Parallel implementation of stochastic simulation for large-scale cellular processes [PDF]
, 2005 Experimental and theoretical studies have shown the importance of stochastic processes in genetic regulatory networks and cellular processes. Cellular networks and genetic circuits often involve small numbers of key proteins such as transcriptional ...
Kevin Burrage +6 more
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Information transfer in signaling pathways: A study using coupled simulated and experimental data [PDF]
BMC Bioinformatics, 2008 Background The topology of signaling cascades has been studied in quite some detail. However, how information is processed exactly is still relatively unknown. Since quite diverse information has to be transported by one and the same signaling cascade (e.
Dixon C Jane +3 more
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Bistability versus bimodal distributions in gene regulatory processes from population balance. [PDF]
PLoS Computational Biology, 2011 In recent times, stochastic treatments of gene regulatory processes have appeared in the literature in which a cell exposed to a signaling molecule in its environment triggers the synthesis of a specific protein through a network of intracellular ...
Che-Chi Shu +4 more
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The role of type 4 phosphodiesterases in generating microdomains of cAMP: Large scale stochastic simulations [PDF]
, 2010 Cyclic AMP (cAMP) and its main effector Protein Kinase A (PKA) are critical for several aspects of neuronal function including synaptic plasticity. Specificity of synaptic plasticity requires that cAMP activates PKA in a highly localized manner despite ...
Terrin, A. +35 more
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G3: Genes, Genomes, Genetics, 2019 Several examples of transcription factors that show stochastic, unsynchronized pulses of nuclear localization have been described. Here we show that under constant calcium stress, nuclear localization pulses of the transcription factor Crz1 follow ...
Ian S. Hsu +3 more
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Noise propagation in two-step series MAPK cascade. [PDF]
PLoS ONE, 2012 Series MAPK enzymatic cascades, ubiquitously found in signaling networks, act as signal amplifiers and play a key role in processing information during signal transduction in cells.
Venkata Dhananjaneyulu +3 more
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Asymmetric stochastic switching driven by intrinsic molecular noise. [PDF]
PLoS ONE, 2012 Low-copy-number molecules are involved in many functions in cells. The intrinsic fluctuations of these numbers can enable stochastic switching between multiple steady states, inducing phenotypic variability.
David Frigola +3 more
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The microRNA mir-71 inhibits calcium signaling by targeting the TIR-1/Sarm1 adaptor protein to control stochastic L/R neuronal asymmetry in C. elegans. [PDF]
PLoS Genetics, 2012 The Caenorhabditis elegans left and right AWC olfactory neurons communicate to establish stochastic asymmetric identities, AWC(ON) and AWC(OFF), by inhibiting a calcium-mediated signaling pathway in the future AWC(ON) cell. NSY-4/claudin-like protein and
Yi-Wen Hsieh +2 more
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Signaling pathways have an inherent need for noise to acquire information
BMC Bioinformatics, 2020 Background All living systems acquire information about their environment. At the cellular level, they do so through signaling pathways. Such pathways rely on reversible binding interactions between molecules that detect and transmit the presence of an ...
Eugenio Azpeitia +2 more
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On the origin and characteristics of noise-induced Lévy walks of E. coli. [PDF]
PLoS ONE, 2011 Lévy walks as a random search strategy have recently attracted a lot of attention, and have been described in many animal species. However, very little is known about one of the most important issues, namely how Lévy walks are generated by biological ...
Franziska Matthäus +3 more
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