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Pattern Recognition in Bioinformatics: 5th IAPR International Conference, PRIB 2010, Nijmegen, The Netherlands, September 22-24, 2010, Proceedings

Pattern Recognition in Bioinformatics: 5th IAPR International Conference, PRIB 2010, Nijmegen, The Netherlands, September 22-24, 2010, Proceedings


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This book constitutes the refereed proceedings of the 5th International Conference on Pattern Recognition in Bioinformatics, PRIB 2010, held in Nijmegen, The Netherlands, in September 2010.
The 38 revised full papers presented were carefully reviewed and selected from 46 submissions. The field of bioinformatics has two main objectives: the creation and maintenance of biological databases and the analysis of life sciences data in order to unravel the mysteries of biological function. Computer science methods such as pattern recognition, machine learning, and data mining have a great deal to offer the field of bioinformatics.

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Product Details

ISBN-13: 9783642160004
Publisher: Springer Berlin Heidelberg
Publication date: 11/04/2010
Series: Lecture Notes in Computer Science , #6282
Edition description: 2010
Pages: 442
Product dimensions: 5.90(w) x 9.30(h) x 0.90(d)

Table of Contents

Part I Classification of Biological Sequences

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 Dick de Ridder 3

Machine Learning Study of DNA Binding by Transcription Factors from the LacI Family Gennady G. Fedonin Mikhail S. Gelfand 15

Joint Loop End Modeling Improves Covariance Model Based Non-coding RNA Gene Search Jennifer Smith 27

Structured Output Prediction of Anti-cancer Drug Activity Hongyu Su Markus Heinonen Juho Rousu 38

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 50

Towards 3D Modeling of Interacting TM Helix Pairs Based on Classification of Helix Pair Sequence Witold Dyrka Jean-Christophe Nebel Malgorzata Kotulska 62

Optimization Algorithms for Identification and Genotyping of Copy Number Polymorphisms in Human Populations Gökhan Yavas Mehmet Koyutürk Thomas LaFramboise 74

Preservation of Statistically Significant Patterns in Multiresolution 0-1 Data Prem Raj Adhikari Jaakko Hollmén 86

Novel Machine Learning Methods for MHC Class I Binding Prediction Christian Widmer Nora C. Toussaint Yasemin Altun Oliver Kohlbacher Gunnar Rätsch 98

Part II Unsupervised Learning Methods for Biological Sequences

SIMCOMP: A Hybrid Soft Clustering of Metagenome Reads Shruthi Prabhakara Raj Acharya 113

The Complexity and Application of Syntactic Pattern Recognition Using Finite Inductive Strings Elijah Myers Paul S. Fisher Keith Irwin Jinsuk Baek Joao Setubal 125

An Algorithm to Find All Identical Motifs in Multiple Biological Sequences Ashish Kishor Bindal R. Sabarinathan J. Sridhar D. Sherlin K. Sekar 137

Discovery of Non-induced Patterns from Sequences Andrew K.C. Wong Dennis Zhuang Gary C.L. Li En-Shiun Annie Lee 149

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 João M.O.S Rodrigues 161

A Maximum-Likelihood Formulation and EM Algorithm for the Protein Multiple Alignment Problem Valentina Sulimova Nikolay Razin Vadim Mottl Ilya Muchnik Casimir Kulikowski 171

Polynomial Supertree Methods Revisited Malte Brinkmeyer Thasso Griebel Sebastian Böcker 183

Enhancing Graph Database Indexing by Suffix Tree Structure Vincenzo Bonnici Alfredo Ferro Rosalba Giugno Alfredo Pulvirenti Dennis Shasha 195

Part III Learning Methods for Gene Expression and Mass Spectrometry Data

Semi-Supervised Graph Embedding Scheme with Active Learning (SSGEAL): Classifying High Dimensional Biomedical Data George Lee Anant Madabhushi 207

Iterated Local Search for Biclustering of Microarray Data Wassim Ayadi Mourad Elloumi Jin-Kao Hao 219

Biologically-aware Latent Dirichlet Allocation (BaLDA) for the Classification of Expression Microarray Alessandro Perina Pietro Lovato Vittorio Murino Manuele Bicego 230

Measuring the Quality of Shifting and Scaling Patterns in Biclusters Beatriz Pontes Raúl Giráldez Jesús S. Aguilar-Ruiz 242

Frequent Episode Mining to Support Pattern Analysis in Developmental Biology Ronnie Bathoorn Monique Welten Michael Richardson Arno Siebes Fons J. Verbeek 253

Time Series Gene Expression Data Classification via L1-norm Temporal SVM Cariotta Orsenigo Carlo Vercellis 264

Part IV Bioimaging

Sub-grid and Spot Detection in DNA Microarray Images Using Optimal Multi-level Thresholding Iman Rezaeian Luis Rueda 277

Quantification of Cytoskeletal Protein Localization from High-Content Images Shiwen Zhu Paul Matsudaira Roy Welsch Jagath C. Rajapakse 289

Pattern Recognition for High Throughput Zebrafish Imaging Using Genetic Algorithm Optimization Alexander E. Nezhinsky Fons J. Verbeek 301

Consensus of Ambiguity: Theory and Application of Active Learning for Biomedical Image Analysis Scott Doyle Anant Madabhushi 313

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 325

Part V Molecular Structure Prediction

A Matrix Algorithm for RNA Secondary Structure Prediction S.P.T. Krishnan Mushfique Junayed Khurshid Bharadwaj Veeravalli 337

Exploiting Long-Range Dependencies in Protein β-Sheet Secondary Structure Prediction Yizhao Ni Mahesan Niranjan 349

Alpha Helix Prediction Based on Evolutionary Computation Alfonso E. Márquez Chamorro Federico Divina Jesús S. Aguilar Ruiz Gualberto Asencio Cortés 358

An On/Off Lattice Approach to Protein Structure Prediction from Contact Maps Stefano Teso Cristina Di Risio Andrea Passerini Roberto Battiti 368

Part VI Protein Protein Interaction and Network Inference

Biological Protein-Protein Interaction Prediction Using Binding Free Energies and Linear Dimensionality Reduction Luis Rueda Carolina Garate Sridip Banerjee Md. Mominul Aziz 383

Employing Publically Available Biological Expert Knowledge from Protein-Protein Interaction Information Kristine A. Pattin Jiang Gui Jason H. Moore 395

SFFS-MR: A Floating Search Strategy for GRNs Inference Fabrício M. Lopes David C. Martins Junior Barrera Roberto M. Cesar 407

Revisiting the Voronoi Description of Protein-Protein Interfaces: Algorithms Frederic Cazals 419

MC4: A Tempering Algorithm for Large-Sample Network Inference Daniel James Barker Steven M. Hill Sach Mukherjee 431

Flow-Based Bayesian Estimation of Nonlinear Differential Equations for Modeling Biological Networks Nicolas J.-B. Brunel Florence d'Alché-Buc 443

Author Index 455

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