[Bioclusters] CBMS 2010 - 5th Special Track Computational Proteomics and Genomics

Mario Cannataro cannataro at unicz.it
Fri Apr 9 16:04:16 EDT 2010

I apologize for any cross-posting of this announcement.
                23rd IEEE International Symposium on
                         Perth, Australia,
                        12-15 October 2010

     5th Special Track Computational Proteomics and Genomics:
                   Data Management and Analysis
* * * CALL FOR PAPERS - Deadline June 17, 2010 * * *

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 and genomics, 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.

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

Data management and analysis in Computational Proteomics and Genomics
o Computational methods for microarray
o Computational methods for mass spectrometry
o Pre-processing and analysis of microarray data
o Pre-processing and analysis of mass-spectrometry data
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 and genomics workflows
o Exploration and visualization of proteomic and genomics data
o Data models and integration for proteomics and genomics
o Querying and retrieval of proteomics and genomics data
o Knowledge management, text mining and ontologies for proteomics and

o System biology ( protein-protein interactions, signalling networks)
o Parallel and Grid-based methods for  proteomics and genomics
o Service Oriented approaches for Life Sciences applications
o Standards in proteomics and genomics

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


We invite original previously unpublished contributions that are not

submitted concurrently to a journal or another conference.
Each paper must be prepared following the IEEE 2-column format and should not

exceed the length of 6 (six) letter-sized pages, submitted electronically

using the paper submission system prior to the submission deadline.
CBMS 2010 submission web site is http://www.cbms2010.debii.curtin.edu.au
All submissions will be peer-reviewed by at least three reviewers. The

proceedings will be published by the IEEE Computer Society Press. At least

one of the authors of accepted papers is required to register and present the

work at the conference; otherwise their papers will be removed from the

digital library after the conference.
Please contact cannataro AT unicz DOT it for any question.

Submission deadline for regular papers: 17 Jun 2010
Notification of acceptation: 2 Aug 2010
Final camera ready due: 2 Sep 2010
Author registration: 2 Sep 2010

* 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)

* 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
* Pietro Hiram Guzzi, University “Magna Græcia” of Catanzaro, 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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