program-07
CIBCB 2007 Program
Plenary Keynote - Pierre Baldi - Chemoinformatics, Machine Learning, and Drug Discovery
Monday, April 2, 8:00AM-9:00AM, Room: South Pacific Ballroom, Speaker: L. Gwenn Volkert
Abstract:
Informatics and computers have not yet become as pervasive in chemistry as they have in physics and biology. Drawing analogies from bioinformatics, key ingredients for progress in chemoinformatics are the availability of large, annotated databases of compounds and reactions, data structures and algorithms to efficiently search these databases, and computational methods to predict the physical, chemical, and biological properties of new compounds and reactions. We will describe the development of: (1) a large public database of compounds and reactions (ChemDB); (2) machine learning kernel methods to predict molecular properties; and (3) the applications of these methods to drug screening/design problems and the identification of new drug leads against a major disease.
Biosketch:
Pierre Baldi is a Professor in the School of Information and Computer Sciences and the Department of Biological Chemistry at the University of California, Irvine and the Director of the UCI Institute for Genomics and Bioinformatics. He received a PhD in Mathematics in 1986 from the California Institute of Technology.
Dr. Baldi has held postdoctoral, faculty, and member of the technical staff positions at UCSD and Caltech, in the Division of Biology and the Jet Propulsion Laboratory. He was CEO of a startup company for a few years and joined UCI in 1999. He is the recipient of a 1993 Lew Allen Award at JPL and a Laurel Wilkening Faculty Innovation Award at UCI. Dr. Baldi's has published over 150 scientific articles and four book. Research in his group focuses on several areas at the intersection of the computational and life sciences, in particular the application of AI/statistical/machine learning methods to problems in bio and chemical informatics. Work in his group has resulted in several databases, software, and web servers that are in wide use.
(see: http://www.igb.uci.edu/servers/servers.html)
Dr. Baldi's main contributions include the development of Hidden Markov Models (HMMPro) for sequence analysis, recursive neural networks for de novo protein structure prediction (SCRATCH), Bayesian statistical methods for DNA microarray analysis (Cyber-T), informatics infrastructure for systems biology (SIGMOID) and, more recently, databases and tools in chemical informatics (ChemDB) for the prediction of molecular properties and applications in chemical synthesis, discovery, and drug design.
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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