ECAI'08 Workshop

“Bioinformatics, Genomics & Proteomics, an Artificial Intelligence Approach”

To be held in conjunction with ECAI 2008
Patras, Greece
Tuesday 22 July, 2008

Objectives  Program Topics and Technical issues Paper Submission Important Dates! Program Committee




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. 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. Hence, this workshop brings the opportunity to discuss applications of AI with an interdisciplinary character, exploring the interactions between sub-areas of AI and Bioinformatics.


Topics and Technical issues

Papers should deal with bio-medical data sets. Computer science and mathematical modelling papers must contain a concise description of the biological problem being solved, and biology papers should show how computation or analysis improves the results.


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

- sequence analysis,
- comparison and alignment methods,
- motif, gene and signal recognition,
- molecular evolution,
- determination or prediction of the structure of RNA and protein in two
and three dimensions,
- gene expression and gene regulatory networks,
- deduction of metabolic pathways,
- microarray design and analysis,
- proteomics,
- functional genomics,
- molecular docking and drug design,
- systems biology,

- miRNA prediction.

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

- Knowledge Discovering techniques and Data Mining,
- 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.

Paper Submission

It is highly recommended to submit papers using the final camera-ready formatting style specified in ECAI 08 Style Guide. Submissions must not exceed 6 pages. All submissions must be sent in PDF or PS format by e-mail to the workshop chairs A. Tsakalides ( and L. Skarlas (

Goals and Intended Audience

The workshop's aim is to discuss computational aspects and challenges of important biological problems and, in doing so, identify new research opportunities. A second goal is to establish a forum that will bring together researchers in Artificial Intelligence face to face with researchers in bioinformatics. The hope is that this workshop will provide a forum where people from the two communities can come together to exchange ideas and discuss different approaches

Important Dates


Deadline for Early Registration

8 June 2008


Deadline for camera-ready paper:

16 June 2008

Workshop Date:

Tuesday 22 July, 2008



Participants to the workshop should register directly to the main ECAI 2008 conference (workshops' early registration

deadline is set to 8 June 2008).


Workshop Proceedings

Each workshop participant will receive a hardcopy of the proceedings of the workshop (s)he participates, as well as a

CD with the proceedings of all ECAI'08 workshops.


Program Chairs:

Prof. Tsakalides Athanasios, Computer & Informatics Department, University of Patras, Greece

Dr. Skarlas Lambros, Pattern Recognition Laboratory, Clinical Oncology Laboratory, University of Patras, Greece


BIGPAIA Workshop Program


Welcome - Introduction

Tsakalides Athanasios, University of Patras, and  Lambros Skarlas, Hellenic Open University


A marginal mixture model for discovering motifs in sequences

Konstantinos Blekas, University of Ioannina


Large-Scale Genetic Network Learning

Andreas Nagele, Technical University of Munich





– Invited Talk -

D.Sanoudou, Bioacademy


Mining Gene Regulatory Networks and Microarray Data: The MinePath Approach

George Potamias, Institute of Computer Science, FORTH


Supervised class prediction in Dukes' B colon cancer

Anna Antonacopoulou, Clinical Oncology Laboratory, University of Patras


A web-server applying Naïve Bayes and SVM for microRNA gene prediction

Malik Yousef, Systems Biology Division, The Wistar Institute, Philadelphia


MAPS: an intelligent learning environment for bioinformatics.

Kalles Dimitris, Hellenic Open University



Tsakalides Athanasios, and  Lambros Skarlas



Program Committee

D. Tsavachidou (USA)

S. Likothanassis (GREECE)

M. Yousef (ISRAEL)

G. Valentini (ITALY)

C. Makris (GREECE)

H. Kalofonos (GREECE)


M. Vrahatis (GREECE)

A. Tsakalides (GREECE)

L. Skarlas (GREECE)

E. Maniataki (USA)

I.  Hatzilygeroudis (GREECE)