Accepted Posters

Category 'V'- Structural Genomics'
Poster V01
Finding co-occurrence of copy number changes in tumors.
Christiaan Klijn- Netherlands Cancer Institute
Jan Bot (Delft University of Technology, The Delft Bioinformatics Lab); Marcel Reinders (Delft University of Technology, The Delft Bioinformatics Lab); David Adams (The Wellcome Trust Sanger Institute, Experimental Cancer Genetics); Lodewyk Wessels (Netherlands Cancer Institute, Molecular Biology); Jos Jonkers (Netherlands Cancer Institute, Molecular Biology);
Short Abstract: Cancer, a genetic disease, is only rarely caused by a single mutation. Often, multiple (epi)genetic mutations have to occur to cause oncogenic transformation. Cancer genes can be disrupted by many different processes of which DNA copy number change due to genomic instability is one. Although many studies have addressed the detection of important single copy number changes in different tumor types, no studies have thoroughly investigated the interdependence of copy number changes.
Our study focuses on the detection of co-occurrent DNA copy number changes. We show that, in lymphoid tumors, there are large networks of related copy number changes over the entire genome. The genomic locations that show significant co-occurrent copy number changes are significantly enriched for functionally related and cancer associated genes. Our observations support the notion that subtle gene dosage changes of many related genes could be an overlooked but important process in cancer.
Long Abstract:Click Here

Poster V02
Protein-ligand interaction network predicts novel targets for known drugs
Olga Kalinina- University of Heidelberg
Robert Russell (University of Heidelberg, Excellencecluster CellNetworks);
Short Abstract: We use the network of interactions in database of three-dimensional structures to predict protein-chemical interactions. Given a pair of proteins sharing a ligand, we used protein and chemical superimpositions and a physicochemical screens to suggest whether additional compounds bound by one protein would bind to the other.
Long Abstract:Click Here

Poster V03
Protein domain assignment from the recurrence of locally similar structures
Chin-Hsien Tai- National Institutes of Health
Vichetra Sam (NIH, CIT); Jean-Francois Gibrat (INRA, Unité Mathématique Informatique et Génome); Jean Garnier (INRA, Unité Mathématique Informatique et Génome); Peter Munson (NIH, CIT); Byungkook Lee (NIH, NCI);
Short Abstract: Protein domains were assigned by using mathematical procedures to cluster protein residues according to the number of padded locally similar structural pieces obtained from VAST structural comparisons. Measured by NDO scores, our procedure gave comparable result to those existing programs using geometrical or structural information.
Long Abstract:Click Here

Poster V04
A Computational Pipeline to Determine the Alternative Secondary Structures for Purine Riboswitches
Yang Ding- Boston College
Peter Clote (Boston College, Biology Department);
Short Abstract: We describe the first computational pipeline to accurately determine the expression platform, alternative secondary structures and ON/OFF logic for purine riboswitches. The pipeline features a novel algorithm to compute the intrinsic transcription terminator based on the computation of Maximum Expected Hybridization. Our results provide compositional properties for intrinsic transcriptional anti-terminators.
Long Abstract:Click Here

Poster V05
Insight into the active site of a Structural Genomics protein – a Phenolic Acid Decarboxylase
Ramya Parasuram- Northeastern University
Mary Jo Ondrechen (Northeastern University, Chemistry and Chemical Biology);
Short Abstract: The computational methods THEMATICS and POOL are used to characterize the active site of a Bacillus subtilis aromatic acid decarboxylase from Structural Genomics. The predicted site of catalysis has been verified by experiment. Comparison of the predicted active site with those of previously characterized decarboxylases reveals some differences.
Long Abstract:Click Here

Poster V06
Protein crystallization analysis on the World Community Grid
Christian Cumbaa- Ontario Cancer Institute
Igor Jurisica (Ontario Cancer Institute, Signaling Biology);
Short Abstract: We have developed a computer vision system that stands to speed
high-throughput X-ray protein structure solution, and lay the
statistical basis for a science of protein crystallization.

Protein crystallization, a major bottleneck in the protein structure
solution via X-ray crystallography, requires a brute-force search
through chemical space for crystallizing conditions. Each trial (1,536
per protein) requires human experts to score the outcome. Our system
automatically scores images from high-throughput trials, assisting or
replacing human experts at the Hauptman-Woodward Institute. The system's
intensive image-analysis step is performed by the World Community Grid
on HWI archives of 110,000,000 images.

Beyond crystal detection, our system distinguishes 10 crystallization
outcomes, including clear, crystal, precipitate, skin, phase separation,
and combinations thereof. Once assembled, the 18,500,000 experiments
will constitute a database of the outcomes of 12,000 proteins across
1,536 cocktails and seven time-points: details of protein
crystallization across time, chemical space, and the protein landscape.
Long Abstract:Click Here

Poster V07
One size doesn’t fit all: The classification of CNV associated genes
K. Cara Woodwark- WTSI
K. Cara Woodwark (WTSI, Pfam);
Short Abstract: Genes associated with copy number variable regions (CNVs) are usually analysed as a single group. Here we show that CNV genes should be classified into three groups each with very distinct characteristics, such as, mode of regulation of expression, 3'UTR length and mutation rate.
Long Abstract:Click Here

Poster V08
Structural Refinement Using Distribution and Correlation of Structural Elements in Proteins
Yuanyuan Huang- Bioinformatics and Computational Biology
No additional authors
Short Abstract: We investigate the distribution and correlation of residue level structural elements such as residue distances and angles and residue torsion angles in proteins, and show important structural properties that can be extracted from these studies.
Long Abstract:Click Here

Poster V09
Extending Three-Dimensional Structural View of Thermotoga maritima
Ying Zhang- Sanford-Burnham Medical Research Institute
Ines Thiele (University of Iceland, Center of Systems Biology); Dana Weeks (Sanford-Burnham Medical Research Institute, Bioinformatics and Systems Biology); Zhanwen Li (Sanford-Burnham Medical Research Institute, Bioinformatics and Systems Biology); Lukasz Jaroszewski (Sanford-Burnham Medical Research Institute, Bioinformatics and Systems Biology); Bernhard Palsson (University of California at San Diego, Department of Bioengineering); Andrei Osterman (Sanford-Burnham Medical Research Institute, Bioinformatics and Systems Biology); Adam Godzik (Sanford-Burnham Medical Research Institute, Bioinformatics and Systems Biology);
Short Abstract: Combining structural genomics and systems biology, we built a three-dimensional structural view of the central metabolic network of a hyperthermophilic bacterium, Thermotoga maritima. This poster presents preliminary results of extending this effort to build a complete image of all the biological processes in a single cell of this bacterium.
Long Abstract:Click Here

Poster V10
The three-dimensional folding of the alpha-globin gene domain reveals formation of chromatin globules
Davide Baù- Prince Felipe Research Center
Marc Marti-Renom (Prince Felipe Research Center, Bioinformatics & Genomics Department);
Short Abstract: We developed a general approach that combines comprehensive chromatin interaction mapping using 5C with the Integrated Modeling Platform to generate high-resolution three-dimensional models of chromatin at the Mb scale. We applied this approach to analyze a 500 Kb gene dense domain (ENm008) on human chromosome 16 that includes the ?-globin locus. We obtained 3D models of this domain in cells that express the ?-globin locus (K562) as well as in lymphoblastoid cells that do not (GM12878). The models accurately reproduce the known looping interactions between the ?-globin genes and their distal regulatory elements. Further, we find that the domain folds into a single globular conformation in GM12878 cells, whereas two globules are formed in K562 cells. The central cores of these globules are enriched for actively transcribed genes, whereas non-transcribed chromatin is more peripheral. We propose that globule formation represents a higher order folding state that is related to clustering of actively transcribed genes around shared transcription machineries.
Long Abstract:Click Here

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