An optimal Bayesian intervention policy in response to unknown dynamic cell stimuli

SH Hosseini, M Imani - Information Sciences, 2024 - Elsevier
Interventions in gene regulatory networks (GRNs) aim to restore normal functions of cells
experiencing abnormal behavior, such as uncontrolled cell proliferation. The dynamic …

Adaptive intervention in probabilistic Boolean networks

R Layek, A Datta, R Pal, ER Dougherty - Bioinformatics, 2009 - academic.oup.com
Motivation: A basic problem of translational systems biology is to utilize gene regulatory
networks as a vehicle to design therapeutic intervention strategies to beneficially alter …

[PDF][PDF] Optimal constrained stationary intervention in gene regulatory networks

B Faryabi, G Vahedi, JF Chamberland, A Datta… - EURASIP Journal on …, 2008 - Springer
A key objective of gene network modeling is to develop intervention strategies to alter
regulatory dynamics in such a way as to reduce the likelihood of undesirable phenotypes …

A comparison study of optimal and suboptimal intervention policies for gene regulatory networks in the presence of uncertainty

MR Yousefi, ER Dougherty - EURASIP Journal on Bioinformatics and …, 2014 - Springer
Perfect knowledge of the underlying state transition probabilities is necessary for designing
an optimal intervention strategy for a given Markovian genetic regulatory network. However …

A CoD-based reduction algorithm for designing stationary control policies on Boolean networks

N Ghaffari, I Ivanov, X Qian, ER Dougherty - Bioinformatics, 2010 - academic.oup.com
Motivation: Gene regulatory networks serve as models from which to derive therapeutic
intervention strategies, in particular, stationary control policies over time that shift the …

Intervention in gene regulatory networks via phenotypically constrained control policies based on long-run behavior

X Qian, ER Dougherty - IEEE/ACM Transactions on …, 2011 - ieeexplore.ieee.org
A salient purpose for studying gene regulatory networks is to derive intervention strategies to
identify potential drug targets and design gene-based therapeutic intervention. Optimal and …

Gene perturbation and intervention in probabilistic Boolean networks

I Shmulevich, ER Dougherty, W Zhang - Bioinformatics, 2002 - academic.oup.com
Motivation: A major objective of gene regulatory network modeling, in addition to gaining a
deeper understanding of genetic regulation and control, is the development of …

Intervention in gene regulatory networks via greedy control policies based on long-run behavior

X Qian, I Ivanov, N Ghaffari, ER Dougherty - BMC systems biology, 2009 - Springer
Background A salient purpose for studying gene regulatory networks is to derive intervention
strategies, the goals being to identify potential drug targets and design gene-based …

On the long-run sensitivity of probabilistic Boolean networks

X Qian, ER Dougherty - Journal of theoretical biology, 2009 - Elsevier
Boolean networks and, more generally, probabilistic Boolean networks, as one class of
gene regulatory networks, model biological processes with the network dynamics …

Intervention in gene regulatory networks with maximal phenotype alteration

MR Yousefi, ER Dougherty - Bioinformatics, 2013 - academic.oup.com
Motivation: A basic issue for translational genomics is to model gene interaction via gene
regulatory networks (GRNs) and thereby provide an informatics environment to study the …