IsoformEx (2011):  IsoformEx is a fast and accurate algorithm to estimate transcript expression levels and gene expression levels, which takes into account short exons and alternative exons with a weighting scheme. The software is available at, (Kim, et al., 2011, BMC Bioinformatics. 2011 Jul 27;12:305.)

TPD (2011):  TPD is a Tree-based Position Weight Matrix based discriminative approach to refine the PWMs from the ChIP-Seq data with a pre-existing PWM. Experiments on both the simulated and real ChIP-Seq data show that the proposed method starting from existing PWM has consistently better performance than existing tools in detecting the TFBSs. The improved accuracy is the result of modelling the complete dependent structure of the motifs and better prediction of true positive rate. The findings could lead to better understanding of the mechanisms of TF-DNA interactions. TPD can be downloaded from