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In this paper, we study the efficacy of a model-based base-calling approach for Illumina's sequencing platforms. In particular, we investigate Genome Analyzer I reads and provide a detailed biochemical model of the sequencing process, incorporating various non-idealities evident in such systems. Parameters of the model are estimated via a supervised learning based on the particle swarm optimization...
Computational structure prediction, including de novo and homology modeling, is an important tool for membrane protein studies. Developing an accurate scoring function that can be used for structure discrimination and assessment remains a challenge. In our previous work, we have analyzed a set of high-resolution membrane protein structures using the network approach developed in our lab and proposed...
System biology is one of the leading edge cross-subjects which requires the cooperation between computer science and biological science. Abstracting complex life phenomenon, like metabolic or transcription regulation pathway, into networks to simulate these processes is one of the hotspots in System biological research. In this paper, we construct a network to simulate one of the most concerned areas...
The available data of complete ordering of genes on each chromosome of organisms is increasing thank to the research in gene hunting and annotation. Researchers like evolutionary biologists and computer scientists are greatly interested in gene order data because it make possible to resolve the ancient branches to fill the tree of life. Inversion based distance metric and the so called DCJ (double-cut-and-join)...
The authors proposed a novel structure representation strategy __ ??Interaction-Distance?? theory to study the quantitative structure-activity relationships (QSARs) of peptide. The ??Interaction-Distance?? theory stated that: I. In a peptide chain, there exists interaction between any two amino acids; II. The value of interaction lies on not only the types the two amino acids, but also the distance...
While much of molecular biology research has led to a wealth of knowledge about individual cellular components and their functions, it has become increasingly clear that most cellular functions are carried out by complex networks of interconnected components, and that the characterization of isolated cellular components is not sufficient to understand the cell's complexity. In recent years, the development...
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