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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)
We consider the problem of learning a local metric in order to enhance the performance of nearest neighbor classification. Conventional metric learning methods attempt to separate data distributions in a purely discriminative manner; here we show how to take advantage of information from parametric generative models. We focus on the bias in the(More)
V Preface CICLing 2006 (www.CICLing.org) was the 7th Annual Conference on Intelligent Text Processing and Computational Linguistics. The CICLing conferences are intended to provide a wide-scope forum for discussion of the internal art and craft of natural language processing research and the best practices in its applications. This volume contains the(More)
Most document classification systems consider only the distribution of content words of the documents, ignoring the syntactic information underlying the documents though it is also an important factor. In this paper, we present an approach for classifying large scale unstructured documents by incorporating both the lexical and the syntactic information of(More)
MOTIVATION An important issue in stem cell biology is to understand how to direct differentiation towards a specific cell type. To elucidate the mechanism, previous studies have focused on identifying the responsible gene regulators, which have, however, failed to provide a systemic view of regulatory modules. To obtain a unified description of the(More)
BACKGROUND MicroRNAs (miRNAs) are small noncoding RNAs, which play significant roles as posttranscriptional regulators. The functions of animal miRNAs are generally based on complementarity for their 5' components. Although several computational miRNA target-gene prediction methods have been proposed, they still have limitations in revealing actual target(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)
Genetic programming is distinguished from other evolutionary algorithms in that it uses tree representations 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 diiculty, h o wever, is that the solutions(More)
Classification of patient samples is a crucial aspect of cancer diagnosis. DNA hybridization arrays simultaneously measure the expression levels of thousands of genes and it has been suggested that gene expression may provide the additional information needed to improve cancer classification and diagnosis. This paper presents methods for analyzing gene(More)