I was a bit disappointed with the readability of this paper to an outsider of computational biology. Even though the paper employs learning/probabilistic methods, it was difficult to even understand these because of the terminology used throughout the paper. Even seemingly simple algorithmic components such as the PSSM, are made complicated by terminology. I realize that I may not be the target audience, but I think the authors limit their audience by using such specific biological terminology throughout the paper without definition or relating these terms to their high level counterparts. I had a very difficult time figuring out how the different components (such as promoter sequence, transcription factor, TF-binding sites, expressions, etc.) were related.