[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.
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23rd IEEE International Symposium on
COMPUTER-BASED MEDICAL SYSTEMS
Perth, Australia,
12-15 October 2010
5th Special Track Computational Proteomics and Genomics:
Data Management and Analysis
http://staff.icar.cnr.it/cannataro/cbms2010
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* * * CALL FOR PAPERS - Deadline June 17, 2010 * * *
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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.
TOPICS OF INTEREST
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
genomics
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
PAPER SUBMISSION AND PUBLICATION
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.
IMPORTANT DATES
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
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
* 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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