[Biodevelopers] CfP IEEE CBMS-07 Computational Proteomics SpecialTrack

[Mario Cannataro]

Please, accept our apologies for multiple postings.

20th IEEE International Symposium on COMPUTER-BASED MEDICAL SYSTEMS
20-22 June 2007, Maribor, Slovenia,
http://cbms2007.uni-mb.si/


Special Track on Computational Proteomics: Management and Analysis of  
Proteomics Data http://bioinformatics.unicz.it/cbms2007/

CALL FOR PAPERS
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. Genome-wide sequencing projects have been completed for many  
organisms, including Homo Sapiens.

Currently thousands of genes have been sequenced but still wait for  
any functional information to be assigned to them:
this suggests that current comprehension of most biological and  
pathological processes is by far incomplete. As a consequence, new  
technological platforms that exploit the genome sequence information  
to explore gene function in a systematic way are evolving at an  
incredibly high pace, e.g. microarray.

Application of the microarray technology has unveiled its enormous  
potential as a diagnostic support to clinical management. Recent works  
exploited gene expression profiling of tumor samples to define sets of  
genes (signatures) whose expression correlates, positively or  
negatively, with specific clinical features, such survival and  
response to therapy. Other types of massive datasets currently  
generated in genomics and projects include: protein expression levels  
measured by proteomics screenings; protein-protein interaction  
datasets in various organisms; protein structure data; genomic  
sequencing of additional organisms, comparative genomics; sequence  
polymorphisms in human populations, mutational analysis in human  
cancer and in hereditary diseases.

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. In medical studies, the  
basic aim of proteomic analysis is the identification of specific  
protein patterns from cells, tissues and biological fluids related to  
physiological or pathological conditions (biomarker discovery). It  
provides a different view as compared to gene expression profiling,  
which does not evaluate post-transcriptional, post-translational  
modifications as well as protein compartimentalization and half-life  
changes (for instance ubiquitination and proteasome-driven  
degradation). All these characteristics make the protein profile much  
more complex but more informative compared to gene expression profiling.

Several approaches have been used to perform proteomic analysis; among  
them, technologies based on Mass Spectrometry (MS) have revolutionized  
proteomics and are heavily used to make high-throughput measurements  
for identifying macromolecules in a specific compound. Some recent  
studies based on mass spectrometry, conducted at the National  
Institutes of Health, USA, have identified in biological samples  
cluster patterns that completely segregated ovarian cancer from  
non-cancer. These results, characterized by a high degree of  
sensitivity and specificity, represent an extraordinary step forward  
in the early detection and diagnosis of ovarian cancer and justify a  
prospective population- based assessment of proteomic pattern  
technology as a screening tool for all stages of ovarian cancer in  
high-risk and general populations. Similar studies performed on  
different types of neoplastic diseases have confirmed the importance  
of identification of "molecular profiles or signatures" (either at RNA  
or protein level) as a powerful tool for innovative diagnostic and  
therapeutic approaches.

Computational Proteomics is about the computational methods,  
algorithms, databases, and methodologies used to manage, analyze and  
interpret the data produced in proteomics experiments. The broad  
application of proteomics in different biological and medical fields,  
as well as the increasing resolution and precision offered by  
technological platforms, make the analysis of proteomics experiments  
difficult and error prone without efficient algorithms and easy-  
to-use tools. This is especially true in Mass Spectrometry-based  
high-throughput proteomics, where the production of huge datasets is  
coupled with the need of on-the-fly data analysis.

The seamless integration of genomic, proteomics and clinical data, and  
the semantic interoperation between bioinformatics tools and health  
management systems, are first steps toward the so-called "Genomic  
Medicine", i.e. the combined use of genomics, proteomics, and clinical  
data to improve healthcare. Future Electronic Patient Records should  
allow the integration of genomic and proteomic data, while  
bioinformatics 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 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 computational proteomics, from  
basic science to clinical practice.
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.


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

Data management and analysis in Computational Proteomics
o	Computational methods for microarray
o	Computational methods for mass spectrometry
o	Florescence-based methods and related image processing techniques
o	Peptide/protein identification
o	Protein structure prediction
o	Applications of Data Mining, Neural Networks, Soft Computing for proteomics
o	Software environments for proteomics workflows
o	Exploration and visualization of proteomic data
o	Data models and integration for proteomics
o	Querying and retrieval of proteomics data
o	Knowledge management, text mining and ontologies for proteomics
o	System biology ( protein-protein interactions, signalling networks)
o	Parallel and Grid-based methods for  proteomics
o	Service Oriented approaches for Life Sciences applications
o	Standards in proteomics

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 genomics, proteomic, and clinical data  
for medical applications
o	Application of proteomics methods in clinical practice
o	Advanced Electronic Patient Records
o	Data quality and provenance
o	Medical Images


IMPORTANT DATES
Paper submission due: January 31, 2007.
Notification of acceptance for papers: March 15, 2007.
Camera ready papers: April 15, 2007.
Pre-registration deadline: April 20, 2007.
CBMS 2007 Symposium: June 20-22, 2007.


PAPER SUBMISSION AND PUBLICATION
Papers can be submitted through the conference web site  
http://cbms2007.uni-mb.si/papers/index.php .
Papers should be submitted in PDF format following the IEEE guidelines  
and formatting instructions http://cbms2007.uni-mb.si/?id=10 .
Submitted papers have to be original, containing new and original  
results. There are two possibilities for initially submitting a paper:

A full paper (6 pages). It is strongly encouraged to submit a full  
paper, which enables reviewers to assess it more objectively and  
authors to substantially improve the paper based on the review  
feedback. In this way, the high quality of this conference series can  
be adequately maintained and/or improved.

A summary (3 pages). CBMS 2007 serves also as a forum for exchanging  
interesting and novel results of a work in progress and in this manner  
provides participants with an opportunity to come up-to-date on  
important issues. In this way, the 3-pages summaries are also accepted  
in the case that a full paper can not be delivered until the deadline.

There are two possibilities for presenting an accepted paper: oral  
presentation (regular papers) or poster presentation (short papers).  
Authors can also indicate their preference when submitting a paper.  
The final decision will be made by the Special Track Program Committee  
based on the reviews. All papers will be peer-reviewed by at least two  
reviewers.
Submission implies the willingness of at least one of the authors to  
register and present the paper at the CBMS 2007 Symposium.
All papers will be peer reviewed by at least two independent referees.  
All accepted papers will be included in the conference proceedings.  
Additionally, selected high quality papers may be invited to submit a  
substantially extended version for the special issue of an  
international journal.
At least one of authors must pre-register to have the paper published  
in the proceedings. If you only plan to attend and are not submitting  
a paper, pre-registration is still strongly encouraged. This  
conference is space-limited, and registration may not be available  
on-site.


TRACK CO-CHAIRS:
*	Mario Cannataro (University "Magna Gr?cia" of Catanzaro, Italy)
*	Giovanni Cuda (University "Magna Gr?cia" of Catanzaro, Italy)
*	Pierangelo Veltri (University "Magna Gr?cia" of Catanzaro, Italy)

PROGRAM COMMITTEE (PROVISIONAL)
*	Gerard Cagney (Conway Institute, University College Dublin, Ireland)
*	Tim Clark (Harvard Medical School - MassGeneral Institute for  
Neurodegenerative Disease, USA)
*	Giuseppe Di Fatta (ICAR-CNR, Italy, and University of Reading, UK)
*	Christine Froidevaux (LRI-Bioinformatics Group - University Paris  
XI, Orsay, France)
*	Marco Gaspari (University "Magna Gr?cia" of Catanzaro, Italy)
*	Concettina Guerra (University of Padova, Italy)
*	Hasan Jamil (Wayne State University, Michigan, USA)
*	Maria Mirto (University of Lecce, Italy)
*	Helen Parkinson (European Bioinformatics Institute, UK)
*	Stephen Pennington (Conway Institute, University College Dublin, Ireland)
*	Omer F. Rana (Cardiff University, UK)
*	Simona Rombo (DEIS-University of Calabria, Italy)
*	Roberto Tagliaferri (University of Salerno, Italy)
*	Domenico Talia (University of Calabria, Italy)
*	Gordon R. Whiteley (National Cancer Institute, USA)

--
Prof. Mario Cannataro,
Informatics and Biomedical Engineering,
University "Magna Græcia" of Catanzaro,
Viale Europa (Località Germaneto), 88100 CATANZARO, ITALY,
Email: cannataro at unicz.it