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Pattern Recognition in Bioinformatics

5th IAPR International Conference, PRIB 2010, Nijmegen, The Netherlands, September 22-24, 2010. Proceedings

  • Tjeerd M. H. Dijkstra
  • Evgeni Tsivtsivadze
  • Elena Marchiori
  • Tom Heskes
Conference proceedings PRIB 2010

Part of the Lecture Notes in Computer Science book series (LNCS, volume 6282)

Also part of the Lecture Notes in Bioinformatics book sub series (LNBI, volume 6282)

Table of contents

  1. Front Matter
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  2. Classification of Biological Sequences

    1. Front Matter
      Pages 1-1
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    2. Sequence-Based Prediction of Protein Secretion Success in Aspergillus niger
      Bastiaan A. van den Berg, Jurgen F. Nijkamp, Marcel J. T. Reinders, Liang Wu, Herman J. Pel, Johannes A. Roubos et al.
      Pages 3-14
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    3. Machine Learning Study of DNA Binding by Transcription Factors from the LacI Family
      Gennady G. Fedonin, Mikhail S. Gelfand
      Pages 15-26
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    4. Joint Loop End Modeling Improves Covariance Model Based Non-coding RNA Gene Search
      Jennifer Smith
      Pages 27-37
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    5. Structured Output Prediction of Anti-cancer Drug Activity
      Hongyu Su, Markus Heinonen, Juho Rousu
      Pages 38-49
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    6. SLiMSearch: A Webserver for Finding Novel Occurrences of Short Linear Motifs in Proteins, Incorporating Sequence Context
      Norman E. Davey, Niall J. Haslam, Denis C. Shields, Richard J. Edwards
      Pages 50-61
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    7. Towards 3D Modeling of Interacting TM Helix Pairs Based on Classification of Helix Pair Sequence
      Witold Dyrka, Jean-Christophe Nebel, Malgorzata Kotulska
      Pages 62-73
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    8. Optimization Algorithms for Identification and Genotyping of Copy Number Polymorphisms in Human Populations
      Gökhan Yavaş, Mehmet Koyutürk, Thomas LaFramboise
      Pages 74-85
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    9. Preservation of Statistically Significant Patterns in Multiresolution 0-1 Data
      Prem Raj Adhikari, Jaakko Hollmén
      Pages 86-97
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    10. Novel Machine Learning Methods for MHC Class I Binding Prediction
      Christian Widmer, Nora C. Toussaint, Yasemin Altun, Oliver Kohlbacher, Gunnar Rätsch
      Pages 98-109
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  3. Unsupervised Learning Methods for Biological Sequences

    1. Front Matter
      Pages 111-111
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    2. SIMCOMP: A Hybrid Soft Clustering of Metagenome Reads
      Shruthi Prabhakara, Raj Acharya
      Pages 113-124
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    3. The Complexity and Application of Syntactic Pattern Recognition Using Finite Inductive Strings
      Elijah Myers, Paul S. Fisher, Keith Irwin, Jinsuk Baek, Joao Setubal
      Pages 125-136
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    4. An Algorithm to Find All Identical Motifs in Multiple Biological Sequences
      Ashish Kishor Bindal, R. Sabarinathan, J. Sridhar, D. Sherlin, K. Sekar
      Pages 137-148
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    5. Discovery of Non-induced Patterns from Sequences
      Andrew K. C. Wong, Dennis Zhuang, Gary C. L. Li, En-Shiun Annie Lee
      Pages 149-160
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    6. Exploring Homology Using the Concept of Three-State Entropy Vector
      Armando J. Pinho, Sara P. Garcia, Paulo J. S. G. Ferreira, Vera Afreixo, Carlos A. C. Bastos, António J. R. Neves et al.
      Pages 161-170
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    7. A Maximum-Likelihood Formulation and EM Algorithm for the Protein Multiple Alignment Problem
      Valentina Sulimova, Nikolay Razin, Vadim Mottl, Ilya Muchnik, Casimir Kulikowski
      Pages 171-182
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    8. Polynomial Supertree Methods Revisited
      Malte Brinkmeyer, Thasso Griebel, Sebastian Böcker
      Pages 183-194
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    9. Enhancing Graph Database Indexing by Suffix Tree Structure
      Vincenzo Bonnici, Alfredo Ferro, Rosalba Giugno, Alfredo Pulvirenti, Dennis Shasha
      Pages 195-203
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  4. Learning Methods for Gene Expression and Mass Spectrometry Data

    1. Front Matter
      Pages 205-205
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    2. Semi-Supervised Graph Embedding Scheme with Active Learning (SSGEAL): Classifying High Dimensional Biomedical Data
      George Lee, Anant Madabhushi
      Pages 207-218
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    3. Iterated Local Search for Biclustering of Microarray Data
      Wassim Ayadi, Mourad Elloumi, Jin-Kao Hao
      Pages 219-229
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    4. Biologically-aware Latent Dirichlet Allocation (BaLDA) for the Classification of Expression Microarray
      Alessandro Perina, Pietro Lovato, Vittorio Murino, Manuele Bicego
      Pages 230-241
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    5. Measuring the Quality of Shifting and Scaling Patterns in Biclusters
      Beatriz Pontes, Raúl Giráldez, Jesús S. Aguilar-Ruiz
      Pages 242-252
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    6. Frequent Episode Mining to Support Pattern Analysis in Developmental Biology
      Ronnie Bathoorn, Monique Welten, Michael Richardson, Arno Siebes, Fons J. Verbeek
      Pages 253-263
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    7. Time Series Gene Expression Data Classification via L1-norm Temporal SVM
      Carlotta Orsenigo, Carlo Vercellis
      Pages 264-274
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  5. Bioimaging

    1. Front Matter
      Pages 275-275
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    2. Sub-grid and Spot Detection in DNA Microarray Images Using Optimal Multi-level Thresholding
      Iman Rezaeian, Luis Rueda
      Pages 277-288
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    3. Quantification of Cytoskeletal Protein Localization from High-Content Images
      Shiwen Zhu, Paul Matsudaira, Roy Welsch, Jagath C. Rajapakse
      Pages 289-300
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    4. Pattern Recognition for High Throughput Zebrafish Imaging Using Genetic Algorithm Optimization
      Alexander E. Nezhinsky, Fons J. Verbeek
      Pages 301-312
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    5. Consensus of Ambiguity: Theory and Application of Active Learning for Biomedical Image Analysis
      Scott Doyle, Anant Madabhushi
      Pages 313-324
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    6. Semi-supervised Learning of Sparse Linear Models in Mass Spectral Imaging
      Fabian Ojeda, Marco Signoretto, Raf Van de Plas, Etienne Waelkens, Bart De Moor, Johan A. K. Suykens
      Pages 325-334
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  6. Molecular Structure Prediction

    1. Front Matter
      Pages 335-335
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    2. A Matrix Algorithm for RNA Secondary Structure Prediction
      S. P. T. Krishnan, Mushfique Junayed Khurshid, Bharadwaj Veeravalli
      Pages 337-348
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    3. Exploiting Long-Range Dependencies in Protein β-Sheet Secondary Structure Prediction
      Yizhao Ni, Mahesan Niranjan
      Pages 349-357
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    4. Alpha Helix Prediction Based on Evolutionary Computation
      Alfonso E. Márquez Chamorro, Federico Divina, Jesús S. Aguilar Ruiz, Gualberto Asencio Cortés
      Pages 358-367
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    5. An On/Off Lattice Approach to Protein Structure Prediction from Contact Maps
      Stefano Teso, Cristina Di Risio, Andrea Passerini, Roberto Battiti
      Pages 368-379
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  7. Protein Protein Interaction and Network Inference

    1. Front Matter
      Pages 381-381
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    2. Biological Protein-Protein Interaction Prediction Using Binding Free Energies and Linear Dimensionality Reduction
      L. Rueda, Carolina Garate, Sridip Banerjee, Md. Mominul Aziz
      Pages 383-394
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    3. Employing Publically Available Biological Expert Knowledge from Protein-Protein Interaction Information
      Kristine A. Pattin, Jiang Gui, Jason H. Moore
      Pages 395-406
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    4. SFFS-MR: A Floating Search Strategy for GRNs Inference
      Fabrício M. Lopes, David C. Martins Jr., Junior Barrera, Roberto M. Cesar Jr.
      Pages 407-418
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    5. Revisiting the Voronoi Description of Protein-Protein Interfaces: Algorithms
      Frederic Cazals
      Pages 419-430
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    6. MC4: A Tempering Algorithm for Large-Sample Network Inference
      Daniel James Barker, Steven M. Hill, Sach Mukherjee
      Pages 431-442
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    7. Flow-Based Bayesian Estimation of Nonlinear Differential Equations for Modeling Biological Networks
      Nicolas J. -B. Brunel, Florence d’Alché-Buc
      Pages 443-454
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  8. Back Matter
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About these proceedings

Keywords

DNA signature algorithm complexity biclustering bioinformatics biomedical informatics classification clustering computational geometry convex optimization data mining databases dynamic programming evolutionary algorithms gene expression gene network

Editors and affiliations

  • Tjeerd M. H. Dijkstra
    • 1
  • Evgeni Tsivtsivadze
    • 2
  • Elena Marchiori
    • 1
  • Tom Heskes
    • 1
  1. 1.Institute for Computing and Information SciencesRadboud University NijmegenNijmegenThe Netherlands
  2. 2.Institute for Computing and Information SciencesTurku Centre for Computer Science, Radboud University NijmegenNijmegenThe Netherlands

Bibliographic information

  • DOI https://doi.org/10.1007/978-3-642-16001-1
  • Copyright Information Springer Berlin Heidelberg 2010
  • Publisher Name Springer, Berlin, Heidelberg
  • eBook Packages Computer Science
  • Print ISBN 978-3-642-16000-4
  • Online ISBN 978-3-642-16001-1
  • Series Print ISSN 0302-9743
  • Series Online ISSN 1611-3349
  • Buy this book on publisher's site