A linear reformulation of Boolean optimization problems and structure identification of gene regulation networks

2013 ◽  
Author(s):  
Christian Breindl ◽  
Madalena Chaves ◽  
Frank Allgower
Keyword(s):  
Gene Regulation ◽  
Optimization Problems ◽  
Structure Identification ◽  
Gene Regulation Networks ◽  
Boolean Optimization ◽  
Linear Reformulation

ELECTRONIC DESIGN OF SYNTHETIC GENETIC NETWORKS

2007 ◽  
Vol 17 (10) ◽  
pp. 3507-3511 ◽  
Author(s):  
JAVIER M. BULDÚ ◽  
JORDI GARCÍA-OJALVO ◽  
ALEXANDRE WAGEMAKERS ◽  
MIGUEL A. F. SANJUÁN
Keyword(s):  
Gene Regulation ◽  
Genetic Networks ◽  
Nonlinear Circuits ◽  
Synthetic Gene ◽  
Electronic Circuits ◽  
Biochemical System ◽  
Gene Regulation Networks ◽  
Electronic Elements ◽  
Electronic Design

We propose the use of nonlinear electronic circuits to study synthetic gene regulation networks. Specifically, we have designed two electronic versions of a synthetic genetic clock, known as the "repressilator," making use of appropriate electronic elements linked in the same way as the original biochemical system. We study the effects of coupling in a population of electronic repressilators, with the aim of observing coherent oscillations of the whole population. With these results, we show that this kind of nonlinear circuits can be helpful in the design and understanding of synthetic genetic networks.

Reverse Engineering of Gene Regulation Networks with an Application to the DREAM4 in silico Network Challenge

2011 ◽  
pp. 461-477 ◽  
Author(s):  
Hyonho Chun ◽  
Jia Kang ◽  
Xianghua Zhang ◽  
Minghua Deng ◽  
Haisu Ma ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Reverse Engineering ◽  
In Silico ◽  
Gene Regulation Networks

scholarly journals Adaptive memory search for Boolean optimization problems

2004 ◽  
Vol 142 (1-3) ◽  
pp. 99-109 ◽  
Author(s):  
Lars M. Hvattum ◽  
Arne Løkketangen ◽  
Fred Glover
Keyword(s):  
Optimization Problems ◽  
Memory Search ◽  
Adaptive Memory ◽  
Boolean Optimization

Estimating time‐varying directed gene regulation networks

Biometrics ◽  
2017 ◽  
Vol 73 (4) ◽  
pp. 1231-1242 ◽  
Author(s):  
Yunlong Nie ◽  
LiangLiang Wang ◽  
Jiguo Cao
Keyword(s):  
Gene Regulation ◽  
Time Varying ◽  
Gene Regulation Networks
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