Juan F. Poyatos

A transformer-based language model reveals developmental constraint and network complexity during zebrafish embryogenesis

The paper uses a transformer-based model to analyze zebrafish embryogenesis data, revealing network-level regulatory constraints during the phylotypic stage.

Development positions malignant cellular states but does notexplain their diversification

The paper develops a framework to analyze how malignant cellular states in pancreatic ductal adenocarcinoma relate to normal developmental trajectories, finding that while developmental programs help locate cancer states, they do not explain their diversification.

Cell atlases and the Developmental Foundations of the Phenotype

The paper introduces the [D]-[P] rule to quantify the relationship between developmental gene expression and phenotypic similarity, using C. elegans to show that genes with broad expression have systemic phenotypes and those with specific expression have specialized roles.

Redefining Housekeeping Genes in the Context of Vertebrate Development

The paper redefines housekeeping genes to include those essential across developmental stages, not just adult tissues, using zebrafish data.

Polygenic prediction and gene regulation networks

This paper combines gene regulation network models with polygenic prediction to explore how phenotypic variation can be captured using statistical methods, identifying key regulatory connections and linking findings to concepts like global sensitivity and epistasis.

Disentangling protein metabolic costs in human cells and tissues.

The paper examines how protein length and amino acid costs influence gene expression in human cells and tissues, finding that cancer tissues overexpress cheap, compact genes.

The limitations of phenotype prediction in metabolism

The paper presents a framework using genome-scale metabolic reconstructions to interpret genotype-to-phenotype associations and identifies limitations in phenotype prediction in metabolism.

Predicting the fitness costs of complex mutations

The paper develops a statistical framework to predict fitness costs of complex mutations by identifying key molecular predictors using RNA polymerase mutations in E. coli.

Tolerance to NADH/NAD+ imbalance anticipates aging and anti-aging interventions

The paper introduces a computational method to assess tolerance to NADH/NAD+ redox imbalances in yeast, linking it to aging and anti-aging interventions.

Genetic buffering and potentiation in metabolism

The paper uses an in silico model of yeast metabolism to identify modifier genes that buffer or potentiate the effects of mutations on growth, revealing pleiotropy, epistasis, and environmental dependencies.

The impact of global transcriptional regulation on bacterial gene order

The paper quantifies how global transcriptional regulation affects gene expression across 700 genes in E. coli and shows that gene position near the origin of replication correlates with sensitivity to transcriptional resources.

Complex genetic and epigenetic regulation deviates gene expression from a unifying global transcriptional program

The paper examines how genetic and epigenetic regulation deviates from a global transcriptional program in yeast under different nutrient conditions, identifying distinct regulatory strategies across gene classes.

Dual autogenous control of the multiple antibiotic resistance phenotype in Escherichia coli

This study investigates how dual autogenous control regulates the multiple antibiotic resistance phenotype in Escherichia coli, revealing mechanisms for rapid induction, pulse generation, and sensing range.