Revealing neuronal function through microelectrode array recordings

MEJ Obien, K Deligkaris, T Bullmann… - Frontiers in …, 2015 - frontiersin.org
Microelectrode arrays and microprobes have been widely utilized to measure neuronal
activity, both in vitro and in vivo. The key advantage is the capability to record and stimulate …

Approximation and inference methods for stochastic biochemical kinetics—a tutorial review

D Schnoerr, G Sanguinetti… - Journal of Physics A …, 2017 - iopscience.iop.org
Stochastic fluctuations of molecule numbers are ubiquitous in biological systems. Important
examples include gene expression and enzymatic processes in living cells. Such systems …

Quantitative and logic modelling of molecular and gene networks

N Le Novere - Nature Reviews Genetics, 2015 - nature.com
Behaviours of complex biomolecular systems are often irreducible to the elementary
properties of their individual components. Explanatory and predictive mathematical models …

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 …

Systems medicine: the future of medical genomics and healthcare

C Auffray, Z Chen, L Hood - Genome medicine, 2009 - Springer
High-throughput technologies for DNA sequencing and for analyses of transcriptomes,
proteomes and metabolomes have provided the foundations for deciphering the structure …

Modelling the molecular mechanisms of synaptic plasticity using systems biology approaches

JH Kotaleski, KT Blackwell - Nature Reviews Neuroscience, 2010 - nature.com
Synaptic plasticity is thought to underlie learning and memory, but the complexity of the
interactions between the ion channels, enzymes and genes that are involved in synaptic …

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 …

Diffusion-controlled reactions modeling in Geant4-DNA

M Karamitros, S Luan, MA Bernal, J Allison… - Journal of …, 2014 - Elsevier
Context Under irradiation, a biological system undergoes a cascade of chemical reactions
that can lead to an alteration of its normal operation. There are different types of radiation …

[HTML][HTML] Space in systems biology of signaling pathways–towards intracellular molecular crowding in silico

K Takahashi, SNV Arjunan, M Tomita - FEBS letters, 2005 - Elsevier
How cells utilize intracellular spatial features to optimize their signaling characteristics is still
not clearly understood. The physical distance between the cell-surface receptor and the …

Rule-based multi-level modeling of cell biological systems

C Maus, S Rybacki, AM Uhrmacher - BMC systems biology, 2011 - Springer
Background Proteins, individual cells, and cell populations denote different levels of an
organizational hierarchy, each of which with its own dynamics. Multi-level modeling is …