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Article
Open AccessRepresentation and quantification of module activity from omics data with rROMA
The efficiency of analyzing high-throughput data in systems biology has been demonstrated in numerous studies, where molecular data, such as transcriptomics and proteomics, offers great opportunities for under...
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Article
Open AccessPhysiBoSS 2.0: a sustainable integration of stochastic Boolean and agent-based modelling frameworks
In systems biology, mathematical models and simulations play a crucial role in understanding complex biological systems. Different modelling frameworks are employed depending on the nature and scales of the sy...
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Article
Open AccessConvergent network effects along the axis of gene expression during prostate cancer progression
Tumor-specific genomic aberrations are routinely determined by high-throughput genomic measurements. It remains unclear how complex genome alterations affect molecular networks through changing protein levels ...
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Article
Open AccessExact solving and sensitivity analysis of stochastic continuous time Boolean models
Solutions to stochastic Boolean models are usually estimated by Monte Carlo simulations, but as the state space of these models can be enormous, there is an inherent uncertainty about the accuracy of Monte Car...
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Chapter and Conference Paper
Synthesis and Simulation of Ensembles of Boolean Networks for Cell Fate Decision
The construction of models of biological networks from prior knowledge and experimental data often leads to a multitude of candidate models. Devising a single model from them can require arbitrary choices, whi...
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Article
Open AccessClassification of gene signatures for their information value and functional redundancy
Gene signatures are more and more used to interpret results of omics data analyses but suffer from compositional (large overlap) and functional (correlated read-outs) redundancy. Moreover, many gene signatures...
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Article
Open AccessQualitative dynamics semantics for SBGN process description
Qualitative dynamics semantics provide a coarse-grain modeling of networks dynamics by abstracting away kinetic parameters. They allow to capture general features of systems dynamics, such as attractors or rea...
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Article
Open AccessDeDaL: Cytoscape 3 app for producing and morphing data-driven and structure-driven network layouts
Visualization and analysis of molecular profiling data together with biological networks are able to provide new mechanistic insights into biological functions. Currently, it is possible to visualize high-thro...
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Article
Open AccessNaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps
Molecular biology knowledge can be formalized and systematically represented in a computer-readable form as a comprehensive map of molecular interactions. There exist an increasing number of maps of molecular ...
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Article
On Circuit Functionality in Boolean Networks
It has been proved, for several classes of continuous and discrete dynamical systems, that the presence of a positive (resp. negative) circuit in the interaction graph of a system is a necessary condition for ...
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Article
Open AccessBiNoM 2.0, a Cytoscape plugin for accessing and analyzing pathways using standard systems biology formats
Public repositories of biological pathways and networks have greatly expanded in recent years. Such databases contain many pathways that facilitate the analysis of high-throughput experimental work and the for...
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Reference Work Entry In depth
Cell Cycle Transition, Detailed Regulation of Restriction Point
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Protocol
From a Biological Hypothesis to the Construction of a Mathematical Model
Mathematical models serve to explain complex biological phenomena and provide predictions that can be tested experimentally. They can provide plausible scenarios of a complex biological behavior when intuition...
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Chapter and Conference Paper
How Cell Decides Between Life and Death: Mathematical Modeling of Epigenetic Landscapes of Cellular Fates
We present a mathematical model of cell fate decision between survival, necrosis and apoptosis as a concrete implementation of the Waddington’s metaphor of epigenetic landscape determining cellular behaviour. ...
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Chapter
Understanding Different Types of Cell Death Using Systems Biology
This chapter is devoted to the mathematical modeling of cellular decisions between death and life (referred to as cell fate decision). These decisions determine many cell events in multicellular and unicellula...
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Protocol
Practical Use of BiNoM: A Biological Network Manager Software
The Biological Network Manager (BiNoM) is a software tool for the manipulation and analysis of biological networks. It facilitates the import and conversion of a set of well-established systems biology file fo...
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Article
Open AccessContinuous time boolean modeling for biological signaling: application of Gillespie algorithm
Mathematical modeling is used as a Systems Biology tool to answer biological questions, and more precisely, to validate a network that describes biological observations and predict the effect of perturbations....
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Chapter and Conference Paper
Cell Death and Life in Cancer: Mathematical Modeling of Cell Fate Decisions
Tumor development is characterized by a compromised balance between cell life and death decision mechanisms, which are tightly regulated in normal cells. Understanding this process provides insights for develo...
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Article
Erratum: The Systems Biology Graphical Notation
Nat. Biotechnol. 27 735–741 (2009); published online 7 August 2009; corrected after print 11 August 2009 In the version of this article initially published, the wrong versions of Figures 1, 2 and 3 were used. ...
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Article
The Systems Biology Graphical Notation
A group of scientists in the systems biology community propose visual conventions for drawing biological diagrams.
