• Rahul Siddharthan

      Articles written in Journal of Biosciences

    • Parsing regulatory DNA: General tasks, techniques, and the PhyloGibbs approach

      Rahul Siddharthan

      More Details Abstract Fulltext PDF

      In this review, we discuss the general problem of understanding transcrip tional regulation from DNA sequence and prior information. The main tasks we discuss are predicting local regions of DNA, cis-regulatory modules (CRMs) that contain binding sites for transcription factors (TFs), and predicting individ ual binding sites. We review various existing methods, and then describe the approach taken by PhyloGibbs, a recent motif-finding algorithm that we developed to predict TF binding sites, and PhyloGibbs-MP, an extension to PhyloGibbs that tackles other tasks in regulatory genomics, particularly prediction of CRMs.

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