-
1
-
-
33947508946
-
Modelling and simulation of signal transduction in an apoptosis pathway by using times Petri nets
-
Chen, L., Qi-Wei, G., Nakata, M., Matsuno, H., and Miyano, S. (2007) Modelling and simulation of signal transduction in an apoptosis pathway by using times Petri nets. J. Biosci., 32, 113-127.
-
(2007)
J. Biosci.
, vol.32
, pp. 113-127
-
-
Chen, L.1
Qi-Wei, G.2
Nakata, M.3
Matsuno, H.4
Miyano, S.5
-
2
-
-
62349126975
-
Hybrid modeling in biochemical systems theory by means of functional Petri nets
-
Wu, J. and Voit, E. (2009) Hybrid modeling in biochemical systems theory by means of functional Petri nets. J. Bioinform. Comput. Biol., 7, 107-134.
-
(2009)
J. Bioinform. Comput. Biol.
, vol.7
, pp. 107-134
-
-
Wu, J.1
Voit, E.2
-
3
-
-
48949100951
-
Computational systems analysis of dopamine metabolism
-
Qi, Z., Miller, G.W., and Voit, E.O. (2008) Computational systems analysis of dopamine metabolism. PLoS ONE, 3, e2444.
-
(2008)
PLoS ONE
, vol.3
-
-
Qi, Z.1
Miller, G.W.2
Voit, E.O.3
-
4
-
-
65649102679
-
Recent developments in parameter estimation and structure identification of biochemical and genomic systems
-
Chou, I.-C. and Voit, E.O. (2009) Recent developments in parameter estimation and structure identification of biochemical and genomic systems. Math. Biosci., 219, 57-83.
-
(2009)
Math. Biosci.
, vol.219
, pp. 57-83
-
-
Chou, I.-C.1
Voit, E.O.2
-
5
-
-
0002862462
-
Enzyme kinetics in vitro and in vivo: Michaelis-Menten revisited
-
in Principles of Medical Biology (ed. E.E. Bittar), JAI Press,Greenwich, CT
-
Savageau, M.A. (1995) Enzyme kinetics in vitro and in vivo: Michaelis-Menten revisited, in Principles of Medical Biology (ed. E.E. Bittar), JAI Press,Greenwich, CT, pp. 93-146.
-
(1995)
, pp. 93-146
-
-
Savageau, M.A.1
-
6
-
-
0025760713
-
Biochemical systems theory: increasing predictive power by using second-order derivatives measurements
-
Cascante, M., Sorribas, A., Franco, R., and Canela, E.I. (1991) Biochemical systems theory: increasing predictive power by using second-order derivatives measurements. J. Theor. Biol., 1991, 521-535.
-
(1991)
J. Theor. Biol.
, vol.1991
, pp. 521-535
-
-
Cascante, M.1
Sorribas, A.2
Franco, R.3
Canela, E.I.4
-
7
-
-
0342349799
-
Recasting nonlinear differential equations as S-systems: a canonical nonlinear form
-
Savageau, M.A. and Voit, E.O. (1987) Recasting nonlinear differential equations as S-systems: a canonical nonlinear form. Math. Biosci., 87, 83-115.
-
(1987)
Math. Biosci.
, vol.87
, pp. 83-115
-
-
Savageau, M.A.1
Voit, E.O.2
-
8
-
-
0027533062
-
S-system modeling of complex systems with chaotic input
-
Voit, E.O. (1993) S-system modeling of complex systems with chaotic input. Environmetrics, 4, 153-186.
-
(1993)
Environmetrics
, vol.4
, pp. 153-186
-
-
Voit, E.O.1
-
11
-
-
16744368260
-
Biochemical Systems Analysis: A Study of Function and Design in Molecular Biology
-
Addison-Wesley, Reading, MA
-
Savageau, M.A. (1976) Biochemical Systems Analysis: A Study of Function and Design in Molecular Biology, Addison-Wesley, Reading, MA, p. 379.
-
(1976)
, pp. 379
-
-
Savageau, M.A.1
-
12
-
-
0003801925
-
Canonical Nonlinear Modeling. S-System Approach to Understanding Complexity
-
Van Nostrand Reinhold, New York
-
Voit, E.O. (ed.) (1991) Canonical Nonlinear Modeling. S-System Approach to Understanding Complexity, Van Nostrand Reinhold, New York, p. 365.
-
(1991)
, pp. 365
-
-
Voit, E.O.1
-
13
-
-
0004297938
-
Pathway Analysis and Optimization in Metabolic Engineering
-
Cambridge University Press, Cambridge.
-
Torres, N.V. and Voit, E.O. (2002) Pathway Analysis and Optimization in Metabolic Engineering, Cambridge University Press, Cambridge.
-
(2002)
-
-
Torres, N.V.1
Voit, E.O.2
-
14
-
-
0004151462
-
Computational Analysis of Biochemical Systems: A Practical Guide for Biochemists and Molecular Biologists
-
Cambridge University Press, Cambridge
-
Voit, E.O. (2000) Computational Analysis of Biochemical Systems: A Practical Guide for Biochemists and Molecular Biologists, Cambridge University Press, Cambridge, p. 530.
-
(2000)
, pp. 530
-
-
Voit, E.O.1
-
15
-
-
0344099105
-
Integration of kinetic information on yeast sphingolipid metabolism in dynamical pathway models
-
Alvarez-Vasquez, F., Sims, K.J., Hannun, Y.A., and Voit, E.O. (2004) Integration of kinetic information on yeast sphingolipid metabolism in dynamical pathway models. J. Theor. Biol., 226, 265-291.
-
(2004)
J. Theor. Biol.
, vol.226
, pp. 265-291
-
-
Alvarez-Vasquez, F.1
Sims, K.J.2
Hannun, Y.A.3
Voit, E.O.4
-
16
-
-
0002465693
-
A spline least squares method for numerical parameter estimation in differential equations
-
Varah, J.M. (1982) A spline least squares method for numerical parameter estimation in differential equations. SIAM J. Sci. Stat. Comput., 3, 28-46.
-
(1982)
SIAM J. Sci. Stat. Comput.
, vol.3
, pp. 28-46
-
-
Varah, J.M.1
-
18
-
-
4444351989
-
Decoupling dynamical systems for pathway identification from metabolic profiles
-
Voit, E.O. and Almeida, J. (2004) Decoupling dynamical systems for pathway identification from metabolic profiles. Bioinformatics, 20, 1670-1681.
-
(2004)
Bioinformatics
, vol.20
, pp. 1670-1681
-
-
Voit, E.O.1
Almeida, J.2
-
19
-
-
84863776020
-
Parameter estimation in canonical biological systems model
-
Voit, E.O. and Chou, I.C. (2010) Parameter estimation in canonical biological systems models. Int. J. Syst. Synth. Biol., 1 (1), 1-19.
-
(2010)
Int. J. Syst. Synth. Biol., 1 (1)
, pp. 1-19
-
-
Voit, E.O.1
Chou, I.C.2
-
20
-
-
33749340654
-
Parameter estimation in biochemical systems models with alternating regression
-
Chou, I.C., Martens, H., Voit, E.O. (2006) Parameter estimation in biochemical systems models with alternating regression. Theor. Biol. Med. Model, 3, 25.
-
(2006)
Theor. Biol. Med. Model
, vol.3
, pp. 25
-
-
Chou, I.C.1
Martens, H.2
Voit, E.O.3
-
21
-
-
42649134526
-
Parameter optimization in Ssystem models
-
Vilela, M., Chou, I.C., Vinga, S. et al. (2008) Parameter optimization in Ssystem models. BMC Syst. Biol., 2, 35.
-
(2008)
BMC Syst. Biol.
, vol.2
, pp. 35
-
-
Vilela, M.1
Chou, I.C.2
Vinga, S.3
-
22
-
-
77950788346
-
Parameter estimation of ODE's via nonparameteric estimators
-
Brunel, N.J.-B. (2008) Parameter estimation of ODE's via nonparameteric estimators. Electr. J. Stat., 2, 1242-1267.
-
(2008)
Electr. J. Stat.
, vol.2
, pp. 1242-1267
-
-
Brunel, N.J.-B.1
-
23
-
-
28844453869
-
A fitting based method for parameter estimation in S-systems
-
Seatzu, C. (2000) A fitting based method for parameter estimation in S-systems. Dyn. Syst. Appl., 9, 77-98.
-
(2000)
Dyn. Syst. Appl.
, vol.9
, pp. 77-98
-
-
Seatzu, C.1
-
24
-
-
0242669997
-
A perfect smoother
-
Eilers, P.H. (2003) A perfect smoother. Anal. Chem., 75, 3631-3636.
-
(2003)
Anal. Chem.
, vol.75
, pp. 3631-3636
-
-
Eilers, P.H.1
-
25
-
-
35448979185
-
Automated smoother for the numerical decoupling of dynamics models
-
Vilela, M., Borges, C.C., Vinga, S. et al. (2007) Automated smoother for the numerical decoupling of dynamics models. BMC Bioinformatics, 8, 305.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 305
-
-
Vilela, M.1
Borges, C.C.2
Vinga, S.3
-
26
-
-
35648981518
-
Parameter estimation for differential equations: a generalized smoothing approach
-
Ramsay, J.O., Hooker, G., Cao, J., and Campbell, D. (2007) Parameter estimation for differential equations: a generalized smoothing approach. J. Roy. Stat. Soc. B, 69, 741-796.
-
(2007)
J. Roy. Stat. Soc. B
, vol.69
, pp. 741-796
-
-
Ramsay, J.O.1
Hooker, G.2
Cao, J.3
Campbell, D.4
-
27
-
-
0003973174
-
Applied Linear Statistical Models, Irwin, Homewood, IL.
-
Neter, J. and Wasserman, W. (1974) Applied Linear Statistical Models, Irwin, Homewood, IL.
-
(1974)
-
-
Neter, J.1
Wasserman, W.2
-
28
-
-
36248970060
-
Extracting falsifiable predictions from sloppy models
-
Gutenkunst, R.N., Casey, F.P., Waterfall, J.J., Myers, C.R., and Sethna, J.P. (2007) Extracting falsifiable predictions from sloppy models. Ann. NY Acad. Sci., 1115, 203-211.
-
(2007)
Ann. NY Acad. Sci.
, vol.1115
, pp. 203-211
-
-
Gutenkunst, R.N.1
Casey, F.P.2
Waterfall, J.J.3
Myers, C.R.4
Sethna, J.P.5
-
29
-
-
35748977901
-
Universally sloppy parameter sensitivities in systems biology models
-
Gutenkunst, R.N., Waterfall, J.J., Casey, F.P. et al. (2007) Universally sloppy parameter sensitivities in systems biology models. PLoS Comput. Biol., 3, 1871-1878.
-
(2007)
PLoS Comput. Biol.
, vol.3
, pp. 1871-1878
-
-
Gutenkunst, R.N.1
Waterfall, J.J.2
Casey, F.P.3
-
30
-
-
67649663892
-
Identification of neutral sets of biochemical systems models from time series data
-
Vilela, M., Vinga, S., Mattoso Maia, M.A.G., Voit, E.O., and Almeida, J. (2009) Identification of neutral sets of biochemical systems models from time series data. BMC Syst. Biol., 3, 47.
-
(2009)
BMC Syst. Biol.
, vol.3
, pp. 47
-
-
Vilela, M.1
Vinga, S.2
Mattoso Maia, M.A.G.3
Voit, E.O.4
Almeida, J.5
-
31
-
-
67650760503
-
Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihood
-
Raue, A., Kreutz, C., Maiwald, T. et al. (2009) Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihood. Bioinformatics, 25, 1923-1929.
-
(2009)
Bioinformatics
, vol.25
, pp. 1923-1929
-
-
Raue, A.1
Kreutz, C.2
Maiwald, T.3
-
32
-
-
54949136572
-
System estimation from metabolic time series data
-
Goel, G., Chou, I.-C., and Voit, E.O. (2008) System estimation from metabolic time series data. Bioinformatics, 24, 2505-2511.
-
(2008)
Bioinformatics
, vol.24
, pp. 2505-2511
-
-
Goel, G.1
Chou, I.-C.2
Voit, E.O.3
-
33
-
-
72049107766
-
Estimation of metabolic pathway systems from different data sources
-
Voit, E.O., Goel, G., Chou, I.-C., and da Fonseca, L. (2009) Estimation of metabolic pathway systems from different data sources. IET Syst. Biol., 3, 513-522.
-
(2009)
IET Syst. Biol.
, vol.3
, pp. 513-522
-
-
Voit, E.O.1
Goel, G.2
Chou, I.-C.3
da Fonseca, L.4
-
34
-
-
84885536794
-
Dynamic Flux Estimation: a novel framework for metabolic pathway analysis. Dissertation, Department of Biomedical Engineering
-
Georgia Institute of Technology, Atlanta, GA.
-
Goel, G. (2009) Dynamic Flux Estimation: a novel framework for metabolic pathway analysis. Dissertation, Department of Biomedical Engineering. Georgia Institute of Technology, Atlanta, GA.
-
(2009)
-
-
Goel, G.1
-
35
-
-
0035578429
-
Design principles for elementary gene circuits: elements, methods, and examples
-
Savageau, M.A. (2001) Design principles for elementary gene circuits: elements, methods, and examples. Chaos, 11, 142-159.
-
(2001)
Chaos
, vol.11
, pp. 142-159
-
-
Savageau, M.A.1
-
36
-
-
0021776306
-
A theory of alternative designs for biochemical control systems
-
Savageau, M.A. (1985) A theory of alternative designs for biochemical control systems. Biomed. Biochim. Acta, 44, 875-880.
-
(1985)
Biomed. Biochim. Acta
, vol.44
, pp. 875-880
-
-
Savageau, M.A.1
-
37
-
-
0031904590
-
Demand theory for gene regulation: quantitative development of the theory
-
Savageau, M.A. (1998) Demand theory for gene regulation: quantitative development of the theory. Genetics, 149, 1665-1676.
-
(1998)
Genetics
, vol.149
, pp. 1665-1676
-
-
Savageau, M.A.1
-
38
-
-
0031927611
-
Demand theory for gene regulation: quantitative application to the lactose and maltose operons of Escherichia coli
-
Savageau, M.A. (1998) Demand theory for gene regulation: quantitative application to the lactose and maltose operons of Escherichia coli. Genetics, 149, 1677-1691.
-
(1998)
Genetics
, vol.149
, pp. 1677-1691
-
-
Savageau, M.A.1
-
39
-
-
63549119474
-
Quantifying global tolerance of biochemical systems: design implications for moiety-transfer cycles
-
Coelho, P.M., Salvador, A., and Savageau, M.A. (2009) Quantifying global tolerance of biochemical systems: design implications for moiety-transfer cycles. PLoS Comput. Biol., 5, e1000319.
-
(2009)
PLoS Comput. Biol.
, vol.5
-
-
Coelho, P.M.1
Salvador, A.2
Savageau, M.A.3
-
40
-
-
33745197543
-
Signalling network with a bistable hysteretic switch controls developmental activation of the sigma transcription factor in Bacillus subtilis
-
Igoshin, O.A., Price, C.W., and Savageau, M.A. (2006) Signalling network with a bistable hysteretic switch controls developmental activation of the sigma transcription factor in Bacillus subtilis. Mol. Microbiol., 61, 165-184.
-
(2006)
Mol. Microbiol.
, vol.61
, pp. 165-184
-
-
Igoshin, O.A.1
Price, C.W.2
Savageau, M.A.3
-
41
-
-
0033748085
-
Effect of overall feedback inhibition in unbranched biosynthetic pathways
-
Alves, R. and Savageau, M.A. (2000) Effect of overall feedback inhibition in unbranched biosynthetic pathways. Biophys. J., 79, 2290-2304.
-
(2000)
Biophys. J.
, vol.79
, pp. 2290-2304
-
-
Alves, R.1
Savageau, M.A.2
-
42
-
-
0030002954
-
Rules for coupled expression of regulator and effector genes in inducible circuits
-
Hlavacek,W.S. and Savageau, M.A. (1996) Rules for coupled expression of regulator and effector genes in inducible circuits. J. Mol. Biol., 255, 121-139.
-
(1996)
J. Mol. Biol.
, vol.255
, pp. 121-139
-
-
Hlavacek, W.S.1
Savageau, M.A.2
-
43
-
-
0021925233
-
Network regulation of the immune response: alternative control points for suppressor modulation of effector lymphocytes
-
Irvine, D.H. and Savageau, M.A. (1985) Network regulation of the immune response: alternative control points for suppressor modulation of effector lymphocytes. J. Immunol., 134, 2100-2116.
-
(1985)
J. Immunol.
, vol.134
, pp. 2100-2116
-
-
Irvine, D.H.1
Savageau, M.A.2
-
44
-
-
15244353650
-
Improved methods for the mathematically controlled comparison of biochemical systems
-
Schwacke, J.H. and Voit, E.O. (2004) Improved methods for the mathematically controlled comparison of biochemical systems. Theor. Biol. Med. Model., 1, 1.
-
(2004)
Theor. Biol. Med. Model.
, vol.1
, pp. 1
-
-
Schwacke, J.H.1
Voit, E.O.2
-
45
-
-
33947719803
-
Concentration-dependent effects on the rapid and efficient activation of MAPK
-
Schwacke, J.H. and Voit, E.O. (2007) Concentration-dependent effects on the rapid and efficient activation of MAPK. Proteomics, 7, 890-899.
-
(2007)
Proteomics
, vol.7
, pp. 890-899
-
-
Schwacke, J.H.1
Voit, E.O.2
-
46
-
-
6344277099
-
Predictive reconstruction of the mitochondrial iron-sulfur cluster assembly metabolism
-
Alves, R., Herrero, E., and Sorribas, A. (2004) Predictive reconstruction of the mitochondrial iron-sulfur cluster assembly metabolism. II. Role of glutaredoxin Grx5. Proteins Struct. Funct. Bioinformat., 57, 481-492.
-
(2004)
II. Role of glutaredoxin Grx5. Proteins Struct. Funct. Bioinformat.
, vol.57
, pp. 481-492
-
-
Alves, R.1
Herrero, E.2
Sorribas, A.3
-
47
-
-
54749089036
-
A mathematical model of presynaptic dopamine homeostasis: implications for schizophrenia
-
Qi, Z., Miller, G.W., and Voit, E.O. (2008) A mathematical model of presynaptic dopamine homeostasis: implications for schizophrenia. Pharmacopsychiatry, 41, S89-S98.
-
(2008)
Pharmacopsychiatry
, vol.41
-
-
Qi, Z.1
Miller, G.W.2
Voit, E.O.3
-
48
-
-
70349859885
-
Computational analysis of determinants of dopamine dysfunction
-
Qi, Z., Miller, G.W., and Voit, E.O. (2009) Computational analysis of determinants of dopamine dysfunction. Synapse, 63, 1133-1142.
-
(2009)
Synapse
, vol.63
, pp. 1133-1142
-
-
Qi, Z.1
Miller, G.W.2
Voit, E.O.3
-
49
-
-
57749210069
-
The role of systems biology in predictive health and personalized medicine
-
Voit, E.O. and Brigham, K.L. (2008) The role of systems biology in predictive health and personalized medicine. Open Path J., 2, 68-70.
-
(2008)
Open Path J.
, vol.2
, pp. 68-70
-
-
Voit, E.O.1
Brigham, K.L.2
-
50
-
-
67949089784
-
Predicting clinical physiology: aMarkov chain model of heart rate recovery after spontaneous breathing trials in mechanically ventilated patients
-
Lu, Y., Burykin, A., Deem, M.W., and Buchman, T.G. (2009) Predicting clinical physiology: aMarkov chain model of heart rate recovery after spontaneous breathing trials in mechanically ventilated patients. J. Crit. Care, 24, 347-361.
-
(2009)
J. Crit. Care
, vol.24
, pp. 347-361
-
-
Lu, Y.1
Burykin, A.2
Deem, M.W.3
Buchman, T.G.4
-
51
-
-
0035578429
-
Design principles for elementary gene circuits: elements, methods, and examples
-
Savageau, M.A. (2001) Design principles for elementary gene circuits: elements, methods, and examples. Chaos, 11, 142.
-
(2001)
Chaos
, vol.11
, pp. 142
-
-
Savageau, M.A.1
-
52
-
-
84902204803
-
A new learning method for piecewise linear regression
-
Ferrari-Trecate, G. and Muselli, M. (2002) A new learning method for piecewise linear regression. Lecture Notes Comput. Sci., 2415, 444-449.
-
(2002)
Lecture Notes Comput. Sci.
, vol.2415
, pp. 444-449
-
-
Ferrari-Trecate, G.1
Muselli, M.2
-
53
-
-
77956009783
-
Automated piecewise power-law modeling of biological systems
-
Machina, A., Ponosov, A., and Voit, E.O. (2010) Automated piecewise power-law modeling of biological systems. J. Biotechnol., 149, 154-165.
-
(2010)
J. Biotechnol.
, vol.149
, pp. 154-165
-
-
Machina, A.1
Ponosov, A.2
Voit, E.O.3
-
54
-
-
51749105256
-
Kinetic model of phosphofructokinase-1 from Escherichia coli
-
Peskov, K., Goryanin, I., and Demin, O. (2008) Kinetic model of phosphofructokinase-1 from Escherichia coli. J. Bioinform. Comput. Biol., 6, 843-867.
-
(2008)
J. Bioinform. Comput. Biol.
, vol.6
, pp. 843-867
-
-
Peskov, K.1
Goryanin, I.2
Demin, O.3
|