Timothy Fuqua

The paper compares the emergence of de-novo promoters in random DNA versus genomic DNA, finding that random DNA generates them more readily due to fewer proto-binding sites in genomic DNA.

The paper investigates interallelic cis-regulatory dominance in Drosophila, showing it promotes robustness by masking deleterious variants and enables evolutionary innovation through cell-type-specific activity.

This study shows that strong prokaryotic promoters are more mutationally robust, with robustness influenced by box spacing and sequence flexibility.

This study shows that transposable elements in E. coli can evolve de-novo promoter activity through mutations, highlighting their latent cis-regulatory potential.

This paper introduces a method to quantify intensity distribution in 3D and 2D microscopy data using spherical harmonics, demonstrating its application across various biological systems.

This study investigates how promoter motifs influence promoter emergence and evolution by mutagenizing promoter islands and measuring gene expression in mutants.

The paper shows that mutations in developmental enhancers in Drosophila mostly alter existing expression patterns, while random sequences can act as enhancers with broader expression, suggesting constraints on phenotypic novelty from existing enhancers.