-
1
-
-
84872668453
-
Making sense-data-based simulations of vertebrate limb development
-
Iber, D. & Zeller, R. Making sense-data-based simulations of vertebrate limb development. Curr Opin Genet Dev 22, 570-577 (2012).
-
(2012)
Curr Opin Genet Dev
, vol.22
, pp. 570-577
-
-
Iber, D.1
Zeller, R.2
-
2
-
-
84885116840
-
Predictive models for cellular signaling networks
-
Springer
-
Iber, D. Fengos, G. Predictive models for cellular signaling networks. Methods in molecular biology 880, 1-22 (Springer 2012).
-
(2012)
Methods in Molecular Biology
, vol.880
, pp. 1-22
-
-
Iber, D.1
Fengos, G.2
-
3
-
-
0037213006
-
Computational modeling of the EGF-receptor system: A paradigm for systems biology
-
DOI 10.1016/S0962-8924(02)00009-0, PII S0962892402000090
-
Wiley,HS., Shvartsman, S. Y. & Lauffenburger, D. A. Computational modeling of the EGF-receptor system: a paradigm for systems biology. Trends in cell biology 13, 43-50 (2003). (Pubitemid 35453894)
-
(2003)
Trends in Cell Biology
, vol.13
, Issue.1
, pp. 43-50
-
-
Wiley, H.S.1
Shvartsman, S.Y.2
Lauffenburger, D.A.3
-
4
-
-
0035815743
-
The influence of macromolecular crowding and macromolecular confinement on biochemical reactions in physiological media
-
DOI 10.1074/jbc.R100005200
-
Minton, A. P. The influence of macromolecular crowding and macromolecular confinement on biochemical reactions in physiological media. Journal of biological chemistry 276, 10577-10580 (2001). (Pubitemid 38089223)
-
(2001)
Journal of Biological Chemistry
, vol.276
, Issue.14
, pp. 10577-10580
-
-
Minton, A.P.1
-
6
-
-
58849137994
-
Systems biology: Experimental design
-
Kreutz, C. & Timmer, J. Systems biology: experimental design. FEBS Journal 276, 923-942 (2009).
-
(2009)
FEBS Journal
, vol.276
, pp. 923-942
-
-
Kreutz, C.1
Timmer, J.2
-
7
-
-
1342265607
-
Experimental design in systems biology, based on parameter sensitivity analysis using a monte carlo method: A case study for the tnfa-mediated nf-k b signal transduction pathway
-
Cho, K.-H., Shin, S.-Y., Kolch, W. & Wolkenhauer, O. Experimental design in systems biology, based on parameter sensitivity analysis using a monte carlo method: A case study for the tnfa-mediated nf-k b signal transduction pathway. Simulation 79, 726-739 (2003).
-
(2003)
Simulation
, vol.79
, pp. 726-739
-
-
Cho, K.-H.1
Shin, S.-Y.2
Kolch, W.3
Wolkenhauer, O.4
-
8
-
-
1342286938
-
Simulation methods for optimal experimental design in systems biology
-
Faller, D., Klingmüller, U. & Timmer, J. Simulation methods for optimal experimental design in systems biology. Simulation 79, 717-725 (2003).
-
(2003)
Simulation
, vol.79
, pp. 717-725
-
-
Faller, D.1
Klingmüller, U.2
Timmer, J.3
-
9
-
-
33750374139
-
Linking data to models: Data regression
-
DOI 10.1038/nrm2030, PII NRM2030
-
Jaqaman, K. & Danuser, G. Linking data to models: data regression. Nat Rev Mol Cell Biol 7, 813-819 (2006). (Pubitemid 44627474)
-
(2006)
Nature Reviews Molecular Cell Biology
, vol.7
, Issue.11
, pp. 813-819
-
-
Jaqaman, K.1
Danuser, G.2
-
10
-
-
84885166438
-
And constraining signaling networks: Parameter estimation for the user
-
Springer
-
Geier, F., Fengos, G., Felizzi, F. & Iber, D. Analyzing and constraining signaling networks: parameter estimation for the user. Methods in molecular biology 880, 23-39 (Springer 2012).
-
(2012)
Methods in Molecular Biology
, vol.880
, pp. 23-39
-
-
Geier, F.1
Fengos, G.2
Felizzi, F.3
Analyzing, I.D.4
-
11
-
-
33947641481
-
Parameter estimation in ordinary differential equations for biochemical processes using the method of multiple shooting
-
DOI 10.1049/iet-syb:20060067
-
Peifer, M. & Timmer, J. Parameter estimation in ordinary differential equations for biochemical processes using the method of multiple shooting. Systems Biology, IET 1, 78-88 (2007). (Pubitemid 46488241)
-
(2007)
IET Systems Biology
, vol.1
, Issue.2
, pp. 78-88
-
-
Peifer, M.1
Timmer, J.2
-
12
-
-
0041815593
-
Nonlinear dynamical system identification from uncertain and indirect measurements
-
DOI 10.1142/S0218127404010345, PII S0218127404010345
-
Voss, H. U., Timmer, J. & Kurths, J. Nonlinear dynamical system identification from uncertain and indirect measurements. International Journal of Bifurcation and Chaos 14, 1905-1933 (2004). (Pubitemid 40253155)
-
(2004)
International Journal of Bifurcation and Chaos in Applied Sciences and Engineering
, vol.14
, Issue.6
, pp. 1905-1933
-
-
Voss, H.U.1
Timmer, J.2
Kurths, J.3
-
13
-
-
0242574982
-
Parameter estimation in biochemical pathways: A comparison of global optimization methods
-
DOI 10.1101/gr.1262503
-
Moles, C. G., Mendes, P. & Banga, J. R. Parameter estimation in biochemical pathways: a comparison of global optimization methods. Genome research 13, 2467-2474 (2003). (Pubitemid 37428271)
-
(2003)
Genome Research
, vol.13
, Issue.11
, pp. 2467-2474
-
-
Moles, C.G.1
Mendes, P.2
Banga, J.R.3
-
14
-
-
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. Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation. Bioinformatics 14, 869-883 (1998). (Pubitemid 29041543)
-
(1998)
Bioinformatics
, vol.14
, Issue.10
, pp. 869-883
-
-
Mendes, P.1
Kell, D.B.2
-
15
-
-
84858736880
-
Sensitivity analysis approaches applied to systems biology models
-
Zi, Z. Sensitivity analysis approaches applied to systems biology models. Systems Biology, IET 5, 336-346 (2011).
-
(2011)
Systems Biology, IET
, vol.5
, pp. 336-346
-
-
Zi, Z.1
-
16
-
-
51049105974
-
A new strategy for assessing sensitivities in biochemical models
-
Sahle, S., Mendes, P., Hoops, S. & Kummer, U. A new strategy for assessing sensitivities in biochemical models. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 366, 3619-3631 (2008).
-
(2008)
Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences
, vol.366
, pp. 3619-3631
-
-
Sahle, S.1
Mendes, P.2
Hoops, S.3
Kummer, U.4
-
17
-
-
35748931160
-
Data-based identifiability analysis of non-linear dynamical models
-
DOI 10.1093/bioinformatics/btm382
-
Hengl, S., Kreutz, C., Timmer, J. Maiwald, T. Data-based identifiability analysis of non-linear dynamical models. Bioinformatics 23, 2612-2618 (2007). (Pubitemid 350048365)
-
(2007)
Bioinformatics
, vol.23
, Issue.19
, pp. 2612-2618
-
-
Hengl, S.1
Kreutz, C.2
Timmer, J.3
Maiwald, T.4
-
18
-
-
36248970060
-
Extracting falsifiable predictions from sloppy models
-
DOI 10.1196/annals.1407.003, Reverse Engineering Biological Networks: Opportunities and Challenges in Computational Methods for Pathway Inference
-
Gutenkunst, R. N., Casey, F. P., Waterfall, J. J., Myers, C. R. & Sethna, J. P. Extracting falsifiable predictions from sloppy models. Annals of the New York Academy of Sciences 1115, 203-211 (2007). (Pubitemid 350134793)
-
(2007)
Annals of the New York Academy of Sciences
, 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
-
19
-
-
33845424529
-
A rate equation approach to elucidate the kinetics and robustness of the TGF-β pathway
-
DOI 10.1529/biophysj.105.080408
-
Melke, P., Jönsson, H., Pardali, E., ten Dijke, P. & Peterson, C. A rate equation approach to elucidate the kinetics and robustness of the TGF-beta pathway. Biophysical journal 91, 4368-4380 (2006). (Pubitemid 44904224)
-
(2006)
Biophysical Journal
, vol.91
, Issue.12
, pp. 4368-4380
-
-
Melke, P.1
Jonsson, H.2
Pardali, E.3
Ten Dijke, P.4
Peterson, C.5
-
20
-
-
34948840834
-
Ensemble modeling for analysis of cell signaling dynamics
-
DOI 10.1038/nbt1330, PII NBT1330
-
Kuepfer, L., Peter, M., Sauer, U. & Stelling, J. Ensemble modeling for analysis of cell signaling dynamics. Nature biotechnology 25, 1001-1006 (2007). (Pubitemid 47517639)
-
(2007)
Nature Biotechnology
, vol.25
, Issue.9
, pp. 1001-1006
-
-
Kuepfer, L.1
Peter, M.2
Sauer, U.3
Stelling, J.4
-
21
-
-
33744976080
-
The mechanism of cell differentiation in Bacillus subtilis
-
DOI 10.1038/nature04666, PII NATURE04666
-
Iber, D., Clarkson, J., Yudkin, M. D. & Campbell, I. D. The mechanism of cell differentiation in bacillus subtilis. Nature 441, 371-374 (2006). (Pubitemid 44050204)
-
(2006)
Nature
, vol.441
, Issue.7091
, pp. 371-374
-
-
Iber, D.1
Clarkson, J.2
Yudkin, M.D.3
Campbell, I.D.4
-
22
-
-
33745254228
-
A Computational Analysis of the Impact of the Transient Genetic Imbalance on Compartmentalized Gene Expression During Sporulation in Bacillus subtilis
-
DOI 10.1016/j.jmb.2006.05.011, PII S0022283606005778
-
Iber, D. A computational analysis of the impact of the transient genetic imbalance on compartmentalized gene expression during sporulation in Bacillus subtilis. Journal of molecular biology 360, 15-20 (2006). (Pubitemid 43927820)
-
(2006)
Journal of Molecular Biology
, vol.360
, Issue.1
, pp. 15-20
-
-
Iber, D.1
-
23
-
-
33748878811
-
A quantitative study of the benefits of co-regulation using the spoIIa operon as an example
-
Iber, D. A quantitative study of the benefits of co-regulation using the spoIIa operon as an example. Molecular systems biology 2, 43 (2006).
-
(2006)
Molecular Systems Biology
, vol.2
, pp. 43
-
-
Iber, D.1
-
24
-
-
0037592480
-
Evolution strategies-A comprehensive introduction
-
Beyer, H.-G. & Schwefel, H.-P. Evolution strategies-a comprehensive introduction. Natural computing 1, 3-52 (2002).
-
(2002)
Natural Computing
, vol.1
, pp. 3-52
-
-
Beyer, H.-G.1
Schwefel, H.-P.2
-
25
-
-
84858237475
-
A computational analysis of the dynamic roles of talin, Dok1, and PIPKI for integrin activation
-
Geier, F., Fengos, G. & Iber, D. A computational analysis of the dynamic roles of talin, Dok1, and PIPKI for integrin activation. PloS One 6, e24808 (2011).
-
(2011)
PloS One
, vol.6
-
-
Geier, F.1
Fengos, G.2
Iber, D.3
-
26
-
-
0037168597
-
An ensemble method for identifying regulatory circuits with special reference to the qa gene cluster of Neurospora crassa
-
DOI 10.1073/pnas.262658899
-
Battogtokh, D., Asch, D., Case, M., Arnold, J. & Schüttler, H.-B. An ensemble method for identifying regulatory circuits with special reference to the qa gene cluster of neurospora crassa. Proceedings of the National Academy of Sciences 99, 16904-16909 (2002). (Pubitemid 36034071)
-
(2002)
Proceedings of the National Academy of Sciences of the United States of America
, vol.99
, Issue.26
, pp. 16904-16909
-
-
Battogtokh, D.1
Asch, D.K.2
Case, M.E.3
Arnold, J.4
Schuttler, H.-B.5
-
27
-
-
80155201059
-
The plasticity of TGF-b signaling
-
Cellière, G., Fengos, G., Hervé, M. & Iber, D. The plasticity of TGF-b signaling. BMC systems biology 5, 184 (2011).
-
(2011)
BMC Systems Biology
, vol.5
, pp. 184
-
-
Cellière, G.1
Fengos, G.2
Hervé, M.3
Iber, D.4
-
28
-
-
33747366698
-
Rules for modeling signal-transduction systems
-
Hlavacek, W. S. et al. Rules for modeling signal-transduction systems. Science Signaling 2006, re6 (2006).
-
(2006)
Science Signaling
, vol.2006
-
-
Hlavacek, W.S.1
-
29
-
-
65649154507
-
Rule-based modeling of biochemical systems with BioNetGen
-
Springer
-
Faeder, J. R., Blinov, M. L. & Hlavacek, W. S. Rule-based modeling of biochemical systems with BioNetGen. Methods Mol Biol. 113-167 (Springer, 2009).
-
(2009)
Methods Mol Biol
, pp. 113-167
-
-
Faeder, J.R.1
Blinov, M.L.2
Hlavacek, W.S.3
-
30
-
-
35748977901
-
Universally sloppy parameter sensitivities in systems biology models
-
Gutenkunst, R. N. et al. Universally sloppy parameter sensitivities in systems biology models. PLoS computational biology 3, e189 (2007).
-
(2007)
PLoS Computational Biology
, vol.3
-
-
Gutenkunst, R.N.1
-
32
-
-
0034995375
-
Complex biology with no parameters
-
DOI 10.1038/89204
-
Bailey, J. E. Complex biology with no parameters. Nature biotechnology 19, 503-504 (2001). (Pubitemid 32521173)
-
(2001)
Nature Biotechnology
, vol.19
, Issue.6
, pp. 503-504
-
-
Bailey, J.E.1
|