[Biodevelopers] IEEE CBMS 2009 Computational Proteomics Deadline Ext. April 22nd, 2009

[Mario Cannataro]

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22nd IEEE International Symposium on
COMPUTER-BASED MEDICAL SYSTEMS
August 3-4 2009
Albuquerque, New Mexico, USA.

Submission Deadline Extended to April 22nd, 2009
Special Track Computational Proteomics: Management and Analysis of  
Proteomics Data

http://staff.icar.cnr.it/cannataro/cbms2009/

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


PAPER SUBMISSION AND PUBLICATION

We invite original previously unpublished contributions that are not  
submitted concurrently to a journal or another conference. Paper  
submissions for IEEE CBMS 2009 will be handled through the easychair  
conference management system.

TO CREATE AN EASYCHAIR ACCOUNT
- Go to http://www.easychair.org/conferences/account_apply.cgi?iid=
- Create an account. Note the username and the secret word.
- Easychair will send you an e-mail to the address you indicate.  
Respond to the confirming email with the secret word that you  
selected. This will complete the account creation.

TO SUBMIT A PAPER TO IEEE CBMS2009
- Login to easychair http://www.easychair.org/conferences/?conf=ieeecbms2009
- Select ?New Submission?
- Select the Computational Proteomics Special Track
- Fill in the requested information, attach a PDF file, and hit ?Submit Paper?
- A confirming e-mail will be sent to your preferred address.
- Each contribution must be prepared following the IEEE 2-column  
format and should not exceed the length of 6 (or approximately 3000  
words).
- Presented material should include sufficient detail to enable the  
program committee in reviewing the article.
- The article should be submitted as a PDF document.
- The article review is double blind and as such personally  
identifying information is discouraged. Author name and address should  
be withheld from the article text for review purposes.
- All submissions will be peer-reviewed by at least three reviewers of  
the Special Track Program Committee.
- All accepted papers will be included in the conference proceedings  
published by IEEE CS Press.
- Article text should be in font size of at least 10 point. Authors  
should follow the IEEE style guide found at:
-  
ftp://pubftp.computer.org/press/outgoing/proceedings/8.5x11%20-%20Formatting%20files/
- At least one author must pay the registration fee before June 21,  
2009 for each accepted paper.

Please consult http://cvial.ee.ttu.edu/cbms2009 or  
http://staff.icar.cnr.it/cannataro/cbms2009 for further information.


IMPORTANT DATES
Paper submission due: Extended to April 22nd , 2009
Notification of acceptance for papers: May 25, 2009
Final camera-ready paper due: June 21, 2009
Pre-registration deadline: June 21, 2009
Hotel room reservations due: July 1, 2009 (see  
http://mcmelegantealbuquerque.com/)
Please visit http://cvial.ee.ttu.edu/cbms2009 for details.

TRACK CO-CHAIRS:
* Mario Cannataro	(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)

PROGRAM COMMITTEE (PROVISIONAL)
* 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
* 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
* Domenico Talia, University of Calabria, Italy
* Jason Wong, University of New South Wales, Australia