A perspective on bridging scales and design of models using low-dimensional manifolds and data-driven model inference
Systems in nature capable of collective behaviour are nonlinear, operating across several
scales. Yet our ability to account for their collective dynamics differs in physics, chemistry …
scales. Yet our ability to account for their collective dynamics differs in physics, chemistry …
[HTML][HTML] Iterative Systems Biology for Medicine–Time for advancing from network signatures to mechanistic equations
D Gomez-Cabrero, J Tegnér - Current Opinion in Systems Biology, 2017 - Elsevier
The rise and growth of Systems Biology following the sequencing of the human genome has
been astounding. Early on, an iterative wet-dry methodology was formulated which turned …
been astounding. Early on, an iterative wet-dry methodology was formulated which turned …
Segregation and crosstalk of D1 receptor-mediated activation of ERK in striatal medium spiny neurons upon acute administration of psychostimulants
O Gutierrez-Arenas, O Eriksson… - PLoS computational …, 2014 - journals.plos.org
The convergence of corticostriatal glutamate and dopamine from the midbrain in the striatal
medium spiny neurons (MSN) triggers synaptic plasticity that underlies reinforcement …
medium spiny neurons (MSN) triggers synaptic plasticity that underlies reinforcement …
A checkpoints capturing timing-robust Boolean model of the budding yeast cell cycle regulatory network
Background Cell cycle process of budding yeast (Saccharomyces cerevisiae) consists of
four phases: G1, S, G2 and M. Initiated by stimulation of the G1 phase, cell cycle returns to …
four phases: G1, S, G2 and M. Initiated by stimulation of the G1 phase, cell cycle returns to …
Modeling and model simplification to facilitate biological insights and predictions
O Eriksson, J Tegnér - Uncertainty in Biology: A Computational Modeling …, 2016 - Springer
Mathematical dynamical models of intracellular signaling networks are continuously
increasing in size and model complexity due in large part to the data explosion in biology …
increasing in size and model complexity due in large part to the data explosion in biology …
Robustness of cell cycle control and flexible orders of signaling events
H Zhu, Y Mao - Scientific Reports, 2015 - nature.com
The highly robust control of cell cycles in eukaryotes enables cells to undergo strictly
ordered G1/S/G2/M phases and respond adaptively to regulatory signals; however the …
ordered G1/S/G2/M phases and respond adaptively to regulatory signals; however the …
Global sensitivity analysis of a model related to memory formation in synapses: Model reduction based on epistemic parameter uncertainties and related issues
D Kulasiri, J Liang, Y He, S Samarasinghe - Journal of theoretical biology, 2017 - Elsevier
We investigate the epistemic uncertainties of parameters of a mathematical model that
describes the dynamics of CaMKII-NMDAR complex related to memory formation in …
describes the dynamics of CaMKII-NMDAR complex related to memory formation in …
Dynamics of the cell-cycle network under genome-rewiring perturbations
Y Katzir, Y Elhanati, I Averbukh, E Braun - Physical Biology, 2013 - iopscience.iop.org
The cell-cycle progression is regulated by a specific network enabling its ordered dynamics.
Recent experiments supported by computational models have shown that a core of genes …
Recent experiments supported by computational models have shown that a core of genes …