-
1
-
-
84941736224
-
BioSimWare: a software for the modeling, simulation and analysis of biological systems
-
In: Gheorghe M, Hinze T, Pǎun G, Rozenberg G, Salomaa A, editors. 11th International Conference, CMC 2010, Jena, Germany, August 24-27, 2010. Membrane Computing. 11th International Conference, CMC 2010, Jena, Germany, August 24--27, 2010. Revised Selected Papers. LNCS 6501, Springer-Verlag;
-
Besozzi D, Cazzaniga P, Mauri G, Pescini D. BioSimWare: a software for the modeling, simulation and analysis of biological systems. In: Gheorghe M, Hinze T, Pǎun G, Rozenberg G, Salomaa A, editors. 11th International Conference, CMC 2010, Jena, Germany, August 24-27, 2010. Membrane Computing. 11th International Conference, CMC 2010, Jena, Germany, August 24-27, 2010. Revised Selected Papers. LNCS 6501, Springer-Verlag; 2010. p. 119-43.
-
(2010)
, pp. 119-43
-
-
Besozzi, D.1
Cazzaniga, P.2
Mauri, G.3
Pescini, D.4
-
2
-
-
52949098296
-
Frequency-modulated nuclear localization bursts coordinate gene regulation
-
Cai L.O., Dalal C.K., Elowitz B. Frequency-modulated nuclear localization bursts coordinate gene regulation. Nature 2008, 455:485-490.
-
(2008)
Nature
, vol.455
, pp. 485-490
-
-
Cai, L.O.1
Dalal, C.K.2
Elowitz, B.3
-
3
-
-
31544465969
-
Efficient step size selection for the tau-leaping simulation method
-
Cao Y., Gillespie D.T., Petzold L.T. Efficient step size selection for the tau-leaping simulation method. J Chem Phys 2006, 124:044109.
-
(2006)
J Chem Phys
, vol.124
, pp. 044109
-
-
Cao, Y.1
Gillespie, D.T.2
Petzold, L.T.3
-
4
-
-
37449025422
-
Modeling and stochastic simulation of the Ras/cAMP/PKA pathway in the yeast Saccharomyces cerevisiae evidences a key function for intracellular guanine nucleotide pools
-
Cazzaniga P., Pescini D., Besozzi D., Mauri G., Colombo S., Martegani E. Modeling and stochastic simulation of the Ras/cAMP/PKA pathway in the yeast Saccharomyces cerevisiae evidences a key function for intracellular guanine nucleotide pools. J Biotechnol 2008, 133:377-385.
-
(2008)
J Biotechnol
, vol.133
, pp. 377-385
-
-
Cazzaniga, P.1
Pescini, D.2
Besozzi, D.3
Mauri, G.4
Colombo, S.5
Martegani, E.6
-
5
-
-
84887123070
-
Monitoring cAMP changes in a single yeast cell
-
Colombo S., Broggi S., D'Alfonso L., Collini M., Chirico G., Martegani E. Monitoring cAMP changes in a single yeast cell. FEBS J 2011, 278(Suppl. 1):362.
-
(2011)
FEBS J
, vol.278
, Issue.SUPPL. 1
, pp. 362
-
-
Colombo, S.1
Broggi, S.2
D'Alfonso, L.3
Collini, M.4
Chirico, G.5
Martegani, E.6
-
6
-
-
0032526715
-
Involvement of distinct G-proteins, Gpa2 and Ras in glucose- and intracellular acidification-induced cAMP signaling in the yeast Saccharomyces cerevisiae
-
Colombo S., Ma P., Cauwenberg L., Winderickx J., Crauwels M., Teunissen A., et al. Involvement of distinct G-proteins, Gpa2 and Ras in glucose- and intracellular acidification-induced cAMP signaling in the yeast Saccharomyces cerevisiae. EMBO J 1998, 17:3326-3341.
-
(1998)
EMBO J
, vol.17
, pp. 3326-3341
-
-
Colombo, S.1
Ma, P.2
Cauwenberg, L.3
Winderickx, J.4
Crauwels, M.5
Teunissen, A.6
-
7
-
-
6344256284
-
Activation state of the Ras2 protein and glucose-induced signaling in Saccharomyces cerevisiae
-
Colombo S., Ronchetti D., Thevelein J.M., Winderickx J., Martegani E. Activation state of the Ras2 protein and glucose-induced signaling in Saccharomyces cerevisiae. J Biol Chem 2004, 279:46715-46722.
-
(2004)
J Biol Chem
, vol.279
, pp. 46715-46722
-
-
Colombo, S.1
Ronchetti, D.2
Thevelein, J.M.3
Winderickx, J.4
Martegani, E.5
-
8
-
-
67449152160
-
Computational systems biology of the cell cycle
-
Csikász-Nagy A. Computational systems biology of the cell cycle. Brief Bioinform 2009, 10(4):424-434.
-
(2009)
Brief Bioinform
, vol.10
, Issue.4
, pp. 424-434
-
-
Csikász-Nagy, A.1
-
9
-
-
0025755609
-
The overexpression of the 3' terminal region of the CDC25 gene of Saccharomyces cerevisiae causes growth inhibition and alteration of purine nucleotides pools
-
Frascotti G., Coccetti P., Vanoni M.A., Alberghina L., Martegani E. The overexpression of the 3' terminal region of the CDC25 gene of Saccharomyces cerevisiae causes growth inhibition and alteration of purine nucleotides pools. Biochim Biophys Acta 1991, 1089(2):206-212.
-
(1991)
Biochim Biophys Acta
, vol.1089
, Issue.2
, pp. 206-212
-
-
Frascotti, G.1
Coccetti, P.2
Vanoni, M.A.3
Alberghina, L.4
Martegani, E.5
-
10
-
-
34250155259
-
Nucleocytoplasmic oscillations of the yeast transcription factor Msn2: evidence for periodic PKA activation
-
Garmendia-Torres C., Goldbeter A., Jacquet M. Nucleocytoplasmic oscillations of the yeast transcription factor Msn2: evidence for periodic PKA activation. Curr Biol 2007, 17:1044-1049.
-
(2007)
Curr Biol
, vol.17
, pp. 1044-1049
-
-
Garmendia-Torres, C.1
Goldbeter, A.2
Jacquet, M.3
-
11
-
-
33845466196
-
Computational methodologies for modelling, analysis and simulation of signalling networks
-
Gilbert D., Fuß H., Gu X., Orton R., Robinson S., Vyshemirsky V., et al. Computational methodologies for modelling, analysis and simulation of signalling networks. Brief Bioinform 2006, 7(4):339-353.
-
(2006)
Brief Bioinform
, vol.7
, Issue.4
, pp. 339-353
-
-
Gilbert, D.1
Fuß, H.2
Gu, X.3
Orton, R.4
Robinson, S.5
Vyshemirsky, V.6
-
12
-
-
46249127273
-
Stochastic modeling of nucleocytoplasmic oscillations of the transcription factor Msn2 in yeast
-
Gonze D., Jacquet M., Goldbeter A. Stochastic modeling of nucleocytoplasmic oscillations of the transcription factor Msn2 in yeast. J R Soc Interface 2008, 5:S95-S109.
-
(2008)
J R Soc Interface
, vol.5
-
-
Gonze, D.1
Jacquet, M.2
Goldbeter, A.3
-
13
-
-
0027054644
-
Phosphorylation of the S. cerevisiae Cdc25 in response to glucose results in its dissociation from Ras
-
Gross E., Goldberg D., Levitzki A. Phosphorylation of the S. cerevisiae Cdc25 in response to glucose results in its dissociation from Ras. Nature 1992, 360:762-765.
-
(1992)
Nature
, vol.360
, pp. 762-765
-
-
Gross, E.1
Goldberg, D.2
Levitzki, A.3
-
14
-
-
0028365073
-
Cdc25p, the guanine nucleotide exchange factor for the Ras proteins of Saccharomyces cerevisiae, promotes exchange by stabilizing Ras in a nucleotide-free state
-
Haney S.A., Broach J.R. Cdc25p, the guanine nucleotide exchange factor for the Ras proteins of Saccharomyces cerevisiae, promotes exchange by stabilizing Ras in a nucleotide-free state. J Biol Chem 1994, 269:16541-16548.
-
(1994)
J Biol Chem
, vol.269
, pp. 16541-16548
-
-
Haney, S.A.1
Broach, J.R.2
-
15
-
-
0038612842
-
Oscillatory nucleocytoplasmic shuttling of the general stress response transcriptional activators Msn2 and Msn4 in Saccharomyces cerevisiae
-
Jacquet M., Renaulkt G., Lallet R., De Mey J., Goldbeter A. Oscillatory nucleocytoplasmic shuttling of the general stress response transcriptional activators Msn2 and Msn4 in Saccharomyces cerevisiae. J Cell Biol 2003, 161:497-505.
-
(2003)
J Cell Biol
, vol.161
, pp. 497-505
-
-
Jacquet, M.1
Renaulkt, G.2
Lallet, R.3
De Mey, J.4
Goldbeter, A.5
-
16
-
-
78649642171
-
Feedback regulation of Ras2 guanine nucleotide exchange factor (Ras2-GEF) activity of Cdc25p by Cdc25p phosphorylation in the yeast Saccharomyces cerevisiae
-
Jian D., Aili Z., Xiaojia B., Huansheng Z., Yun H. Feedback regulation of Ras2 guanine nucleotide exchange factor (Ras2-GEF) activity of Cdc25p by Cdc25p phosphorylation in the yeast Saccharomyces cerevisiae. FEBS Lett 2010, 584:4745-4750.
-
(2010)
FEBS Lett
, vol.584
, pp. 4745-4750
-
-
Jian, D.1
Aili, Z.2
Xiaojia, B.3
Huansheng, Z.4
Yun, H.5
-
17
-
-
0034019315
-
Negative feedback and ultrasensitivity can bring about oscillations in the mitogen-activated protein kinase cascades
-
Kholodenko B.N. Negative feedback and ultrasensitivity can bring about oscillations in the mitogen-activated protein kinase cascades. Eur J Biochem 2000, 267:1583-1588.
-
(2000)
Eur J Biochem
, vol.267
, pp. 1583-1588
-
-
Kholodenko, B.N.1
-
18
-
-
36949034670
-
Stochastic noise and synchronisation during Dictyostelium aggregation make cAMP oscillations robust
-
Kim J., Heslop-Harrison P., Postlethwaite I., Bates D.G. Stochastic noise and synchronisation during Dictyostelium aggregation make cAMP oscillations robust. PLoS Comput Biol 2007, 3(11):e218.
-
(2007)
PLoS Comput Biol
, vol.3
, Issue.11
-
-
Kim, J.1
Heslop-Harrison, P.2
Postlethwaite, I.3
Bates, D.G.4
-
19
-
-
71149108764
-
-
Wiley-VCH
-
Klipp E., Liebermeister W., Wierling C., Kowald A., Lehrach H., Herwig R. Systems Biology: A Textbook 2009, Wiley-VCH.
-
(2009)
Systems Biology: A Textbook
-
-
Klipp, E.1
Liebermeister, W.2
Wierling, C.3
Kowald, A.4
Lehrach, H.5
Herwig, R.6
-
20
-
-
0032896365
-
The PDE1-encoded low-affinity phosphodiesterase in the yeast Saccharomyces cerevisiae has a specific function in controlling agonist-induced cAMP signaling
-
Ma P., Wera S., Van Dijck P., Thevelein J.M. The PDE1-encoded low-affinity phosphodiesterase in the yeast Saccharomyces cerevisiae has a specific function in controlling agonist-induced cAMP signaling. Mol Biol Cell 1999, 10:91-104.
-
(1999)
Mol Biol Cell
, vol.10
, pp. 91-104
-
-
Ma, P.1
Wera, S.2
Van Dijck, P.3
Thevelein, J.M.4
-
21
-
-
35648995939
-
MSN2 and MSN4 link calorie restriction and TOR to sirtuin-mediated lifespan extension in Saccharomyces cerevisiae
-
Medvedik O., Lamming D.W., Kim K.D., Sinclair D.A. MSN2 and MSN4 link calorie restriction and TOR to sirtuin-mediated lifespan extension in Saccharomyces cerevisiae. PLoS Biol 2007, 5:2330-2341.
-
(2007)
PLoS Biol
, vol.5
, pp. 2330-2341
-
-
Medvedik, O.1
Lamming, D.W.2
Kim, K.D.3
Sinclair, D.A.4
-
23
-
-
0023442858
-
Rigorous feedback control of cAMP levels in Saccharomyces cerevisiae
-
Nikawa J., Cameron S., Toda T., Ferguson K.M., Wigler M. Rigorous feedback control of cAMP levels in Saccharomyces cerevisiae. Genes Dev 1987, 1:931-937.
-
(1987)
Genes Dev
, vol.1
, pp. 931-937
-
-
Nikawa, J.1
Cameron, S.2
Toda, T.3
Ferguson, K.M.4
Wigler, M.5
-
24
-
-
77955374442
-
The role of type 4 phosphodiesterases in generating microdomains of cAMP: large scale stochastic simulations
-
Oliveira R.F., Terrin A., Di Benedetto G., Cannon R.C., Koh W., Kim M.S., et al. The role of type 4 phosphodiesterases in generating microdomains of cAMP: large scale stochastic simulations. PLoS One 2010, 5(7):e11725.
-
(2010)
PLoS One
, vol.5
, Issue.7
-
-
Oliveira, R.F.1
Terrin, A.2
Di Benedetto, G.3
Cannon, R.C.4
Koh, W.5
Kim, M.S.6
-
25
-
-
12144282761
-
Detecting cAMP-induced Epac activation by fluorescence resonance energy transfer: Epac as a novel cAMP indicator
-
Ponsioen B., Zhao J., Riedl J., Zwartkruis F., van der Krogt G., Zaccolo M., et al. Detecting cAMP-induced Epac activation by fluorescence resonance energy transfer: Epac as a novel cAMP indicator. EMBO Rep 2004, 5:1176-1180.
-
(2004)
EMBO Rep
, vol.5
, pp. 1176-1180
-
-
Ponsioen, B.1
Zhao, J.2
Riedl, J.3
Zwartkruis, F.4
van der Krogt, G.5
Zaccolo, M.6
-
26
-
-
0037078982
-
Control, exploitation and tolerance of intracellular noise
-
Rao C.V., Wolf D.M., Arkin A.P. Control, exploitation and tolerance of intracellular noise. Nature 2002, 420:231-237.
-
(2002)
Nature
, vol.420
, pp. 231-237
-
-
Rao, C.V.1
Wolf, D.M.2
Arkin, A.P.3
-
27
-
-
0035938253
-
Role of guanine mucleotides in the regulation of the Ras/cAMP pathway in Saccharomyces cerevisiae
-
Rudoni S., Colombo S., Coccetti P., Martegani E. Role of guanine mucleotides in the regulation of the Ras/cAMP pathway in Saccharomyces cerevisiae. Biochim Biophys Acta 2001, 1538:181-189.
-
(2001)
Biochim Biophys Acta
, vol.1538
, pp. 181-189
-
-
Rudoni, S.1
Colombo, S.2
Coccetti, P.3
Martegani, E.4
-
28
-
-
71449121678
-
Rapid and sustained nuclear-cytoplasmic ERK oscillations induced by epidermal growth factor
-
Shankaran H., Ippolito D.L., Chrisler W.B., Resat H., Bollinger N., Opresko L.K., et al. Rapid and sustained nuclear-cytoplasmic ERK oscillations induced by epidermal growth factor. Mol Syst Biol 2009, 5:332.
-
(2009)
Mol Syst Biol
, vol.5
, pp. 332
-
-
Shankaran, H.1
Ippolito, D.L.2
Chrisler, W.B.3
Resat, H.4
Bollinger, N.5
Opresko, L.K.6
-
29
-
-
65249103982
-
Positive- and negative-feedback regulations coordinate the dynamic behavior of the Ras-Raf-MEK-ERK signal transduction pathway
-
Shin S.Y., Rath O., Choo S.M., Fee F., McFerran B., Kolch W., et al. Positive- and negative-feedback regulations coordinate the dynamic behavior of the Ras-Raf-MEK-ERK signal transduction pathway. J Cell Sci 2009, 122:425-435.
-
(2009)
J Cell Sci
, vol.122
, pp. 425-435
-
-
Shin, S.Y.1
Rath, O.2
Choo, S.M.3
Fee, F.4
McFerran, B.5
Kolch, W.6
-
30
-
-
0037200116
-
A role for phosphorylation of inositol 1,4,5-trisphosphate receptors in defining calcium signals induced by peptide agonists in pancreatic acinar cells
-
Straub S.V., Giovannucci R.D., Bruce J.I.E., Yule D.I. A role for phosphorylation of inositol 1,4,5-trisphosphate receptors in defining calcium signals induced by peptide agonists in pancreatic acinar cells. J Biol Chem 2002, 277:31949-31956.
-
(2002)
J Biol Chem
, vol.277
, pp. 31949-31956
-
-
Straub, S.V.1
Giovannucci, R.D.2
Bruce, J.I.E.3
Yule, D.I.4
-
32
-
-
0025232840
-
S. cerevisiae IRA1 and IRA2 encode proteins that may be functionally equivalent to mammalian ras GTPase activating protein
-
Tanaka K., Nakafuku M., Satoh T., Marshall M.S., Gibbs J.B., Matsumoto K., et al. S. cerevisiae IRA1 and IRA2 encode proteins that may be functionally equivalent to mammalian ras GTPase activating protein. Cell 1990, 60:803-807.
-
(1990)
Cell
, vol.60
, pp. 803-807
-
-
Tanaka, K.1
Nakafuku, M.2
Satoh, T.3
Marshall, M.S.4
Gibbs, J.B.5
Matsumoto, K.6
-
33
-
-
0032835137
-
Novel sensing mechanisms and targets for the cAMP-protein kinase A pathway in the yeast Saccharomyces cerevisiae
-
Thevelein J.M., de Winde J.H. Novel sensing mechanisms and targets for the cAMP-protein kinase A pathway in the yeast Saccharomyces cerevisiae. Mol Microbiol 1999, 33:904-918.
-
(1999)
Mol Microbiol
, vol.33
, pp. 904-918
-
-
Thevelein, J.M.1
de Winde, J.H.2
-
34
-
-
0037376655
-
Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell
-
Tyson J.J., Chen K.C., Novak B. Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell. Curr Opin Cell Biol 2003, 15(2):221-231.
-
(2003)
Curr Opin Cell Biol
, vol.15
, Issue.2
, pp. 221-231
-
-
Tyson, J.J.1
Chen, K.C.2
Novak, B.3
-
35
-
-
45749108672
-
Integration of global signaling pathways, cAMP-PKA, MAPK and TOR in the regulation of FLO11
-
Vinod P.K., Sengupta N., Bhat P.J., Venkatesh K.V. Integration of global signaling pathways, cAMP-PKA, MAPK and TOR in the regulation of FLO11. PLoS One 2008, 3(2):e1663.
-
(2008)
PLoS One
, vol.3
, Issue.2
-
-
Vinod, P.K.1
Sengupta, N.2
Bhat, P.J.3
Venkatesh, K.V.4
-
36
-
-
6444221171
-
Stress induces depletion of Cdc25p and decreases the cAMP producing capability in Saccharomyces cerevisiae
-
Wang L., Renault G., Garreau H., Jacquet M. Stress induces depletion of Cdc25p and decreases the cAMP producing capability in Saccharomyces cerevisiae. Microbiology 2004, 150:3383-3391.
-
(2004)
Microbiology
, vol.150
, pp. 3383-3391
-
-
Wang, L.1
Renault, G.2
Garreau, H.3
Jacquet, M.4
-
37
-
-
4544321024
-
Modeling and simulation of intracellular dynamics: choosing an appropriate framework
-
Wolkenhauer O., Ullah M., Kolch W., Kwang-Hyun C. Modeling and simulation of intracellular dynamics: choosing an appropriate framework. IEEE Trans Nanobioscience 2004, 3(3):200-207.
-
(2004)
IEEE Trans Nanobioscience
, vol.3
, Issue.3
, pp. 200-207
-
-
Wolkenhauer, O.1
Ullah, M.2
Kolch, W.3
Kwang-Hyun, C.4
|