Posters Accepted for Presentation

Data Integration

Classifier Fusion for Poorly-Differentiated Tumor Classification using Both Messenger RNA and MicroRNA Expression Profiles Yuhang Wang, Margaret H. Dunham, James A. Waddle, Monnie McGee

Modeling and storing scientific protocols Zoe Lacroix, Yi Chen, and Natalia Kwasnikowska

Querying Consolidated miRNA data: A Comparative Study S. Lopez, Z. Chen

Benefits and costs of bioinformatics pipelines : an experiment B. A. Eckman, T. Gaasterland, Z. Lacroix, L. Raschid, B. Snyder, and M.-E. Vidal

Pathway Knowledge Base: Integrating and querying pathways using BioPAX and RDF Kyle Bruck, Nikesh Kotecha, and William Lu

Data Mining

Information Mining over Heterogeneous Microarray and Clinical Data Fatih Altiparmak, Ozgur Ozturk, Selnur Erdal, Hakan Ferhatosmanoglu, Donald C. Trost

In silico identification of mitochondrial proteins using EST data Yaoqing Shen, Gertraud Burger

Feature filtering to improve predictions of RNA interference activities by support vector machine regression Andrew S. Peek

Web-Based Tools for Gene Comparison and Clustering James Z. Wang, Rapeeporn Payattakool, Chin-fu Chen

A Two-Phase Hybrid Method for Biological Sequence Clustering Wei-Bang Chen, Chengcui Zhang

Learning SNP Dependencies using Embedded Bayesian Networks Ara V. Nefian

FOCUS Discovery: An Asynchronous, Parallel, Non-Linear Software Program for Gene Association Studies Matthew Frome, Gerri Shaw and Jim Shaw

Data Visualization

Phylo-mLogo: An interactive multiple-logo tool for visualization of large-number sequence alignment Arthur Chun-Chieh Shih, D.T. Lee, Chin-Lin Peng, and Yu-Wei Wu

3D Phylogeny Explorer: Distinguishing paralogs, lateral transfer, and violations of the “molecular clock” assumption with 3D visualization Namshin Kim and Christopher Lee

Tools for Integrated Sequence-Structure Analysis with UCSF Chimera Elaine C. Meng, Eric F. Pettersen, Conrad C. Huang, John "Scooter" Morris, and Thomas E. Ferrin

Gene Expression

A bioinformatics approach to identify recoding events of A-to-I RNA editing Stefan Maas, Daniel Lopresti, Derek Drake, Rikhi Kaushal, Steven Hookway, Walter Scheirer, Mark Strohmaier, and Christopher Wojciechowski

Use generalized Procrustes analysis for be-tween-slide normalization of microarray data Huiling Xiong, Dapeng Zhang, Crhstopher J. Martyniuk, Vance L. Tru-deau, Xuhua Xia

An Automated Pipeline for Regulatory Motif Detection Tool Assessment Daniel Quest, Kathryn Dempsey, Dhundy Bastola, and Hesham Ali

Extension of SVM-RFE for multiclass gene selection on DNA microarray data Xin Zhou and David P. Tuck

DNA Aberration and RNA Expression Pattern Detection Using Affymetrix Gene Expression Arrays Guoliang (Leon) Xing, Cristina R. Antonescu, Kai Wu1, Manqiu Cao, Yaron Turpaz, Earl Hubbell, Nicholas Socci, Robert G. Maki, C. Garrett Miyada, and Raji Pillai

Genomic Annotation

A Noncoding RNA Gene Finder for Bacteria Brian Tjaden

Splign: a Tool for cDNA-to-Genome Compartmentization and Alignment Yu.Kapustin, A.Souvorov, T.Tatusova

goldMINER: an efficient automatic sequence annotation platform Xuhua Xia, Pingchao Ma, Christopher Martyniuk, Kate Werry, Huiling Xiong, Vance L. Trudeau

Computational pipeline for the analysis of genome-wide experimental data Gabriel Renaud, Ingeborg Holt, James Malley, Tyra Wolfsberg

Integrating Multiple Genome Builds into an Automated Sequence Annotation Pipeline Conrad Huang, John "Scooter" Morris, Susan Johns, Michiko Kawamoto, Doug Stryke, Courtney Harper, Thomas Ferrin, Patricia Babbitt

Genotyping and SNPs

Graphic Models: Approaches for Mining Genetic Epidemiology Data in Complex Trait Analysis Lu-yong Wang, Dorin Comaniciu, Daniel Fasulo

Designing a Rapid SNP-Based Genomic Screening Tool for Common Diseases Lu-yong Wang, Dorin Comaniciu, Daniel Fasulo

Morphometric Analysis of Imaging Genetics in Mild Cognitive Impairment Li Shen, Andrew Saykin, Heng Huang, Moo K. Chung, James Ford, Fillia Makedon

SIDACS: An integrated computational system for SNP/indel discovery and classification Stephen M. Beckstrom-Sternberg and Raymond K. Auerbach

Molecular Simulation

A Computational RNA Evolution Simulator based on thermodynamic stability, mutational robustness, and linguistic complexity Nir Dromi, Assaf Avihoo, and Danny Barash

Other

Chemical molecular similarity analysis and its applications in structure-activity visualization Weiguo Fan, Xin Lin, Yu-wei Hsieh, Boren Lin, Paul Durand, Johnnie Baker and Chun-Che Tsai

A Comparison Study of Signal Extensions Methods for Wavelet Denoising of Array CGH Data Yuhang Wang

Grid-based Secure Web Service Framework for Bioinformatics Dawei Sun and Xiaoyu Zhang

OptiPNAFinder: A Sequence Designing Tool for Peptide Nucleic Acid (PNA) with Minimized Off-target Effect Seungpyo Hong, Hosang Jeon, Seongjo Kim, Hyon Chang Kim, Dong Soon Choi, Han Jip Kim, Hyun Joo, Churl K. Min

Using Pathway Logic to Integrate Signal Transduction and Gene Expression Data Linda Briesemeister, Joe Gray, Laura Heiser, Merrill Knapp, Keith Laderoute, Andy Poggio, Paul Spellman, Carolyn Talcott

Predictive Methods

Prediction of catalytic residues in proteins using machine-learning techniques Natalia V. Petrova, Cathy H. Wu

Distinctive Compositional Features for Extracellular Levansucrases of Proteobacteria Inara Andersone, Martina Baltkalne and Peteris Zikmanis

DomainDiscovery: A Novel Algorithm for Protein Domain Boundary Assignment Using Support Vector Machine Abdur R. Sikder, Stella Veretnik, Albert Y. Zomaya and Philip E. Bourne

On the Prediction of Biomineralization Proteins in the Absence of Sequence Homologies Xiaoyu Zhang and Betsy Read

Semi-Supervised Learning for Protein Subcellular Localization Prediction Leon French, Martin Ester, Fiona Brinkman

A statistical approach using network structure in the prediction of protein characteristics Pao-Yang Chen, Charlotte M. Deane, Gesine Reinert

Classification and Prediction of Antisense Oligonucleotide Efficiency using global structure information with support vector machines Roger Craig and Li Liao

Prediction of disulfide patterns from protein sequences Yu-Ching Chen and Jenn-Kang Hwang

A Base Stacking Energetics Centered Dynamic Programming Algorithm for the Computational Prediction of Thermodynamic Interaction Potentials between Nucleic Acid Sequences Yuan Lin, Jeffrey A. Manthey, Andrew S. Peek

Modelling eukaryotic promoters with an evolving HMM method Kyoung Jae Won, Troels Torben Marstrand, Anders Krogh

Prediction of Protein Subcellular Localization Chin-Sheng Yu and Jenn-Kang Hwang

Recommending pathway genes using a compendium of clustering solutions David M. Ng, Marcos H. Woehrmann, and Josh Stuart

The Evolutionary Origins of Phosphorylation Samuel M. Pearlman, Zach Serber, James E. Ferrell, Jr.

Proteomics

Modeling Protein Complexes Using Comparative Patch Analysis Dmitry Korkin, Fred P. Davis, Frank Alber, and Andrej Sali

Mathematical Models and Extensions of Ramachandran Plots Kiran B. Chilakamarri, Nathaniel Dean, and Charu Malhotra

Sequence Comparison

An Assessment of Phylogenetic Capacity for Bacterial Levansucrases Martina Baltkalne, Ieva Minicha, Inara Andersone and Peteris Zikmanis

A Web-Based Tool for Protein Thermostability Han-Kuen Liang, Chia-Mao Huang, Ming-Tat Ko, Jenn-Kang Hwang

Scoring Alignment Gaps in the Twilight Zone Barbara S. Chapman, Ph.D

Tools for Identification of Sequence and Structurally Conserved Environments Brandon Peters , Eunseog Youn, Charlie Moad, Randy Heiland, Sean D. Mooney

Quantum Based Evolutionary Algorithm for Multiple Sequence Alignments Hongwei Huo, Vojislav Stojkovic, and Qiuli Lin

Strings, Graphs, and Algorithms

DNA-Based Addition and Subtraction of Two Unsigned Integer Numbers Inspired by Unrestricted Grammars Implemented in Prolog Programming Language Elizabeth Britto

A Novel Method for Clustering Internal Transcribed Spacer (ITS) Sequences from Fungi using Computer-simulated Restriction Enzyme Cut Patterns Rajib Sengupta, Dhundy Bastola and Hesham Ali

A Linear-Time Algorithm for Suffix Sorting and Its Applications Fei Nan and Don Adjeroh

Functional modules from protein interaction network via local optimization Feng Luo, Xiu-Feng Wan, Chin-Fu Chen, Richard Scheuermann

On the approximation of optimal structures for RNA-RNA interaction Saad Mneimneh

Structural Biology

Evaluation of Features for Catalytic Residue Prediction in Novel Folds Eunseog Youn, Brandon Peters, Predrag Radivojac, and Sean D. Mooney

The fragment transformation method to detect the protein structural motifs Chih Hao

A Semantic Map to select Structural Bioinformatics services Zoé Lacroix, Hervé Ménager, and Pierre Tufféry

Computation of Conformational Entropy from Protein Sequences Shao-Wei Huang and Jenn-Kang Hwang

Finding all plausible pairing partners for a stem-forming RNA region with the PRPVS algorithm Xiaolu Huang, William Tappriach and Hesham Ali

Accurate prediction of protein complex structures through machine learning Andrew J. Bordner and Andrey Gorin

Severe supersecondary regularities in beta sandwich proteins Y-S. Chiang and A.E. Kister

Protein Structure Prediction using Integer Programming and new Residue Pair Energy Functions Kyle Ellrott, Jun-Tao Guo, Victor Olman, Ying Xu

Systems Biology

Global Computational Regulatory Analysis of Anti-endotoxin Effect of LL-37 Simon Chan, Gregory Doho, Neeloffer Mookherjee, Kelly Brown, Fiona Roche, Fiona S.L. Brinkman, and Robert E.W. Hancock

S. pombe Regulatory Network Construction Using the Fuzzy Logic Network Yingjun Cao, Paul P. Wang, Alade Tokuta

Assessing Hierarchical Modularity in Protein Interaction Networks Young-Rae Cho, Woochang Hwang, Aidong Zhang and Murali Ramanathan

Simulation of Leukocyte Interactions with a P-Selectin Coated Substrate Jon Tang and C. Anthony Hunt

A local clustering algorithm for discovering functional modules from the synthetic lethal interaction network in yeast Ping Ye, Joel Bader

Agent-Directed DEVS Modeling of Adaptive Cellular Immunity Sunwoo Park, Sean H. J. Kim, and C. Anthony Hunt

Agent-Based Simulations of In Vitro Epithelial Morphogenesis in Multiple Environments Mark R. Grant, Sean H. J. Kim, and C. Anthony Hunt

Stochastic, Agent-Based Analogues of Primary Rat Hepatocytes: Prediction of In Vitro Biliary Excretion Shahab Sheikh-Bahaei and C. Anthony Hunt

Axiom Based in Silico Analogues of In Vitro Tumor Spheroids Jesse Engelberg, C. Anthony Hunt

Global Analysis of Protein Translation Networks in Yeast Daniel D. Wu, Xiaohua Hu

Proteins’ large indel mutations tend to reside in the internal regions Fengfeng Zhou, Ying Xu

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Poster Abstracts