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Mario Cannataro <[log in to unmask]>
Reply To:
Thu, 24 Nov 2011 00:23:33 +0100
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         I apologize for any cross-posting of this announcement.
25th IEEE International Symposium on COMPUTER-BASED MEDICAL SYSTEMS
      June 20-22, Università Campus Bio-Medico di Roma, Italy

                          7th Special Track
    Bioinformatics: towards personalized medicine from omics data


The study of biological systems is the process that study the basic
biological elements (e.g., proteins, genes and metabolites) as well as the
interactions among such components (e.g., protein interactions, genetic
interactions). Such a study currently requires the integration of
interdisciplinary approaches e.g., integrating computational methods and
experiences with biological and life science knowledge.

This process starts from the production of experimental biological
results, mostly reported in raw data, both from in vitro or in vivo wet 
lab experiments. Results data need to be stored, preprocessed, integrated
with semantic information and prior knowledge, e.g. through annotations or
ontology data. Analysis is performed by using computational methods to
extract behavior and information from biological systems. Computational
methods lead also to building accurate models of such systems and that
give feedback to the scientist to perform new experiments or to
re&#64257;ne current ones.

Computational methods strongly depend on biological “omics” experimentally
analysed data. For instance Genomics is the study of the genome, i.e. the
whole hereditary information of an organism that is encoded in the DNA
(or, for some viruses, RNA). Investigation of single genes, their
functions and roles is becoming common practice in today's medical and
biological research. More recently, Next Generation Sequencing (NGS)
methods are accumulating large amounts of data that encode biologically
meaningful knowledge. Proteomics is a fastly developing area of
biochemical investigation and regards the study of the proteins expressed
in an organism or a cell. Proteomics studies include: protein
identification and quantification, structural genomics, protein-to-protein
interaction, post-translational modifications, and so on.  Interactomics
focuses on the modeling, storage, and retrieval of protein-to-protein
interactions (PPI), as well as on algorithms for analyzing protein
interaction networks (PIN) or for predicting interactions. Since the
majority of protein functions are performed when proteins interact with
each other, interactomics is a key discipline to explain and interpret
protein functions. Finally, novel omics areas, such as metabolomics and
trascriptomics are becoming more important due to the introduction of
novel technologies producing raw data requiring additional computational
methods and studies.

The maturity and experiences of the collaboration among biologists and
computer scientists brings today to additional interests on integrating
omics data with clinical data, e.g. through the integration of omics data
into Electronic Patent Records. The combined use of genomics, proteomics,
and clinical data will thus improve healthcare  management. Tools and
databases used for genomics and proteomics studies should be able to
furnish input to clinical practice, enabling the so called
“from-bench-to-bed” paradigm.

This workshop aims to bring together computer scientists, biologists and
clinicians for exploring the current state-of-the-art of computational
methods for analysis and management of “omics” data, including acquisition
and preprocessing of omics data coming from biological laboratory
experiments, annotation and analysis of data results, and finally
integration into clinical data practices and applications. The workshop
intends to provide a forum for the presentation of original research,
valuable software tools (basic algorithms, modelling, analysis, and
visualization tools, databases), and clinical fallouts, on topics of
importance to computational genomics and proteomics.

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

Data management and analysis of omics data
o Pre-processing and analysis of omics data
o Pre-processing and analysis  for next generation sequencing data
o Pattern extraction from omics data
o Software environments for proteomics and genomics workflows
o Exploration and visualization of omics data
o Data models and integration for proteomics and genomics
o Querying and retrieval of omics data
o Knowledge management, text mining and ontologies for proteomics and
o Parallel and Grid-based methods for  proteomics and genomics
o Service Oriented approaches for Life Sciences applications
o Standards in proteomics and genomics
o Cloud computing in bioinformatics

Applications of Genomics and Proteomics in Clinical Practice
o Biomarker discovery (identification of molecular targets for early
detection, prognosis and treatment of diseases)
o Technologies and data models for phenotype, genotype and proteotype data
o Integration and analysis of omics and medical data for clinical
o Data quality and provenance
o Biomedical Images analysis

Papers should be submitted electronically using EasyChair online
submission system. The papers must be prepared following the IEEE
two-column format and should not exceed the length of 6 (six) Letter-sized
pages. LaTeX or Microsoft Word templates can be used when preparing the
papers. Please, note that only PDF format of submissions is allowed.
Submission through EasyChair requires that an account in the system be
created by a prospective author first. In order to create a new account,
select the "I have no EasyChair account" option and follow the
instructions given. When submitting, please, select the Bioinformatics:
towards personalized medicine from omics data special track.

After the workshop, selected papers may be invited for a special issue of
an international journal or for an edited book. Selected papers (extended
and revised versions) accepted on the previous editions of the workshop
have been published on a special section of Briefings in Bioinformatics
(Oxford University Press).

Paper submission due	 	January 15, 2012
Notification of acceptance	March 15, 2012
Final camera-ready paper due 	April 10, 2012
Pre-registration deadline 	April 10, 2012
CBMS symposium days 		June 20-22 2012

* Pietro Hiram Guzzi  (University “Magna Græcia” of Catanzaro, Italy)
* Giovanni Cuda  (University “Magna Græcia” of Catanzaro, Italy)
* Marco Gaspari  (University “Magna Græcia” of Catanzaro, Italy)
* Pierangelo Veltri  (University “Magna Græcia” of Catanzaro, Italy)
* Mario Cannataro  (University “Magna Græcia” of Catanzaro, Italy)

* Tim Clark, Harvard Medical School - MassGeneral Institute for
Neurodegenerative Disease, USA
* Giuseppe Di Fatta, University of Reading, UK
* Cesare Furlanello, FBK - Fondazione Bruno Kessler, Italy
* Christine Froidevaux, LRI-Bioinformatics Group - University Paris XI,
Orsay, France
* Concettina Guerra, University of Padova, Italy
* Hasan Jamil, Wayne State University, Michigan, USA
* Ela Hunt, ETHZ, Switzerland
* Maria Mirto, University of Salento, Italy
* Stephen Pennington, Conway Institute, University College Dublin, Ireland
* Simona Rombo, University of Calabria, Italy
* Dennis Shields, Conway Institute, University College Dublin, Ireland
* Roberto Tagliaferri, University of Salerno, Italy
* Jason Wong, University of New South Wales, Australia

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