-
1
-
-
84873801934
-
High-throughput sequencing for biology and medicine
-
3340846,.;; ()
-
Soon WW, Hariharan M, Snyder MP, High-throughput sequencing for biology and medicine. Mol Syst Biol; 2013;9(640). doi: 10.1038/msb.2012.6123340846
-
(2013)
Mol Syst Biol
, vol.9
, Issue.640
-
-
Soon, W.W.1
Hariharan, M.2
Snyder, M.P.3
-
2
-
-
84858433310
-
Personal omics profiling reveals dynamic molecular and medical phenotypes
-
2424236,.;; (): –
-
Chen R, et al. Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell; 2012;148(6):1293–1307. doi: 10.1016/j.cell.2012.02.00922424236
-
(2012)
Cell
, vol.148
, Issue.6
, pp. 1293-1307
-
-
Chen, R.1
-
3
-
-
84884997982
-
Emerging landscape of oncogenic signatures across human cancers
-
Ciriello G, Miller ML, Aksoy BA, Senbabaoglu Y, Schultz N, Sander C, Emerging landscape of oncogenic signatures across human cancers. Nat Gen; 2013;45(10):1127–1133. doi: 10.1038/ng.2762
-
(2013)
Nat Gen
, vol.45
, Issue.10
, pp. 1127-1133
-
-
Ciriello, G.1
Miller, M.L.2
Aksoy, B.A.3
Senbabaoglu, Y.4
Schultz, N.5
Sander, C.6
-
4
-
-
0037079054
-
Computational Systems Biology
-
2432404,.;; (): –
-
Kitano H, Computational Systems Biology. Nature; 2002;420(6912):206–210. doi: 10.1038/nature0125412432404
-
(2002)
Nature
, vol.420
, Issue.6912
, pp. 206-210
-
-
Kitano, H.1
-
5
-
-
33845368513
-
COPASI—a COmplex PAthway SImulator
-
Hoops S, Sahle S, Gauges R, Lee C, Pahle J, Simus N, et al. COPASI—a COmplex PAthway SImulator. Bioinf; 2006;22:3067–3074. doi: 10.1093/bioinformatics/btl485
-
(2006)
Bioinf
, vol.22
, pp. 3067-3074
-
-
Hoops, S.1
Sahle, S.2
Gauges, R.3
Lee, C.4
Pahle, J.5
Simus, N.6
-
6
-
-
79961185589
-
AMIGO, a toolbox for advanced model identification in systems biology using global optimization
-
Balsa-Canto E, Banga JR, AMIGO, a toolbox for advanced model identification in systems biology using global optimization. Bioinf; 2011;27(16):2311–2313. doi: 10.1093/bioinformatics/btr370
-
(2011)
Bioinf
, vol.27
, Issue.16
, pp. 2311-2313
-
-
Balsa-Canto, E.1
Banga, J.R.2
-
7
-
-
84947575588
-
Data2Dynamics: a modeling environment tailored to parameter estimation in dynamical systems
-
Raue A, Steiert B, Schelker M, Kreutz C, Maiwald T, Hass H, et al. Data2Dynamics: a modeling environment tailored to parameter estimation in dynamical systems. Bioinf; 2015;31(21):3558–3560. doi: 10.1093/bioinformatics/btv405
-
(2015)
Bioinf
, vol.31
, Issue.21
, pp. 3558-3560
-
-
Raue, A.1
Steiert, B.2
Schelker, M.3
Kreutz, C.4
Maiwald, T.5
Hass, H.6
-
8
-
-
0033982936
-
KEGG: Kyoto Encyclopedia of Genes and Genomes
-
0592173,.;; (): –
-
Kanehisa M, Goto S, KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res; 2000;28(1):27–30. doi: 10.1093/nar/28.1.2710592173
-
(2000)
Nucleic Acids Res
, vol.28
, Issue.1
, pp. 27-30
-
-
Kanehisa, M.1
Goto, S.2
-
9
-
-
78651275182
-
Reactome: a database of reactions, pathways and biological processes
-
1067998,.;; (): –
-
Croft D, O’Kelly G, Wu G, Haw R, Gillespie M, Matthews L, et al. Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res; 2011;39(Database issue):D691–7. doi: 10.1093/nar/gkq101821067998
-
(2011)
Nucleic Acids Res
, vol.39
, Issue.Database issue
, pp. D691-D967
-
-
Croft, D.1
O’Kelly, G.2
Wu, G.3
Haw, R.4
Gillespie, M.5
Matthews, L.6
-
10
-
-
84876515907
-
STRING v9.1: protein-protein interaction networks, with increased coverage and integration
-
3203871,.;; (): –
-
Franceschini A, Szklarczyk D, Frankild S, Kuhn M, Simonovic M, Roth A, et al. STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res; 2013;41(Database issue):D808–15. doi: 10.1093/nar/gks109423203871
-
(2013)
Nucleic Acids Res
, vol.41
, Issue.Database issue
, pp. D808-D815
-
-
Franceschini, A.1
Szklarczyk, D.2
Frankild, S.3
Kuhn, M.4
Simonovic, M.5
Roth, A.6
-
11
-
-
84886740491
-
Path2Models: large-scale generation of computational models from biochemical pathway maps
-
Büchel F, Rodriguez N, Swainston N, Wrzodek C, Czauderna T, Keller R, et al. Path2Models: large-scale generation of computational models from biochemical pathway maps. BMC Syst Biol; 2013;7(116).
-
(2013)
BMC Syst Biol
, vol.7
, Issue.116
-
-
Büchel, F.1
Rodriguez, N.2
Swainston, N.3
Wrzodek, C.4
Czauderna, T.5
Keller, R.6
-
12
-
-
84877315835
-
A community-driven global reconstruction of human metabolism
-
3455439,.;; (): –
-
Thiele I, Swainston N, Fleming RMT, Hoppe A, Sahoo S, Aurich MK, et al. A community-driven global reconstruction of human metabolism. Nat Biotechnol; 2013;31(5):419–25. doi: 10.1038/nbt.248823455439
-
(2013)
Nat Biotechnol
, vol.31
, Issue.5
, pp. 419-425
-
-
Thiele, I.1
Swainston, N.2
Fleming, R.M.T.3
Hoppe, A.4
Sahoo, S.5
Aurich, M.K.6
-
13
-
-
84938721639
-
Predicting network functions with nested patterns
-
4398547,.;;:
-
Ganter M, Kaltenbach HM, Stelling J, Predicting network functions with nested patterns. Nat Commun; 2014;5:3006. doi: 10.1038/ncomms400624398547
-
(2014)
Nat Commun
, vol.5
, pp. 3006
-
-
Ganter, M.1
Kaltenbach, H.M.2
Stelling, J.3
-
14
-
-
84943302689
-
SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks
-
6452770,.;;:
-
Dräger A, Zielinski DC, Keller R, Rall M, Eichner J, Palsson BO, et al. SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks. BMC Syst Biol; 2015;9:68. doi: 10.1186/s12918-015-0212-926452770
-
(2015)
BMC Syst Biol
, vol.9
, pp. 68
-
-
Dräger, A.1
Zielinski, D.C.2
Keller, R.3
Rall, M.4
Eichner, J.5
Palsson, B.O.6
-
15
-
-
84893707475
-
Systematic construction of kinetic models from genome-scale metabolic networks
-
4324546,.;; ():
-
Stanford NJ, Lubitz T, Smallbone K, Klipp E, Mendes P, Liebermeister W, Systematic construction of kinetic models from genome-scale metabolic networks. PLoS ONE; 2013;8(11):e79195. doi: 10.1371/journal.pone.007919524324546
-
(2013)
PLoS ONE
, vol.8
, Issue.11
, pp. e79195
-
-
Stanford, N.J.1
Lubitz, T.2
Smallbone, K.3
Klipp, E.4
Mendes, P.5
Liebermeister, W.6
-
16
-
-
84924607090
-
A consensus approach for estimating the predictive accuracy of dynamic models in biology
-
5716416,.;; (): –
-
Villaverde AF, Bongard S, Mauch K, Müller D, Balsa-Canto E, Schmid J, et al. A consensus approach for estimating the predictive accuracy of dynamic models in biology. Computer Methods and Programs in Biomedicine; 2015;119(1):17–28. doi: 10.1016/j.cmpb.2015.02.00125716416
-
(2015)
Computer Methods and Programs in Biomedicine
, vol.119
, Issue.1
, pp. 17-28
-
-
Villaverde, A.F.1
Bongard, S.2
Mauch, K.3
Müller, D.4
Balsa-Canto, E.5
Schmid, J.6
-
18
-
-
84884755942
-
Lessons learned from quantitative dynamical modeling in systems biology
-
4098642,.;; ():
-
Raue A, Schilling M, Bachmann J, Matteson A, Schelke M, Kaschek D, et al. Lessons learned from quantitative dynamical modeling in systems biology. PLoS ONE; 2013;8(9):e74335. doi: 10.1371/journal.pone.007433524098642
-
(2013)
PLoS ONE
, vol.8
, Issue.9
, pp. e74335
-
-
Raue, A.1
Schilling, M.2
Bachmann, J.3
Matteson, A.4
Schelke, M.5
Kaschek, D.6
-
21
-
-
26444479778
-
Optimization by simulated annealing
-
7813860,.;; (): –
-
Kirkpatrick S, Gelatt CD, JrM P Vecchi MP, Optimization by simulated annealing. Science; 1983;220(4598):671–680. doi: 10.1126/science.220.4598.67117813860
-
(1983)
Science
, vol.220
, Issue.4598
, pp. 671-680
-
-
Kirkpatrick, S.1
Gelatt, C.D.2
M P Vecchi, M.P.3
-
22
-
-
41849104688
-
Hybrid optimization method with general switching strategy for parameter estimation
-
8366722,.;; ()
-
Balsa-Canto E, Peifer M, Banga JR, Timmer J, Fleck C, Hybrid optimization method with general switching strategy for parameter estimation. BMC Syst Biol; 2008;2(26). doi: 10.1186/1752-0509-2-2618366722
-
(2008)
BMC Syst Biol
, vol.2
, Issue.26
-
-
Balsa-Canto, E.1
Peifer, M.2
Banga, J.R.3
Timmer, J.4
Fleck, C.5
-
23
-
-
34548479280
-
A particle swarm pattern search method for bound constrained global optimization
-
Vaz A, Vicente L, A particle swarm pattern search method for bound constrained global optimization. J Global Optim; 2007;39(2):197–219. doi: 10.1007/s10898-007-9133-5
-
(2007)
J Global Optim
, vol.39
, Issue.2
, pp. 197-219
-
-
Vaz, A.1
Vicente, L.2
-
24
-
-
0242574982
-
Parameter estimation in biochemical pathways: A comparison of global optimization methods
-
4559783,.;;: –
-
Moles CG, Mendes P, Banga JR, Parameter estimation in biochemical pathways: A comparison of global optimization methods. Genome Res; 2003;13:2467–2474. doi: 10.1101/gr.126250314559783
-
(2003)
Genome Res
, vol.13
, pp. 2467-2474
-
-
Moles, C.G.1
Mendes, P.2
Banga, J.R.3
-
25
-
-
46349105936
-
Optimization in computational systems biology
-
Banga JR, Optimization in computational systems biology. BMC Syst Biol; 2008;2(47).
-
(2008)
BMC Syst Biol
, vol.2
, Issue.47
-
-
Banga, J.R.1
-
27
-
-
84924534693
-
BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology
-
5880925,.;; ()
-
Villaverde AF, Henriques D, Smallbone K, Bongard S, Schmid J, Cicin-Sain D, et al. BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology. BMC Syst Biol; 2015;9(8). doi: 10.1186/s12918-015-0144-425880925
-
(2015)
BMC Syst Biol
, vol.9
, Issue.8
-
-
Villaverde, A.F.1
Henriques, D.2
Smallbone, K.3
Bongard, S.4
Schmid, J.5
Cicin-Sain, D.6
-
30
-
-
33745217791
-
SUNDIALS: Suite of Nonlinear and Differential/Algebraic Equation Solvers
-
Hindmarsh AC, Brown PN, Grant KE, Lee SL, Serban R, Shumaker DE, et al. SUNDIALS: Suite of Nonlinear and Differential/Algebraic Equation Solvers. ACM T Math Software; 2005;31(3):363–396. doi: 10.1145/1089014.1089020
-
(2005)
ACM T Math Software
, vol.31
, Issue.3
, pp. 363-396
-
-
Hindmarsh, A.C.1
Brown, P.N.2
Grant, K.E.3
Lee, S.L.4
Serban, R.5
Shumaker, D.E.6
-
32
-
-
33847185388
-
On fitting of mathematical models of cell signaling pathways using adjoint systems
-
0369938,.;; (): –
-
Fujarewicz K, Kimmel M, Swierniak A, On fitting of mathematical models of cell signaling pathways using adjoint systems. MBE; 2005;2(3):527–534. doi: 10.3934/mbe.2005.2.52720369938
-
(2005)
MBE
, vol.2
, Issue.3
, pp. 527-534
-
-
Fujarewicz, K.1
Kimmel, M.2
Swierniak, A.3
-
33
-
-
84878917873
-
Inverse problems from biomedicine: Inference of putative disease mechanisms and robust therapeutic strategies
-
2526835,.;; (): –
-
Lu J, August E, Koeppl H, Inverse problems from biomedicine: Inference of putative disease mechanisms and robust therapeutic strategies. J Math Biol; 2012;67(1):143–168. doi: 10.1007/s00285-012-0523-z22526835
-
(2012)
J Math Biol
, vol.67
, Issue.1
, pp. 143-168
-
-
Lu, J.1
August, E.2
Koeppl, H.3
-
34
-
-
0035374241
-
Inverse problems light: Numerical differentiation
-
Hanke M, Scherzer O, Inverse problems light: Numerical differentiation. The American Mathematical Monthly; 2001;108(6):512–521. doi: 10.2307/2695705
-
(2001)
The American Mathematical Monthly
, vol.108
, Issue.6
, pp. 512-521
-
-
Hanke, M.1
Scherzer, O.2
-
35
-
-
33750722128
-
A review of the adjoint-state method for computing the gradient of a functional with geophysical applications
-
Plessix RE, A review of the adjoint-state method for computing the gradient of a functional with geophysical applications. Geophys J Int; 2006;167(2):495–503. doi: 10.1111/j.1365-246X.2006.02978.x
-
(2006)
Geophys J Int
, vol.167
, Issue.2
, pp. 495-503
-
-
Plessix, R.E.1
-
36
-
-
84900329958
-
Single-cell mRNA transfection studies: Delivery, kinetics and statistics by numbers
-
Leonhardt C, Schwake G, Stögbauer TR, Rappl S, Kuhr JT, Ligon TS, et al. Single-cell mRNA transfection studies: Delivery, kinetics and statistics by numbers. Nanomedicine: Nanotechnology, Biology, and Medicine; 2014;10(4):679–688.
-
(2014)
Nanomedicine: Nanotechnology, Biology, and Medicine
, vol.10
, Issue.4
, pp. 679-688
-
-
Leonhardt, C.1
Schwake, G.2
Stögbauer, T.R.3
Rappl, S.4
Kuhr, J.T.5
Ligon, T.S.6
-
37
-
-
77953934646
-
BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models
-
0587024,.;;:
-
Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, et al. BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol; 2010;4:92. doi: 10.1186/1752-0509-4-9220587024
-
(2010)
BMC Syst Biol
, vol.4
, pp. 92
-
-
Li, C.1
Donizelli, M.2
Rodriguez, N.3
Dharuri, H.4
Endler, L.5
Chelliah, V.6
-
38
-
-
84878005602
-
Computational modelling of the regulation of Insulin signalling by oxidative stress
-
Smith GR, Shanley DP, Computational modelling of the regulation of Insulin signalling by oxidative stress. BMC Syst Biol; 2013;7(1):1. doi: 10.1186/1752-0509-7-41
-
(2013)
BMC Syst Biol
, vol.7
, Issue.1
, pp. 1
-
-
Smith, G.R.1
Shanley, D.P.2
-
39
-
-
70349574614
-
Monte carlo analysis of an ode model of the sea urchin endomesoderm network
-
Kühn C, Wierling C, Kühn A, Klipp E, Panopoulou G, Lehrach H, et al. Monte carlo analysis of an ode model of the sea urchin endomesoderm network. BMC Syst Biol; 2009;3(1):1.
-
(2009)
BMC Syst Biol
, vol.3
, Issue.1
, pp. 1
-
-
Kühn, C.1
Wierling, C.2
Kühn, A.3
Klipp, E.4
Panopoulou, G.5
Lehrach, H.6
-
40
-
-
58549083142
-
Input–output behavior of ErbB signaling pathways as revealed by a mass action model trained against dynamic data
-
Chen WW, Schoeberl B, Jasper PJ, Niepel M, Nielsen UB, Lauffenburger DA, et al. Input–output behavior of ErbB signaling pathways as revealed by a mass action model trained against dynamic data. Mol Syst Biol; 2009;5(239).
-
(2009)
Mol Syst Biol
, vol.5
, Issue.239
-
-
Chen, W.W.1
Schoeberl, B.2
Jasper, P.J.3
Niepel, M.4
Nielsen, U.B.5
Lauffenburger, D.A.6
-
41
-
-
0037025146
-
Dynamic modeling of the central carbon metabolism of Escherichia coli
-
7590932,.;; (): –
-
Chassagnole C, Noisommit-Rizzi N, Schmid JW, Mauch K, Reuss M, Dynamic modeling of the central carbon metabolism of Escherichia coli. Biotechnol Bioeng; 2002;79(1):53–73. doi: 10.1002/bit.1028817590932
-
(2002)
Biotechnol Bioeng
, vol.79
, Issue.1
, pp. 53-73
-
-
Chassagnole, C.1
Noisommit-Rizzi, N.2
Schmid, J.W.3
Mauch, K.4
Reuss, M.5
-
42
-
-
77949385752
-
Bacterial adaptation through distributed sensing of metabolic fluxes
-
0212527,.;; ()
-
Kotte O, Zaugg JB, Heinemann M, Bacterial adaptation through distributed sensing of metabolic fluxes. Mol Syst Biol; 2010;6(1). doi: 10.1038/msb.2010.1020212527
-
(2010)
Mol Syst Biol
, vol.6
, Issue.1
-
-
Kotte, O.1
Zaugg, J.B.2
Heinemann, M.3
-
43
-
-
84921813087
-
-
Villaverde AF, Bongard S, Mauch K, Müller D, Balsa-Canto E, Schmid J, et al. High-Confidence Predictions in Systems Biology Dynamic Models. In: 8th International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB 2014). Cham: Springer International Publishing; 2014. p. 161–171.
-
(2014)
High-Confidence Predictions in Systems Biology Dynamic Models
, vol.2014
, pp. 161-171
-
-
Villaverde, A.F.1
Bongard, S.2
Mauch, K.3
Müller, D.4
Balsa-Canto, E.5
Schmid, J.6
-
44
-
-
84864952677
-
State–time spectrum of signal transduction logic models
-
2871648,.;; ():
-
MacNamara A, Terfve C, Henriques D, Bernabé BP, Saez-Rodriguez J, State–time spectrum of signal transduction logic models. Phys Biol; 2012;9(4):045003. doi: 10.1088/1478-3975/9/4/04500322871648
-
(2012)
Phys Biol
, vol.9
, Issue.4
, pp. 045003
-
-
MacNamara, A.1
Terfve, C.2
Henriques, D.3
Bernabé, B.P.4
Saez-Rodriguez, J.5
-
45
-
-
84881518999
-
Large-scale metabolic models: From reconstruction to differential equations
-
Smallbone K, Mendes P, Large-scale metabolic models: From reconstruction to differential equations. Ind Biotechnol; 2013;9(4):179–184. doi: 10.1089/ind.2013.0003
-
(2013)
Ind Biotechnol
, vol.9
, Issue.4
, pp. 179-184
-
-
Smallbone, K.1
Mendes, P.2
-
46
-
-
77956887650
-
A fast scoring algorithm for maximum likelihood estimation in unbalanced mixed models with nested random effects
-
Longford NT, A fast scoring algorithm for maximum likelihood estimation in unbalanced mixed models with nested random effects. Biometrika; 1987;74(4):817–827. doi: 10.1093/biomet/74.4.817
-
(1987)
Biometrika
, vol.74
, Issue.4
, pp. 817-827
-
-
Longford, N.T.1
-
47
-
-
0000387235
-
A rapidly convergent descent method for minimization
-
Fletcher R, Powell MJ, A rapidly convergent descent method for minimization. Comp J; 1963;6(2):163–168. doi: 10.1093/comjnl/6.2.163
-
(1963)
Comp J
, vol.6
, Issue.2
, pp. 163-168
-
-
Fletcher, R.1
Powell, M.J.2
-
48
-
-
84966251980
-
A Family of Variable-Metric Methods Derived by Variational Means
-
Goldfarb D, A Family of Variable-Metric Methods Derived by Variational Means. Math Comp; 1970;24(109):23–26. doi: 10.1090/S0025-5718-1970-0258249-6
-
(1970)
Math Comp
, vol.24
, Issue.109
, pp. 23-26
-
-
Goldfarb, D.1
-
49
-
-
0001484947
-
Optimization and sensitivity analysis for multiresponse parameter estimation in systems of ordinary differential equations
-
(): –. An International Journal of Computer Application in Chemical Engineering
-
Guay M, McLean DD, Optimization and sensitivity analysis for multiresponse parameter estimation in systems of ordinary differential equations. Comp and Chem Eng; 1995;19(12):1271–1285. An International Journal of Computer Application in Chemical Engineering. doi: 10.1016/0098-1354(94)00120-0
-
(1995)
Comp and Chem Eng
, vol.19
, Issue.12
, pp. 1271-1285
-
-
Guay, M.1
McLean, D.D.2
-
50
-
-
25444433053
-
Cheap Second Order Directional Derivatives of Stiff ODE Embedded Functionals
-
Özyurt DB, Barton PI, Cheap Second Order Directional Derivatives of Stiff ODE Embedded Functionals. SIAM Journal on Scientific Computing; 2005;26(5):1725–1743. doi: 10.1137/030601582
-
(2005)
SIAM Journal on Scientific Computing
, vol.26
, Issue.5
, pp. 1725-1743
-
-
Özyurt, D.B.1
Barton, P.I.2
-
52
-
-
0040763312
-
ATOMFT: Solving ODEs and DAEs using Taylor series
-
Chang YF, Corliss GF, ATOMFT: Solving ODEs and DAEs using Taylor series. Comp Math App; 1994;28(10–12):209–233. doi: 10.1016/0898-1221(94)00193-6
-
(1994)
Comp Math App
, vol.28
, Issue.10-12
, pp. 209-233
-
-
Chang, Y.F.1
Corliss, G.F.2
-
53
-
-
0017254690
-
Taylor expansion of the accumulated rounding error
-
Linnainmaa S, Taylor expansion of the accumulated rounding error. BIT; 1976;16(2):146–160. doi: 10.1007/BF01931367
-
(1976)
BIT
, vol.16
, Issue.2
, pp. 146-160
-
-
Linnainmaa, S.1
-
54
-
-
84900846604
-
MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics
-
Egea JA, Henriques D, Cokelaer T, Villaverde AF, MacNamara A, Danciu DP, et al. MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics. BMC Bioinf; 2014;15(136).
-
(2014)
BMC Bioinf
, vol.15
, Issue.136
-
-
Egea, J.A.1
Henriques, D.2
Cokelaer, T.3
Villaverde, A.F.4
MacNamara, A.5
Danciu, D.P.6
-
55
-
-
32544443964
-
Systems biology toolbox for MATLAB: a computational platform for research in systems biology
-
Schmidt H, Jirstrand M, Systems biology toolbox for MATLAB: a computational platform for research in systems biology. Bioinf; 2006;22(4):514–515. doi: 10.1093/bioinformatics/bti799
-
(2006)
Bioinf
, vol.22
, Issue.4
, pp. 514-515
-
-
Schmidt, H.1
Jirstrand, M.2
-
56
-
-
84861147460
-
A specialized ODE integrator for the efficient computation of parameter sensitivities
-
2607742,.;; ()
-
Gonnet P, Dimopoulos S, Widmer L, Stelling J, A specialized ODE integrator for the efficient computation of parameter sensitivities. BMC Syst Biol; 2012;6(46). doi: 10.1186/1752-0509-6-4622607742
-
(2012)
BMC Syst Biol
, vol.6
, Issue.46
-
-
Gonnet, P.1
Dimopoulos, S.2
Widmer, L.3
Stelling, J.4
-
57
-
-
84945919257
-
Robust and efficient parameter estimation in dynamic models of biological systems
-
6515482,.;;:
-
Gábor A, Banga JR, Robust and efficient parameter estimation in dynamic models of biological systems. BMC Syst Biol; 2015;9:74. doi: 10.1186/s12918-015-0219-226515482
-
(2015)
BMC Syst Biol
, vol.9
, pp. 74
-
-
Gábor, A.1
Banga, J.R.2
-
58
-
-
84862214722
-
SABIO-RK—database for biochemical reaction kinetics
-
2102587,.;; (): –
-
Wittig U, Kania R, Golebiewski M, Rey M, Shi L, Jong L, et al. SABIO-RK—database for biochemical reaction kinetics. Nucl Acids Res; 2012;40(D1):D790–D796. doi: 10.1093/nar/gkr104622102587
-
(2012)
Nucl Acids Res
, vol.40
, Issue.D1
, pp. D790-D796
-
-
Wittig, U.1
Kania, R.2
Golebiewski, M.3
Rey, M.4
Shi, L.5
Jong, L.6
-
59
-
-
58149185126
-
BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009
-
8984617,.;; (): –
-
Chang A, Scheer M, Grote A, Schomburg I, Schomburg D, BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009. Nucleic Acids Res; 2009;37(Database issue):D588–92. doi: 10.1093/nar/gkn82018984617
-
(2009)
Nucleic Acids Res
, vol.37
, Issue.Database issue
, pp. D588-D592
-
-
Chang, A.1
Scheer, M.2
Grote, A.3
Schomburg, I.4
Schomburg, D.5
-
60
-
-
84984978138
-
-
In:.:;. London, United Kingdom Chapman & Hall / CRC Pres
-
Neal RM, Brooks S, Gelman A, Jones G, Meng XL, MCMC using Hamiltonian dynamics. In: Handbook of Markov Chain Monte Carlo. London, United Kingdom: Chapman & Hall / CRC Press; 2011.
-
(2011)
Handbook of Markov Chain Monte Carlo
-
-
Neal, R.M.1
Brooks, S.2
Gelman, A.3
Jones, G.4
Meng, X.L.5
-
61
-
-
79952295497
-
Riemann manifold Langevin and Hamiltonian Monte Carlo methods
-
Girolami M, Calderhead B, Riemann manifold Langevin and Hamiltonian Monte Carlo methods. J R Statist Soc B; 2011;73(2):123–214. doi: 10.1111/j.1467-9868.2010.00765.x
-
(2011)
J R Statist Soc B
, vol.73
, Issue.2
, pp. 123-214
-
-
Girolami, M.1
Calderhead, B.2
-
62
-
-
85011415617
-
-
an S, Bui-Thanh T, Christie M, Girolami M. Emulation of higher-order tensors in manifold Monte Carlo methods for Bayesian inverse problems.; 2015. [stat.CO]
-
Lan S, Bui-Thanh T, Christie M, Girolami M. Emulation of higher-order tensors in manifold Monte Carlo methods for Bayesian inverse problems. arXiv; 2015. arXiv:1507.06244v2 [stat.CO].
-
-
-
-
63
-
-
84910146580
-
-
Fröhlich F, Hross S, Theis FJ, Hasenauer J. Radial basis function approximation of Bayesian parameter posterior densities for uncertainty analysis. In: Mendes P, Dada JO, Smallbone KO, editors. Proceedings of the 12th International Conference on Computational Methods in Systems Biology (CMSB 2014), Manchester, UK. Lecture Notes in Bioinformatics. Springer International Publishing Switzerland; 2014. p. 73–85.
-
(2014)
Radial basis function approximation of Bayesian parameter posterior densities for uncertainty analysis
, vol.2014
, pp. 73-85
-
-
Fröhlich, F.1
Hross, S.2
Theis, F.J.3
Hasenauer, J.4
Mendes, P.5
Dada, J.O.6
Smallbone, K.O.7
-
64
-
-
77953839617
-
Inferring signaling pathway topologies from multiple perturbation measurements of specific biochemical species
-
Xu TR, Vyshemirsky V, Gormand A, von Kriegsheim A, Girolami M, Baillie GS, et al. Inferring signaling pathway topologies from multiple perturbation measurements of specific biochemical species. Sci Signal; 2010;3(113):ra20. doi: 10.1126/scisignal.2000517
-
(2010)
Sci Signal
, vol.3
, Issue.113
, pp. ra20
-
-
Xu, T.R.1
Vyshemirsky, V.2
Gormand, A.3
von Kriegsheim, A.4
Girolami, M.5
Baillie, G.S.6
-
65
-
-
84888027235
-
High-dimensional Bayesian parameter estimation: Case study for a model of JAK2/STAT5 signaling
-
3602931,.;; (): –
-
Hug S, Raue A, Hasenauer J, Bachmann J, Klingmüller U, Timmer J, et al. High-dimensional Bayesian parameter estimation: Case study for a model of JAK2/STAT5 signaling. Math Biosci; 2013;246(2):293–304. doi: 10.1016/j.mbs.2013.04.00223602931
-
(2013)
Math Biosci
, vol.246
, Issue.2
, pp. 293-304
-
-
Hug, S.1
Raue, A.2
Hasenauer, J.3
Bachmann, J.4
Klingmüller, U.5
Timmer, J.6
-
66
-
-
84963973421
-
Data-driven modelling of biological multi-scale processes
-
Hasenauer J, Jagiella N, Hross S, Theis FJ, Data-driven modelling of biological multi-scale processes. Journal of Coupled Systems and Multiscale Dynamics; 2015;3(2):101–121. doi: 10.1166/jcsmd.2015.1069
-
(2015)
Journal of Coupled Systems and Multiscale Dynamics
, vol.3
, Issue.2
, pp. 101-121
-
-
Hasenauer, J.1
Jagiella, N.2
Hross, S.3
Theis, F.J.4
-
67
-
-
84876576325
-
Computational solutions for omics data
-
3594911,.;; (): –
-
Berger B, Peng J, Singh M, Computational solutions for omics data. Nat Rev Genet; 2013;14(5):333–346. doi: 10.1038/nrg343323594911
-
(2013)
Nat Rev Genet
, vol.14
, Issue.5
, pp. 333-346
-
-
Berger, B.1
Peng, J.2
Singh, M.3
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