-
3
-
-
0035775725
-
A new approach to decoding life: Systems biology
-
T. Ideker, T. Galitski and L. Hood, A new approach to decoding life: Systems biology, Annu Rev Genomics Hum Genet., 2 (2001), 343-372.
-
(2001)
Annu Rev Genomics Hum Genet.
, vol.2
, pp. 343-372
-
-
Ideker, T.1
Galitski, T.2
Hood, L.3
-
4
-
-
0037079054
-
Computational systems biology
-
H. Kitano, Computational systems biology, Nature, 420 (2002), 206-210.
-
(2002)
Nature
, vol.420
, pp. 206-210
-
-
Kitano, H.1
-
5
-
-
0037288767
-
Systems biology: Integrating technology, biology, and computation
-
L. Hood, Systems biology: Integrating technology, biology, and computation, Mech Ageing Dev., 124 (2003), 9-16.
-
(2003)
Mech Ageing Dev.
, vol.124
, pp. 9-16
-
-
Hood, L.1
-
8
-
-
0030797355
-
Robustness in simple biochemical networks
-
N. Barkai and S. Leibler, Robustness in simple biochemical networks, Nature, 387 (1997), 913-917.
-
(1997)
Nature
, vol.387
, pp. 913-917
-
-
Barkai, N.1
Leibler, S.2
-
9
-
-
33644524741
-
Cell-signalling dynamics in time and space
-
B. N. Kholodenko, Cell-signalling dynamics in time and space, Nat. Rev. Mol. Cell Biol., 7 (2006), 165-176.
-
(2006)
Nat. Rev. Mol. Cell Biol.
, vol.7
, pp. 165-176
-
-
Kholodenko, B.N.1
-
10
-
-
64349110975
-
Systems-level interactions between insulin-EGF networks amplify mitogenic signaling
-
N. Borisov, E. Aksamitiene, A. Kiyatkin, S. Legewie, J. Berkhout, T. Maiwald, N. P. Kaimachnikov, J. Timmer, J. B. Hoek and B. N. Kholodenko, Systems-level interactions between insulin-EGF networks amplify mitogenic signaling, Mol Syst Biol., 5 (2009), 256.
-
(2009)
Mol Syst Biol.
, vol.5
, pp. 256
-
-
Borisov, N.1
Aksamitiene, E.2
Kiyatkin, A.3
Legewie, S.4
Berkhout, J.5
Maiwald, T.6
Kaimachnikov, N.P.7
Timmer, J.8
Hoek, J.B.9
Kholodenko, B.N.10
-
11
-
-
84860285346
-
A multi-scale approach to colorectal cancer: From a biochemical- interaction signaling network level, to multi-cellular dynamics of malignant transformation. Interplay with mutations and onco-protein inhibitor drugs
-
L. Tortolina, N. Castagnino, C. De Ambrosi, E. Moran, F. Patrone, A. Ballestrero and S. Parodi, A multi-scale approach to colorectal cancer: From a biochemical-interaction signaling network level, to multi-cellular dynamics of malignant transformation. Interplay with mutations and onco-protein inhibitor drugs, Current Cancer Drug Target (CCDT), 12 (2012), 339-355.
-
(2012)
Current Cancer Drug Target (CCDT)
, vol.12
, pp. 339-355
-
-
Tortolina, L.1
Castagnino, N.2
De Ambrosi, C.3
Moran, E.4
Patrone, F.5
Ballestrero, A.6
Parodi, S.7
-
12
-
-
0037069467
-
Analysis of optimality in natural and perturbed metabolic networks
-
D. Segré, D. Vitkup and G. M. Church, Analysis of optimality in natural and perturbed metabolic networks, Proc Natl Acad Sci U S A., 99 (2002), 15112-15117.
-
(2002)
Proc Natl Acad Sci U S A.
, vol.99
, pp. 15112-15117
-
-
Segré, D.1
Vitkup, D.2
Church, G.M.3
-
13
-
-
11244297914
-
Modular epistasis in yeast metabolism
-
D. Segré, A. Deluna, G. M. Church and R. Kishony, Modular epistasis in yeast metabolism, Nat Genet., 37 (2005), 77-83.
-
(2005)
Nat Genet.
, vol.37
, pp. 77-83
-
-
Segré, D.1
Deluna, A.2
Church, G.M.3
Kishony, R.4
-
14
-
-
33947507091
-
Computational systems biology in drug discovery and development: Methods and applications
-
W. Materi and D. S. Wishart, Computational systems biology in drug discovery and development: methods and applications, Drug Discov Today, 12 (2007), 295-303.
-
(2007)
Drug Discov Today
, vol.12
, pp. 295-303
-
-
Materi, W.1
Wishart, D.S.2
-
15
-
-
33645429016
-
Exact stochastic simulation of coupled chemical reactions
-
D. T. Gillespie, Exact stochastic simulation of coupled chemical reactions, J. Phys.Chem., 81 (1977), 2340-2361.
-
(1977)
J. Phys.Chem.
, vol.81
, pp. 2340-2361
-
-
Gillespie, D.T.1
-
16
-
-
58549110252
-
Stochastic modelling for quantitative description of heterogeneous biological systems
-
D. J. Wilkinson, Stochastic modelling for quantitative description of heterogeneous biological systems, Nat Rev Genet., 10 (2009), 122-33.
-
(2009)
Nat Rev Genet.
, vol.10
, pp. 122-133
-
-
Wilkinson, D.J.1
-
17
-
-
33749993417
-
The consensus coding sequences of human breast and colorectal cancers
-
T. Sjöblom, S. Jones, L. D. Wood, D. W. Parsons, J. Lin, T. D. Barber, D. Mandelker, R. J. Leary, J. Ptak, N. Silliman, S. Szabo, P. Buckhaults, C. Farrell, P. Meeh, S. D. Markowitz, J. Willis, D. Dawson, J. K. Willson, A. F. Gazdar, J. Hartigan, L. Wu, C. Liu, G. Parmigiani, B. H. Park, K. E. Bachman, N. Papadopoulos, B. Vogelstein, K. W. Kinzler and V. E. Velculescu, The consensus coding sequences of human breast and colorectal cancers, Science, 314 (2006), 268-274.
-
(2006)
Science
, vol.314
, pp. 268-274
-
-
Sjöblom, T.1
Jones, S.2
Wood, L.D.3
Parsons, D.W.4
Lin, J.5
Barber, T.D.6
Mandelker, D.7
Leary, R.J.8
Ptak, J.9
Silliman, N.10
Szabo, S.11
Buckhaults, P.12
Farrell, C.13
Meeh, P.14
Markowitz, S.D.15
Willis, J.16
Dawson, D.17
Willson, J.K.18
Gazdar, A.F.19
Hartigan, J.20
Wu, L.21
Liu, C.22
Parmigiani, G.23
Park, B.H.24
Bachman, K.E.25
Papadopoulos, N.26
Vogelstein, B.27
Kinzler, K.W.28
Velculescu, V.E.29
more..
-
18
-
-
36248962105
-
The genomic landscapes of human breast and colorectal cancers
-
L. D. Wood, D. W. Parsons, S. Jones, J. Lin, T. Sjöblom, R. J. Leary, D. Shen, S. M. Boca, T. Barber, J. Ptak, N. Silliman, S. Szabo, Z. Dezso, V. Ustyanksky, T. Nikolskaya, Y. Nikolsky, R. Karchin, P. A. Wilson, J. S. Kaminker, Z. Zhang, R. Croshaw, J. Willis, D. Dawson, M. Shipitsin, J. K Willson, S. Sukumar, K. Polyak, B. H. Park, C. L. Pethiyagoda, P. V. Pant, D. G. Ballinger, A. B. Sparks, J. Hartigan, D. R. Smith, E. Suh, N. Papadopoulos, P. Buckhaults, S. D. Markowitz, G. Parmigiani, K. W. Kinzler, V. E. Velculescu and B. Vogelstein, The genomic landscapes of human breast and colorectal cancers, Science, 318 (2007), 1108-1113.
-
(2007)
Science
, vol.318
, pp. 1108-1113
-
-
Wood, L.D.1
Parsons, D.W.2
Jones, S.3
Lin, J.4
Sjöblom, T.5
Leary, R.J.6
Shen, D.7
Boca, S.M.8
Barber, T.9
Ptak, J.10
Silliman, N.11
Szabo, S.12
Dezso, Z.13
Ustyanksky, V.14
Nikolskaya, T.15
Nikolsky, Y.16
Karchin, R.17
Wilson, P.A.18
Kaminker, J.S.19
Zhang, Z.20
Croshaw, R.21
Willis, J.22
Dawson, D.23
Shipitsin, M.24
Willson, J.K.25
Sukumar, S.26
Polyak, K.27
Park, B.H.28
Pethiyagoda, C.L.29
Pant, P.V.30
Ballinger, D.G.31
Sparks, A.B.32
Hartigan, J.33
Smith, D.R.34
Suh, E.35
Papadopoulos, N.36
Buckhaults, P.37
Markowitz, S.D.38
Parmigiani, G.39
Kinzler, K.W.40
Velculescu, V.E.41
Vogelstein, B.42
more..
-
19
-
-
48749118242
-
Combinatorial patterns of somatic gene mutations in cancer
-
C. H. Yeang, F. McCormick and A. Levine, Combinatorial patterns of somatic gene mutations in cancer, FASEB J., 22 (2008), 2605-2622.
-
(2008)
FASEB J.
, vol.22
, pp. 2605-2622
-
-
Yeang, C.H.1
McCormick, F.2
Levine, A.3
-
20
-
-
1542286612
-
Molecular interaction maps - A diagrammatic graphical language for bioregulatory networks
-
M. I. Aladjem, S. Pasa, S. Parodi, J. N. Weinstein, Y. Pommier and K. W.Kohn, Molecular interaction maps-a diagrammatic graphical language for bioregulatory networks, Sci STKE., 222 (2004), pe8.
-
(2004)
Sci STKE.
, vol.222
-
-
Aladjem, M.I.1
Pasa, S.2
Parodi, S.3
Weinstein, J.N.4
Pommier, Y.5
Kohn, K.W.6
-
21
-
-
30044440098
-
Molecular interaction maps of bioregulatory networks: A general rubric for systems biology
-
K. W. Kohn, M. I. Aladjem, J. N. Weinstein and Y. Pommier, Molecular interaction maps of bioregulatory networks: A general rubric for systems biology, Mol. Biol. Cell, 17 (2006), 1-13.
-
(2006)
Mol. Biol. Cell
, vol.17
, pp. 1-13
-
-
Kohn, K.W.1
Aladjem, M.I.2
Weinstein, J.N.3
Pommier, Y.4
-
22
-
-
33750735728
-
Depicting combinatorial complexity with the molecular interaction map notation
-
K. W. Kohn, M. I. Aladjem, S. Kim, J. N.Weinstein and Y. Pommier, Depicting combinatorial complexity with the molecular interaction map notation, Mol Syst Biol., 2 (2006), 51.
-
(2006)
Mol Syst Biol.
, vol.2
, pp. 51
-
-
Kohn, K.W.1
Aladjem, M.I.2
Kim, S.3
Weinstein, J.N.4
Pommier, Y.5
-
23
-
-
79955968330
-
A formal MIM specification and tools for the common exchange of MIM diagrams: An XML-Based format, an API, and a validation method
-
A. Luna, E. I. Karac, M. Sunshine, L. Chang, R. Nussinov, M. I. Aladjem and K. W. Kohn, A formal MIM specification and tools for the common exchange of MIM diagrams: An XML-Based format, an API, and a validation method, BMC Bioinformatics, 12 (2011), 167.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 167
-
-
Luna, A.1
Karac, E.I.2
Sunshine, M.3
Chang, L.4
Nussinov, R.5
Aladjem, M.I.6
Kohn, K.W.7
-
26
-
-
0029056755
-
The use of estrogens and progestins and the risk of breast cancer in postmenopausal women
-
G. A. Colditz, S. E. Hankinson, D. J. Hunter, W. C. Willett, J. E. Manson, M. J. Stampfer, C. Hennekens, B. Rosner and F. E. Speizer, The use of estrogens and progestins and the risk of breast cancer in postmenopausal women, N Engl J Med., 332 (1995), 1589-1593.
-
(1995)
N Engl J Med.
, vol.332
, pp. 1589-1593
-
-
Colditz, G.A.1
Hankinson, S.E.2
Hunter, D.J.3
Willett, W.C.4
Manson, J.E.5
Stampfer, M.J.6
Hennekens, C.7
Rosner, B.8
Speizer, F.E.9
-
28
-
-
33846009481
-
A phosphoproteomic analysis of the ErbB2 receptor tyrosine kinase signaling pathways
-
M. Mukherji, L. M. Brill, S. B. Ficarro, G. M. Hampton and P. G. Schultz, A phosphoproteomic analysis of the ErbB2 receptor tyrosine kinase signaling pathways, Biochemistry, 45 (2006), 15529-15540.
-
(2006)
Biochemistry
, vol.45
, pp. 15529-15540
-
-
Mukherji, M.1
Brill, L.M.2
Ficarro, S.B.3
Hampton, G.M.4
Schultz, P.G.5
-
29
-
-
4344684649
-
PTEN function: How normal cells control it and tumour cells lose it
-
N. R. Leslie and C. P. Downes, PTEN function: how normal cells control it and tumour cells lose it, Biochem. J., 382 (2004), 1-11.
-
(2004)
Biochem. J.
, vol.382
, pp. 1-11
-
-
Leslie, N.R.1
Downes, C.P.2
-
30
-
-
33846557325
-
Coexistence of the loss of heterozygosity at the PTEN locus and HER2 overexpression enhances the Akt activity thus leading to a negative progesterone receptor expression in breast carcinoma
-
E. Tokunaga, E. Oki, Y. Kimura, T. Yamanaka, A. Egashira, K. Nishida, T. Koga, M. Morita, Y. Kakeji and Y. Maehara, Coexistence of the loss of heterozygosity at the PTEN locus and HER2 overexpression enhances the Akt activity thus leading to a negative progesterone receptor expression in breast carcinoma, Breast Cancer Res. Treat., 101 (2007), 249-257.
-
(2007)
Breast Cancer Res. Treat.
, vol.101
, pp. 249-257
-
-
Tokunaga, E.1
Oki, E.2
Kimura, Y.3
Yamanaka, T.4
Egashira, A.5
Nishida, K.6
Koga, T.7
Morita, M.8
Kakeji, Y.9
Maehara, Y.10
-
31
-
-
78649258925
-
Dynamic simulations of pathways downstream of ERBB-family, including mutations and treatments: Concordance with experimental results
-
N. Castagnino, L. Tortolina, A. Balbi, R. Pesenti, R. Montagna, A. Ballestrero, D. Soncini, A. Nencioni and S. Parodi, Dynamic simulations of pathways downstream of ERBB-family, including mutations and treatments: Concordance with experimental results, Current Cancer Drug Targets (CCDT), 10 (2010), 737-757.
-
(2010)
Current Cancer Drug Targets (CCDT)
, vol.10
, pp. 737-757
-
-
Castagnino, N.1
Tortolina, L.2
Balbi, A.3
Pesenti, R.4
Montagna, R.5
Ballestrero, A.6
Soncini, D.7
Nencioni, A.8
Parodi, S.9
-
32
-
-
0034194467
-
Why cytoplasmic signalling proteins should be recruited to cell membranes
-
B. N. Kholodenko, J. B. Hoek and H. V. Westerhoff, Why cytoplasmic signalling proteins should be recruited to cell membranes, Trends Cell Biol., 10 (2000), 173-178.
-
(2000)
Trends Cell Biol.
, vol.10
, pp. 173-178
-
-
Kholodenko, B.N.1
Hoek, J.B.2
Westerhoff, H.V.3
-
33
-
-
35448954932
-
The impact of the regulatory design on the response of epidermal growth factor receptor-mediated signal transduction towards oncogenic mutations
-
J. Wolf, S. Dronov, F. Tobin and I. Goryanin, The impact of the regulatory design on the response of epidermal growth factor receptor-mediated signal transduction towards oncogenic mutations, FEBS J., 274 (2007), 5505-5517.
-
(2007)
FEBS J.
, vol.274
, pp. 5505-5517
-
-
Wolf, J.1
Dronov, S.2
Tobin, F.3
Goryanin, I.4
-
34
-
-
0033570090
-
Quantification of short term signaling by the epidermal growth factor receptor
-
B. N. Kholodenko, O. V. Demin, G. Moehren and J. B. Hoek, Quantification of short term signaling by the epidermal growth factor receptor, J Biol. Chem., 274 (1999), 30169-30181.
-
(1999)
J Biol. Chem.
, vol.274
, pp. 30169-30181
-
-
Kholodenko, B.N.1
Demin, O.V.2
Moehren, G.3
Hoek, J.B.4
-
35
-
-
23244446113
-
Signal processing at the Ras circuit: What shapes Ras activation patterns?
-
N. I. Markevich, G. Moehren, O. V. Demin, A. Kiyatkin, J. B. Hoek and B. N. Kholodenko, Signal processing at the Ras circuit: what shapes Ras activation patterns?, Syst Biol (Stevenage), 1 2004, 104-113.
-
(2004)
Syst Biol (Stevenage)
, vol.1
, pp. 104-113
-
-
Markevich, N.I.1
Moehren, G.2
Demin, O.V.3
Kiyatkin, A.4
Hoek, J.B.5
Kholodenko, B.N.6
-
36
-
-
33746021158
-
Scaffolding protein Grb2-associated binder 1 sustains epidermal growth factor-induced mitogenic and survival signaling by multiple positive feedback loops
-
A. Kiyatkin, E. Aksamitiene, N. I. Markevich, N. M. Borisov, J. B. Hoek and B. N. Kholodenko, Scaffolding protein Grb2-associated binder 1 sustains epidermal growth factor-induced mitogenic and survival signaling by multiple positive feedback loops, J. Biol. Chem., 281 (2006), 19925-19938.
-
(2006)
J. Biol. Chem.
, vol.281
, pp. 19925-19938
-
-
Kiyatkin, A.1
Aksamitiene, E.2
Markevich, N.I.3
Borisov, N.M.4
Hoek, J.B.5
Kholodenko, B.N.6
-
37
-
-
36248988538
-
Ligand-dependent responses of the ErbB signaling network: Experimental and modeling analyses
-
M. R. Birtwistle, M. Hatakeyama, N. Yumoto, B. A. Ogunnaike, J. B. Hoek and B. N. Kholodenko, Ligand-dependent responses of the ErbB signaling network: experimental and modeling analyses, Mol. Syst. Biol., 3 (2007), e144.
-
(2007)
Mol. Syst. Biol.
, vol.3
-
-
Birtwistle, M.R.1
Hatakeyama, M.2
Yumoto, N.3
Ogunnaike, B.A.4
Hoek, J.B.5
Kholodenko, B.N.6
-
38
-
-
58549083142
-
Input-output behavior of ErbB signaling pathways as revealed by a mass action model trained against dynamic data
-
W. W. Chen, B. Schoeberl, P. J. Jasper, M. Niepel, U. B. Nielsen, D. A. Lauffenburger and P. K. Sorger, Input-output behavior of ErbB signaling pathways as revealed by a mass action model trained against dynamic data, Mol. Syst. Biol., 5 (2009), e239.
-
(2009)
Mol. Syst. Biol.
, vol.5
-
-
Chen, W.W.1
Schoeberl, B.2
Jasper, P.J.3
Niepel, M.4
Nielsen, U.B.5
Lauffenburger, D.A.6
Sorger, P.K.7
-
39
-
-
77952902183
-
Ligand-specific c-Fos expression emerges from the spatiotemporal control of ErbB network dynamics
-
T. Nakakuki, M. R. Birtwistle, Y. Saeki, N. Yumoto, K. Ide, T. Nagashima, L. Brusch, B. A. Ogunnaike, M. Okada-Hatakeyama and B. N. Kholodenko, Ligand-specific c-Fos expression emerges from the spatiotemporal control of ErbB network dynamics, Cell., 141 (2010), 884-896.
-
(2010)
Cell
, vol.141
, pp. 884-896
-
-
Nakakuki, T.1
Birtwistle, M.R.2
Saeki, Y.3
Yumoto, N.4
Ide, K.5
Nagashima, T.6
Brusch, L.7
Ogunnaike, B.A.8
Okada-Hatakeyama, M.9
Kholodenko, B.N.10
-
41
-
-
0029979217
-
Chemical kinetic theory: Understanding cell-cycle regulation
-
J. J. Tyson, B. Novak, G. G.M. Odell, K. Chen and C. D. Thron, Chemical kinetic theory: understanding cell-cycle regulation, Trends Biochem. Sci., 21 (1996), 89-96.
-
(1996)
Trends Biochem. Sci.
, vol.21
, pp. 89-96
-
-
Tyson, J.J.1
Novak, B.2
Odell, G.G.M.3
Chen, K.4
Thron, C.D.5
-
42
-
-
72149109797
-
Phosphatidylinositol 3-kinase signaling does not activate the Wnt cascade
-
S. S. Ng, T. Mahmoudi, E. Danenberg, I. Bejaoui, W. de Lau, H. C. Korswagen, M. Schutte and H. Clevers, Phosphatidylinositol 3-kinase signaling does not activate the Wnt cascade, J Biol Chem., 284 (2009), 35308-35313.
-
(2009)
J Biol Chem.
, vol.284
, pp. 35308-35313
-
-
Ng, S.S.1
Mahmoudi, T.2
Danenberg, E.3
Bejaoui, I.4
De Lau, W.5
Korswagen, H.C.6
Schutte, M.7
Clevers, H.8
-
43
-
-
78650656329
-
Does GSK-3 provide a shortcut for PI3K activation of Wnt signalling?
-
D. Voskas, L. S. Ling and J. R.Woodgett, Does GSK-3 provide a shortcut for PI3K activation of Wnt signalling?, F1000 Biol Rep., 2 (2010), 82.
-
(2010)
F1000 Biol Rep.
, vol.2
, pp. 82
-
-
Voskas, D.1
Ling, L.S.2
Woodgett, J.R.3
|