Attractors in Boolean networks: a tutorial

被引：34

作者：

Hopfensitz, Martin ^{[1
]}

Muessel, Christoph ^{[1
]}

Maucher, Markus ^{[1
]}

Kestler, Hans A. ^{[1
]}

机构：

[1] Univ Ulm, Res Grp Bioinformat & Syst Biol, Inst Neural Informat Proc, D-89069 Ulm, Germany

来源：

COMPUTATIONAL STATISTICS | 2013年 / 28卷 / 01期

关键词：

Systems biology; Boolean networks; Attractors; REGULATORY NETWORKS; GENETIC NETWORKS; MODEL;

D O I：

10.1007/s00180-012-0324-2

中图分类号：

O21 [概率论与数理统计]; C8 [统计学];

学科分类号：

020208 ; 070103 ; 0714 ;

摘要：

Boolean networks are a popular class of models for the description of gene-regulatory networks. They model genes as simple binary variables, being either expressed or not expressed. Simulations of Boolean networks can give insights into the dynamics of cellular systems. In particular, stable states and cycles in the networks are thought to correspond to phenotypes. This paper presents approaches to identify attractors in synchronous, asynchronous and probabilistic Boolean networks and gives examples of their usage in the BoolNet R package.

引用

页码：19 / 36

页数：18

共 50 条

[41] Stochastic Local Search to Automatically Design Boolean Networks with Maximally Distant Attractors
Benedettini, Stefano
Roli, Andrea
Serra, Roberto
Villani, Marco
[J]. APPLICATIONS OF EVOLUTIONARY COMPUTATION, PT I, 2011, 6624 : 22 - +
[42] An Improved Method for Finding Attractors of Large-Scale Asynchronous Boolean Networks
Trinh Van Giang
Hiraishi, Kunihiko
[J]. 2021 IEEE CONFERENCE ON COMPUTATIONAL INTELLIGENCE IN BIOINFORMATICS AND COMPUTATIONAL BIOLOGY (CIBCB), 2021, : 246 - 254
[43] Local Negative Circuits and Cyclic Attractors in Boolean Networks with at most Five Components
Tonello, Elisa
Farcot, Etienne
Chaouiya, Claudine
[J]. SIAM JOURNAL ON APPLIED DYNAMICAL SYSTEMS, 2019, 18 (01): : 68 - 79
[44] Integer programming-based method for observability of singleton attractors in Boolean networks
Cheng, Xiaoqing
Qiu, Yushan
Hou, Wenpin
Ching, Wai-Ki
[J]. IET SYSTEMS BIOLOGY, 2017, 11 (01) : 30 - 35
[45] Edgetic perturbations to eliminate fixed-point attractors in Boolean regulatory networks
Campbell, Colin
Albert, Reka
[J]. CHAOS, 2019, 29 (02)
[46] Singleton and 2-periodic attractors of sign-definite Boolean networks
Akutsu, Tatsuya
Melkman, Avraham A.
Tamura, Takeyuki
[J]. INFORMATION PROCESSING LETTERS, 2012, 112 (1-2) : 35 - 38
[47] FINDING ATTRACTORS IN ASYNCHRONOUS BOOLEAN DYNAMICS
Skodawessely, Thomas
Klemm, Konstantin
[J]. ADVANCES IN COMPLEX SYSTEMS, 2011, 14 (03): : 439 - 449
[48] ILP/SMT-Based Method for Design of Boolean Networks Based on Singleton Attractors
Kobayashi, Koichi
Hiraishi, Kunihiko
[J]. IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, 2014, 11 (06) : 1253 - 1259
[49] On the dynamics of random Boolean networks subject to noise: Attractors, ergodic sets and cell types
Serra, R.
Villani, M.
Barbieri, A.
Kauffman, S. A.
Colacci, A.
[J]. JOURNAL OF THEORETICAL BIOLOGY, 2010, 265 (02) : 185 - 193
[50] Detecting small attractors of large Boolean networks by function-reduction-based strategy
Zheng, Qiben
Shen, Liangzhong
Shang, Xuequn
Liu, Wenbin
[J]. IET SYSTEMS BIOLOGY, 2016, 10 (02) : 49 - 56

← 1 2 3 4 5 →