One of the significant topics in systems biology is to develop control theory of gene regulatory networks (GRNs). In typical control of GRNs, expression of some genes is inhibited (activated) by manipulating external stimuli and expression of other genes. It is expected to apply control theory of GRNs to gene therapy technologies in the future. In this paper, a control method using a Boolean ne...

BACKGROUND The cytologic accuracy in assessing malignancy in papillary breast neoplasms (PBNs) is controversial. This is further complicated by overlapping features observed in other breast lesions that produce papillary-like tissue fragments. METHODS The authors reviewed 22 fine-needle aspirates (FNAs) from histologically proven papillary neoplasms: papillary carcinoma (PCA; 10 aspirates) an...

MOTIVATION Ranking gene feature sets is a key issue for both phenotype classification, for instance, tumor classification in a DNA microarray experiment, and prediction in the context of genetic regulatory networks. Two broad methods are available to estimate the error (misclassification rate) of a classifier. Resubstitution fits a single classifier to the data, and applies this classifier in t...

High-throughput genomic technologies such as microarrays are now allowing scientists to acquire extensive information on gene activities of thousands of genes in cells at any physiological state. It has long been known that genes and their products in cells are not independent in the sense that the activation of genes with subsequent production of proteins is typically jointly dependent on the ...

Bayes nets (BNs) for relational databases are a major research topic in machine learning and artificial intelligence. When the database exhibits cyclic probabilistic dependencies, measuring the fit of a BN model to relational data with a likelihood function is a challenge [5, 36, 28, 9]. A common approach to difficulties in defining a likelihood function is to employ a pseudo-likelihood; a prom...

The inference of gene regulatory networks is a key issue for genomic signal processing. This paper addresses the inference of probabilistic Boolean networks (PBNs) from observed temporal sequences of network states. Since a PBN is composed of a finite number of Boolean networks, a basic observation is that the characteristics of a single Boolean network without perturbation may be determined by...

Introduction: Increased detection of organ-confined prostate cancer has led to an increased demand for nervesparing surgery. Most studies of erectile dysfunction (ED) following nerve-sparing radical prostatectomy (RRP) use single-item assessment, and potency rates differ widely among various groups. We aimed to investigate the use of the IIEF-5, a validated questionnaire, for reporting ED follo...