Bilena L.B. Almeida

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.