BIBM 2008 Conference Program Regular Papers: 20 minutes Short papers: 15 minutes Nov. 3, Monday 8:00 – 10:00 Tutorial Session 1: Luke Huan and Deepak Bandyopadhyay, Geometric Pattern Mining and Its Applications in Protein Structure and Function Analysis 8:00 – 10:00 Workshop 1: Biomedical and Health Informatics Workshop 2: Data Mining in Functional Genomics 10:00 – 10:15 Coffee Break 10:15 – 12:00 Workshop 2: Data Mining in Functional Genomics Workshop 3: Systems Biology and Medicine Workshop 4: Computational Structural Bioinformatics 12:00 – 1:30 Lunch 1:30 – 2:30 Keynote Speech: Steven Salzberg, Assembling Genomes from Very Short Reads 2:30 – 2:50 Coffee Break 2:50 – 5:50 Workshop 1: Biomedical and Health Informatics 2:50 – 5:50 Tutorial Session 2: Prof. Iosif Vaisman and Dr. Majid Masso, Statistical Geometry of Protein Structure and Computational Mutagenesis Tutorial Session 3 Saket Kharsikar and Asawari Samant, Computational Biology using MATLAB products‐A Focus on Bioinformatics and Systems Biology 6:30 – 8:30 Industry poster and Keynote Nov. 4, Tuesday 8:00 – 9:00 Keynote Speech: Zoran Obradovic, Functions of Intrinsically Disordered Proteins and Relationship with Human Disease Network 9:05 – 10:25 Session 1: Computational Systems Biology Reverse Engineering of gene regulatory network by integration of prior global gene regulatory information Baikang Pei, David Rowe, and Dong‐Guk Shin Invariance Kernel of Biological Regulatory Networks Jamil Ahmad and Olivier Roux Synthetic Gene Design with a Large Number of Hidden Stop Codons Vinhthuy Phan, Sudip Saha, Ashutosh Pandey, and Tit‐Yee Wong Fast Alignments of Metabolic Networks Qiong Cheng, Piotr Berman, Robert Harrison, and Alexander Zelikovsky Session 2: Gene Regulation and Transcriptomics Heart of the Matter: discovering the consensus of multiple clustering results Alex Kosorukoff and Saurabh Sinha Probe Design for Compressive Sensing DNA Microarrays Wei Dai, Mona Sheikh, Olgica Milenkovic, and Richard Baraniuk Detecting significantly expressed genes from time‐course expression profiles and its validation Fang‐Xiang Wu 10:25 – 10:40 Coffee break 10:40 – 11:40 Session 1: Biological Databases and Ontologies bcnQL: A Query Language for Biochemical Networks Hong Yang, Rajshekhar Sunderraman, and Hao Tian A Mixture Language Model for Class‐Attribute Mining from Biomedical Literature Digital Library Xiaohua Zhou, Xiaohua Hu, Xiaodan Zhang, Daniel Wu, Tingting He, Aijin Lou ANALYSIS OF MULTIPLEX GENE EXPRESSION MAPS OBTAINED BY VOXELATION Li An, Hongbo Xie, Mark Chin, Zoran Obradovic, Desmond Smith, and Vasileios Megalooikonomou Session 2: Bioinformatics of Diseases and Comparative Genomics Functional Proteomic Pattern Identification Under Low Dose Ionizing Radiation Jean Gao, Young Bun Kim, Johanne Pastor, and Kevin Rosenblatt Robust Composite Interval Mapping for QTL Analysis by Minimum‐Divergence Method Md. Nurul Haque MOLLAH and Shinto Eguchi The Effectiveness of Applying Codon Usage Bias for Translational Initiation Sites Predictionʺ Jia Zeng, Reda Alhajj, and Douglas Demetrick 11:40 – 1:00 Lunch 1:00 – 2:00 Keynote Speech: Yuan‐Ting Zhang, Telemedicine: Wearable Intelligent Sensors and Systems (WISS) for Mobile Healthcare 2:00 – 2:20 Coffee break 2:20 – 4:00 Session 1: Protein Structure, function, and interactions Exploring core/periphery structures in protein interaction networks provides structure‐property relation insights Thomas Grindinger, Feng Luo, Xiufeng Wan, and Richard Scheuermann Protein‐protein Interaction Prediction and Assessment from Model Organisms Xiaotong Lin, Mei Liu, and Xue‐wen Chen Towards Site‐based Protein Functional Annotationsʺ Seak Lei and Jun Huan Functional Neighbors: Relationships between Non‐homologous Protein Families Inferred Using Family‐Specific Fingerprints Deepak Bandyopadhyay, Luke Huan, Jinze Liu, Jan Prins, Jack Snoeyink, Wei Wang, and Alexander Tropsha Discrimination of insoluble‐carbohydrate binding proteins and their binding sites using a 3D motif detection methodʺ Andrew Doxey, Zhenyu Cheng, and Brendan McConkey Session 2: Sequence Analysis, Evolution and Phylogeny On the role of local matching for efficient semi‐supervised protein sequence classification Pavel Kuksa, Pai‐Hsi Huang, and Vladimir Pavlovic Uncovering Genomic Reassortments Among Influenza Strains by Enumerating Maximal Bicliques Niranjan Nagarajan and Carl Kingsford Exploring Alternative Splicing Features using Support Vector Machines Jing Xia, Doina Caragea, and Susam Brown New Approaches to Compare Phylogenetic Search Heuristics Seung‐Jin Sul, Suzanne Matthews, and Tiffani Williams Biological data outlier detection based on Kullback‐Leibler divergence Jean Gao, Jung Hun Oh, and Kevin Rosenblatt 4:00 – 4:20 Coffee break 4:20 – 5:40 Session 1: BiomedicaI Informatics/Data Mining and Visualization Multi‐way Association Extraction from Biological Text Documents Using Hyper‐ graphs Snehasis Mukhopadhyay, Mathew Palakal, and Kalyan Maddu Figure classification in biomedical literature towards figure mining Natsu Ishii, Asako Koike, Yasunori Yamamoto, and Toshihisa Takagi Energy Profile and Secondary Structure Impact shRNA Efficacy Hong Zhou and Xiao Zeng Meta Analysis of Microarray Data Using Gene Regulation Pathways Saira Kazmi, Bikang Pei, Alan Wong, Nori Ravi, Hsin‐Wei Wang, Dong‐Guk Shin, Yoo‐Ah Kim, and David Rowe Session 2: Biological Data Mining and Visualization Frequency Sorting Method for Spectral Analysis of DNA Sequences Anca Bucur, Jasper van Leeuwen, Nevenka Dimitrova, and Chetan Mittal Knowledge Discovery in Clinical Performance of Cancer Patients John Hayward, Sergio Alvarez, Carolina Ruiz, Mary Sullivan, Jennifer Tseng, and Giles Whalen Discovering frequent patterns of functional associations in protein interaction networks for function predictionʺ Young‐Rae Cho and Aidong Zhang Using Gene Ontology to Enhance Effectiveness of Similarity Measures for Microarray Dataʺ Zheng Chen and Jian Tang 6:00 – 8:00 Banquet Nov. 5, Wednesday 8:00 – 9:00 Keynote Speech: Olivier Bodenreider, Ontologies for Mining Biomedical Data 9:05 – 10:05 Session 1: Biological Data Mining and Visualization Correlations of length distributions between non‐coding and coding sequences of the Arabidopsis thaliana Rachel Amber Caldwell, Yan‐Xia Lin, and Ren Zhang Identifying interface elements implied in protein‐protein interactions using statistical tests and Frequent Item Sets Christine Martin and Antoine Cornuols Mining Fuzzy Association Patterns in Gene Expression Data for Gene Function Prediction Patrick C.H. Ma and Keith C.C. Chan Session 2: Biological Data Mining and Visualization Applying Clustering and Phylogeny Analysis to Study Dinoflagellates based on Sterol Composition Jeffrey Leblond, Andrew Lasiter, Cen Li, Ramiro Logares, Karin Rengefors, and Terence Evens Protein Sequence Motif Super‐Rule‐Tree (SRT) Structure Constructed by Hybrid Hierarchical K‐means Clustering Algorithm Bernard Chen, Jieyue He, Steven Pellicer, and Yi Pan Using Global Sequence Similarity to Enhance Biological Sequence Labeling Cornelia Caragea, Jivko Sinapov, Drena Dobbs, and Vasant Honavar 10:05 – 10:20 Coffee break 10:20 – 11:35 Session 1: Bioinformatics of Diseases and Health Informatics Editing Bayesian Networks: A New Approach for Combining Prior Knowledge and Gene Expression Measurements for Researching Diseases Udi Rubinstein, Yifat Felder, Nana Ginzbourg, Michael Gurevich, and Tamir Tuller Multi‐Agent Model Analysis of the Containment Strategy for Avian Influenza (AI) in South Korea Taehyong Kim, Woochang Hwang, Aidong Zhang, Surajit Sen, and Murali Ramanathan Predicting Protective Linear B‐cell Epitopes using Evolutionary Information Yasser EL‐Manzalawy, Drena Dobbs, and Vasant Honavar Towards the Mental Health Ontology Maja Hadzic, Meifania Chen, and Tharam S. Dillon Data Integration on Multiple Data Sets Tian Mi, Robert Aseltine, and Sanguthevar Rajasekaran Session 2: Biological Data Mining PhyQL: A Web‐Based Phylogenetic Visual Query Engine Shahriyar Hossain, Munirul Islam, Jesmin, and Hasan Jamil A Changing Window Approach to Exploring Gene Expression Patterns Qiang Wang, yunming ye, and Joshua Zhexue Huang Sample Clustering of Flow Cytometry Data Lin Liu, Li Xiong, James Lu, Kim Gernert, and Vicki Hertzberg Feature selection for tandem mass spectrum quality assessment Jiarui Ding, Jinhong Shi, AnMin Zou, and Fang‐Xiang Wu Integrative Protein Function Transfer using Factor Graphs and Heterogeneous Data Sources Antonina Mitrofanova, Vladimir Pavlovic, and Bud Mishra Session 3: Sequence Analysis and Systems Biology Systems Biology via Redescription and Ontologies (III): Protein Classification using Malaria Parasiteʹs Temporal Transcriptomic Profiles Antonina Mitrofanova, Samantha Kleinberg, Jane Carlton, Simon Kasif, and Bud Mishra Sampling Based Meta‐Algorithms for Accurate Multiple Sequence Alignment Vishal Thapar and Sanguthevar Rajasekaran Conservative, Non‐Conservative and Average Pairwise Statistical Significance of Local Sequence Alignment Ankit Agrawal and Xiaoqiu Huang A Graph Mining Algorithm for Classifying Chemical Compounds Winnie W. M. Lam and Keith C. C. Chan Synthetic Biology Design and Analysis: a Case Study of Frequency Entrained Biological Clock Peng Yu, Xi Chen, David Pan, and Andrew Ellington 11:35 – 1:00 Lunch 1:00 – 2:30 Panel Discussion with Program Managers/Directors 2:30 – 2:50 Coffee break 2:50 – 4:50 Session 1: Protein Structure, Function, and Interaction Boosting methods for Protein Fold Recognition:An Empirical Comparison Yazhene Krishnaraj and Chandan Reddy