Research graph
References from Stochastic simulation in systems biology. Local targets link to admitted publications; unresolved targets remain external evidence.
10.1128/iai.01343-10
10.1128/iai.01343-10 · External reference
So what do we really mean when we say that systems biology is holistic?
10.1186/1752-0509-4-22 · 2010 · External reference
10.1093/oso/9780195124415.001.0001
10.1093/oso/9780195124415.001.0001 · 2009 · External reference
10.1038/nature01254
10.1038/nature01254 · External reference
Why model?
2008 · External reference
The edges of understanding
10.1186/1741-7007-8-40 · 2010 · External reference
10.1017/cbo9780511819872
10.1017/cbo9780511819872 · 2006 · External reference
10.1016/b978-0-12-438150-6.50018-2
10.1016/b978-0-12-438150-6.50018-2 · 1979 · External reference
Some lessons about models from Michaelis and Menten
10.1091/mbc.e11-07-0643 · 2012 · External reference
Models in biology: accurate descriptions of our pathetic thinking
10.1186/1741-7007-12-29 · 2014 · External reference
Unresolved reference
2013 · External reference
10.2976/1.3244985
10.2976/1.3244985 · External reference
10.1038/nphys2474
10.1038/nphys2474 · External reference
Molecular dynamics simulations and drug discovery
10.1186/1741-7007-9-71 · 2011 · External reference
Unresolved reference
1993 · External reference
10.1093/oso/9780198534327.001.0001
10.1093/oso/9780198534327.001.0001 · 1995 · External reference
Unresolved reference
1991 · External reference
10.1146/annurev.physchem.58.032806.104637
10.1146/annurev.physchem.58.032806.104637 · External reference
Biochemical simulations: stochastic, approximate stochastic and hybrid approaches
10.1093/bib/bbn050 · 2009 · External reference
Modeling and simulating chemical reactions
10.1137/060666457 · 2008 · External reference
10.1016/j.physrep.2013.03.004
10.1016/j.physrep.2013.03.004 · External reference
10.1038/nrg2509
10.1038/nrg2509 · External reference
10.1201/b11812
10.1201/b11812 · 2011 · External reference
10.1016/s0168-9525(98)01659-x
10.1016/s0168-9525(98)01659-x · External reference
10.1242/dev.035139
10.1242/dev.035139 · External reference
10.1038/nrmicro1460
10.1038/nrmicro1460 · External reference
Unresolved reference
2010 · External reference
Unresolved reference
2000 · External reference
10.1126/science.1105891
10.1126/science.1105891 · External reference
10.1016/j.cell.2008.09.050
10.1016/j.cell.2008.09.050 · External reference
10.1111/j.1558-5646.2011.01289.x
10.1111/j.1558-5646.2011.01289.x · External reference
Convergence in pigmentation at multiple levels: mutations, genes and function
10.1098/rstb.2010.0104 · 2010 · External reference
10.1038/nrg3483
10.1038/nrg3483 · External reference
10.1038/nature12511
10.1038/nature12511 · External reference
Unresolved reference
2007 · External reference
10.1038/nrg1615
10.1038/nrg1615 · External reference
10.1371/journal.pone.0000394
10.1371/journal.pone.0000394 · External reference
10.1038/nature04281
10.1038/nature04281 · External reference
10.1371/journal.pcbi.1002416
10.1371/journal.pcbi.1002416 · External reference
Adaptive noise
10.1098/rspb.2013.1104 · 2013 · External reference
10.1038/262467a0
10.1038/262467a0 · External reference
10.1371/journal.pbio.0040309
10.1371/journal.pbio.0040309 · External reference
10.1146/annurev.biophys.36.040306.132705
10.1146/annurev.biophys.36.040306.132705 · External reference
10.1126/science.1070919
10.1126/science.1070919 · External reference
10.1073/pnas.162041399
10.1073/pnas.162041399 · External reference
A common repressor pool results in indeterminacy of extrinsic noise
10.1063/1.3658618 · 2011 · External reference
10.1126/science.1099390
10.1126/science.1099390 · External reference
10.1111/j.1365-2958.2009.06605.x
10.1111/j.1365-2958.2009.06605.x · External reference
10.1016/j.cell.2011.01.030
10.1016/j.cell.2011.01.030 · External reference
10.1371/journal.pone.0002372
10.1371/journal.pone.0002372 · External reference
10.1371/journal.pcbi.1002480
10.1371/journal.pcbi.1002480 · External reference
10.1126/science.1161427
10.1126/science.1161427 · External reference
10.1093/genetics/149.4.1633
10.1093/genetics/149.4.1633 · External reference
10.1038/ng.110
10.1038/ng.110 · External reference
10.1038/nature06965
10.1038/nature06965 · External reference
Unresolved reference
2006 · External reference
10.1038/ng2051
10.1038/ng2051 · External reference
10.1007/s12052-009-0128-1
10.1007/s12052-009-0128-1 · External reference
High genomic deleterious mutation rates in hominids
10.1038/16915 · 1999 · External reference
10.1038/nature12477
10.1038/nature12477 · External reference
Evolutionary dynamics of feedback escape and the development of stem-cell driven cancers
10.1073/pnas.1107621108 · 2011 · External reference
10.1126/science.1106914
10.1126/science.1106914 · External reference
10.1038/nature01258
10.1038/nature01258 · External reference
10.1016/j.molcel.2007.11.013
10.1016/j.molcel.2007.11.013 · External reference
Noise minimization in eukaryotic gene expression
10.1371/journal.pbio.0020137 · 2004 · External reference
10.1038/msb.2008.11
10.1038/msb.2008.11 · External reference
10.1101/gad.1945410
10.1101/gad.1945410 · External reference
Unresolved reference
2007 · External reference
10.1073/pnas.151588598
10.1073/pnas.151588598 · External reference
10.1038/nature02257
10.1038/nature02257 · External reference
10.1126/science.1216379
10.1126/science.1216379 · External reference
10.1038/nature04785
10.1038/nature04785 · External reference
10.1038/ng1807
10.1038/ng1807 · External reference
10.1126/science.1188308
10.1126/science.1188308 · External reference
10.1073/pnas.94.3.814
10.1073/pnas.94.3.814 · External reference
Unresolved reference
1999 · External reference
10.1137/s0036144500378302
10.1137/s0036144500378302 · External reference
10.1063/1.481811
10.1063/1.481811 · External reference
Chemical reaction models for nonequilibrium phase-transitions
10.1007/bf01379769 · 1972 · External reference
Conditioned averages in chemical kinetics
10.1063/1.442111 · 1981 · External reference
General method for numerically simulating stochastic time evolution of coupled chemical-reactions
10.1016/0021-9991(76)90041-3 · 1976 · External reference
10.1021/j100540a008
10.1021/j100540a008 · External reference
10.1063/1.1378322
10.1063/1.1378322 · External reference
Bayesian methods in bioinformatics and computational systems biology
10.1093/bib/bbm007 · 2007 · External reference
10.1016/0378-4371(92)90283-v
10.1016/0378-4371(92)90283-v · External reference
Unresolved reference
1992 · External reference
10.1083/jcb.200903097
10.1083/jcb.200903097 · External reference
Perspective: stochastic algorithms for chemical kinetics
10.1063/1.4801941 · 2013 · External reference
A diffusional bimolecular propensity function
10.1063/1.3253798 · 2009 · External reference
10.1016/s0968-0004(01)01938-7
10.1016/s0968-0004(01)01938-7 · External reference
10.1146/annurev.biophys.37.032807.125817
10.1146/annurev.biophys.37.032807.125817 · External reference
Models of macromolecular crowding effects and the need for quantitative comparisons with experiment
10.1016/j.sbi.2010.01.008 · 2010 · External reference
10.1049/iet-syb.2011.0049
10.1049/iet-syb.2011.0049 · External reference
10.1088/0034-4885/76/4/046602
10.1088/0034-4885/76/4/046602 · External reference
Colored extrinsic fluctuations and stochastic gene expression
10.1038/msb.2008.31 · 2008 · External reference
10.1007/s00285-006-0034-x
10.1007/s00285-006-0034-x · External reference
10.1063/1.2145882
10.1063/1.2145882 · External reference
10.1137/060678154
10.1137/060678154 · External reference
Stochastic modeling of naïve T cell homeostasis for competing clonotypes via the master equation
10.1137/09077182x · 2010 · External reference
10.1007/s11538-008-9346-x
10.1007/s11538-008-9346-x · External reference
Direct solution of the chemical master equation using quantized tensor trains
10.1371/journal.pcbi.1003359 · 2014 · External reference
10.1073/pnas.0811999106
10.1073/pnas.0811999106 · External reference
Approximate moment dynamics for chemically reacting systems
10.1109/tac.2010.2088631 · 2011 · External reference
Moment closure approximations for stochastic kinetic models with rational rate laws
10.1016/j.mbs.2011.02.006 · 2011 · External reference
A general moment expansion method for stochastic kinetic models
10.1063/1.4802475 · 2013 · External reference
Linear noise approximation is valid over limited times for any chemical system that is sufficiently large
10.1049/iet-syb.2011.0038 · 2012 · External reference
10.1073/pnas.0503858102
10.1073/pnas.0503858102 · External reference
Oscillatory regulation of hes1: discrete stochastic delay modelling and simulation
10.1371/journal.pcbi.0020117 · 2006 · External reference
10.1021/jp993732q
10.1021/jp993732q · External reference
10.1063/1.1778376
10.1063/1.1778376 · External reference
Recycling random numbers in the stochastic simulation algorithm
10.1063/1.4792207 · 2013 · External reference
Improved leap-size selection for accelerated stochastic simulation
10.1063/1.1613254 · 2003 · External reference
Efficient step size selection for the tau-leaping simulation method
10.1063/1.2159468 · 2006 · External reference
Binomial leap methods for simulating stochastic chemical kinetics
10.1063/1.1810475 · 2004 · External reference
Binomial distribution based tau-leap accelerated stochastic simulation
10.1063/1.1833357 · 2005 · External reference
Efficient binomial leap method for simulating chemical kinetics
10.1063/1.2741252 · 2007 · External reference
Multinomial tau-leaping method for stochastic kinetic simulations
10.1063/1.2432326 · 2007 · External reference
Look before you leap: a confidence-based method for selecting species criticality while avoiding negative populations in tau-leaping
10.1063/1.3554385 · 2011 · External reference
10.1137/040603206
10.1137/040603206 · External reference
10.1137/06066792x
10.1137/06066792x · External reference
A weak second order tau-leaping method for chemical kinetic systems
10.1063/1.3609119 · 2011 · External reference
Highly accurate tau-leaping methods with random corrections
10.1063/1.3091269 · 2009 · External reference
Weak error analysis of numerical methods for stochastic models of population processes
10.1137/110849699 · 2012 · External reference
A higher-order numerical framework for stochastic simulation of chemical reaction systems
10.1186/1752-0509-6-85 · 2012 · External reference
Efficient simulation of stochastic chemical kinetics with the Stochastic Bulirsch–Stoer extrapolation method
10.1186/1752-0509-8-71 · 2014 · External reference
Unbiased tau-leap methods for stochastic simulation of chemically reacting systems
10.1063/1.2894479 · 2008 · External reference
10.1063/1.1627296
10.1063/1.1627296 · External reference
The adaptive explicit-implicit tau-leaping method with automatic tau selection
10.1063/1.2745299 · 2007 · External reference
Simulation methods with extended stability for stiff biochemical kinetics
10.1186/1752-0509-4-110 · 2010 · External reference
Avoiding negative populations in explicit Poisson tau-leaping
10.1063/1.1992473 · 2005 · External reference
Quasiequilibrium approximation of fast reaction kinetics in stochastic biochemical systems
10.1063/1.1889434 · 2005 · External reference
Approximate simulation of coupled fast and slow reactions for stochastic chemical kinetics
10.1063/1.1505860 · 2002 · External reference
Stochastic chemical kinetics and the quasi-steady-state assumption: application to the Gillespie algorithm
10.1063/1.1545446 · 2003 · External reference
Hybrid simulation of cellular behavior
10.1093/bioinformatics/btg409 · 2004 · External reference
Nested stochastic simulation algorithm for chemical kinetic systems with disparate rates
10.1063/1.2109987 · 2005 · External reference
Accurate hybrid stochastic simulation of a system of coupled chemical or biochemical reactions
10.1063/1.1835951 · 2005 · External reference
10.1016/j.pbiomolbio.2004.01.014
10.1016/j.pbiomolbio.2004.01.014 · External reference
Gene regulatory networks: a coarse-grained, equation-free approach to multiscale computation
10.1063/1.2149854 · 2006 · External reference
A constrained approach to multiscale stochastic simulation of chemically reacting systems
10.1063/1.3624333 · 2011 · External reference
10.1017/cbo9780511624094
10.1017/cbo9780511624094 · 1991 · External reference
Unresolved reference
2001 · External reference
10.1016/0021-9991(75)90060-1
10.1016/0021-9991(75)90060-1 · External reference
Stochastic chemical kinetics and the total quasi-steady-state assumption: application to the stochastic simulation algorithm and chemical master equation
10.1063/1.2971036 · 2008 · External reference
COPASI — a COmplex PAthway SImulator
10.1093/bioinformatics/btl485 · 2006 · External reference
10.1093/bioinformatics/btr401
10.1093/bioinformatics/btr401 · External reference
STOCKS: STOChastic Kinetic Simulations of biochemical systems with gillespie algorithm
10.1093/bioinformatics/18.3.470 · 2002 · External reference
Biochemical network stochastic simulator (BioNetS): software for stochastic modeling of biochemical networks
10.1186/1471-2105-5-24 · 2004 · External reference
The slow-scale stochastic simulation algorithm
10.1063/1.1824902 · 2005 · External reference
10.1371/journal.pcbi.1000705
10.1371/journal.pcbi.1000705 · External reference
Stochastic modelling of reaction-diffusion processes: algorithms for bimolecular reactions
10.1088/1478-3975/6/4/046001 · 2009 · External reference
10.1088/1478-3967/1/3/001
10.1088/1478-3967/1/3/001 · External reference
10.1137/070692017
10.1137/070692017 · External reference
Stochastic reaction-diffusion simulation with MesoRD
10.1093/bioinformatics/bti431 · 2005 · External reference
Binomial tau-leap spatial stochastic simulation algorithm for applications in chemical kinetics
10.1063/1.2771548 · 2007 · External reference
10.1186/1752-0509-6-76
10.1186/1752-0509-6-76 · External reference
10.1039/a702602a
10.1039/a702602a · External reference
Unresolved reference
2009 · External reference
Inferring diffusion in single live cells at the single-molecule level
10.1098/rstb.2012.0029 · 2013 · External reference
10.1371/journal.pcbi.1000696
10.1371/journal.pcbi.1000696 · External reference
10.1098/rsif.2008.0172
10.1098/rsif.2008.0172 · External reference
Stochastic simulation of chemically reacting systems using multi-core processors
10.1063/1.3670416 · 2012 · External reference
STOCHSIMGPU: parallel stochastic simulation for the systems biology toolbox 2 for MATLAB
10.1093/bioinformatics/btr068 · 2011 · External reference
10.1016/j.parco.2014.03.009
10.1016/j.parco.2014.03.009 · External reference
10.1371/journal.pone.0091963
10.1371/journal.pone.0091963 · External reference
10.1158/1541-7786.mcr-10-0264
10.1158/1541-7786.mcr-10-0264 · External reference
