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Thursday - Nov 1, 2007
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15.30 - 18.30
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Conference
on-site Registration
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Friday - Nov 2, 2007
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7.30 - 9.00
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Conference
on-site Registration, , 8:45-9am
Opening ceremony
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9.00 - 9.45
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BIBM Keynote Speech
"Combining Simulation and Machine
Learning to Recognize Function in 4D"
by Prof. Russ Altman (Chair : Aydin Tozeren )
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9.45 - 10.30
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GrC Keynote Speech
"Linguistic Summaries of Static and
Dynamic Data : Granularity and Computing with Words"
by Prof. Janusz
Kacprzyk (Chair: T.Y.Lin)
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10.30 - 11.00
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Coffee Break
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11.00 - 11.45
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GrC Keynote Speech
"Granular Computing - Computing with
Information which is Imprecise, Uncertain, Incomplete or Partially True"
by L. Zadeh
(Chair: T.Y.Lin)
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11.45 - 12.30
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GrC Keynote Speech
"On Genetic-Fuzzy Data Mining
Techniques"
by Tzung-Pei
Hong (Chair: Janus Kacprzyk)
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11:00-12:30
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Parallel
Sessions
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Salon A: Biological Data Mining
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Session Chair : Sun Kim
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Lei Yu,
"Feature Cluster Selection for High-Throughput Data Analysis"
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Ricardo Martinez, Claude Pasquier,
and Nicolas Pasquier, "GenMiner:
Mining Informative Association Rules from Genomic Data"
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Sun Kim, Ankita
Bhan, Bharat Kumar Maryada,
Kwangmin Choi, and Yves
Brun, "EGGS: Extraction of Gene clusters
using Genome context based Sequence matching techniques"
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Mutlu Mete, Xiaowei
Xu, Chun-Yang Fan, and Gal Shafirstein,
"A Machine Learning Approach for Identification of Head and Neck Squamous Cell Carcinoma"
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Salon B: Proteomics, Computational proteomics
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Session Chair : Jean Gao
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Tingting Li, Hu
Fu, and Xuegong Zhang, "Prediction of Kinase-Specific Phosphorylation
Sites by One-Class SVMs"
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Byung-Hoon Park, Bing Zhang, Tatiana Karpinets, and Nagiza F. Samatova,
"Multi-Stage framework to infer protein functional modules from
mass spectrometry pull-down data with assessment of biological
relevance"
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Karin Noy
and Daniel Fasulo, "Robust Estimation and Graph-based
Meta Clustering for LC-MS Feature Extraction"
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Jung Hun Oh,
Young Bun Kim, Prem Gurnani,
Kevin Rosenblatt, and Jean Gao, "A Novel Classification Method for
Analyzing Multi-Stage Diseases Using MALDI-TOF Mass Spectra"
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12:30-1:30
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Conference Lunch : Salon V
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1:30-3:45
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Parallel
Sessions
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Salon A: Workshop High-throughput data analysis for proteomics and
genomics
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Salon B: Biological Data Mining
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Session Chair : Min Song
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Feihong Wu, Fadi
Towfic, Drena Dobbs,
and Vasant Honavar,
"Analysis of Protein Protein Dimeric Interfaces"
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Min Song and Illhoi
yoo, "A Hybrid Abbreviation Extraction
Technique for Biomedical Literature"
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Dharmesh Thakkar,
Carolina
Ruiz, and Elizabeth Ryder, "Hypothesis-Driven Specialization of Gene
Expression Association Rules"
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Razvan Andonie,
Levente Fabry-Asztalos,
Lukas Magill, and Sarah Abdul-Wahid, "A New Fuzzy ARTMAP Approach for
Predicting Biological Activity of Potential HIV-1 Protease Inhibitors"
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Yutaka Sasaki, Brian Rea, and
Sophia Ananiadou, "Multi-Topic Aspects in
Clinical Text Classification"
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Salon C: Healthcare Informatics
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Session Chair: Shusaku Tsumoto
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Shusaku Tsumoto,
Kimiko Matsuoka, and Shigeki Yokoyama,
"Mining Rules for Risk Factors on Blood Stream Infection in Hospital
Information System"
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Soo-Yeon Ji, Toan Huynh, and Kayvan Najarian , "A Comparative Medical Informatics
Approach to Traumatic Pelvic Injuries"
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Oliver Amft,
Martin Kusserow, and Gerhard Troester,
"Identification of temporal structures in chewing sounds"
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Sai Moturu,
William Johnson, and Huan Liu, "Predicting
Future High-Cost Patients: A Real-World Risk Modeling Application"
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Aaron Smalter,
Seak Fei Lei, and Xue-wen Chen,
"Human Disease-gene Classification with Integrative
Sequence-based and Topological Features of Protein-protein Interaction
Networks"
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15:45-16:15
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Coffee break
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16.15 - 18.15
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Parallel
Sessions
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Salon A: Workshop High-throughput data analysis for proteomics and
genomics
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Salon B: Gene networks, Pathways, Networks, Systems Biology
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Session Chair : Jason Li
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Leonardo Bobadilla, Fernando Niño,
Edilberto Cepeda, and
Manuel Patarroyo, "A Novel Methodology for
Characterizing and Predicting Protein Functional Sites"
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Valeria Fionda,
Luigi Palopoli, Simona Panni, and Simona E. Rombo, "Bi-GRAPPIN: Bipartite GRAph
based Protein-Protein Interaction Networks similarity search."
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Younhee Ko,
Sandra Zas, and Chengxiang
Zhai, "Inference of Gene Pathways Using
Gaussian Mixture Models"
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Xin Li, Jiexun
Li, Zhu Zhang, and Hsinchun Chen, "Graph
Kernel-based Learning for Gene Function Prediction from Gene Interaction
Network"
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Fang Fang,
Xiangjun Liu, and Robert Grossman, "Generate
Unique Keys for Metabolic Pathways"
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Salon C: Biological Databases and Ontologies,
Data Integration and Visualization
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Session Chair : Illhoi Yoo
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Denise Jones, Ying Jin, and Huaqin Xu, "An Active
Rule-Based Approach for Constraint Management of Biological Data in XML
Documents"
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Paul Gordon, Edward Kawas, Mark Wilkinson, and Christoph
Sensen, "Using a novel data transformation
technique to provide the EMBOSS software suite as Semantic Web
Services"
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Dragana Veljkovic,
Kay Robbins, Doug Rubino, and Nicholas Hatsopoulos, "Exploring and Organizing
Spatiotemporal Features such as Waves in High Throughput Brain Recordings
by Lifting to Feature Space"
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Sachin Mathur
and Deendayal Dinakarpandian,
"A New Metric to Measure Gene Product Similarity"
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Oliver Ruebenacker,
Ion Moraru, James Schaff,
and Michael Blinov, "Kinetic Modeling using BioPAX ontology"
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18.30 - 21.00
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Welcome
Reception: Salon IV and V
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Saturday - Nov 3, 2007
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8.00 - 8.45
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Conference
on-site Registration
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9.00 - 9.45
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BIBM Keynote Speech (Salon I, II…IX)
"Computer science as a Lens on the
Sciences: The Example of Computational Molecular Biology"
by Prof. Richard Karp (Chair
: Xiaohua Tony Hu)
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9.45 - 10.30
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GrC Feature Speech
"Information Granulation and
Integration: Impact on Web"
by Prof. Tsau
Young Lin (Chair: Xiaohua Tony Hu)
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10.30 - 11.00
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Coffee Break
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11.00 - 11.45
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WI/IAT Keynote Speech
"How Relevant is Game Theory to
Intelligent Agent Technology"
by Prof. Yoav
Shoham
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11.45 - 12.30
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WI/IAT Keynote Speech
"Service Web 3.0"
by Prof. Dieter Fensel
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12.30 - 13.30
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Conference
Lunch (Salon V)
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13.30 - 15.45
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Parallel
Sessions
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Salon A: Tutorial: Minimum Redundancy Feature Selection and Extraction
By Chris Ding, University of Texas at Arlington, chqding@uta.edu, Hanchuan Peng, Howard Hughes Medical Institute,
pengh@janelia.hhmi.org
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Salon B: Protein structure
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Session Chair : Xue-wen Chen
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Satu Jääskeläinen,
Pentti Riikonen, Tapio Salakoski, and Mauno Vihinen,
"Evaluation of protein hydropathy
scales"
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Christophe Nicolas Magnan, Cécile Capponi, and François Denis, "A Protocol to Detect
Local Affinities Involved in Proteins Distant Interactions"
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Frank DiMaio,
Ameet Soni, George
Phillips, and Jude Shavlik, "Improved
Methods for Template-Matching in Electron Density Maps Using Spherical
Harmonics"
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Yhi Shiau, Jia-Nan Wang, Yu-Feng Huang,
and Chien-Kang Huang, "Heuristic Strategy
for Geometric Hashing based Protein Structure Comparison of Ellipsoidal
Representation"
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Quan Wen and
Jean Gao, "Multiple Interacting Subcellular Structure Tracking By Sequential Monte Carlo Method"
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Salon C: Genomics, Comparative Genomics
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Session Chair : Reda Alhajj
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Thanh Phuong Nguyen and Tu Bao Ho, "A
Semi-Supervised Learning Approach to Disease Gene Prediction"
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Jaegul Choo, Hyunsoo Kim, Haesun Park,
and Hongyuan Zha, “A
Comparison of Unsupervised Dimension Reduction Algorithms for
Classification"
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Winnie W.M. Lam, Keith C.C. Chan,
David K.Y. Chiu, and Andrew K.C. Wong, "MAGMA: AN ALGORITHM FOR MINING
MULTI-LEVEL PATTERNS"
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Arnaud Fontaine and Hélène TOUZET,
"Computational identification of protein-coding sequences by
comparative analysis"
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Reda Alhajj,
"Multi-Agent System for Translation Initiation Site Prediction"
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15.45 - 16.15
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Coffee Break
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16.15 - 18.45
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Parallel
Sessions
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Salon A: Tutorial: From sequences, structures, to interactions of
proteins: some recent development
By Yaoqi Zhou, Professor of School
of Informatics, IUPUI and Center
for Computational Biology and Bioinformatics, IU School of Medicine.
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Salon B: Molecular sequence analysis
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Session Chair : Kaizhong Zhang
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Shengyin Gu,
Olivier Poch, Bernd Hamann,
and Patrice Koehl, "The Geometric Representation
of Protein Sequences"
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Feng Yue and
jijun Tang, "A Divide-and-Conquer
Implementation of Three Sequence Alignment and Ancestor
Inference"
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Dan He and Xindong
Wu, "SAIL-APPROX: An Efficient On-line Algorithm for Approximate Pattern
Matching with Wildcards and Length Constraints"
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Lenwood Heath and Amrita Pati, "Predicting Markov chain order in genomic
sequences"
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Abanish Singh, Cedric Feschotte,
and Nikola Stojanovic, "Micro-repetitive
structure of genomic sequences and the identification of ancient repeat
elements"
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Shihyen Chen, Bin Ma, and Kaizhong Zhang, "The Normalized Similarity Metric
and Its Applications"
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Salon C: Computational systems biology
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Session Chair : Xin Li
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Duong Doan and Patricia Evans,
"A Haplotyping Algorithm for Non-Recombinant
Pedigree Data Containing Missing Members"
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Dumitru Brinza
and Alexander Zelikovsky, "Risk Factor
Searching Heuristics for SNP Case-Control Studies"
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Luca Bortolussi,
Simone Fonda, and Alberto Policriti,
"Constraint-based simulation of bological
systems described by Molecular Interaction Maps”
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Yudong Sun, Steve McKeever,
Kia Balali-Mood, and Mark Sansom,
"A Multiscale Model for Efficient Simulation
of a Membrane Bound Viral Fusion Peptide"
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Jiaxing Xue,
Jean Gao, and Liping
Tang, "Mathematical modeling of phagocyte chemotaxis
toward and adherence to biomaterial implants"
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18.30 - 20.00
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Banquet: Salon
IV and V
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Sunday - Nov 4, 2007
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9.00 - 9.45
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GrC Keynote Speech (Salon IV and V)
"Towards Mobile Internet: Privacy
Threats and Challenges"
by Prof. Ling Liu (Chair; Xiaohua Tony Hu)
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9.45 - 10.30
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BIBM Keynote Speech
"Statistical Machine Learning and
Computational Biology"
by Prof. Michael I. Jordan (Chair: Ion
Mandoiu)
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10.30 - 11.00
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Coffee Break
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11:00 – 18:00
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Salon A: Workshop Computational Structural Bioinformatics
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11:00 - 12:30
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Parallel Sessions
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Salon B: Microarray design and
data analysis
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Session Chair : Ion Mandoiu
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Fatih Altiparmak,
Selnur Erdal, Ozgur Ozturk, and Hakan Ferhatosmanoglu,
"A Multi-Metric Similarity Based Analysis of Microarray Data"
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Brandon Smith, Sandra Rodriguez-Zas, and Bruce Southey, "Smoothing Spline Mixed Effects Modelings
of Multifactorial Gene Expression Profiles"
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Samik Ghosh, Preetam Ghosh, Kalyan Basu, and Sajal Das, "Modeling the stochastic dynamics of
gene expression in single cells: A Birth and Death Markov Chain
Analysis"
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Salon C: Signal and Image Processing in BioMedicine
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Session Chair : Aydin Tozeren
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Antonio Ruiz, Olcay
Sertel, Manuel Ujaldon,
Umit Catalyurek, Joel Saltz, and Metin Gurcan, "Pathological Image Analysis Using the
GPU: Stroma Classification for Neuroblastoma"
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Hara Stefanou,
Thanasis Margaritis, Dimitris Kafetzopoulos,
Kostas Marias, and Panagiotis Tsakalides,
"Microarray Image Denoising Using a
Two-Stage Multiresolution Technique"
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SANTA DI CATALDO, ELISA FICARRA,
and ENRICO MACII, "SELECTION OF TUMOR AREAS AND SEGMENTATION OF
NUCLEAR MEMBRANES IN TISSUE CONFOCAL IMAGES: A FULLY-AUTOMATED
APPROACH"
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12.30 - 13.30
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Conference
Lunch
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13.30 - 15.45
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Parallel
Sessions
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Salon B: Workshop Data
Mining in Bioinformatics (DMB 2007),
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Salon C: Workshop Knowledge Discovery and Management in Hearth
Informatics,
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Salon A: Workshop Computational Structural Bioinformatics
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Livemore Valley: BioMedical
Databases & Information Systems, BioMedical
Information
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Session Chair : James Wang
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Chetan Mittal,
Nevenka Dimitrova, and Bhaskar Azad, "MDDM: A Resource for Differential Methylation in Cancer"
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James Z. Wang, Zhidian
Du, Philip S. Yu, and Chin-Fu Chen, "An Efficient Online Tool to
Search Top-N Genes with Similar Biological Functions in Gene Ontology
Database"
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Fusheng Wang, Cornelius Rabsch, and Peiya Liu,
"Using SVG to Model and Query Image Annotations and their
History"
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Michele Berlingerio,
Francesco Bonchi, Fosca
Giannotti, and Franco Turini,
"Mining Clinical Data with a Temporal Dimension: a Case Study"
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15:45 - 16:15
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Coffee break
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16:15 - 18:15
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Parallel
Sessions
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