Adaptive laboratory evolution (ALE) has emerged as an effective tool for scientific discovery
and addressing biotechnological needs. Much of ALE's utility is derived from reproducibly …

The ferric uptake regulator (Fur) plays a critical role in the transcriptional regulation of iron
metabolism. However, the full regulatory potential of Fur remains undefined. Here we …

Comprehensive and systematic analysis of airway gene expression represents a strategy
for addressing the multiple, complex, and largely untested hypotheses that exist for disease …

Underlying cellular responses is a transcriptional regulatory network (TRN) that modulates
gene expression. A useful description of the TRN would decompose the transcriptome into …

Three transcription factors (TFs), OxyR, SoxR, and SoxS, play a critical role in transcriptional
regulation of the defense system for oxidative stress in bacteria. However, their full genome-…

Rapid growth in size and complexity of biological data sets has led to the ‘Big Data to
Knowledge’ challenge. We develop advanced data integration methods for multi-level analysis of …

The regulators GadE, GadW and GadX (which we refer to as GadEWX) play a critical role in
the transcriptional regulation of the glutamate-dependent acid resistance (GDAR) system in …

The ability of Staphylococcus aureus to infect many different tissue sites is enabled, in part,
by its transcriptional regulatory network (TRN) that coordinates its gene expression to …

… The repair rate v repair is constrained by the concentrations of the set of repair proteins R = {
YggX, … F = 2 ⋅ p r e c i s i o n ⋅ r e c a l l / ( p r e c i s i o n + r e c a l l ) (SI Appendix, Fig. S3). …

Biological regulatory network architectures are multi-scale in their function and can
adaptively acquire new functions. Gene knockout (KO) experiments provide an established …