49 citations · 129 across the 5 of their papers we have counts for
5 papers
Reliable scaling of Position Weight Matrices for binding strength comparisons between transcription factors
Xiaoyan Ma, Daphne Ezer, Carmen Navarro +1
Scoring DNA sequences against Position Weight Matrices (PWMs) is a widely adopted method to identify putative transcription factor binding sites. While common bioinformatics tools…
Physical constraints determine the logic of bacterial promoter architectures
Daphne Ezer, Nicolae Radu Zabet, Boris Adryan
Site-specific transcription factors (TFs) bind to their target sites on the DNA, where they regulate the rate at which genes are transcribed. Bacterial TFs undergo facilitated diff…
The influence of transcription factor competition on the relationship between occupancy and affinity
Nicolae Radu Zabet, Robert Foy, Boris Adryan
Transcription factors (TFs) are proteins that bind to specific sites on the DNA and regulate gene activity. Identifying where TF molecules bind and how much time they spend on thei…
The effects of transcription factor competition on gene regulation
Nicolae Radu Zabet, Boris Adryan
Transcription factor (TF) molecules translocate by facilitated diffusion (a combination of 3D diffusion around and 1D random walk on the DNA). Despite the attention this mechanism…
A comparative analysis of transcription factor expression during metazoan embryonic development
Alicia Schep, Boris Adryan
During embryonic development, a complex organism is formed from a single starting cell. These processes of growth and differentiation are driven by large transcriptional changes, w…