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author = {P. Wellstead and E. Bullinger and D. Kalamatianos and O. Mason and M. Verwoerd},
date-added = {2009-06-10 11:41:11 +0100},
date-modified = {2009-06-10 11:41:59 +0100},
journal = {Annual Reviews in Control},
pages = {33-47},
title = {The Role of Control and System Theory in Systems Biology},
volume = {32},
year = {2008}
}
@article{Verwoerd:2009hi,
author = {M. Verwoerd and O. Mason},
date-added = {2009-06-10 11:39:44 +0100},
date-modified = {2009-06-10 11:40:20 +0100},
journal = {SIAM Journal of Applied Dynamics },
number = {1},
pages = {417--453},
title = {On computing the critical coupling coefficient for the Kuramoto model on a complete Bipartite graph},
volume = {8},
year = {2009}
}
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author = {S. N. Sreenath and K.-H. Cho and P. Wellstead.},
date-added = {2009-06-09 16:33:01 +0100},
date-modified = {2009-06-10 11:37:02 +0100},
editor = {O. Wolkenhauer, P. Wellstead and K-H Cho},
pages = {1--15},
publisher = {Portland Press},
series = {Essays in Biochemistry: Systems Biology, Lecture Notes in Control and Information Sciences},
title = {Modelling the dynamics of signalling pathways. },
volume = {357},
year = {2008}
}
@inproceedings{Wellstead:2009uk,
author = {M. Cloutier and Pierre O. Poliquin and Mario Jolicoeur and P. Wellstead},
booktitle = {Foundations of Systems Biology in Engineering (FOSBE), Denver, USA, to appear},
date-added = {2009-06-09 16:31:52 +0100},
date-modified = {2009-06-09 16:32:36 +0100},
title = {An integrative modelling approach for the implications of energy metabolism in neurodegeneration},
year = {2009}
}
@inproceedings{krippendorff_etal09c,
author = {B.-F. Krippendorff and D. A. Oyarz\'un and W. Huisinga},
booktitle = {Proceedings of the 3rd Foundations of Systems Biology and Engineering (FOSBE), Denver, USA, to appear},
date-added = {2009-06-09 16:29:45 +0100},
date-modified = {2009-06-09 16:31:19 +0100},
title = {Ligand accumulation counteracts therapeutic inhibition of receptor systems.},
year = {2009}
}
@article{D.-Oyarzun:2009vf,
author = {D. A. Oyarz\'un and Brian P. Ingalls and R. H. Middleton and D. Kalamatianos},
date-added = {2009-06-09 16:23:35 +0100},
date-modified = {2009-06-09 16:29:24 +0100},
doi = {10.1007/s11538-009-9427-5},
journal = {Bulletin of Mathematical Biology},
title = {Sequential activation of metabolic pathways: a dynamic optimization approach.},
year = {2009},
bdsk-url-1 = {http://dx.doi.org/10.1007/s11538-009-9427-5}
}
@article{Wellstead:2009hb,
author = {M. Cloutier and Fiachra B. Bolger and John P. Lowry and P. Wellstead},
date-added = {2009-06-09 16:21:29 +0100},
date-modified = {2009-06-09 16:23:11 +0100},
doi = {10.1007/s10827-009-0152-8},
journal = {Journal of Computational Neuroscience},
title = {An integrative dynamic model of brain energy metabolism using in vivo neurochemical measurements},
year = {2009},
bdsk-url-1 = {http://dx.doi.org/10.1007/s10827-009-0152-8}
}
@inproceedings{Rutjes_etal07,
author = {T. Rutjes and O. Mason and M. Verwoerd},
booktitle = {Foundations of Systems Biology in Engineering (FOSBE), Stuttgart, Germany},
owner = {Administrador},
pubtype = {proceedings},
title = {On the growth of the largest component in duplication-divergence models of protein interaction networks},
year = {2007}
}
@article{MasVer08,
author = {M. Verwoerd and O. Mason},
journal = {to appear in Siam Journal of Applied Dynamical Systems},
pubtype = {journal},
title = {Global phase-locking in finite populations of phase-coupled oscillators},
url = {http://arxiv.org/abs/0709.1558v1},
year = {2007},
bdsk-url-1 = {http://arxiv.org/abs/0709.1558v1}
}
@incollection{Bull_etal07,
author = {E. Bullinger and R. Findeisen and D. Kalamatianos and and P. Wellstead},
booktitle = {Biology and control theory: current challenges},
editor = {I. Queinnec and S. Tarbouriech and G. Garcia and S.-I. Niculescu},
owner = {d.o},
publisher = {Springer-Verlag, Berlin, Germany},
pubtype = {journal},
series = {Lecture Notes in Control and Information Sciences},
title = {System and control theory furthers the understanding of biological signal transduction},
volume = {357},
year = {2007}
}
@article{Vera_etal07,
author = {J. Vera and E. Balsa-Canto and P. Wellstead and J.R. Banga and O. Wolkenhauer},
journal = {Cellular Signalling},
pages = {1531--1541},
pubtype = {journal},
title = {Power-Law models of signal transduction pathways},
url = {http://dx.doi.org/10.1016/j.cellsig.2007.01.029},
volume = {19},
year = {2007},
bdsk-url-1 = {http://dx.doi.org/10.1016/j.cellsig.2007.01.029}
}
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author = {Ei\ss{}ing, T. and Waldherr, S. and Allg\"{o}wer, F. and Scheurich, P. and Bullinger, E.},
date = {4/2/2007},
date-modified = {2009-06-10 19:53:37 +0100},
journal = {Biophys. J.},
note = {In press},
owner = {eric},
project = {sysbio},
pubtype = {journal},
reviewed = {y},
title = {Response to Bistability in Apoptosis: Roles of {Bax}, {Bcl-2}, and Mitochondrial Permeability Transition Pores},
url = {http://www.biophysj.org/cgi/content/abstract/biophysj.106.100362v1},
year = 2007,
bdsk-url-1 = {http://www.biophysj.org/cgi/content/abstract/biophysj.106.100362v1}
}
@article{eissing2007a,
author = {Ei\ss{}ing, T. and Waldherr, S. and Allg\"{o}wer, F. and Scheurich, P. and Bullinger, E.},
date = {11/1/2007},
date-modified = {2009-06-10 19:53:49 +0100},
journal = {BioSystems},
note = {In press},
owner = {eric},
project = {sysbio},
pubtype = {journal},
reviewed = {y},
title = {Steady state and (bi-)stability evaluation of simple protease signalling networks},
url = {http://www.sciencedirect.com/science/article/B6T2K-4MTK97M-1/2/4ceef3c319208dcadf52105e16d6d92e},
year = {2007},
bdsk-url-1 = {http://www.sciencedirect.com/science/article/B6T2K-4MTK97M-1/2/4ceef3c319208dcadf52105e16d6d92e}
}
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annote = {hui},
author = {T. Jahnke and W. Huisinga},
journal = {J. Math. Biol.},
owner = {d.o},
pages = {1--26},
pdf = {http://compphysiol.mi.fu-berlin.de/pub/JaHu2005MasterEquation.pdf},
pubtype = {journal},
timestamp = {2007.02.07},
title = {Solving the chemical master equation for monomolecular reaction systems analytically},
volume = {54},
year = {2007}
}
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author = {O. Mason and M.H.A. Verwoerd},
journal = {IET Systems Biology},
number = {2},
pages = {89--119},
pubtype = {journal},
title = {Graph Theory and Networks in Biology},
volume = {1},
year = {2007}
}
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annote = {hui - ehemals husc:05,husc:02},
author = {W. Huisinga and B. Schmidt},
booktitle = {Advances in Algorithms for Macromolecular Simulation},
editor = {Benedict Leimkuhler et al.},
owner = {d.o},
pages = {167--182},
pdf = {http://www.hamilton.ie/compphysiol/pub/MetastabDominantEV.pdf},
publisher = {Springer},
pubtype = {journal},
series = {Lecture Notes in Computational Science and Engineering},
timestamp = {2007.02.07},
title = {Metastability and Dominant Eigenvalues of Transfer Operators},
volume = {49},
year = {2006}
}
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annote = {hui},
author = {W. Huisinga and R. Telgmann and M. Wulkow},
journal = {Drug Discovery Today},
number = {17 \& 18},
owner = {d.o},
pages = {800--805},
pdf = {http://www.hamilton.ie/compphysiol/pub/VirtualLab.pdf},
pubtype = {journal},
timestamp = {2007.02.07},
title = {The virtual lab approach to pharmacokinetic: Design principles and concepts},
volume = {11},
year = {2006}
}
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annote = {hui},
author = {B.F. Krippendorff and P. Lienau and A. Reichel and W. Huisinga},
journal = {J. Biomolecular Screening},
note = {in press, online Nov 27},
owner = {d.o},
pdf = {http://www.hamilton.ie/compphysiol/pub/TwoPointAssay.pdf},
pubtype = {journal},
timestamp = {2007.02.07},
title = {Optimizing Classification of Drug-Drug Interaction Potential for {CYP450} Iso-Enzymes Inhibition Assays in Early Drug Discovery},
year = {2006}
}
@incollection{WolkMesWell:06,
address = {Berlin},
author = {O. Wolkenhauer and M. Mesarovic and P. Wellstead},
booktitle = {Systems Biology - Applications and Perspectives},
date = {2006-01-23},
editor = {E. Butcher and P. Bringmann and B. Weiss},
owner = {peter},
project = {sysbio},
publisher = {Springer Verlag},
pubtype = {book},
reviewed = {y},
title = {A Plea for More Theory in Molecular Biology},
year = 2006
}
@article{eb:millat06a,
author = {T. Millat and E. Bullinger and J. Rohwer and O. Wolkenhauer},
date = {9 Mai 2006},
journal = {Math Bioscience},
note = {In press},
owner = {eric},
pmid = 17070871,
project = {sysbio},
pubtype = {journal},
reviewed = {y},
title = {Approximations and their Consequences for Dynamic Modelling of Signal Transduction Pathways},
url = {http://dx.doi.org/10.1016/j.mbs.2006.08.012},
year = 2006,
bdsk-url-1 = {http://dx.doi.org/10.1016/j.mbs.2006.08.012}
}
@article{eb:nickel06a,
author = {M. Nickel and E. Bullinger and F. Beckmann},
date = {9 February 2006},
journal = {Zoomorphology},
number = 4,
owner = {eric},
pages = {225--239},
project = {sysbio},
pubtype = {journal},
reviewed = {y},
title = {Functional Morphology of {{\em Tethya}} species (Porifera): 2.\ Three-dimensional morphometrics on Spicules and Skeleton Superstructures of {{\em T.\ minuta}}},
url = {http://dx.doi.org/10.1007/s00435-006-0022-0},
volume = 125,
year = 2006,
bdsk-url-1 = {http://dx.doi.org/10.1007/s00435-006-0022-0}
}
@article{ChoWell:05,
author = {K-H. Cho and S-M. Choo and P. Wellstead and O. Wolkenhauer},
date = {2006-01-23},
journal = {FEBS Letters},
number = 20,
owner = {peter},
pages = {4520--4528},
project = {sysbio},
pubtype = {journal},
reviewed = {y},
title = {A Unified Framework For Unravelling The Functional Interaction Structure Of A Biomolecular Network Based On Stimulus-Response Experiment Data},
volume = 579,
year = 2005
}
@article{BIOCHEM05,
author = {Wolkenhauer, O. and Sreenath, S. N. and Wellstead, P. and Ullar, M. and Cho, K-H.},
date = {2006-01-23},
journal = {Biochemical Society Trans.},
number = 3,
owner = {peter},
pages = {505--515},
pmid = {15916553},
project = {sysbio},
pubtype = {journal},
reviewed = {y},
title = {A Systems and Signal-Oriented Approach to Intracellular Dynamics},
volume = 33,
year = 2005
}
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