Nobuo Ogawa

TL;DR: Surprisingly, for five of the six factors, their recognition sites are not unambiguously more constrained evolutionarily than the immediate flanking DNA, even in more highly bound and presumably functional regions, indicating that comparative DNA sequence analysis is limited in its ability to identify functional transcription factor targets.

TL;DR: The model demonstrated that elevated expression driven by a fusion of MSE2 and MSE3 was a consequence of the recruitment of a portion of Mse3 to become a functional component of M SE2, demonstrating that cis-regulatory “elements” are not elementary objects.

TL;DR: A robust version of the SELEX protocol is presented for high-throughput analysis, providing a powerful way to determine the in vitro binding specificities of DNA-binding proteins such as transcription factors.

TL;DR: The SELEX model outperformed other published methods for predicting putative binding sites for Bicoid as indicated by the results of an in-vivo ChIP-chip experiment.

TL;DR: In this paper, a biochemical parametrization of SELEX data is presented to estimate the affinities of the oligonucleotides and aligns them with the target.