Kinetic models of gene expression including non-coding RNAs

VP Zhdanov - Physics Reports, 2011 - Elsevier
In cells, genes are transcribed into mRNAs, and the latter are translated into proteins. Due to
the feedbacks between these processes, the kinetics of gene expression may be complex …

Dose response relationship in anti-stress gene regulatory networks

Q Zhang, ME Andersen - PLoS computational biology, 2007 - journals.plos.org
To maintain a stable intracellular environment, cells utilize complex and specialized defense
systems against a variety of external perturbations, such as electrophilic stress, heat shock …

Counter-intuitive stochastic behavior of simple gene circuits with negative feedback

TT Marquez-Lago, J Stelling - Biophysical journal, 2010 - cell.com
It has often been taken for granted that negative feedback loops in gene regulation work as
homeostatic control mechanisms. If one increases the regulation strength a less noisy signal …

Accuracy of positional information provided by multiple morphogen gradients with correlated noise

Y Morishita, Y Iwasa - Physical Review E—Statistical, Nonlinear, and Soft …, 2009 - APS
Normal development of multicellular organisms requires cells to respond properly according
to their positions. Positional information is often provided to cells as concentrations of …

Multiple feedback loop design in the tryptophan regulatory network of Escherichia coli suggests a paradigm for robust regulation of processes in series

S Bhartiya, N Chaudhary… - Journal of the …, 2006 - royalsocietypublishing.org
Biological networks have evolved through adaptation in uncertain environments. Of the
different possible design paradigms, some may offer functional advantages over others …

Intrinsic noise in post-transcriptional gene regulation by small non-coding RNA

Y Jia, W Liu, A Li, L Yang, X Zhan - Biophysical Chemistry, 2009 - Elsevier
Small non-coding RNA (sRNA) plays very important role in the post transcriptional
regulation in various organisms. In complex regulatory networks, highly significant relative …

An optimal number of molecules for signal amplification and discrimination in a chemical cascade

Y Morishita, TJ Kobayashi, K Aihara - Biophysical journal, 2006 - cell.com
Understanding the information processing ability of signal transduction pathways is of great
importance because of their crucial roles in triggering various cellular responses. Despite …

Large-scale on-off switching of genetic activity mediated by the folding-unfolding transition in a giant DNA molecule: An hypothesis

Y Takenaka, H Nagahara, H Kitahata… - Physical Review E …, 2008 - APS
We present a model to describe the on-off switching of transcriptional activity in a genetic
assembly by considering the intrinsic characteristics of a giant genomic DNA molecule …

Mutational robustness of gene regulatory networks

ADJ van Dijk, S van Mourik, RCHJ van Ham - PloS one, 2012 - journals.plos.org
Mutational robustness of gene regulatory networks refers to their ability to generate constant
biological output upon mutations that change network structure. Such networks contain …

Transient stochastic bistable kinetics of gene transcription during the cellular growth

VP Zhdanov - Chemical physics letters, 2006 - Elsevier
The feedback between mRNA and regulatory-protein production may result in bistability of
gene transcription. If the mRNA and/or protein number are low, one can observe …