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.
ABSTRACT:
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.
ABSTRACT:
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
ABSTRACT:
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
ABSTRACT:
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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