Journal ArticleDOI
Dynamical behaviour of biological regulatory networks--I. Biological role of feedback loops and practical use of the concept of the loop-characteristic state.
TLDR
The recent concept of the loop-characteristic state, defined as the logical state located at the level of the thresholds involved in the loop, together with its application, are presented and their applications are discussed.About:
This article is published in Bulletin of Mathematical Biology.The article was published on 1995-03-01. It has received 488 citations till now. The article focuses on the topics: Biological regulation.read more
Citations
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Journal ArticleDOI
Modeling and simulation of genetic regulatory systems: a literature review.
TL;DR: This paper reviews formalisms that have been employed in mathematical biology and bioinformatics to describe genetic regulatory systems, in particular directed graphs, Bayesian networks, Boolean networks and their generalizations, ordinary and partial differential equations, qualitative differential equation, stochastic equations, and so on.
Journal ArticleDOI
Structure and function of the feed-forward loop network motif
S. Mangan,Uri Alon +1 more
TL;DR: This study defines the function of one of the most significant recurring circuit elements in transcription networks, the feed-forward loop (FFL), which is a three-gene pattern composed of two input transcription factors, both jointly regulating a target gene.
Journal ArticleDOI
Probabilistic Boolean networks: a rule-based uncertainty model for gene regulatory networks
TL;DR: Probabilistic Boolean Networks (PBN) are introduced that share the appealing rule-based properties of Boolean networks, but are robust in the face of uncertainty.
Proceedings ArticleDOI
Identification of genetic networks from a small number of gene expression patterns under the Boolean network model.
TL;DR: A much simpler algorithm is devised that is conceptually so simple that it is extensible for more realistic network models and shows that the Boolean network of size 100,000 can be identified by the algorithm from about 100 INPUT/OUTPUT pairs if the maximum indegree is bounded by 2.
Journal ArticleDOI
Engineered gene circuits
TL;DR: Synthetic gene networks will lead to new logical forms of cellular control, which could have important applications in functional genomics, nanotechnology, and gene and cell therapy.
References
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Book
Stability and Complexity in Model Ecosystems
Robert M. May,N. MacDonald +1 more
TL;DR: Preface vii Preface to the Second Edition Biology Edition 1.
Journal ArticleDOI
Metabolic stability and epigenesis in randomly constructed genetic nets
TL;DR: The hypothesis that contemporary organisms are also randomly constructed molecular automata is examined by modeling the gene as a binary (on-off) device and studying the behavior of large, randomly constructed nets of these binary “genes”.
Journal ArticleDOI
The logical analysis of continuous, non-linear biochemical control networks.
Leon Glass,Stuart A. Kauffman +1 more
TL;DR: A mapping to study the qualitative properties of continuous biochemical control networks which are invariant to the parameters used to describe the networks but depend only on the logical structure of the networks.
Journal ArticleDOI
Boolean formalization of genetic control circuits
TL;DR: This paper is an attempt to formalize in Boolean terms genetic situations, from simple concepts like recessitivity and cis-dominance, to models describing complex control circuits, to describe in compact and unambiguous way, systems which become more and more difficult to describe as their complexity is being unravelled.
Related Papers (5)
Metabolic stability and epigenesis in randomly constructed genetic nets
The logical analysis of continuous, non-linear biochemical control networks.
Leon Glass,Stuart A. Kauffman +1 more