Rubén Perez‐Carrasco

A Bayesian framework reveals heterogeneous and stochastic decision-making in NK cell cytotoxicity

This study develops a Bayesian framework to analyze NK cell cytotoxicity and identifies distinct mechanisms underlying variability in killing responses.

Entropy Sorting Feature Selection: information-theoretic gene set identification improves single-cell RNA sequencing data interpretability

ESFS improves scRNA-seq data interpretability by identifying gene sets with complex expression dynamics, outperforming traditional methods in diverse biological contexts.

MIMIQ: Fast mutual information calculation and significance testing for single-cell RNA sequencing analysis

The paper introduces MIMIQ, a method for fast mutual information calculation and significance testing in single-cell RNA sequencing to study gene rewiring in T-cells during SARS-CoV-2 infection.

Protein-protein interactions drive differences in the spatiotemporal dynamics of transcription factors NANOG and SOX2 in naïve pluripotent cells

The paper tracks SOX2 and NANOG dynamics in live cells using advanced microscopy and analysis pipelines, revealing differences in their spatiotemporal behavior due to protein-protein interactions.

Epigenetic-metabolic axis in the temporal scaling of mammalian cortical neurogenesis across species

The paper identifies H3K27me3-mediated repression and -ketoglutarate as key regulators of species-specific neurogenesis timescales across mammals.

Let there be multifunctionality: Uncovering the criticality zoo of the AC-DCgenetic circuit

The paper analyzes the AC-DC genetic circuit to show it can exhibit diverse multifunctional dynamics, including coexisting oscillations and multistability, challenging traditional views of network constraints.

Local Nearby Bifurcations Lead to Synergies in Critical Slowing Down: the Case of Mushroom Bifurcations

The paper studies transient dynamics near multiple bifurcations in gene regulatory networks, showing synergistic effects and noise-driven control of transition timing.

A Mathematical Framework for Measuring and Tuning Tempo in Developmental Gene Regulatory Networks

This paper develops a mathematical framework to measure and tune tempo in developmental gene regulatory networks by analyzing perturbations that preserve dynamical orbits.

Automated design of gene circuits with optimal mushroom-bifurcation behaviour

This paper presents an optimization-based method to design synthetic gene circuits with specified bifurcation diagrams, focusing on mushroom bifurcation for applications in biosensors and synthetic biology.

"Neighbourhood watch" model: embryonic epiblast cells assess positional information in relation to their neighbours

The paper shows that chick embryo cells use neighborhood-based positional information to position the primitive streak, solving the French Flag Problem.

Levels of p53 expression determine the competitive ability of embryonic stem cells during the onset of differentiation.

The paper shows that p53-deficient embryonic stem cells outcompete wild-type cells during differentiation, eliminating them via apoptosis through local interactions.

Precision of Tissue Patterning is Controlled by Dynamical Properties of Gene Regulatory Networks

The paper shows that gene regulatory network structure influences boundary precision in tissue patterning by modulating stochastic fluctuations, not reducing noise.

Effects of cell cycle variability on lineage and population measurements of mRNA abundance

The paper quantifies how cell cycle variability affects mRNA abundance measurements and shows it can introduce errors in transcription rate inference.

Controlling spatiotemporal pattern formation in a concentration gradient with a synthetic toggle switch

This study builds a synthetic toggle switch in E. coli to control spatiotemporal gene expression patterns using diffusible molecules and mathematical modeling.

Species-specific developmental timing is associated with global differences in protein stability in mouse and human

The paper shows that slower human embryonic development compared to mice is due to higher protein stability and longer cell cycle duration in human cells.

A multiscale model of epigenetic heterogeneity reveals the kinetic routes of pathological cell fate reprogramming

This paper introduces a multiscale model of epigenetic heterogeneity to study the kinetic routes of pathological cell fate reprogramming and identifies strategies to control the transition between pluripotent and differentiated states.

Neuronal differentiation affects tissue mechanics and progenitor arrangement in the vertebrate neuroepithelium

The paper develops a mechanical model of the neuroepithelium to show how neuronal differentiation rates affect tissue growth anisotropy and cell arrangement.