Workshop on Computational Methods in Bioinformatics and Systems Biology

The success of bioinformatics in recent years has been prompted by research in molecular biology and molecular medicine in initiatives like the human genome project. The volume and diversification of data has increased so much that is hard if not impossible to analyse by human experts. Systems Biology is a related  research area that has been replacing the reductionist view that dominated biology research in the last decades, requiring the coordinated efforts of biological researchers with those related to data analysis, mathematical modelling, computer simulation and optimization.

The growth of large-scale data bases prompts for new computational technology and for research in this arena. Computational methods methods have been helping in tasks related to knowledge discovery, modeling and optimization tasks. This workshop brings the opportunity to discuss applications of AI exploring the interactions between this field, Bioinformatics and Systems Biology.

Topics of Interest

Computational areas of interest include, but are not limited to:

- Knowledge Discovery and Data Mining techniques for the Analysis of high-throughput biological data (trancriptomics, proteomics, metabolomics, fluxomics)
- Text Mining and Language Processing;
- Machine Learning and Pattern Recognition;
- Rough, Fuzzy and Hybrid Techniques;
- Hidden Markov Models;
- Bayesian Approaches;
- Artificial Neural Networks;
- Support Vector Machines;
- Evolutionary Computing;
- Non-linear dynamical analysis methods and Intelligent signal processing;
- Feature selection.

Biological areas of interest include, but are not limited to:

- Sequence analysis,
- Comparison and alignment methods;
- Motif, gene and signal recognition;
- Molecular evolution;
- Phylogenetics and phylogenomics;
- Determination or prediction of the structure of RNA and protein in two and three dimensions;
- DNA twisting and folding;
- Gene expression and gene regulatory networks;
- Deduction of metabolic pathways;
- Microarray design and analysis;
- Proteomics;
- Functional genomics;
- Molecular docking and drug design;
- Computational problems in genetics such as linkage and QTL analysis, linkage disequilibrium analysis in populations, and haplotype determination;
- Molecular and cellular interactions;
- Emergence of properties in complex biological systems;
- Visualization of biological systems and networks;
- Data and softwqare integration;
- In silico optimization of biological systems;
- Metabolic engineering applications;
- Cell simulation and modelling;
- Metabolic, regulatory and signalling networks: properties, dynamics, inference and reverse engineering;
- Metabonomics.

Scope

The success of bioinformatics in recent years has been prompted by research in molecular biology and molecular medicine in initiatives like the human genome project. These initiatives gave rise to an exponential increase in the volume and diversification of data, including protein and gene data, nucleotide sequences and biomedical literature.

Systems Biology is a related  research area that has been replacing the reductionist view that dominated biology research in the last decades, requiring the coordinated efforts of biological researchers with those related to data analysis, mathematical modelling, computer simulation and optimization.

The accumulation and exploitation of large-scale data bases prompts for new computational technology and for research into these issues. In this context, many widely successful computational models and tools used by biologists in these initiatives, such as clustering and classification methods for gene expression data, are based on artificial intelligence (AI) techniques.

In fact, these methods have been helping in tasks related to knowledge discovery, modeling and optimization tasks, aiming at the development of computational models so that the response of biological complex systems to any perturbation can be predicted. Hence, this workshop brings the opportunity to discuss applications of AI with an interdisciplinary character, exploring the interactions between sub-areas of AI, Bioinformatics and Systems Biology.

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Invited speaker:

1st: "Protein folding and unfolding simulations: new challenges in data mining and data warehousing", Rui Brito, (Universidade de Coimbra, Portugal)

2nd: (to be anounced)

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Journal special issue:

We will have a special issue in the Journal of Computational Intelligence in Bioinformatics (JCIB) with selected and extended papers from the workshop. 

Organising Committee

Program Chairs

Rui Camacho                           Miguel Rocha
LIACC and FEUP,                       Dep. Informática / CCTC,
Universidade do Porto, Portugal       Universidade do Minho, Portugal
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Yonghong Peng                          Isabel Rocha
Department of Computing,               Dep. Engenharia Biologica,
University of Bradford, U. K.          Universidade do Minho, Portugal
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Nuno Fonseca                          Kiran Patil
LIACC and FCUP,                       Biocentrum,
Universidade do Porto, Portugal       Technical University of Denmark, Denmark
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Alexessander Alves                    Florentino Fdez-Riverola
Imperial College London, UK           Escuela Superior de Ingeniería Informática, Ourense, Spain
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Program Committee