Parity and time reversal elucidate both decision-making in empirical models and attractor scaling in critical Boolean networks

JC Rozum, J Gómez Tejeda Zañudo, X Gan… - Science …, 2021 - science.org
We present new applications of parity inversion and time reversal to the emergence of
complex behavior from simple dynamical rules in stochastic discrete models. Our parity …

Improving the efficiency of attractor cycle identification in Boolean networks

DJ Irons - Physica D: Nonlinear Phenomena, 2006 - Elsevier
Boolean network models provide a computationally efficient way of studying dynamical
processes on networks and are most frequently used to study the dynamical properties of …

AEON. py: Python library for attractor analysis in asynchronous Boolean networks

N Beneš, L Brim, O Huvar, S Pastva, D Šafránek… - …, 2022 - academic.oup.com
AEON. py is a Python library for the analysis of the long-term behaviour in very large
asynchronous Boolean networks. It provides significant computational improvements over …

Bayesian inference in ring attractor networks

A Kutschireiter, MA Basnak, RI Wilson… - Proceedings of the …, 2023 - National Acad Sciences
Working memories are thought to be held in attractor networks in the brain. These attractors
should keep track of the uncertainty associated with each memory, so as to weigh it properly …

An evaluation of methods for inferring Boolean networks from time-series data

N Berestovsky, L Nakhleh - PloS one, 2013 - journals.plos.org
Regulatory networks play a central role in cellular behavior and decision making. Learning
these regulatory networks is a major task in biology, and devising computational methods …

Steady-state probabilities for attractors in probabilistic Boolean networks

M Brun, ER Dougherty, I Shmulevich - Signal Processing, 2005 - Elsevier
Boolean networks form a class of disordered dynamical systems that have been studied in
physics owing to their relationships with disordered systems in statistical mechanics and in …

State reduction for network intervention in probabilistic Boolean networks

X Qian, N Ghaffari, I Ivanov, ER Dougherty - Bioinformatics, 2010 - academic.oup.com
Motivation: A key goal of studying biological systems is to design therapeutic intervention
strategies. Probabilistic Boolean networks (PBNs) constitute a mathematical model which …

Criticality distinguishes the ensemble of biological regulatory networks

BC Daniels, H Kim, D Moore, S Zhou, HB Smith… - Physical review …, 2018 - APS
The hypothesis that many living systems should exhibit near-critical behavior is well
motivated theoretically, and an increasing number of cases have been demonstrated …

Scaling in ordered and critical random Boolean networks

JES Socolar, SA Kauffman - Physical review letters, 2003 - APS
Random Boolean networks, originally invented as models of genetic regulatory networks,
are simple models for a broad class of complex systems that show rich dynamical structures …

pystablemotifs: Python library for attractor identification and control in Boolean networks

JC Rozum, D Deritei, KH Park… - …, 2022 - academic.oup.com
Abstract Summary pystablemotifs is a Python 3 library for analyzing Boolean networks. Its
non-heuristic and exhaustive attractor identification algorithm was previously presented in …