International Workshop on Bioinformatics Research and Applications

University of Reading, UK, May 28-31, 2006
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IWBRA 2006 Technical Program

Session 1
Session Chair: I. Mandoiu 		Mon, 29 May 2006
10:20 - 12:00
  1. Efficient and Practical Algorithms for Deducing the History of Recombination in Populations
    Author(s): D. Gusfield
    Presenter: D. Gusfield, University of California, Davis
  2. Chordal Graphs in Computational Biology - New Insights and Applications
    Author(s): T.M. Przytycka
    Presenter: T.M. Przytycka, NCBI
Session 2
Session Chair: R. Harrison 		Mon, 29 May 2006
13:20 - 15:00
  1. Exemplar Longest Common Subsequence
    Author(s): P.B. Bonizzoni, G.D.V. Della Vedova, R.D. Dondi, G.F. Fertin, S.V. Vialette
    Presenter: P.B. Bonizzoni, DISCo, Univ. Milano-Bicocca
  2. Synonymous Codon Substitution Matrices
    Author(s): A. Schneider, G.H. Gonnet, G.M. Cannarozzi
    Presenter: A. Schneider, ETH Zurich
  3. SEPA: Approximate Non-Subjective Empirical p-Value Estimation for Nucleotide Sequence Alignment
    Author(s): O.H.G. Hirsch Gill, B.M. Mishra
    Presenter: O.H.G. Hirsch Gill, New York University
  4. Multiple Sequence Alignment by Ant Colony Optimization and Divide-and-conquer
    Author(s): Y. Chen, Y. Pan, J. Chen, W. Liu, L. Chen
    Presenter: Y. Pan, Georgia State University
  5. COMBAT: Search Rapidly For Highly Similar Protein-Coding Sequences Using Bipartite Graph Matching
    Author(s): B.S. Sun, J.T.S. Schwartz, O.H.G. Gill, B.M. Mishra
    Presenter: B.S. Sun, Courant Institute of Mathematical Sciences, New York University, USA
Session 3
Session Chair: P. Bonizzoni 		Mon, 29 May 2006
16:20 - 18:00
  1. Missing Values Estimation in Microarray data with Partial Least Squares Regression
    Author(s): K. Yang, J.Z. Li, C.K. Wang
    Presenter: K. Yang
  2. Boost Feature Subset Selection: A New Gene Selection Algorithm for Microarray Dataset
    Author(s): X.X. Xu, A.Z. Zhang
    Presenter: X.X. Xu, State University of New York at Buffalo
  3. A Self-Supervised Learning Framework for Classifying Microarray Gene Expression Data
    Author(s): Y.J.L. Lu, Q.T. Tian, F.L. Liu, M.S. Sanchez, Y.F.W. Wang
    Presenter: Y.J.L. Lu, University of Texas at San Antonio
  4. A Hybrid Feature Selection Approach for Microarray Gene Expression Data
    Author(s): F.T. Tan, X.Z.F. Fu, H.W. Wang, Y.Q.Z. Zhang, A.B. Bourgeois
    Presenter: F.T. Tan, Georgia State University
  5. Pooling Evidence to Identify Cell Cycle–Regulated Genes
    Author(s): G. Zheng, T. Milledge, E. George, G. Narasimhan
    Presenter: G. Zheng, Florida International University
Session 4
Session Chair: M.T. Hajiaghayi 		Tue, 30 May 2006
10:20 - 12:00
  1. Discovering Sequence-Structure Patterns in Proteins with Variable Secondary
    Author(s): T. Milledge, G. Zheng, G. Narasimhan
    Presenter: T. Milledge, Florida International University
  2. Clustering Support Vector Machines and Its Application to Local Protein Tertiary Structure Prediction
    Author(s): J. He, W. Zhong, R. Harrison, P. Tai, Y. Pan
    Presenter: J. He, Southeast University, China
  3. Extracting Protein-Protein Interactions from the Literature
    Author(s): D.Y. Zhou, Y.L. He, C.K. Kwoh
    Presenter: Y.L. He, School of Computer Engineering, Nanyang Technological University
  4. A Multilevel Approach to Identify Functional Modules in a Yeast Protein-Protein Interaction Network
    Author(s): S. Oliveira, S.C. Seok
    Presenter: S.C. Seok, University of Iowa
  5. Towards Detecting Protein Complexes from Protein Interaction Data
    Author(s): P. Pei, A. Zhang
    Presenter: P. Pei, Department of Computer Science and Engineering, State University of New York at Buffalo
Session 5
Session Chair: D. Gusfield 		Tue, 30 May 2006
13:20 - 15:00
  1. High-Throughput SNP Genotyping by SBE/SBH
    Author(s): I.I. Mandoiu, C. Prajescu
    Presenter: I.I. Mandoiu, University of Connecticut
  2. Tag SNP Selection Based on Multivariate Linear Regression
    Author(s): J.H. He, A.Z. Zelikovsky
    Presenter: A.Z. Zelikovsky, Georgia State University
  3. Minimum Multicolored Subgraph Problem in Multiplex PCR Primer Set Selection and Population Haplotyping
    Author(s): M.T. Hajiaghayi, K. Jain, L.C. Lau, I.I. Mandoiu, A. Russell, V.V. Vazirani
    Presenter: M.T. Hajiaghayi, CMU
  4. Phasing of 2-SNP Genotypes based on Non-Random Mating Model
    Author(s): D. Brinza, A. Zelikovsky
    Presenter: A. Zelikovsky, Georgia State University
  5. Event Models for Tumor Classification with SAGE Gene Expression Data
    Author(s): X. Jin, A. Xu, G. Zhao, J. Ma, R. Bie
    Presenter: G. Zhao, School of Mathematical Sciences, Beijing Normal University, Beijing 100875, P.R. China
Session 6
Session Chair: T. Przytycka 		Tue, 30 May 2006
16:20 - 18:00
  1. Genomes containing Duplicates are Hard to compare (Extended Abstract)
    Author(s): C. Chauve, G. Fertin, R. Rizzi, S. Vialette
    Presenter: G. Fertin, LINA, FRE CNRS 2729, Université de Nantes
  2. Rearrangement of Noisy Genomes
    Author(s): C. Zheng, D. Sankoff
    Presenter: C. Zheng
  3. Simple Reconstruction of Binary Near-Perfect Phylogenetic Trees
    Author(s): S. Sridhar, K. Dhamdhere, G.E. Blelloch, E. Halperin, R. Ravi, R. Schwartz
    Presenter: S. Sridhar, Computer Science Department, Carnegie Mellon University
  4. Reconstructing ancestor-descendant lineages from serially-sampled data: a comparison study
    Author(s): P. Buendia, T.M. Collins, G. Narasimhan
    Presenter: P. Buendia, Florida International University
  5. Robustness of Greedy Type Minimum Evolution Algorithms
    Author(s): T. Shigezumi
    Presenter: T. Shigezumi, Dept. of Mathematical and Computing Sciences Tokyo Institute of Technology
Session 7
Session Chair: D. Brinza 		Wed, 31 May 2006
10:20 - 12:00
  1. Space and Time Efficient Algorithms for Planted Motif Search
    Author(s): J. Davila, S. Balla, S. Rajasekaran
    Presenter: J. Davila, CSE Department at University of Connecticut, Storrs, CT
  2. Predictability of Rules in HIV-1 Protease Cleavage Site Analysis
    Author(s): H. Kim, T.S. Yoon, Y. Zhang, A. Dikshit, S.S. Chen
    Presenter: H. Kim, Korea University
  3. Statistical Feature Selection From Chaos Game Representation for Promoter Recognition
    Author(s): O. TINNUNGWATTANA, C. LURSINSAP
    Presenter: O. Tinnungwattana, Advanced Virtual and Intelligent Computing (AVIC) Center, Chulalongkorn University
  4. Blue Matter: Strong Scaling of Molecular Dynamics on Blue Gene/L
    Author(s): B.G. Fitch, A. Rayshubskiy, M. Eleftheriou, T.J.C. Ward, M.E. Giampapa, Y. Zhestkov, M.C. Pitman, F. Suits, A. Grossfield, J.W. Pitera, W.C. Swope, R. Zhou, S. Feller, R.S. Germain
    Presenter: B.G. Fitch, IBM T.J. Watson Research Center
  5. DigitalTree: A Tool for Displaying Biological Data in Tree Structure
    Author(s): R. Kramer, V. Olman, Y. Xu, D. Xu
    Presenter: R. Kramer, University of Missouri-Columbia
Session 8
Session Chair: I. Mandoiu 		Wed, 31 May 2006
13:20 - 15:00
  1. HiSP: A Probabilistic Data Mining Technique for Protein Classification
    Author(s): L.H.C.M. Merschmann, A.P. Plastino
    Presenter: L.H.C.M. Merschmann, Universidade Federal Fluminense
  2. Cross-Ontological Analytics: Combining Associative and Hierarchical Relations in the Gene Ontologies to Assess Gene Product Similarity
    Author(s): C.P. Posse, A.S. Sanfilippo, B.G. Gopalan, R.R. Riensche, N.B. Beagley, B.B. Baddeley
    Presenter: C.P. Posse, Pacific Northwest National Laboratory
  3. A GO-based Method for Assessing the Biological Plausibility of Regulatory Hypotheses
    Author(s): J. Gamalielsson, P. Nilsson, B. Olsson
    Presenter: B. Olsson, Systems Biology Group, University of Skövde, Sweden
  4. Delays in Biological Regulatory Networks (BRN)
    Author(s): J. Ahmad, A. Richard, G. Bernot, J.P. Comet, O. Roux
    Presenter: J. Ahmad, IRCCyN
  5. Phase Transitions in Gene Knockdown Networks of Transitive RNAi
    Author(s): S. Qiu, T. Lane
    Presenter: S. Qiu, University of New Mexico
Full ICCS 2006 schedue