Advances in Bioinformatics and Computational Biology

1. Front Matter

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2. Algorithmic Approaches for Molecular Biology Problems

   1. Genotype Tagging with Limited Overfitting

      • Irina Astrovskaya, Alex Zelikovsky

      Pages 1-12

   2. Constraint Programming Models for Transposition Distance Problem

      • Ulisses Dias, Zanoni Dias

      Pages 13-23

   3. Comparison of Spectra in Unsequenced Species

      • Freddy Cliquet, Guillaume Fertin, Irena Rusu, Dominique Tessier

      Pages 24-35

3. Micro-array Analysis

   1. BiHEA: A Hybrid Evolutionary Approach for Microarray Biclustering

      • Cristian Andrés Gallo, Jessica Andrea Carballido, Ignacio Ponzoni

      Pages 36-47

   2. Using Supervised Complexity Measures in the Analysis of Cancer Gene Expression Data Sets

      • Ivan G. Costa, Ana C. Lorena, Liciana R. M. P. y Peres, Marcilio C. P. de Souto

      Pages 48-59

   3. Quantitative Improvements in cDNA Microarray Spot Segmentation

      • Mónica G. Larese, Juan Carlos Gómez

      Pages 60-72

4. Machine Learning Methods for Classification

   1. SOM-PORTRAIT: Identifying Non-coding RNAs Using Self-Organizing Maps

      • Tulio C. Silva, Pedro A. Berger, Roberto T. Arrial, Roberto C. Togawa, Marcelo M. Brigido, Maria Emilia M. T. Walter

      Pages 73-85

   2. Automatic Classification of Enzyme Family in Protein Annotation

      • Cássia T. dos Santos, Ana L. C. Bazzan, Ney Lemke

      Pages 86-96

   3. Representations for Evolutionary Algorithms Applied to Protein Structure Prediction Problem Using HP Model

      • Paulo H. R. Gabriel, Alexandre C. B. Delbem

      Pages 97-108

   4. Comparing Methods for Multilabel Classification of Proteins Using Machine Learning Techniques

      • Ricardo Cerri, Renato R. O. da Silva, André C. P. L. F. de Carvalho

      Pages 109-120

   5. Comparative Study of Classification Algorithms Using Molecular Descriptors in Toxicological DataBases

      • Max Pereira, Vítor Santos Costa, Rui Camacho, Nuno A. Fonseca, Carlos Simões, Rui M. M. Brito

      Pages 121-132

5. In Silico Simulation

   1. Influence of Antigenic Mutations in Time Evolution of the Immune Memory – A Dynamic Modeling

      • Alexandre de Castro, Carlos Frederico Fronza, Poliana Fernanda Giachetto, Domingos Alves

      Pages 133-142

6. Short Papers

   1. FReDD: Supporting Mining Strategies through a Flexible-Receptor Docking Database

      • Ana T. Winck, Karina S. Machado, Osmar Norberto-de-Souza, Duncan D. D. Ruiz

      Pages 143-146

   2. A Wide Antimicrobial Peptides Search Method Using Fuzzy Modeling

      • Fabiano C. Fernandes, William F. Porto, Octavio L. Franco

      Pages 147-150

   3. Identification of Proteins from Tuberculin Purified Protein Derivative (PPD) with Potential for TB Diagnosis Using Bioinformatics Analysis

      • Sibele Borsuk, Fabiana Kommling Seixas, Daniela Fernandes Ramos, Caroline Rizzi, Odir Antonio Dellagostin

      Pages 151-155

   4. Mapping HIV-1 Subtype C gp120Epitopes Using a Bioinformatic Approach

      • Dennis Maletich Junqueira, Rúbia Marília de Medeiros, Sabrina Esteves de Matos Almeida, Vanessa Rodrigues Paixão-Cortez, Paulo Michel Roehe, Fernando Rosado Spilki

      Pages 156-159

   5. MHC: Peptide Analysis: Implications on the Immunogenicity of Hantaviruses’ N protein

      • Maurício Menegatti Rigo, Dinler Amaral Antunes, Gustavo Fioravanti Vieira, José Artur Bogo Chies

      Pages 160-163

   6. An Ontology to Integrate Transcriptomics and Interatomics Data Involved in Gene Pathways of Genome Stability

      • Giovani Rubert Librelotto, José Carlos Mombach, Marialva Sinigaglia, Éder Simão, Heleno Borges Cabral, Mauro A. A. Castro

      Pages 164-167

7. Back Matter

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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.

• In silico
• algorithms
• bioinformatics
• biology
• classification
• learning
• machine learning
• simulation

• Center of Informatics, Av. Prof. Luiz Freire, Federal University of Pernambuco, Recife, Brazil

  Katia S. Guimarães

• National Library of Medicine, National Institutes of Health, National Center for Biotechnology Information, USA

  Anna Panchenko

• National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, USA

  Teresa M. Przytycka

Policies and ethics