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 …
been widely applied in molecular biology. In particular, alignment-free sequence analysis …
Dynamical criticality: overview and open questions
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 …
condition, poised between order and disorder. This observation is at the core of the so …
Quantifying hidden order out of equilibrium
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 …
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
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 …
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 …
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 …
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
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 …
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 …
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 …
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 …
patterns. This organization emerges during development from the coupling of dynamic intra …