25
, pp. 1822-1830
-
-
Chen, B.S.1
Chang, C.H.2
Lee, H.C.3
-
53
-
-
69549091790
-
A systematic design method for robust synthetic biology to satisfy design specifications
-
Chen, B.S.; Wu, C.H. A systematic design method for robust synthetic biology to satisfy design specifications. BMC Syst. Biol. 2009, 3, 66-83.
-
(2009)
BMC Syst. Biol
, vol.3
, pp. 66-83
-
-
Chen, B.S.1
Wu, C.H.2
-
54
-
-
77953495214
-
GA-based Design Algorithms for the Robust Synthetic Genetic Oscillators with Prescribed Amplitude, Period and Phase
-
Chen, B.S.; Chen, P.W. GA-based Design Algorithms for the Robust Synthetic Genetic Oscillators with Prescribed Amplitude, Period and Phase. Gene Regul. Syst. Bio. 2010, 4, 35-52.
-
(2010)
Gene Regul. Syst. Bio
, vol.4
, pp. 35-52
-
-
Chen, B.S.1
Chen, P.W.2
-
55
-
-
77953487043
-
Robust optimal reference-tracking design method for stochastic synthetic biology systems, T-S fuzzy approach
-
Chen, B.S.; Wu, C.H. Robust optimal reference-tracking design method for stochastic synthetic biology systems, T-S fuzzy approach. IEEE T. Fuzzy Syst. 2010, 18, 1144-1159.
-
(2010)
IEEE T. Fuzzy Syst
, vol.18
, pp. 1144-1159
-
-
Chen, B.S.1
Wu, C.H.2
-
56
-
-
80052544125
-
Multiobjective H-2/H-infinity synthetic gene network design based on promoter libraries
-
Wu, C.H.; Zhang, W.H.; Chen, B.S. Multiobjective H-2/H-infinity synthetic gene network design based on promoter libraries. Math. Biosci. 2011, 233, 111-125.
-
(2011)
Math. Biosci
, vol.233
, pp. 111-125
-
-
Wu, C.H.1
Zhang, W.H.2
Chen, B.S.3
-
57
-
-
80052526091
-
Robust synthetic gene network design via library-based search method
-
Wu, C.H.; Lee, H.C.; Chen, B.S. Robust synthetic gene network design via library-based search method. Bioinformatics 2011, 27, 2700-2706.
-
(2011)
Bioinformatics
, vol.27
, pp. 2700-2706
-
-
Wu, C.H.1
Lee, H.C.2
Chen, B.S.3
-
58
-
-
84862908629
-
Robust design of biological circuits, Evolutionary systems biology approach
-
Chen, B.S.; Hsu, C.Y.; Liou, J.J. Robust design of biological circuits, Evolutionary systems biology approach. J. Biomed. Biotechnol. 2011, 2011, 30423.
-
(2011)
J. Biomed. Biotechnol. 2011
, pp. 30423
-
-
Chen, B.S.1
Hsu, C.Y.2
Liou, J.J.3
-
59
-
-
84874577390
-
A unifying mathematical framework for genetic robustness, Environmental robustness, Network robustness and their trade-offs on phenotype robustness in biological networks. Part III, Synthetic gene networks in synthetic biology
-
Chen, B.S.; Lin, Y.P. A unifying mathematical framework for genetic robustness, Environmental robustness, Network robustness and their trade-offs on phenotype robustness in biological networks. Part III, Synthetic gene networks in synthetic biology. Evol. Bioinform 2013, 9, 87-109.
-
(2013)
Evol. Bioinform
, vol.9
, pp. 87-109
-
-
Chen, B.S.1
Lin, Y.P.2
-
60
-
-
84867768286
-
Robust synchronization control scheme of a population of nonlinear stochastic synthetic genetic oscillators under intrinsic and extrinsic molecular noise via quorum sensing
-
Chen, B.S.; Hsu, C.Y. Robust synchronization control scheme of a population of nonlinear stochastic synthetic genetic oscillators under intrinsic and extrinsic molecular noise via quorum sensing. BMC Systems Biology 2012, 6, 136-150.
-
(2012)
BMC Systems Biology
, vol.6
, pp. 136-150
-
-
Chen, B.S.1
Hsu, C.Y.2
-
61
-
-
35348893696
-
Metabolite essentiality elucidates robustness of Escherichia coli metabolism
-
Kim, P.J.; Lee, D.Y.; Kim, T.Y.; Lee, K.H.; Jeong, H.; Lee, S.Y.; Park, S. Metabolite essentiality elucidates robustness of Escherichia coli metabolism. Proc. Natl. Acad. Sci. USA 2007, 104, 13638-13642.
-
(2007)
Proc. Natl. Acad. Sci. USA
, vol.104
, pp. 13638-13642
-
-
Kim, P.J.1
Lee, D.Y.2
Kim, T.Y.3
Lee, K.H.4
Jeong, H.5
Lee, S.Y.6
Park, S.7
-
62
-
-
0037069467
-
Analysis of optimality in natural and perturbed metabolic networks
-
Segre, D.; Vitkup, D.; Church, G.M. Analysis of optimality in natural and perturbed metabolic networks. Proc. Natl. Acad. Sci. USA 2002, 99, 15112-15117.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 15112-15117
-
-
Segre, D.1
Vitkup, D.2
Church, G.M.3
-
63
-
-
71849110254
-
Mathematical modeling and synthetic biology
-
Chandran, D.; Copeland, W.B.; Sleight, S.C.; Sauro, H.M. Mathematical modeling and synthetic biology. Drug Discovery Today 2008, 5, 299-309.
-
(2008)
Drug Discovery Today
, vol.5
, pp. 299-309
-
-
Chandran, D.1
Copeland, W.B.2
Sleight, S.C.3
Sauro, H.M.4
-
64
-
-
37549034954
-
Engineering a native homoethanol pathway in Escherichia coli B for ethanol production
-
Zhou, S.; Iverson, A.G.; Grayburn, W.S. Engineering a native homoethanol pathway in Escherichia coli B for ethanol production. Biotechnol. Lett. 2008, 30, 335-342.
-
(2008)
Biotechnol. Lett
, vol.30
, pp. 335-342
-
-
Zhou, S.1
Iverson, A.G.2
Grayburn, W.S.3
-
65
-
-
34247183123
-
A genome-scale computational study of the interplay between transcriptional regulation and metabolism
-
Shlomi, T.; Eisenberg, Y.; Sharan, R.; Ruppin, E. A genome-scale computational study of the interplay between transcriptional regulation and metabolism. Mol. Syst. Biol. 2007, 3, 101-107.
-
(2007)
Mol. Syst. Biol
, vol.3
, pp. 101-107
-
-
Shlomi, T.1
Eisenberg, Y.2
Sharan, R.3
Ruppin, E.4
-
66
-
-
42949164125
-
Formulating genome-scale kinetic models in the post-genome era
-
Jamshidi, N.; Palsson, B.O. Formulating genome-scale kinetic models in the post-genome era. Mol. Syst. Biol. 2008, 4, 171-186.
-
(2008)
Mol. Syst. Biol
, vol.4
, pp. 171-186
-
-
Jamshidi, N.1
Palsson, B.O.2
-
67
-
-
37349099750
-
A predictive model for transcriptional control of physiology in a free living cell
-
Bonneau, R.; Facciotti, M.T.; Reiss, D.J.; Schmid, A.K.; Pan, M.; Kaur, A.; Thorsson, V.; Shannon, P.; Johnson, M.H.; Bare, J.C., et al. A predictive model for transcriptional control of physiology in a free living cell. Cell 2007, 131, 1354-1365.
-
(2007)
Cell
, vol.131
, pp. 1354-1365
-
-
Bonneau, R.1
Facciotti, M.T.2
Reiss, D.J.3
Schmid, A.K.4
Pan, M.5
Kaur, A.6
Thorsson, V.7
Shannon, P.8
Johnson, M.H.9
Bare, J.C.10
-
68
-
-
33847134821
-
Efficient classification of complete parameter regions based on semidefinite programming
-
Kuepfer, L.; Sauer, U.; Parrilo, P.A. Efficient classification of complete parameter regions based on semidefinite programming. BMC Bioinf. 2007, 8, 12-22.
-
(2007)
BMC Bioinf
, vol.8
, pp. 12-22
-
-
Kuepfer, L.1
Sauer, U.2
Parrilo, P.A.3
-
69
-
-
80051511593
-
Constructing gene regulatory networks for long term photosynthetic light acclimation in Arabidopsis thaliana
-
Yao, C.W.; Hsu, B.D.; Chen, B.S. Constructing gene regulatory networks for long term photosynthetic light acclimation in Arabidopsis thaliana. BMC Bioinf. 2011, 12, 335.
-
(2011)
BMC Bioinf
, vol.12
, pp. 335
-
-
Yao, C.W.1
Hsu, B.D.2
Chen, B.S.3
-
70
-
-
78650897194
-
A network-based biomarker approach for molecular investigation and diagnosis of lung cancer
-
Wang, Y.C.; Chen, B.S. A network-based biomarker approach for molecular investigation and diagnosis of lung cancer. BMC Med. Genomics 2011, 4, 2-16.
-
(2011)
BMC Med. Genomics
, vol.4
, pp. 2-16
-
-
Wang, Y.C.1
Chen, B.S.2
-
71
-
-
77951162860
-
Integrated cellular network of transcription regulations and protein-protein interactions
-
Wang, Y.C.; Chen, B.S. Integrated cellular network of transcription regulations and protein-protein interactions. BMC Syst. Biol. 2010, 4, 20-36.
-
(2010)
BMC Syst. Biol
, vol.4
, pp. 20-36
-
-
Wang, Y.C.1
Chen, B.S.2
-
72
-
-
84860920283
-
Synthetic biology devices as tools for metabolic engineering
-
Shiue, E.; Prather, K.L.J. Synthetic biology devices as tools for metabolic engineering. Biochem. Eng. J. 2012, 65, 82-89.
-
(2012)
Biochem. Eng. J
, vol.65
, pp. 82-89
-
-
Shiue, E.1
Prather, K.L.J.2
-
73
-
-
0742269301
-
Stochastic H(2)/H(infinity) control with state-dependent noise
-
Chen, B.S.; Zhang, W.H. Stochastic H(2)/H(infinity) control with state-dependent noise. IEEE T Automat. Contr. 2004, 49, 45-57.
-
(2004)
IEEE T Automat. Contr
, vol.49
, pp. 45-57
-
-
Chen, B.S.1
Zhang, W.H.2
-
74
-
-
13244258477
-
Robust H-infinity filtering for nonlinear stochastic systems
-
Zhang, W.H.; Chen, B.S.; Tseng, C.S. Robust H-infinity filtering for nonlinear stochastic systems. IEEE T Signal. Proces. 2005, 53, 589-598.
-
(2005)
IEEE T Signal. Proces
, vol.53
, pp. 589-598
-
-
Zhang, W.H.1
Chen, B.S.2
Tseng, C.S.3
-
75
-
-
33645831442
-
State feedback H(infinity) control for a class of nonlinear stochastic systems
-
Zhang, W.H.; Chen, B.S. State feedback H(infinity) control for a class of nonlinear stochastic systems. Siam J. Control. Optim 2006, 44, 1973-1991.
-
(2006)
Siam J. Control. Optim
, vol.44
, pp. 1973-1991
-
-
Zhang, W.H.1
Chen, B.S.2
-
76
-
-
0034616930
-
Functional discovery via a compendium of expression profiles
-
Hughes, T.R.; Marton, M.J.; Jones, A.R.; Roberts, C.J.; Stoughton, R.; Armour, C.D.; Bennett, H.A.; Coffey, E.; Dai, H.Y.; He, Y.D.D., et al. Functional discovery via a compendium of expression profiles. Cell 2000, 102, 109-126.
-
(2000)
Cell
, vol.102
, pp. 109-126
-
-
Hughes, T.R.1
Marton, M.J.2
Jones, A.R.3
Roberts, C.J.4
Stoughton, R.5
Armour, C.D.6
Bennett, H.A.7
Coffey, E.8
Dai, H.Y.9
He, Y.D.D.10
-
78
-
-
34447500791
-
Construction and clarification of dynamic gene regulatory network of cancer cell cycle via microarray data
-
Li, C.W.; Chu, Y.H.; Chen, B.S. Construction and clarification of dynamic gene regulatory network of cancer cell cycle via microarray data. Cancer Informatics 2006, 2, 223-241.
-
(2006)
Cancer Informatics
, vol.2
, pp. 223-241
-
-
Li, C.W.1
Chu, Y.H.2
Chen, B.S.3
-
80
-
-
7644238181
-
Biological robustness
-
Kitano, H. Biological robustness. Nat. Rev. Genet. 2004, 5, 826-837.
-
(2004)
Nat. Rev. Genet
, vol.5
, pp. 826-837
-
-
Kitano, H.1
-
81
-
-
67651148398
-
Robust H-2/H-infinity global linearization filter design for nonlinear stochastic systems
-
Chen, B.S.; Chen, W.H.; Wu, H.L. Robust H-2/H-infinity global linearization filter design for nonlinear stochastic systems. IEEE T Circuits-I 2009, 56, 1441-1454.
-
(2009)
IEEE T Circuits-I
, vol.56
, pp. 1441-1454
-
-
Chen, B.S.1
Chen, W.H.2
Wu, H.L.3
-
82
-
-
84947634865
-
A nonlinear H-Infinity control design in robotic systems under parameter perturbation and external disturbance
-
Chen, B.S.; Lee, T.S.; Feng, J.H. A nonlinear H-Infinity control design in robotic systems under parameter perturbation and external disturbance. Int J. Control. 1994, 59, 439-461.
-
(1994)
Int J. Control
, vol.59
, pp. 439-461
-
-
Chen, B.S.1
Lee, T.S.2
Feng, J.H.3
-
83
-
-
0034204782
-
Mixed H-2/H-infinity fuzzy output feedback control design for nonlinear dynamic systems, An LMI approach
-
Chen, B.S.; Tseng, C.S.; Uang, H.J. Mixed H-2/H-infinity fuzzy output feedback control design for nonlinear dynamic systems, An LMI approach. IEEE T. Fuzzy Syst. 2000, 8, 249-265.
-
(2000)
IEEE T. Fuzzy Syst
, vol.8
, pp. 249-265
-
-
Chen, B.S.1
Tseng, C.S.2
Uang, H.J.3
-
84
-
-
57049159362
-
A fast, robust and tunable synthetic gene oscillator
-
Stricker, J.; Cookson, S.; Bennett, M.R.; Mather, W.H.; Tsimring, L.S.; Hasty, J. A fast, robust and tunable synthetic gene oscillator. Nature 2008, 456, 516-519.
-
(2008)
Nature
, vol.456
, pp. 516-519
-
-
Stricker, J.1
Cookson, S.2
Bennett, M.R.3
Mather, W.H.4
Tsimring, L.S.5
Hasty, J.6
-
85
-
-
58249117722
-
A tunable synthetic mammalian oscillator
-
Tigges, M.; Marquez-Lago, T.T.; Stelling, J.; Fussenegger, M. A tunable synthetic mammalian oscillator. Nature 2009, 457, 309-312.
-
(2009)
Nature
, vol.457
, pp. 309-312
-
-
Tigges, M.1
Marquez-Lago, T.T.2
Stelling, J.3
Fussenegger, M.4
-
86
-
-
17844374314
-
A synthetic multicellular system for programmed pattern formation
-
Basu, S.; Gerchman, Y.; Collins, C.H.; Arnold, F.H.; Weiss, R. A synthetic multicellular system for programmed pattern formation. Nature 2005, 434, 1130-1134.
-
(2005)
Nature
, vol.434
, pp. 1130-1134
-
-
Basu, S.1
Gerchman, Y.2
Collins, C.H.3
Arnold, F.H.4
Weiss, R.5
-
87
-
-
46849090495
-
Robust, Tunable biological oscillations from interlinked positive and negative feedback loops
-
Tsai, T.Y.; Choi, Y.S.; Ma, W.; Pomerening, J.R.; Tang, C.; Ferrell, J.E., Jr. Robust, Tunable biological oscillations from interlinked positive and negative feedback loops. Science 2008, 321, 126-129.
-
(2008)
Science
, vol.321
, pp. 126-129
-
-
Tsai, T.Y.1
Choi, Y.S.2
Ma, W.3
Pomerening, J.R.4
Tang, C.5
Ferrell Jr., J.E.6
-
89
-
-
66149172363
-
Diversity-based, Model-guided construction of synthetic gene networks with predicted functions
-
Ellis, T.; Wang, X.; Collins, J.J. Diversity-based, Model-guided construction of synthetic gene networks with predicted functions. Nat. Biotechnol 2009, 27, 465-471.
-
(2009)
Nat. Biotechnol
, vol.27
, pp. 465-471
-
-
Ellis, T.1
Wang, X.2
Collins, J.J.3
-
90
-
-
80052498962
-
Entrainment of a Population of Synthetic Genetic Oscillators
-
Mondragon-Palomino, O.; Danino, T.; Selimkhanov, J.; Tsimring, L.; Hasty, J. Entrainment of a Population of Synthetic Genetic Oscillators. Science 2011, 333, 1315-1319.
-
(2011)
Science
, vol.333
, pp. 1315-1319
-
-
Mondragon-Palomino, O.1
Danino, T.2
Selimkhanov, J.3
Tsimring, L.4
Hasty, J.5
-
91
-
-
81355123249
-
Software for systems biology, from tools to integrated platforms
-
Ghosh, S.; Matsuoka, Y.; Asai, Y.; Hsin, K.Y.; Kitano, H. Software for systems biology, from tools to integrated platforms. Nat. Rev. Genet. 2011, 12, 821-832.
-
(2011)
Nat. Rev. Genet
, vol.12
, pp. 821-832
-
-
Ghosh, S.1
Matsuoka, Y.2
Asai, Y.3
Hsin, K.Y.4
Kitano, H.5
-
92
-
-
16344385431
-
Evolutionary optimization with data collocation for reverse engineering of biological networks
-
Tsai, K.Y.; Wang, F.S. Evolutionary optimization with data collocation for reverse engineering of biological networks. Bioinformatics 2005, 21, 1180-1188.
-
(2005)
Bioinformatics
, vol.21
, pp. 1180-1188
-
-
Tsai, K.Y.1
Wang, F.S.2
-
93
-
-
0033205006
-
Robustness design of nonlinear dynamic systems via fuzzy linear control
-
Chen, B.S.; Tseng, C.S.; Uang, H.J. Robustness design of nonlinear dynamic systems via fuzzy linear control. IEEE T. Fuzzy Syst. 1999, 7, 571-585.
-
(1999)
IEEE T. Fuzzy Syst
, vol.7
, pp. 571-585
-
-
Chen, B.S.1
Tseng, C.S.2
Uang, H.J.3
-
94
-
-
0037079054
-
Computational systems biology
-
Kitano, H. Computational systems biology. Nature 2002, 420, 206-210.
-
(2002)
Nature
, vol.420
, pp. 206-210
-
-
Kitano, H.1
|