CIBCB 2008 Program
Plenary Lecture:
Monday, September 15, 8:20AM-9:30AM, Room: Limelight B Ballroom, Chair: Scott Smith
Keynote: "Computational Discovery of Noncoding RNA", Professor Walter L. Ruzzo, University of Washington, Department of Computer Science & Engineering and Adjunct Professor in the Department of Genome Sciences
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Prof. Ruzzo received a B.S. (Mathematics) from the California Institute of Technology in 1968, Ph.D. (Computer Science) from the University of California at Berkeley in 1978, and has been with the University of Washington since 1977. His research interests initially were focused on algorithms and computational complexity theory, but migrated to computational biology more than a decade ago. |
Abstract: The famous "Central Dogma" of molecular biology posits that "DNA makes RNA makes protein," and proteins comprise the molecular machines enabling life. In the face of this, recent discoveries from the genome projects are puzzling: the vast majority of the human DNA is transcribed to RNA, but only a few percent of it codes for proteins. The overall significance of this remains unclear and controversial, but there are increasingly many cases where noncoding RNA (ncRNA) has proven to be functional in its own right, in diverse, sophisticated and unexpected ways, in all domains of life. Many ncRNAs belong to "families" defined by similarities in sequence, structure and function. Although function is not directly accessible computationally, shared sequence and structure motifs are, and development of computational tools is critical for their effective discovery. This is a challenging and multifaceted problem. Motif representation, inference and search are all important, as are algorithmic efficiency and incorporation of relevant biological knowledge. I will describe work in my lab on specific tools suited to various aspects of these problems, as well as their integration into comparative genomics "pipelines" for discovery of RNA elements, one focused on cis-regulatory elements in bacteria, another on vertebrates. These strategies recover most known cis-regulatory RNAs in bacteria. More importantly, we have discovered 5 new riboswitch families, now experimentally verified, plus over 20 other elements in a wide variety of bacteria (Yao, et al., 2007; Weinberg, et al. 2007). In vertebrate genomes, we have identified thousands of candidate regions that show stronger evidence for conservation at the RNA level than at the primary sequence level (Torarinsson, et al. 2008). Many biological and computational challenges remain.
Session M-AM1: RNA
Monday, September 15, 9:45AM-10:45AM, Room: Limelight B Ballroom, Chair: Scott Smith
| 9:45AM | SARNA-Predict-pk: Predicting RNA Secondary Structures Including Pseudoknots [#42] |
| Herbert H. Tsang and Kay C. Wiese | |
| Simon Fraser University, Canada | |
| 10:05AM | Classification of Mouse fRNA Genes Using Evolved Neural Networks [#43] |
| Mars Cheung and Gary B. Fogel | |
| Natural Selection, Inc., United States | |
| 10:25AM | A Hybrid Clustering/Evolutionary Algorithm for RNA Folding [#44] |
| Kay C. Wiese and Andrew Hendriks | |
| Simon Fraser University, Canada |
Session M-AM2: Sequence Analysis
Monday, September 15, 11:00AM-12:20PM, Room: Limelight B Ballroom, Chair: Gwenn Volkert
| 11:00AM | Classifying Synthetic and Biological DNA Sequences with Side Effect Machines [#10] |
| Daniel Ashlock and Elizabeth Warner | |
| University of Guelph, Canada; University of Guelph, Canada | |
| 11:20AM | An Information Theoretic Approach for the Discovery of Irregular and Repetitive Patterns in Genomic Data [#54] |
| Willard Davis, Ananth Kalyanaraman and Diane Cook | |
| Washington State University, United States | |
| 11:40AM | Exploring Chaos Automata for Protein Sequences [#59] |
| Deborah Stoffer and L. Gwenn Volkert | |
| Kent State University, United States | |
| 12:00PM | PCA-based Linear Combinations of Oligonucleotide Frequencies for Metagenomic DNA Fragment Binning [#12] |
| Hongwei Wu | |
| Georgia Institute of Technology, United States |
Session M-PM1: Microarray Analysis
Monday, September 15, 2:00PM-3:20PM, Room: Limelight B Ballroom, Chair: Gary Fogel
| 2:00PM | Evolution Strategy with Greedy Probe Selection Heuristics for the Non-Unique Oligonucleotide Probe Selection Problem [#8] |
| Lili Wang, Alioune Ngom, Robin Gras and Luis Rueda | |
| University of Windsor, Canada; Universidad de Concepcion, Chile | |
| 2:20PM | Temporal and Structural Analysis of Biological Networks in Combination with Microarray Data [#37] |
| Chang hun You, Lawrence Holder and Diane Cook | |
| Washington State University, United States | |
| 2:40PM | Cancer Classification with Incremental Gene Selection based on DNA Microarray Data [#46] |
| Jin-Hyuk Hong and Sung-Bae Cho | |
| Yonsei University, Korea (South) | |
| 3:00PM | A Graph-Based Representation of Gene Expression Profiles in DNA Microarrays [#25] |
| Alfredo Benso, Stefano Di Carlo, Gianfranco Politano and Luca Sterpone | |
| Politecnico di Torino, Italy |
Session M-PM2 : Network Analysis
Monday, September 15, 3:40PM-5:00PM, Room: Limelight B Ballroom, Chair: Kay Wiese
| 3:40PM | Network Motifs in Context: An Exploration of the Evolution of Oscillatory Dynamics in Transcriptional Networks [#56] |
| Jennifer Hallinan and Anil Wipat | |
| Newcastle University, United Kingdom | |
| 4:00PM | Combining Multiple Types of Biological Data in Constraint-Based Learning of Gene Regulatory Networks [#30] |
| Mehmet Tan, Mohammed AlShalalfa, Reda Alhajj and Faruk Polat | |
| University of Calgary, Canada; Middle East Technical University, Turkey | |
| 4:20PM | Reverse Engineering Time Series of Gene Expression Data Using Dynamic Bayesian Networks And Covariance Matrix Adaptation Evolution Strategy with Explicit Memory [#34] |
| Maryam Salehi, Alan Ableson and Parvin Mousavi | |
| First author, Canada; Second author, Canada; Third author, Canada | |
| 4:40PM | Reverse Engineering of the Transcriptional Subnetwork in the Yeast Cell Cycle Pathway Using Dynamic Bayesian Networks and Evolutionary Search [#47] |
| Maryam Salehi, Paul G. Young and Parvin Mousavi | |
| First author, Canada; Second author, Canada; Third author, Canada |
Special Session T-AM1: Data Mining Special Session I
Tuesday, September 16, 9:00AM-10:00AM, Room: Limelight B Ballroom, Chair: Sumeet Dua
| 9:00AM | Very Large Scale ReliefF for Genome-Wide Association Analysis [#7] |
| Margaret Eppstein and Paul Haake | |
| University of Vermont, United States | |
| 9:20AM | Fitness Directed Intervention Crossover Approaches applied to Bio-Scheduling Problems [#23] |
| Paul Godley, David Cairns, Julie Cowie and John McCall | |
| University of Stirling, Scotland; The Robert Gordon University, Scotland | |
| 9:40AM | Reassessing the genomic data integration limits for the prediction of protein-protein interactions in Saccharomyces Cerevisiae [#28] |
| Fiona Browne, Haiying Wang, Huiru Zheng and Francisco Azuaje | |
| University of Ulster, United Kingdom; Research Centre for Public Health, Luxembourg |
Special Session T-AM2: Data Mining Special Session II
Tuesday, September 16, 10:20AM-11:20AM, Room: Limelight B Ballroom, Chair: Sumeet Dua
| 10:20AM | Gene Ranking through the Integration of Synchronization Experiments [#57] |
| Alan Alex, Sumeet Dua and Pradeep Chowriappa | |
| Louisiana Tech University, United States | |
| 10:40AM | Distributed Peer-to-Peer Cooperative Partitional-Divisive Clustering for Gene Expression Datasets [#52] |
| Rasha Kashef and Mohamed Kamel | |
| University of Waterloo, ECE Department, Canada | |
| 11:00AM | 3D-Shape Analysis of the HIV-1 Protease Ligand Binding Site [#38] |
| Sunil Kumar, Rajni Garg, Srinivas Alla, Xiaoyu Zhang and Vivek Jalahalli | |
| San Diego State University, United States; California State University, San Marcos, United States |
Session T-PM1: Novel Problems/Approaches
Tuesday, September 16, 2:10PM-2:50PM, Room: Limelight B Ballroom, Chair: Dan Ashlock
| 2:10PM | Neuro-Fuzzy Classification of the Rhagoletis pomonella Species Group Using Digitized Wing Structure [#26] |
| Chengpeng Bi, Michael Saunders and Bruce McPheron | |
| Children's Mercy Hospital and Univ. of Missouri, United States; The Pennsylvania State University, United States | |
| 2:30PM | Methods and Strategies for Construction of a Phylogeny-Adaptive Hormone Response Element Consensus Model [#18] |
| Feng Lin, Jesslyn Saw and Maria Stepanova | |
| Nanyang Technological University, Singapore |
Session T-PM2: Proteins and Small Molecule Discovery
Tuesday, September 16, 3:10PM-4:30PM, Room: Limelight B Ballroom, Chair: Gary Fogel
| 3:10PM | Parallel multi-objective algorithms for the molecular docking problem [#36] |
| Jean-Charles Boisson, Laetitia Jourdan, El-Ghazali Talbi and Horvath Dragos | |
| INRIA Dolphin Project team, France; Bat. C9, USTL, France | |
| 3:30PM | A Wrapper Feature Selection Method Based on Simulated Annealing Algorithm for Prostate Protein Mass Spectrometry Data [#20] |
| Yifeng Li and Yihui Liu | |
| Shandong Institute of Light Industry, China | |
| 3:50PM | ProLoc-rGO: Using rule-based knowledge with Gene Ontology terms for prediction of protein subnuclear localization [#17] |
| Wen-Lin Huang, Chun-Wei Tung, Shih-Wen Ho and Shinn-Ying Ho | |
| WLH, Taiwan; CWT, Taiwan; SWH, Taiwan; SYH, Taiwan | |
| 4:10PM | Exploring 3D-QSAR Pharmacophore Mapping of Azaphenanthrenone derivatives for mPGES-1 inhibition Using HypoGen Technique [#35] |
| Winston Yu-Chen Chen, Po-Yuan Chen, Calvin Yu-Chian Chen and Jing-Gung Chung | |
| Department of Biological Science and Technology, Taiwan |
Plenary Poster Session Posters: Poster Presentations
Tuesday, September 16, 4:30PM-5:30PM, Room: Limelight B Ballroom, Chair: Gwenn Volkert
| Granular Decision Fusion Systems for Effective Protein Methylation Prediction [#55] | |
| Zejin Ding, You Feng, Yujun Zheng and Yan-Qing Zhang | |
| Computer Science Dept., Georgia State University, United States; Chemistry Dept., Georgia State University, United States | |
| Mining sequence features for DNA-binding site prediction [#16] | |
| Jing Hu and Yan Changhui | |
| Utah State University, United States | |
| Numerical Representation of DNA Sequences Based on Genetic Code Context [#3] | |
| Changchuan Yin and Stephen Yau | |
| University of Illinois at Chicago, United States | |
| Automated Optic Nerve Head Image Fusion of Nonhuman Primate Eyes Using Heuristic Optimization Algorithm [#45] | |
| Hua Cao, Bahram Khoobehi and S.S. Iyengar | |
| Louisiana State University, United States; LSUHSC, United States |
Session W-AM1: Hybrid Approachs
Wednesday, September 17, 9:00AM-10:00AM, Room: Limelight B Ballroom, Chair: Jennifer Hallinan
| 9:00AM | Discovering Novel Cancer Therapies: A Computational Modeling and Search Approach [#48] |
| Arthur Mahoney, Brian Smith, Nicholas Flann and Gregory Podgorski | |
| Utah State University, United States; Utah State Univesity, United States | |
| 9:20AM | Predicting Translation Initiation Sites Using a Multi-Agent Architecture Empowered with Reinforcement Learning [#15] |
| Jia Zeng and Reda Alhajj | |
| University of Calgary, Canada | |
| 9:40AM | Using Hybrid GA-ANN to Predict Biological Activity of HIV Protease Inhibitors [#51] |
| Srinivas Alla, Akmal Aulia, Sunil Kumar and Rajni Garg | |
| San Diego State University, United States; Cal State San Marcos, United States |
Special Session W-AM2: Special Session on EcoInformatics
Wednesday, September 17, 10:20AM-11:20AM, Room: Limelight B Ballroom, Chair: Gary Fogel
| 10:20AM | Transience in the Simulation of Ring Species [#11] |
| Daniel Ashlock, Taika VonKonigslow, Elizabeth Clare and Wendy Ashlock | |
| University of Guelph, Canada | |
| 10:40AM | Characterization of Extremal Epidemic Networks with Diffusion Characters [#13] |
| Daniel Ashlock and Colin Lee | |
| University of Guelph, Canada | |
| 11:00AM | A Model of Emotion in the Prisoner's Dilemma [#27] |
| Daniel Ashlock and Nicolas Rogers | |
| University of Guelph, Canada |
Special Lecture W-Close: Closing Remarks
Wednesday, September 17, 11:20AM-11:30AM, Room: Limelight B Ballroom, Speaker: Scott Smith
