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CIBCB 2007 Program
Special Lecture KEY: Keynote - Pierre Baldi - Chemoinformatics, Machine Learning, and Drug Discovery
Monday, April 2, 8:00AM-9:00AM, Room: South Pacific Ballroom, Speaker: L. Gwenn Volkert
Session AM1-M: Genetics
Monday, April 2, 9:00AM-10:00AM, Room: South Pacific Ballroom, Chair: L. Gwenn Volkert
| 9:00AM | Linkage Disequilibrium in Genetic Association Studies Improves the Performance of Grammatical Evolution Neural Networks [#80] |
| Alison Motsinger, David Reif, Theresa Fanelli, Anna Davis and Marylyn Ritchie |
| Vanderbilt University, United States; Environmental Protection Agency, United States; Vanderbilt Univerisity, United States |
| 9:30AM | Novel Data Mining Techniques in aCGH based Breast Cancer Subtypes Profiling: the Biological Perspective [#49] |
| Filippo Menolascina, Stefania Tommasi, Angelo Paradiso, Marco Cortellino and Vitoantonio Bevilacqua |
| National Cancer Institute, Polytechnic of Bari, Italy; National Cancer Institute, Italy; Polytechnic of Bari, Italy |
Session AM2-M: Gene expression & Microarrays
Monday, April 2, 10:15AM-12:15PM, Room: South Pacific Ballroom, Chair: Gary Fogel
| 10:15AM | Associative Artificial Neural Network for Discovery of Highly Correlated Gene Groups Based on Gene Ontology and Gene Expression [#78] |
| Ji He, Xinbin Dai and Xuechun Zhao |
| Samuel Robers Noble Foundation, United States; Samuel Roberts Noble Foundation, United States |
| 10:45AM | Evolutionary Parameter Setting of Multi-clustering [#26] |
| Daniel Ashlock and Ling Guo |
| University of Guelph, Canada; Iowa State University, United States |
| 11:15AM | Boosting Evolutionary Support Vector Machine for Designing Tumor Classifiers from Microarray Data [#67] |
| Hui-Ling Huang, Yi-Hsiung Chen, Dwight D. Koeberl and Shinn-Ying Ho |
| Department of Information Management, Jin Wen In, Taiwan; Institute of Bioinformatics, National Chiao Tun, Taiwan; Duke University Medical School, Durham, NC, United States; Department of Biological Science and Technology,, Taiwan |
| 11:45AM | Two-way Clustering using Fuzzy ASI for Knowledge Discovery in Microarrays [#14] |
| Jahangheer Shaik and Mohammed Yeasin |
| University of Memphis, United States |
Session PM1-M: Special Session 1 - Biomedical Engineering - Part 1
Monday, April 2, 1:15PM-3:15PM, Room: South Pacific Ballroom, Chair: Julia Chung and D.J. Lee
| 1:15PM | Cluster Methodology Defines Archetype Sentinel Consomic Rats [#29] |
| Nancy Sobczak, George Corliss, Martin Seitz and Peter Tonellato |
| Marquette University, Milwaukee, WI, United States; Medical College of WI, Marquette University, United States |
| 1:45PM | Combining Neural Network and Wavelet Transform for Trigger Asynchrony Detection [#112] |
| Lan Chang, Pau-Choo Chung and Chang-Wen Chen |
| Institute of CCE, National Cheng-Kung University, Taiwan; T.I.M Dept., National Cheng-Kung Univ. Hospital, Taiwan |
| 2:15PM | Predicting Tumor Malignancies using Combined Computational Intelligence, Bioinformatics and Laboratory Molecular Biology Approaches [#100] |
| Jack Yang, Mary Yang, Zuojie Luo, Andrzej Niemierko and Jianling Li |
| Harvard Univ. and Massachusetts General Hosp, United States; National Human Genome Research Inst., NIH-USDHHS, United States; Harvard, Joslin Diabetes Ctr - Guangxi Medical U, United States; Guangxi Medical Univ., First Affiliated Hospital, China |
| 2:45PM | Analysis and Prevention of Dispension Errors by Using Data Mining Techniques [#18] |
| Vincent S. Tseng, Chun-Hao Chen, Hsiao-Ming Chen, Hui-Jen Chang and Chin-Tai Yu |
| National Cheng-Kung University, Taiwan; National Cheng Kung University Hospital, Taiwan |
Session PM2-M: Regulatory Pathways and Networks
Monday, April 2, 3:30PM-5:30PM, Room: South Pacific Ballroom, Chair: Jennifer Hallinan
| 3:30PM | Spectral Decomposition of Signaling Networks [#105] |
| Bahram Parvin, Nirmalya Ghosh, Laura Heiser, Joe Gray and Paul Spellman |
| Lawrence Berkeley National Laboratory, United States |
| 4:00PM | Inference of Gene Regulatory Networks using S-System: A Unified Approach [#41] |
| Haixin Wang, Lijun Qian and Edward Dougherty |
| PVAMU, United States; Translational Genomics Research Institute, United States |
| 4:30PM | Optimization of Bacterial Strains with Variable-Sized Evolutionary Algorithms [#131] |
| Miguel Rocha, Jose P. Pinto, Isabel Rocha and Eugenio C. Ferreira |
| Dep. Informatics/ CCTC - Univ. Minho, Portugal; IBB-Inst. Biot. and Bioeng.- CEB- Univ. Minho, Portugal; BB-Inst. Biot. and Bioeng.- CEB -Univ. Minho, Portugal |
| 5:00PM | Gene-Gene Interaction Tests Using SVM and Neural Network Modeling [#35] |
| Nelli Matchenko-Shimko and Marie-Pierre Dube |
| Montreal Heart Institute, Canada; Universite de Montreal, Montreal Heart Institute, Canada |
Plenary Poster Session PS-M: Poster Session 1
Monday, April 2, 7:00PM-9:00PM, Room: South Pacific Ballroom, Chair: L. Gwenn Volkert
| | Clustering Microarrays with Predictive Weighted Ensembles [#12] |
| Christine Smyth and Danny Coomans |
| James Cook University, Australia |
| | Gene Relation Discovery by Mining Similar Subsequences in Time-Series Microarray Data [#22] |
| Vincent S. Tseng, Lien-Chin Chen and Jian-Jie Liu |
| National Cheng-Kung University, Taiwan |
| | Discovering Connected Patterns in Gene Expression Arrays [#83] |
| Noha Yousri, Mohamed Ismail and Mohamed Kamel |
| University of Waterloo, Ontario, Canada; University of Alexandria, Alexandria, Egypt |
| | Matching and Visualization of Multiple Overlapping Clustering of Microarray Data [#127] |
| Chase Krumpelman and Joydeep Ghosh |
| University of Texas at Austin, United States |
| | Geometrical probability approach for analyis of 3D chromatin structure in interphase cell nuclei [#1] |
| Evgeny Gladilin, Sandra Goetze, Jose Mateos-Langerak, Roel van Driel and Karl Rohr |
| DKFZ Heidelberg, Germany; SILS Amsterdam, Netherlands |
| | Operon Prediction in Microbial Genomes Using Decision Tree Approach [#13] |
| Dongsheng Che, Jizhen Zhao, Liming Cai and Ying Xu |
| University of Georgia, United States |
| | An ACGT-Words Tree for Efficient Data Access in Genomic Databases [#17] |
| Ye-In Chang, Wei-Horng Yeh, Jiun-Rung Chen and Jen-Wei Hu |
| National Sun Yet-Sen University, Taiwan |
| | An Experimental Evaluation of Inversion- and Transposition-Based Genomic Distances through Simulations [#23] |
| Moulik Kothari and Bernard M.E. Moret |
| University of New Mexico, United States; Ecole Polytechnique Federale de Lausanne, Switzerland |
| | Overestimation for Multiple Sequence Alignment [#28] |
| Tristan Cazenave |
| Universite Paris 8, France |
| | Biological Sequence Mining Using Plausible Neural Network and its Application to Exon/intron Boundaries Prediction [#30] |
| Kuochen Li, Dar-jen Chang, Eric Rouchka and Yuan Yan Chen |
| University of Louisville, United States; PNN Technologies Inc, United States |
| | Terminator Detection by Support Vector Machine Utilizing a Stochastic Context-Free Grammar [#32] |
| Patricia Francis-Lyon, Nello Cristianini and Stephen Holbrook |
| University of California at Davis, United States; University of Bristol, United Kingdom; Lawrence Berkeley National Laboratory, United States |
| | Prediction of Co-Regulated Gene Groups through Gene Ontology [#62] |
| Zuojian Tang, Sieu Phan, Youlian Pan and Fazel Famili |
| National Research Council of Canada, Canada |
| | Genetic Regulatory Network Modeling Using Network Component Analysis and Fuzzy Clustering [#125] |
| Fatemeh Bakouie and Mohammad. Hassan Moradi |
| Ms.c student in Biomedical ingineering, Iran; Associate prof of Biomedical engineering, Iran |
| | Motifs and Modules in Fractured Functional Yeast Networks [#130] |
| Jennifer Hallinan and Anil Wipat |
| Newcastle University, United Kingdom |
| | Efficient and Scalable Motif Discovery using Graph-based Search [#86] |
| Amit Sinha and Raj Bhatnagar |
| University of Cincinnati, United States |
| | Inferring Regulatory Interactions between Transcriptional Factors and Genes by Propagating Known Regulatory Links [#88] |
| Qian Zhong, Riccardo Boscolo, Timothy Gardner and Vwani Roychowdhury |
| University of California, Los Angeles, United States; Boston University, United States |
| | Semantic Analysis of Genome Annotations using Weighting Schemes [#94] |
| Bogdan Done, Purvesh Khatri, Arina Done and Sorin Draghici |
| Wayne State University, United States |
| | Comparison of Human and Mouse Pseudogenes [#107] |
| Pooja Pooja and Jagath Rajapakse |
| Nanyang Technological University, Singapore |
| | Modularization of Protein Interaction Networks by Incorporating Gene Ontology Annotations [#56] |
| Young-Rae Cho, Woochang Hwang and Aidong Zhang |
| State University of New York at Buffalo, United States |
Session AM1-T: RNA/Protein Structure and Function
Tuesday, April 3, 8:30AM-10:00AM, Room: South Pacific Ballroom, Chair: Scott Smith
| 8:30AM | SARNA-Predict: A Study of RNA Secondary Structure Prediction Using Different Annealing Schedules [#117] |
| Herbert H. Tsang and Kay C. Wiese |
| Simon Fraser University, Canada |
| 9:00AM | Prediction of Enzyme Catalytic Sites from Sequence Using Neural Networks [#11] |
| Swati Pande, Raheja Amar and Dennis Livesay |
| California State Polytechnic University, Pomona, United States; University of North Carolina at Charlotte, United States |
| 9:30AM | Predicting Peptide Binders of Flexible Lengths with Genetic Annealing Algorithm [#118] |
| Menaka Rajapakse and Lin Feng |
| Institute for Infocomm Research, Singapore; Nanyang Technological University, Singapore |
Session AM2-T: Sequence Analysis
Tuesday, April 3, 10:15AM-12:15PM, Room: South Pacific Ballroom, Chair: Kay Wiese
| 10:15AM | RNA Gene Finding with Biased Mutation Operators [#106] |
| Scott Smith |
| Boise State University, United States |
| 10:45AM | A Genetic-Based EM Motif-Finding Algorithm for Biological Sequence Analysis [#24] |
| Chengpeng Bi |
| Children Mercy Hospitals, United States |
| 11:15AM | Computational Prediction of Replication Origins in Herpesviruses [#37] |
| Raul Cruz-Cano, Deepak Chandran and Ming-Ying Leung |
| Bioinformatics Prog., Univ. of Texas at El Paso, United States |
| 11:45AM | Evolutionary-Progressive Method for Multiple Sequence Alignment [#72] |
| Pawel Kupis and Jacek Mandziuk |
| Warsaw University of Technology, Poland |
Session PM1-T: Special Session 2 - Fuzzy Systems in Bioinformatics
Tuesday, April 3, 1:15PM-3:15PM, Room: South Pacific Ballroom, Chair: Mihail Popescu
| 1:15PM | GoFuzzKegg: Mapping Genes to KEGG Pathways Using an Ontological Fuzzy Rule System [#16] |
| Mihail Popescu,, Dong Xu and Erik Taylor |
| University of Missouri, Columbia, United States; University of Texas, Houston, United States |
| 1:45PM | Multiple Sequence Alignment using Fuzzy Logic [#79] |
| Sara Nasser, Gregory Vert, Monica Nicolescu and Alison Murray |
| University of Nevada Reno, United States; Desert Research Institute, United States |
| 2:15PM | Cost-sensitive Fuzzy Classification for Medical Diagnosis [#113] |
| Gerald Schaefer, Tomoharu Nakashima, Yasuyuki Yokota and Hisao Ishibuchi |
| Aston University, United Kingdom; Osaka Prefecture University, Japan |
| 2:45PM | Super Granular SVM Feature Elimination (Super GSVM-FE) Model for Protein Sequence Motif Information Extraction [#82] |
| Bernard Chen, Stephen Pellicer, Phang C. Tai, Robert Harrison and Yi Pan |
| Georgia State University Computer Science Depart, United States; Georgia State University Biology Department, United States |
Session PM2-T: Computational Biology
Tuesday, April 3, 3:30PM-5:30PM, Room: South Pacific Ballroom, Chair: Clare Bates Congdon
| 3:30PM | Hybrid Architecture for Accelerating DNA Codeword Library Searching [#68] |
| Qinru Qiu, Daniel Burns, Qing Wu and Prakash Mukre |
| Binghamton University, United States; Air Force Research Laboratory, Rome Site, United States |
| 4:00PM | Evolving Extremal Epidemic Networks [#21] |
| Daniel Ashlock and Fatemeh Jafargholi |
| University of Guelph, Canada |
| 4:30PM | Building Smart Machines by Utilizing Spiking Neural Networks [#93] |
| Heike Sichtig |
| Binghamton University, United States |
| 5:00PM | Multi-Criterion Phylogenetic Inference using Evolutionary Algorithms [#9] |
| Waldo Cancino and A.C.B. Delbem |
| ICMC USP, Brazil; ICMC-USP, Brazil |
Plenary Poster Session PS2: Poster Session
Tuesday, April 3, 7:00PM-9:00PM, Room: South Pacific Ballroom, Chair: L. Gwenn Volkert
| | A Framework for Discrete Modeling of Juxtacrine Signaling Systems [#33] |
| Luiz Rozante, Marco Gubitoso and Sergio Matioli |
| Imes University, Brazil; University of Sao Paulo, Brazil |
| | A Comparison of Sequence Kernels for Localization Prediction of Transmembrane Proteins [#39] |
| Stefan Maetschke, Marcus Gallagher and Boden Mikael |
| University of Queensland, Australia |
| | Feature Sensitivity on Biochemical Signaling Pathways [#40] |
| George Papadopoulos and Martin Brown |
| The University of Manchester, United Kingdom |
| | In vivo Intracellular Metabolite Dynamics Estimation by Sequential Monte Carlo Filter [#46] |
| Jing Yang, Visakan Kadirkamanathan and Stephen Billings |
| The University of Sheffield, United Kingdom |
| | Real Value Solvent Accessibility Prediction using Adaptive Support Vector Regression [#52] |
| Jayavardhana Gubbi, Alistair Shilton, Marimuthu Palaniswami and Michael Parker |
| The University of Melbourne, Australia; St. Vincent's Institute of Medical Research,, Australia |
| | Active Learning for Network Estimation [#61] |
| Shotaro Akaho and Kenji Fukumizu |
| AIST, Japan; Institute of Statistical Mathematics, Japan |
| | Metabolic Flux Estimation from Incomplete Labelling Measurements Using the Expectation/Conditional-Maximisation Algorithm [#64] |
| Sarawan Wongsa, Visakan Kadirkamanathan, Stephen A. Billings and Phillip Wright |
| University of Sheffield, United Kingdom |
| | Understanding the Prediction of Transmembrane Proteins by Support Vector Machine using Association Rule Mining [#84] |
| Hae-Jin Hu, Hao Wang, Robert Harrison, Phang C. Tai and Yi Pan |
| Georgia State University, United States |
| | Synchronization in Complex Dynamical Networks [#101] |
| Karsten Kube, Andreas Herzog, Bernd Michaelis, Ana de Lima and Thomas Voigt |
| Otto-von-Guericke Univ. Magdeburg, Germany |
| | Modeling protein-DNA binding time in Stochastic Discrete Event Simulation of Biological Processes [#104] |
| Preetam Ghosh, Samik Ghosh, Kalyan Basu and Sajal Das |
| University of Texas at Arlington, United States |
| | Channel Selection in EEG-based Prediction of Shoulder/Elbow Movement Intentions involving Stroke Patients: A Computational Approach [#120] |
| Jie Zhou and Sundeep Yedida |
| Northern Illinois University, United States |
| | A Closer Look on Protein Unfolding Simulations through Hierarchical Clustering [#122] |
| Pedro G. Ferreira, Candida G. Silva, Rui M. M. Brito and Paulo J. Azevedo |
| University of Minho, Portugal; University of Coimbra, Portugal |
| | Integrating Drosophila Data to Discover Disease-Related Protein Interactions in Human [#123] |
| James Costello, Jade Buchanan-Carter, Mehmet Dalkilic and Justen Andrews |
| Indiana University, United States |
| | A Flexible Fully-Multiplicative Orthogonal-Group Based ICA Algorithm [#19] |
| Yalan Ye, Jing Wan, Zhi-Lin Zhang, Jia Chen and Lei Wu |
| University of Electronic Science and Technology, China; Shanghai Jiao Tong University, China |
| | The Difference of Bilateral Limbs Involvement During Trunk Bending and Reaching in Stroke Patients [#20] |
| Jen-Suh Chern, Saiwei Yang, Chi-Wen Long and Chen-Yu Lo |
| Chang Gung University, Taiwan; Yang Ming University, Taiwan; Chinese Medicine University, Taiwan |
| | Color-Texture Segmentation of Medical Images Based on Local Contrast Information [#25] |
| Yuchou Chang, Dah-Jye Lee and Yong-Gang Wang |
| ECE Department, Brigham Young University, United States; Samsung Electronics Co. Ltd, Korea (South) |
| | Towards an Automated Analysis of Neuroleptics' Impact on Human Hand Motor Skills [#53] |
| Matthias Dose, Christian Gruber, Ariane Grunz, Christian Hook and Juergen Kempf |
| Mental Health Institution Taufkirchen, Germany; University of Passau, Germany; University of Applied Sciences Regensburg, Germany |
| | Extracting Efficient Fuzzy If-Then Rules From Mass Spectra of Blood SamplesTo Early Diagnosis of Ovarian Cancer [#60] |
| Amin Assareh and Mohammad Hasan Moradi |
| MSc Student, Iran; Associative Professor, Iran |
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