IEEE CIBCB 2006 Program
CIBCB 2006 Program
Plenary Talk PL1: Genome-Wide Genetic Analysis using Computational Intelligence:The Importance of Expert Knowledge
Thursday, September 28, 9:00AM-10:00AM, Room: Northern Lights Ballroom, Speaker: Dan Ashlock
Session A: Protein-Protein Interaction
Thursday, September 28, 10:20AM-12:00PM, Room: Northern Lights Ballroom, Chair: Jagath Rajapakse
| 10:20AM | Predicting Protein-Protein Interface using Desolvation Energy Similarity Matching [#1043] |
| Yasir Arafat, Gour Karmakar, Joarder Kamruzzaman and Juan Fernandez-Recio | |
| FIT, Monash University, Australia; Institute of Biomedical Research, IRB-PCB, Spain | |
| 10:40AM | A Hidden Markov Model Approach to Identifying HTH Motifs Using Protein Sequence and Predicted Solvent Accessibility [#1046] |
| Changhui Yan and Jing Hu | |
| Utah State University, United States | |
| 11:00AM | A method to integrate, assess and characterize the protein-protein interactions [#1051] |
| Fa Zhang, Lin Xu, Jingchun Chen, Liu Zhiyong and Bo Yuan | |
| The Institute of Computing Technology, China; The Ohio State University, United States; National Natural Science Foundation of China, China | |
| 11:20AM | Fuzzy C-means for inferring functional coupling of proteins from their phylogenetic profiles [#1118] |
| Juan Carlos Fernandez, Edgar E. Vallejo and Enrique Morett | |
| ITESM Campus Estado de Mexico, Mexico; Instituto de Biotecnologia UNAM, Mexico | |
| 11:40AM | Protein-Protein Interface Residue Prediction with SVM Using Evolutionary Profiles and Accessible Surface Areas [#1042] |
| Minh Nguyen and Jagath Rajapakse | |
| Nanyang Technological University, Singapore |
Session B: Cancer and Disease Informatics
Thursday, September 28, 1:30PM-3:10PM, Room: Northern Lights Ballroom, Chair: Hu Pingahao
| 1:30PM | Classification of Relapse Ovarian Cancer on MALDI-TOF Mass Spectrometry Data [#1087] |
| Jung Hun Oh, Animesh Nandi, Prem Gurnani, Lynne Knowles and John Schorge | |
| The University of Texas at Arlington, United States; UT Southwestern Medical Center, United States | |
| 1:50PM | A Swarm Intelligence Based Algorithm for Proteomic Pattern Detection of Ovarian Cancer [#1050] |
| Yan Meng | |
| Stevens Institute of Technology, United States | |
| 2:10PM | Aggregating Homologous Protein Families in Evolutionary Reconstructions of Herpesviruses [#1032] |
| Boris Mirkin, Renata Camargo, Trevor Fenner, George Loizou and Paul Kellam | |
| Birkbeck University of London, United Kingdom; University College of London, United Kingdom | |
| 2:30PM | Feature Selection Approach for Quantitative Prediction of Transcriptional Activities [#1104] |
| Ashish Anand, Gary Fogel, Ke Tang and Ponnuthurai Nagaratnam Suganthan | |
| Nanyang Technological University, Singapore; Natural Selection Inc., La Jolla, CA, United States | |
| 2:50PM | Integrating Affymetrix microarray data sets using probe-level test statistic for predicting prostate cancer [#1023] |
| Pingzhao Hu, Celia Greenwood and Joseph Beyene | |
| The Hospital for Sick Children, Canada; University of Toronto, Canada |
CIBCB Poster Session
Thursday, September 28, 4:00PM-6:00PM, Room: Northern Lights Ballroom, Chair: Dan Ashlock
| A Fuzzy Kohonen SOM Implementation and Clustering of Bio-active Compound Structures for Drug Discovery [#1069] | |
| Jehan Zeb Shah and Naomie bt Salim | |
| FSKSM, Universiti Teknologi Malaysia, Malaysia | |
| Optimization of the Sliding Window Size for Protein Structure Prediction [#1028] | |
| Ke Chen, Lukasz Kurgan and Jishou Ruan | |
| University of Alberta, Canada; Nankai University, China | |
| Iris Recognition Algorithm Optimized for Hardware Implementation [#1039] | |
| Kamil Grabowski, Wojciech Sankowski, Malgorzata Napieralska, Mariusz Zubert and Andrzej Napieralski | |
| Technical University of Lodz, DMCS, Poland | |
| Using Artificial Neural Networks to Predict Claim Duration in a Work Injury Compensation Environment [#1061] | |
| Anthony Almudevar | |
| University of Rochester, United States | |
| A Systematic Computational Approach for Transcription Factor Target Gene Prediction [#1090] | |
| Ji He, Xinbin Dai and Xuechun Zhao | |
| Samuel Roberts Noble Foundation, United States | |
| A Stochastic model to estimate the time taken for Protein-Ligand Docking [#1106] | |
| Preetam Ghosh, Samik Ghosh, Kalyan Basu, Sajal Das and Simon Daefler | |
| Student, University of Texas at Arlington, United States; Professor, University of Texas at Arlington, United States; Professor, Mount Sinai School of Medicine, United States | |
| Inferring functional coupling of proteins using the Evolutionary Bond Energy Algorithm [#1108] | |
| Ryosuke Watanabe, Edgar E. Vallejo and Enrique Morett | |
| ITESM Campus Estado de Mexico, Mexico; IBT Universidad Nacional Autonoma de Mexico, Mexico | |
| A Model-Free Greedy Gene Selection for Microarray Sample Class Prediction [#1017] | |
| Yi Shi, Zhipeng Cai, Lizhe Xu, Wei Ren, Randy Goebel and Lin Guohui | |
| University of Alberta, Canada; University of New Orleans, United States; Chinese Academy of Sciences, China | |
| A Systematic Statistical Process for Microarray Data Analysis: Countering the Limitations in the Public Data Sets [#1045] | |
| Jarukit Lertbantanawong and Jonathan Chan | |
| Department of Mathematics, Assumption University, Thailand; Sch. of IT, King Mongkut's Univ of Tech Thonburi, Thailand | |
| E2D: A Novel Tool for Annotating Protein Domains in Expressed Sequence Tags [#1035] | |
| Guo-Hsing Lee, Nai-Yu Chuang, Wen-Dar Lin, Hahn-Ming Lee and Chung-Der Hsiao | |
| Academia Sinica, Taiwan; National Taiwan University of Sci. and Tech., Taiwan | |
| Gene Ontology Driven Feature Selection from Microarray Gene Expression Data [#1078] | |
| Jianlong Qi and Jian Tang | |
| Memorial University of Newfoundland, Canada | |
| Inference of Gene Regulatory Networks from Time Course Gene Expression Data Using Neural Networks and Swarm Intelligence [#1074] | |
| Habtom Ressom, Yuji Zhang, Jianhua Xuan, Yue Wang and Robert Clarke | |
| Georgetown University, United States; Virginia Tech, United States | |
| The Image Registration of TME Biomedical Images in variant Creutzfeldt-Jakob Diseases [#1031] | |
| Mariusz Zubert, Napieralska Malgorzata, Napieralski Andrzej and Sikorska Beata | |
| Technical University of Lodz, DMCS, Poland; Medical University of Lodz,Dep.ofMolecularBiol.., Poland | |
| A Fast Algorithm for Detecting Frame Shifts in DNA sequences [#1071] | |
| Hassan Masoom, Suprakash Datta, Amir Asif, Lesley Cunningham and Gillian Wu | |
| York University, Toronto., Canada; York University, Toronto, Canada | |
| Prediction of the Number of Helices for the Twilight Zone Proteins [#1026] | |
| Kanaka Durga Kedarisetti, Ke Chen, Aashima Kapoor and Lukasz Kurgan | |
| University of Alberta, Canada | |
| SARNA-Predict: A Simulated Annealing Algorithm for RNA Secondary Structure Prediction [#1099] | |
| Herbert H. Tsang and Kay C. Wiese | |
| Simon Fraser University, Canada | |
| Developing Antibiotic Regimens Using Evolutionary Algorithms [#1101] | |
| Steven Corns, Scott Hurd, Daniel Ashlock and Mark Bryden | |
| Iowa State University, United States; University of Guelph, Canada | |
| A Novel Graphical Model Approach to Segmenting Cell Images [#1079] | |
| Shann-Ching Chen, Ting Zhao, Geoffrey J. Gordon and Robert F. Murphy | |
| Dept. of Biomedical Eng., Carnegie Mellon Univ., United States; Dept. of Machine Learning, Carnegie Mellon Univ., United States | |
| G Protein-Coupled Receptor Classification at the Subfamily Level with Probabilistic Suffix Tree [#1110] | |
| Jingyi Yang and Jitender Deogun | |
| CSE Department, University of Nebraska-lincoln, United States |
Special Lecture: Banquet, Sylvia Spengler
Thursday, September 28, 7:00PM-9:00PM, Room: Northern Lights Ballroom, Speaker: Dan Ashlock
Session C: Protein Folding
Friday, September 29, 8:30AM-10:10AM, Room: Northern Lights Ballroom, Chair: Candida G. Silva
| 8:30AM | Non-Isomorphic Coding in Lattice Model and its Impact for Protein Folding Prediction Using Genetic Algorithm [#1008] |
| Md Tamjidul Hoque, Madhu Chetty and Laurence S Dooley | |
| MONASH UNIVERSITY, Australia | |
| 8:50AM | Bayesian Segmentation using Residue Proximity for Secondary Structure and Contact Prediction [#1029] |
| Niranjan Bidargaddi, Madhu Chetty and Joarder Kamruzzaman | |
| student member IEEE CIS, Australia; senior member IEEE, Australia; member IEEE, Australia | |
| 9:10AM | A Differential Evolution Approach for Protein Folding [#1077] |
| Reginaldo Bitello and Heitor Lopes | |
| BIOINFO / UTFPR, Brazil | |
| 9:30AM | Identification of non Random Motifs in Loops Using a Structural Alphabet [#1092] |
| Leslie Regad, Juliette Martin and Anne-Claude Camproux | |
| EBGM INSERM U726 Universite Paris 7, France; EBGM INSERM U726/ INRA MIG, France | |
| 9:50AM | P-found: The Protein Folding and Unfolding Simulation Repository [#1096] |
| Candida G. Silva, Vitaliy Ostropytskyy, Nuno Loureiro-Ferreira, Martin Swain, Daniel Berrar, Werner Dubitzky and Rui M. M. Brito | |
| University of Coimbra, Portugal; University of Ulster, United Kingdom |
Session D: Gene Networks
Friday, September 29, 8:30AM-10:10AM, Room: Aurora Room, Chair: Jennifer Hallinan
| 8:30AM | A Systematic Approach for Identifying Regulatory Interactions in Large Temporal Gene Expression Datasets from Peripheral Blood [#1116] |
| Simon Knott, Parvin Mousavi and Sergio Baranzini | |
| Queen's University, Canada; University of California, San Francisco, United States | |
| 8:50AM | A New Approach to Identify Functional Modules Using Random Matrix Theory [#1027] |
| Mengxia Zhu, Qishi Wu, Yunfeng Yang and Jizhong Zhou | |
| Southern Illinois University, United States; University of Memphis, United States; Oak Ridge National Laboratory, United States; University of Oklahoma, United States | |
| 9:10AM | A Fuzzy Data Mining Technique for the Reconstruction of Gene Regulatory Networks from Time Series Expression Data [#1102] |
| Patrick C.H. Ma and Keith C.C. Chan | |
| The Hong Kong Polytechnic University, Hong Kong | |
| 9:30AM | Causal Modeling of Gene Regulatory Network [#1103] |
| Ramesh Ram, Madhu Chetty and Trevor Dix | |
| Gippsland School of IT, Monash University, Australia; Clayton School of IT, Monash University, Australia | |
| 9:50AM | Clustering and Cross-talk in a Yeast Functional Interaction Network [#1113] |
| Jennifer Hallinan and Anil Wipat | |
| Newcastle University, United Kingdom, United Kingdom |
Session E: Feature Selection
Friday, September 29, 10:40AM-12:20PM, Room: Northern Lights Ballroom, Chair: Stefan C. Kremer
| 10:40AM | Visualization of Support Vector Machines with Unsupervised Learning [#1009] |
| Lutz Hamel | |
| University of Rhode Island, United States | |
| 11:00AM | Data Visualization with Simultaneous Feature Selection [#1075] |
| Dharmesh Maniyar and Ian Nabney | |
| Aston University, United Kingdom | |
| 11:20AM | Biomarker Identification and Rule Extraction from Mass Spectral Serum Profiles [#1073] |
| Habtom Ressom, Rency Varghese, Edward Orvisky, Steven Drake and Glen Hortin | |
| Georgetown University, United States; NIH, United States | |
| 11:40AM | Feature Selection using a Random Forests Classifier for the Integrated Analysis of Multiple Data Types [#1117] |
| David Reif, Alison Motsinger, Brett McKinney, James Crowe, Jr. and Jason Moore | |
| Vanderbilt University, United States; Dartmouth Medical School, United States | |
| 12:00PM | Detecting Similarities between Families of Bio-Sequences Using the Steady-State of a PCA Neural Network [#1085] |
| Mosaab Daoud and Stefan C. Kremer | |
| Dept. of CIS, University of Guelph, Canada |
Session F: Biosequence Analysis and Biochemical Modeling
Friday, September 29, 10:40AM-12:20PM, Room: Aurora Room, Chair: Cindy Y. Li
| 10:40AM | Motif Evaluation Using Leave-One-Out Scoring [#1025] |
| Audrey Girouard, Noah Smith and Donna Slonim | |
| Tufts University, United States | |
| 11:00AM | A profile-based protein sequence alignment algorithm for a domain clustering database [#1052] |
| Xu Lin, Zhang Fa and Liu Zhiyong | |
| The Institute of Computing Technology, China; the Institute of Computing Technology, China; National Natural Science Foundation of China, China | |
| 11:20AM | A Comparative Study on Feature Extraction from Protein Sequences for Subcellular Localization Prediction [#1053] |
| Wen-Yun Yang, Bao-Liang Lu and Yang Yang | |
| Shanghai Jiao Tong University, China | |
| 11:40AM | Machine Learning in Basecalling - Decoding trace peak behaviour [#1093] |
| David Thornley and Stavros Petridis | |
| Imperial College London, United Kingdom | |
| 12:00PM | A Random Walk Modelling Approach for Passive Metabolic Pathways in Gram-Negative Bacteria [#1072] |
| Amin Mazloom, Kalyan Basu and Sajal Das | |
| Ph.D. student, United States; Professor, United States |
Session G: Microarray Analysis
Friday, September 29, 2:00PM-3:20PM, Room: Northern Lights Ballroom, Chair: Dan Ashlock
| 2:00PM | Bicluster Analysis of Genome-Wide Gene Expression [#1018] |
| Kuanchung Chen and Yuh-Jyh Hu | |
| National Chiao Tung University, Taiwan | |
| 2:20PM | Bottom-Up Biclustering of Expression Data [#1022] |
| Kenneth Bryan and Padraig Cunningham | |
| Trinity College Dublin, Ireland | |
| 2:40PM | A New Hybrid Approach for Unsupervised Gene Selection [#1088] |
| Young Bun Kim and Jean Gao | |
| The University of Texas at Arlington, United States | |
| 3:00PM | Efficient Probe Selection in Microarray Design [#1091] |
| Leszek Gasieniec, Cindy Y. Li, Paul Sant and Prudence W.H. Wong | |
| The University of Liverpool, United Kingdom; University of Luton, United Kingdom |
Session H: Biological Theory
Friday, September 29, 2:00PM-3:00PM, Room: Aurora Room, Chair: Dan Ashlock
| 2:00PM | Understanding the Evolutionary Process of Grammatical Evolution Neural Networks for Feature Selection in Genetic Epidemiology [#1068] |
| Alison Motsinger, David Reif, Scott Dudek and Marylyn Ritchie | |
| Vanderbilt University, United States | |
| 2:20PM | An Exploration of Differential Utility in Iterated Prisoner's Dilemma [#1097] |
| Dan Ashlock, Wendy Ashlock and Gary Umphrey | |
| University of Guelph, Canada | |
| 2:40PM | An Evolutionary Algorithm for the Selection of Geographically Informative Species [#1066] |
| Daniel Ashlock, Karl Cottenie, Lindsey Carson, Kenneth Bryden and Steven Corns | |
| University of Guelph, Canada; Iowa State University, United States |
Session I: Medical Informatics
Friday, September 29, 3:40PM-5:20PM, Room: Northern Lights Ballroom, Chair: Nelli Martchenko-Shimko
| 3:40PM | PSpice Simulation of Cardiac Impulse Propagation: studying the mechanisms of action potential propagation [#1012] |
| Somayeh Mahdavi, Shahriar Gharibzadeh, Mostafa Rezaei-Tavirani, Farzad Towhidkhah and Soheil Shafiee | |
| Khatam university, Iran; Amirkabir University of Technology, Iran; Ilam Medical Sciences University - Asre novin, Iran | |
| 4:00PM | Clinical Characterization of Electromyographic Data Using Computational Tools [#1016] |
| Andrew Hamilton-Wright and Daniel Stashuk | |
| University of Guelph, Canada; University of Waterloo, Canada | |
| 4:20PM | Bootstrap Inference with Neural-Network Modeling for Gene-Disease Association Testing [#1041] |
| Nelli Martchenko-Shimko and Marie-Pierre Dube | |
| Montreal Heart Institute, Canada; Universite de Montreal, Montreal Heart Institute, Canada | |
| 4:40PM | Classification of Scleroderma and Normal Biopsy Data and Identification of Possible Biomarkers of the Disease [#1119] |
| Topon Paul and Hitoshi Iba | |
| The University of Tokyo, Japan | |
| 5:00PM | A Fast Multivariate Feature-Selection/Classification Approach for Prediction of Therapy Response in Multiple Sclerosis [#1033] |
| Sara Mostafavi, Sergio Baranzini, Jorge Oksenberg and Parvin Mousavi | |
| Queen's University, Canada; University of California, San Francisco, United States |
Session J: RNA Structure and Function
Friday, September 29, 3:40PM-5:20PM, Room: Aurora Room, Chair: Dan Ashlock
| 3:40PM | Covariance Searches for ncRNA Gene Finding [#1007] |
| Scott Smith | |
| Boise State University, United States | |
| 4:00PM | A Bayesian approach to pairwise RNA Secondary Structure Alignment [#1105] |
| Zhuozhi Wang and Ellizabeth Tillier | |
| University Health Network, Canada; University of Toronto, Canada | |
| 4:20PM | Determination of the Relative Importance of Gene Function or Taxonomic Grouping to Codon Usage Bias Using Cluster Analysis and SVMs [#1095] |
| Jianmin Ma, Ngoc Minh Nguyen, Gary Fogel and Jagath Rajapakse | |
| Nanyang Technological University, Singapore; Natural Selection, Inc., United States | |
| 4:40PM | Analysis of Thermodynamic Models and Performance in RnaPredict - An Evolutionary Algorithm for RNA Folding [#1100] |
| Kay C. Wiese, Andrew Hendriks and Alain Deschenes | |
| Simon Fraser University, Canada; Chemical Computing Group, Inc., Canada | |
| 5:00PM | Filtration and Depth Annotation Improve Non-linear Projection for RNA Motif Discovery [#1112] |
| Justin Schonfeld and Daniel Ashlock | |
| Iowa State University, United States; University of Guelph, Canada |
