REG1: Registration
Sunday, May 2, 5:00PM-7:00PM, Room: Petit Opus, Chair: Daniel Ashlock
REG2: Registration
Monday, May 3, 7:30AM-3:00PM, Room: Petit Opus, Chair: Andrew McEachern
Tutorial T1: Molecular Biology for Computer Scientists
Monday, May 3, 8:00AM-9:30AM, Room: Printemps, Instructor: Suprakash Datta
Tutorial T2: R for Bioinformaticians
Monday, May 3, 9:30AM-11:00AM, Room: Printemps, Instructor: Paul McNicholas
Tutorial T3: Opportunities in computational biology presented by DNA barcoding
Monday, May 3, 11:00AM-12:30PM, Room: Printemps, Instructor: Taika von Konigslow
Workshop LUNCH1: Lunch Break
Monday, May 3, 12:30PM-2:00PM, Room: Printemps, Chair: Daniel Ashlock
Tutorial T4: Phylogenetic Inference and Evolutionary Computation
Monday, May 3, 2:00PM-3:30PM, Room: Printemps, Instructor: Clair Bates-Congdon
Tutorial T6: Representation for Evolutionary Computation in Bioinformatics
Monday, May 3, 3:30PM-5:00PM, Room: Printemps, Instructor: Daniel Ashlock
Tutorial T5: Making Sense of Support Vector Machines
Monday, May 3, 5:00PM-6:30PM, Room: Printemps, Instructor: Stefan Kremer
REG3: Registration
Tuesday, May 4, 7:30AM-3:00PM, Room: Petit Opus, Chair: Taika von Konigslow
AMN1: Welcome
Tuesday, May 4, 8:00AM-8:30AM, Room: Printemps, Chair: Daniel Ashlock
Plenary Talk PL: Keynote Speech
Tuesday, May 4, 8:30AM-9:30AM, Room: Printemps, Speaker: Daniel Ashlock
Tutorial BK1: Coffee Break
Tuesday, May 4, 9:30AM-10:00AM, Room: Printemps, Instructor: Daniel Ashlock
Session TK1: Microarray Technology
Tuesday, May 4, 10:00AM-12:00PM, Room: Printemps, Chair: Steve Corns
| 10:00AM | New Approaches to Clustering Microarray Time-Series Data Using Multiple Expression Profile Alignment [#36] |
| Numanul Subhani, Luis Rueda, Alioune Ngom and Conrad Burden | |
| University of Windsor, Canada; The Australian National University, Australia | |
| 10:20AM | Supervised Learning of Maternal Cigarette-Smoking Signatures from Placental Gene Expression Data: A Case Study [#1] |
| Chengpeng Bi, Carrie Vyhlidal and Steve Leeder | |
| Children's Mercy Hospital, United States | |
| 10:40AM | Towards a Temporal Modeling of the Genetic Network Controlling Systemic Acquired Resistance in Arabidopsis thaliana [#4] |
| Alain Tchagang, Heather Shearer, Sieu Phan, Hugo Berube, Fazel Famili, Pierre Fobert and Youlian Pan | |
| Institute for Information Technology, National Research Council, Canada; Plant Biotechnology Institute, National Research Council, Canada | |
| 11:00AM | Support Vectors Based Correlation Coefficient for Gene and Sample Selection in Cancer Classification [#19] |
| Piyushkumar Mundra and Jagath Rajapakse | |
| Nanyang Technological University, Singapore | |
| 11:20AM | Additive Noise Analysis on Microarray Data via SVM Classification [#60] |
| Zejin Ding and Yan-Qing Zhang | |
| Department of Computer Science, GSU, United States; Georgia State University, United States | |
| 11:40AM | Missing Value Imputation Methods for Gene-Sample-Time Microarray Data Analysis [#40] |
| Yifeng Li, Alioune Ngom and Luis Rueda | |
| University of Windsor, Canada |
Workshop Lunch2: Luncheon Break
Tuesday, May 4, 12:00PM-1:30PM, Room: Printemps, Chair: Daniel Ashlock
Session TK2: Proteomics and Protein Structure
Tuesday, May 4, 1:30PM-3:30PM, Room: Printemps, Chair: Gary Fogel
| 1:30PM | Searching for a Single Mathematical Function to Address the Nonlinear Retention Time Shifts Problem in nanoLC-MS Data: Fuzzy-Evolutionary Computational Proteomics Approach [#11] |
| Alan Barton | |
| National Research Council Canada, Canada | |
| 1:50PM | Exploring structural modeling of proteins for kernel-based enzyme discrimination [#3] |
| Marco Alvarez and Changhui Yan | |
| Utah State University, United States; North Dakota State University, United States | |
| 2:10PM | DGA: Decomposition with Genetic Algorithm for Multiple Sequence Alignment [#8] |
| Farhana Naznin, Ruhul Sarker and Daryl Essam | |
| University of New South Wales at the Australian Defence Force Academy, Australia | |
| 2:30PM | Integrating Multiple Scoring Functions to Improve Protein Loop Structure Conformation Space Sampling [#10] |
| Yaohang Li, Ionel Rata and Jakobsson Eric | |
| North Carolina Agricultural and Technical State University, United States; University of Illinois at Urbana-Champaign, United States | |
| 2:50PM | Classification of HIV-1 Protease Crystal Structures Using Random Forest, Linear Discriminant Analysis and Logistic Regression [#12] |
| Gene M. Ko, A. Srinivas Reddy, Sunil Kumar, Barbara A. Bailey and Rajni Garg | |
| San Diego State University, United States | |
| 3:10PM | Speeding up Subcellular Localization by Extracting Informative Regions of Protein Sequences for Profile Alignment [#31] |
| Wei Wang, Manwai Mak and Sunyuan Kung | |
| The Hong Kong Polytechnic University, Hong Kong; Hong Kong Polytechnic University, Hong Kong; Princeton University, United States |
Session TK3: Molecular Dynamics
Tuesday, May 4, 3:30PM-4:50PM, Room: Printemps, Chair: Wendy Ashlock
| 3:30PM | Improved PCR Design for Mouse DNA by Training Finite State Machines [#54] |
| Steven Corns and Salik Yadav | |
| Missouri University of Science and Technology, United States | |
| 3:50PM | Predicting Chemical Activities From Structures by Attributed Molecular Graph Classification [#20] |
| Qian Xu, Hao Hu, Hong Xue and Qiang Yang | |
| Hong Kong University of Science and Technology, Hong Kong | |
| 4:10PM | Machine Learning Approaches for Customized Docking Scores: Modeling of Inhibition of Mycobacterium tuberculosis Enoyl Acyl Carrier Protein Reductase [#53] |
| Gary B. Fogel, Jonathan Tran, Stephen Johnson and David Hecht | |
| Natural Selection, Inc., United States; Southwestern College, United States | |
| 4:30PM | Principal Components Analysis Filters Functionally Significant Peroxidase Motions [#65] |
| Monique Laberge and Istvan Kovesi | |
| RMC St-Jean, Canada; Semmelweis University, Hungary |
Session TK4: RNA Structure and Function
Tuesday, May 4, 4:50PM-5:50PM, Room: Printemps, Chair: Kay Weise
| 4:50PM | Expanded Study of efn2 Thermodynamic Model Performance on RnaPredict, an Evolutionary Algorithm for RNA Folding [#32] |
| Kay Wiese and Andrew Hendriks | |
| Simon Fraser University, Canada | |
| 5:10PM | Computation Intelligence Method to Find Generic Non-coding RNA Search Models [#44] |
| Jennifer Smith | |
| Boise State University, United States | |
| 5:30PM | An Exploration of Individual RNA Structural Elements in RNA Gene Finding [#45] |
| Nicholas Erho and Kay Wiese | |
| Simon Fraser University, Canada |
Plenary Poster Session POS: Poster Session
Tuesday, May 4, 7:30PM-8:00PM, Room: Automne, Chair: Daniel Ashlock
| P101 | Functional Data Classification for Temporal Gene Expression Data with Kernel-Induced Random Forests [#16] |
| Guangzhe Fan, Jiguo Cao and Jiheng Wang | |
| University of Waterloo, Canada; Simon Fraser University, Canada | |
| P102 | A Comparative Study of the Time-Series Data for Inference of Gene Regulatory Networks Using B-Spline [#9] |
| Haixin Wang, James Glover and Lijun Qian | |
| Fort Valley State University, United States; Prairie View AM University, United States | |
| P103 | A Discrete Fourier Transform Method for Alignment of Visual Evoked Potentials [#59] |
| Ismet Sahin and Nuri Yilmazer | |
| University of Maryland, United States; Texas A and M University-Kingsville, United States | |
| P104 | Paroxysmal Atrial Fibrillation Diagnosis Based on Feature Extraction and Classification [#56] |
| Bahareh Pourbabaee and Caro Lucas | |
| Center of Nonlinear Dynamics, Department of Physiology, McGill University, Canada; Control and Intelligent Processing Center of Excellence, Electrical and Computer Engineering Department, University of Tehran, Iran | |
| P105 | Identification Of A Gene Expression Core Signature For Duchenne Muscular Dystrophy (DMD) Via Integrative Analysis Reveals Novel Potential Compounds For Treatment [#17] |
| Noru Ichim-Moreno, Manuel Aranda and Christian Voolstra | |
| KAUST, Saudi Arabia | |
| P106 | Applying neural networks to classify influenza virus antigenic types and hosts [#62] |
| Pavan Kumar Attaluri, Zhengxin Chen and Guoqing Lu | |
| University of Nebraska at Omaha, United States | |
| P107 | Issues with the PipeAlign Phylogenomics Toolkit in Identifying Protein Subfamilies [#38] |
| Christine Kehyayan and Gregory Butler | |
| Concordia University, Canada | |
| P108 | Using Decision Tree Learning to Study the Convergence of Phylogenetic Analyses [#50] |
| Grant Brammer and Tiffani Williams | |
| TAMU, United States | |
| P109 | Sequence Transformation to a Complex Signature Form for Consistent Phylogenetic Tree Using Extensible Markov Model [#13] |
| Rao M. Kotamarti, Michael Hahsler, Douglas W. Raiford and Margaret H. Dunham | |
| Southern Methodist University, United States; University of Montana, United States | |
| P110 | Modular Clustering of Protein-Protein Interaction Networks [#5] |
| Nassim Sohaee and Christian Forst | |
| University of Texas, Southwestern Medical Center, United States; University of Texas Southwestern Medical Center, United States |
BNQ: Banquet
Tuesday, May 4, 8:00PM-10:00PM, Room: Ete, Chair: Gary Yen
Session D1: Side Effect Machines
Wednesday, May 5, 8:00AM-9:20AM, Room: Printemps, Chair: Justin Shonfeld
| 8:00AM | Side Effect Machines for Quaternary Edit Metric Decoding [#21] |
| Joseph Brown, Sheridan Hougthen and Daniel Ashlock | |
| University of Guelph, Canada; Brock University, Canada | |
| 8:20AM | Nearest Neighbor Training of Side Effect Machines for Sequence Classification [#23] |
| Daniel Ashlock and Andrew McEachern | |
| University of Guelph, Canada | |
| 8:40AM | Detecting Retroviruses Using Reading Frame Information And Side Effect Machines [#52] |
| Wendy Ashlock and Suprakash Datta | |
| York University, Canada | |
| 9:00AM | Classifying Cytochrome C Oxidase Subunit 1 by Translation Initiation Mechanism using Side Effect Machines [#58] |
| Daniel Ashlock and Justin Schonfeld | |
| University of Guelph, Canada |
Tutorial BK4: Coffee Break
Wednesday, May 5, 9:20AM-9:50AM, Room: Printemps, Instructor: Daniel Ashlock
Session D2: Medical Informatics
Wednesday, May 5, 9:50AM-11:50AM, Room: Printemps, Chair: Stefan Kremer
| 9:50AM | Simulation of Oscillatory Dynamics of Blood Testosterone Levels Using the Crossover Method [#26] |
| Amit Sabnis and Robert Harrison | |
| Georgia State University, United States | |
| 10:10AM | Modeling Treatment and Drug Effects at The Molecular Level Using Hybrid System Theory [#29] |
| Xiangfang Li, Lijun Qian and Edward Dougherty | |
| Texas A and M University, United States; Prairie View AM University, United States; Texas A and M University and TGEN, United States | |
| 10:30AM | Mixing Patterns in a Global Influenza A Virus Network using Whole Genome Comparisons [#43] |
| Adrienne E Breland, Mehmet H Gunes, Karen A Schlauch and Frederick C. Harris | |
| University of Nevada, Reno, United States | |
| 10:50AM | Neural Grammar Networks for Toxicology [#48] |
| Christopher Cameron, Eddie Ma and Stefan Kremer | |
| University of Guelph, Canada; University of Waterloo, Canada | |
| 11:10AM | A fitness-independent evolvability measure for evolutionary developmental systems [#15] |
| Yaochu Jin and Jens Trommler | |
| Honda Research Institute Europe, Germany; Technical University of Darmstadt, Germany | |
| 11:30AM | Super-Resolution of Mammograms [#35] |
| Jun Zheng, Olac Fuentes and Ming-Ying Leung | |
| The University of Texas at El Paso, United States |
Session D3: Machine Learning in Bioinformatics
Wednesday, May 5, 11:50AM-12:50PM, Room: Printemps, Chair: Daniel Ashlock
| 11:50AM | Identifying Essential Features for the Classification of Real and Pseudo MicroRNAs Precursors Using Fuzzy Decision Trees [#24] |
| Na'el Abu-halaweh and Robert Harrison | |
| Georgia State University, United States | |
| 12:10PM | A Regression Tree-based Gibbs Sampler to Learn the Regulation Programs in a Transcription Regulatory Module Network [#25] |
| Jianlong Qi, Tom Michoel and Gregory Butler | |
| Concordia University, Canada; Ghent University, Belgium | |
| 12:30PM | Improved Prediction of Transcription Binding Sites from Chromatin Modification Data [#49] |
| Kengo Sato, Tom Whitington, Timothy Bailey and Paul Horton | |
| AIST, Japan; University of Queensland, IMB, Australia |