Advances in Bioinformatics and Computational Biology: 4th Brazilian Symposium on Bioinformatics, BSB 2009, Porto Alegre, Brazil, July 29-31, 2009, Proceedings (Lecture Notes in Computer Science, 5676)

This book constitutes the refereed proceedings of the 4th Brazilian Symposium on Bioinformatics, BSB 2009, held in Porto Alegre, Brazil, in July 2009. The 12 revised full papers and 6 extended abstracts were carefully reviewed and selected from 55 submissions. The papers are organized in topical sections on algorithmic approaches for molecular biology problems; micro-array analysis; machine learning methods for classification; and in silico simulation. Cover......Page 1 ISBN-10 3-642-03222-2......Page 4 Preface......Page 5 Organization......Page 6 Table of Contents......Page 9 Introduction......Page 12 Correlation for a Triple of SNPs......Page 14 The Minimum Tag Selection Problem......Page 16 LP Formulation for M2TS Problem......Page 17 BLP Relaxation......Page 18 Measuring Overfit via 2-Cross Validation......Page 19 Missing Data Results......Page 21 Conclusions......Page 22 Introduction......Page 24 Definitions......Page 25 CLP Models for Sorting by Transposition......Page 27 Computational Experiments......Page 30 Conclusion and Future Works......Page 32 Introduction......Page 35 Definitions and Notations......Page 37 Our Method......Page 38 Symmetry......Page 40 Packet......Page 41 PacketSpectralAlignment Algorithm......Page 42 Results......Page 43 Conclusion......Page 45 Introduction......Page 47 Microarray Biclustering......Page 48 GEDM: Main Biclustering Methods......Page 49 BiHEA: Biclustering via a Hybrid Evolutionary Algorithm......Page 50 Experimental Framework and Results......Page 53 Conclusions......Page 57 References......Page 58 Introduction......Page 59 Classification of Gene Expression Data......Page 60 Data Sets......Page 61 Data Complexity Measures......Page 62 Classification Algorithms......Page 64 Experiments and Results......Page 65 Conclusions......Page 67 Introduction......Page 71 Dataset Description......Page 72 K-means Initial Segmentation......Page 73 Gaussian Mixture Model (GMM) Initial Segmentation......Page 74 Markov Random Field (MRF) Segmentation......Page 75 Quantitative Accuracy Assessment......Page 76 Discussion......Page 77 Concluding Remarks......Page 81 Introduction......Page 84 About ncRNAs and SVM-PORTRAIT......Page 85 Self-Organizing Maps......Page 86 Training Set Construction......Page 87 Model Configuration and Implementation Details......Page 88 A Case Study: The Paracoccidioidis Brasiliensis Fungus......Page 90 Experiment 1: Two Classes......Page 91 Experiment 2: Three Classes......Page 92 Comparing Two and Three Classes SOM-PORTRAIT......Page 93 Conclusions and Future Work......Page 94 Introduction......Page 97 Databases of Motifs......Page 99 Data Processing......Page 101 Methods......Page 102 Results and Discussion......Page 103 Related Work......Page 104 Conclusion and Future Work......Page 106 Introduction......Page 108 HP Model for Protein Structure Prediction......Page 109 Evolutionary Algorithms to Protein Structure Prediction......Page 110 Direct Representation......Page 112 Conformation Matrix......Page 113 Results and Discussion......Page 114 Conclusions......Page 116 Introduction......Page 120 Multilabel Classification......Page 121 Algorithm Independent Approach......Page 122 Evaluation Metrics......Page 123 Implemented Methods......Page 125 Experiments......Page 126 Conclusion......Page 130 Introduction......Page 132 Data Sets......Page 134 Machine Learning Methods......Page 135 Classification......Page 137 Related Work......Page 140 Conclusions......Page 141 Introduction......Page 144 Extended Model and Methodology......Page 145 Results......Page 148 Conclusion......Page 151 Introduction......Page 154 Developing FReDD Data Base: Towards Mining Experiments......Page 155 Final Considerations and Future Work......Page 156 References......Page 157 Materials and Methods......Page 158 Results......Page 160 References......Page 161 Introdution......Page 162 In Silico Analysis......Page 163 Results and Discussion......Page 164 Introduction......Page 167 Results......Page 168 Discussion......Page 169 References......Page 170 Introduction......Page 171 Results......Page 172 Discussion......Page 173 References......Page 174 Introduction......Page 175 Ontocancro......Page 176 Conclusion......Page 177 Author Index......Page 179 This volume contains the papers selected for presentation at the 4th Brazilian Sym- sium on Bioinformatics, BSB 2009, which was held in Porto Alegre, Brazil, during August 29–31, 2009. The BSB symposium had its origins in the Brazilian Workshop on Bioinformatics (WOB). WOB had three editions, in 2002 (Gramado, RS), in 2003 (Macaé, RJ), and in 2004 (Brasília, DF). The change in the designation from wo- shop to symposium reflects the increase in the quality of the contributions and also in the interest of the scientific community for the meeting. The previous editions of BSB took place in São Leopoldo, RS, in 2005, in Angra dos Reis, RJ, in 2007, and in Santo André, SP, in 2008. As evidence of the internationalization of the event, BSB 2009 had 55 submissions from seven countries. Of the 55 papers submitted, 36 were full papers, with up to 12 pages each, and 19 were extended abstracts, with up to 4 pages each. The articles submitted were carefully reviewed and selected by an international Program Comm- tee, comprising three chairs and 45 members from around the world, with the help of 21 additional reviewers. The Program Committee Chairs are very thankful to the - thors of all submitted papers, and especially to the Program Committee members and the additional reviewers, who helped select the 12 full papers and the six extended abstracts that make up this book.