The 2007 IEEE International Conference on Bioinformatics and Biomedicine

BIBM 2007 Program


Fremont, California, USA

November 2-4, 2007

IEEE BIBM 2007 Program

Thursday - Nov 1, 2007

15.30 - 18.30

Conference on-site Registration

Friday - Nov 2, 2007

7.30 - 9.00

Conference on-site Registration, ,    8:45-9am Opening ceremony

9.00 - 9.45

BIBM Keynote Speech
"Combining Simulation and Machine Learning to Recognize Function in 4D"
by Prof. Russ Altman (Chair : Aydin Tozeren )

9.45 - 10.30

GrC Keynote Speech
"Linguistic Summaries of Static and Dynamic Data : Granularity and Computing with Words"
by Prof. Janusz Kacprzyk
(Chair: T.Y.Lin)

10.30 - 11.00

Coffee Break

11.00 - 11.45

GrC Keynote Speech
"Granular Computing - Computing with Information which is Imprecise, Uncertain, Incomplete or Partially True"
by L. Zadeh
(Chair: T.Y.Lin)

11.45 - 12.30

GrC Keynote Speech
"On Genetic-Fuzzy Data Mining Techniques"
by Tzung-Pei Hong
(Chair: Janus Kacprzyk)


Parallel Sessions

Salon A: Biological Data Mining

Session Chair : Sun Kim

Lei Yu, "Feature Cluster Selection for High-Throughput Data Analysis"

Ricardo Martinez, Claude Pasquier, and Nicolas Pasquier, "GenMiner: Mining Informative Association Rules from Genomic Data"    

Sun Kim, Ankita Bhan, Bharat Kumar Maryada, Kwangmin Choi, and Yves Brun, "EGGS: Extraction of Gene clusters using Genome context based Sequence matching techniques"

Mutlu Mete, Xiaowei Xu, Chun-Yang Fan, and Gal Shafirstein, "A Machine Learning Approach for Identification of Head and Neck Squamous Cell Carcinoma"

Salon B: Proteomics, Computational proteomics

Session Chair : Jean Gao

Tingting Li, Hu Fu, and Xuegong Zhang, "Prediction of Kinase-Specific Phosphorylation Sites by One-Class SVMs"

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"

Karin Noy and Daniel Fasulo,  "Robust Estimation and Graph-based Meta Clustering for LC-MS Feature Extraction"

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"


Conference Lunch : Salon V


Parallel Sessions

Salon A: Workshop High-throughput data analysis for proteomics and genomics

Salon B: Biological Data Mining

Session Chair : Min Song

Feihong Wu, Fadi Towfic, Drena Dobbs, and Vasant Honavar, "Analysis of Protein Protein Dimeric Interfaces"

Min Song and Illhoi yoo, "A Hybrid Abbreviation Extraction Technique for Biomedical Literature"

Dharmesh Thakkar, Carolina Ruiz, and Elizabeth Ryder, "Hypothesis-Driven Specialization of Gene Expression Association Rules"

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"

Yutaka Sasaki, Brian Rea, and Sophia Ananiadou, "Multi-Topic Aspects in Clinical Text Classification"

Salon C: Healthcare Informatics

Session Chair: Shusaku Tsumoto

Shusaku Tsumoto, Kimiko Matsuoka, and Shigeki Yokoyama, "Mining Rules for Risk Factors on Blood Stream Infection in Hospital Information System"

Soo-Yeon Ji, Toan Huynh, and Kayvan Najarian , "A Comparative Medical Informatics Approach to Traumatic Pelvic Injuries"

Oliver Amft, Martin Kusserow, and Gerhard Troester, "Identification of temporal structures in chewing sounds"

Sai Moturu, William Johnson, and Huan Liu, "Predicting Future High-Cost Patients: A Real-World Risk Modeling Application"

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"


Coffee break

16.15 - 18.15

Parallel Sessions

Salon A: Workshop High-throughput data analysis for proteomics and genomics

Salon B: Gene networks, Pathways, Networks, Systems Biology

Session Chair : Jason Li

Leonardo Bobadilla, Fernando Niño, Edilberto Cepeda, and Manuel Patarroyo, "A Novel Methodology for Characterizing and Predicting Protein Functional Sites"

Valeria Fionda, Luigi Palopoli, Simona Panni, and Simona E. Rombo, "Bi-GRAPPIN: Bipartite GRAph based Protein-Protein Interaction Networks similarity search."   

Younhee Ko, Sandra Zas, and Chengxiang Zhai, "Inference of Gene Pathways Using Gaussian Mixture Models"

Xin Li, Jiexun Li, Zhu Zhang, and Hsinchun Chen, "Graph Kernel-based Learning for Gene Function Prediction from Gene Interaction Network"

Fang Fang, Xiangjun Liu, and Robert Grossman, "Generate Unique Keys for Metabolic Pathways"

Salon C: Biological Databases and Ontologies, Data Integration and Visualization

Session Chair : Illhoi Yoo

Denise Jones, Ying Jin, and Huaqin Xu, "An Active Rule-Based Approach for Constraint Management of Biological Data in XML Documents"

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"

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"

Sachin Mathur and Deendayal Dinakarpandian, "A New Metric to Measure Gene Product Similarity"

Oliver Ruebenacker, Ion Moraru, James Schaff, and Michael Blinov, "Kinetic Modeling using BioPAX ontology"

18.30 - 21.00

Welcome Reception: Salon IV and V

Saturday - Nov 3, 2007

8.00 - 8.45

Conference on-site Registration

9.00 - 9.45

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)

9.45 - 10.30

GrC Feature Speech
"Information Granulation and Integration: Impact on Web"
by Prof. Tsau Young Lin
(Chair: Xiaohua Tony Hu)

10.30 - 11.00

Coffee Break

11.00 - 11.45

WI/IAT Keynote Speech
"How Relevant is Game Theory to Intelligent Agent Technology"
by Prof. Yoav Shoham

11.45 - 12.30

WI/IAT Keynote Speech
"Service Web 3.0"
by Prof. Dieter Fensel

12.30 - 13.30

Conference Lunch (Salon V)

13.30 - 15.45

Parallel Sessions

Salon A: Tutorial: Minimum Redundancy Feature Selection and Extraction

By Chris Ding, University of Texas at Arlington,,  Hanchuan Peng, Howard Hughes Medical Institute,

Salon B: Protein structure

Session Chair : Xue-wen Chen

Satu Jääskeläinen, Pentti Riikonen, Tapio Salakoski, and Mauno Vihinen, "Evaluation of protein hydropathy scales"    

Christophe Nicolas Magnan, Cécile Capponi, and François Denis, "A Protocol to Detect Local Affinities Involved in Proteins Distant Interactions"

Frank DiMaio, Ameet Soni, George Phillips, and Jude Shavlik, "Improved Methods for Template-Matching in Electron Density Maps Using Spherical Harmonics"

Yhi Shiau, Jia-Nan Wang, Yu-Feng Huang, and Chien-Kang Huang, "Heuristic Strategy for Geometric Hashing based Protein Structure Comparison of Ellipsoidal Representation"

Quan Wen and Jean Gao, "Multiple Interacting Subcellular Structure Tracking By Sequential Monte Carlo Method"

Salon C: Genomics, Comparative Genomics

Session Chair : Reda Alhajj

Thanh Phuong Nguyen and Tu Bao Ho, "A Semi-Supervised Learning Approach to Disease Gene Prediction"

Jaegul Choo, Hyunsoo Kim, Haesun Park, and Hongyuan Zha, “A Comparison of Unsupervised Dimension Reduction Algorithms for Classification"

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"

Arnaud Fontaine and Hélène TOUZET, "Computational identification of protein-coding sequences by comparative analysis"

Reda Alhajj, "Multi-Agent System for Translation Initiation Site Prediction"

15.45 - 16.15

Coffee Break

16.15 - 18.45

Parallel Sessions

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.

Salon B: Molecular sequence analysis

Session Chair : Kaizhong Zhang

Shengyin Gu, Olivier Poch, Bernd Hamann, and Patrice Koehl, "The Geometric Representation of Protein Sequences"      

Feng Yue and jijun Tang, "A Divide-and-Conquer Implementation of Three Sequence Alignment and Ancestor Inference"    

Dan He and Xindong Wu, "SAIL-APPROX: An Efficient On-line Algorithm for Approximate Pattern Matching with Wildcards and Length Constraints"    

Lenwood Heath and Amrita Pati, "Predicting Markov chain order in genomic sequences"  

Abanish Singh, Cedric Feschotte, and Nikola Stojanovic, "Micro-repetitive structure of genomic sequences and the identification of ancient repeat elements" 

Shihyen Chen, Bin Ma, and Kaizhong Zhang, "The Normalized Similarity Metric and Its Applications"

Salon C: Computational systems biology

Session Chair : Xin Li

Duong Doan and Patricia Evans, "A Haplotyping Algorithm for Non-Recombinant Pedigree Data Containing Missing Members"

Dumitru Brinza and Alexander Zelikovsky, "Risk Factor Searching Heuristics for SNP Case-Control Studies"   

Luca Bortolussi, Simone Fonda, and Alberto Policriti, "Constraint-based simulation of bological systems described by Molecular Interaction Maps”      

Yudong Sun, Steve McKeever, Kia Balali-Mood, and Mark Sansom, "A Multiscale Model for Efficient Simulation of a Membrane Bound Viral Fusion Peptide"

Jiaxing Xue, Jean Gao, and Liping Tang, "Mathematical modeling of phagocyte chemotaxis toward and adherence to biomaterial implants"

18.30 - 20.00

Banquet: Salon IV and V

Sunday - Nov 4, 2007

9.00 - 9.45

GrC Keynote Speech (Salon IV and V)
"Towards Mobile Internet: Privacy Threats and Challenges"
by Prof. Ling Liu
(Chair; Xiaohua Tony Hu)

9.45 - 10.30

BIBM Keynote Speech
"Statistical Machine Learning and Computational Biology"
by Prof. Michael I. Jordan (Chair: Ion Mandoiu)



10.30 - 11.00

Coffee Break

11:00 – 18:00

 Salon A: Workshop Computational Structural Bioinformatics

11:00 - 12:30

Parallel Sessions

Salon B: Microarray design and data analysis

Session Chair : Ion Mandoiu

Fatih Altiparmak, Selnur Erdal, Ozgur Ozturk, and Hakan Ferhatosmanoglu, "A Multi-Metric Similarity Based Analysis of Microarray Data"

Brandon Smith, Sandra Rodriguez-Zas, and Bruce Southey, "Smoothing Spline Mixed Effects Modelings of Multifactorial Gene Expression Profiles"

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"

Salon C: Signal and Image Processing in BioMedicine

Session Chair : Aydin Tozeren

Antonio Ruiz, Olcay Sertel, Manuel Ujaldon, Umit Catalyurek, Joel Saltz, and Metin Gurcan, "Pathological Image Analysis Using the GPU: Stroma Classification for Neuroblastoma"   

Hara Stefanou, Thanasis Margaritis, Dimitris Kafetzopoulos, Kostas Marias, and Panagiotis Tsakalides, "Microarray Image Denoising Using a Two-Stage Multiresolution Technique"


12.30 - 13.30

Conference Lunch

13.30 - 15.45

Parallel Sessions

Salon B: Workshop Data Mining in Bioinformatics (DMB 2007),

Salon C: Workshop Knowledge Discovery and Management in Hearth Informatics,

Salon A: Workshop Computational Structural Bioinformatics

Livemore Valley: BioMedical Databases & Information Systems, BioMedical Information

Session Chair : James Wang

Chetan Mittal, Nevenka Dimitrova, and Bhaskar Azad, "MDDM: A Resource for Differential Methylation in Cancer"

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"    

Fusheng Wang, Cornelius Rabsch, and Peiya Liu, "Using SVG to Model and Query Image Annotations and their History"

Michele Berlingerio, Francesco Bonchi, Fosca Giannotti, and Franco Turini, "Mining Clinical Data with a Temporal Dimension: a Case Study"

15:45 - 16:15

Coffee break

16:15 - 18:15

Parallel Sessions

Salon B: Workshop Data Mining in Bioinformatics (DMB 2007)

Salon C: Workshop Knowledge Discovery and Management in Hearth Informatics

Salon A: Workshop Computational Structural Bioinformatics