scholarly journals Incorporating Time Delays in Process Hitting Framework for Dynamical Modeling of Large Biological Regulatory Networks

2019 ◽  
Vol 10 ◽  
Author(s):  
Iftikhar Ali Sheikh ◽  
Jamil Ahmad ◽  
Morgan Magnin ◽  
Olivier Roux
Keyword(s):  
Time Delays ◽  
Regulatory Networks ◽  
Dynamical Modeling ◽  
Biological Regulatory Networks

scholarly journals Learning Delays in Biological Regulatory Networks from Time Series Data

2017 ◽  
Vol 3 (2) ◽  
pp. 43
Author(s):  
Emna Ben Abdallah ◽  
Tony Ribeiro ◽  
Morgan Magnin ◽  
Olivier Roux ◽  
Katsumi Inoue
Keyword(s):  
Time Delays ◽  
Regulatory Networks ◽  
Time Series Data ◽  
Series Data ◽  
Learning Approach ◽  
Direct Integration ◽  
Biological Models ◽  
High Throughput Data ◽  
Biological Regulatory Networks ◽  
Manual Analysis

Models of Biological Regulatory Networks are generally based on prior knowledge, either derived from literature and/or the manual analysis of biological observations. With the development of high-throughput data, there is a growing need for methods that automatically generate admissible models. To have a better understanding of the dynamical phenomena at stake in the influences between biological components, it would be necessary to include delayed influences in the model. The main purpose of this work is to have a resulting network as consistent as possible with the observed datasets regarding the conflicts and the simultaneity between transitions. The originality of our work is threefold: (i) the identification the sign of the interactions, (ii) the direct integration of quantitative time delays in the learning approach and (iii) the identification of the qualitative discrete levels that lead to the systems dynamics.In this work the precision of our automatic approach is discussed by applying it on dynamical biological models coming from the DREAM4 Challenge datasets.

Dynamical modeling of biological regulatory networks

Biosystems ◽  
2006 ◽  
Vol 84 (2) ◽  
pp. 77-80 ◽  
Author(s):  
Claudine Chaouiya ◽  
Hidde de Jong ◽  
Denis Thieffry
Keyword(s):  
Regulatory Networks ◽  
Dynamical Modeling ◽  
Biological Regulatory Networks

Modulation of Biological Regulatory Networks During Nephrogenesis

2006 ◽  
Vol 38 (4) ◽  
pp. 677-683 ◽  
Author(s):  
Kenneth S. Ramos ◽  
M. Hadi Falahatpisheh ◽  
Adrian Nanez ◽  
Qiang He
Keyword(s):  
Regulatory Networks ◽  
Biological Regulatory Networks

Stability Criteria for Genetic Regulatory Networks with Time Delays

2018 ◽  
Author(s):  
Shasha Xiao ◽  
Yantao Wang ◽  
Xian Zhang
Keyword(s):  
Time Delays ◽  
Regulatory Networks ◽  
Genetic Regulatory Networks ◽  
Stability Criteria

Stability and Bifurcation Analysis of Cyclic Genetic Regulatory Networks with Mixed Time Delays

2015 ◽  
Vol 14 (1) ◽  
pp. 202-220 ◽  
Author(s):  
Guang Ling ◽  
Zhi-Hong Guan ◽  
Rui-Quan Liao ◽  
Xin-Ming Cheng
Keyword(s):  
Bifurcation Analysis ◽  
Time Delays ◽  
Regulatory Networks ◽  
Genetic Regulatory Networks ◽  
Mixed Time Delays ◽  
Stability And Bifurcation ◽  
Stability And Bifurcation Analysis

Robust stability analysis of Markov jump standard genetic regulatory networks with mixed time delays and uncertainties

2013 ◽  
Vol 110 ◽  
pp. 44-50 ◽  
Author(s):  
Yanzheng Zhu ◽  
Qingrui Zhang ◽  
Zuolong Wei ◽  
Lixian Zhang
Keyword(s):  
Stability Analysis ◽  
Robust Stability ◽  
Time Delays ◽  
Regulatory Networks ◽  
Genetic Regulatory Networks ◽  
Markov Jump ◽  
Mixed Time Delays ◽  
Robust Stability Analysis

Robustness in biological regulatory networks IV: Application to genetic networks controlling the cell cycle

2012 ◽  
Vol 350 (5-6) ◽  
pp. 293-298 ◽  
Author(s):  
Jacques Demongeot ◽  
Jules Waku
Keyword(s):  
Cell Cycle ◽  
Regulatory Networks ◽  
Genetic Networks ◽  
Biological Regulatory Networks
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