Kiyoko F. Aoki-Kinoshita

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The increasing amount of genomic and molecular information is the basis for understanding higher-order biological systems, such as the cell and the organism, and their interactions with the environment, as well as for medical, industrial and other practical applications. The KEGG resource (http://www.genome.jp/kegg/) provides a reference knowledge base for(More)
Mining frequent patterns is a general and important issue in data mining. Complex and unstructured (or semi-structured) datasets have appeared in major data mining applications, including text mining, web mining and bioinformatics. Mining patterns from these datasets is the focus of many of the current data mining approaches. We focus on labeled ordered(More)
Bioinformatics approaches to carbohydrate research have recently begun using large amounts of protein and carbohydrate data. In this field called glycome informatics, the foremost necessity is a comprehensive resource for genome-scale bioinformatics analysis of glycan data. Although the accumulation of experimental data may be useful as a reference of(More)
KCaM (KEGG Carbohydrate Matcher) is a tool for the analysis of carbohydrate sugar chains, or glycans. It consists of a web-based graphical user interface that allows users to enter glycans easily with the mouse. The glycan structure is then transformed into our KCF (KEGG Chemical Function) file format and sent to our program which implements an efficient(More)
MOTIVATION Various computational methods have been proposed to tackle the problem of predicting the peptide binding ability for a specific MHC molecule. These methods are based on known binding peptide sequences. However, current available peptide databases do not have very abundant amounts of examples and are highly redundant. Existing studies show that(More)
The UniCarb KnowledgeBase (UniCarbKB; http://unicarbkb.org) offers public access to a growing, curated database of information on the glycan structures of glycoproteins. UniCarbKB is an international effort that aims to further our understanding of structures, pathways and networks involved in glycosylation and glyco-mediated processes by integrating(More)
MOTIVATION Glycans are the third major class of biomolecules following DNA and proteins. They are extremely vital for the functioning of multicellular organisms. However, comparing the fast development of sequence analysis techniques, informatics work on glycans have a long way to go. Alignment algorithms for glycan tree structures are one of the foremost(More)
We propose a novel general-purpose tree kernel and apply it to glycan structure analysis. Our kernel measures the similarity between two labeled trees by counting the number of common q-length substrings (tree q-grams) embedded in the trees for all possible lengths q. We apply our tree kernel using a support vector machine (SVM) to classification and(More)
Introduction Carbohydrates are considered the third class of information-encoding biological macromolecules. ''Glycomics,'' the scientific attempt to characterize and study carbohydrates , is a rapidly emerging branch of science, for which informatics is just beginning. Glycomics requires sophisticated algo-rithmic approaches. Several algorithms and models(More)