90 citations · 168 across the 5 of their papers we have counts for
6 papers
Long-term evolution of regulatory DNA sequences. Part 1: Simulations on global, biophysically-realistic genotype-phenotype maps
Elia Mascolo, Réka Borbély, Santiago Herrera-Álvarez +3
Promoters and enhancers are cis-regulatory elements (CREs), DNA sequences that bind transcription factor (TF) proteins to up- or down-regulate target genes. Decades-long efforts yi…
Statistical mechanics for metabolic networks during steady-state growth
Daniele De Martino, Anna MC Andersson, Tobias Bergmiller +2
Which properties of metabolic networks can be derived solely from stoichiometric information about the network's constituent reactions? Predictive results have been obtained by Flu…
Intrinsic limits to gene regulation by global crosstalk
Tamar Friedlander, Roshan Prizak, Călin C. Guet +2
Gene regulation relies on the specificity of transcription factor (TF) - DNA interactions. In equilibrium, limited specificity may lead to crosstalk: a regulatory state in which a…
Efficient reduction of Kappa models by static inspection of the rule-set
Andreea Beica, Calin Guet, Tatjana Petrov
When designing genetic circuits, the typical primitives used in major existing modelling formalisms are gene interaction graphs, where edges between genes denote either an activati…
Model Checking Gene Regulatory Networks
Mirco Giacobbe, Calin C. Guet, Ashutosh Gupta +3
The behaviour of gene regulatory networks (GRNs) is typically analysed using simulation-based statistical testing-like methods. In this paper, we demonstrate that we can replace th…
Modeling network dynamics: the lac operon, a case study
J. M. G. Vilar, C. C. Guet, S. Leibler
We use the lac operon in Escherichia coli as a prototype system to illustrate the current state, applicability, and limitations of modeling the dynamics of cellular networks. We in…