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

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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 proteomi=
cs
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=3D
- 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=3Dieeecbms2=
009
- Select ?New Submission?
- Select the Computational Proteomics Special Track
- Fill in the requested information, attach a PDF file, and hit ?Submit Pap=
er?
- 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-%20Formattin=
g%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 Gr=E6cia? of Catanzaro, Italy)
* Giovanni Cuda		(University ?Magna Gr=E6cia? of Catanzaro, Italy)
* Marco Gaspari		(University ?Magna Gr=E6cia? of Catanzaro, Italy)
* Pierangelo Veltri	(University ?Magna Gr=E6cia? 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