-
1
-
-
3343020085
-
Integrative analysis of cell cycle control in budding yeast
-
10.1091/mbc.E03-11-0794, 491841, 15169868
-
Chen K, Calzone L, Csikasz-Nagy A, Cross F, Novak B, Tyson J. Integrative analysis of cell cycle control in budding yeast. Molecular Biology of the Cell 2004, 15(8):3841-3862. 10.1091/mbc.E03-11-0794, 491841, 15169868.
-
(2004)
Molecular Biology of the Cell
, vol.15
, Issue.8
, pp. 3841-3862
-
-
Chen, K.1
Calzone, L.2
Csikasz-Nagy, A.3
Cross, F.4
Novak, B.5
Tyson, J.6
-
2
-
-
38949110777
-
A quantitative study of the division cycle of Caulobacter crescentus stalked cells
-
10.1371/journal.pcbi.0040009, 2217572, 18225942
-
Li S, Brazhnik P, Sobral B, Tyson J. A quantitative study of the division cycle of Caulobacter crescentus stalked cells. PLoS Comput Biol 2008, 4:e9. 10.1371/journal.pcbi.0040009, 2217572, 18225942.
-
(2008)
PLoS Comput Biol
, vol.4
-
-
Li, S.1
Brazhnik, P.2
Sobral, B.3
Tyson, J.4
-
3
-
-
29544448913
-
Extension of a genetic network model by iterative experimentation and mathematical analysis
-
2005.0013
-
Locke JCW, Southern MM, Kozma-Bognar L, Hibberd V, Brown PE, Turner MS, Millar AJ. Extension of a genetic network model by iterative experimentation and mathematical analysis. Mol Syst Biol 2005, 1. 2005.0013.
-
(2005)
Mol Syst Biol
, vol.1
-
-
Locke, J.C.W.1
Southern, M.M.2
Kozma-Bognar, L.3
Hibberd, V.4
Brown, P.E.5
Turner, M.S.6
Millar, A.J.7
-
4
-
-
0037686112
-
The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in Drosophila melanogaster
-
10.1016/S0022-5193(03)00035-3, 12782112
-
Albert R, Othmer HG. The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in Drosophila melanogaster. J Theor Biol 2003, 223:1-18. 10.1016/S0022-5193(03)00035-3, 12782112.
-
(2003)
J Theor Biol
, vol.223
, pp. 1-18
-
-
Albert, R.1
Othmer, H.G.2
-
5
-
-
33747874092
-
Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle
-
10.1093/bioinformatics/btl210, 16873462
-
Fauré A, Naldi A, Chaouiya C, Thieffry D. Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle. Bioinformatics 2006, 22(14):e124-e131. 10.1093/bioinformatics/btl210, 16873462.
-
(2006)
Bioinformatics
, vol.22
, Issue.14
-
-
Fauré, A.1
Naldi, A.2
Chaouiya, C.3
Thieffry, D.4
-
6
-
-
34447551397
-
Structural and functional analysis of cellular networks with CellNetAnalyzer
-
10.1186/1752-0509-1-2, 1847467, 17408509
-
Klamt S, Saez-Rodriguez J, Gilles ED. Structural and functional analysis of cellular networks with CellNetAnalyzer. BMC Syst Biol 2007, 1:2. 10.1186/1752-0509-1-2, 1847467, 17408509.
-
(2007)
BMC Syst Biol
, vol.1
, pp. 2
-
-
Klamt, S.1
Saez-Rodriguez, J.2
Gilles, E.D.3
-
7
-
-
70049105859
-
The logic of EGFR/ErbB signaling: theoretical properties and analysis of high-throughput data
-
10.1371/journal.pcbi.1000438, 2710522, 19662154
-
Samaga R, Saez-Rodriguez J, Alexopoulos LG, Sorger PK, Klamt S. The logic of EGFR/ErbB signaling: theoretical properties and analysis of high-throughput data. PLoS Comput Biol 2009, 5(8):e1000438. 10.1371/journal.pcbi.1000438, 2710522, 19662154.
-
(2009)
PLoS Comput Biol
, vol.5
, Issue.8
-
-
Samaga, R.1
Saez-Rodriguez, J.2
Alexopoulos, L.G.3
Sorger, P.K.4
Klamt, S.5
-
8
-
-
70449481350
-
Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling
-
10.1186/1752-0509-3-98, 2764636, 19785753
-
Wittmann DM, Krumsiek J, Saez-Rodriguez J, Lauffenburger DA, Klamt S, Theis FJ. Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling. BMC Syst Biol 2009, 3:98. 10.1186/1752-0509-3-98, 2764636, 19785753.
-
(2009)
BMC Syst Biol
, vol.3
, pp. 98
-
-
Wittmann, D.M.1
Krumsiek, J.2
Saez-Rodriguez, J.3
Lauffenburger, D.A.4
Klamt, S.5
Theis, F.J.6
-
9
-
-
0003043542
-
The possible effects of the aggregation of the molecules of haemoglobin on its dissociation curves
-
Hill A. The possible effects of the aggregation of the molecules of haemoglobin on its dissociation curves. J Physiol 1910, 40:4-7.
-
(1910)
J Physiol
, vol.40
, pp. 4-7
-
-
Hill, A.1
-
11
-
-
51449094260
-
Rapidly exploring structural and dynamic properties of signaling networks using PathwayOracle
-
10.1186/1752-0509-2-76, 2527501, 18713463
-
Ruths D, Nakhleh L, Ram PT. Rapidly exploring structural and dynamic properties of signaling networks using PathwayOracle. BMC Syst Biol 2008, 2:76. 10.1186/1752-0509-2-76, 2527501, 18713463.
-
(2008)
BMC Syst Biol
, vol.2
, pp. 76
-
-
Ruths, D.1
Nakhleh, L.2
Ram, P.T.3
-
12
-
-
84874663136
-
YED graph editor
-
yED graph editor. , http://www.yworks.com/products/yed/
-
-
-
-
13
-
-
67049098922
-
Hypergraphs and cellular networks
-
10.1371/journal.pcbi.1000385, 2673028, 19478865
-
Klamt S, Haus UU, Theis F. Hypergraphs and cellular networks. PLoS Comput Biol 2009, 5(5):e1000385. 10.1371/journal.pcbi.1000385, 2673028, 19478865.
-
(2009)
PLoS Comput Biol
, vol.5
, Issue.5
-
-
Klamt, S.1
Haus, U.U.2
Theis, F.3
-
14
-
-
33646352954
-
GINsim: a software suite for the qualitative modelling, simulation and analysis of regulatory networks
-
10.1016/j.biosystems.2005.10.003, 16434137
-
Gonzalez AG, Naldi A, Sánchez L, Thieffry D, Chaouiya C. GINsim: a software suite for the qualitative modelling, simulation and analysis of regulatory networks. Biosystems 2006, 84(2):91-100. 10.1016/j.biosystems.2005.10.003, 16434137.
-
(2006)
Biosystems
, vol.84
, Issue.2
, pp. 91-100
-
-
Gonzalez, A.G.1
Naldi, A.2
Sánchez, L.3
Thieffry, D.4
Chaouiya, C.5
-
15
-
-
84888274605
-
Probabilistic Boolean Networks toolbox
-
Probabilistic Boolean Networks toolbox. , http://personal.systemsbiology.net/ilya/PBN/PBN.htm
-
-
-
-
16
-
-
32544443964
-
Systems Biology Toolbox for MATLAB: a computational platform for research in systems biology
-
10.1093/bioinformatics/bti799, 16317076
-
Schmidt H, Jirstrand M. Systems Biology Toolbox for MATLAB: a computational platform for research in systems biology. Bioinformatics 2006, 22(4):514-515. 10.1093/bioinformatics/bti799, 16317076.
-
(2006)
Bioinformatics
, vol.22
, Issue.4
, pp. 514-515
-
-
Schmidt, H.1
Jirstrand, M.2
-
17
-
-
0345269975
-
Genetic Network Analyzer: qualitative simulation of genetic regulatory networks
-
10.1093/bioinformatics/btf851, 12584118
-
de Jong H, Geiselmann J, Hernandez C, Page M. Genetic Network Analyzer: qualitative simulation of genetic regulatory networks. Bioinformatics 2003, 19(3):336-344. 10.1093/bioinformatics/btf851, 12584118.
-
(2003)
Bioinformatics
, vol.19
, Issue.3
, pp. 336-344
-
-
de Jong, H.1
Geiselmann, J.2
Hernandez, C.3
Page, M.4
-
18
-
-
38949210153
-
Dynamic simulation of regulatory networks using SQUAD
-
10.1186/1471-2105-8-462, 2238325, 18039375
-
Di Cara A, Garg A, De Micheli G, Xenarios I, Mendoza L. Dynamic simulation of regulatory networks using SQUAD. BMC Bioinformatics 2007, 8:462. 10.1186/1471-2105-8-462, 2238325, 18039375.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 462
-
-
Di Cara, A.1
Garg, A.2
De Micheli, G.3
Xenarios, I.4
Mendoza, L.5
-
19
-
-
34548431024
-
A Logical Model Provides Insights into T Cell Receptor Signaling
-
10.1371/journal.pcbi.0030163, 1950951,1950951, 17722974
-
Saez-Rodriguez J, Simeoni L, Lindquist JA, Hemenway R, Bommhardt U, Arndt B, Haus UU, Weismantel R, Gilles ED, Klamt S, Schraven B. A Logical Model Provides Insights into T Cell Receptor Signaling. PLoS Comput Biol 2007, 3(8):e163. 10.1371/journal.pcbi.0030163, 1950951,1950951, 17722974.
-
(2007)
PLoS Comput Biol
, vol.3
, Issue.8
-
-
Saez-Rodriguez, J.1
Simeoni, L.2
Lindquist, J.A.3
Hemenway, R.4
Bommhardt, U.5
Arndt, B.6
Haus, U.U.7
Weismantel, R.8
Gilles, E.D.9
Klamt, S.10
Schraven, B.11
-
20
-
-
33845368513
-
COPASI-a COmplex PAthway SImulator
-
10.1093/bioinformatics/btl485, 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. 10.1093/bioinformatics/btl485, 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
-
21
-
-
47949099328
-
CellDesigner 3.5: A Versatile Modeling Tool for Biochemical Networks
-
Funahashi A, Matsuoka Y, Jouraku A, Morohashi M, Kikuchi N, Kitano H. CellDesigner 3.5: A Versatile Modeling Tool for Biochemical Networks. Proceedings of the IEEE 2008, 96(8):1254-1265.
-
(2008)
Proceedings of the IEEE
, vol.96
, Issue.8
, pp. 1254-1265
-
-
Funahashi, A.1
Matsuoka, Y.2
Jouraku, A.3
Morohashi, M.4
Kikuchi, N.5
Kitano, H.6
-
22
-
-
0035480007
-
Hematopoietic development: a balancing act
-
10.1016/S0959-437X(00)00226-4, 11532392
-
Cantor AB, Orkin SH. Hematopoietic development: a balancing act. Curr Opin Genet Dev 2001, 11(5):513-519. 10.1016/S0959-437X(00)00226-4, 11532392.
-
(2001)
Curr Opin Genet Dev
, vol.11
, Issue.5
, pp. 513-519
-
-
Cantor, A.B.1
Orkin, S.H.2
-
23
-
-
33746040437
-
Towards an understanding of lineage specification in hematopoietic stem cells: a mathematical model for the interaction of transcription factors GATA-1 and PU.1
-
Roeder I, Glauche I. Towards an understanding of lineage specification in hematopoietic stem cells: a mathematical model for the interaction of transcription factors GATA-1 and PU.1. J Theor Biol 2006, 241(4):852-865.
-
(2006)
J Theor Biol
, vol.241
, Issue.4
, pp. 852-865
-
-
Roeder, I.1
Glauche, I.2
-
24
-
-
34248199004
-
Bifurcation dynamics in lineage-commitment in bipotent progenitor cells
-
10.1016/j.ydbio.2007.02.036, 17412320
-
Huang S, Guo YP, May G, Enver T. Bifurcation dynamics in lineage-commitment in bipotent progenitor cells. Dev Biol 2007, 305(2):695-713. 10.1016/j.ydbio.2007.02.036, 17412320.
-
(2007)
Dev Biol
, vol.305
, Issue.2
, pp. 695-713
-
-
Huang, S.1
Guo, Y.P.2
May, G.3
Enver, T.4
-
25
-
-
59149091124
-
Computational modeling of the hematopoietic erythroid-myeloid switch reveals insights into cooperativity, priming, and irreversibility
-
10.1371/journal.pcbi.1000268, 2613533, 19165316
-
Chickarmane V, Enver T, Peterson C. Computational modeling of the hematopoietic erythroid-myeloid switch reveals insights into cooperativity, priming, and irreversibility. PLoS Comput Biol 2009, 5:e1000268. 10.1371/journal.pcbi.1000268, 2613533, 19165316.
-
(2009)
PLoS Comput Biol
, vol.5
-
-
Chickarmane, V.1
Enver, T.2
Peterson, C.3
-
26
-
-
0037438387
-
Transcriptional accessibility for genes of multiple tissues and hematopoietic lineages is hierarchically controlled during early hematopoiesis
-
10.1182/blood-2002-06-1780, 12393558
-
Akashi K, He X, Chen J, Iwasaki H, Niu C, Steenhard B, Zhang J, Haug J, Li L. Transcriptional accessibility for genes of multiple tissues and hematopoietic lineages is hierarchically controlled during early hematopoiesis. Blood 2003, 101(2):383-389. 10.1182/blood-2002-06-1780, 12393558.
-
(2003)
Blood
, vol.101
, Issue.2
, pp. 383-389
-
-
Akashi, K.1
He, X.2
Chen, J.3
Iwasaki, H.4
Niu, C.5
Steenhard, B.6
Zhang, J.7
Haug, J.8
Li, L.9
-
27
-
-
73449138248
-
Spatial Analysis of Expression Patterns Predicts Genetic Interactions at the Mid-Hindbrain Boundary
-
10.1371/journal.pcbi.1000569, 2774268, 19936059
-
Wittmann DM, Bölchl F, Trümbach D, Wurst W, Prakash N, Theis FJ. Spatial Analysis of Expression Patterns Predicts Genetic Interactions at the Mid-Hindbrain Boundary. PLoS Comput Biol 2009, 5(11):e1000569. 10.1371/journal.pcbi.1000569, 2774268, 19936059.
-
(2009)
PLoS Comput Biol
, vol.5
, Issue.11
-
-
Wittmann, D.M.1
Bölchl, F.2
Trümbach, D.3
Wurst, W.4
Prakash, N.5
Theis, F.J.6
-
28
-
-
5444240078
-
Specification of midbrain territory
-
10.1007/s00441-004-0955-x, 15322917
-
Prakash N, Wurst W. Specification of midbrain territory. Cell Tissue Res 2004, 318:5-14. 10.1007/s00441-004-0955-x, 15322917.
-
(2004)
Cell Tissue Res
, vol.318
, pp. 5-14
-
-
Prakash, N.1
Wurst, W.2
-
29
-
-
0034644270
-
The segment polarity network is a robust developmental module
-
10.1038/35018085, 10910359
-
von Dassow G, Meir E, Munro EM, Odell GM. The segment polarity network is a robust developmental module. Nature 2000, 406(6792):188-192. 10.1038/35018085, 10910359.
-
(2000)
Nature
, vol.406
, Issue.6792
, pp. 188-192
-
-
von Dassow, G.1
Meir, E.2
Munro, E.M.3
Odell, G.M.4
|