Cristina S.D. Palma

The paper models the σE biochemical network to show how transcriptional and post-translational regulation interact to control σE activity under stress, revealing context-dependent feedback mechanisms.

This paper shows that Spo0A~P pulsing frequency controls biofilm matrix deactivation in B. subtilis, independent of growth rate effects on gene dosage and protein dilution.

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

The paper develops a biophysical model to elucidate how Spo0A[~]P binding to its regulatory boxes affects spo0A transcription in Bacillus subtilis, revealing repressive effects and the role of RNAP holoenzyme levels in expression increase.

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 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.

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.

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