Andre Sanches Ribeiro

Hierarchical organization in sparse gene regulatory networks shapes structural coherence and emergent regulatory coordination

The paper introduces a coherence matrix to analyze directional regulatory coordination in gene regulatory networks, showing how hierarchical structures mitigate scaling penalties in sparse networks.

Thermal shifts can override the effects of Transcription-targeting Antibiotics

The paper shows that thermal shifts override antibiotic effects in E. coli by altering transcriptomes and physiological responses across multiple levels.

Single-cell Analysis of Attenuation-Driven Transcription Reveals New Principles of Bacterial Gene Regulation

The paper shows that transcription attenuation modulates both burst size and frequency from a σ70 promoter, challenging previous views on frequency modulation and revealing cross-feeding as a strategy for controlling gene expression variation.

Mechanisms shaping the transcriptome of E. coli to non-lethal rifampicin stress

This study identifies genome-wide transcriptional mechanisms in E. coli under non-lethal rifampicin stress, showing gene regulatory network structure influences response dynamics and phenotypic adaptations.

Dynamics of bacterial operons during genome-wide stresses is influenced by premature terminations and internal promoters

The paper investigates how premature terminations and internal promoters affect operon responses during genome-wide stresses in bacteria.

Transcription attenuation in synthetic promoters in tandem formation

The paper studies transcription attenuation in synthetic tandem promoters in E. coli, finding that promoter positioning and factors like rifampicin influence attenuation through RNAP collisions.

A library of reporters of the global regulators of gene expression of Escherichia coli

The paper develops a library of fluorescent reporters for 16 global regulators in E. coli to track their activity under various growth and stress conditions.

Sequence-dependent model of genes with dual σ factor preference

The paper models gene promoters with dual σ factor preference in E. coli, showing sequence-dependent sensitivity to σ70 and σ38 and proposing a generalizable framework for synthetic biology applications.

The transcription factor network of E. coli steers global responses to shifts in RNAP concentration

The paper examines how changes in RNA polymerase concentration affect gene expression in E. coli, finding that mid-term responses correlate with transcription factor network topology.

Analytical kinetic model of native tandem promoters in E. coli

The paper develops an analytical model of gene expression dynamics for tandem promoters in E. coli, showing that transcription interference depends on RNAP occupancy time and distance between transcription start sites.

Positive supercoiling buildup is a trigger of E. coli's short-term response to cold shock

The paper identifies cold shock repressed genes in E. coli and shows their responsiveness is linked to positive supercoiling buildup and Gyrase inhibition.