Elena R Alvarez-Buylla

Analytical approach of synchronous and asynchronous update schemes applied to solving biological Boolean networks

This paper analyzes synchronous and asynchronous update schemes in Boolean networks and shows that the canonical form can only be obtained with the synchronous scheme.

Extended discrete gene regulatory network model for the Arabidopsis thaliana root-hair cell fate

The paper extends a gene regulatory network model for Arabidopsis thaliana root-hair cell fate to better recover mutant phenotypes and quantify cell type distribution patterns.

Genome-Wide Association Studies meta-analysis uncovers NOJO and SGS3 novel genes involved in Arabidopsis thaliana primary root development and plasticity

The paper performs a GWAS meta-analysis to identify novel genes involved in Arabidopsis thaliana primary root development and plasticity, finding new loci and confirming the role of SGS3 and a SAM-containing gene.

Uncovering the role that specific genes play in reachability properties of complex biological Gene Regulatory Networks (GRNs): The Arabidopsis thaliana flower development case

The paper introduces a method to analyze the role of specific genes in reachability properties of GRNs using the Arabidopsis thaliana flower development GRN, finding 79 inducible attractor transitions with external control inputs.

In vivo and in vitro human gene essentiality estimations capture contrasting functional constraints

The paper compares in vivo and in vitro gene essentiality estimates to assess functional constraints and identifies genes with contrasting mutational tolerance.

Spatio-temporal Dynamics of the Patterning of Arabidopsis Flower Meristem

This paper presents a qualitative model that explains the spatio-temporal dynamics of Arabidopsis flower meristem patterning, showing how pre-patterns and gene interactions generate positional information for floral organ development.

Structural robustness of mammalian transcription factor networks reveals plasticity across development

The paper analyzes tissue-specific transcription factor networks to reveal structural plasticity and robustness across development.

A quantitative network modeling approach to evaluate the role of cytokine combinations on CD4+ T cell differentiation, partial polarization, and plasticity

The paper extends a Boolean network model of CD4+ T cell differentiation to a continuous model to assess how cytokine concentrations and combinations influence differentiation and plasticity.