ISMB 2008 ISCB

16th Annual
International Conference
Intelligent Systems
for Molecular Biology


Metro Toronto Convention Centre (South Building)
Toronto, Canada


 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

















Accepted Posters
Category 'T'- Other (includes posters with fewer than 10 submissions)'
Poster T01
Computational protein function prediction: Are we making progress?
Iddo Friedberg- University of California San Diego
Adam Godzik (Burnham Institute for Medical Research, Bioinformatics and Systems Biology); Martin Jambon (Wink Technologies, );
Short Abstract: None On File
Long Abstract: Click Here

Poster T02
Making the Semantic Web Usable for Biologists
Paul Gordon- University of Calgary
Mark Wilkinson (University of British Columbia, James Hogg iCAPTURE Centre for Cardiopulmonary Research); Christoph Sensen (University of Calgary, Biochemistry and Molecular Biology);
Short Abstract: None On File
Long Abstract: Click Here

Poster T03
Molecular Mechanics Analysis of Minimal Energy RNA Conformational Change Pathways
Keith Van Nostrand- University of Rochester
David Mathews (University of Rochester, Department of Biochemistry and Biophysics);
Short Abstract: Nudged Elastic Band and targeted molecular dynamics were explored to determine low potential energy pathways for conformational change of an AA non-canonical pair, which was shown to be in conformational exchange by NMR. The pathways revealed a reaction coordinate along which free energy changes were determined by umbrella sampling.
Long Abstract: Click Here

Poster T04
Response of calyces yield and quality of four Roselle genotypes under different nitrogen fertilizer rates
Mohamed Shaheen- King Abdul Aziz University
No additional authors
Short Abstract: Four Roselle genotypes were studied under four nitrogen rates in 2006 and 2007 in Saudia. Asswan cv. produced the highest dry calyces yield under 276 and 368 kg N/ha. Sewa cv. had highest vit. C and lowest calcium oxalate. The 276 kg N/ha produced highest vit. C and calcium oxalate.
Long Abstract: Click Here

Poster T05
From genes to drug targets: Applications for parasitic organisms
Adhemar Zerlotini- FIOCRUZ - IRR
Guilherme Oliveira (FIOCRUZ, Instituto René Racho); Jessica Kissinger (UGA, Genetics);
Short Abstract: Genomics technologies have contributed to further understand biological processes, but the field has yet to effectively tackle the drug discovery challenge. In this review, we describe computational approaches aiming to improve the exploitation of these resources to gain insights into mechanisms that underlie diseases and drug target discovery.
Long Abstract: Click Here

Poster T06
Towards an automatic classification of protein structural domains based on structural similarity
Chin-Hsien Tai- National Cancer Institute, NIH
Vichetra Sam (CIT, NIH, DHHS); Jean Garnier (MIG, INRA, INRA); Jean-Francois Gibrat (MIG, INRA, INRA); Byungkook Lee (NCI, NIH, DHHS); Peter Munson (CIT, NIH, DHHS);
Short Abstract: Manually curated protein classifications like SCOP and CATH are different from automatic classifications. We investigated the reasons for this difference and conclude that the difference arises mainly from the computed pairwise similarities rather than from any partition procedure that needs to be used for the classification.
Long Abstract: Click Here

Poster T07
The networks of sequence flow and the stability gap
Baoqiang Cao- University of Texas at Austin
Ron Elber (University of Texas at Austin, Department of Chemistry and Biochemistry and Institute of Computational and Engineering Sciences);
Short Abstract: We investigated the sensitivity of the network of sequence flow between proteins structures to the stability gap.
Long Abstract: Click Here

Poster T08
Structural Classification Databases and Automated Structure Alignment Programs: Can’t We All Just Get Along?
Michael Sierk- Saint Vincent College
No additional authors
Short Abstract: Protein structural classification databases such as SCOP frequently differ from automatic structural alignment programs. Recent studies have probed these differences, either attempting a reconciliation or rationalizing the divergence. I will provide an overview of this literature, emphasizing the sometimes implicit assumptions behind the metrics used to determine classification boundaries.
Long Abstract: Click Here

Poster T09
The Jena Library of Biological Macromolecules - JenaLib: New Features
Rolf Huehne- Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI)
Thomas Koch (Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI), Biocomputing);
Short Abstract: The JenaLib (www.fli-leibniz.de/IMAGE.html) offers value-added
information for all PDB and NDB database entries, e.g.:
PDB/NDB atlas pages, QuickSearch, PDB/UniProt alignments, Jmol-based
molecule viewer, SNP and PROSITE motif mapping.

Most recent new features are:
PFAM domain mapping, sequence pattern search, integration of various
data (SAPs, Exons, Domains etc.) into PDB/UniProt alignments
Long Abstract: Click Here

Poster T10
Molecular design with full flexibility: Incorporating homology modeling, molecular dynamics simulations, and virtual screening to identify inhibitors of the HTRA1 serine protease
Yat Tang- Washington University School of Medicine
No additional authors
Short Abstract: HTRA1 is a serine protease identified as a major genetic risk factor for age-related macular degeneration. A homology model was created, molecular dynamics simulations were performed in explicit solvent, and snapshots at different time intervals were extracted and employed in virtual screening to improve hit identification.
Long Abstract: Click Here

Poster T11
Genotyping and the search for the genetic basis for common diseases
Simon Potter- Wellcome Trust Sanger Institute
No additional authors
Short Abstract: With the reference human genomc sequence established, an
area of research which has recently flourished
is the analysis of genetic variation with the aim of
identifying the genes linked to common human diseases.
We present a general overview of the methods and highlight
some current projects.
Long Abstract: Click Here

Poster T12
A Multi-regional Analysis of Contact Maps towards Understanding Protein Similarity Relationships
Hazem Ahmed- MSc. Student, Queen's University
Tony Kuo (PhD Student, Queen's University , School of Computing); Janice Glasgow (Professor, Queen's University , School of Computing);
Short Abstract: Understanding protein similarity relationships would lead to understand protein functional similarity and evolutionary relationships. Therefore, a multi-regional analysis of contact maps is performed towards understanding sequence/contact map relationships by studying the amount of similarity between a pair of sequences and the amount of similarity between their corresponding contact maps.
Long Abstract: Click Here

Poster T13
Utilizing the Ontology of Biomedical Investigations (OBI) for Influenza Sequence and Surveillance Analysis
Richard Squires- UT Southwestern Medical Center at Dallas
Richard Scheuermann (UT Southwestern, Pathology); Lynn Schriml (University of Maryland School of Medicine, Institute for Genome Sciences); Eric Bortz (Mount Sinai School of Medicine, Microbiology); Torsten Staab (Los Alamos National Laboratory, Applied Engineering and Technology ); Marc Colosimo (Mitre Corporation, Information Technology); Joanne Luciano (Mitre Corporation, Information Technology);
Short Abstract: The Influenza Ontology captures influenza virus sequence metadata. Research and surveillance terms describe Investigator, Event, Location, Strain Specimen, Amplified Strain Specimen, Virion RNA, Treatment, and Host. Once completed, a database schema based upon the OBI will serves as the repository for influenza sequence and surveillance data through the BioHealthBase portal.
Long Abstract: Click Here

Poster T14
Eighteen months and counting: A status update of activities at Iowa State University’s BCBLab initiative
Yves Sucaet- Iowa State University
Deepak Reyon (Iowa State University, Bioinformatics & Computational Biology Laboratory); Fadi Towfic (Iowa State University, Bioinformatics & Computational Biology Laboratory);
Short Abstract: Bioinformatics and Computational Biology Laboratory (BCBLab: http://lab.bcb.iastate.edu) serves wet-labs throughout
campus with bioinformatics expertise.
Involvements range from legacy
Fortran applications to structure determination
and microarray analysis. The BCBLab is open to students
with an interest in bioinformatics and who wish to develop breadth and depth
in diverse research areas.
Long Abstract: Click Here

Poster T15
Vaccine Ontology Development and its Application on Vaccine Data Standardization and exchange
Yongqun He- University of Michigan
Zuoshuang Xiang (University of Michigan, Lab Animal Medicine, Microbiology and Immunology); Boyang Zhao (University of Michigan, Engineering); Lindsay Cowell (Duke University, Biostatistics and Bioinformatics); Barry Smith (University at Buffalo, Philosophy);
Short Abstract: A prototype of Vaccine Ontology has been developed based on a collaborative effect among three universities. XML and RDF/OWL-based vaccine data exchange formats have been standardized by Vaccine Ontology and used to represent vaccine data in the VIOLIN vaccine database system (http://www.violinet.org/).
Long Abstract: Click Here

Poster T16
Between order and disorder: The origin of increased radius of gyration of proteins
Zsuzsanna Dosztanyi- Columbia University
Burkhard Rost (Columbia University, Department of Biochemistry & Molecular Biophysics);
Short Abstract: Radius of gyration describes the effective size of molecules. In proteins, its increase is usually associated with unfolding or disorder, however, many proteins with known structures also deviates form the ideal compact conformation. We developed a prediction method to recognize the increased radius of gyration from the amino acid sequence.
Long Abstract: Click Here

Poster T17
The Environment Ontology (EnvO) & Gazetteer (Gaz): two community-based projects for describing the environments of organisms and biological samples.
Lynn Schriml- University of Maryland, School of Medicine
The Environment Ontology Consortium (none, none);
Short Abstract: The community-based efforts of the Environmental Ontology consortium (www.environmentontology.org) have produced two artifacts that support consistent annotation of the environment of an organism. The Environment Ontology (EnvO) describes the environments of organisms and the Gazetteer (Gaz) describes places and place names.
Long Abstract: Click Here

Poster T18
Snowflock: Virtual Cluster Technology for Bioinformatics Applications
Joe Whitney- University of Toronto
Andres Lagar-Cavilla (University of Toronto, Computer Science); Eyal DeLara (University of Toronto, Computer Science); Adin Scannell (University of Toronto, Computer Science); Stephen Rumble (University of Toronto, Computer Science); Michael Brudno (University of Toronto, Terrence Donnelly Centre for Cell and Biomolecular Research, Computer Science, Banting and Best Department of Computational Biology);
Short Abstract: Virtual machines (VMs) are widely used to share hardware compute and storage resources among many users. In bioinformatics, typical applications leverage grid computing, where tasks are run in parallel on many machines (a cluster). Snowflock provides dynamic cloning of individual VMs into virtual clusters for bioinformatics grid computing.
Long Abstract: Click Here

Poster T19
OBI: the Ontology for Biomedical Investigations
Melanie Courtot- Terry Fox Laboratory - BCCRC
James Malone (EMBL-EBI, Microarray); various various (various, various);
Short Abstract: The Ontology for Biomedical Investigations (OBI) Consortium is developing an integrated ontology to describe biological and biomedical investigations. Researchers from a variety of biological and technological domains have collaborated to create a shared source of terms for consistent representation of the experiments and studies. OBI is available at http://purl.org/obo/obi/.
Long Abstract: Click Here

Poster T20
A Stability Diagram for the Charged Flexible Surfaces in a Polyelectrolyte
Adriano Ferrari- McGill University
No additional authors
Short Abstract: Like-charged surfaces in aqueous solution can attract each other when surrounded by ions of opposite charge. We performed Brownian dynamics simulations to examine the force between two infinite flexible chains with discrete charges, and examined their stability against deformation. We have also computed the stability diagram.
Long Abstract: Click Here

Poster T21
Structural Face of the Metabolic Reconstruction of Thermotoga Maritima
Ying Zhang- Burnham Institute for Medical Research
Ines Thiele (University of California, San Diego, Bioinformatics); Dana Weekes (Burnham Institute for Medical Research, Bioinformatics and Systems Biology Program); Zhanwen Li (Burnham Institute for Medical Research, Bioinformatics and Systems Biology Program); Andrei Osterman (Burnham Institute for Medical Research, Bioinformatics and Systems Biology Program); Adam Godzik (Burnham Institute for Medical Research, Bioinformatics and Systems Biology Program);
Short Abstract: Combining efforts of structural genomics and molecular modeling centers we modeled 3D protein structure of core metabolic network of a hyperthermophilic bacterium, Thermotoga maritima, thus connecting metabolic simulations and structural biology. Exploring synergies between these two research fields opens up applications from detailed analysis of enzyme-substrate interactions to the study of evolution of metabolic networks.
Long Abstract: Click Here

Poster T22
A Cell Line Knowledgebase
David States- University of Michigan
Sirarat Sarntivijai (University of Michigan, National Center for Integrative Biomedical Informatics); Alex Ade (University of Michigan, National Center for Integrative Biomedical Informatics); Brian Athey (University of Michigan, National Center for Integrative Biomedical Informatics);
Short Abstract: The Cell Line Knowledgebase (CLKB) was created to assist data exploration and comparison of different cell lines in biomedical research and to begin to develop a controlled vocabulary of cell line names. Both linguistic and experimental issues are addressed.
Long Abstract: Click Here

Poster T23
A Review on Feature Selection Methods in Model Building
Shuzlina Rahman- Universiti Teknologi MARA
Azuraliza Abu Bakar (Dr, Systems Information and Technology); Zeti Azura Mohamed Hussein (Dr, Department of Biosciences & Biotechnology);
Short Abstract: Literatures have shown that feature selection is vital prior to building a model as it improves model performance, provide faster and reliable model etc. The study reviewed various feature selection methods in model building and highlights its importance. The concepts, merits, demerits, and scoring criteria of each method are described.
Long Abstract: Click Here

Poster T24
Phylogeny-based scoring of structural coverage in protein families
Natasha Sefcovic- University of California
Christian M. Zmasek (Burnham Institute for Medical Research, Program in Bioinformatics and Systems Biology); Adam Godzik (Burnham Institute for Medical Research, Program in Bioinformatics and Systems Biology);
Short Abstract: To assess the structural coverage of particular protein families (in the context of structural genomics), we propose a metric, which uses distances along a phylogenetic tree to calculate and compare the impact of specific proteins on the structural coverage. We report how this metric "performs" on some protein families.
Long Abstract: Click Here

Poster T25
Brainstorm: a new tool for analysing neuronal's activity.
Anne Segonds-Pichon- The Babraham Institute
Simon Andrews (Babraham Institute, Bioinformatics); Alister Nicol (Babraham Institute, Laboratory of Cognitive & Behavioural Neuroscience); Keith Kendrick (Babraham Institute, Laboratory of Cognitive & Behavioural Neuroscience);
Short Abstract: Brainstorm aims to analyse neuronal activity sampled from electrodes in a microelectrode array.
It allows quantification of changes in mean spike rate between the pre- and the post-stimulus periods and calculation of correlation between spatially identified neurons pairs.
Graphical representations of changes in neuron activity and correlation are available.
Long Abstract: Click Here

Poster T26
Compositional enrichment of bio-ontologies
Andrea Splendiani- University of Rennes 1
Scott Piao (University of Manchester, Text Mining Group); Elena Beisswanger (University of Jena, Julie Lab); Yutaka Sasaki (University of Manchester, Text Mining Group); Sophia Ananiadou (University of Manchester, The National Center for Text Mining); John McNaught (University of Manchester, The National Center for Text Mining);
Short Abstract: With the increasing number of ontologies developed in the bio-domain, it is important to identify relations between terms in different ontologies. We propose a modular approach for this task, that can benefit on existing frameworks while focusing on the specifics of bio-ontologies.
Long Abstract: Click Here

Poster T27
Stability of A-G Non-Canonical Pair Conformations in RNA Duplexes
Matthew Seetin- University of Rochester Medical Center
John Serafini (University of Rochester, Physics); David Mathews (University of Rochester Medical Center, Biochemistry and Biophysics);
Short Abstract: We investigated the free energy surface of conformational changes of the A-G non-canonical pairs two self-complimentary RNA duplexes using umbrella sampling and the Weighted Histogram Analysis Method. These calculations quantify the favorability of each conformation for each sequence using the AMBER99 molecular dynamics force field
Long Abstract: Click Here

Poster T28
Histone modifications and transcriptional regulation
Rosa Karlic- Max Planck Institute for Molecular Genetics
No additional authors
Short Abstract: This review focuses on recent studies that investigate the combinatorial nature of histone modifications and it's impact on gene regulation, with special attention paid to the effect of CpG‐content‐specific histone modification patterns of different promoter classes on gene expression levels.
Long Abstract: Click Here

Poster T29
Internal coordinate methods for macromolecular structure and dynamics
Samuel Flores- Stanford University
No additional authors
Short Abstract: RNAs play a pervasive role in gene expression and regulation. Their structure and dynamics are crucially important for understanding function. An internal coordinate representation allows us to freeze bond length and angle vibrations and rigidify secondary structure, leading us to recover observed motions of RNA at low computational cost.
Long Abstract: Click Here

Poster T30
3-dimensional Protein Structure Alignment: A Review
Shweta Shah- Carnegie Mellon University
Nikolaos Sahinidis (Carnegie Mellon University, Chemical Engineering);
Short Abstract: Properties of proteins are strongly dependent on their structure. Since protein sequences are often unable to provide sufficient structural information, structural alignment becomes important in function elucidation. Many approaches have been developed for protein structure alignment. We discuss these approaches, and provide a critical review of their strengths and weaknesses.
Long Abstract: Click Here

Poster T31
Crystallization Image Analysis on the World Community Grid
Christian Cumbaa- Ontario Cancer Institute
Igor Jurisica (Ontario Cancer Institute, Signaling Biology);
Short Abstract: High-throughput protein X-ray crystallography requires massively parallel searches through chemical space for suitable crystallization conditions. Automatic classification of resulting protein crystallization trial images improves throughput and optimization. Our system is running on the World Community Grid, extracting and evaluating 12,375 image features from 70 million crystallization images.
Long Abstract: Click Here

Poster T32
3D-Fun/PDB-UF: web-based tool for predicting enzyme function from structure.
Marcin von Grotthuss- BioInfoBank Institute
Dariusz Plewczynski (BioInfoBank Institute, Bioinformatics Laboratory); Gert Vriend (Radboud University Nijmegen, Centre for Molecular and Biomolecular Informatics); Leszek Rychlewski (BioInfoBank Institute, Bioinformatics Laboratory);
Short Abstract: Here we present software for determining enzyme function based on structural similarity. The system is freely available for everybody at http://3dfun.bioinfo.pl/ and http://3dfun.cmbi.ru.nl/. The tool was used to infer EC numbers for over 2000 protein structures from structural genomics. The predictions can be accessed at http://bioinfo.pl/PDB-UF/ or http://paradox.harvard.edu/PDB-UF/.
Long Abstract: Click Here

Poster T33
ZBTB16 (PLZF), a GC-induced repressor of the apoptotic GC response?
Muhammad Wasim- Medical University
Michela Carlet (Medical University, Biocenter, Div. Molecular Pathophysiology); Muhammad Mansha (Medical University, Biocenter, Div. Molecular Pathophysiology); Harald Niederegger (Medical University, Biocenter, Div. Molecular Pathophysiology); Reinhard Kofler (Medical University, Biocenter, Div. Molecular Pathophysiology);
Short Abstract: ZBTB16(PLZF) was appeared best glucocorticoid-response candidate gene after whole genome expression profiling of childhood ALL. Functional analysis of it in stable CEM C7H2 celllines proved it as pro-survival in GC-induced apoptosis which came as a surprise but was in good agreement with the fact that GCs activate pro-and anti-apoptotic signaling in different tissues.
Long Abstract: Click Here

Poster T34
β-glucan stimulate prolactin synthesis in GH3/B6 via Dectin-1 receptor
Houri Sepehri- university of Tehran, faculty of Biology
Fatemeh Shaerzadeh (university of Tehran, faculty of Biology, animal physiology department ); Ladan Delphi (university of Tehran, faculty of Biology, animal physiology department );
Short Abstract: Dectin-1 recognizes β-glucans and an endogenous undefined ligand on T cells. Dectin-1 expresses in immune and non-immune tissues. β-glucan is the main ligand of dectin-1 and potential of prolactin secretion from GH3/B6 cells. In the present study expression of Dectin-1 in GH3B6 cells is demonstrated.
Long Abstract: Click Here

Poster T35
RNAStructVis - A RNA structure visualizer
Daniel Jurczak- University of Applied Sciences, Hagenberg
Andreas Heinzel (University of Applied Sciences, Hagenberg, Bioinformatics); Martina Kutmon (University of Applied Sciences, Hagenberg, Bioinformatics); Stefan Luger (University of Applied Sciences, Hagenberg, Bioinformatics); Susanne Schaller (University of Applied Sciences, Hagenberg, Bioinformatics); Andreas Schönegger (University of Applied Sciences, Hagenberg, Bioinformatics); Verena Hoenninger (Medical University of Vienna, Clinical Institute of Virology); Regina Kofler (Medical University of Vienna, Clinical Institute of Virology); Christian Siehs (University of Applied Sciences, Hagenberg, Bioinformatics);
Short Abstract: RNA StructVis provides a comprehensive way to produce journal-quality images of RNA secondary structures, as well as permitting its users to perform further manipulations, such as sequence/structure alterations or custom graphical annotations. The result can be exported in a variety of popular graphical formats.
Long Abstract: Click Here

Poster T36
Exploring the functional dynamics of P-loop NTPases
Barry Grant- University of California, San Diego
Alemayehu Gorfe (University of California, San Diego, Chemistry & Biochemistry); J. Andrew McCammon (University of California, San Diego, Chemistry & Biochemistry);
Short Abstract: Structural informatics and molecular modelling were used to probe sequence-structure-function relationships in P-loop NTPases. This study provides information on conformational changes, allosteric modulation, protein-protein interactions and evolutionary relationships. The work illustrates the powerful interplay of informatics and simulation in relation to structural and biochemical experiments on this important class of enzymes.
Long Abstract: Click Here

Poster T37
Mobyle: a new full web bioinformatics framework
Hervé Ménager- Institut Pasteur
Bertrand Néron (Institut Pasteur, Biological Software and Databanks); Corinne Maufrais (Institut Pasteur, Biological Software and Databanks); Nicolas Joly (Institut Pasteur, Biological Software and Databanks); Pierre Tufféry (Université Paris Diderot, Ressource Parisienne en Bioinformatique Structurale); Catherine Letondal (Institut Pasteur, Biological Software and Databanks);
Short Abstract: We present Mobyle, a system that aims at providing biologists a Web environment to run various bioinformatics tools and services. While being specifically targeted towards usability and understandability, it should also provide an integration framework to enable advanced features such as workflow or remote services management.
Long Abstract: Click Here

Poster T38
High Performance Life Sciences Computing on the TeraGrid
Richard Repasky- Indiana University
No additional authors
Short Abstract: High-throughput experiments and large molecular simulations have fueled the "omics" revolution, and Life Scientists increasingly turn to high performance computing to meet exploding data and computational needs. The TeraGrid is a national computational grid that provides supercomputing and massive data storage that support such data analysis/storage and visualization needs.
Long Abstract: Click Here

Poster T39
Counting differing clusters in trees
Lavanya Kannan- Stowers Institute for Medical Research
Hua Li (Stowers Institute for Medical Research, Bioinformatics); Arcady Mushegian (Stowers Institute for Medical Research- Bioinformatics; University of Kansas Medical Center, Department of Microbiology, Molecular Genetics, and Immunology);
Short Abstract: Clusters in trees are structural units that are of biological importance. We propose a new tree distance measure, partial-cluster-index(PCI), which counts non-redundant differing clusters in two trees. We show that PCI is unique among tree distance measures in giving a heuristic on the number of Subtree Pruning and Re-grafting(SPR) reconstructions.
Long Abstract: Click Here

Poster T40
T-RF Manager: a web-based tool
Robert Bukowski- Cornell University
Steven Culman (Cornell University, Crop and Soil Siences); Daniel Ripoll (Cornell University, CBSU);
Short Abstract: T-RF manager is a web-based tool for processing of T-RFLP data. The program eliminates the need for tedious and error-prone manual raw data manipulation and performs multivariate analysis using the Additive Main Effects and Multiplicative Interaction (AMMI) model to investigate the relatioships between microbial communities and their environments.
Long Abstract: Click Here

Poster T41
NCIBI Portal - Collaborative Biomedical Research Environment
Yuri Ikeda- The University of Michigan
Zach Wright (The University of Michigan, National Center for Integrative Biomedical Informatics); Barbara Mirel (The University of Michigan, National Center for Integrative Biomedical Informatics); Aaron Bookvich (The University of Michigan, National Center for Integrative Biomedical Informatics); Paul Trombley (The University of Michigan, National Center for Integrative Biomedical Informatics); James Cavalcoli (The University of Michigan, National Center for Integrative Biomedical Informatics); Beth Kirschner (The University of Michigan, National Center for Integrative Biomedical Informatics);
Short Abstract: The National Center for Integrative Biomedical Informatics (NCIBI) at the University of Michigan developed a Sakai-based portal for biomedical and bioinformatics researchers. The NCIBI Portal promises to uniquely integrate three purposes: public dissemination, research collaboration, and a repository of available tools and resources.
Long Abstract: Click Here

Poster T42
Biological applications of AIDA knowledge management components
Marco Roos- Faculty of Science, University of Amsterdam (UvA)
Piter T. de Boer (University of Amsterdam, Informatics Institute); M. Scott Marshall (University of Amsterdam, Informatics Institute); Kasper van den Berg (University of Amsterdam, Informatics Institute); Sophia Katrenko (University of Amsterdam, Informatics Institute); Edgar Meij (University of Amsterdam, Informatics Institute); Willem R. van Hage (TNO, Science & Industry); Pieter W. Adriaans (University of Amsterdam, Informatics Institute);
Short Abstract: Knowledge can be important for bioinformatics. We consider a ‘knowledge space’ and present two applications of AIDA, a collection of knowledge management components: (i) a workflow that extends a knowledge model with relations extracted from literature, (ii) vBrowser, a virtual resource browser that can find biological resources via semantic relationships.
Long Abstract: Click Here

Poster T43
PATA: a new generative model for alternative splicing
Sepand Mavandadi- University of Toronto
No additional authors
Short Abstract: Alternative splicing (AS) is a key cellular mechanism for expanding the number of unique transcripts produced from a single gene. Here, we present PATA, a leading generative model used to greatly reduce negative effects cross-hybridization when examining AS using microarray experiments.
Long Abstract: Click Here

Poster T44
The methods of affiliation classification for the annual report of biological papers
Myungguen Chung- Korea Institute of Science and Technology Information
DongSoo Jung (Korea Institute of Science and Technology Information, Super Computing Center);
Short Abstract: Our cooperator had published out an annual report for the papers of biological fields. They have wanted to a fully automatic system. We turn their hand-made works into just a mouse click event with the fully automatic system to publish annual reports. we reduced the unclassified notation more than before.
Long Abstract: Click Here

Poster T45
Pathway-based diagnosis of cancer and metastasis
Han-Yu Chuang- Univ. Of California San Diego
Eunjung Lee (Korea Advanced Institute of Science and Technology, Bio and Brain Engineering); Doheon Lee (Korea Advanced Institute of Science and Technology, Bio and Brain Engineering); Yu-Tsueng Liu (Univ. of California San Diego, Moores cancer center); Trey Ideker (Univ. of California San Diego, Bioengineering);
Short Abstract: None On File
Long Abstract: Click Here

Poster T46
Rwui: A web application to create user friendly web interfaces for R scripts
Richard Newton- MRC Biostatistics Unit
Lorenz Wernisch (MRC, Biostatistics);
Short Abstract: Rwui creates web interfaces for running R scripts. Rwui is aimed at bioinformaticians who are developing a statistical analysis of experimental data for collaborators and want to automate their analysis in a user friendly way. Rwui allows them to do this without the need for any web application programming.
Long Abstract: Click Here

Poster T47
Assessing the functional structure of genomic data
Curtis Huttenhower- Princeton University
Olga G. Troyanskaya (Princeton University, Computer Science);
Short Abstract: We analyze the functional structure of S. cerevisiae datasets from over 950 publications in the context of over 140 biological processes. This includes a coverage analysis of biological processes given current high-throughput data, a data-driven map of associations between processes, and a measure of similar functional activity between genome-scale datasets.
Long Abstract: Click Here

Poster T48
A topological mechanism for gene descrambling in stichotrichous ciliates
Mark Daley- The University of Western Ontario
Ian McQuillan (University of Saskatchewan, Computer Science); Nicholas Stover (Bradley University, Biology);
Short Abstract: Through the application of the theory of rational knots, we show that the unique gene descrambling process in stichotrichous ciliates can be explained by considering the topology of DNA molecules. Our model is also demonstrated to be consistent with all current experimental results.
Long Abstract: Click Here

Poster T49
Maximizing the Extent of Spread in a Dynamic Network
Habiba Habiba- University of Illinois at Chicago
Tanya Y. Berger-Wolf (Univeristy of Illinois, Computer Science);
Short Abstract: We present a method for identifying the top individuals to initiate processes, such as diseases and behavior, dynamically spreading in populations, so as to maximize the resulting extent of spread. Under the standard models of propagation from mathematical epidemiology we validate and demonstrate applicability of our approach on animal populations.
Long Abstract: Click Here

Poster T50
Dynamics of communities in fission-fusion species
Chayant Tantipathananandh- University of Illinois at Chicago
Tanya Berger-Wolf (University of Illinois at Chicago, Department of Computer Science); Siva Sundaresan (Princeton University, Department of Ecology and Evolutionary Biology); Ilya Fischhoff (Princeton University, Department of Ecology and Evolutionary Biology); Daniel Rubenstein (Princeton University, Department of Ecology and Evolutionary Biology);
Short Abstract: We use a novel method for identifying communities in dynamic social networks to study two equid species: Grevy's zebra and onagers. Our result confirms previous ecological studies suggesting different social drives for group formation in the two species. Moreover, our approach quantifies the difference and provides visual supporting evidence.
Long Abstract: Click Here

Poster T51
Gene Designer: a synthetic biology tool for constructing artificial DNA segments
Alan Villalobos- DNA2.0
No additional authors
Short Abstract: Gene Designer is an expandable Synthetic Biology workbench suitable for molecular biologists interested in the de novo
creation of genetic constructs. Users can easily add, edit and combine genetic elements such as promoters, open reading frames
and tags through an intuitive drag-and-drop graphic interface and a hierarchical DNA/Protein object map.
Long Abstract: Click Here

Poster T52
Bridging Existing Bioinformatics Resources Into the Semantic Web To Facilitate Integrative Analysis and Workflows
Paul Gordon- University of Calgary
No additional authors
Short Abstract: We present work within the BioMoby project to facilitate the use of existing data and the use of legacy bioinformatics applications in Semantic Web Services. Frameworks for simply wrapping ACD, CGI and WSDL-based analysis interfaces are available, as is a client (Seahawk) for integrated analysis and workflow construction.
Long Abstract: Click Here



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