-
1
-
-
14844289540
-
Illuminating drug discovery with biological pathways
-
G. Apic, T. Ignjatovic, S. Boyer, and R.B. Russell Illuminating drug discovery with biological pathways FEBS Lett 579 2005 1872 1877
-
(2005)
FEBS Lett
, vol.579
, pp. 1872-1877
-
-
Apic, G.1
Ignjatovic, T.2
Boyer, S.3
Russell, R.B.4
-
3
-
-
13844267123
-
Integrating cell-level kinetic modeling into the design of engineered protein therapeutics
-
B.M. Rao, D.A. Lauffenburger, and K.D. Wittrup Integrating cell-level kinetic modeling into the design of engineered protein therapeutics Nat Biotechnol 23 2005 191 194
-
(2005)
Nat Biotechnol
, vol.23
, pp. 191-194
-
-
Rao, B.M.1
Lauffenburger, D.A.2
Wittrup, K.D.3
-
4
-
-
12344250438
-
Structural genomics of GPCRs
-
K. Lundstrom Structural genomics of GPCRs Trends Biotechnol 23 2005 103 108
-
(2005)
Trends Biotechnol
, vol.23
, pp. 103-108
-
-
Lundstrom, K.1
-
5
-
-
11144252286
-
Intracoronary administration of FGF-2: a computational model of myocardial deposition and retention
-
R.J. Filion, and A.S. Popel Intracoronary administration of FGF-2: a computational model of myocardial deposition and retention Am J Physiol Heart Circ Physiol 288 2005 H263 H279
-
(2005)
Am J Physiol Heart Circ Physiol
, vol.288
-
-
Filion, R.J.1
Popel, A.S.2
-
6
-
-
14644399153
-
The kinetics of FGF-2 binding to heparan sulfate proteoglycans and MAP kinase signaling
-
K. Forsten-Williams, C.C. Chua, and M.A. Nugent The kinetics of FGF-2 binding to heparan sulfate proteoglycans and MAP kinase signaling J Theor Biol 233 2005 483 499
-
(2005)
J Theor Biol
, vol.233
, pp. 483-499
-
-
Forsten-Williams, K.1
Chua, C.C.2
Nugent, M.A.3
-
7
-
-
0037133306
-
Pharmacological treatment of coronary artery disease with recombinant fibroblast growth factor-2: double-blind, randomized, controlled clinical trial
-
M. Simons, B.H. Annex, R.J. Laham, N. Kleiman, T. Henry, H. Dauerman, J.E. Udelson, E.V. Gervino, M. Pike, and M.J. Whitehouse Pharmacological treatment of coronary artery disease with recombinant fibroblast growth factor-2: double-blind, randomized, controlled clinical trial Circulation 105 2002 788 793
-
(2002)
Circulation
, vol.105
, pp. 788-793
-
-
Simons, M.1
Annex, B.H.2
Laham, R.J.3
Kleiman, N.4
Henry, T.5
Dauerman, H.6
Udelson, J.E.7
Gervino, E.V.8
Pike, M.9
Whitehouse, M.J.10
-
8
-
-
0037213006
-
Computational modeling of the EGF-receptor system: a paradigm for systems biology
-
H.S. Wiley, S.Y. Shvartsman, and D.A. Lauffenburger Computational modeling of the EGF-receptor system: a paradigm for systems biology Trends Cell Biol 13 2003 43 50
-
(2003)
Trends Cell Biol
, vol.13
, pp. 43-50
-
-
Wiley, H.S.1
Shvartsman, S.Y.2
Lauffenburger, D.A.3
-
9
-
-
17844372539
-
Critical update and emerging trends in epidermal growth factor receptor targeting in cancer
-
J. Baselga, and C.L. Arteaga Critical update and emerging trends in epidermal growth factor receptor targeting in cancer J Clin Oncol 23 2005 2445 2459
-
(2005)
J Clin Oncol
, vol.23
, pp. 2445-2459
-
-
Baselga, J.1
Arteaga, C.L.2
-
10
-
-
0037931402
-
Quantitative analysis of HER2-mediated effects on HER2 and epidermal growth factor receptor endocytosis: distribution of homo- and heterodimers depends on relative HER2 levels
-
B.S. Hendriks, L.K. Opresko, H.S. Wiley, and D. Lauffenburger Quantitative analysis of HER2-mediated effects on HER2 and epidermal growth factor receptor endocytosis: distribution of homo- and heterodimers depends on relative HER2 levels J Biol Chem 278 2003 23343 23351
-
(2003)
J Biol Chem
, vol.278
, pp. 23343-23351
-
-
Hendriks, B.S.1
Opresko, L.K.2
Wiley, H.S.3
Lauffenburger, D.4
-
11
-
-
2942588906
-
Mathematical and computational models of immune-receptor signalling
-
B. Goldstein, J.R. Faeder, and W.S. Hlavacek Mathematical and computational models of immune-receptor signalling Nat Rev Immunol 4 2004 445 456
-
(2004)
Nat Rev Immunol
, vol.4
, pp. 445-456
-
-
Goldstein, B.1
Faeder, J.R.2
Hlavacek, W.S.3
-
12
-
-
2942683015
-
An algebra of dimerization and its implications for G-protein coupled receptor signaling
-
P.J. Woolf, and J.J. Linderman An algebra of dimerization and its implications for G-protein coupled receptor signaling J Theor Biol 229 2004 157 168
-
(2004)
J Theor Biol
, vol.229
, pp. 157-168
-
-
Woolf, P.J.1
Linderman, J.J.2
-
13
-
-
0033555859
-
Emergent properties of networks of biological signaling pathways
-
U.S. Bhalla, and R. Iyengar Emergent properties of networks of biological signaling pathways Science 283 1999 381 387
-
(1999)
Science
, vol.283
, pp. 381-387
-
-
Bhalla, U.S.1
Iyengar, R.2
-
14
-
-
0037079054
-
Computational systems biology
-
H. Kitano Computational systems biology Nature 420 2002 206 210
-
(2002)
Nature
, vol.420
, pp. 206-210
-
-
Kitano, H.1
-
15
-
-
0034693459
-
Mathematical modeling of epidermal growth factor receptor signaling through the phospholipase C pathway: mechanistic insights and predictions for molecular interventions
-
J.M. Haugh, A. Wells, and D.A. Lauffenburger Mathematical modeling of epidermal growth factor receptor signaling through the phospholipase C pathway: mechanistic insights and predictions for molecular interventions Biotechnol Bioeng 70 2000 225 238
-
(2000)
Biotechnol Bioeng
, vol.70
, pp. 225-238
-
-
Haugh, J.M.1
Wells, A.2
Lauffenburger, D.A.3
-
16
-
-
0032731892
-
Tumor invasion: role of growth factor-induced cell motility
-
A. Wells Tumor invasion: role of growth factor-induced cell motility Adv Cancer Res 78 2000 31 101
-
(2000)
Adv Cancer Res
, vol.78
, pp. 31-101
-
-
Wells, A.1
-
17
-
-
0037044575
-
The IkappaB-NF-kappaB signaling module: temporal control and selective gene activation
-
A. Hoffmann, A. Levchenko, M.L. Scott, and D. Baltimore The IkappaB-NF-kappaB signaling module: temporal control and selective gene activation Science 298 2002 1241 1245 This is an excellent example of how modeling and experimental studies complement each other to advance a field. Their predictive NF-κB model has inspired many studies in cancer, apoptosis and other clinically relevant systems. Sung et al. [18] have adapted this model to explore alternative drug targets and treatment schedules in the NF-κB pathway for cancer therapy.
-
(2002)
Science
, vol.298
, pp. 1241-1245
-
-
Hoffmann, A.1
Levchenko, A.2
Scott, M.L.3
Baltimore, D.4
-
18
-
-
3042668006
-
In silico simulation of inhibitor drug effects on nuclear factor-kappaB pathway dynamics
-
M.H. Sung, and R. Simon In silico simulation of inhibitor drug effects on nuclear factor-kappaB pathway dynamics Mol Pharmacol 66 2004 70 75
-
(2004)
Mol Pharmacol
, vol.66
, pp. 70-75
-
-
Sung, M.H.1
Simon, R.2
-
19
-
-
0346850834
-
Modeling beta-adrenergic control of cardiac myocyte contractility in silico
-
J.J. Saucerman, L.L. Brunton, A.P. Michailova, and A.D. McCulloch Modeling beta-adrenergic control of cardiac myocyte contractility in silico J Biol Chem 278 2003 47997 48003 This study integrates both the electrical and chemical signals in a cell, and uses network properties of the β-AR signaling system to arrive at optimal sites for drug intervention.
-
(2003)
J Biol Chem
, vol.278
, pp. 47997-48003
-
-
Saucerman, J.J.1
Brunton, L.L.2
Michailova, A.P.3
McCulloch, A.D.4
-
20
-
-
2942576105
-
Data-driven computer simulation of human cancer cell
-
R. Christopher, A. Dhiman, J. Fox, R. Gendelman, T. Haberitcher, D. Kagle, G. Spizz, I.G. Khalil, and C. Hill Data-driven computer simulation of human cancer cell Ann N Y Acad Sci 1020 2004 132 153 This cancer cell simulation is one of the largest and most detailed models in the literature. The authors have explored the connectivity of signal transduction pathways with gene-expression networks, in silico and in vivo, in unicellular and multicellular systems. The model has undergone extensive validation steps through multiple iterations between experiments and simulations. Using the model, the authors are in a position to test drug efficacy, most importantly, in a patient-specific manner; in line with the ideal of personalized medicine.
-
(2004)
Ann N Y Acad Sci
, vol.1020
, pp. 132-153
-
-
Christopher, R.1
Dhiman, A.2
Fox, J.3
Gendelman, R.4
Haberitcher, T.5
Kagle, D.6
Spizz, G.7
Khalil, I.G.8
Hill, C.9
-
21
-
-
0035397515
-
Roles of triosephosphate isomerase and aerobic metabolism in Trypanosoma brucei
-
S. Helfert, A.M. Estevez, B. Bakker, P. Michels, and C. Clayton Roles of triosephosphate isomerase and aerobic metabolism in Trypanosoma brucei Biochem J 357 2001 117 125
-
(2001)
Biochem J
, vol.357
, pp. 117-125
-
-
Helfert, S.1
Estevez, A.M.2
Bakker, B.3
Michels, P.4
Clayton, C.5
-
22
-
-
4744347322
-
Heart mitochondria signaling pathways: appraisal of an emerging field
-
J. Marin-Garcia, and M.J. Goldenthal Heart mitochondria signaling pathways: appraisal of an emerging field J Mol Med 82 2004 565 578
-
(2004)
J Mol Med
, vol.82
, pp. 565-578
-
-
Marin-Garcia, J.1
Goldenthal, M.J.2
-
23
-
-
0036037788
-
Virtual mitochondria: metabolic modelling and control
-
M. Aimar-Beurton, B. Korzeniewski, T. Letellier, S. Ludinard, J.P. Mazat, and C. Nazaret Virtual mitochondria: metabolic modelling and control Mol Biol Rep 29 2002 227 232
-
(2002)
Mol Biol Rep
, vol.29
, pp. 227-232
-
-
Aimar-Beurton, M.1
Korzeniewski, B.2
Letellier, T.3
Ludinard, S.4
Mazat, J.P.5
Nazaret, C.6
-
24
-
-
0037380954
-
An integrated model of cardiac mitochondrial energy metabolism and calcium dynamics
-
S. Cortassa, M.A. Aon, E. Marban, R.L. Winslow, and B. O'Rourke An integrated model of cardiac mitochondrial energy metabolism and calcium dynamics Biophys J 84 2003 2734 2755
-
(2003)
Biophys J
, vol.84
, pp. 2734-2755
-
-
Cortassa, S.1
Aon, M.A.2
Marban, E.3
Winslow, R.L.4
O'Rourke, B.5
-
25
-
-
4544288672
-
Reconstruction and functional characterization of the human mitochondrial metabolic network based on proteomic and biochemical data
-
T.D. Vo, H.J. Greenberg, and B.O. Palsson Reconstruction and functional characterization of the human mitochondrial metabolic network based on proteomic and biochemical data J Biol Chem 279 2004 39532 39540
-
(2004)
J Biol Chem
, vol.279
, pp. 39532-39540
-
-
Vo, T.D.1
Greenberg, H.J.2
Palsson, B.O.3
-
26
-
-
1042302103
-
Early prediction of drug metabolism and toxicity: systems biology approach and modeling
-
A. Bugrim, T. Nikolskaya, and Y. Nikolsky Early prediction of drug metabolism and toxicity: systems biology approach and modeling Drug Discov Today 9 2004 127 135
-
(2004)
Drug Discov Today
, vol.9
, pp. 127-135
-
-
Bugrim, A.1
Nikolskaya, T.2
Nikolsky, Y.3
-
27
-
-
0027475656
-
Prostacyclin agonists reduce early atherosclerosis in hyperlipidemic hamsters. Octimibate and BMY 42393 suppress monocyte chemotaxis, macrophage cholesteryl ester accumulation, scavenger receptor activity, and tumor necrosis factor production
-
M.C. Kowala, C.E. Mazzucco, K.S. Hartl, S.M. Seiler, G.A. Warr, S. Abid, and R.I. Grove Prostacyclin agonists reduce early atherosclerosis in hyperlipidemic hamsters. Octimibate and BMY 42393 suppress monocyte chemotaxis, macrophage cholesteryl ester accumulation, scavenger receptor activity, and tumor necrosis factor production Arterioscler Thromb 13 1993 435 444
-
(1993)
Arterioscler Thromb
, vol.13
, pp. 435-444
-
-
Kowala, M.C.1
Mazzucco, C.E.2
Hartl, K.S.3
Seiler, S.M.4
Warr, G.A.5
Abid, S.6
Grove, R.I.7
-
28
-
-
0017094798
-
An enzyme isolated from arteries transforms prostaglandin endoperoxides to an unstable substance that inhibits platelet aggregation
-
S. Moncada, R. Gryglewski, S. Bunting, and J.R. Vane An enzyme isolated from arteries transforms prostaglandin endoperoxides to an unstable substance that inhibits platelet aggregation Nature 263 1976 663 665
-
(1976)
Nature
, vol.263
, pp. 663-665
-
-
Moncada, S.1
Gryglewski, R.2
Bunting, S.3
Vane, J.R.4
-
29
-
-
0028268947
-
Endogenous nitric oxide enhances prostaglandin production in a model of renal inflammation
-
D. Salvemini, K. Seibert, J.L. Masferrer, T.P. Misko, M.G. Currie, and P. Needleman Endogenous nitric oxide enhances prostaglandin production in a model of renal inflammation J Clin Invest 93 1994 1940 1947
-
(1994)
J Clin Invest
, vol.93
, pp. 1940-1947
-
-
Salvemini, D.1
Seibert, K.2
Masferrer, J.L.3
Misko, T.P.4
Currie, M.G.5
Needleman, P.6
-
30
-
-
0015889354
-
On the organization and mechanism of prostaglandin synthetase
-
P. Wlodawer, and B. Samuelsson On the organization and mechanism of prostaglandin synthetase J Biol Chem 248 1973 5673 5678
-
(1973)
J Biol Chem
, vol.248
, pp. 5673-5678
-
-
Wlodawer, P.1
Samuelsson, B.2
-
31
-
-
0031300886
-
Organizing and computing metabolic pathway data in terms of binary relations
-
S. Goto, H. Bono, H. Ogata, W. Fujibuchi, T. Nishioka, K. Sato, and M. Kanehisa Organizing and computing metabolic pathway data in terms of binary relations Pac Symp Biocomput 1997 175 186
-
(1997)
Pac Symp Biocomput
, pp. 175-186
-
-
Goto, S.1
Bono, H.2
Ogata, H.3
Fujibuchi, W.4
Nishioka, T.5
Sato, K.6
Kanehisa, M.7
-
32
-
-
1242298712
-
Modeling approaches to type 2 diabetes
-
A.R. Kansal Modeling approaches to type 2 diabetes Diabetes Technol Ther 6 2004 39 47
-
(2004)
Diabetes Technol Ther
, vol.6
, pp. 39-47
-
-
Kansal, A.R.1
-
33
-
-
7644241654
-
Metabolic syndrome and robustness tradeoffs
-
H. Kitano, K. Oda, T. Kimura, Y. Matsuoka, M. Csete, J. Doyle, and M. Muramatsu Metabolic syndrome and robustness tradeoffs Diabetes 53 Suppl 3 2004 S6 S15 This paper is of particular interest because the authors discuss a very novel approach to treat diabetes, an age-old disorder. This model spans multiple cell types and signaling pathways and shows that it might be better to target properties of a system (robustness) rather than single molecules. This is an interesting perspective that shows the power and relevance of systems modeling in therapeutics, and can be extended to other robust systemic diseases such as cancer and AIDS.
-
(2004)
Diabetes
, vol.53
, Issue.SUPPL. 3
-
-
Kitano, H.1
Oda, K.2
Kimura, T.3
Matsuoka, Y.4
Csete, M.5
Doyle, J.6
Muramatsu, M.7
-
34
-
-
0037107986
-
Small- and large-scale biosimulation applied to drug discovery and development
-
C.J. Musante, A.K. Lewis, and K. Hall Small- and large-scale biosimulation applied to drug discovery and development Drug Discov Today 7 2002 S192 S196
-
(2002)
Drug Discov Today
, vol.7
-
-
Musante, C.J.1
Lewis, A.K.2
Hall, K.3
-
35
-
-
6644229440
-
Effects of an interleukin-5 blocking monoclonal antibody on eosinophils, airway hyper-responsiveness, and the late asthmatic response
-
M.J. Leckie, A. ten Brinke, J. Khan, Z. Diamant, B.J. O'Connor, C.M. Walls, A.K. Mathur, H.C. Cowley, K.F. Chung, and R. Djukanovic Effects of an interleukin-5 blocking monoclonal antibody on eosinophils, airway hyper-responsiveness, and the late asthmatic response Lancet 356 2000 2144 2148
-
(2000)
Lancet
, vol.356
, pp. 2144-2148
-
-
Leckie, M.J.1
Ten Brinke, A.2
Khan, J.3
Diamant, Z.4
O'Connor, B.J.5
Walls, C.M.6
Mathur, A.K.7
Cowley, H.C.8
Chung, K.F.9
Djukanovic, R.10
-
36
-
-
14844302652
-
Using models of the myocyte for functional interpretation of cardiac proteomic data
-
R.L. Winslow, S. Cortassa, and J.L. Greenstein Using models of the myocyte for functional interpretation of cardiac proteomic data J Physiol 563 2005 73 81
-
(2005)
J Physiol
, vol.563
, pp. 73-81
-
-
Winslow, R.L.1
Cortassa, S.2
Greenstein, J.L.3
-
37
-
-
3042716105
-
The computational integrated myocyte: a view into the virtual heart
-
J.B. Bassingthwaighte, and K.C. Vinnakota The computational integrated myocyte: a view into the virtual heart Ann N Y Acad Sci 1015 2004 391 404
-
(2004)
Ann N Y Acad Sci
, vol.1015
, pp. 391-404
-
-
Bassingthwaighte, J.B.1
Vinnakota, K.C.2
-
38
-
-
10944234639
-
Integration from proteins to organs: the IUPS Physiome Project
-
P. Hunter, N. Smith, J. Fernandez, and M. Tawhai Integration from proteins to organs: the IUPS Physiome Project Mech Ageing Dev 126 2005 187 192
-
(2005)
Mech Ageing Dev
, vol.126
, pp. 187-192
-
-
Hunter, P.1
Smith, N.2
Fernandez, J.3
Tawhai, M.4
-
39
-
-
0036051992
-
High-throughput crystallography for lead discovery in drug design
-
T.L. Blundell, H. Jhoti, and C. Abell High-throughput crystallography for lead discovery in drug design Nat Rev Drug Discov 1 2002 45 54
-
(2002)
Nat Rev Drug Discov
, vol.1
, pp. 45-54
-
-
Blundell, T.L.1
Jhoti, H.2
Abell, C.3
-
40
-
-
0033987746
-
Lessons learned from the development of an abl tyrosine kinase inhibitor for chronic myelogenous leukemia
-
B.J. Druker, and N.B. Lydon Lessons learned from the development of an abl tyrosine kinase inhibitor for chronic myelogenous leukemia J Clin Invest 105 2000 3 7
-
(2000)
J Clin Invest
, vol.105
, pp. 3-7
-
-
Druker, B.J.1
Lydon, N.B.2
-
41
-
-
0037441560
-
Fulfilling the promise: drug discovery in the post-genomic era
-
S.K. Chanda, and J.S. Caldwell Fulfilling the promise: drug discovery in the post-genomic era Drug Discov Today 8 2003 168 174
-
(2003)
Drug Discov Today
, vol.8
, pp. 168-174
-
-
Chanda, S.K.1
Caldwell, J.S.2
-
42
-
-
8844232706
-
Functional genomics to new drug targets
-
R. Kramer, and D. Cohen Functional genomics to new drug targets Nat Rev Drug Discov 3 2004 965 972
-
(2004)
Nat Rev Drug Discov
, vol.3
, pp. 965-972
-
-
Kramer, R.1
Cohen, D.2
-
43
-
-
2442636351
-
Computational analysis of Plasmodium falciparum metabolism: organizing genomic information to facilitate drug discovery
-
I. Yeh, T. Hanekamp, S. Tsoka, P.D. Karp, and R.B. Altman Computational analysis of Plasmodium falciparum metabolism: organizing genomic information to facilitate drug discovery Genome Res 14 2004 917 924
-
(2004)
Genome Res
, vol.14
, pp. 917-924
-
-
Yeh, I.1
Hanekamp, T.2
Tsoka, S.3
Karp, P.D.4
Altman, R.B.5
-
44
-
-
0036195958
-
Metabolic control analysis in drug discovery and disease
-
M. Cascante, L.G. Boros, B. Comin-Anduix, P. de Atauri, J.J. Centelles, and P.W. Lee Metabolic control analysis in drug discovery and disease Nat Biotechnol 20 2002 243 249
-
(2002)
Nat Biotechnol
, vol.20
, pp. 243-249
-
-
Cascante, M.1
Boros, L.G.2
Comin-Anduix, B.3
De Atauri, P.4
Centelles, J.J.5
Lee, P.W.6
-
45
-
-
0036371443
-
Modelling viral and immune system dynamics
-
A.S. Perelson Modelling viral and immune system dynamics Nat Rev Immunol 2 2002 28 36
-
(2002)
Nat Rev Immunol
, vol.2
, pp. 28-36
-
-
Perelson, A.S.1
-
46
-
-
0037364162
-
ADMET in silico modelling: towards prediction paradise?
-
H. van de Waterbeemd, and E. Gifford ADMET in silico modelling: towards prediction paradise? Nat Rev Drug Discov 2 2003 192 204
-
(2003)
Nat Rev Drug Discov
, vol.2
, pp. 192-204
-
-
Van De Waterbeemd, H.1
Gifford, E.2
-
47
-
-
5044232226
-
Can complexity be commercialized?
-
G.S. Mack Can complexity be commercialized? Nat Biotechnol 22 2004 1223 1229
-
(2004)
Nat Biotechnol
, vol.22
, pp. 1223-1229
-
-
Mack, G.S.1
-
48
-
-
0037342537
-
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models
-
M. Hucka, A. Finney, H.M. Sauro, H. Bolouri, J.C. Doyle, H. Kitano, A.P. Arkin, B.J. Bornstein, D. Bray, and A. Cornish-Bowden The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models Bioinformatics 19 2003 524 531
-
(2003)
Bioinformatics
, vol.19
, pp. 524-531
-
-
Hucka, M.1
Finney, A.2
Sauro, H.M.3
Bolouri, H.4
Doyle, J.C.5
Kitano, H.6
Arkin, A.P.7
Bornstein, B.J.8
Bray, D.9
Cornish-Bowden, A.10
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