-
1
-
-
0037079054
-
Computational systems biology
-
Kitano H. Computational systems biology. Nature 2002;420:206-10.
-
(2002)
Nature
, vol.420
, pp. 206-210
-
-
Kitano, H.1
-
2
-
-
3042678959
-
Computational challenges of systems biology
-
Finkelstein A, Hetherington J, Li L, et al. Computational challenges of systems biology. Computer 2004;37:26-33.
-
(2004)
Computer
, vol.37
, pp. 26-33
-
-
Finkelstein, A.1
Hetherington, J.2
Li, L.3
-
3
-
-
33845500836
-
-
Russel J (ed). Framingham MA: Bio-IT World, (20 April 2006, date last accessed)
-
Russel J (ed). Bio-IT World Briefing on: System Biology. http://cms.bioitworld.com/whitepapers#briefings.Framingham MA: Bio-IT World, 2005 (20 April 2006, date last accessed).
-
(2005)
Bio-IT World Briefing On: System Biology
-
-
-
4
-
-
33645279713
-
-
Emmott S (ed). Cambridge UK: Microsoft Research (20 April 2006, date last accessed)
-
Emmott S (ed). Towards 2020 Science. Cambridge UK: Microsoft Research, 2006. http://research.microsoft.com/towards2020science (20 April 2006, date last accessed).
-
(2006)
Towards 2020 Science
-
-
-
5
-
-
29244482315
-
Barriers to progress in systems biology
-
Cassman M. Barriers to progress in systems biology. Nature 2005;438:1079.
-
(2005)
Nature
, vol.438
, pp. 1079
-
-
Cassman, M.1
-
6
-
-
33845476358
-
TeraGrid project
-
(26 August date last accessed)
-
TeraGrid project. http://www.teragrid.org (26 August 2006, date last accessed)
-
(2006)
-
-
-
8
-
-
0014800108
-
Distinguishing homologous from analogous proteins
-
Fitch WM. Distinguishing homologous from analogous proteins. Syst Zool 1970;19:99-113.
-
(1970)
Syst Zool
, vol.19
, pp. 99-113
-
-
Fitch, W.M.1
-
9
-
-
0029789824
-
A minimal gene set for cellular life derived by comparison of complete bacterial genomes
-
Mushegian AR, Koonin EV. A minimal gene set for cellular life derived by comparison of complete bacterial genomes. Proc Natl Acad Sci USA 1996;93:10268-73.
-
(1996)
Proc Natl Acad Sci USA
, vol.93
, pp. 10268-10273
-
-
Mushegian, A.R.1
Koonin, E.V.2
-
11
-
-
2942513067
-
A hybrid clustering approach to recognition of protein families in 114 microbial genomes
-
Harlow TJ, Gogarten JP, Ragan MA. A hybrid clustering approach to recognition of protein families in 114 microbial genomes. BMC Bioinform 2004;5:45.
-
(2004)
BMC Bioinform
, vol.5
, pp. 45
-
-
Harlow, T.J.1
Gogarten, J.P.2
Ragan, M.A.3
-
12
-
-
33845508927
-
-
(20 April date last accessed)
-
van Dongen S. The MCL FAQ. http://micans.org/mcl/man/mclfaq.html (20 April 2006, date last accessed).
-
(2006)
The MCL FAQ
-
-
van Dongen, S.1
-
13
-
-
19544381576
-
A word-oriented approach to alignment validation
-
Beiko RG, Chan CX, Ragan MA. A word-oriented approach to alignment validation. Bioinformatics 2005;21:2230-9.
-
(2005)
Bioinformatics
, vol.21
, pp. 2230-2239
-
-
Beiko, R.G.1
Chan, C.X.2
Ragan, M.A.3
-
14
-
-
0035861456
-
Bayesian inference of phylogeny and its impact on evolutionary biology
-
Huelsenbeck JP, Ronquist F, Nielsen R, et al. Bayesian inference of phylogeny and its impact on evolutionary biology. Science 2001;294:2310-4.
-
(2001)
Science
, vol.294
, pp. 2310-2314
-
-
Huelsenbeck, J.P.1
Ronquist, F.2
Nielsen, R.3
-
15
-
-
15244352063
-
Bayesian and maximum likelihood phylogenetic analyses of protein sequence data under relative branch-length differences and model violation
-
Mar JC, Harlow TJ, Ragan MA. Bayesian and maximum likelihood phylogenetic analyses of protein sequence data under relative branch-length differences and model violation. BMC Bioinform 2005;5:8.
-
(2005)
BMC Bioinform
, vol.5
, pp. 8
-
-
Mar, J.C.1
Harlow, T.J.2
Ragan, M.A.3
-
16
-
-
0041386108
-
MrBayes 3: Bayesian phylogenetic inference under mixed models
-
Ronquist F, Huelsenbeck JP. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003;19:1572-4.
-
(2003)
Bioinformatics
, vol.19
, pp. 1572-1574
-
-
Ronquist, F.1
Huelsenbeck, J.P.2
-
17
-
-
33845489241
-
Taverna project
-
Taverna 1.3.1. (21 April date last accessed)
-
Taverna project. Taverna 1.3.1. http://taverna.sourceforge.net (21 April 2006, date last accessed).
-
(2006)
-
-
-
18
-
-
2942544409
-
Pegasys: Software for executing and integrating analyses of biological sequences
-
Shah SP, He DYM, Sawkins JN, et al. Pegasys: Software for executing and integrating analyses of biological sequences. BMC Bioinform 2004;5:40.
-
(2004)
BMC Bioinform
, vol.5
, pp. 40
-
-
Shah, S.P.1
He, D.Y.M.2
Sawkins, J.N.3
-
19
-
-
25444447098
-
Workflows in bioinformatics: Meta-analysis and prototype implementation of a workflow generator
-
Garcia A, Thoraval S, Garcia LJ, et al. Workflows in bioinformatics: meta-analysis and prototype implementation of a workflow generator. BMC Bioinform 2005;6:87.
-
(2005)
BMC Bioinform
, vol.6
, pp. 87
-
-
Garcia, A.1
Thoraval, S.2
Garcia, L.J.3
-
20
-
-
33645324703
-
REMORA: A pilot in the ocean of BioMoby web-services
-
Carrere S, Gouzy J. REMORA: A pilot in the ocean of BioMoby web-services. Bioinformatics 2006;22:900-1.
-
(2006)
Bioinformatics
, vol.22
, pp. 900-901
-
-
Carrere, S.1
Gouzy, J.2
-
22
-
-
0035371624
-
Whole-cell simulation: A grand challenge of the 21st century
-
Tomita M. Whole-cell simulation: A grand challenge of the 21st century. Trends Biotechnol 2001;19:205-10.
-
(2001)
Trends Biotechnol
, vol.19
, pp. 205-210
-
-
Tomita, M.1
-
24
-
-
0345863934
-
The CyberCell Database (CCDB): A comprehensive, self-updating, relational database to coordinate and facilitate in silico modelling of Escherichia coli
-
Sundararaj S, Guo A, Habibi-Nazhad B, et al. The CyberCell Database (CCDB): A comprehensive, self-updating, relational database to coordinate and facilitate in silico modelling of Escherichia coli. Nucl Acids Res 2004;32:D293-5.
-
(2004)
Nucl Acids Res
, vol.32
-
-
Sundararaj, S.1
Guo, A.2
Habibi-Nazhad, B.3
-
25
-
-
2642527148
-
Genomic Object Net: II. Modeling biopathways by hybrid functional Petri net with extension
-
Doi A, Nagasaki M, Fujita S, et al. Genomic Object Net: II. Modeling biopathways by hybrid functional Petri net with extension. Appl Bioinform 2004;2:185-8.
-
(2004)
Appl Bioinform
, vol.2
, pp. 185-188
-
-
Doi, A.1
Nagasaki, M.2
Fujita, S.3
-
27
-
-
84947292082
-
-
SDSC TR-1999-2. October (20 April 2006, date last accessed)
-
Moore R. Persistent Archives for Data Collections. SDSC TR-1999-2. October 1999. http://www.sdsc.edu/dice/Pubs/sdsc-tr-1999-2.pdf (20 April 2006, date last accessed).
-
(1999)
Persistent Archives for Data Collections
-
-
Moore, R.1
-
28
-
-
0031879114
-
Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cell
-
Arkin A, Ross J, McAdams HH. Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cell. Genetics 1998;149:1633-48.
-
(1998)
Genetics
, vol.149
, pp. 1633-1648
-
-
Arkin, A.1
Ross, J.2
McAdams, H.H.3
-
29
-
-
0035319006
-
Computational studies of gene regulatory networks: In numero molecular biology
-
Hasty J, McMillen D, Isaacs F, et al. Computational studies of gene regulatory networks: In numero molecular biology. Nat Rev Genet 2001;2:268-79.
-
(2001)
Nat Rev Genet
, vol.2
, pp. 268-279
-
-
Hasty, J.1
McMillen, D.2
Isaacs, F.3
-
30
-
-
19544379881
-
Stochasticity in gene expression: From theories to phenotypes
-
Kærn M, Elston TC, Blake WJ, et al. Stochasticity in gene expression: from theories to phenotypes. Nat Rev Genet 2005;6:451-64.
-
(2005)
Nat Rev Genet
, vol.6
, pp. 451-464
-
-
Kærn, M.1
Elston, T.C.2
Blake, W.J.3
-
31
-
-
0031029852
-
Stochastic mechanisms in gene expression
-
McAdams HH, Arkin A. Stochastic mechanisms in gene expression. Proc Natl Acad Sci USA 1997;94:814-9.
-
(1997)
Proc Natl Acad Sci USA
, vol.94
, pp. 814-819
-
-
McAdams, H.H.1
Arkin, A.2
-
32
-
-
33645429016
-
Exact stochastic simulation of coupled chemical reactions
-
Gillespie DT. Exact stochastic simulation of coupled chemical reactions. J Phys Chem 1977;81:340-61.
-
(1977)
J Phys Chem
, vol.81
, pp. 340-361
-
-
Gillespie, D.T.1
-
33
-
-
0036204115
-
STOCKS: Stochastic kinetic simulations of biochemical systems with Gillespie algorithm
-
Kierzek AM. STOCKS: Stochastic kinetic simulations of biochemical systems with Gillespie algorithm. Bioinformatics 2002;18:470-81.
-
(2002)
Bioinformatics
, vol.18
, pp. 470-481
-
-
Kierzek, A.M.1
-
34
-
-
0022429106
-
The OR control system of bacteriophage lambda: A physical-chemical model for gene regulation
-
Shea MA, Ackers GK. The OR control system of bacteriophage lambda: A physical-chemical model for gene regulation. J Mol Biol 1985;181:211-30.
-
(1985)
J Mol Biol
, vol.181
, pp. 211-230
-
-
Shea, M.A.1
Ackers, G.K.2
-
35
-
-
0035933994
-
Approximate accelerated stochastic simulation of chemically reacting systems
-
Gillespie DT. Approximate accelerated stochastic simulation of chemically reacting systems. J Chem Phys 2001;115:1716-33.
-
(2001)
J Chem Phys
, vol.115
, pp. 1716-1733
-
-
Gillespie, D.T.1
-
36
-
-
3142543968
-
Binomial leap methods for simulating stochastic chemical kinetics
-
Tian T, Burrage K. Binomial leap methods for simulating stochastic chemical kinetics. J Chem Phys 2004;121:10356-64.
-
(2004)
J Chem Phys
, vol.121
, pp. 10356-10364
-
-
Tian, T.1
Burrage, K.2
-
37
-
-
0037109565
-
Approximate simulation of coupled fast and slow reactions for stochastic chemical kinetics
-
Haseltine EL, Rawlings JB. Approximate simulation of coupled fast and slow reactions for stochastic chemical kinetics. J Chem Phys 2002;117:6959-69.
-
(2002)
J Chem Phys
, vol.117
, pp. 6959-6969
-
-
Haseltine, E.L.1
Rawlings, J.B.2
-
38
-
-
18844402156
-
Quasiequilibrium approximation of fast reaction kinetics in stochastic biochemical systems
-
Goutsias J. Quasiequilibrium approximation of fast reaction kinetics in stochastic biochemical systems. J Chem Phys 2005;122:1-15.
-
(2005)
J Chem Phys
, vol.122
, pp. 1-15
-
-
Goutsias, J.1
-
39
-
-
0037444724
-
Stochastic chemical kinetics and the quasi-steady-state assumption: Application to the Gillespie algorithm
-
Rao C, Arkin A. Stochastic chemical kinetics and the quasi-steady-state assumption: Application to the Gillespie algorithm. J Chem Phys 2003;118:4999-5010.
-
(2003)
J Chem Phys
, vol.118
, pp. 4999-5010
-
-
Rao, C.1
Arkin, A.2
-
40
-
-
2442438819
-
A multi-scaled approach for simulating chemical reaction systems
-
Burrage K, Tian T, Burrage P. A multi-scaled approach for simulating chemical reaction systems. Prog Biophys Mol Biol 2004;85:217-34.
-
(2004)
Prog Biophys Mol Biol
, vol.85
, pp. 217-234
-
-
Burrage, K.1
Tian, T.2
Burrage, P.3
-
41
-
-
4344657452
-
A grid implementation of chemical kinetic simulation methods in genetic regulation
-
In: ISBN 0-9579303
-
Burrage K, Burrage P, Jeffrey S, et al. A grid implementation of chemical kinetic simulation methods in genetic regulation. In: Proceedings of APAC03 Conference on Advanced Computing, Grid Applications and e-Research, ISBN 0-9579303, 2003, 1-3.
-
(2003)
Proceedings of APAC03 Conference on Advanced Computing, Grid Applications and E-Research
, pp. 1-3
-
-
Burrage, K.1
Burrage, P.2
Jeffrey, S.3
-
42
-
-
33751347484
-
The finite state projection algorithm for the solution of the chemical master equation
-
Munsky B, Khammash M. The finite state projection algorithm for the solution of the chemical master equation. J Chem Phys 2006;124:044104.
-
(2006)
J Chem Phys
, vol.124
, pp. 044104
-
-
Munsky, B.1
Khammash, M.2
-
43
-
-
35348848671
-
A Krylov-based finite state projection algorithm for solving the chemical master equation arising in the discrete modelling of biological systems
-
In: in press
-
Burrage K, Hegland M, MacNamara S, et al. A Krylov-based finite state projection algorithm for solving the chemical master equation arising in the discrete modelling of biological systems. In: Proceedings of the Markov 150th Anniversary Conference, in press.
-
Proceedings of the Markov 150th Anniversary Conference
-
-
Burrage, K.1
Hegland, M.2
MacNamara, S.3
-
44
-
-
0032010619
-
Expokit: Software package for computing matrix exponentials
-
Sidje RBS. Expokit: Software package for computing matrix exponentials. ACM Trans Math Software 1998;24:130-56.
-
(1998)
ACM Trans Math Software
, vol.24
, pp. 130-156
-
-
Sidje, R.B.S.1
-
45
-
-
2942614884
-
Programmable cells: Interfacing natural and engineered gene networks
-
Kobayashi H, Kærn M, Araki M, et al. Programmable cells: Interfacing natural and engineered gene networks. Proc Natl Acad Sci USA 2004;101:8414-9.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 8414-8419
-
-
Kobayashi, H.1
Kærn, M.2
Araki, M.3
-
46
-
-
33845506760
-
Modelling the cardiac calcium transient using grid refinement and an ADI algorithm
-
Technical Report, Deptment of Mathematics, University of Auckland, New Zealand
-
Higgins E, Sneyd J. Modelling the cardiac calcium transient using grid refinement and an ADI algorithm. Technical Report, Deptment of Mathematics, University of Auckland, New Zealand, 2006.
-
(2006)
-
-
Higgins, E.1
Sneyd, J.2
-
47
-
-
29144435996
-
Computational modeling of the receptor-tyrosine-kinase-activated MAPK pathway
-
Orton RJ, Sturm OE, Vyshemirsky V, et al. Computational modeling of the receptor-tyrosine-kinase-activated MAPK pathway. Biochem J 2005;392:249-61.
-
(2005)
Biochem J
, vol.392
, pp. 249-261
-
-
Orton, R.J.1
Sturm, O.E.2
Vyshemirsky, V.3
-
48
-
-
0036212767
-
Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors
-
Schoeberl B, Eichler-Jonsson C, Gillies ED, et al. Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors. Nature Biotechnol 2002;20:370-5.
-
(2002)
Nature Biotechnol
, vol.20
, pp. 370-375
-
-
Schoeberl, B.1
Eichler-Jonsson, C.2
Gillies, E.D.3
-
50
-
-
25144497122
-
Towards a Grid infrastructure to support integrative approaches to biological research
-
Gavaghan DJ, Simpson AC, Lloyd S, et al. Towards a Grid infrastructure to support integrative approaches to biological research. Phil Trans R Soc Lond A 2005;363:1829-41.
-
(2005)
Phil Trans R Soc Lond A
, vol.363
, pp. 1829-1841
-
-
Gavaghan, D.J.1
Simpson, A.C.2
Lloyd, S.3
-
51
-
-
2442595958
-
CellML: Its future, present and past
-
Lloyd CM, Halstead MDB, Nielsen PF, et al. CellML: Its future, present and past. Prog Biophys Mol Biol 2004;85:433-50.
-
(2004)
Prog Biophys Mol Biol
, vol.85
, pp. 433-450
-
-
Lloyd, C.M.1
Halstead, M.D.B.2
Nielsen, P.F.3
-
52
-
-
33746269919
-
-
Components for Grid security. (20 April date last accessed)
-
Globus Alliance. Components for Grid security. http://www.globus.org/ grid_software/security/ (20 April 2006, date last accessed).
-
(2006)
Globus Alliance
-
-
-
53
-
-
34548256977
-
-
Shibboleth. (20 April date last accessed)
-
Internet2. Shibboleth. http://shibboleth.internet2.edu/ (20 April 2006, date last accessed).
-
(2006)
Internet2
-
-
-
54
-
-
27144457492
-
Semantic web roadmap
-
(2 May date last accessed)
-
Berners-Lee T. Semantic web roadmap. http://www.w3.org/DesignIssues/ Semantic.html (2 May 2006, date last accessed).
-
(2006)
-
-
Berners-Lee, T.1
-
55
-
-
1842550305
-
-
W3C. (2 May date last accessed)
-
W3C. OWL Web Ontology Language Overview. http://www.w3.org/TR/ owl-features/ (2 May 2006, date last accessed).
-
(2006)
OWL Web Ontology Language Overview
-
-
-
56
-
-
33845496860
-
Moby
-
(2 May date last accessed)
-
Wilkinson M. moby. http://biomoby.org (2 May 2006, date last accessed).
-
(2006)
-
-
Wilkinson, M.1
|