Modelling and analysis of gene regulatory networks

G Karlebach, R Shamir - Nature reviews Molecular cell biology, 2008 - nature.com
Gene regulatory networks have an important role in every process of life, including cell
differentiation, metabolism, the cell cycle and signal transduction. By understanding the …

Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project

M Hucka, A Finney, BJ Bornstein, SM Keating… - Systems biology, 2004 - IET
Biologists are increasingly recognising that computational modelling is crucial for making
sense of the vast quantities of complex experimental data that are now being collected. The …

Efficient step size selection for the tau-leaping simulation method

Y Cao, DT Gillespie, LR Petzold - The Journal of chemical physics, 2006 - pubs.aip.org
The tau-leaping method of simulating the stochastic time evolution of a well-stirred
chemically reacting system uses a Poisson approximation to take time steps that leap over …

Petri nets for systems and synthetic biology

M Heiner, D Gilbert, R Donaldson - … school on formal methods for the …, 2008 - Springer
We give a description of a Petri net-based framework for modelling and analysing
biochemical pathways, which unifies the qualitative, stochastic and continuous paradigms …

Gillespie-driven kinetic Monte Carlo algorithms to model events for bulk or solution (bio) chemical systems containing elemental and distributed species

AD Trigilio, YW Marien… - Industrial & …, 2020 - ACS Publications
Stochastic modeling techniques have emerged as a powerful tool to study the time evolution
of processes in many research fields including (bio) chemical engineering and biology. One …

Computation with finite stochastic chemical reaction networks

D Soloveichik, M Cook, E Winfree, J Bruck - natural computing, 2008 - Springer
A highly desired part of the synthetic biology toolbox is an embedded chemical
microcontroller, capable of autonomously following a logic program specified by a set of …

Avoiding negative populations in explicit Poisson tau-leaping

Y Cao, DT Gillespie, LR Petzold - The Journal of chemical physics, 2005 - pubs.aip.org
The explicit tau-leaping procedure attempts to speed up the stochastic simulation of a
chemically reacting system by approximating the number of firings of each reaction channel …

Binomial leap methods for simulating stochastic chemical kinetics

T Tian, K Burrage - The Journal of chemical physics, 2004 - pubs.aip.org
This paper discusses efficient simulation methods for stochastic chemical kinetics. Based on
the τ-leap and midpoint τ-leap methods of Gillespie [DT Gillespie, J. Chem. Phys. 115, 1716 …

Mathematical modeling of intracellular signaling pathways

E Klipp, W Liebermeister - BMC neuroscience, 2006 - Springer
Dynamic modeling and simulation of signal transduction pathways is an important topic in
systems biology and is obtaining growing attention from researchers with experimental or …

[HTML][HTML] Stochastic simulation in systems biology

T Székely Jr, K Burrage - Computational and structural biotechnology …, 2014 - Elsevier
Natural systems are, almost by definition, heterogeneous: this can be either a boon or an
obstacle to be overcome, depending on the situation. Traditionally, when constructing …