-
1
-
-
2942514591
-
Biochemical Network Stochastic Simulator (BioNetS): software for stochastic modeling of biochemical networks
-
Adalsteinsson D, McMillen D, Elston TC. 2004. Biochemical Network Stochastic Simulator (BioNetS): software for stochastic modeling of biochemical networks. BMC Bioinformatics, 5: 1-24 (http://www.biomedcentral.com/1471-2105/5124)
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 1-24
-
-
Adalsteinsson, D.1
McMillen, D.2
Elston, T.C.3
-
2
-
-
58149472976
-
Metabolomics
-
Marcel-Dekker, NY, USA
-
Arnold J, Schuttler H-B, Logan D, et al. 2004. Metabolomics. In: Handbook of Industrial Mycology. 597-633, Marcel-Dekker, NY, USA
-
(2004)
In: Handbook of Industrial Mycology
, pp. 597-633
-
-
Arnold, J.1
Schuttler, H.-B.2
Logan, D.3
-
3
-
-
58149464983
-
KINSOLVER: A simulator for computing large ensembles of biochemical and gene regulatory networks
-
Aleman-Meza B, Yu YH, Schuttler HB, et al. 2009. KINSOLVER: A simulator for computing large ensembles of biochemical and gene regulatory networks. Computers and Mathematics with Applications, 57(3): 420- 435
-
(2009)
Computers and Mathematics with Applications
, vol.57
, Issue.3
, pp. 420- 435
-
-
Aleman-Meza, B.1
Yu, Y.H.2
Schuttler, H.B.3
-
4
-
-
0020740241
-
Analysis of numerical methods for computer simulation of kinetic processes: development of KINSIM-a flexible, portable system
-
Barshop BA, Wrenn RF, Frieden C.1983. Analysis of numerical methods for computer simulation of kinetic processes: development of KINSIM-a flexible, portable system. Analytical Biochemistry, 130(1): 134-145
-
(1983)
Analytical Biochemistry
, vol.130
, Issue.1
, pp. 134-145
-
-
Barshop, B.A.1
Wrenn, R.F.2
Frieden, C.3
-
5
-
-
0037168597
-
An ensemble method for identifying regulatory circuits with special reference to the qa gene cluster of Neurospora crassa
-
Battogtokh D, Asch DK, Case ME, et al. 2002. An ensemble method for identifying regulatory circuits with special reference to the qa gene cluster of Neurospora crassa. Proceedings of the National Academy of Sciences of the USA, 99(26): 16904-16909
-
(2002)
Proceedings of the National Academy of Sciences of the USA
, vol.99
, Issue.26
, pp. 16904-16909
-
-
Battogtokh, D.1
Asch, D.K.2
Case, M.E.3
-
7
-
-
0035003178
-
A graph layout algorithm for drawing metabolic pathways
-
Becker MY, Rojas I. 2001. A graph layout algorithm for drawing metabolic pathways. Bioinformatics, 17(5): 461-467
-
(2001)
Bioinformatics
, vol.17
, Issue.5
, pp. 461-467
-
-
Becker, M.Y.1
Rojas, I.2
-
8
-
-
0033555859
-
Emergent properties of networks of biological signaling pathways
-
Bhalla US, Iyengar R. 1999. Emergent properties of networks of biological signaling pathways. Science, 283(5400): 381-387
-
(1999)
Science
, vol.283
, Issue.5400
, pp. 381-387
-
-
Bhalla, U.S.1
Iyengar, R.2
-
9
-
-
85035221677
-
Statistical mechanical approaches to models with many poorly known parameters
-
Brown KS, Sethna JP. 2003. Statistical mechanical approaches to models with many poorly known parameters. Physics Review E, 68(2).
-
(2003)
Physics Review E
, vol.68
, Issue.2
-
-
Brown, K.S.1
Sethna, J.P.2
-
11
-
-
0026023024
-
MetaModel: a program for modelling and control analysis of metabolic pathways on the IBM PC and compatibles
-
Cornish-Bowden A, Hofmeyr JH. 1991. MetaModel: a program for modelling and control analysis of metabolic pathways on the IBM PC and compatibles. Comput Appl Biosci, 7(1): 89-93
-
(1991)
Comput Appl Biosci
, vol.7
, Issue.1
, pp. 89-93
-
-
Cornish-Bowden, A.1
Hofmeyr, J.H.2
-
12
-
-
0030669030
-
Exploring the metabolic and genetic control of gene expression on a genomic scale
-
DeRisi JL, Iyer VR, Brown PO. 1997. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science, 278(5338): 680-686
-
(1997)
Science
, vol.278
, Issue.5338
, pp. 680-686
-
-
DeRisi, J.L.1
Iyer, V.R.2
Brown, P.O.3
-
13
-
-
51849120153
-
Systems biology of the clock in Neurospora crassa
-
Dong W, Tang X, Yu Y, et al. 2008. Systems biology of the clock in Neurospora crassa. PloS One, 3(8): e3105
-
(2008)
PloS One
, vol.3
, Issue.8
-
-
Dong, W.1
Tang, X.2
Yu, Y.3
-
14
-
-
0029073341
-
MIST: a user-friendly metabolic simulator
-
Ehlde M, Zacchi G.1995. MIST: a user-friendly metabolic simulator. Comput Appl Biosci, 11(2): 201-207
-
(1995)
Comput Appl Biosci
, vol.11
, Issue.2
, pp. 201-207
-
-
Ehlde, M.1
Zacchi, G.2
-
15
-
-
0026802334
-
Metabolic control analysis: a survey of its theoretical and experimental development
-
Fell D. 1992. Metabolic control analysis: a survey of its theoretical and experimental development. Biochemistry Journal, 266: 313-330
-
(1992)
Biochemistry Journal
, vol.266
, pp. 313-330
-
-
Fell, D.1
-
16
-
-
0033707946
-
Using Bayesian networks to analyze expression data
-
Friedman N, Linial M, Nachman I, et al. 2000. Using Bayesian networks to analyze expression data. Journal of Computational Biology, 7(3-4): 601-620
-
(2000)
Journal of Computational Biology
, vol.7
, Issue.3-4
, pp. 601-620
-
-
Friedman, N.1
Linial, M.2
Nachman, I.3
-
17
-
-
47949099328
-
CellDesigner 3.5: A versatile modeling tool for biochemical networks
-
Funahashi A, Matsuoka Y, Jouraku A, et al. 2008. CellDesigner 3.5: A versatile modeling tool for biochemical networks. IEEE P, 96(8): 1254-1265
-
(2008)
IEEE P
, vol.96
, Issue.8
, pp. 1254-1265
-
-
Funahashi, A.1
Matsuoka, Y.2
Jouraku, A.3
-
18
-
-
0038048325
-
Collins JJ: Inferring genetic networks and identifying compound mode of action via expression profiling
-
Gardner TS, di Bernardo D, Lorenz D, et al. 2003. Collins JJ: Inferring genetic networks and identifying compound mode of action via expression profiling. Science, 301(5629): 102-105
-
(2003)
Science
, vol.301
, Issue.5629
, pp. 102-105
-
-
Gardner, T.S.1
di Bernardo, D.2
Lorenz, D.3
-
19
-
-
0032825010
-
Mathematical simulation and analysis of cellular metabolism and regulation
-
Goryanin I, Hodgman TC, Selkov E. 1999. Mathematical simulation and analysis of cellular metabolism and regulation. Bioinformatics, 15(9): 749-758
-
(1999)
Bioinformatics
, vol.15
, Issue.9
, pp. 749-758
-
-
Goryanin, I.1
Hodgman, T.C.2
Selkov, E.3
-
20
-
-
33845368513
-
COPASI: a complex pathway simulator
-
Hoops S, Sahle S, Gauges R, et al. 2006. COPASI: a complex pathway simulator. Bioinformatics, 22(24): 3067-3074
-
(2006)
Bioinformatics
, vol.22
, Issue.24
, pp. 3067-3074
-
-
Hoops, S.1
Sahle, S.2
Gauges, R.3
-
21
-
-
0032809387
-
Gene expression profiling, genetic networks, and cellular states: an integrating conectp for tumorigenesis and drug discovery
-
Huang S. 1999. Gene expression profiling, genetic networks, and cellular states: an integrating conectp for tumorigenesis and drug discovery. Journal of Mol Med-Jmm, 77, 469-480
-
(1999)
Journal of Mol Med-Jmm
, vol.77
, pp. 469-480
-
-
Huang, S.1
-
22
-
-
0037342537
-
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models
-
Hucka M, Finney A, Sauro HM, et al. 2003. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics, 19(4): 524-531
-
(2003)
Bioinformatics
, vol.19
, Issue.4
, pp. 524-531
-
-
Hucka, M.1
Finney, A.2
Sauro, H.M.3
-
23
-
-
84877740253
-
The role of protein interaction domains in the human cancer network
-
Ibrahim SS, Eldeeb MAR, Rady MAH, et al. 2011. The role of protein interaction domains in the human cancer network. Network Biology, 1(1): 59-71
-
(2011)
Network Biology
, vol.1
, Issue.1
, pp. 59-71
-
-
Ibrahim, S.S.1
Eldeeb, M.A.R.2
Rady, M.A.H.3
-
24
-
-
0035805255
-
Integrated genomic and proteomic analyses of a systematically perturbed metabolic network
-
Ideker T, Thorsson V, Ranish JA, et al. 2001. Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science, 292(5518): 929-934
-
(2001)
Science
, vol.292
, Issue.5518
, pp. 929-934
-
-
Ideker, T.1
Thorsson, V.2
Ranish, J.A.3
-
25
-
-
4544227574
-
Toward large-scale modeling of the microbial cell for computer simulation
-
Ishii N, Robert M, Nakayama Y, et al. 2004. Toward large-scale modeling of the microbial cell for computer simulation. Journal of Biotechnology, 113(1-3): 281-294
-
(2004)
Journal of Biotechnology
, vol.113
, Issue.1-3
, pp. 281-294
-
-
Ishii, N.1
Robert, M.2
Nakayama, Y.3
-
26
-
-
70449504296
-
A computational framework for qualitative simulation of nonlinear dynamical models of gene-regulatory networks
-
Ironi L, Panzeri L. 2009. A computational framework for qualitative simulation of nonlinear dynamical models of gene-regulatory networks. BMC Bioinformatics, 10(Suppl): 12: S14
-
(2009)
BMC Bioinformatics
, vol.10
, Issue.12
, pp. S14
-
-
Ironi, L.1
Panzeri, L.2
-
27
-
-
79960942688
-
Mathematical modeling deciphering balance between cell survival and cell death using insulin
-
Jain S, Bhooshan SV, Naik PK. 2011. Mathematical modeling deciphering balance between cell survival and cell death using insulin. Network Biology, 1(1): 46-58
-
(2011)
Network Biology
, vol.1
, Issue.1
, pp. 46-58
-
-
Jain, S.1
Bhooshan, S.V.2
Naik, P.K.3
-
28
-
-
0037316342
-
FluxAnalyzer: exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps
-
Klamt S, Stelling J, Ginkel M, et al. 2003. FluxAnalyzer: exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps. Bioinformatics, 19(2): 261-269
-
(2003)
Bioinformatics
, vol.19
, Issue.2
, pp. 261-269
-
-
Klamt, S.1
Stelling, J.2
Ginkel, M.3
-
29
-
-
67650911355
-
Estimating parameters for generalized mass action models with connectivity information
-
Ko CL, Voit EO, Wang FS. 2009. Estimating parameters for generalized mass action models with connectivity information. BMC Bioinformatics, 10: 140
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 140
-
-
Ko, C.L.1
Voit, E.O.2
Wang, F.S.3
-
30
-
-
0036462215
-
IntelliGEN: A distributed workflow system for discovering proteinprotein interactions
-
Kochut K, Arnold J, Sheth A, et al. 2003. IntelliGEN: A distributed workflow system for discovering proteinprotein interactions. Distributed and Parallel Databases, 13(1): 43-72
-
(2003)
Distributed and Parallel Databases
, vol.13
, Issue.1
, pp. 43-72
-
-
Kochut, K.1
Arnold, J.2
Sheth, A.3
-
32
-
-
38349133639
-
Automated manipulation of systems biology models using libSBML within Taverna workflows
-
Li P, Oinn T, Soiland S, et al. 2008. Automated manipulation of systems biology models using libSBML within Taverna workflows. Bioinformatics, 24(2): 287-289
-
(2008)
Bioinformatics
, vol.24
, Issue.2
, pp. 287-289
-
-
Li, P.1
Oinn, T.2
Soiland, S.3
-
33
-
-
50549103571
-
Computational design of synthetic gene circuits with composable parts
-
Marchisio MA, Stelling J. 2008. Computational design of synthetic gene circuits with composable parts. Bioinformatics, 24(17): 1903-1910
-
(2008)
Bioinformatics
, vol.24
, Issue.17
, pp. 1903-1910
-
-
Marchisio, M.A.1
Stelling, J.2
-
34
-
-
84867371815
-
Escherichia coli transcriptional regulatory network
-
Martinez-Antonio A. 2011. Escherichia coli transcriptional regulatory network. Network Biology, 1(1): 21-33
-
(2011)
Network Biology
, vol.1
, Issue.1
, pp. 21-33
-
-
Martinez-Antonio, A.1
-
35
-
-
0027370376
-
GEPASI: a software package for modelling the dynamics, steady states and control of biochemical and other systems
-
Mendes P. 1993. GEPASI: a software package for modelling the dynamics, steady states and control of biochemical and other systems. Comput Appl Biosci, 9(5): 563-571
-
(1993)
Comput Appl Biosci
, vol.9
, Issue.5
, pp. 563-571
-
-
Mendes, P.1
-
36
-
-
0030921160
-
Biochemistry by numbers: simulation of biochemical pathways with Gepasi 3
-
Mendes P. 1997. Biochemistry by numbers: simulation of biochemical pathways with Gepasi 3. Trends in Biochemical Sciences, 22(9): 361-363
-
(1997)
Trends in Biochemical Sciences
, vol.22
, Issue.9
, pp. 361-363
-
-
Mendes, P.1
-
37
-
-
61449140264
-
PROMOT: modular modeling for systems biology
-
Mirschel S, Steinmetz K, Rempel M, et al. 2009. PROMOT: modular modeling for systems biology. Bioinformatics, 25(5): 687-689
-
(2009)
Bioinformatics
, vol.25
, Issue.5
, pp. 687-689
-
-
Mirschel, S.1
Steinmetz, K.2
Rempel, M.3
-
39
-
-
84865863301
-
The polarity sub-network in the yeast network of protein-protein interactions
-
Paris L, Bazzoni G. 2011.The polarity sub-network in the yeast network of protein-protein interactions. Network Biology, 1(3-4): 149-158
-
(2011)
Network Biology
, vol.1
, Issue.3-4
, pp. 149-158
-
-
Paris, L.1
Bazzoni, G.2
-
41
-
-
0027178664
-
SCAMP: a general-purpose simulator and metabolic control analysis program
-
Sauro HM. 1993. SCAMP: a general-purpose simulator and metabolic control analysis program. Comput Appl Biosci, 9(4): 441-450
-
(1993)
Comput Appl Biosci
, vol.9
, Issue.4
, pp. 441-450
-
-
Sauro, H.M.1
-
42
-
-
0347511691
-
Next generation simulation tools: the Systems Biology Workbench and BioSPICE integration
-
Sauro HM, Hucka M, Finney A, et al. 2003. Next generation simulation tools: the Systems Biology Workbench and BioSPICE integration. Omics, 7(4): 355-372
-
(2003)
Omics
, vol.7
, Issue.4
, pp. 355-372
-
-
Sauro, H.M.1
Hucka, M.2
Finney, A.3
-
44
-
-
71749113685
-
TIde: a software for the systematic scanning of drug targets in kinetic network models
-
Schulz M, Bakker B, Klipp E. 2009. TIde: a software for the systematic scanning of drug targets in kinetic network models. BMC Bioinformatics, 10: 344
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 344
-
-
Schulz, M.1
Bakker, B.2
Klipp, E.3
-
45
-
-
0036184629
-
Probabilistic Boolean Networks: a rule-based uncertainty model for gene regulatory networks
-
Shmulevich I, Dougherty ER, Kim S, et al. 2002. Probabilistic Boolean Networks: a rule-based uncertainty model for gene regulatory networks. Bioinformatics, 18(2): 261-274
-
(2002)
Bioinformatics
, vol.18
, Issue.2
, pp. 261-274
-
-
Shmulevich, I.1
Dougherty, E.R.2
Kim, S.3
-
48
-
-
84995515754
-
Immunoregulatory network and cancer-associated genes: molecular links and relevance to aging
-
Tacutu R, et al. 2011.Immunoregulatory network and cancer-associated genes: molecular links and relevance to aging. Network Biology, 1(2): 112-120
-
(2011)
Network Biology
, vol.1
, Issue.2
, pp. 112-120
-
-
Tacutu, R.1
-
49
-
-
79958786873
-
Systems Biology of the qa Gene Cluster in Neurospora crassa
-
Tang XJ, Dong WB, Griffith J, et al. 2011. Systems Biology of the qa Gene Cluster in Neurospora crassa. PloS One, 6(6): e20671
-
(2011)
PloS One
, vol.6
, Issue.6
-
-
Tang, X.J.1
Dong, W.B.2
Griffith, J.3
-
50
-
-
0033031386
-
E-CELL: software environment for whole-cell simulation
-
Tomita M, Hashimoto K, Takahashi K, et al. 1999. E-CELL: software environment for whole-cell simulation. Bioinformatics, 15(1): 72-84
-
(1999)
Bioinformatics
, vol.15
, Issue.1
, pp. 72-84
-
-
Tomita, M.1
Hashimoto, K.2
Takahashi, K.3
-
51
-
-
18844475514
-
The E-CELL project: towards integrative simulation of cellular processes
-
Tomita M, Hashimoto K, Takahashi K, et al. 2000. The E-CELL project: towards integrative simulation of cellular processes. New Generation Computing, 18: 1-12
-
(2000)
New Generation Computing
, vol.18
, pp. 1-12
-
-
Tomita, M.1
Hashimoto, K.2
Takahashi, K.3
-
52
-
-
58149142997
-
Approximate Bayesian computation scheme for parameter inference and model selection in dynamical systems
-
Toni T, Welch D, Strelkowa N, et al. 2009. Approximate Bayesian computation scheme for parameter inference and model selection in dynamical systems. J R Soc Interface 6(31): 187-202
-
(2009)
J R Soc Interface
, vol.6
, Issue.31
, pp. 187-202
-
-
Toni, T.1
Welch, D.2
Strelkowa, N.3
-
54
-
-
41449088987
-
beta(2)-adrenergic receptor signaling and desensitization elucidated by quantitative modeling of real time cAMP dynamics
-
Violin JD, DiPilato LM, Yildirim N, et al. 2008. beta(2)-adrenergic receptor signaling and desensitization elucidated by quantitative modeling of real time cAMP dynamics. Journal of Biological Chemistry, 283(5): 2949-2961
-
(2008)
Journal of Biological Chemistry
, vol.283
, Issue.5
, pp. 2949-2961
-
-
Violin, J.D.1
DiPilato, L.M.2
Yildirim, N.3
-
55
-
-
0028085745
-
Transient state kinetics tutorial using the kinetics simulation program, KINSIM
-
Wachsstock DH, Pollard TD. 1994. Transient state kinetics tutorial using the kinetics simulation program, KINSIM. Biophysical Journal, 67(3): 1260-1273
-
(1994)
Biophysical Journal
, vol.67
, Issue.3
, pp. 1260-1273
-
-
Wachsstock, D.H.1
Pollard, T.D.2
-
56
-
-
0036138322
-
How to reconstruct a large genetic network from n gene perturbations in fewer than n(2) easy steps
-
Wagner A. 2001. How to reconstruct a large genetic network from n gene perturbations in fewer than n(2) easy steps. Bioinformatics, 17(12): 1183-1197
-
(2001)
Bioinformatics
, vol.17
, Issue.12
, pp. 1183-1197
-
-
Wagner, A.1
-
58
-
-
45449110775
-
SYCAMORE - a systems biology computational analysis and modeling research environment
-
Weidemann A, Richter S, Stein M, et al. 2008. SYCAMORE - a systems biology computational analysis and modeling research environment. Bioinformatics, 24(12): 1463-1464
-
(2008)
Bioinformatics
, vol.24
, Issue.12
, pp. 1463-1464
-
-
Weidemann, A.1
Richter, S.2
Stein, M.3
-
59
-
-
1642403354
-
Identification of genetic networks
-
Xiong MM, Li J, Fang XZ. 2004. Identification of genetic networks. Genetics, 166(2): 1037-1052
-
(2004)
Genetics
, vol.166
, Issue.2
, pp. 1037-1052
-
-
Xiong, M.M.1
Li, J.2
Fang, X.Z.3
-
60
-
-
33847335120
-
A genetic network for the clock of Neurospora crassa
-
Yu Y, Dong W, Altimus C, et al. 2007. A genetic network for the clock of Neurospora crassa. Proceedings of the National Academy of Sciences of the USA, 104(8): 2809-2814
-
(2007)
Proceedings of the National Academy of Sciences of the USA
, vol.104
, Issue.8
, pp. 2809-2814
-
-
Yu, Y.1
Dong, W.2
Altimus, C.3
-
61
-
-
33847719830
-
Computer inference of network of ecological interactions from sampling data
-
Zhang WJ. 2007. Computer inference of network of ecological interactions from sampling data. Environmental Monitoring and Assessment, 124: 253-261
-
(2007)
Environmental Monitoring and Assessment
, vol.124
, pp. 253-261
-
-
Zhang, W.J.1
-
62
-
-
84895301995
-
A Java software for drawing graphs
-
Zhang WJ. 2012. A Java software for drawing graphs. Network Biology, 2(1): 38-44
-
(2012)
Network Biology
, vol.2
, Issue.1
, pp. 38-44
-
-
Zhang, W.J.1
|