Information theory applications for biological sequence analysis

S Vinga - Briefings in bioinformatics, 2014 - academic.oup.com
Abstract Information theory (IT) addresses the analysis of communication systems and has
been widely applied in molecular biology. In particular, alignment-free sequence analysis …

Dynamical criticality: overview and open questions

A Roli, M Villani, A Filisetti, R Serra - Journal of Systems Science and …, 2018 - Springer
Abstract Systems that exhibit complex behaviours are often found in a particular dynamical
condition, poised between order and disorder. This observation is at the core of the so …

Quantifying hidden order out of equilibrium

S Martiniani, PM Chaikin, D Levine - Physical Review X, 2019 - APS
While the equilibrium properties, states, and phase transitions of interacting systems are well
described by statistical mechanics, the lack of suitable state parameters has hindered the …

Describing the complexity of systems: Multivariable “set complexity” and the information basis of systems biology

DJ Galas, NA Sakhanenko, A Skupin… - Journal of Computational …, 2014 - liebertpub.com
Context dependence is central to the description of complexity. Keying on the pairwise
definition of “set complexity,” we use an information theory approach to formulate general …

Biological data analysis as an information theory problem: Multivariable dependence measures and the Shadows algorithm

NA Sakhanenko, DJ Galas - Journal of Computational Biology, 2015 - liebertpub.com
Abstract Information theory is valuable in multiple-variable analysis for being model-free and
nonparametric, and for the modest sensitivity to undersampling. We previously introduced a …

Studying software evolution using artefacts' shared information content

T Arbuckle - Science of Computer Programming, 2011 - Elsevier
In order to study software evolution, it is necessary to measure artefacts representative of
project releases. If we consider the process of software evolution to be copying with …

Information density, structure and entropy in equilibrium and non-equilibrium systems

M Zu, A Bupathy, D Frenkel… - Journal of Statistical …, 2020 - iopscience.iop.org
During a spontaneous change, a macroscopic physical system will evolve towards a macro-
state with more realizations. This observation is at the basis of the statistical mechanical …

Canalizing Boolean functions maximize mutual information

JG Klotz, D Kracht, M Bossert… - IEEE Transactions on …, 2014 - ieeexplore.ieee.org
Information processing in biologically motivated Boolean networks is of interest in recent
information theoretic research. One measure to quantify this ability is the well-known mutual …

A multilayer structure facilitates the production of antifragile systems in boolean network models

H Kim, OK Pineda, C Gershenson - Complexity, 2019 - Wiley Online Library
Antifragility is a property from which systems are able to resist stress and furthermore benefit
from it. Even though antifragile dynamics is found in various real‐world complex systems …

Kolmogorov complexity of epithelial pattern formation: The role of regulatory network configuration

NS Flann, H Mohamadlou, GJ Podgorski - Biosystems, 2013 - Elsevier
The tissues of multicellular organisms are made of differentiated cells arranged in organized
patterns. This organization emerges during development from the coupling of dynamic intra …