Computational Methods in Bioinformatics and Systems Biology (3rd edition)

a thematic track of
EPIA 2013, the XVI Portuguese Conference on Artificial Intelligence
Angra do Heroísmo, Azores, Portugal, September 9-13, 2013
http://www.epia2013.uac.pt/?page_id=597

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Call for Papers
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The success of bioinformatics in recent years has been prompted by research in molecular biology and medicine in initiatives like the human genome project.
These initiatives gave rise to an enormous increase in the volume and diversification of data, including protein and genomic sequences, high-throughput experimental and biomedical literature.
Systems Biology is a related field, devoted mainly to efforts in cell modelling, that require the coordinated work of biological researchers with those related to data analysis, mathematical modelling, computer simulation and optimization.
The accumulation and exploitation of large-scale databases prompts for new computational technologies 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 experimental data, are based on Artificial Intelligence (AI) techniques.
In fact, these methods have been helping in tasks related to knowledge discovery, modelling 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.


Topics and Technical issues
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Computational areas of interest include, but are not limited to:
- Knowledge Discovery and Data Mining techniques
- 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:
- Analysis of high-throughput biological data (transcriptomics/ gene expression, proteomics, metabolomics, fluxomics)
- 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;
- Prediction of metabolic pathways and metabolic engineering applications;
- 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;
- Visualisation of biological systems and networks;
- Data and software integration;
- In silico optimisation of biological systems;
- Cell simulation and modelling;
- Metabolic, regulatory and signalling networks: properties, dynamics, inference and reverse engineering.

Submissions should address relevant biological/ biomedical research problems, through computational techniques, making original
contributions at the fundamental or applied levels.

Paper submission
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Submitted papers should be full-length papers with a maximum length of 12 pages.
The best papers will be published in a volume of Lecture Notes in Artificial Intelligence (LNAI) by Springer (proceedings indexed by the Thomson ISI Web of Knowledge).
All other accepted papers will be published in the local proceedings.

All papers should be submitted in PDF format through EPIA’2013 Conference Management Website:
https://www.easychair.org/conferences/?conf=epia2013

All papers should be prepared according to the formatting instructions of Springer LNAI series.
The review process is double-blind. Therefore, authors must remove their names from the submitted papers and should take reasonable care not to indirectly disclose their identity.
References to own work may be included in the paper, as long as referred to in the third person. Three program committee members will be assigned to review each paper.
Acceptance will be based on the paper’s significance, technical quality, clarity, relevance and originality.
Accepted papers must be presented at the conference by one of the authors and at least one author of each accepted paper must register for the conference.


Important Dates:
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- Deadline for paper submission: March 15, 2013
- Notification of paper acceptance: April 30, 2013
- Deadline for final versions: May 31, 2013


Organising comittee
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Miguel Rocha
Universidade do Minho, Portugal
mrocha@di.uminho.pt

Rui Camacho
Universidade do Porto, Portugal
rcamacho@fe.up.pt

Sara Madeira
Instituto Superior Técnico, Portugal
smadeira@kdbio.inesc-id.pt

Jose Luis Oliveira
Universidade de Aveiro, Portugal
jlo@ua.pt