Boolean modeling in systems biology: an overview of methodology and applications
Mathematical modeling of biological processes provides deep insights into complex cellular
systems. While quantitative and continuous models such as differential equations have been …
systems. While quantitative and continuous models such as differential equations have been …
Boolean modeling: a logic‐based dynamic approach for understanding signaling and regulatory networks and for making useful predictions
The biomolecules inside or near cells form a complex interacting system. Cellular
phenotypes and behaviors arise from the totality of interactions among the components of …
phenotypes and behaviors arise from the totality of interactions among the components of …
Benchmarking algorithms for gene regulatory network inference from single-cell transcriptomic data
We present a systematic evaluation of state-of-the-art algorithms for inferring gene
regulatory networks from single-cell transcriptional data. As the ground truth for assessing …
regulatory networks from single-cell transcriptional data. As the ground truth for assessing …
Symmetry and simplicity spontaneously emerge from the algorithmic nature of evolution
Engineers routinely design systems to be modular and symmetric in order to increase
robustness to perturbations and to facilitate alterations at a later date. Biological structures …
robustness to perturbations and to facilitate alterations at a later date. Biological structures …
Inferring gene regulatory network from single-cell transcriptomes with graph autoencoder model
The gene regulatory structure of cells involves not only the regulatory relationship between
two genes, but also the cooperative associations of multiple genes. However, most gene …
two genes, but also the cooperative associations of multiple genes. However, most gene …
SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools
Background Qualitative frameworks, especially those based on the logical discrete
formalism, are increasingly used to model regulatory and signalling networks. A major …
formalism, are increasingly used to model regulatory and signalling networks. A major …
Boolean modeling of biological regulatory networks: a methodology tutorial
Given the complexity and interactive nature of biological systems, constructing informative
and coherent network models of these systems and subsequently develo** efficient …
and coherent network models of these systems and subsequently develo** efficient …
Criticality distinguishes the ensemble of biological regulatory networks
The hypothesis that many living systems should exhibit near-critical behavior is well
motivated theoretically, and an increasing number of cases have been demonstrated …
motivated theoretically, and an increasing number of cases have been demonstrated …
Modeling approaches for qualitative and semi-quantitative analysis of cellular signaling networks
R Samaga, S Klamt - Cell communication and signaling, 2013 - Springer
A central goal of systems biology is the construction of predictive models of bio-molecular
networks. Cellular networks of moderate size have been modeled successfully in a …
networks. Cellular networks of moderate size have been modeled successfully in a …
BTR: training asynchronous Boolean models using single-cell expression data
Background Rapid technological innovation for the generation of single-cell genomics data
presents new challenges and opportunities for bioinformatics analysis. One such area lies in …
presents new challenges and opportunities for bioinformatics analysis. One such area lies in …