-
1
-
-
0037044575
-
The IkappaB-NF-kappaB signaling module: Temporal control and selective gene activation
-
12424381
-
Hoffmann A Levchenko A Scott ML Baltimore D The IkappaB-NF-kappaB signaling module: Temporal control and selective gene activation Science 2002, 298(5596):1241-1245. 12424381
-
(2002)
Science
, vol.298
, Issue.5596
, pp. 1241-1245
-
-
Hoffmann, A.1
Levchenko, A.2
Scott, M.L.3
Baltimore, D.4
-
2
-
-
4544246088
-
Mathematical modeling reveals threshold mechanism in CD95-induced apoptosis
-
2172102 15364960
-
Bentele M Lavrik I Ulrich M Stosser S Heermann DW Kalthoff H Krammer PH Eils R Mathematical modeling reveals threshold mechanism in CD95-induced apoptosis J Cell Biol 2004, 166(6):839-851. 2172102 15364960
-
(2004)
J Cell Biol
, vol.166
, Issue.6
, pp. 839-851
-
-
Bentele, M.1
Lavrik, I.2
Ulrich, M.3
Stosser, S.4
Heermann, D.W.5
Kalthoff, H.6
Krammer, P.H.7
Eils, R.8
-
5
-
-
33749137281
-
Quantitative and predictive model of transcriptional control of the Drosophila melanogaster even skipped gene
-
16980977
-
Janssens H Hou S Jaeger J Kim AR Myasnikova E Sharp D Reinitz J Quantitative and predictive model of transcriptional control of the Drosophila melanogaster even skipped gene Nat Genet 2006, 38(10):1159-1165. 16980977
-
(2006)
Nat Genet
, vol.38
, Issue.10
, pp. 1159-1165
-
-
Janssens, H.1
Hou, S.2
Jaeger, J.3
Kim, A.R.4
Myasnikova, E.5
Sharp, D.6
Reinitz, J.7
-
6
-
-
34447523907
-
Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli
-
1949037 17625511
-
Schuetz R Kuepfer L Sauer U Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli Mol Syst Biol 2007, 3:119. 1949037 17625511
-
(2007)
Mol Syst Biol
, vol.3
, pp. 119
-
-
Schuetz, R.1
Kuepfer, L.2
Sauer, U.3
-
7
-
-
13844296861
-
In silico identification of the key components and steps in IFN-gamma induced JAK-STAT signaling pathway
-
15710397
-
Zi Z Cho KH Sung MH Xia X Zheng J Sun Z In silico identification of the key components and steps in IFN-gamma induced JAK-STAT signaling pathway FEBS Lett 2005, 579(5):1101-1108. 15710397
-
(2005)
FEBS Lett
, vol.579
, Issue.5
, pp. 1101-1108
-
-
Zi, Z.1
Cho, K.H.2
Sung, M.H.3
Xia, X.4
Zheng, J.5
Sun, Z.6
-
9
-
-
21344476293
-
Sensitivity and Uncertainty Analysis of Complex-Models of Disease Transmission - An Hiv Model, as an Example
-
Blower SM Dowlatabadi H Sensitivity and Uncertainty Analysis of Complex-Models of Disease Transmission - an Hiv Model, as an Example International Statistical Review 1994, 62(2):229-243.
-
(1994)
International Statistical Review
, vol.62
, Issue.2
, pp. 229-243
-
-
Blower, S.M.1
Dowlatabadi, H.2
-
10
-
-
0031051892
-
Metabolic Control Analysis of glycolysis in tuber tissue of potato (Solanum tuberosum): Explanation for the low control coefficient of phosphofructokinase over respiratory flux
-
1218166 9078251
-
Thomas S Mooney PJ Burrell MM Fell DA Metabolic Control Analysis of glycolysis in tuber tissue of potato (Solanum tuberosum): Explanation for the low control coefficient of phosphofructokinase over respiratory flux Biochem J 1997, 322 (Pt 1):119-127. 1218166 9078251
-
(1997)
Biochem J
, vol.322
, Issue.PART 1
, pp. 119-127
-
-
Thomas, S.1
Mooney, P.J.2
Burrell, M.M.3
Fell, D.A.4
-
11
-
-
0036789922
-
Untangling the wires: A strategy to trace functional interactions in signaling and gene networks
-
130547 12242336
-
Kholodenko BN Kiyatkin A Bruggeman FJ Sontag E Westerhoff HV Hoek JB Untangling the wires: A strategy to trace functional interactions in signaling and gene networks Proc Natl Acad Sci U S A 2002, 99(20):12841-12846. 130547 12242336
-
(2002)
Proc Natl Acad Sci U S A
, vol.99
, Issue.20
, pp. 12841-12846
-
-
Kholodenko, B.N.1
Kiyatkin, A.2
Bruggeman, F.J.3
Sontag, E.4
Westerhoff, H.V.5
Hoek, J.B.6
-
12
-
-
1342265607
-
Experimental design in systems biology based on parameter sensitivity analysis using a Monte Carlo method: A case study for the TNF alpha-mediated NF-kappaB signal transduction pathway
-
Cho KH Shin SY Kolch W Wolkenhauer O Experimental design in systems biology based on parameter sensitivity analysis using a Monte Carlo method: A case study for the TNF alpha-mediated NF-kappaB signal transduction pathway SIMULATION 2003, 79:726-739.
-
(2003)
SIMULATION
, vol.79
, pp. 726-739
-
-
Cho, K.H.1
Shin, S.Y.2
Kolch, W.3
Wolkenhauer, O.4
-
13
-
-
14844364430
-
Optimizing genetic circuits by global sensitivity analysis
-
1304645 15454422
-
Feng XJ Hooshangi S Chen D Li G Weiss R Rabitz H Optimizing genetic circuits by global sensitivity analysis Biophys J 2004, 87(4):2195-2202. 1304645 15454422
-
(2004)
Biophys J
, vol.87
, Issue.4
, pp. 2195-2202
-
-
Feng, X.J.1
Hooshangi, S.2
Chen, D.3
Li, G.4
Weiss, R.5
Rabitz, H.6
-
14
-
-
33646432753
-
Time-dependent sensitivity analysis of biological networks: Coupled MAPK and PI3K signal transduction pathways
-
16623463
-
Hu D Yuan JM Time-dependent sensitivity analysis of biological networks: coupled MAPK and PI3K signal transduction pathways J Phys Chem A 2006, 110(16):5361-5370. 16623463
-
(2006)
J Phys Chem A
, vol.110
, Issue.16
, pp. 5361-5370
-
-
Hu, D.1
Yuan, J.M.2
-
15
-
-
33746618464
-
Comparative study of parameter sensitivity analyses of the TCR-activated Erk-MAPK signalling pathway
-
16986622
-
Zheng Y Rundell A Comparative study of parameter sensitivity analyses of the TCR-activated Erk-MAPK signalling pathway Syst Biol (Stevenage) 2006, 153(4):201-211. 16986622
-
(2006)
Syst Biol (Stevenage)
, vol.153
, Issue.4
, pp. 201-211
-
-
Zheng, Y.1
Rundell, A.2
-
16
-
-
34547570814
-
Sensitivity Analysis of Intracellular Signaling Pathway Kinetics Predicts Targets for Stem Cell Fate Control
-
1913098 17616983
-
Mahdavi A Davey RE Bhola P Yin T Zandstra PW Sensitivity Analysis of Intracellular Signaling Pathway Kinetics Predicts Targets for Stem Cell Fate Control PLoS Comput Biol 2007, 3(7):e130. 1913098 17616983
-
(2007)
PLoS Comput Biol
, vol.3
, Issue.7
-
-
Mahdavi, A.1
Davey, R.E.2
Bhola, P.3
Yin, T.4
Zandstra, P.W.5
-
17
-
-
0348049802
-
Systems biology markup language: Level 2 and beyond
-
14641091
-
Finney A Hucka M Systems biology markup language: Level 2 and beyond Biochem Soc Trans 2003, 31(Pt 6):1472-1473. 14641091
-
(2003)
Biochem Soc Trans
, vol.31
, Issue.PART 6
, pp. 1472-1473
-
-
Finney, A.1
Hucka, M.2
-
18
-
-
33845368513
-
COPASI - A COmplex PAthway SImulator
-
17032683
-
Hoops S Sahle S Gauges R Lee C Pahle J Simus N Singhal M Xu L Mendes P Kummer U COPASI - a COmplex PAthway SImulator Bioinformatics 2006, 22(24):3067-3074. 17032683
-
(2006)
Bioinformatics
, vol.22
, Issue.24
, pp. 3067-3074
-
-
Hoops, S.1
Sahle, S.2
Gauges, R.3
Lee, C.4
Pahle, J.5
Simus, N.6
Singhal, M.7
Xu, L.8
Mendes, P.9
Kummer, U.10
-
19
-
-
32544443964
-
Systems Biology Toolbox for MATLAB: A computational platform for research in systems biology
-
16317076
-
Schmidt H Jirstrand M Systems Biology Toolbox for MATLAB: A computational platform for research in systems biology Bioinformatics 2005/12/01 2006, 22(4):514-515. 16317076
-
(2006)
Bioinformatics
, vol.22
, Issue.4
, pp. 514-515
-
-
Schmidt, H.1
Jirstrand, M.2
-
20
-
-
33750415038
-
SBML-PET: A Systems Biology Markup Language-based parameter estimation tool
-
16926221
-
Zi Z Klipp E SBML-PET: A Systems Biology Markup Language-based parameter estimation tool Bioinformatics 2006, 22(21):2704-2705. 16926221
-
(2006)
Bioinformatics
, vol.22
, Issue.21
, pp. 2704-2705
-
-
Zi, Z.1
Klipp, E.2
-
21
-
-
8844269072
-
MathSBML: A package for manipulating SBML-based biological models
-
1409765 15087311
-
Shapiro BE Hucka M Finney A Doyle J MathSBML: A package for manipulating SBML-based biological models Bioinformatics 2004, 20(16):2829-2831. 1409765 15087311
-
(2004)
Bioinformatics
, vol.20
, Issue.16
, pp. 2829-2831
-
-
Shapiro, B.E.1
Hucka, M.2
Finney, A.3
Doyle, J.4
-
23
-
-
0034926426
-
Global sensitivity indices for nonlinear mathematical models and their Monte Carlo estimates
-
Sobol IM Global sensitivity indices for nonlinear mathematical models and their Monte Carlo estimates Mathematics and Computers in Simulation 2001, 55(1-3):271-280.
-
(2001)
Mathematics and Computers in Simulation
, vol.55
, Issue.1-3
, pp. 271-280
-
-
Sobol, I.M.1
-
24
-
-
34548684135
-
Cellular signaling is potentially regulated by cell density in receptor trafficking networks
-
17825822
-
Zi Z Klipp E Cellular signaling is potentially regulated by cell density in receptor trafficking networks FEBS Lett 2007, 581(24):4589-4595. 17825822
-
(2007)
FEBS Lett
, vol.581
, Issue.24
, pp. 4589-4595
-
-
Zi, Z.1
Klipp, E.2
-
25
-
-
33646884848
-
SBMLToolbox: An SBML toolbox for MATLAB users
-
16574696
-
Keating SM Bornstein BJ Finney A Hucka M SBMLToolbox: An SBML toolbox for MATLAB users Bioinformatics 2006/04/01 2006, 22(10):1275-1277. 16574696
-
(2006)
Bioinformatics
, vol.22
, Issue.10
, pp. 1275-1277
-
-
Keating, S.M.1
Bornstein, B.J.2
Finney, A.3
Hucka, M.4
-
26
-
-
84886753732
-
-
Matlab http://www.mathworks.com
-
-
-
-
27
-
-
33745217791
-
SUNDIALS: Suite of nonlinear and differential/algebraic equation solvers
-
Hindmarsh AC Brown PN Grant KE Lee SL Serban R Shumaker DE Woodward CS SUNDIALS: Suite of nonlinear and differential/algebraic equation solvers Acm Transactions on Mathematical Software 2005, 31(3):363-396.
-
(2005)
Acm Transactions on Mathematical Software
, vol.31
, Issue.3
, pp. 363-396
-
-
Hindmarsh, A.C.1
Brown, P.N.2
Grant, K.E.3
Lee, S.L.4
Serban, R.5
Shumaker, D.E.6
Woodward, C.S.7
-
28
-
-
84886761529
-
-
SUNDIALS https://computation.llnl.gov/casc/sundials/main.html
-
-
-
-
29
-
-
9444266171
-
CellDesigner: A process diagram editor for gene-regulatory and biochemical networks
-
Funahashi A Tanimura, N., Morohashi, M., and Kitano, H CellDesigner: A process diagram editor for gene-regulatory and biochemical networks BIOSILICO 2003, 1:159.
-
(2003)
BIOSILICO
, vol.1
, pp. 159
-
-
Funahashi Tanimura, N.1
Morohashi, M.2
Kitano, H.A.3
-
30
-
-
33947623106
-
SBMLeditor: Effective creation of models in the Systems Biology Markup language (SBML)
-
1831489 17341299
-
Rodriguez N Donizelli M Le Novere N SBMLeditor: Effective creation of models in the Systems Biology Markup language (SBML) BMC Bioinformatics 2007, 8:79. 1831489 17341299
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 79
-
-
Rodriguez, N.1
Donizelli, M.2
Le Novere, N.3
-
31
-
-
22144498043
-
Sensitivity analysis of discrete stochastic systems
-
1305350 15695639
-
Gunawan R Cao Y Petzold L Doyle FJ 3rd Sensitivity analysis of discrete stochastic systems Biophys J 2005/02/08 2005, 88(4):2530-2540. 1305350 15695639
-
(2005)
Biophys J
, vol.88
, Issue.4
, pp. 2530-2540
-
-
Gunawan, R.1
Cao, Y.2
Petzold, L.3
Doyle III, F.J.4
-
32
-
-
0019392712
-
An Approach to the Preliminary-Analysis of Environmental Systems
-
Hornberger GM Spear RC An Approach to the Preliminary-Analysis of Environmental Systems Journal of Environmental Management 1981, 12(1):7-18.
-
(1981)
Journal of Environmental Management
, vol.12
, Issue.1
, pp. 7-18
-
-
Hornberger, G.M.1
Spear, R.C.2
-
33
-
-
0018468345
-
Comparison of 3 Methods for Selecting Values of Input Variables in the Analysis of Output from a Computer Code
-
Mckay MD Beckman RJ Conover WJ Comparison of 3 Methods for Selecting Values of Input Variables in the Analysis of Output from a Computer Code Technometrics 1979, 21(2):239-245.
-
(1979)
Technometrics
, vol.21
, Issue.2
, pp. 239-245
-
-
Mckay, M.D.1
Beckman, R.J.2
Conover, W.J.3
-
35
-
-
34548825690
-
Towards a theory of biological robustness
-
2013924 17882156
-
Kitano H Towards a theory of biological robustness Mol Syst Biol 2007, 3:137. 2013924 17882156
-
(2007)
Mol Syst Biol
, vol.3
, pp. 137
-
-
Kitano, H.1
-
36
-
-
0030797355
-
Robustness in simple biochemical networks
-
917 9202124
-
Barkai N Leibler S Robustness in simple biochemical networks Nature 1997, 387:6636-913. 917 9202124
-
(1997)
Nature
, vol.387
, pp. 913-917
-
-
Barkai, N.1
Leibler, S.2
-
37
-
-
17644446947
-
How robust are switches in intracellular signaling cascades?
-
14604583
-
Bluthgen N Herzel H How robust are switches in intracellular signaling cascades? Journal of Theoretical Biology 2003, 225(3):293-300. 14604583
-
(2003)
Journal of Theoretical Biology
, vol.225
, Issue.3
, pp. 293-300
-
-
Bluthgen, N.1
Herzel, H.2
-
38
-
-
32944481448
-
Robustness analysis of the IFN-gamma induced JAK-STAT signaling pathway
-
Zi ZK Sun ZR Robustness analysis of the IFN-gamma induced JAK-STAT signaling pathway Journal of Computer Science and Technology 2005, 20(4):491-495.
-
(2005)
Journal of Computer Science and Technology
, vol.20
, Issue.4
, pp. 491-495
-
-
Zi, Z.K.1
Sun, Z.R.2
-
39
-
-
33644877164
-
BioModels Database: A free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems
-
(Database issue): 1347454 16381960
-
Le Novere N Bornstein B Broicher A Courtot M Donizelli M Dharuri H Li L Sauro H Schilstra M Shapiro B Snoep JL Hucka M BioModels Database: A free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems Nucleic Acids Res 2006, 34(Database issue):D689-91. 1347454 16381960
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Le Novere, N.1
Bornstein, B.2
Broicher, A.3
Courtot, M.4
Donizelli, M.5
Dharuri, H.6
Li, L.7
Sauro, H.8
Schilstra, M.9
Shapiro, B.10
Snoep, J.L.11
Hucka, M.12
-
40
-
-
48549097369
-
Steady state analysis of signal response in receptor trafficking networks
-
18546478
-
Zi Z Klipp E Steady state analysis of signal response in receptor trafficking networks Genome Inform 2008/06/12 2007, 18:100-108. 18546478
-
(2007)
Genome Inform
, vol.18
, pp. 100-108
-
-
Zi, Z.1
Klipp, E.2
-
43
-
-
0034019315
-
Negative feedback and ultrasensitivity can bring about oscillations in the mitogen-activated protein kinase cascades
-
10712587
-
Kholodenko BN Negative feedback and ultrasensitivity can bring about oscillations in the mitogen-activated protein kinase cascades Eur J Biochem 2000, 267(6):1583-1588. 10712587
-
(2000)
Eur J Biochem
, vol.267
, Issue.6
, pp. 1583-1588
-
-
Kholodenko, B.N.1
-
44
-
-
0035579883
-
Mathematical model of the cell division cycle of fission yeast
-
12779461
-
Novak B Pataki Z Ciliberto A Tyson JJ Mathematical model of the cell division cycle of fission yeast Chaos 2001, 11(1):277-286. 12779461
-
(2001)
Chaos
, vol.11
, Issue.1
, pp. 277-286
-
-
Novak, B.1
Pataki, Z.2
Ciliberto, A.3
Tyson, J.J.4
-
45
-
-
33750701480
-
NFAT and NFkappaB activation in T lymphocytes: A model of differential activation of gene expression
-
1764593 17031595
-
Fisher WG Yang PC Medikonduri RK Jafri MS NFAT and NFkappaB activation in T lymphocytes: A model of differential activation of gene expression Ann Biomed Eng 2006, 34(11):1712-1728. 1764593 17031595
-
(2006)
Ann Biomed Eng
, vol.34
, Issue.11
, pp. 1712-1728
-
-
Fisher, W.G.1
Yang, P.C.2
Medikonduri, R.K.3
Jafri, M.S.4
|