Byoung-Tak Zhang

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The Drosha-DGCR8 complex initiates microRNA maturation by precise cleavage of the stem loops that are embedded in primary transcripts (pri-miRNAs). Here we propose a model for this process that is based upon evidence from both computational and biochemical analyses. A typical metazoan pri-miRNA consists of a stem of approximately 33 bp, with a terminal loop(More)
DNA computing relies on biochemical reactions of DNA molecules and may result in incorrect or undesirable computations. Therefore, much work has focused on designing the DNA sequences to make the molecular computation more reliable. Sequence design involves with a number of heterogeneous and conflicting design criteria and traditional optimization methods(More)
MicroRNAs (miRNAs) are small regulatory RNAs of approximately 22 nt. Although hundreds of miRNAs have been identified through experimental complementary DNA cloning methods and computational efforts, previous approaches could detect only abundantly expressed miRNAs or close homologs of previously identified miRNAs. Here, we introduce a probabilistic(More)
MOTIVATION Most previous approaches to model biochemical networks have focused either on the characterization of a network structure with a number of components or on the estimation of kinetic parameters of a network with a relatively small number of components. For system-level understanding, however, we should examine both the interactions among the(More)
Genetic programming is distinguished from other evolutionary algorithms in that it uses tree representa tions of variable size instead of linear strings of xed length The exible representation scheme is very important because it allows the underlying structure of the data to be discovered automatically One primary di culty however is that the solutions may(More)
Genetic algorithms have been used for neural networks in two main ways to optimize the network architecture and to train the weights of a xed architecture While most previous work focuses on only one of these two options this paper investigates an alternative evo lutionary approach called Breeder Genetic Programming BGP in which the architecture and the(More)
Most DNA computing algorithms for mathematical problems start with combinatorial generation of an initial pool. Several methods for initialpool generation have been proposed, including hybridization/ligation and mix/split methods. Here, we implement and compare parallel overlap assembly with the hybridization/ligation method. We applied these methods to the(More)
Bilinear models provide rich representations compared with linear models. They have been applied in various visual tasks, such as object recognition, segmentation, and visual question-answering, to get state-of-the-art performances taking advantage of the expanded representations. However, bilinear representations tend to be high-dimensional, limiting the(More)
Protein-protein interaction (PPI) extraction has been an important research topic in bio-text mining area, since the PPI information is critical for understanding biological processes. However, there are very few open systems available on the Web and most of the systems focus on keyword searching based on predefined PPIs. PIE (Protein Interaction(More)
We introduce a DNA encoding method to represent numerical values and a biased molecular algorithm based on the thermodynamic properties of DNA. DNA strands are designed to encode real values by variation of their melting temperatures. The thermodynamic properties of DNA are used for effective local search of optimal solutions using biochemical techniques,(More)