The Community for Technology Leaders
2005 IEEE Computational Systems Bioinformatics Conference - Workshops (2005)
Stanford, California
Aug. 8, 2005 to Aug. 11, 2005
ISBN: 0-7695-2442-7
TABLE OF CONTENTS
Workshop: BioImage data Mining and Informatics
Cover
Biomedical Research

Sequential Classification for Microarray and Clinical Data (Abstract)

Guenter Tusch , Grand Valley State University
pp. 5-6

Diagnosis and Biomarker Identi.cation on SELDI proteomics data by ADTBoost (Abstract)

Lu-yong Wang , Siemens Corporate Research
Amit Chakraborty , Siemens Corporate Research
Dorin Comaniciu , Siemens Corporate Research
pp. 9-10

Inverse Design of Large Molecules using Linear Diophantine Equations (Abstract)

W. Michael Brown , Sandia National Laboratories
Shawn Martin , Sandia National Laboratories
Jean-Loup Faulon , Sandia National Laboratories
Donald Visco , Tennessee Technological University
Derick Weis , Tennessee Technological University
pp. 11-16
Cellular Multicelluar Systems

Reducing Gene Regulatory Networks by Decomposition (Abstract)

Kazuyuki Aihara , The University of Tokyo
Ruiqi Wang , The University of Tokyo
Luonan Chen , Osaka Sangyo University
pp. 17-18

A Diffusion Model to Estimate the Inter-arrival Time of Charged Molecules in Stochastic Event based Modeling of Complex Biological Networks (Abstract)

Preetam Ghosh , The University of Texas at Arlington
Samik Ghosh , The University of Texas at Arlington
Kalyan Basu , The University of Texas at Arlington
Sajal Das , The University of Texas at Arlington
pp. 19-22
Comporative Genomics

Operon Prediction in Cyanobacteria using Comparative Genomics (Abstract)

Natalia Khuri , Carnegie Institution, DPB
Nikhila S Rao , San Jose State University
pp. 23-24

Patterns of Gene Deletion following Genome Duplication in Yeast (Abstract)

Jake K. Byrnes , University of Chicago
Wen-Hsiung Li , University of Chicago
pp. 25-26

PLATCOM: a Platform for Computational Comparative Genomics on the Web (Abstract)

Zhiping Wang , Indiana University
Amit Saple , Indiana University
Jason Lee , Indiana University
Jeong-Hyeon Choi , Indiana University
Sun Kim , Indiana University
Kwangmin Choi , Indiana University
pp. 27-30
Data Mining

Classification Methods for HIV-1 Medicated Neuronal Damage (Abstract)

Yong Shi , Graduate University of the Chinese Academy of Sciences
Mengjun Wang , Heart and Vascular Institute, Henry Ford Health System
Zhengxin Chen , University of Nebraska at Omaha
Jialin Zheng , University of Nebraska Medical Center
pp. 31-32

Key Features of the UCSC Genome Site (Abstract)

Heather Trumbower , UCSC Genome Bioinformatics Group
Jennifer Jackson , UCSC Genome Bioinformatics Group
pp. 33-34

PROMOCO: a New Program for Prediction of cis Regulatory Elements: From High-Information Content Analysis to Clique Identification (Abstract)

Ying Xu , University of Georgia
Jizhu Lu , University of Georgia
Victor Olman , University of Georgia
Guojun Li , University of Georgia
pp. 35-36

Data Integration in the Mouse Genome Informatics (MGI) Database (Abstract)

Jim A. Kadin , The Jackson Laboratory
Joel E. Richardson , The Jackson Laboratory
Jannan E. Eppig , The Jackson Laboratory
Donnie Qi , The Jackson Laboratory
Carol J. Bult , The Jackson Laboratory
Martin Ringwald , The Jackson Laboratory
Judith A. Blake , The Jackson Laboratory
pp. 37-38

HIV Structural and Biothermodynamics Databases: a Resource for the Pharmaceutical and Biotechnology Industry (Abstract)

Robert N. Goldberg , Biotechnology Division, NIST, 100 Bureau Drive
Talapady N. Bhat , Biotechnology Division, NIST, 100 Bureau Drive
Henry Rodriguez , Biotechnology Division, NIST, 100 Bureau Drive
Yadu B. Tewari , Biotechnology Division, NIST, 100 Bureau Drive
pp. 39-40

A New Clustering Strategy with Stochastic Merging and Removing Based on Kernel Functions (Abstract)

Hesham Ali , University of Nebraska at Omaha
Huimin Geng , University of Nebraska Medical Center
pp. 41-42

Head and Neck Cancer Metastasis Prediction via Artificial Neural Networks (Abstract)

Eveleen Darby , University of Houston
Shilpa Kodali , University of Houston
Liwen Shih , University of Houston
Tezeswari Nettimi , University of Houston
pp. 43-44

Cluster Utility: A New Metric for Clustering Biological Sequences (Abstract)

Sun Kim , Center for Genomics and Bioinformatics,Indiana University
Jason Lee , School of Informatics,Indiana University
pp. 45-46

Problem Solving Environment Approach to Integrating Diverse Biological Data Sources (Abstract)

Eric G. Stephan , Pacific Northwest National Laboratory
Mudita Singhal , Pacific Northwest National Laboratory
Kyle R. Klicker , Pacific Northwest National Laboratory
Heidi J. Sofia , Pacific Northwest National Laboratory
pp. 47-50
Evolution and Phylogenetics

Predicting functional gene-links from phylogenetic-statistical analyses of whole genomes (Abstract)

Daniel Barker , University of Reading, Whiteknights
Mark Pagel , University of Reading, Whiteknights
pp. 51-52

Whole Genome Phylogeny Based on Clustered Signature String Composition (Abstract)

Dong Xu , University of Missouri
Xiu-Feng Wan , University of Missouri
Guohui Lin , University of Alberta
Xiaomeng Wu , University of Alberta
pp. 53-54

A Polynomial Algorithm for the Minimum Quartet Inconsistency Problem with O(n) Quartet Errors (Abstract)

Gang Wu , University of Alberta
Guohui Lin , University of Alberta
Jia-Huai You , University of Alberta
pp. 55-56

Phylogenetic Postprocessing (Abstract)

Nicholas D. Pattengale , University of New Mexico
Bernard M.E. Moret , University of New Mexico
pp. 57-58

A Novel Quartet-Based Method for Phylogenetic Inference (Abstract)

R. P. Brent , Australian National University, Canberra, ACT 0200, Australia
B. B. Zhou , University of Sydney, NSW 2006, Australia
C. Wang , University of Sydney, NSW 2006, Australia
M. Tarawneh , University of Sydney, NSW 2006, Australia
pp. 59-60

Consensus Methods Using Phylogenetic Databases (Abstract)

Mahesh M. Kulkarni , University of New Mexico
Bernard M.E. Moret , University of New Mexico
pp. 61-62

Bacterial Whole Genome Phylogeny Using Proteome Comparison and Optimal Reversal Distance (Abstract)

Noppadon Khiripet , National Electronics and Computer Technology Center, Thailand
pp. 63-64

Identifying Orthologs: Cycle Splitting on the Breakpoint Graph (Abstract)

Krister M. Swenson , University of New Mexico
Nicholas D. Pattengale , University of New Mexico
Bernard M.E. Moret , University of New Mexico
pp. 65-68
Functional Genomics

Improving Operon Prediction in E. coli (Abstract)

Victor Olman , Computational Biology, Institute, Oak Ridge National Laboratory
Ying Xu , Computational Biology, Institute, Oak Ridge National Laboratory
Phuongan. Dam , University of Georgia at Athens
pp. 69-70

Relating transcription factors, modules of genes and cultivation conditions in Saccharomyces cerevisiae (Abstract)

T.A. Knijnenburg , Delft University of Technology
J.M. Daran , Kluyver Centre for Genomics of Industrial Fermentation Delft The Netherlands
P. Daran-Lapujade , Kluyver Centre for Genomics of Industrial Fermentation Delft The Netherlands
L.F.A. Wessels , Department of Pathology The Netherlands Cancer Institute, The Netherlands
M.J.T. Reinders , Delft University of Technology
pp. 71-72

Automatic Protein Function Annotation through Candidate Ortholog Clusters from Incomplete Genomes (Abstract)

Rutgers University , DIMACS, Rutgers University
Casimir Kulikowski , Rutgers University, Piscataway
Akshay Vashist , Rutgers University, Piscataway
pp. 73-74

EST-Based Analysis of Gene Expression in the Human Cochea (Abstract)

Anne B.S. Giersch , Harvard University
Richard J. Carter , Hewlett-Packard Labs
Irene S. Gabashvili , Hewlett-Packard Labs
Peter Markstein , Hewlett-Packard Labs
pp. 75-76

EigenPhenotypes: Towards an Algorithmic Framework for Phenotype Discovery (Abstract)

Rahul Rahul Singh , Department of Computer Science,San Francisco State University
Ilmi Yoon , Department of Computer Science,San Francisco State University
Alexander Vaughan , Department of Biology,San Francisco State University
Megumi Fuse , Department of Biology,San Francisco State University
pp. 77-78

A Novel Approach for Prediction of Multi-Labeled Protein Subcellular Localization for Prokaryotic Bacteria (Abstract)

Fu Chang , Institute of Information Science, Academia Sinica, Taiwan
Wen-Lian Hsu , Institute of Information Science, Academia Sinica, Taiwan
Chin-Chin Lin , Institute of Information Science, Academia Sinica, Taiwan
Chia-Yu Su , Institute of Information Science, Academia Sinica, Taiwan
Allan Lo , Institute of Information Science, Academia Sinica, Taiwan
pp. 79-82
High Performance Computing

A generic algorithm to find all common intervals of two permutations (Abstract)

Guiliang Feng , University of Louisiana at Lafayette
Yujiang Shan , Southern Arkansas University
pp. 85-88
Microarray Analysis

M@CBETH: Optimizing Clinical Microarray Classi.cation (Abstract)

Ignace B. Vergote , Division of Gynecologic Oncology,University Hospitals Leuven, Belgium
Frizo A.L. Janssens , Department of Electrical Engineering ESAT-SCD,Belgium
Frank De Smet , Department of Electrical Engineering ESAT-SCD,Belgium
Bart L.R. De Moor , Department of Electrical Engineering ESAT-SCD, Belgium
Kathleen Marchal , Department of Electrical Engineering ESAT-SCD,Belgium
Nathalie L.M.M. Pochet , Department of Electrical Engineering ESAT-SCD,Belgium
Johan A.K. Suykens , Department of Electrical Engineering ESAT-SCD, Belgium
pp. 89-90

Similarity and cluster analysis algorithms for Microarrays using R trees (Abstract)

Jiaxiong Pi , University of Nebraska at Omaha, Omaha
Zhengxin Chen , University of Nebraska at Omaha
Yong Shi , Graduate University of the Chinese Academy of Sciences
pp. 91-92

Maximum signi.cance clustering of oligonucleotide microarrays (Abstract)

Marcel J.T. Reinders , Delft University of Technology
Dick de Ridder , Delft University of Technology
Jacques J.M. van Dongen , Department of Immunology, Erasmus MC, University Medical Center, Netherlands
Frank J.T. Staal , Department of Immunology, Erasmus MC, University Medical Center, Netherlands
pp. 93-94

Gene-Ontology-based analysis of gene expression changes in early development of Ceratopteris spores (Abstract)

Mari L. Salmi , University of Texas at Austin
Stanley J. Roux , University of Texas at Austin
Ann E. Loraine , University of Alabama at Birmingham
Stephen C. Stout , University of Texas at Austin
pp. 95-96

Fractal Clustering for Microarray Data Analysis (Abstract)

Dorin Comaniciu , Siemens Corporate Research
Ammaiappan Balasubramanian , Siemens Corporate Research
Lu-yong Wang , Siemens Corporate Research
Amit Chakraborty , Siemens Corporate Research
pp. 97-98

Multivariate gene selection: Does it help (Abstract)

Carmen Lai , Delft University of Technology
Marcel Reinders , The Netherlands Cancer Institute, Amsterdam
pp. 99-100

Considerations in Making Microarray Cross-Platform Correlations (Abstract)

Sudeshna Adak , GE Global Research, Bangalore, India
Manohar Kollegal , GE Global Research, Bangalore, India
Timothy Sendera , GE Healthcare Bio-Sciences, Chandler, Arizona, US
Richard Shippy , GE Healthcare Bio-Sciences, Chandler, Arizona, US
pp. 101-102

Two-way clustering of gene expression profiles by sparse matrix factorization (Abstract)

J.M. Carazo , National Center of Biotechnology. CNB-CSIC. Universidad Aut?noma de Madrid
P. Carmona-S?ez , National Center of Biotechnology. CNB-CSIC. Universidad Aut?noma de Madrid
A. Pascual-Montano , Computer Architecture Department. Universidad Complutense de Madrid
R.D. Pascual-Marqui , The KEY Institute for Brain-Mind Research. Lenggstr, Switzerland
F. Tirado , Computer Architecture Department. Universidad Complutense de Madrid.
pp. 103-104

Novel Hybrid Hierarchical-K-means Clustering Method (H-K-means) for Microarray Analysis (Abstract)

R. Harrison , Department of Computer Science, Georgia State University, Atlanta
Yi Pan , Department of Computer Science, Georgia State University, Atlanta
Phang C. Tai , Department of Biology, Georgia State University, Atlanta
Bernard Chen , Department of Computer Science, Georgia State University, Atlanta
pp. 105-108

A General Methodology for Integration of Microarray Data (Abstract)

Olga Troyanskaya , Princeton University
Curtis Huttenhower , Princeton University
pp. 109

K-means+ Method for Improving Gene Selection for Classification of Microarray Data (Abstract)

Fei Xiong , Computer Science Department Dartmouth College
Bruce Hettleman , Department of Cardiology Dartmouth Medical School
Li Shen , Computer and Information Science Department University of Massachusetts Dartmouth
Fillia Makedon , Computer Science Department Dartmouth College
Rong Zhang , Computer Science Department Dartmouth College
Justin Pearlman , Department of Cardiology Dartmouth Medical School
Heng Huang , Computer Science Department Dartmouth College
pp. 110-111

Sequential Diagonal Linear Discriminant Analysis (SeqDLDA) for Microarray Classification and Gene Identification (Abstract)

Antonio Ortega , University of Southern California
Shahab Asgharzadeh , Children's Hospital of Los Angeles
Roger Pique-Regi , University of Southern California
pp. 112-116
Other

A Storage, Processing, and Retrieval System for Microtubule Tracking Data (Abstract)

Robert John Coulier , Undergraduate, California State University at San Bernardino
pp. 117

BioMap: Discovering Schema Mapping Using Ontologies (Abstract)

Herve Menager , Arizona State University
Zoe Lacroix , Arizona State University
Sumedha Gholba , Arizona State University
pp. 118-119

Minimal Marker Sets to Discriminate Among Seedlines (Abstract)

Thomas C. Hudson , University of North Carolina at Wilmington
Amy M. Curley , University of North Carolina at Wilmington
Ann E. Stapleton , University of North Carolina at Wilmington
pp. 120-121

A Fast Shotgun Assembly Heuristic (Abstract)

Christopher Wilks , San Jose State University
Sami Khuri , San Jose State University
pp. 122-123

Simulated Pharmacogenomics Exercises for the Cybertory Virtual Molecular Biology Laboratory (Abstract)

Robert M. Horton , Attotron Biotechnologies Corporation
Bill Martin , Attotron Biotechnologies Corporation
Camille Bodley Troup , Attotron Biotechnologies Corporation
Carl E. McMillan , Attotron Biotechnologies Corporation
pp. 124-125

Lossless Compression of DNA Microarray Images (Abstract)

Rahul Parthe , West Virginia University, Morgantown
Don Adjeroh , West Virginia University, Morgantown
Yong Zhang , West Virginia University, Morgantown
pp. 128-132

Predicting Continuous Epitopes in Proteins (Abstract)

Jeremy Heil , Celera Genomics
Sudeshna Adak , GE Global Research, Bangalore, India
Vaibhav A. Narayan , Celera Genomics
Brion Sarachan , GE Global Research, Niskayuna,NY
William FitzHugh , Celera Genomics
Reeti Tandon , GE Global Research, Bangalore, India
pp. 133-134

BioNavigation: Using Ontologies to Express Meaningful Navigational Queries Over Biological Resources (Abstract)

Natalia Marquez , Universidad Simon Bol?var,Venezuela
Kaushal Parekh , Arizona State University, Tempe
Louiqa Raschid , University of Maryland
Marelis Cardenas , Universidad Simon Bol?var,Venezuela
Maria-Esther Vidal , Universidad Simon Bol?var,Venezuela
Zoe Lacroix , Arizona State University
pp. 137-138

RNAMute: RNA Secondary Structure Mutation Analysis Tool (Abstract)

Alexander Churkin , Ben-Gurion University
Ornit Elgad , Ben-Gurion University
Danny Barash , Ben-Gurion University
Oshrat Petgho , Ben-Gurion University
pp. 139-141

Data Mining in situ Gene Expression Patterns at Cellular Resolution (Abstract)

Gregor Eichele , Baylor College of Medicine
Tao Ju , Rice University
Christina Thaller , Baylor College of Medicine
Musodiq Bello , The University of Houston
James Carson , Baylor College of Medicine,
Ioannis Kakadiaris , The University of Houston
Joe Warren , Rice University
Wah Chiu , Baylor College of Medicine
pp. 141-142

Adapting Support Vector Machines to Predict Translation Initiation Sites the Human Genome (Abstract)

Stephen Kwek , University of Texas at San Antonio
Rehan Akbani , University of Texas at San Antonio
pp. 143-148
Pathways Networks System Biology

Semantic Similarity-based Validation of Human Protein-Protein Interactions (Abstract)

Michael N. Liebman , Windber Research Institute
Hai Hu , Windber Research Institute
Xiang Guo , Windber Research Institute
Craig D. Shriver , Walter Reed Army Medical Center
pp. 149-150

A Protein Interaction Verification System Based on a Neural Network Algorithm (Abstract)

Seung Soo Park , Ewha Womans University, Korea
Min Kyung Kim , Ewha Womans University, Korea
Min Su Lee , Ewha Womans University, Korea
pp. 151-154

Pathway Logic Helping Biologists Understand and Organize Pathway Information (Abstract)

Patrick Lincoln , SRI International, Menlo Park,CA
Keith Laderoute , SRI International, Menlo Park,CA
Carolyn Talcott , SRI International, Menlo Park,CA
Merrill Knapp , SRI International, Menlo Park,CA
Andy Poggio , SRI International, Menlo Park,CA
Steven Eker , SRI International, Menlo Park,CA
Linda Briesemeister , SRI International, Menlo Park,CA
pp. 155-156

MassTRAQ: a Fully Automated Tool for iTRAQ-labeled Protein Quantification (Abstract)

Wen-Lian Hsu , Institute of Information Science, Academia Sinica
Wei-Neng Hung , Institute of Information Science and Academia Sinica
Wen-Ting Lin , Institute of Information Science and Academia Sinica
Yu-Ju Chen , Institute of Chemistry, Academia Sinica
Yet-Ran Chen , Institute of Chemistry, Academia Sinica
Yi-Hwa Yian , Institute of Information Science and Academia Sinica
Kuen-Pin Wu , Institute of Information Science and Academia Sinica
Ting-Yi Sung , Institute of Information Science and Academia Sinica
pp. 157-158

Biological Pathway Prediction from Multiple Data Sources Using Iterative Bayesian Updating (Abstract)

Corey Powell , University of California, Santa Cruz
Joshua Stuart , University of California, Santa Cruz
pp. 159-160

Functional Modularity in a Large-Scale Mammalian Molecular Interaction Network (Abstract)

Daniel R. Richards , Ingenuity Systems
James O. Bowlby , Ingenuity Systems
Ramon M. Felciano , Ingenuity Systems
Andreas Kramer , Ingenuity Systems
pp. 161-163

Oscillatory dynamics in the mitogen-activated protein kinase cascade (Abstract)

Vipul Bhargava , Bioinformatics Institute, Singapore
K.-H. Chiam , Bioinformatics Institute, Singapore
Gunaretnam Rajagopal , Bioinformatics Institute, Singapore
pp. 164-165

Predicting gene function by combining expression and interaction data (Abstract)

S.D.C. Martes , Delft University of Technology
L.F.A. Wessels , Delft University of Technology
M.J.T. Reinders , Delft University of Technology
R.J.P. van Berlo , Delft University of Technology
pp. 166-167

A symbolic approach to the simulation of biochemical models: application to circadian rhythms (Abstract)

Vincenzo Manca , University of Verona
Federico Fontana , University of Verona
Luca Bianco , University of Verona
pp. 168-169

iSimBioSys :An ?In Silico? Discrete Event Simulation Framework for Modeling Biological Systems (Abstract)

Samik Ghosh , University of Texas at Arlington
Sajal Das , University of Texas at Arlington
Preetam Ghosh , University of Texas at Arlington
Kalyan Basu , University of Texas at Arlington
pp. 170-171

Unravelling the murine osteoblast differentiation pathway by network structure analysis using time-series microarray data (Abstract)

B.L.T. Vaes , Univ. of Nijmegen
W.T. Steegenga , Wageningen University
E.P. van Someren , Delft Univ. of Technology
M.J.T. Reinders , Delft Univ. of Technology
K.J. Dechering , Target Discovery Unit N.V. Organon
A.M. Sijbers , Target Discovery Unit N.V. Organon
pp. 172-173

A Parallel Algorithm for Clustering Protein-Protein Interaction Networks (Abstract)

Stefano Lonardi , University of California, Riverside
Qiaofeng Yang , University of California, Riverside
pp. 174-177

Discovering Functional Transcription Factor Binding from Superimposed Gene Networks (Abstract)

Matt Weirauch , University of California at Santa Cruz
Josh Stuart , University of California at Santa Cruz
pp. 178-179

Identifying Local Gene Expression Patterns in Biomolecular Networks (Abstract)

N. Daraselia , Ariadne Genomics, Inc.
A. Y. Sivachenko , Ariadne Genomics, Inc.
I. Mazo , Ariadne Genomics, Inc.
A. Yuryev , Ariadne Genomics, Inc.
pp. 180-184
Pattern Recognition

Artificial Neural Networks to Predict Daylily Hybrids (Abstract)

Ramana M. Gosukonda , Fort Valley State University,GA
Masoud Naghedolfeizi , Fort Valley State University,GA
Johnny Carter , Fort Valley State University,GA
pp. 187-188

Combinatorial method of splice sites prediction (Abstract)

Hesham Ali , University of Nebraska at Omaha
Alexander Churbanov , University of Nebraska at Omaha
pp. 189-190

Computational identi?cation and characterization of Type III secretion substrates (Abstract)

David J. Schneider , USDA Agricultural Research Service
Samuel W. Cartinhour , USDA Agricultural Research Service
Monica Vencato , Department of Plant Pathology Cornell University
Eric Sakk , Morgan State University
Christopher R. Myers , Cornell Theory Center, Cornell University
Alan Collmer , Department of Plant Pathology Cornell University
pp. 191-192

Integration of RNA Search methods for Identifying Novel Riboswitch Patterns in Eukaryotes (Abstract)

Danny Barash , Department of Life Science, Ben-Gurion University
Klara Kedem , Department of Computer Science, Ben-Gurion University
Michal Shapira , Department of Life Science, Ben-Gurion University
Adaya N. Cohen , Department of Computer Science, Ben-Gurion University
pp. 193-195

Joint Genomic and Metabolomic Analysis of Toxic Dose-Response Experiments (Abstract)

Nicholas DelRaso , Air Force Research Laboratory
Mark P. Westrick , Air Force Research Laboratory
Victor Chan , Air Force Research Laboratory
Gary L. Jahns , BAE Systems Advanced Information Technologies
Timothy R. Zacharewski , Michigan State University, Lansing
Nicholas V. Reo , Wright State University
pp. 195-198
Promoter Analysis

cis-Regulatory Element Prediction in Mammalian Genomes (Abstract)

Erin Pleasance , British Columbia Cancer Agency
Asim Siddiqui , British Columbia Cancer Agency
Kevin Teague , British Columbia Cancer Agency
Maik Hassel , British Columbia Cancer Agency
Neil Robertson , British Columbia Cancer Agency
Stephen Montgomery , British Columbia Cancer Agency
Richard Varhol , British Columbia Cancer Agency
Steven Jones , British Columbia Cancer Agency
Keven Lin , British Columbia Cancer Agency
Monica C. Sleumer , British Columbia Cancer Agency
Maggie Zhang , British Columbia Cancer Agency
Mehrdad Oveisi , British Columbia Cancer Agency
Gordon Robertson , British Columbia Cancer Agency
Misha Bilenky , British Columbia Cancer Agency
Tamara Astakhova , British Columbia Cancer Agency
Obi L. Griffith , British Columbia Cancer Agency
pp. 203-206
Protiend Structure Analysis

TPR Packing Analysis and 3D Modeling for the HAT Domain of Human Crooked Neck Protein (Abstract)

Odd-Arne Olsen , Pioneer Hi-bred International Inc.
Cunxi Wang , Pioneer Hi-bred International Inc.
Zhenglin Hou , Pioneer Hi-bred International Inc.
pp. 207-208

Protein Secondary Structure Prediction Using Support Vector Machine With a PSSM Profile and an Advanced Tertiary Classifier (Abstract)

Hae-Jin Hu , Department of Computer Science,Georgia State University, Atlanta
Robert Harrison , Department of Biology,Georgia State University, Atlanta
Yi Pan , Department of Computer Science, Georgia State University, Atlanta
Phang C. Tai , Department of Biology,Georgia State University, Atlanta
Jieyue He , Southeast University, Nanjing
pp. 213-214

Mining Protein Sequence Motifs Representing Common 3D Structures (Abstract)

Phang C. Tai , Georgia State University, Atlanta
Gulsah Altum , Georgia State University, Atlanta
Wei Zhong , Georgia State University, Atlanta
Yi Pan , Georgia State University, Atlanta
Robert Harrison , Georgia State University, Atlanta
pp. 215-216

Structural genomics analysis of alternative splicing and its application in modeling structures of alternatively spliced variants (PDF)

Bo Yan , Bioinformatics, University of Georgia, Athens, GA
Juntao Guo , Bioinformatics, University of Georgia, Athens, GA
Chindo Hicks , Bioinformatics, University of Georgia, Athens, GA
Ying Xu , Bioinformatics, University of Georgia, Athens, GA
Peng Wang , Bioinformatics, University of Georgia, Athens, GA
pp. 217-

GANAA Genetic Algorithm for NMR Backbone Resonance Assignment (Abstract)

Hsin-Nan Lin , Institute of Information Science, Academia Sinica, Taipei
Ting-Yi Sung , Institute of Information Science, Academia Sinica, Taipei
Kuen-Pin Wu , Institute of Information Science, Academia Sinica, Taipei
Jia-Ming Chang , Institute of Information Science, Academia Sinica, Taipei
Wen-Lian Hsu , Institute of Information Science, Academia Sinica, Taipei
pp. 218-219

Creating a Protein Ontology Resource (Abstract)

Amandeep S. Sidhu , University of Technology Sydney
Tharam S. Dillon , University of Technology Sydney
Elizabeth Chang , School of Information Systems, Curtin University of Technology, Perth, Australia
pp. 220-221

Efficient Sampling of Protein Folding Pathways using HMMSTR and Efficient Sampling of Protein Folding Pathways using HMMSTR and (Abstract)

Yogesh A. Girdhar , Dept. of Computer Science,Rensselaer Polytechnic Institute
Srinivas Akella , Dept. of Computer Science,Rensselaer Polytechnic Institute
Srinivas Akella Srinivas Akella , Biology, Rensselaer Polytechnic Institute, Troy,
pp. 222-223

Rule Clustering and Super-rule Generation for Transmembrane Segments Prediction (Abstract)

Yisheng Dong , Department of Computer Science, Southeast University, Nanjing
Hae-Jin Hu , Department of Computer Science, Georgia State University, Atlanta
Phang C. Tai , Department of Biology, Georgia State University, Atlanta
Yi Pan , Department of Computer Science, Southeast University, Nanjing
Jieyue He , Department of Computer Science, Southeast University, Nanjing
Bernard Chen , Department of Computer Science, Georgia State University, Atlanta
Yisheng Dong , Department of Computer Science, Southeast University, Nanjing
Robert Harrison , GCC Distinguished Cancer Scholar
pp. 224-227

Analysis of four different sets of predictive features for metalloproteins (Abstract)

Parvez I. Haris , Faculty of Health and Life Sciences, De Montfort University
Huseyin Seker , De Montfort University
pp. 228-232
RNAi Analysis

Temperature and Mutation Switches in the Secondary Structure of Small RNAs (Abstract)

Assaf Avihoo , Ben-Gurion University
Danny Barash , Ben-Gurion University
pp. 235-238
Sequence Alignment

Using Parallel Algorithms for Searching Molecular Sequence Databases (Abstract)

Carla Correa Tavares dos Reis , Oswaldo Cruz Foundation
Rubem Mondaini , Federal University of Rio de Janeiro
pp. 239-240

Massive Multiple Sequence Alignment of 16S Bacterial Ribosomal RNAs Using ClustalW-Message Passing Interface (MPI) Based on Beowulf Linux System (Abstract)

Ji Hwan Song , Division of Information and Computer Engineering,,Ajou University, South Korea
Hyon Chang Kim , Department of Biological Sciences,Ajou University, South Korea
Churl K. Min , Department of Molecular Science and Technology,,Ajou University, South Korea
Han Jip Kim , Department of Biological Sciences, Ajou University, South Korea
Dong Soon Choi , Department of Molecular Science and Technology,,Ajou University, South Korea
Yong Beom Seo , Division of Information and Computer Engineering,,Ajou University, South Korea
pp. 241-242

Improved pairwise alignment of proteins in the Twilight Zone using local structure predictions (Abstract)

Christopher Bystroff , RENSSELAER POLYTECHNIC INSTITUTE, TROY, NEW YORK
Yao-ming Huang , RENSSELAER POLYTECHNIC INSTITUTE, TROY, NEW YORK
pp. 243-246
SNPs and Haplotyping

Classification method for prediction of multifactorial disease development using interaction between genetic and environmental factors (Abstract)

Yasuyuki Tomita , Department of Biotechnology, School of Engineering, Nagoya University
Hiroyuki Honda , Department of Biotechnology, School of Engineering, Nagoya University
Mitsuhiro Yokota , Department of Cardiovascular Genome Science, School of Medicine, Nagoya University
pp. 247-248

Mapping SNP association results into type 2 DM Pathways-Metabolic Syndrome as a robust system (Abstract)

Guijin Ji , HuBit Genomix, Inc , Tokyo, Japan
Masaaki Muramatsu , HuBit Genomix, Inc , Tokyo, Japan
Hidenori Satoh , HuBit Genomix, Inc , Tokyo, Japan
Masanori Baba , HuBit Genomix, Inc , Tokyo, Japan
Takashi Kido , HuBit Genomix, Inc , Tokyo, Japan
pp. 249-250

ssahaSNP A Polymorphism Detection Tool on a Whole Genome Scale (Abstract)

Zemin Ning , The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus
Mario Caccamo , The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus
James C. Mullikin , Genome Technology Branch/NHGRI, NIH
pp. 251-254
Synthetic Biological Systems

Noise Propagation in Transcriptional Cascades (PDF)

R. Weiss , Princeton University
S. Hooshangi , Princeton University
S. Thiberge , Princeton University
pp. 255

The Synthetic Gene Designer: a Flexible Web Platform to Explore Sequence Space of Synthetic Genes for Heterologous Expression (Abstract)

Stephen Freeland , University of Maryland at Baltimore
Nabila Bashir-Bello , University of Maryland at Baltimore
Gang Wu , University of Maryland at Baltimore
pp. 258-259

ECOME: A simple model for an evolving consumption web (Abstract)

Christopher Bystroff , Biology Department, Rensselaer Polytechnic Institute
Sam DeLuca , Biology Department, Rensselaer Polytechnic Institute
Carl N. McDaniel , Biology Department, Rensselaer Polytechnic Institute
pp. 260-261

Engineering a 1:2 Bio-multiplexer for controlled stem cell differentiation (PDF)

Ron Weiss , Engineering and Dept. of Molecular Biology, Princeton University
Sairam Subramanian , Engineering, Princeton University
Ihor Lemischka , Biology Dept, Princeton University
pp. 262

Engineering Multi-signal Systems for Complex Pattern Formation (Abstract)

Ron Weiss , Dept. of Electrical Engineering and Dept. of Molecular Biology, Princeton University
Jerome Ku , Dept. of Electrical Engineering, Princeton University
David Karig , Dept. of Electrical Engineering, Princeton University
pp. 263-266
Visualization

Chemical Structure-Activity Relationship Visualization Using Structure Activity Maps (Abstract)

Xin Lin , Department of Computer Science, Kent State University
Johnnie W. Baker , Department of Computer Science, Kent State University
Weiguo Fan , Department of Computer Science, Kent State University
Chun-che Tsai , Department of Chemistry, Kent State University
Boren Lin , Department of Chemistry, Kent State University
Yu-Wei Hsieh , Department of Computer Science, Kent State University
pp. 267-268

SinicView: An Interactive Visualization Tool for Comparison of Multiple Sequence Alignment Results (Abstract)

Tze-Chang Shiao , Institute of Information Science and Genomics Research Center, Academia Sinica, Taiwan
Laurent Lin , Institute of Information Science and Genomics Research Center, Academia Sinica, Taiwan
Chun-Yi Wong , Institute of Information Science and Genomics Research Center, Academia Sinica, Taiwan
Shiang-Heng Chen , Institute of Information Science and Genomics Research Center, Academia Sinica, Taiwan
D.T. Lee , Institute of Information Science and Genomics Research Center, Academia Sinica, Taiwan
Meng-Yuan Chou , Institute of Information Science and Genomics Research Center, Academia Sinica, Taiwan
Arthur Chun-Chieh Shih , Institute of Information Science and Genomics Research Center, Academia Sinica, Taiwan
Chin-Lin Peng , Institute of Information Science and Genomics Research Center, Academia Sinica, Taiwan
pp. 269-270

DockingShop: a Tool for Interactive Protein Docking (Abstract)

Ting-Cheng Lu , California Institute for Quantitative Biomedical Research
Silvia N. Crivelli , California Institute for Quantitative Biomedical Research
JinHui Ding , California Institute for Quantitative Biomedical Research
pp. 271-272

ProteinShop and POSE: Bringing Robotics and Intelligent Systems into the Field of Molecular Modeling (Abstract)

Nelson L. Max , University of California, Davis
Silvia N. Crivelli , California Institute for Quantitative Biomedical Research
Ting-Cheng Lu , California Institute for Quantitative Biomedical Research
pp. 273-274

Visualization of Logic Analysis of Phylogenetic Profiles (LAPP) (Abstract)

Kay A. Robbins , Cajal Neuroscience Research Institute University of Texas at San Antonio
Li Zhao , Department of Computer Science, University of Texas at San Antonio
pp. 275-276

The Significance of Linearity of Quantities in Electrophoresed and Blotted Materials Demonstrated by BandScan© - an Analytical Program (Abstract)

Yasantha Rajakarunanayake , Baylor University Medical Center
Hari Damodaran , University of Houston
Keith Hyland , Baylor University Medical Center
Richard S. Gunasekera , University of Houston
pp. 277-282
Workshop: Controlling Complexity

Autonomicity An Antidote for Complexity? (Abstract)

Roy Sterritt , University of Ulster, Ireland
Mike Hinchey , NASA Goddard Space Flight Center Software Engineering Laboratory
pp. 283-291

An Information Fusion Approach to Controlling Complexity in Bioinformatics Research (Abstract)

Tom Ziemke , School of Humanities and Informatics,University of Sk?vde
Sten F. Andler , School of Humanities and Informatics,University of Sk?vde
Barbara Gawronska , School of Humanities and Informatics,University of Sk?vde
Patric Nilsson , School of Life Sciences,,University of Sk?vde
Bj?rn Olsson , School of Humanities and Informatics,University of Sk?vde
Anne Persson , School of Technology and Society,University of Sk?vde
pp. 299-304

An Approach to Generating and Verifying Complex Scripts and Procedures (PDF)

Michael G. Hinchey , NASA Goddard Space Flight Center Information Systems Division
James L. Rash , NASA Goddard Space Flight Center Information Systems Division
Denis Gracanin , Virginia Tech
pp. 305-313

Clustering Gene Expression Data using Continuous Markov Models (Abstract)

Roy Sterritt , University of Ulster at Jordanstown
Adele H. Marshall , Queen?s University of Belfast
pp. 314-321

Computing MEG Signal Sources (Abstract)

Jonathan Sprinkle , University of California, Berkeley
Ruzena Bajcsy , University of California, Berkeley
J. Mikael Eklund , University of California, Berkeley
Gregory V. Simpson , University of California, San Francisco
pp. 332-338
Workshop: BioImage data Mining and Informatics

PET Imaging of Tumor Integrin Expression (Abstract)

Weibo Cai , University School of Medicine, Stanford
Xiaoyuan Chen , University School of Medicine, Stanford
pp. 340-349

Volume Measurements in the Embryonic Zebrafish Heart using 4D Confocal Microscopy (PDF)

Scott E. Fraser , Biological Imaging Center, Beckman Institute, California Institute of Technology
Michael Liebling , Biological Imaging Center, Beckman Institute, California Institute of Technology
Arian Forouhar , Option of Bioengineering and Aeronautics, California Institute of Technology
Mary E. Dickinson , Biological Imaging Center, Beckman Institute, California Institute of Technology
Morteza Gharib , Option of Bioengineering and Aeronautics, California Institute of Technology
pp. 350

Image Data Mining of Fruitfly Gene Expression Patterns (Abstract)

Hanchuan Peng , University of California at Berkeley
pp. 352

Toward Automatic Annotation of in situ mRNA Expression Patterns of Drosophila Embryos (PDF)

Hanchuan Peng , Genomics Division, Lawrence Berkeley National Laboratory
Jie Zhou , Northern Illinois University
pp. 353

Data Mining in situ Gene Expression Patterns at Cellular Resolution (PDF)

Christina Thaller , Biochemistry and Molecular Biology, Baylor College of Medicine
Gregor Eichele , Max Planck Institute of Experimental Endocrinology, Hannover, Germany
M. Bello , Dept. of Computer Science, University of Houston
Joe Warren , Dept. of Computer Science, Rice University, Houston TX.
Wah Chiu , Biochemistry and Molecular Biology, Baylor College of Medicine
Tao Ju , Dept. of Computer Science, Rice University, Houston TX.
James Carson , National Center for Macromolecular Imaging
pp. 358

Content-Based Tissue Image Mining (Abstract)

Abhi Gholap , BioImagene, Inc.
Gauri Naik , BioImagene, Inc.
CVK Rao , BioImagene, Inc.
Aparna Joshi , BioImagene, Inc.
pp. 359-363

Efficient 3D Binary Image Skeletonization (Abstract)

Liwen Shih , University of Houston
Son Tran , University of Houston
pp. 364-372

Digital Pathological Image Analysis and Cell Segmentation (PDF)

George Collins , University of Houston
Luis Hernandez , University of Houston
Liwen Shih , University of Houston
Gerald Campbell , University of Texas Medical Branch
Paula Gothreaux , University of Houston
pp. 373

Cell Phenotype Classification Based on 3D Cell Image Analysis (PDF)

Hanchuan Peng , Lawrence Berkeley National Lab, Berkeley, CA
Sophie Leli?vre , Lawrence Berkeley National Lab, Berkeley, CA
Fuhui Long , Lawrence Berkeley National Lab, Berkeley, CA
David Knowles , Lawrence Berkeley National Lab, Berkeley, CA
Damir Sudar , Lawrence Berkeley National Lab, Berkeley, CA
pp. 374

Current Challenges in Bioimage Database Design (Abstract)

Vebjorn Ljosa , University of California, Santa Barbara
Arnab Bhattacharya , University of California, Santa Barbara
Ambuj K. Singh , University of California, Santa Barbara
pp. 375-379

Open Microscopy Environment (PDF)

Ilya Goldberg , Laboratory of Genetics, NIH, National Institute on Aging
pp. 380
Workshop: BioSpice and Use Case

Large-scale Drug Function Prediction by Integrating QIS D2 and BioSpice (Abstract)

Cliff Zhou , Quantum Intelligence, Inc.
Ying Zhao , Quantum Intelligence, Inc.
Ian Oglesby , Quantum Intelligence, Inc.
Charles Zhou , Quantum Intelligence, Inc.
pp. 391-394

Drug Characteristics Prediction (Abstract)

Charles Zhou , Quantum Intelligence, Inc.
Ying Zhao , Quantum Intelligence, Inc.
pp. 395-398
Author Index

Author Index (PDF)

pp. 399
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