CIBCB 2009 Program
Session CIBCB-1: Keynote Lecture
Monday, March 30, 9:30AM-10:30AM, Room: Hermitage D, Chair: Kay C. Wiese, Simon Fraser University, Canada
| 9:30AM | Bringing Biological Models to Life: The Power of Agent-based Modeling and Visualization |
| Christian Jacob | |
| University of Calgary, Canada |
Session CIBCB-2: NIH Invited Special Session and Panel
Monday, March 30, 11:00AM-1:00PM, Room: Hermitage D, Chair: Gary Fogel, Natural Selection, Inc., USA
| 11:00AM | CyberInfrastructure and Computational Intelligence: Recent Experience and Current Activities at NSF in Fostering Transformative Cyber-Enabled Research |
| Fahmida Chowdhury and Edward Seidel | |
| National Science Foundation, United States | |
| 11:30AM | Transforming Behavioral Medicine: Cyberinfrastructure in Cancer Prevention and Control |
| Abdul R. Shaikh and Bradford W. Hesse | |
| National Cancer Institute, National Institutes of Health, United States | |
| 12:00PM | A Role for Systems Science Methodologies in Addressing Complexity in Population Health |
| Patricia L. Mabry and Stephane Philogene | |
| National Institutes of Health, United States | |
| 12:30PM | NIH and BBTC Panel and Open Discussion |
| Gary Fogel and Fahmida Chowdhury | |
| NSI, United States; NSF, United States |
Session CIBCB-3: AI and Machine Learning in Bioinformatics 1
Monday, March 30, 2:00PM-4:00PM, Room: Hermitage D, Chair: Gary Fogel, Natural Selection, Inc., USA
| 2:00PM | rnaDesign: Local Search for RNA Secondary Structure Design [#6069] |
| Denny C. Dai, Herbert H. Tsang and Kay C. Wiese | |
| Simon Fraser University, Canada | |
| 2:24PM | SARNA-Ensemble-Predict: The Effect of Different Dissimilarity Metrics on a Novel Ensemble-based RNA Secondary Structure Prediction Algorithm [#6063] |
| Herbert H. Tsang and Kay C. Wiese | |
| Simon Fraser University, Canada | |
| 2:48PM | Performance Prediction for RNA Design Using Parametric and Non-Parametric Regression Model [#6012] |
| Denny C. Dai and Kay C. Wiese | |
| Simon Fraser University, Canada | |
| 3:12PM | An Approach for RNA Secondary Structure Prediction Based on Bayesian Network [#6033] |
| Tianhua Wu, Zhidong Deng and Dandan Song | |
| Tsinghua University, China |
Session CIBCB-4: Sequence and Phylogenetic Analysis
Monday, March 30, 4:30PM-6:30PM, Room: Hermitage D, Chair: Gwenn Volkert, Kent State University, USA
| 4:30PM | Haplotype Inference Using A Genetic Algorithm [#6026] |
| Dongsheng Che, Haibao Tang and Yinglei Song | |
| East Stroudsburg University, United States; University of Georgia, United States; University of Maryland Eastern Shore, United States | |
| 4:54PM | DNA Error Correcting Codes: No Crossover. [#6015] |
| Daniel Ashlock and Sheridan Houghten | |
| University of Geulph, Canada; Brock University, Canada | |
| 5:18PM | Detecting Sequence and Structure Homology via an Integrative Kernel: A Case-Study in Recognizing Enzymes [#6018] |
| Isye Arieshanti, Mikael Boden, Stefan Maetschke and Fabian Buske | |
| The University of Queensland, Institute for Molecular Bioscience, Australia | |
| 5:42PM | A Novel LDA and PCA-based Hierarchical Scheme for Metagenome Fragment Binning [#6074] |
| Hao Zheng and Hongwei Wu | |
| Georgia Institute of Technology, United States | |
| 6:06PM | Using Diffusion Characters for the Taxonomy of Self-Organizing Social Networks [#6032] |
| Daniel Ashlock and Colin Lee | |
| University of Geulph, Canada; University of Guelph, Canada |
Session CIBCB-5: Protein and RNA Structure Prediction, Folding and Docking
Tuesday, March 31, 8:30AM-10:30AM, Room: Hermitage D, Chair: Kay C. Wiese, Simon Fraser University, Canada
| 8:30AM | Improved Prediction of Trans-Membrane Spans in Proteins using an Artificial Neural Network [#6052] |
| Julia Koehler, Ralf Mueller and Jens Meiler | |
| Vanderbilt University, United States | |
| 8:54AM | Protein Fold Recognition with Adaptive Local Hyperplane Algorithm [#6006] |
| Vojislav Kecman and Tao Yang | |
| The Virginia Commonwealth University, United States; The University of Auckland, New Zealand | |
| 9:18AM | Protein Secondary Structure Prediction Using Rule Induction from Coverings [#6039] |
| Leong Lee, Jennifer L. Leopold, Ronald L. Frank and Anne M. Maglia | |
| Missouri University of Science and Technology, United States | |
| 9:42AM | Bioinformatics: Implementation of a proposed upgraded Smith-Waterman Algorithm for local alignment [#6013] |
| Md. Shihabuddin Sadi, Abu Zafar Mohammad Sami, Imtiaz Uddin Ahmed, Abdullahil Baki Md. Ruhunnabi and Nirmalendu Das | |
| Shah Jalal University of Science and Technology, Bangladesh |
Session CIBCB-6: AI and Machine Learning in Bioinformatics 2
Tuesday, March 31, 11:00AM-1:00PM, Room: Hermitage D, Chair: Kay C. Wiese, Simon Fraser University, Canada
| 11:00AM | Diagnostic Character Location within the Cryptic Skipper Butterfly Species Complex with an Evolutionary Algorithm [#6056] |
| Daniel Ashlock and Taika von Konigslow | |
| University of Geulph, Canada | |
| 11:24AM | A Method for Improving Protein Localization Prediction from Datasets with Outliers [#6022] |
| Jiang Tian, Hong Gu and WenQi Liu | |
| Dalian University of Technology, China | |
| 11:48AM | A Framework for the Application of Decision Trees to the Analysis of SNPs Data [#6048] |
| Linda Fiaschi, Jon Garibaldi and Natalio Krasnogor | |
| University of Nottingham, United Kingdom | |
| 12:12PM | Predicting Protein Subcellular Locations for Gram-Negative Bacteria Using Neural Networks Ensemble [#6076] |
| Junwei Ma, WenQi Liu and Hong Gu | |
| Dalian University of Technology, China |
Session CIBCB-7: AI and Machine Learning in Bioinformatics 3
Tuesday, March 31, 2:00PM-4:00PM, Room: Hermitage D, Chair: Kay C. Wiese, Simon Fraser University, Canada
| 2:00PM | A System for Recognition of Biological Patterns in Toxins Using Computational Intelligence [#6050] |
| Bernardo Carvalho, Thais Mendes, Ricardo Ribeiro, Ricardo Fortuna, Jose Veneroso and Mauricio Mudado | |
| ABG Information Systems, Brazil; Fundacao Ezequiel Dias, Brazil | |
| 2:24PM | Comparison of Feature Selection Techniques for Viral DNA Replication Origins Prediction [#6064] |
| Raul Cruz-Cano and Ming-Ying Leung | |
| Texas A and M University - Texarkana, United States; The University of Texas at El Paso, United States | |
| 2:48PM | Predicting Protein-Protein Interactions using Numerical Associational Features [#6070] |
| Waleed Aljandal, William Hsu and Jing Xia | |
| kansas State University, United States |
Session CIBCB-8: Gene Finding and Microarray Analysis 1
Tuesday, March 31, 4:30PM-6:30PM, Room: Hermitage D, Chair: Wendy Ashlock, University of Geulph, Canada
| 4:30PM | Simulation of the Impact of Retroviruses on Genome Organization of an Artificial Organism [#6041] |
| Daniel Ashlock and Wendy Ashlock | |
| University of Geulph, Canada; York University, Canada | |
| 4:54PM | A Simple Algorithm for (l, d) Motif Search [#6062] |
| Dolly Sharma and Sanguthevar Rajasekaran | |
| University of Connecticut, United States | |
| 5:18PM | Degenerate Primer Selection Algorithms [#6061] |
| Dolly Sharma, Sudha Balla, Sanguthevar Rajasekaran and Nikoletta DiGirolamo | |
| University of Connecticut, United States; 2Sloan-Kettering Institute, United States; Hunter College, United States | |
| 5:42PM | An Automatic Gene Ontology Software Tool for Bicluster and Cluster Comparisons [#6073] |
| Fadhl Al-Akwaa and Yasser Kadah | |
| University of Science and Technology, Yemen; Cairo University and Nile University, Egypt |
Session CIBCB-9: Gene Finding and Microarray Analysis 2
Wednesday, April 1, 8:30AM-10:30AM, Room: Hermitage D, Chair: Jennifer Hallinan, Newcastle University, UK
| 8:30AM | A Multi-Threaded DNA Tag/Anti-tag Library Generator for Multi-Core Platforms [#6051] |
| Arun Ravindran and Daniel Burns | |
| University of North Carolina at Charlotte, United States; Air Force Research Laboratory, Rome, NY, United States | |
| 8:54AM | The Analysis of Microarray Datasets Using a Genetic Programming [#6028] |
| Chun-Gui Xu, Kun-Hong Liu, Jie Gui and De-Shuang Huang | |
| Intelligent Computing Lab, Hefei Institute of Intelligent Machines, Chinese Academy of Sciences, China; Software Department, Xiamen University, China | |
| 9:18AM | Steady-state Analysis of Genetic Regulatory Networks Modeled by Nonlinear Ordinary Differential Equations [#6036] |
| Haixin Wang, Lijun Qian and Edward Dougherty | |
| Fort Valley State Univeristy, United States; Prairie View AM University, United States; Translational Genomics Research Institute, United States | |
| 9:42AM | Goal Driven Analysis of cDNA Microarray Data [#6025] |
| Youlian Pan, Jitao Zou, Yi Huang, Ziying Liu and Sieu Phan | |
| National Research Council Canada, Canada |
Session CIBCB-10: Analysis of Very Large Biological Data Sets 1
Wednesday, April 1, 11:00AM-1:00PM, Room: Hermitage D, Chair: Daniel Ashlock, University of Guelph, Canada
| 11:00AM | Fuzzy Rule Base Classifier Fusion for Protein Mass Spectra Based Ovarian Cancer Diagnosis [#6079] |
| Amin Assareh and L. Gwenn Volkert | |
| Kent State Universtiy, United States; Kent State University, United States | |
| 11:24AM | Assessing the Impact of Network Depth on the Analysis of PPI Networks: A Case Study [#6046] |
| Jaine Blayney, Haiying Wang, Huiru Zheng and Francisco Azuaje | |
| University of Ulster, Northern Ireland; Public Research Centre for Health, Luxembourg | |
| 11:48AM | Nerve Graft Selection for Peripheral Nerve Regeneration using Neural Networks Trained by a Hybrid ACO/PSO Method [#6009] |
| Matthew Conforth, Yan Meng, Chandra Valmikinathan and Xiaojun Yu | |
| Stevens Institute of Technology, United States | |
| 12:12PM | An Assignment Walk through 3D NMR Spectrum [#6040] |
| Marta Szachniuk, Mariusz Popenda, Ryszard Adamiak and Jacek Blazewicz | |
| Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poland; Institute of Computing Science, Poznan University of Technology, Poland | |
| 12:36PM | An Application of the Metric Access Methods to the Mass Spectrometry Data [#6005] |
| Jiri Novak and David Hoksza | |
| Charles University in Prague, Czech Republic |
Session CIBCB-11: Analysis of Very Large Biological Data Sets 2
Wednesday, April 1, 2:00PM-4:00PM, Room: Hermitage D, Chair: Anil Wipat, Newcastle University, Canada
| 2:00PM | Clustering Incorporating Shortest Paths Identifies Relevant Modules in Functional Interaction Networks [#6071] |
| Jennifer Hallinan, Matthew Pocock, Steven Addinall, David Lydall and Anil Wipat | |
| Newcastle University, United Kingdom | |
| 2:24PM | Modeling oncology gene pathways network with multiple genotypes and phenotypes via a copula method [#6019] |
| Le Bao, Zhou Zhu and Jingjing Ye | |
| Department of Statistics, University of Washington, Seattle, United States; Pfizer Global Research and Development, Pfizer Inc., United States | |
| 2:48PM | Fast Algorithms for Detecting Overlapping Functional Modules in PPI Networks [#6007] |
| Peng gang Sun and Lin Gao | |
| Xidian University, China | |
| 3:12PM | Application of Machine Learning Approaches on Quantitative Structure Activity Relationships [#6067] |
| Mariusz Butkiewicz, Ralf Mueller, Danilo Selic, Eric Dawson and Jens Meiler | |
| Vanderbilt University, United States | |
| 3:36PM | DDPIn - Distance and Density Based Protein Indexing [#6030] |
| David Hoksza | |
| Charles University in Prague, Czech Republic |
Session CIBCB-12: Medical Imaging
Wednesday, April 1, 4:30PM-6:30PM, Room: Hermitage D, Chair: Daniel Ashlock, University of Guelph, Canada
| 4:30PM | Knee MR Image Segmentation Combining Contextual Constrained Neural Network and Level Set Evolution [#6047] |
| Lan Haw-Chang, Chang Tsai-Rong, Liao Wen-Ching, Chung Yi-Nung and Chung Pau-Choo | |
| Dept. of Radiology, Taichung Veterans General Hospital, Taiwan; Dept. of Computer Science and Information Engineering, South Taiwan University, Taiwan; Dept. of Electrical Engineering, National Cheng Kung University, Taiwan; Dept. of Electrical Engineering, National Changhua University of Education, Taiwan |
|
| 4:54PM | Emotion Recognition with Consideration of Facial Expressions and Physiological Signals [#6044] |
| Chuan-Yu Chang, Jeng-Shiun Tsai, Chi-Jane Wang and Pau-Choo Chung | |
| National Yunlin University of Science and Technology, Taiwan; National Cheng Kung University, Taiwan | |
| 5:18PM | Statistical Comparison of Color Model Classifier Pairs in Hematoxylin and Eosin Stained Histological Images [#6058] |
| Mutlu Mete and Umit Topaloglu | |
| University of Arkansas for Medical Sciences, United States | |
| 5:42PM | Shape Modeling and Clustering of White Matter Fiber Tracts Using Fourier Descriptors [#6023] |
| Xuwei Liang, Qi Zhuang, Ning Cao and Jun Zhang | |
| University of Kentucky, United States | |
| 6:06PM | Data Synthesis and Tool Development for Exploring Imaging Genomic Patterns [#6068] |
| Sungeun Kim, Li Shen, Andrew Saykin and John West | |
| Indiana University, United States |
IEEE SSCI 2009 March 30 – April 2, 2009 Sheraton Music City Hotel, Nashville, TN, USA
