Modeling stochasticity and robustness in gene regulatory networks
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Procedural modeling allows for the generation of innumerable variations of models from a parameterized, conditional or stochastic rule set. Due to the abstractness, complexity and stochastic nature of rule sets, it is often very difficult to have an unders ...
Wiley-Blackwell2014
The external control of Gene Regulatory Networks (GRNs) has received much attention in recent years. In this paper, we propose a novel algorithm for controlling partially observable GRNs coupling utility based state learning methods and Batch Mode Reinforc ...
The precise tuning of gene expression levels is essential for the optimal performance of transcriptional regulatory networks. We created 209 variants of the Saccharomyces cerevisiae PHO5 promoter to quantify how different binding sites for the transcriptio ...
The goal of controlling a gene regulatory network (GRN) is to generate an intervention strategy, i.e., a control policy, such that by applying the policy the system will avoid undesirable states. In this work, we propose a method to control GRNs by using B ...
Mapping gene regulatory networks is a significant challenge in systems biology, yet only a few methods are currently capable of systems-level identification of transcription factors (TFs) that bind a specific regulatory element. We developed a microfluidic ...
Over the last decade, modeling and controlling gene regulation has received much attention. In this thesis, we have attempted to solve (i) controlling gene regulation systems and (ii) generating high quality artificial gene expression data problems. For co ...
Gene regulatory networks control gene expression levels, and therefore play an essential role in mammalian development and function. Regulation of gene expression is the result of a complex interplay between DNA regulatory elements and their binding partne ...
Regulation of gene expression is a carefully regulated phenomenon in the cell. “Reverse-engineering” algorithms try to reconstruct the regulatory interactions among genes from genome-scale measurements of gene expression profiles (microarrays). Mammalian c ...
Cognitive abilities and disorders unique to humans are thought to result from adaptively driven changes in brain transcriptomes, but little is known about the role of cis-regulatory changes affecting transcription start sites (TSS). Here, we mapped in huma ...
Numerous methods have been developed for inference of gene regulatory networks from expression data, however, their strengths and weaknesses remain poorly understood. Accurate and systematic evaluation of these methods is hampered by the difficulty of cons ...
