An Information Theoretic Approach to Constructing Robust Boolean Gene Regulatory Networks

2012 ◽  
Vol 9 (1) ◽  
pp. 52-65 ◽  
Author(s):  
B. Vasic ◽  
V. Ravanmehr ◽  
A. R. Krishnan
Keyword(s):  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Theoretic Approach ◽  
Information Theoretic ◽  
Gene Regulatory ◽  
Information Theoretic Approach

scholarly journals MapReduce Algorithms for Inferring Gene Regulatory Networks from Time-Series Microarray Data Using an Information-Theoretic Approach

2017 ◽  
Vol 2017 ◽  
pp. 1-8 ◽  
Author(s):  
Yasser Abduallah ◽  
Turki Turki ◽  
Kevin Byron ◽  
Zongxuan Du ◽  
Miguel Cervantes-Cervantes ◽  
...  
Keyword(s):  
Time Series ◽  
Gene Regulatory Networks ◽  
Microarray Data ◽  
Regulatory Networks ◽  
Experimental Results ◽  
Theoretic Approach ◽  
Information Theoretic ◽  
Gene Regulatory ◽  
Information Theoretic Approach ◽  
Time Series Microarray

Gene regulation is a series of processes that control gene expression and its extent. The connections among genes and their regulatory molecules, usually transcription factors, and a descriptive model of such connections are known as gene regulatory networks (GRNs). Elucidating GRNs is crucial to understand the inner workings of the cell and the complexity of gene interactions. To date, numerous algorithms have been developed to infer gene regulatory networks. However, as the number of identified genes increases and the complexity of their interactions is uncovered, networks and their regulatory mechanisms become cumbersome to test. Furthermore, prodding through experimental results requires an enormous amount of computation, resulting in slow data processing. Therefore, new approaches are needed to expeditiously analyze copious amounts of experimental data resulting from cellular GRNs. To meet this need, cloud computing is promising as reported in the literature. Here, we propose new MapReduce algorithms for inferring gene regulatory networks on a Hadoop cluster in a cloud environment. These algorithms employ an information-theoretic approach to infer GRNs using time-series microarray data. Experimental results show that our MapReduce program is much faster than an existing tool while achieving slightly better prediction accuracy than the existing tool.

scholarly journals SELF-ORGANIZING PARTICLE SYSTEMS

2013 ◽  
Vol 16 (02n03) ◽  
pp. 1250089
Author(s):  
MALTE HARDER ◽  
DANIEL POLANI
Keyword(s):  
Regulatory Networks ◽  
Particle System ◽  
Living Organism ◽  
Quantitative Information ◽  
Particle Systems ◽  
Self Organization ◽  
Theoretic Approach ◽  
Information Theoretic ◽  
Differential Adhesion ◽  
Information Theoretic Approach

The self-organization of cells into a living organism is a very intricate process. Under the surface of orchestrating regulatory networks there are physical processes which make the information processing possible, that is required to organize such a multitude of individual entities. We use a quantitative information theoretic approach to assess self-organization of a collective system. In particular, we consider an interacting particle system, that roughly mimics biological cells by exhibiting differential adhesion behavior. Employing techniques related to shape analysis, we show that these systems in most cases exhibit self-organization. Moreover, we consider spatial constraints of interactions, and additionaly show that particle systems can self-organize without the emergence of pattern-like structures. However, we will see that regular pattern-like structures help to overcome limitations of self-organization that are imposed by the spatial structure of interactions.

scholarly journals Time lagged information theoretic approaches to the reverse engineering of gene regulatory networks

2010 ◽  
Vol 11 (S6) ◽  
Author(s):  
Vijender Chaitankar ◽  
Preetam Ghosh ◽  
Edward J Perkins ◽  
Ping Gong ◽  
Chaoyang Zhang
Keyword(s):  
Reverse Engineering ◽  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Information Theoretic ◽  
Gene Regulatory ◽  
Time Lagged
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