BSB 2012 Program

Invited Talk 1
Fernando D. Gonzáles-Nilo - Universidad Andrés Bello, Chile
Neuroscience: Synergy between Molecular Simulations and Computational Biology
Chair: Maricel Kann (Univ. of Maryland, USA)

Invited Talk 2
Maricel Kann, Univ. of Maryland, USA
Protein Domain-Centric Approach to Study Cancer Somatic Mutations from High-throughput Sequencing Studies 
Chair: Marcilio C.P. de Souto (UFPE, Brazil)

Invited Talk 3
Jens Stoye - Bielefeld University, Germany
Genome Rearrangement by Double Cut and Join
Chair: João C. Setubal (USP, Brazil)

Invited Talk 4
José Fernando Garcia - Unesp, Brazil
From the Assembly of a "de novo" Genome to its Functional Exploration: The Short Story of Bos indicus
Chair: Marcelo M. Brigido (UnB, Brazil)

Invited Talk 5
Marcos Vinicius G.B. da Silva - Embrapa Gado de Leite, Brazil
How Genomics can be Applied for Sustainable Livestock Production
Chair: Cleber Oliveira Soares (Embrapa Gado de Corte, Brazil) 

Industry Talk
Leonardo Varuzza, Ph.D. - Life Technologies Brazil
Introduction to Semiconductor Sequencing
Chair: Marcelo M. Brigido (Unb, Brazil) 

Technical Session 1
Sequence Analysis and Motifs
Chair: Maria Emilia T. Walter (UnB, Brazil)

1. Transposition Diameter and Lonely Permutations
   Luis Cunha (UFRJ), Luis Kowada (Universidade Federal Fluminense), Rodrigo Hausen (USP) & Celina Figueiredo (UFRJ)
2. Extending the Algebraic Formalism for Genome Rearrangements to Include Linear Chromosomes
   Pedro Feijao (Universidade Estadual de Campinas), João Meidanis (Instituto de Computação - Unicamp)
3. On the Approximation Ratio of Algorithms for Sorting by Transpositions without Using Cycle Graphs
   Gustavo Galvão (University of Campinas), Zanoni Dias (University of Campinas)
4. A comparison of three heuristic methods for solving the parsing problem for tandem repeats
   Atheer Matroud (Massey University), Christopher Tuffley (Massey University), David Bryant (University of Otago),  Michael Hendy (University of Otago)

Technical Session 2
Algorithms for Problems in Computational Biology
Chair: Maricel Kann (Univ. of Maryland, USA)

1. A Probabilistic Model Checking Approach to Investigate the Palytoxin Effects on the Na+/K+-ATPase
   Fernando Braz (Universidade Federal de Minas Gerais), Jáder Cruz (Universidade Federal de Minas Gerais),  Alessandra Faria-Campos (Universidade Federal de Minas Gerais), Sergio Campos (Universidade Federal de Minas Gerais)
2. A Bioconductor based workflow for Z-DNA region detection and biological inference
   Halian Vilela (Universidade de Brasília), Taina Raiol Alencar (University Of Brasilia), Andrea Maranhao (UnB), Maria Emilia Walter (University of Brasilia (UnB) & Marcelo Brigido (Universidade de Brasília
3. Molecular Dynamics for simulating the Protein Folding Process using the 3D AB off-lattice Model
   César Benítez (UTFPR), Heitor Lopes (Universidade Tecnológica Federal do Paraná)
4. RNA Folding Algorithms with G-Quadruplexes
   Ronny Lorenz (Theoretical Chemistry, Univ. of Vienna), Stephan H. Bernhart (Bioinformatics, Dept of Comp. Sci., Uni Leipzig), Fabian Externbrink (Bioinformatics, Dept
   of Comp. Sci., Uni Leipzig), Jing Qin (Bioinformatics, Dept of Comp. Sci., Uni Leipzig), Christian Hoener zu Siederdissen (Theoretical Chemistry, Univ. of Vienna), Fabian Amman (Theoretical Chemistry, Univ. of Vienna), Ivo L. Hofacker (Theoretical Chemistry, Univ. of Vienna), Peter Stadler (University of Leipzig)

Technical Session 3
Gene identification, Regulation and Expression Analysis, and Personal Genomics
Chair: Marcilio C. P. de Souto (UFPE, Brazil)

1. RFMirTarget: a random forest classifier for Human miRNA target gene prediction
   Mariana Mendoza (Universidade Federal do Rio Grande do Sul), Guilherme C. da Fonseca (Universidade Federal do Rio Grande do Sul, Centro de Biotecnologia), Guilherme L. de Morais (Universidade Federal do Rio Grande do Sul, Centro de Biotecnologia),  Ronnie Alves (UFRGS), Ana Bazzan (UFRGS), Rogerio Margis (Universidade Federal do Rio Grande do Sul, Centro de Biotecnologia)
2. Prediction of Transcription Factor Binding Sites by Integrating DNase digestion and Histone Modification
   Eduardo Gusmão (Universidade Federal de Pernambuco),  Christoph Dieterich (Berlin Institute for Medical Systems Biology), Ivan Gesteira Costa (Universidade Federal de Pernambuco)
3. Evaluating Correlation Coefficients for Clustering Gene Expression Profiles of Cancer
   Pablo Jaskowiak (University of São Paulo), Ricardo Campello (SCC / ICMC / USP), Ivan Gesteira Costa (Universidade Federal de Pernambuco)
4. Associating Genotype Sequence Properties to Haplotype Inference Errors
   Rogério Rosa (Federal University of Pernambuco), Rafael Santos (Universidade Federal de Pernambuco), Katia Guimarães (Universidade Federal de Pernambuco)

Technical Session 4
Biological Databases, and Applications in Evolution and Phylogenetics
Chair: Said S. Adi (UFMS, Brazil)

1. Design and Implementation of ProteinWorldDB
   Sergio Lifschitz (PUC-Rio), Carlos Juliano M. Viana (PUC-Rio), Cristian Tristao (PUC-Rio), Marcos Catanho (Instituto Oswaldo Cruz), Wim M. Degrave (Instituto Oswaldo Cruz), Antonio Basilio de Miranda (Instituto Oswaldo Cruz), Marcia Bezerra (Instituto Oswaldo Cruz), & Thomas D. Otto (Wellcome Trust Sanger Institute, UK)
2. A Comparative Analysis of Public Ligand Databases based on Molecular Descriptors
   Ana Trindade Winck (PUC-RS), Christian Quevedo (PUC-RS), Karina Machado (Fundação Universidade Federal do Rio Grande), Osmar Norberto de Souza (PUC-RS) &  Duncan Ruiz (PUC-RS)
3. Phylogenetic distance computation using CUDA
   Wellington Martins (Universidade Federal de Goiás), Thiago Rangel (Universidade Federal de Goiás), Divino Lucas (Unicamp), Elias Ferreira (Universidade Federal de Goiás), Edson Cáceres (UFMS)
4. Exploring Molecular Evolution Reconstruction Using a Parallel Cloud-based Scientific Workflow - Kary Ocaña (COPPE/UFRJ), Daniel de Oliveira (COPPE/UFRJ), Felipe Horta (POLI/UFRJ), Jonas Dias (COPPE/UFRJ), Eduardo Ogasawara (CEFET/RJ), Marta Mattoso (COPPE/UFRJ)