No abstract available.
Biology*

No abstract available.
Biology

Local alignment is an important task in molecular biology to see if two sequences contain regions that are similar. The most popular approach to local alignment is the use of dynamic programming due to Smith and Waterman, but the alignment reported by the Smith-Waterman algorithm has some undesirable properties. The recent approach to fix these problems is to use the notion of normalized scores for local alignments by Arslan, Egecioglu and Pevzner. In this paper we consider the problem of finding all local alignments whose normalized scores are above a given threshold, and present a fast heuristic algorithm. Our algorithm is 180-330 times faster than Arslan et al.''s for sequences of length about 120 kbp and about 40-50 times faster for sequences of length about 30 kbp.
Molecular Biology

In the 21st century, proteomics, a new science, appears in the biology. Proteomics studies the human protein, opens a new era of molecular pathology. The scientists suggest that the human being is determined by 2 factors: the genetic system or human genome and various influences of surrounding environment. From which, proteomics have been become the turning point of the biology at the beginning of 21st century.
Proteomics ; Biology

No abstract available.
Biology* ; Eosinophils*

No abstract available.
Molecular Biology

No abstract available.
Molecular Biology*

Integrating various pathway data collections to create new biological knowledge is a challenge, for which novel computational tools play a key role. For this purpose, we developed the Java-based conversion modules KGML2SBML and KGML2BioPAX to translate KGML (KEGG Markup Language) into a couple of common data exchange formats: SBML (Systems Biology Markup Language) and BioPAX (Biological Pathway Exchange). We hope that our work will be beneficial for other Java developers when they extend their bioinformatics system into SBML- or BioPAX-aware analysis tools. This is part of our ongoing effort to develop an ultimate KEGG-based pathway enrichment analysis system.
2,5-Dimethoxy-4-Methylamphetamine ; Biology ; Computational Biology ; Indonesia ; Systems Biology

The basic graph layout technique, one of many visualization techniques, deals with the problem of positioning vertices in a way to maximize some measure of desirability in a graph. The technique is becoming critically important for further development of the field of systems biology. However, applying the appropriate automatic graph layout techniques to the genomic scale flow of metabolism requires an understanding of the characteristics and patterns of duplicate and shared vertices, which is crucial for bioinformatics software developers. In this paper, we provide the results of parsing KEGG XML files from a graph-theoretical perspective, for future research in the area of automatic layout techniques in biological pathway domains.
Computational Biology ; Metabolic Networks and Pathways ; Systems Biology

Advances in molecular biology have made it possible to understand the tumor biology of breast cancer at the molecular level and have revealed molecular targets for the therapy of breast cancer. Nowadays, targeting agents are used as mono-therapy or as combined therapy with other anti-cancer drugs for the treatment of breast cancer. Much more efforts is also being made in the development of better therapeutic agents targeting molecules having an important role in tumor biology. In this article, promising molecules for targeted therapy are reviewed for their roles in the pathophysiology and the treatment of breast cancer. We also introduce and summarize new preclinical agents, developed or on developing, with preliminary results from clinical trials. Given the progress currently being made, targeted therapy could become a main strategy for the treatment of breast cancer in the near future.
Biology ; Breast ; Breast Neoplasms ; Molecular Biology