Advances in Bioinformatics and Computational Biology

1. Front Matter

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2. The Trouble with Long-Range Base Pairs in RNA Folding

   • Fabian Amman, Stephan H. Bernhart, Gero Doose, Ivo L. Hofacker, Jing Qin, Peter F. Stadler et al.

   Pages 1-11

3. Roles of RORα on Transcriptional Expressions in the Mammalian Circadian Regulatory System

   • Hiroshi Matsuno, Makoto Akashi

   Pages 12-23

4. HybHap: A Fast and Accurate Hybrid Approach for Haplotype Inference on Large Datasets

   • Rogério S. Rosa, Katia S. Guimarães

   Pages 24-35

5. Restricted DCJ-Indel Model Revisited

   • Marília D. V. Braga, Jens Stoye

   Pages 36-46

6. MSA-GPU: Exact Multiple Sequence Alignment Using GPU

   • Daniel Sundfeld, Alba C. M. A. de Melo

   Pages 47-58

7. MultiSETTER - Multiple RNA Structure Similarity Algorithm

   • David Hoksza, Peter Szépe, Daniel Svozil

   Pages 59-70

8. Assessing the Accuracy of the SIRAH Force Field to Model DNA at Coarse Grain Level

   • Pablo D. Dans, Leonardo Darré, Matías R. Machado, Ari Zeida, Astrid F. Brandner, Sergio Pantano

   Pages 71-81

9. How to Multiply Dynamic Programming Algorithms

   • Christian Höner zu Siederdissen, Ivo L. Hofacker, Peter F. Stadler

   Pages 82-93

10. Influence of Scaffold Stability and Electrostatics on Top7-Based Engineered Helical HIV-1 Epitopes

    • Isabelle F. T. Viana, Rafael Dhalia, Marco A. Krieger, Ernesto T. A. Marques, Roberto D. Lins

    Pages 94-103

11. Random Forest and Gene Networks for Association of SNPs to Alzheimer’s Disease

    • Gilderlanio S. Araújo, Manuela R. B. Souza, João Ricardo M. Oliveira, Ivan G. Costa

    Pages 104-115

12. Multilayer Cluster Heat Map Visualizing Biological Tensor Data

    • Atsushi Niida, Georg Tremmel, Seiya Imoto, Satoru Miyano

    Pages 116-125

13. On the 1.375-Approximation Algorithm for Sorting by Transpositions in O(n logn) Time

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

    Pages 126-135

14. ncRNA-Agents: A Multiagent System for Non-coding RNA Annotation

    • Wosley Arruda, Célia G. Ralha, Tainá Raiol, Marcelo M. Brígido, Maria Emília M. T. Walter, Peter F. Stadler

    Pages 136-147

15. Inference of Genetic Regulatory Networks Using an Estimation of Distribution Algorithm

    • Thyago Salvá, Leonardo R. Emmendorfer, Adriano V. Werhli

    Pages 148-159

16. A Network-Based Meta-analysis Strategy for the Selection of Potential Gene Modules in Type 2 Diabetes

    • Ronnie Alves, Marcus Mendes, Diego Bonnato

    Pages 160-169

17. RAIDER: Rapid Ab Initio Detection of Elementary Repeats

    • Nathaniel Figueroa, Xiaolin Liu, Jiajun Wang, John Karro

    Pages 170-180

18. A Probabilistic Model Checking Analysis of the Potassium Reactions with the Palytoxin and Na + /K + -ATPase Complex

    • Fernando Braz, João Amaral, Bruno Ferreira, Jader Cruz, Alessandra Faria-Campos, Sérgio Campos

    Pages 181-193

19. False Discovery Rate for Homology Searches

    • Hyrum D. Carroll, Alex C. Williams, Anthony G. Davis, John L. Spouge

    Pages 194-201

20. A Pipeline to Characterize Virulence Factors in Mycobacterium Massiliense Genome

    • Guilherme Menegói, Tainá Raiol, João Victor de Araújo Oliveira, Edans Flávius de Oliveira Sandes, Alba Cristina Magalhães Alves de Melo, Andréa Queiroz Maranhão et al.

    Pages 202-213

This book constitutes the refereed proceedings of the 8th Brazilian Symposium on Bioinformatics, BSB 2013, held in Recife, Brazil, in November 2013. The 18 regular papers presented were carefully reviewed and selected for inclusion in this book. The papers cover all aspects of bioinformatics and computational biology.

• RNA folding
• algorithms
• data mining
• gene expressions
• sequence analysis
• algorithm analysis and problem complexity

• Institute of Chemistry, University of São Paulo, São Paulo, Brazil

  João C. Setubal

• School of Computing, Facom-UFMS, Federal University of Mato Grosso do Sul, Brazil

  Nalvo F. Almeida

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