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2007
2007 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2007)
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2007 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2007)
Fremont, California
November 02-November 04
ISBN: 0-7695-3031-1
Table of Contents
Introduction
Preface
(PDF)
pp. xi
ABSTRACT
PDF
Organizing Committee
(PDF)
pp. xii
ABSTRACT
PDF
Program Committee
(PDF)
pp. xiii
ABSTRACT
PDF
Sponsors
(PDF)
pp. xvii
ABSTRACT
PDF
Keynotes
Combining Simulation and Machine Learning to Recognize Function in 4D
(PDF)
Russ Biagio Altman
pp. 3
ABSTRACT
PDF
Statistical Machine Learning and Computational Biology
(PDF)
Michael I. Jordan
pp. 4
ABSTRACT
PDF
Computer Science as a Lens on the Sciences: The Example of Computational Molecular Biology
(PDF)
Richard M. Karp
pp. 5
ABSTRACT
PDF
Session 1: Biological Data Mining
Feature Cluster Selection for High-Throughput Data Analysis
(Abstract)
Lei Yu
Hao Li
pp. 9-14
ABSTRACT
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GenMiner: Mining Informative Association Rules from Genomic Data
(Abstract)
Ricardo Martinez
Claude Pasquier
Nicolas Pasquier
pp. 15-22
ABSTRACT
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EGGS: Extraction of Gene Clusters Using Genome Context Based Sequence Matching Techniques
(Abstract)
Sun Kim
Ankita Bhan
Bharath K. Maryada
Kwangmin Choi
Yves V. Brun
pp. 23-28
ABSTRACT
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A Machine Learning Approach for Identification of Head and Neck Squamous Cell Carcinoma
(Abstract)
Mutlu Mete
Xiaowei Xu
Chun-Yang Fan
Gal Shafirstein
pp. 29-34
ABSTRACT
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Analysis of Protein Protein Dimeric Interfaces
(Abstract)
Feihong Wu
Fadi Towfic
Drena Dobbs
Vasant Honavar
pp. 35
ABSTRACT
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A Hybrid Abbreviation Extraction Technique for Biomedical Literature
(Abstract)
Min Song
Illhoi Yoo
pp. 42-47
ABSTRACT
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Hypothesis-Driven Specialization of Gene Expression Association Rules
(Abstract)
Dharmesh Thakkar
Carolina Ruiz
Elizabeth F. Ryder
pp. 48-55
ABSTRACT
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A New Fuzzy ARTMAP Approach for Predicting Biological Activity of Potential HIV-1 Protease Inhibitors
(Abstract)
Razvan Andonie
Levente Fabry-Asztalos
Lukas Magill
Sarah Abdul-Wahid
pp. 56-61
ABSTRACT
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Multi-topic Aspects in Clinical Text Classification
(Abstract)
Yutaka Sasaki
Brian Rea
Sophia Ananiadou
pp. 62-70
ABSTRACT
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Session 2: High Performance Bio-computing
A Comparison of Unsupervised Dimension Reduction Algorithms for Classification
(Abstract)
Jaegul Choo
Hyunsoo Kim
Haesun Park
Hongyuan Zha
pp. 71-77
ABSTRACT
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Pathological Image Analysis Using the GPU: Stroma Classification for Neuroblastoma
(Abstract)
Antonio Ruiz
Olcay Sertel
Manuel Ujaldon
Umit Catalyurek
Joel Saltz
Metin Gurcan
pp. 78-88
ABSTRACT
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Session 3: Genomics, Comparative Genomics
MAGMA: An Algorithm for Mining Multi-level Patterns in Genomic Data
(Abstract)
Winnie W. M. Lam
Keith C. C. Chan
David K. Y. Chiu
Andrew K. C. Wong
pp. 89-94
ABSTRACT
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Computational Identification of Protein-Coding Sequences by Comparative Analysis
(Abstract)
Arnaud Fontaine
H?l?ne Touzet
pp. 95-102
ABSTRACT
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Multi-agent System for Translation Initiation Site Prediction
(Abstract)
Jia Zeng
Reda Alhajj
pp. 103-110
ABSTRACT
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Session 4: Biological Databases, Data Integration and Visualization
An Active Rule-Based Approach for Constraint Management of Biological Data in XML Documents
(Abstract)
Denise Jones
Ying Jin
Huaqin Xu
pp. 111-116
ABSTRACT
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Using a Novel Data Transformation Technique to Provide the EMBOSS Software Suite as Semantic Web Services
(Abstract)
Paul M. K. Gordon
Edward Kawas
Mark Wilkinson
Christoph W. Sensen
pp. 117-124
ABSTRACT
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Exploring and Organizing Spatiotemporal Features such as Waves in High Throughput Brain Recordings by Lifting to Feature Space
(Abstract)
Dragana Veljkovic
Kay A. Robbins
Doug Rubino
Nicholas G. Hatsopoulos
pp. 125-134
ABSTRACT
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Session 5: Molecular Sequence Analysis
A Geometric Representation of Protein Sequences
(Abstract)
Shengyin Gu
Olivier Poch
Bernd Hamann
Patrice Koehl
pp. 135-142
ABSTRACT
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A Divide-and-Conquer Implementation of Three Sequence Alignment and Ancestor Inference
(Abstract)
Feng Yue
Jijun Tang
pp. 143-150
ABSTRACT
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SAIL-APPROX: An Efficient On-Line Algorithm for Approximate Pattern Matching with Wildcards and Length Constraints
(Abstract)
Dan He
Xindong Wu
Xingquan Zhu
pp. 151-158
ABSTRACT
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Predicting Markov Chain Order in Genomic Sequences
(Abstract)
Lenwood S. Heath
Amrita Pati
pp. 159-164
ABSTRACT
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Micro-repetitive Structure of Genomic Sequences and the Identification of Ancient Repeat Elements
(Abstract)
Abanish Singh
Cedric Feschotte
Nikola Stojanovic
pp. 165-171
ABSTRACT
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The Normalized Similarity Metric and Its Applications
(Abstract)
Shihyen Chen
Bin Ma
Kaizhong Zhang
pp. 172-180
ABSTRACT
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Session 6: Healthcare Informatics
Mining Rules for Risk Factors on Blood Stream Infection in Hospital Information System
(Abstract)
Kimiko Matsuoka
Shigeki Yokoyama
Kunitomo Watanabe
Shusaku Tsumoto
pp. 181-187
ABSTRACT
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A Comparative Medical Informatics Approach to Traumatic Pelvic Injuries
(Abstract)
Soo-Yeon Ji
Toan Huynh
Kayvan Najarian
pp. 188-193
ABSTRACT
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Automatic Identification of Temporal Sequences in Chewing Sounds
(Abstract)
Oliver Amft
Martin Kusserow
Gerhard Tr?ster
pp. 194-201
ABSTRACT
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Predicting Future High-Cost Patients: A Real-World Risk Modeling Application
(Abstract)
Sai T. Moturu
William G. Johnson
Huan Liu
pp. 202-208
ABSTRACT
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Human Disease-Gene Classification with Integrative Sequence-Based and Topological Features of Protein-Protein Interaction Networks
(Abstract)
Aaron Smalter
Seak Fei Lei
Xue-wen Chen
pp. 209-216
ABSTRACT
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Session 7: Proteomics, Computational Proteomics
Prediction of Kinase-Specific Phosphorylation Sites by One-Class SVMs
(Abstract)
Tingting Li
Hu Fu
Xuegong Zhang
pp. 217-222
ABSTRACT
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Multi-stage Framework to Infer Protein Functional Modules from Mass Spectrometry Pull-Down Data with Assessment of Biological Relevance
(Abstract)
Byung-Hoon Park
Bing Zhang
Tatiana Karpinets
Nagiza F. Samatova
pp. 223-229
ABSTRACT
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Robust Estimation and Graph-Based Meta Clustering for LC-MS Feature Extraction
(Abstract)
Karin Noy
Daniel Fasulo
pp. 230-236
ABSTRACT
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A Novel Classification Method for Analysis of Multi-stage Diseases via Mass Spectrometric Data
(Abstract)
Jung Hun Oh
Young Bun Kim
Jean Gao
pp. 237-244
ABSTRACT
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Session 8: Protein Structure
Evaluation of Protein Hydropathy Scales
(Abstract)
Satu J??skel?inen
Pentti Riikonen
Tapio Salakoski
Mauno Vihinen
pp. 245-251
ABSTRACT
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A Protocol to Detect Local Affinities Involved in Proteins Distant Interactions
(Abstract)
Christophe N. Magnan
C?cile Capponi
Fran?ois Denis
pp. 252-257
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Improved Methods for Template-Matching in Electron-Density Maps Using Spherical Harmonics
(Abstract)
Frank DiMaio
Ameet Soni
George N. Phillips
Jude W. Shavlik
pp. 258-265
ABSTRACT
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Heuristic Strategy for Geometric Hashing Based Protein Structure Comparison of Ellipsoidal Representation
(Abstract)
Yhi Shiau
Jia-Nan Wang
Yu-Feng Huang
Chien-Kang Huang
pp. 266-274
ABSTRACT
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Session 9: Computational Systems Biology
A Haplotyping Algorithm for Non-recombinant Pedigree Data Containing Missing Members
(Abstract)
Doan Dai Duong
Patricia A. Evans
pp. 275-281
ABSTRACT
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Risk Factor Searching Heuristics for SNP Case-Control Studies
(Abstract)
Dumitru Brinza
Alexander Zelikovsky
pp. 282-287
ABSTRACT
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Constraint-Based Simulation of Biological Systems Described by Molecular Interaction Maps
(Abstract)
Luca Bortolussi
Simone Fonda
Alberto Policriti
pp. 288-293
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A Multiscale Model for Efficient Simulation of a Membrane Bound Viral Fusion Peptide
(Abstract)
Yudong Sun
Steve McKeever
Kia Balali-Mood
Mark S. P. Sansom
pp. 294-301
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Mathematical Modeling of Phagocyte Chemotaxis toward and Adherence to Biomaterial Implants
(Abstract)
Jiaxing Xue
Jean Gao
Liping Tang
pp. 302-307
ABSTRACT
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Modeling the Stochastic Dynamics of Gene Expression in Single Cells: A Birth and Death Markov Chain Analysis
(Abstract)
Samik Ghosh
Preetam Ghosh
Kalyan Basu
Sajal K. Das
pp. 308-316
ABSTRACT
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Session 10: Microarray Design and Data Analysis
A Multi-metric Similarity Based Analysis of Microarray Data
(Abstract)
Fatih Altiparmak
Selnur Erdal
Ozgur Ozturk
Hakan Ferhatosmanoglu
pp. 317-324
ABSTRACT
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Smoothing Spline Mixed Effects Modeling of Multifactorial Gene Expression Profiles
(Abstract)
Brandon J. Smith
Bruce R. Southey
Sandra L. Rodriguez-Zas
pp. 325-332
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Session 11: BioOntologies
A New Metric to Measure Gene Product Similarity
(Abstract)
Sachin Mathur
Deendayal Dinakarpandian
pp. 333-338
ABSTRACT
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Kinetic Modeling Using BioPAX Ontology
(Abstract)
Oliver Ruebenacker
Ion I. Moraru
James C. Schaff
Michael L. Blinov
pp. 339-348
ABSTRACT
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Session 12: Gene Networks, Pathways, Networks, Systems Biology
A Novel Methodology for Characterizing and Predicting Protein Functional Sites
(Abstract)
Leonardo Bobadilla
Fernando Ni?
Edilberto Cepeda
Manuel A. Patarroyo
pp. 349-354
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GRAPPIN: Bipartite GRAph Based Protein-Protein Interaction Network Similarity Search
(Abstract)
Valeria Fionda
Luigi Palopoli
Simona Panni
Simona E. Rombo
pp. 355-361
ABSTRACT
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Inference of Gene Pathways Using Gaussian Mixture Models
(Abstract)
Younhee Ko
Chengxiang Zhai
Sandra L. Rodriguez-Zas
pp. 362-367
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Graph Kernel-Based Learning for Gene Function Prediction from Gene Interaction Network
(Abstract)
Xin Li
Zhu Zhang
Hsinchun Chen
Jiexun Li
pp. 368-373
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An Algorithm for Assigning Unique Keys to Metabolic Pathways
(Abstract)
Fang Fang
Robert L. Grossman
Xiangjun Liu
pp. 374-382
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Session 13: Signal and Image Processing in BioMedicine
Microarray Image Denoising Using a Two-Stage Multiresolution Technique
(Abstract)
Hara Stefanou
Thanasis Margaritis
Dimitris Kafetzopoulos
Konstantinos Marias
Panagiotis Tsakalides
pp. 383-389
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Selection of Tumor Areas and Segmentation of Nuclear Membranes in Tissue Confocal Images: A Fully Automated Approach
(Abstract)
Santa Di Cataldo
Elisa Ficarra
Enrico Macii
pp. 390-398
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Session 14: BioMedical Databases and Information Systems, BioMedical Information
MDDM: A Resource for Differential Methylation in Cancer
(Abstract)
Chetan Mittal
Nevenka Dimitrova
Vijaykumar Channakeshava
pp. 399-405
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An Efficient Online Tool to Search Top-N Genes with Similar Biological Functions in Gene Ontology Database
(Abstract)
James Z. Wang
Zhidian Du
Philip S. Yu
Chin-Fu Chen
pp. 406-411
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Using SVG to Model and Query Image Annotations and Their History
(Abstract)
Fusheng Wang
Cornelius Rabsch
Peiya Liu
pp. 412-422
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Session 15: Intelligent Biomedical Knowledge Discovery
A Semi-supervised Learning Approach to Disease Gene Prediction
(Abstract)
Thanh Phuong Nguyen
Tu Bao Ho
pp. 423-428
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Mining Clinical Data with a Temporal Dimension: A Case Study
(Abstract)
Michele Berlingerio
Francesco Bonchi
Fosca Giannotti
Franco Turini
pp. 429-436
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Multiple Interacting Subcellular Structure Tracking by Sequential Monte Carlo Method
(Abstract)
Quan Wen
Jean Gao
Kate Luby-Phelps
pp. 437-442
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Author Index
Author Index
(PDF)
pp. 443
ABSTRACT
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