Víctor H. Tierrafría

The paper maps DNA binding of 139 E. coli TFs using ChIP-Seq and trains BoltzNet, a neural network that predicts TF binding energy from DNA sequence, validated with biophysical experiments.

This study identifies DicC, a cryptic prophage transcription factor in E. coli, and shows it regulates hundreds of host genes, influencing bacterial phenotypes independently of other prophage genes.

The paper analyzes the sources of evidence for transcription factor regulatory interactions in E. coli K-12, classifies them into seven groups, and evaluates confidence levels of interactions using high-throughput data.

The paper creates a similarity corpus for microbial transcriptional regulation sentences, evaluated by curators to aid in biomedical literature curation.

The paper introduces MCO, an ontology for standardized annotation of microbial growth conditions, enabling comparison of gene expression data across experiments.

The paper expands RegulonDB to integrate high-throughput binding data with existing knowledge on gene regulation in E. coli K-12, enhancing its comprehensiveness and utility.