[Bio-matrix] CFP: Workshop on Computational Methods in Bioinformatics and Systems Biology

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Sat Jun 16 08:36:22 EST 2007

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             CALL FOR PAPERS (Reminder)   Deadline: 30 June 2007

        Workshop on Computational Methods in Bioinformatics and Systems Biology

                      epia2007 from appia.pt

                          as part of the
        13th Portuguese Conference on Artificial Intelligence
             Guimaraes, Portugal,  3-7 December 2007
                     email: epia2007 from appia.pt

                           Call for Papers

  		         Invited Speaker:

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

           Second Invited Speaker to be announced

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 optimisation.

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, modelling and optimisation tasks. This
workshop brings the opportunity to discuss applications of AI  
exploring the interactions
between this field, Bioinformatics and Systems Biology.

Topics and Technical issues

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;
   - Metabonomics;
   - 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;
   - Metabolic engineering applications;
   - Cell simulation and modelling;
   - Metabolic, regulatory and signalling networks: properties,  
dynamics, inference and reverse engineering.


The 13th Portuguese Conference on Artificial Intelligence is sponsored by
APPIA, the Portuguese Association of AI (http://www.appia.pt/).


Authors should submit full papers with a maximum of 12 pages reporting on
innovative work, work reported elsewhere, ongoing research or student
projects.  Only innovative full papers are candidate to publications in
the Springer proceedings as specified below. All papers must follow the
Springer instructions for authors as indicated in

A selection of the workshop accepted full papers will be published by Springer
in the Lecture Notes in Artificial Intelligence sub-series of LNCS. All
accepted papers not published in the Springer proceedings will be
published in ta Local Workshop Proceedings, in hard copy, in CD-ROM  
and in the web.

To be a candidate for publication in the main proceedings the
following rules must be met:

* Submissions must be full technical papers on substantial, original,
   and previously unpublished research.

* Submissions must be formatted according to the Springer LNCS Series
   guidelines, and must not exceed 12 pages. Each selected paper will be
   allowed 12 pages in the Proceedings. Up to two additional pages may
   be purchased by the authors.

At least one of the authors must be registered at the conference for
the paper to be published in the proceedings.

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.

Important Dates

Here are some important dates:

   Conference begins      December 3rd, 2007

   Paper submission       June 30th, 2007
   Author notification    July 28th, 2007
   Camera-ready copies    September 1st, 2007

Submission and reviewing Information

Submission is made through the submission page available in the EPIA 2007
website  http://epia2007.appia.pt/


Program Chairs

Rui Camacho                           Miguel Rocha
LIACC and FEUP,                       Dep. Informática / CCTC,
Universidade do Porto, Portugal       Universidade do Minho, Portugal
rcamacho from fe.up.pt                     mrocha from di.uminho.pt


Yonghong Peng                          Isabel Rocha
Department of Computing,               Dep. Engenharia Biologica,
University of Bradford, U. K.          Universidade do Minho, Portugal
y.h.peng from bradford.ac.uk                irocha from deb.uminho.pt

Nuno Fonseca                          Kiran Patil
LIACC and FCUP,                       Biocentrum,
Universidade do Porto, Portugal       Technical University of Denmark, Denmark
nf from ncc.up.pt                          krp from biocentrum.dtu.dk

Alexessander Alves                    Florentino Fdez-Riverola
Imperial College London, UK           Escuela Superior de Ingeniería  
Informática, Ourense, Spain
alves from ieee.org                        riverola from uvigo.es

Program Committee

Alexessander Alves           (Imperial College, London, UK)
Philip Bourne                (University of California, San Diego, USA)
Pavel Brazdil                (University of Porto, Portugal)
Chris Bystroff               (Rensselaer Polytechnic Institute, USA)
Rui Camacho                  (LIACC, FEUP, Universidade do Porto, Portugal)
Andre Carvalho               (University of Sao Paulo Sao Carlos, Brasil)
Vitor Costa                  (LIACC, FCUP, Universidade do Porto, Portugal)
Francisco Couto              (Faculdade de Ciencias da Univ. Lisboa, Portugal)
Luc Dehaspe                  (PharmaDM, Belgium)
Fernando Diaz		     (Univ. Valladolid, Spain)
Ines Dutra                   (UFRJ, Brasil )
Timothy MD Ebbels            (Imperial College London, U.K.)
Fazel Famili                 (NRC Institute for Information  
Technology, Canada)
Eugénio Ferreira	     (Univ. Minho, Portugal)
Nuno Fonseca                 (IBMC/LIACC, Portugal)
Elaine Holmes                (Imperial College London, U.K.)
Eva Iglesias		     (Univ. Vigo, Spain)
Hasan M. Jamil               (Wayne State University, USA )
Alipio Jorge                 (LIACC, FEP, Universidade do Porto, Portugal)
Rui Mendes		     (univ. Minho, Portugal)
José Mendez-Reboredo	     (Univ. VIgo, Spain)
Kiran Patil		     (DTU, Denmark)
Enrique Caso Pelaez          (Fichuvi, Spain)
Yonghong Peng                (Bradford University, UK)
Florentino Riverola	     (Univ. Vigo, Spain)
Isabel Rocha		     (Univ. Minho, Portugal)
Miguel Rocha		     (Univ. Minho, Portugal)
Marie-France Sagot           (Inria Rhone-Alpes, Universite Claude  
Bernard, Lyon I, France)
Mario J. G. Silva            (Faculdade de Ciencias da Univ. Lisboa, Portugal)
Jorge Vieira                 (IBMC, Portugal)
Mohammed Zaki                (Rensselaer Polytechnic Institute, USA)


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