Mohamed N. M. Bahrudeen

The paper presents an optimized Halo-seq protocol to profile nucleoplasmic and nucleolar RNAs in HeLa cells, demonstrating high spatial specificity.

dirCLIP uses nanopore sequencing to profile variant-specific RNA-protein interactions, revealing isoform-selective binding and co-occurring sites with high concordance to short-read data.

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.