Poster Abstracts

Except where noted, all abstracts are pdf files.

Session A (odd-numbered posters)
Tuesday, Aug 9th: 1:30 - 2:15 pm
Wednesday, Aug 10th: 1:20 ?- 2:05 pm

Session B (even-numbered posters)
Tuesday, Aug 9th: 5:45 - 6:30 pm
Thursday, Aug 10th: 1:20 - 2:05 pm

Biomedical Research
Cellular Multicellular Systems
Comparative Genomics
Data Mining
Evolution and Phylogenetics
Functional Genomics
High Performance Computing
Microarray Analysis
Pathways Networks Systems Biology
Pattern Recognition
Promoter Analysis
Protein Structure Analysis
RNAi Analysis
Sequence Alignment
SNPs and Haplotyping
Synthetic Biological Systems
Papers presented as posters

Biomedical Research
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Use of Microarray and Clinical Data for Sequential Classification
Guenter Tusch
Grand Valley State University and Grand Rapids Medical Education and Research Center

Efficient Image Texture Analysis and Classification for Prostate Ultrasound Diagnosis
Mark A. Sheppard and Liwen Shih
Univ. of Houston - Clear Lake

Diagnosis and Biomarker Identification on SELDI proteomics data by ADTBoost
Lu-yong Wang, Amit Chakraborty, Dorin Comaniciu
Siemens Corporate Research

Inverse Design of Large Molecules using Linear Diophantine Equations
Shawn Martin, W. Michael Brown, Derick Weis, John Kenneke, Don Visco, Jean-Loup Faulon
Sandia National Laboratories

Cellular Multicellular Systems
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Reducing Gene Regulatory Networks by Decomposition
Luonan Chen, Ruiqi Wang, Kazuyuki Aihara
Osaka Sangyo University

A Diffusion Model to Estimate the Inter-arrival Time of Charged Molecules in Stochastic Event based Modeling of Complex Biological Networks
Preetam Ghosh, Samik Ghosh, Kalyan Basu and Sajal K Das
University of Texas at Arlington

Comparative Genomics
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Operon Prediction Using Comparative Genomics
Natalia Khuri and Nikhila S. Rao
Carnegie Institution of Washington, Department of Plant Biology

Patterns of Gene Deletion following Genome Duplication in Yeast
Jake K. Byrnes and Wen-Hsiung Li
University of Chicago Department of Ecology and Evolution

Comparative Analysis of Alternative Splicing Events in Human and Mouse

Fang-Rong Hsuchia-Hung Liuhwan-You Chang
TU Delft

Comparative study of amino acid composition, codon usage and gene order in microbial genomes

Natalia Khuri and Scot Close
The Carnegie Institution of Washington, DPB

PLATCOM : A Platform for Computational Comparative Genomics on the Web
Kwangmin Choi and Sun Kim
School of Informatics, Indiana University, Bloomington, Indiana

Data Mining
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Classification Methods for HIV-1 Medicated Neuronal Damage
Mengjun Wang (1), Jialin Zheng (2), Zhengxin Chen (3), and Yong Shi (3,4)
(1) Cardiovascular Research, Heart & Vascular Institute, Henry Ford Health System, Detroit; (2) Departments of Pathology, Microbiology and Pharmacology, University of Nebraska Medical Center; (3) College of Information Science and Technology, University of Nebraska at Omaha; (4) Graduate School of Chinese Academy of Sciences, Beijing

The UCSC Genome Project
Heather Trumbower and Jennifer Jackson
UC Santa Cruz Center for Biomolecular Science and Engineering

PROMOCO: a New Program for Prediction of cis Regulatory Elements: From High-Information Content Analysis to Clique Identification
Guojun Li, Jizhu Lu, Victor Olman, Ying Xu
Yale University

Data Integration in the Mouse Genome Informatics (MGI) Database
Donnie Qi, Carol J. Bult, Judith A. Blake, Jim A. Kadin,Joel E. Richardson, Martin Ringwald, Janan T. Eppig, and the Mouse Genome Informatics Group
The Jackson LaboratoryL

HIV Structural and Bio Thermodynamics databases: A resource for the Pharmaceutical and Biotechnology Industry
Talapady N. Bhat*, Yadu B. Tewari, Henry Rodriguez, and Robert N. Goldberg

A New Clustering Strategy with Stochastic Merging and Removing Based on Kernel Functions
Huimin Geng and Hesham Ali
University of Nebraska Medical Center

Prediction of Head and Neck Cancer Metastasis using Artificial Neural Networks
Eveleen Darby, Tezeswari Nettimi, Shilpa Kodali, Liwen Shih
Univ. of Houston - Clear Lake and Lincoln Gray, Univ. of Texas - Medical School at Houston

Cluster utility: A new relative index for sequence clustering
Jason Lee and Sun Kim
Indiana University, Bloomington

A Problem Solving Environment Approach to Integrating Diverse Biological Data Sources
Eric G. Stephan, Kyle R. Klicker, Mudita Singhal, Heidi J. Sofia
Pacific Northwest National Laboratories

Evolution and Phylogenetics
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Predicting functional gene-links from phylogenetic- statistical analyses of whole genomes
Daniel Barker and Mark Pagel
University of Reading

Whole Genome Phylogeny Based on Clustered Signature String Composition
Xiaomeng Wu (1), Xiufeng Wan (2), Dong Xu (2), and Guohui Lin (1)
(1) Computing Science, University of Alberta; (2) Computer Science, University of Missouri - Columbia

A Polynomial Algorithm for the Minimum Quartet Inconsistency Problem with O(n) Quartet Errors
Gang Wu, Jia-Huai You, and Guohui Lin
Computing Science, University of Alberta

Phylogenetic Postprocessing
Nicholas D. Pattengale
University of New Mexico

A Novel Quartet-Based Method for Phylogenetic Inference
B. B. Zhou, M. Tarawneh, C. Wang, A. Zomaya, and R. P. Brent
University of Sydney

Consensus methods using phylogenetic databases
Mahesh Kulkarni and Bernard M.E. Moret
University of New Mexico

Whole Genome Bacterial Phylogeny Using Proteome Comparison and Optimal Reversal Distance
Noppadon Khiripet
National Electronics and Computer Technology Center, Thailand

Identifying Orthologs: The Cycle Splitting Problem on the Breakpoint Graph
Krister Swenson, Nick Pattengale, and Bernard Moret
University of New Mexico

Functional Genomics
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Improving Operon Prediction in E. coli
Phuongan Dam (1,2), Victor Olman (1), and Ying Xu (1,2)
(1) Department of Biochemistry and Molecular Biology, University of Georgia at Athens; (2) Computational Biology Institute, Oak Ridge National Laboratory

Relating transcription factors, modules of genes and cultivations conditions in Saccharomyces cerevisiae
T.A. Knijnenburg, J.M. Daran, P. Daran-Lapujade, M.J.T. Reinders and L.F.A. Wessels
TU Delft

Automatic protein function annotation through candidate ortholog clusters from incomplete genomes
Akshay Vashist, Casimir Kulikowski, and Ilya Muchnik
Department of Computer Science, Rutgers, The State University of New Jersey

EST-Based Analysis of Gene Expression in the Human Cochlea
Irene Gabashvili, Richard J. Carter, Peter Markstein
Hewlett-Packard Labs

EigenPhenotypes: Towards an Algorithmic Framework for Phenotype Discovery
Alex Vaughan, Rahul Singh, Alan Shimoide, Megumi Fuse, Ilmi Yoon
Department of Computer Science, San Francisco State University

A Novel Approach for Prediction of Multi-class Protein Subcellular Localization in Prokaryotic Bacteria
Chia-Yu Su, Allan Lo, Qing-Qin Lin, Fu Chang
Institute of Information Science, Academia Sinica

High Performance Computing
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Incorporating life sciences applications in the architectural optimizations of next-generation petaflop-system
David A. Bader and Vipin Sachdeva
University of New Mexico

A generic Algorithm to find all common intervals of two permutations
Guiliang Feng and Yujiang Shan
Southern Arkansas University

A Custom Compute Engine to Accelerate Dynamic Programming in Bioinformatics Applications

Paul Hartke and Bill Dally
Stanford University

Microarray Analysis
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M@CBETH: optimizing clinical microarray classification
Nathalie Pochet, Frizo Janssens, Frank De Smet, Kathleen Marchal, Johan Suykens and Bart De Moor
ESAT-SCD (BioI), Katholieke Universiteit Leuven (K.U.Leuven)

Similarity and cluster analysis algorithms for Microarrays using R* trees
Jiaxiong Pi, Yong Shi and Zhengxin Chen
University of Nebraska at Omaha

Maximum significance clustering of oligonucleotide microarrays
Dick de Ridder [1,2], Marcel J.T. Reinders [1], Frank J.T.Staal [2] and Jacques J.M. van Dongen [2]
[1] Information & Communication Theory Group, Faculty of Electrical Engineering, Mathematics & Computer Science, Delft University of Technology, The Netherlands; [2] Department of Immunology, Erasmus MC, University Medical Center, The Netherlands

Gene Ontology-based analysis of gene expression changes in early development in Ceratopteris
Ann E. Loraine, Mari L. Salmi, Stephen C. Stout, Stanley J. Roux
Department of Biostatistics, University of Alabama at Birmingham

Fractal Clustering for Gene Expression Profiling
Lu-yong Wang, Ammaiappan Balasubramanian, Amit Chakraborty, Dorin Comaniciu
Siemens Corporate Research

Multivariate gene selection...does it help?
Carmen Lai, Marcel Reinders, Lodewyk Wessels
Information and Communication Theory Group, Delft University of Technology

Considerations in Making Microarray Cross-Platform Correlations
Manohar Kollegal (1), Sudeshna Adak(1), Richard Shippy(2), Timothy Sendera(2)
(1) GE Global Research, Bangalore, India; (2)GE Healthcare, Chandler, Arizona, US

Two-way clustering of gene expression profiles by sparse matrix factorization
A. Pascual-Montano, P. Carmona-Sez, R.D. Pascual-Marqui, F. Tirado, J.M. Carazo
Universidad Complutense de Madrid, Spain

Novel Hybrid Hierarchical-K-means Clustering Method for Microarray Analysis
Bernard Chen(1) , Phang C. Tai(2) , R. Harrison(1,2) and Yi Pan(1)
(1) Department of Computer Science, Georgia State University; (2) Department of Biology, Georgia State University

A general methodology for integration of microarray data
Curtis Huttenhower, Olga Troyanskaya
Princeton University

K-means+ Method for Improving Gene Selection for Classification of Microarray Data
Heng Huang, Li Shen, Fei Xiong, Fillia Makedon, Justin Pearlman
Dartmouth College, Computer Science Department

Sequential Diagonal Linear Discriminant Analysis (SeqDLDA) for Microarray Classification and Gene Identification
Roger Pique-Regi (1), Antonio Ortega (1), and Shahab Asgharzadeh (2)
(1) University of Southern California; 2) Children's Hospital of Los Angeles

Selective Feature Filtering of Gene Expression using Gene Ontology for Unsupervised Molecular Classification of Cancer

Sumeet Dua and Vijay R. Kukkala
Data Mining Research Laboratory, Louisiana Tech University

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A Data Storage, Processing, and Retrieval System for Microtubule Tracking Data
Robert Coulier
Cal State San Bernardino

BIOMAP: discovering schema mapping using ontologies
Sumedha Gholba, Hervé Métnager, Zoé Lacroix
Arizona State University, U.S.A

Heuristic Selection of Minimal Marker Sets to Discriminate Among Seedlines
Thomas C. Hudson, Ann E. Stapleton, Amy M. Curley, Tristan M. Carland
University of North Carolina at Wilmington

A Fast Shotgun Assembly Heuristic
Chris Wilks and Sami Khuri
San Jose State University

A Simulated Pharmacogenomics Exercise for the Cybertory Virtual Molecular Biology Laboratory
Camille B. Troup, Ph.D., Carl E. McMillan, Robert M. Horton, Ph.D.
Attotron Biotechnologies Corporation

Aligning Peaks Across Multiple Mass Spectrometry Data Sets Using A Scale-Space Based Approach
Weichuan Yu, Xiaoye Li, and Hongyu Zhao
ale University

Lossless Compression of DNA Microarray Images
Yong Zhang, Rahul Parthe, Don Adjeroh
West Virginia University

Predicting Continuous Epitopes in Proteins
Reeti Tandon(1), Sudeshna Adak(1), Brion Sarachan(2), Vaibhav A. Narayan(3), William FitzHugh(3), Jeremy Heil(3)
(1) Computational Biology & Biostatistics Lab, GE Global Research, Bangalore, India; 2) Computational Biology & Biostatistics Lab, GE Global Research, New York, USA; 3) Celera Genomics, Rockville, MD USA

Which normalization method is best? A platform-independent biologically inspired quantitative comparison of normalization methods
E.P. van Someren and M.J.T. Reinders
Delft University of Technology

BioNavigation: Using Ontologies to express meaningful navigational queries over biological resources
Marelis Cardenas, Zoe Lacroix, Natalia Marquez, Kaushal Parekh, Louiqa Raschid, Maria-Esther Vidal
Arizona State University

RNAMute: RNA Secondary Structure Mutation Analysis Tool
Alexander Churkin, Ornit Elgad, Oshrat Petgho, and Danny Barash
Department of Computer Science, Ben-Gurion University

A Transcriptome Atlas of the Mouse Brain at Cellular Resolution
James Carson, Tao Ju, Hui-Chen Lu, Christina Thaller, Musodiq Bello, Ioannis Kakadiaris, Joe Warren, Gregor Eichele, Wah Chiu
Baylor College of Medicine

Adapting Support Vector Machines to Predict Translation Initiation Sites in the Human Genome
Stephen Kwek and Rehan Akbani
University of Texas at San Antonio

Pathways Networks Systems Biology
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Semantic Similarity-based Validation of Protein-Protein Interactions
Xiang Guo, *Craig D. Shriver, Hai Hu, and Michael N. Liebman
Windber Research Institute and *Walter Reed Army Medical Center, Washington, DC

A Protein Interaction Verification System Based on a Neural Network Algorithm
Min Su Lee, Seung Soo Park, Min Kyung Kim
Ewha Womans University

Pathway Logic: Helping Biologists Understand and Organize Pathway Information
M. Knapp, L. Briesemeister, S. Eker, P. Lincoln, A. Poggio, C. Talcott, and K. Laderoute
SRI International

MassTRAQ: a Fully Automated Tool for iTRAQ-labeled Protein Quantification
Keun-Pin Wu, Wen-Ting Lin, Wei-Neng Hung, Yi-Hwa Yian,Yet-Ran Chen, Yu-Ju Chen, Ting-Yi Sung and Wen-Lian Hsu
Institute of Information Science, Academia Sinica

Biological Pathway Prediction from Multiple Data Sources Using Iterative Bayesian Updating
Corey Powell, Joshua Stuart
University of California, Santa Cruz

Functional modularity in a large-scale mammalian molecular interaction network
Andreas Kramer, Daniel R. Richards, James O. Bowlby, and Ramon M. Felciano
Ingenuity Systems

Oscillatory dynamics in the mitogen-activated protein kinase cascade
K.-H. Chiam, Vipul Bhargava, and Gunaretnam Rajagopal
Bioinformatics Institute, University of Louisiana

Predicting gene function by combining expression and interaction data
R.J.P. van Berlo, L.F.A. Wessels, S.D.C. Martes and M.J.T. Reinders
Delft University of Technology

A symbolic approach to the simulation of biochemical models: application to circadian rhythms
Federico Fontana, Luca Bianco, Vincenzo Manca
University of Verona - Dept. Computer Science

Global Dynamics of Nucleosome Arrays, Influence of Variant Histone H2A.Z

Li Wang, Amutha Ramaswamy & Ilya Ioshikhes
Ohio State University

iSimBioSys: An'In Silico' Discrete Event Simulation Framework for Modeling Biological Systems
Samik Ghosh, Preetam Ghosh, Kalyan Basu, Sajal K. Das
Department of Computer Science, University of Texas at Arlington

A parallel algorithm for clustering protein-protein interaction networks
Qiaofeng Yang, Stefano Lonardi
University of California, Riverside

Unravelling the murine osteoblast differentiation pathway by network structure analysis using time-series microarray data
E.P. van Someren, B.L.T. Vaes, K.J. Dechering, A.M. Sijbers and M.J.T. Reinders
Delft University of Technology

Discovering combinatorial transcription factor binding from a joint cis-regulatory and gene expression network
Matt Weirauch and Josh Stuart

Identifying Local Gene Expression Patterns in Biomolecular Networks
A. Y. Sivachenko, A. Yuryev, N. Daraselia, I. Mazo
Ariadne Genomics, Inc

Pattern Recognition
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Automated Characterization of cellular migration phenomena
Christian Beaudry (1), Michael E. Berens (1), Tarek El Doker (2), Anna M. Joy (1), Lina J Karam (2), Zo?t Lacroix (3), Jad A. Lutfi (2), Sai Motoru (4), Rosemary A Renaut (4), Ian Rich (2)
(1) TGen, The Translational Genomics Research Institute, Arizona State University; (2) Department of Electrical Engineering, Northern Arizona University; (3) Department of Mechanical and Aerospace Engineering, Arizona State University; (4) Department of Mathematics, Arizona State University

Artificial Neural Networks to Predict Daylily Hybrids
Ramana M. Gosukonda, Masoud Naghedolfeizi, Johnny Carter
Fort Valley State University

Combinatiorial method of splice sites prediction
Alexander Churbanov, Hesham Ali
University of Nebraska at Omaha

Computational identification and characterization of Type III secretion substrates
Eric Sakk, David Schneider, Monica Vencato, Alan Collmer, and Samuel Cartinhour
Morgan State University

Integration of RNA Search methods for Identifying Novel Riboswitch Patterns in Eukaryotes
Adaya N. Cohen, Klara Kedem, Michal Shapira, and Danny Barash
Department of Computer Science, Ben-Gurion University

Joint Genomic and Metabolomic Analysis of Toxic Dose-Response Experiments
Gary L. Jahns (1), Nicholas DelRaso (2), Mark P. Westric (2), Victor Chan (3), Nicholas V. Reo (4) and Timothy R. Zacharewski (5)
(1) BAE Systems Advanced Information Technologies, San Diego; 2) Air Force Research Laboratory, Wright-Patterson Air Force Base, OH; 3) Alion Science and Technology, Wright-Patterson Air Force Base, OH ; 4) Dept. of Biochemistry and Molecular Biology, Wright State University; 5) Dept. of Biochemistry and Molecular Biology, Michigan State University

Promoter Analysis
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Comparing linear classifiers for predicting a Transcription Start Site, A case Study on Different Genome
Raja Loganantharaj
University of Louisiana at Lafayette

On Discriminating TATA-box from putative TATA box, A Case Study Using Plant Genome
Raja Loganantharaj
University of Louisiana at Lafayette
cis-Regulatory Element Prediction in Mammalian Genomes
Asim Siddiqui, Gordon Robertson, Misha Bilenky, Tamara Astakhova, Chris Fjell, Obi L. Griffith, Maik Hassel, Ann He, Bernard Li, Keven Lin, Stephen Montgomery, Mehrdad Oveisi, Erin D. Pleasance, Neil Robertson, Monica C. Sleumer, Richard Varhol, Maggie Zhang and Steven Jones
Canada's Michael Smith Genome Sciences Centre

Protein Structure Analysis
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TPR Packing Analysis and 3D Modeling for the HAT Domain of Human Crooked Neck Protein
Zhenglin Hou, Cunxi Wang, Odd-Arne Olsen
Pioneer Hi-bred, a Dupont company

Extending the incorporation of superfamily structural information in the process of flexible fitting in 3D-EM
Velåzquez-Muriel, J.A., Carazo, J.M.
Centro Nacional de Biotecnologia

Protein Structure Prediction Using Physical-Based Global Optimization and Knowledge-Guided Fragment Packing
Jinhui Ding, Elizabeth Eskow, Nelson Max, Silvia Crivelli
QB3 Institute, UC Berkeley

Protein Secondary Structure Prediction Using Support Vector Machine With a PSSM profile and an Advanced Tertiary Classifier
Hae-Jin Hu, Phang C. Tai, Jieyue He, Robert Harrison and Yi Pan
Georigia State University

Mining Protein Sequence Motifs Representing Common 3D Structures
Wei Zhong, Gulsah Altun, Robert Harrison, Phang C. Tai, and Yi Pan
Georgia State University

Structural genomics analysis of alternative splicing and its application in modeling structures of alternatively spliced variants
Peng Wang, Bo Yan, Juntao Guo, Chindo Hicks, Ying Xu
Institute of Bioinformatics, University of Georgia

GANA -- A Genetic Algorithm for NMR Backbone Resonance Assignment
Hsin-Nan Lin, Kuen-Pin Wu, Jia-Ming Chang, Ting-Yi Sung,Wen-Lian Hsu
Institute of Information Science, Academia Sinica

Creating a Protein Ontology Resource
Amandeep S. Sidhu, Tharam Dillon, Elizabeth Chang
University of Technology, Australia

Efficient Sampling of Protein Folding Pathways using HMMSTR and Probabilistic Roadmaps
Yogesh Girdhar, Edward Carlson, Srinivas Akella, Christopher Bystroff
Rensselaer Polytechnic Institute

Rule clustering and super-rule generation for transmembrane segment prediction
Jieyue He(1,2), Bernard Chen(2), Hae-Jin Hu(2), Robert Harrison(2,3,4), Phang C. Tai,(3), and Yi Pan(2)
(1) Department of Computer Science, Southeast University, China; (2) Department of Computer Science, Ben-Gurion University; (3) Department of Biology, Georgia State University, USA

Analysis of four different sets of predictive features for Metalloproteins
H. Seker and P.I. Haris
School of Computing - De Montfort University

Accurate and Fast Protein Structural Classification using Spatial Aggregation of Orthonormal Coefficients of Structural Geometric Descriptors

Sumeet Dua and Ravikanth Meka
Data Mining Research Laboratory, Louisiana Tech University

RNAi Analysis
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Maximum Sequence Alignment Fails To Predict Off-targeted Gene Regulation by RNAi
Amanda Birmingham, Emily M. Anderson, William S. Marshall, and Anastasia Khvorova
Dharmacon, Inc.

Temperature and Mutation Switches in the Secondary Structure of Small RNAs
Assaf Avihoo and Danny Barash
Department of Computer Science, Ben-Gurion University

Sequence Alignment
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Approximate String Matching Algorithms Using Parallel Methods for Molecular Sequence Comparisons
Carla Corroa Tavares dos Reis and Dr. Rubem Mondaini
Oswaldo Cruz Foundation

Massive multiple sequence alignment of 16S bacterial ribosomal RNAs using Clustal W-Message Passing Interface (MPI) based on Beowulf Linux system
Hyon Chang Kim(1), Yong Beom Seo(2), Ji Hwan Song(2), Dong Soon Choi(3), Churl K. Min(3), Han Jip Kim(1)
(1) Department of Biological Science, (2) Division of Information & Computer Engineering, (3) Department of Molecular Science & Technology, Ajou University

Improved pairwise alignment of proteins in the Twilight Zone using local structure predictions
Yao-ming Huang and Christopher Bystroff
Rensselaer Polytechnic Institute

SNPs and Haplotyping
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Classification method for prediction of multifactorial disease development using interaction between genetic and environmental factors
Yasuyuki Tomita, Mitsuhiro Yokota, Hiroyuki Honda
Nagoya University

Association Mapping of Quantitative Traits Using Haplotypes

Jing Li and Tony Parrado
Case Western Reserve University
107A (Word)
Mapping SNP association results into type 2 DM Pathways -Metabolic Syndrome as a robust system-
Takashi Kido
Hubit Genomix

ssahaSNP - A Mutation Detection Tool on Whole Genome Scale
Zemin Ning*, Mario Caccamo* and James C. Mullikin+
*The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge UK; +Genome Technology Branch/NHGRI, NIH

Synthetic Biological Systems
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Noise Propagation in Transcriptional Cascades
Sara Hooshangi, Stephan Thiberge and Ron Weiss
Princeton University

What Causes Organisms to Fall into Maladaptive Behavior Patterns?

Beth E. Simmons
University of Texas
Non-occurring and rare quads in PDB and translated introns with possible applications in nanostructure design
G. Sampath (Independent) and James TenEyck (Marist College)

The Synthetic Gene Designer: a flexible web platform to explore sequence space of synthetic genes for heterologous expression
Gang Wu, Nabila Bashir-Bello, Stephen Freeland
University of Maryland at Baltimore County

ECOME: A simple model for an evolving consumption web
Christopher Bystroff and Carl N. McDaniel
Rensselaer Polytechnic institute

Engineering a 1:2 bio-multiplexer for controlled stem cell differentiation
Sairam Subramanian, Ihor Lemischka, Ron Weiss
Princeton University

Engineering Multi-signal Systems for Complex Pattern Formation
David Karig and Ron Weiss
Dept. of Electrical Engineering, Princeton University

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Chemical Structure-Activity-Relationship Visualization Using Structure-Activity Maps
Weiguo Fan, Xin Lin, Yu-Wei Hsieh, Boren, Lin, Johnnie W. Baker and Chun-che Tsai
Kent State University

SinicView: An Interactive Visualization Tool for Comparison of Multiple Sequence Alignment Results
Arthur Chun-Chieh Shih, D. T. Lee, Laurent Lin, Chin-Lin Peng, Chun-Yi Wong, Tze-Chang Shiao, Hung-Yi Chen, and Shiang-Heng Chen
Institute of Information Science, Academia Sinica

DockingShop: a Tool for Interactive Protein Docking
Ting-Cheng Lu, Jinhui Ding, Silvia N.Crivelli1

ProteinShop and POSE: Bringing Robotics and Intelligent Systems into the Field of Molecular Modeling
Ting-Cheng Lu and Silvia N. Crivelli

Visualization of Logic Analysis of Phylogenetic Profiles (LAPP)
Kay A. Robbins and Li Zhao
University of Texas at San Antonio and Cajal Neuroscience Research Center

The Significance of Linearity of Quantities in Electrophoresed and Blotted Materials Demonstrated by BandScan(C) - an Analytical Program
Richard S. Gunasekera, Ph.D., Hari Damodaran, B.S., Yasantha Rajakarunanayake, Ph.D., and Keith Hyland, Ph.D.
University of Houston - Victoria

Papers presented as posters
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Accurate Prediction of Orthologous Gene Groups in Microbes
Hongwei Wu (1,2) , Fenglou Mao (1) , Victor Olman (1) and Ying Xu (1,2)
1) Department of Biochemistry and Molecular Biology and Institute of Bioinformatics University of Georgia, 2) Computational Biology Institute, Oak Ridge National Laboratory, Oak Ridge, TN 37831

Discriminative Discovery of Transcription Factor Binding Sites from Location Data
Yuji Kawada and Yasubumi Sakakibara
Department of Biosciences and Informatics, Keio University

TreeRefiner: A Tool for Refining a Multiple Alignment on a Phylogenetic Tree
Aswath Manohar and Serafim Batzoglou
Department of Computer Science, Stanford University

A learned comparative expression measure for Affymetrix GeneChip DNA microarrays
Will Sheffler (Dept. of Genome Sciences, University of Washington), Eli Upfal (Dept. of Computer Science, Brown University), John Sedivy (Dept. of Molecular and Cell, Biology and Biochemistry, Brown University), William Stafford Noble (Dept. of Genome Sciences Dept. of Computer Science and Engineering, University of Washington)

Discover True Association Rates In Multi-protein Complex Proteomics Data Sets
Changyu Shen (1), Lang Li (1), Jake Yue Chen (2)
(1) Division of Biostatistics, Department of Medicine, Indiana University, (2) School of Informatics, Indiana University and Department of Computer and Information Science, Purdue University School of Science

An Algebraic Geometry Approach to Protein Structure Determination from NMR Data
Lincoln Wang (1), Ramgopal R. Mettu (2), Bruce Randall Donald (3)
(1) Dartmouth Computer Science Department, (2) Dartmouth Chemistry Department, (3) Dartmouth Department of Biological Sciences

A Tree-Decomposition Approach to Protein Structure Prediction
Jinbo Xu (1), Feng Jiao (2), Bonnie Berger (3)
(1) Department of Mathematics and CSAIL MIT, (2) School of Computer Science, (3) Department of Mathematics and CSAIL, MIT

Estimating Time-Dependent Gene Networks from Time Series Microarray Data by Dynamic Linear Models with Markov Switching
Ryo Yoshida (1), Seiya Imoto (2), Tomoyuki Higuchi (1)
(1) Institute of Statistical Mathematics, Tokyo, (2) Human Genome Center, Institute of Medical Science, University of Tokyo