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

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, 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, 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 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

Images based system for surface matching in macromolecular screening Ivan Merelli, Paolo Cozzi, Luciano Milanesi, Daniele DʹAgostino, and Andrea Clematis

Structure Based Functional Analysis of Bacteriophage f1 Gene V Protein Majid Masso, Ewy Mathe, Nida Parvez, Kahkeshan Hijazi, and Iosif Vaisman

Identifying Calcium‐binding Sites with Oxygen‐Carbon Shell Geometric and Chemic Criteria ‐ A Graph‐based Approach Hui Liu and Hai Deng

Combining Hierarchical Inference in Ontologies with Heterogeneous Data Sources Improves Gene Function Prediction Xiaoyu Jiang, Naoki Nariai, Martin Steffen, Simon Kasif, David Gold, and Eric Kolaczyk

Evaluating Protein Sequence Signatures Inferred from Protein‐Protein Interaction Data by Gene Ontology Annotations Osamu Maruyama, Hideki Hirakawa, Takao Iwayanagi, Yoshiko Ishida, Shizu Takeda, Jun Otomo, and Satoru Kuhara

Document Classification for Mining Host Pathogen Protein‐Protein Interactions Guixian Xu, Lanlan Yin, Manabu Torii, Zhendong Niu, Cathy Wu, Zhang‐Zhi Hu, and HongFang Liu

LogCHEM: Interactive Discriminative Mining of Chemical Structure Vitor Costa, Nuno Fonseca, and Rui Camacho

Session 2: Genome Data Analysis

Genome‐Scale Functional Annotation from Meta‐Analysis of Microarray Datasets Gyan Srivastava, Jing Qiu, and Dong Xu

Improvement of Survival Prediction from Gene Expression Profiles by Mining of Prior Knowledge Siyuan Ren and Zoran Obradovic

Systematic Evaluation of Scaling Methods for Gene Expression Data Gaurav Pandey, Lakshmi N. Ramakrishnan, Michael Steinbach, and Vipin Kumar Estimating Missing Value in Microarray Data Using Fuzzy Clustering and Gene Ontology Azadeh Mohammadi and Mohammad hossein Saraee

Fast gene selection for microarray data using SVM‐based evaluatin criterion Xin Zhou, Xingye Wu, Kezhi Mao, and David Tuck

Genome‐wide DNA‐binding specificity of PIL5, a Arabidopsis basic helix‐loop‐ helix (bHLH) transcription factor Hyojin Kang, Eunkyoo Oh, Giltsu Choi, and Doheon Lee

Genome alignments using MPI‐LAGAN Ruinan Zhang, Huzefa Rangwala, and George Karypis

2:50 – 4:50 Tutorial Session 4: Jundong Liu, Tutorial on Brain MRI Data Analysis

4:50 – 5:00 Coffee break

5:00 – 6:15 Session 1: Computational Systems Biology

Protein‐protein interaction network alignment by quantitative simulation Perry Evans, Ted Sandler, and Lyle Ungar

Reconstruction of post‐transcriptional regulatory signals in E. coli Rui‐Sheng Wang, Guanxu Jin, Xiang‐Sun Zhang, and Luonan Chen

A Functional Network of Yeast Genes Using Gene Ontology Information Erliang Zeng, Lisa Schneper, Kalai Mathee, and Giri Narasimhan

Estimating regulatory associations of genomic loci and biological pathways in lymphoblastoid cells Jung Hoon Woo, Eunjee Lee, Sung Bum Cho, and Ju Han Kim

Partial Order‐Based Bayesian Network Learning Algorithm for Estimating Gene Networks Kazuyuki Numata, Seiya Imoto, and

Session 2: Biomedical Text Mining and Ontologies Research

Multiway clustering for creating biomedical term sets Vasileios Kandylas, Lyle Ungar, Ted Sandler, and Shane Jensen

Online Biomedical Concept Annotation Using Language Model Mapping Lawrence Reeve, Hyoil Han, and Ari Brooks

Detecting Duplicate Biological Entities using Markov Random Field‐based Edit Distance Min Song

iProLINK: A Framework for Linking Text Mining with Ontology and Systems Biology Zhang‐Zhi Hu, K. Bretonnel Cohen, Lynette Hirschman, , HongFang Liu, and Cathy Wu

Extracting Protein‐Protein Interactions from MEDLINE Using Syntactic Roles Syed Toufeeq Ahmed, Hasan Davulcu, and Chitta Baral

6:15 – 6:25 Coffee break and closing