Posters Accepted for Presentation

Click on title for Abstract
The CSB2006 Conference reserves the right to make scheduling changes.
Comparative Genomics
Identification and evolutionary analysis of alternative splicing events using cross-species EST-to-genome comparisons in human, mouse and rat
Feng-Chi Chen, Chuang-Jong Chen, Sheng-Shun Wang, Jar-Yi Ho, Wen-Hsiung Li, and Trees-Juen Chuang
A likelihood ratio test to identify fast-evolving sites in protein sequences, and its application to phylogenomic analysis
Yu Liu, Franz B. Lang
Virtual-CGH: Prediction of Novel Regions of DNA Segmental Alterations from Microarray Gene Expression in Natural Killer Cell Lymphoma
Huimin Geng, Javeed Iqbal, Wing C. Chan and Hesham Ali
Regulatory Element Prediction in Mammalian Genomes
Bilenky M., Robertson G., Dagpinar M., He A., Lin K., Yuen, W., Bainbridge M., Varhol R., Teague K., Griffith O.L., Zhang X., Pan, Y., Quayle A., Hassel M., Sleumer M.C., Pan, W., Pleasance E.D., Chuang, M., Hao H., Li Y.Y., Tsang E.
New tools for large-scale genome comparison analysis
Heidi J. Sofia, Grant C. Nakamura, Joel M. Malard, and Chris S. Oehmen
Detecting uber-operons in microbes
Fenglou Mao, Guojun Li, DOngsheng Che, Hongwei Wu, Ying Xu
Operon conservation and its function diversity
Ping Wan, Fenglou Mao, Victor Olman, Ying Xu
Hierarchical Clustering of Bacterial Genes for Functional Annotations at Multiple Resolution Levels
Hongwei Wu, Fenglou Mao, Victor Olman, Ying Xu

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

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.

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


Poster Abstracts



Microsoft Research


Journal of Bioinformatics and Computational Biology