Metagenomics enables the characterization of the specific metabolic potential of a microbial community. The common approach towards a quantitative representation of this potential is to count the number of metagenomic sequence fragments that can be assigned to metabolic pathways by means of predicted gene functions. The resulting pathway abundances make up the metabolic profile of the metagenom...

Pancreatic ductal adenocarcinoma (PDAC) is a lethal disease, and the patient has an extremely poor overall survival with a less than 5% 5-year survival rate. Development of potential biomarkers provides a critical foundation for the diagnosis of PDAC. In this project, we have adopted an integrative approach to simultaneously identify biomarker and generate testable hypothesis from multidimensio...

Invasive aspergillosis is characterized by vascular invasion and thrombosis. In order to determine the antifungal activity of human platelets, hyphal elongation and metabolic activity of a clinical A. fumigatus isolate were measured. Genome-wide identification of differentially expressed genes in A. fumigatus was performed after exposure to platelets for 15, 30, 60 and 180 min. Data were analyz...

Figure 1: KEGG Compound Search One of the significant challenges in bioinformatics is to represent and manipulate computationally complex biological information such as metabolic pathways, chemical compounds and protein-protein interactions. This challenge was successfully accomplished by representing biological information with graph objects[1]. On the other hand, these enormous graph structur...

SUMMARY LinkinPath is a pathway mapping and analysis tool that enables users to explore and visualize the list of gene/protein sequences through various Flash-driven interactive web interfaces including KEGG pathway maps, functional composition maps (TreeMaps), molecular interaction/reaction networks and pathway-to-pathway networks. Users can submit single or multiple datasets of gene/protein s...

In recent years, the analysis of orthologous genes based on phylogenetic profiles has received popularity in bioinfomatics. We propose a new method to extract organism groups and their hierarchy from phylogenetic profiles using the independent component analysis (ICA). The method involves first finding independent axes in the projected space from the multivariate data matrix representing phylog...

The KEGG RPAIR database is a collection of biochemical structure transformation patterns, called RDM patterns, and chemical structure alignments of substrate-product pairs (reactant pairs) in all known enzyme-catalyzed reactions taken from the Enzyme Nomenclature and the KEGG PATHWAY database. Here, we present PathPred (http://www.genome.jp/tools/pathpred/), a web-based server to predict plausi...

It is an exciting time for tau researchers as it is now generally accepted that abnormal tau species are required to mediate the toxic effects of amyloid β-peptide oligomers in Alzheimer's disease. Tau may play multiple roles in neurophysiology and there may be further pathologically relevant tau alterations, besides hyperphosphorylation and aggregation. The recent Biology and Pathology of Tau ...

We propose a method for predicting types of protein-protein interactions using a multiple-instance learning (MIL) model. Given an interaction type to be predicted, the MIL model was trained using interaction data collected from biological pathways, where positive bags were constructed from interactions between protein complexes of that type, and negative bags from those of other types. In an ex...

RINGS (Resource for INformatics of Glycomes at Soka), available at http://rings.t.soka.ac.jp/, is the first web resource for analyzing glycan structures, implementing many advanced tools such as data mining and graph algorithm techniques. In order to perform analyses efficiently, structure data from KEGG[1] and GLYCOSCIENCES.de had been imported into RINGS. However, GlycomeDB[2] has been recent...