Advances in Bioinformatics and Computational Biology

1. Front Matter

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2. Transposition Diameter and Lonely Permutations

   • Luís Felipe I. Cunha, Luis Antonio B. Kowada, Rodrigo de A. Hausen, Celina M. H. de Figueiredo

   Pages 1-12

3. Extending the Algebraic Formalism for Genome Rearrangements to Include Linear Chromosomes

   • Pedro Feijao, Joao Meidanis

   Pages 13-24

4. On the Approximation Ratio of Algorithms for Sorting by Transpositions without Using Cycle Graphs

   • Gustavo Rodrigues Galvão, Zanoni Dias

   Pages 25-36

5. A Comparison of Three Heuristic Methods for Solving the Parsing Problem for Tandem Repeats

   • A. A. Matroud, C. P. Tuffley, D. Bryant, M. D. Hendy

   Pages 37-48

6. RNA Folding Algorithms with G-Quadruplexes

   • Ronny Lorenz, Stephan H. Bernhart, Fabian Externbrink, Jing Qin, Christian Höner zu Siederdissen, Fabian Amman et al.

   Pages 49-60

7. Molecular Dynamics for Simulating the Protein Folding Process Using the 3D AB Off-Lattice Model

   • César Manuel Vargas Benítez, Heitor Silvério Lopes

   Pages 61-72

8. A Bioconductor Based Workflow for Z-DNA Region Detection and Biological Inference

   • Halian Vilela, Tainá Raiol, Andrea Queiroz Maranhão, Maria Emília Walter, Marcelo M. Brígido

   Pages 73-83

9. A Probabilistic Model Checking Approach to Investigate the Palytoxin Effects on the Na + /K + -ATPase

   • Fernando A. F. Braz, Jader S. Cruz, Alessandra C. Faria-Campos, Sérgio V. A. Campos

   Pages 84-96

10. RFMirTarget: A Random Forest Classifier for Human miRNA Target Gene Prediction

    • Mariana R. Mendoza, Guilherme C. da Fonseca, Guilherme L. de Morais, Ronnie Alves, Ana L. C. Bazzan, Rogerio Margis

    Pages 97-108

11. Prediction of Transcription Factor Binding Sites by Integrating DNase Digestion and Histone Modification

    • Eduardo G. Gusmão, Christoph Dieterich, Ivan G. Costa

    Pages 109-119

12. Evaluating Correlation Coefficients for Clustering Gene Expression Profiles of Cancer

    • Pablo A. Jaskowiak, Ricardo J. G. B. Campello, Ivan G. Costa

    Pages 120-131

13. Associating Genotype Sequence Properties to Haplotype Inference Errors

    • Rogério S. Rosa, Rafael H. S. Santos, Katia S. Guimarães

    Pages 132-143

14. Design and Implementation of ProteinWorldDB

    • Sérgio Lifschitz, Carlos Juliano M. Viana, Cristian Tristão, Marcos Catanho, Wim M. Degrave, Antonio Basílio de Miranda et al.

    Pages 144-155

15. A Comparative Analysis of Public Ligand Databases Based on Molecular Descriptors

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

    Pages 156-167

16. Phylogenetic Distance Computation Using CUDA

    • Wellington S. Martins, Thiago F. Rangel, Divino C. S. Lucas, Elias B. Ferreira, Edson N. Caceres

    Pages 168-178

17. Exploring Molecular Evolution Reconstruction Using a Parallel Cloud Based Scientific Workflow

    • Kary A. C. S. Ocaña, Daniel de Oliveira, Felipe Horta, Jonas Dias, Eduardo Ogasawara, Marta Mattoso

    Pages 179-191

18. How Bioinformatics Enables Livestock Applied Sciences in the Genomic Era

    • José Fernando Garcia, Adriana Santana do Carmo, Yuri Tani Utsunomiya, Haroldo Henrique de Rezende Neves, Roberto Carvalheiro, Curtis Van Tassell et al.

    Pages 192-201

19. Back Matter

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This book constitutes the refereed proceedings of the 7th Brazilian Symposium on Bioinformatics, BSB 2012, held in Campo Grande, Brazil, in August 2012. The 16 regular papers presented were carefully reviewed and selected for inclusion in this book. It also contains a joint paper from two of the guest speakers. The Brazilian Symposium on Bioinformatics covers all aspects of bioinformatics and computational biology, including sequence analysis; motifs, and pattern matching; biological databases, data management, data integration, and data mining; biomedical text mining; structural, comparative, and functional genomics; personal genomics; protein structure, modeling, and simulation; gene identification, regulation and expression analysis; gene and protein interaction and networks; molecular docking; molecular evolution and phylogenetics; computational systems biology; computational proteomics; statistical analysis of molecular sequences; algorithms for problems in computational biology; applications in molecular biology, biochemistry, genetics, medicine, microbiology and associated subjects.

• dynamic programming
• neural network
• parallel computing
• probabilistic model checking
• target prediction
• algorithm analysis and problem complexity

• Universidade Federal de Pernambuco, Recife, Brazil

  Marcilio C. Souto

• Department of Biological Sciences, University of Maryland/Baltimore County, Baltimore, USA

  Maricel G. Kann

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