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Workshop on Computational Methods in Bioinformatics

rcamacho at fe.up.pt rcamacho at fe.up.pt
Mon May 30 10:49:14 EST 2005

*** We apologise for multiple copies ***

                      *** Deadline extended ***

                **  Paper submission June 3rd, 2005 **

       Workshop on Computational Methods in Bioinformatics

                     cmb.epia05 at di.ubi.pt

                         as part of the
       12th Portuguese Conference on Artificial Intelligence
            Covilha, Portugal,  5-8 December 2005
                    email: epia05 at di.ubi.pt

                      Call for Papers

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;
  - 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;
  - systems biology.

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


The 12th Portuguese Conference on Artificial Intelligence is sponsored by
APPIA, the Portuguese Association of AI (http://www.appia.pt/).

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.


Authors may submit full papers with a maximum of 12 pages or short
papers with a maximum of 4 pages. Both kinds of papers may report 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 by UBI in the 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.


The workshop will have a poster session running during the coffee
breaks. Posters are intended to report on work in progress,
student projects, open problems and research issues, as well as new
application challenges.

Important Dates

Here are some important dates:

  Conference begins      December 5th, 2005

  Paper submission       June 3rd, 2005
  Author notification    July 15th, 2005
  Camera-ready copies    July 28th, 2005

Submission and reviewing Information

The workshop will follow a blind reviewing policy. In order to make
blind reviewing possible, submissions must be anonymous. This requires
that authors exercise some care not to identify themselves in their
contributions. Authors should omit their names and affiliations from
the paper. Also, while the references should include all published
literature relevant to the paper, including previous works of the
authors, it should not include unpublished works. When referring to
one's own work, authors must use the third person rather than the
first person.

To submit a paper the author fills in an electronic form with author's
and papers information and them upload the paper in PDF format.

All papers (short or full papers) will follow the same reviewing process.

Submission is made through the submission page available in the EPIA 2005
website  http://epia05.di.ubi.pt .


Program Chairs

Rui Camacho                           Alexessander Alves
LIACC and FEUP,                       LIACC
Universidade do Porto, Portugal       Universidade do Porto, Portugal
rcamacho at fe.up.pt                     alves at ieee.org

Joaquim Pinto da Costa                Paulo Azevedo
LIACC and FCUP                        Departamento de Informatica
Universidade do Porto, Portugal       Universidade do Minho, Portugal
jpcosta at fc.up.pt                      pja at di.uminho.pt

Program Committee

P. Alexandrino    (Portugal)          T. Freitas        (Portugal)
A. Alves          (Portugal)          H. M. Jamil       (USA)
P. Azevedo        (Portugal)          A. Jorge          (Portugal)
P. Bourne         (USA)               R. King           (Wales, UK)
V. Brusic         (Singapore)         I. C. Lerman      (France)
C. Bystroff       (USA)               M. P. Monteiro    (Portugal)
R. Camacho        (Portugal)          M. Sagot          (France)
E. Costa          (Portugal)          T. Scheffer       (Germany)
A. Carvalho       (Brasil)            S. Schulze-Kremer (Germany)
J. P. Costa       (Portugal)          A. Srinivasan     (India)
V. Costa          (Brasil)            A. Valencia       (Spain)
I. Dutra          (Brasil)            J. Vieira         (Portugal)
L. Dehaspe        (Belgium)           M. Zaki           (USA)
D. Gilbert        (Scotland, UK)


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