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MOTIVATION Molecular biotechnology now makes it possible to build elaborate systems models, but the systems biology community needs information standards if models are to be shared, evaluated and developed cooperatively. RESULTS We summarize the Systems Biology Markup Language (SBML) Level 1, a free, open, XML-based format for representing biochemical(More)
Analysis of cellular components at multiple levels of biological information can provide valuable functional insights. We performed multiple high-throughput measurements to study the response of Escherichia coli cells to genetic and environmental perturbations. Analysis of metabolic enzyme gene disruptants revealed unexpectedly small changes in messenger(More)
A genome-wide computational analysis of overlapping genes in various prokaryotic genomes was conducted to study the evolutionary rates of the formation and degradation of overlapping genes. Overlapping genes are adjacent genes that overlap partially or entirely. Overlapping gene pairs extracted from complete bacterial genome sequences were classified into(More)
BACKGROUND Successful realization of a "systems biology" approach to analyzing cells is a grand challenge for our understanding of life. However, current modeling approaches to cell simulation are labor-intensive, manual affairs, and therefore constitute a major bottleneck in the evolution of computational cell biology. RESULTS We developed the(More)
1 INTRODUCTION The E~ project [38] was launched in 1996 at Kern University m order to model and simulate various cellular processes with the ultimate goal of simulating the cell as a whole. The first version of the E-C~L simulation system, which is a generic software package for cell modeling, was completed m 1997. E-CI~ simulates the behavior of model cell(More)
We consider the cohomological classification of the 4+2-dimensional topological field, which is proposed by Lüscher, for SU(2) L × U(1) Y electroweak theory. The dependence on the admissible abelian gauge field of U(1) Y is determined through topological argument, with SU(2) L gauge field fixed as background. We then show the exact cancellation of the local(More)
In the cyanobacterium, Synechococcus elongatus, most promoters are regulated by a circadian clock under continuous light (LL) conditions. Nevertheless, the basic circadian oscillation is primarily generated by alternating KaiC phosphorylation/dephosphorylation reactions at the posttranslational level. Indeed, the KaiC phosphorylation cycle was recently(More)
The purpose of this study was to investigate the effect of laser irradiation on the enamel surface spectroscopically. Polished bovine enamel surface was irradiated with an Er:YAG laser apparatus and chemically analyzed using X-ray photoelectron spectroscopy (XPS). XPS detected core electron peaks such as carbon (C 1s) and nitrogen (N 1s), as well as calcium(More)