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September 29, 2005

Area chairs: Angel R. Ortiz and Anna Tramontano

OP-1 Augmented cell-graphs for automated cancer diagnosis
Cigdem Demir (1), S. Humayun Gultekin(2), Bulent Yener (1)
1) Rensselaer Polytechnic Institute, 2) Oregon Health and Science University.

This work reports a novel computational method based on Augmented Cell Graphs (ACG), which are constructed from low magnification tissue images for the mathematical diagnosis of brain cancer (malignant glioma). An ACG is a simple, undirected, weighted, and complete graph in which a node represents a cell cluster and an edge between a pair of nodes defines a binary relationship between them. Both the nodes and the edges of an ACG are assigned weights to capture more information about the topology of the tissue. In this work, the experiments are conducted on a data set that comprised of 646 human brain biopsy samples from 60 different patients. It is shown that the ACG approach yields sensitivity of 97.53% and specificities of 93.33% and 98.15% (for the inflamed and healthy, respectively) at the tissue level in glioma diagnosis.

CONTACT: demir@cs.rpi.edu

OP-2 A framework for computational and experimental methods: Identifying dimerization residues in CCR chemokine receptors
Ana Rojas (1), Mario Mellado (1), José Miguel Rodríguez-Frade (1), David de Juan(1), Patricia Hernanz-Falcón (1), Antonio Serrano (1), Antonio del Sol (2), Carlos Martínez (3), Alfonso Valencia (1)
1) CNB, 2) INC, 3) DIO.

Solving relevant biological problems requires answering complex questions. Addressing such questions traditionally implied the design of time-consuming experimental procedures which most of the times are not accessible to average-sized laboratories. The current trends in the actual scientific scenario move towards the multidisciplinary approach integrating both theoretical knowledge and experimental approaches. This combination is a powerful tool that a priori will be sufficient to successfully achieve the goal of shedding light to biological problems.
To illustrate this concept, here we show a descriptive example where the computational methods showed to be a key aspect to detect crucial players in a very important biological problem: the chemokine receptors dimerization. Experimental validation of computational procedures provide with a wealth of valuable information not obtainable by any of the individual approaches alone.
CONTACT: arojas@cnb.uam.es

OP-3 ARTS: Alignment of RNA Tertiary Structures
Oranit Dror (1), Ruth Nussinov (1), Haim Wolfson (1)
Tel Aviv University

Motivation: A fast growing number of non-coding RNAs have recently been discovered to play essential roles in many cellular processes. Similarly to proteins, understanding the functions of these active RNAs requires methods for analyzing their tertiary structures. However, in contrast to the wide range of structurebased approaches available for proteins, there is still a lack of methods for studying RNA structures.
Results: We present a new computational method named ARTS (Alignment of RNA Tertiary Structures). The method compares two nucleic acid structures (RNAs or DNAs) and detects a-priori unknown common substructures. These substructures can be either large global folds containing hundreds and even thousands of nucleotides or small local tertiary motifs with at least two successive base pairs. To the best of our knowledge, this is the first method of this type. The method is highly-efficient and was used to conduct an all-against-all comparison of all the RNA structures currently available in the Protein Data Bank. Keywords: Structural Bioinformatics, Nucleic Acid 3D structurecomparison, an all-against-all comparison.
Availability: The program, a web-server and supplementary informationare available on http://bioinfo3d.cs.tau.ac.il/ARTS.
CONTACT: oranit@post.tau.ac.il

RNA 3D Structure and Function

OP-4 Non-coding RNAs in Ciona intestinalis
Kristin Missal (1), Dominic Rose (1), Peter F. Stadler (1)
1) Bioinformatics Group, Dep. of Computer Science, University of Leipzig

Motivation: The analysis of animal genomes showed that only a minute part of their DNA codes for proteins. Recent experimental results agree, however, that a large fraction of these genomes is transcribed and hence is probably functional at the RNA level. A computational survey of vertebrate genomes has predicted thousands of previously unknown ncRNAs with evolutionary conserved secondary structures. An extension of these comparative studies beyond vertebrates is difficult, however, since most ncRNAs evolve relatively fast at the sequence level while conserving their characteristic secondary structures.
Results: Here we report on a computational screen of structured ncRNAs in the urochordate lineage based on a comparison of the genomic data from Ciona intestinalis, Ciona savignyi, and Oikopleura dioica. We predict more than 1000 ncRNAs with an evolutionarily conserved RNA secondary structure. Of these, about a quarter is located in introns of known protein coding sequences. Only a small fraction of the RNA motifs can be identified as known RNAs, including about 300 tRNAs, some 100 snRNA genes, and a few microRNAs and snoRNAs.
CONTACT: kristin@bioinf.uni-leipzig.de


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