Jong Kyoung Kim

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The N-terminal transit peptides of nuclear-encoded plastid proteins are necessary and sufficient for their import into plastids, but the information encoded by these transit peptides remains elusive, as they have a high sequence diversity and lack consensus sequences or common sequence motifs. Here, we investigated the sequence information contained in(More)
Methods for discriminative motif discovery in DNA sequences identify transcription factor binding sites (TFBSs), searching only for patterns that differentiate two sets (positive and negative sets) of sequences. On one hand, discriminative methods increase the sensitivity and specificity of motif discovery, compared to generative models. On the other hand,(More)
Predicting the destination of a protein in a cell is important for annotating the function of the protein. Recent advances have allowed us to develop more accurate methods for predicting the subcellular localization of proteins. One of the most important factors for improving the accuracy of these methods is related to the introduction of new useful(More)
Tree-dependent component analysis (TCA) is a generalization of independent component analysis (ICA), the goal of which is to model the multivariate data by a linear transformation of latent variables , while latent variables fit by a tree-structured graphical model. In contrast to ICA, TCA allows dependent structure of latent variables and also consider(More)
Accurate prediction of transcription factor binding sites (TFBSs) is a prerequisite for identifying cis-regulatory modules that underlie transcriptional regulatory circuits encoded in the genome. Here, we present a computational framework for detecting TFBSs, when multiple position weight matrices (PWMs) for a transcription factor are available. Grouping(More)
The comprehensive identification of functional transcription factor binding sites (TFBSs) is an important step in understanding complex transcriptional regulatory networks. This study presents a motif-based comparative approach, STAT-Finder, for identifying functional DNA binding sites of STAT3 transcription factor. STAT-Finder combines STAT-Scanner, which(More)
Prediction of the cellular location of a protein plays an important role in inferring the function of the protein. Feature extraction is a critical part in prediction systems, requiring raw sequence data to be transformed into appropriate numerical feature vectors while minimizing information loss. In this paper we present a method for extracting useful(More)