In this paper, we formulate a top-k query that compares objects in a database to a user-provided query object on a novel scoring function. The proposed scoring function combines the idea of attractive and repulsive dimensions into a general framework to overcome the weakness of traditional distance or similarity measures. We study the properties of the proposed class of scoring functions and de...

This project is to combine sequence and structure information of proteins to set up scoring function to classify protein structures whose belongings are unknown. The scoring function is basically explained as distance between two proteins. We began this project with searching useful informations and construct geometric and topological representations and distance metrics of those useful informa...

We developed Græmlin 2.0, a new multiple network aligner with (1) a new multi-stage approach to local network alignment; (2) a novel scoring function that can use arbitrary features of a multiple network alignment, such as protein deletions, protein duplications, protein mutations, and interaction losses; (3) a parameter learning algorithm that uses a training set of known network alignments to...

The analysis of the large volume of tandem mass spectrometry (MS/MS) proteomics data that is generated these days relies on automated algorithms that identify peptides from their mass spectra. An essential component of these algorithms is the scoring function used to evaluate the quality of peptide-spectrum matches (PSMs). In this paper, we present new approach to scoring of PSMs. We argue that...

OBJECTIVE Most chest radiography scoring systems for patients with cystic fibrosis have been developed for children but are also used for adults. Our aim was to evaluate the intra- and interobserver variability of 2 radiographic scoring systems in adults with cystic fibrosis and to assess the correlation of these systems with clinical and spirometric parameters. PATIENTS AND METHODS The chest...

We examine the problem of transmembrane protein structure determination. Like many other questions that arise in biological research, this problem cannot be addressed by traditional laboratory experimentation alone. An approach that integrates experiment and computation is required. We investigate a procedure which states the transmembrane protein structure determination problem as a bound cons...