[Bioclusters] ACM-BCB 2010 - 1st Workshop on Protein-protein interaction data: management, querying and analysis

Mario Cannataro cannataro at unicz.it
Thu Apr 1 11:22:12 EDT 2010

I apologize for any cross-posting of this announcement.
              ACM International Conference on
          Bioinformatics and Computational Biology
       August 2-4, 2010. Niagara Falls, New York, U.S.A.

                       1st Workshop on
Protein-protein interaction data: management, querying and analysis


         Submission deadline extended to April 15, 2010.


Biological macromolecules, such as proteins, play their role by
interacting among them.
Nowadays, many biochemical interactions among biological macromolecules
are known, thanks to the application of different experimental platforms
using different technologies, such as Yeast2Hybrid, Mass Spectrometry,
etc. Results of such interactions may be stored in databases originating a
knowledge base for biochemical reactions among known macromolecules.

A key area in such field is the study of the interactions among proteins,
especially within a cell. Currently, different experiments have lead to
the accumulation of a large amount of data about proteins, also referred
as Protein-Protein Interaction (PPI) data. Nevertheless, as the analysis
of single protein structure requires large computational efforts, also
analysing protein to protein interactions requires algorithms and software
platforms for the modeling, management and analysis of PPI data.

Moreover, thanks to such an interest in interactions, representing a large
base of protein to protein interactions may generate a very large network,
referred to as Protein Interaction Network (PIN), that codes biochemical
and spatial relations among proteins. The analysis of such networks allows
to discover new knowledge about biological functionalities.

PINs can be represented by using (direct) graphs where nodes are
associated to proteins, and edges represent interactions among proteins.
Once that an interaction network is modeled by using a graph, the study of
biological properties can be done using graph-based algorithms and
associating biological properties of the modeled PPI to the topological
properties of the underlying graph.

In recent years many research efforts have produced different databases
for storing interactions (PPI databases), as well as many algorithms for
analyzing PINs and software tool for their visualization. Analysis
algorithms can be grouped in three main classes: (i) algorithms that
predict protein complexes, (ii) algorithms used for the extraction of
functional modules (e.g. pathways), and (iii) algorithms for the alignment
of PPI networks (e.g. belonging to different organisms).

Nevertheless, many research problems are still open such as: the
integration of existing databases in a large map of interaction, the
introduction of semantic technologies to manage, query and analyze data,
the introduction of  novel models able to represent the spatio-temporal
variation of interactome, the integration of PPI information with
biochemical pathways, gene (regulatory) pathways, and transcriptomics.

This Workshop is designed to bring together computer scientists,
biologists and clinicians for exploring the current state-of-the-art
research taking place in all aspects of interactomics, from basic science
to clinical practice. The workshop intends to provide a forum for the
presentation oforiginal research, valuable software tools (basic
algorithms, modelling, analysis, and visualization tools, databases), and
clinical fallouts, on topics of importance to interactomics.


The topics of interest will include but will be not limited to:

Data management and querying in Interactomics
Data management and analysis in Interactomics
Data models and integration for interactomics
Querying and retrieval of PPI  data
Semantic web technologies for Interactomics
Parallel and Grid-based methods for interactomics

Algorithms and software tools for Interactomics
 Computational methods for Interactomics
 Novel interaction identification
 Protein interaction prediction
Alignment of PINs
Applications of Data Mining, Neural Networks, Soft Computing for
 Exploration and visualization of PPI  data

Interactomics and biomedical research

Biomarker discovery (identification of molecular targets for early
detection, prognosis and treatment of diseases
Integration and analysis of genomics, proteomic, and interactomics data
for medical applications


    * Submission deadline: Extended to April 15, 2010.
    * Author notification: April 30, 2010
    * Workshop Data August 2, 2010


ACM-BCB invites authors to submit papers using the link. By submitting
your paper to ACM-BCB, you implicitly state that the paper is based on
your own original research and that it was not and will not be submitted
elsewhere. Papers should not exceed 8 pages in ACM template on 8.5 x 11
inch paper (see ACM templates). All submitted papers should be written in
English. Submission implies the willingness of at least one of the authors
to register and present the work associated with the paper submitted. All
submitted papers will be reviewed by ACM-BCB’s technical program
committee. All accepted papers of registered authors will be included in
the proceedings published by ACM digital libraries. Selected papers will
be invited to adapt their papers for their publication in several

At the end of the workshop, we plan to invite the best 4-6 papers of the
workshop for a special section on an international journal.

Wokshop Chair:
  Pietro Hiram Guzzi, University Magna Graecia of Catanzaro, Italy
General Chair:
  Mario Cannataro, University Magna Græcia of Catanzaro, Italy
Publicity Chair:
  Pierangelo Veltri, University Magna Graecia of Catanzaro, Italy

Alejanda Gonzales Beltran, University College of London, UK
Giovanni Ciriello, University of Padova, Italy
Fabrizio Silvestri, ISTI-CNR, Italy

New book release
Handbook of Research on Computational Grid Technologies for Life Sciences,
Biomedicine, and Healthcare
ISBN: 978-1-60566-374-6; 1,050 pp; May 2009 Published under Medical
Information Science Reference an imprint of IGI Global
Edited by: Mario Cannataro, University Magna Graecia of Catanzaro, Italy
Prof. Mario Cannataro,
Informatics and Biomedical Engineering,
University "Magna Græcia" of Catanzaro,
Viale Europa (Località Germaneto), 88100 CATANZARO, ITALY,
Tel: 0961-369 4100, Fax: 0961-369 4073/4090, Email: cannataro at unicz.it,
Web: http://bioingegneria.unicz.it/~cannataro/

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