[BiO BB] CBMS 2011 - Computational Proteomics and Genomics Special Track

Mario Cannataro cannataro at unicz.it
Fri Feb 25 13:10:34 EST 2011

      24th IEEE International Symposium on

               June 27th - 30th,
  University of the West of England, Bristol, UK

               6th Special Track
     Computational Proteomics and Genomics:
    Management and Analysis of “omics” Data

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

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 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

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.

The integrated application of bioinformatics methods to clinical data is
at the basis of Translational Research and Translational Medicine, whose
goals is to translate the findings in basic research into medical
practice. Wang and Liotta recently introduced the concept of Clinical
Bioinformatics, i.e. "clinical application of bioinformatics-associated
sciences and technologies to understand molecular mechanisms and potential
therapies for human diseases", as a new and important concept for the
development of disease-specific biomarkers and individualized medicine.

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 translational research and medicine. 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
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 Translational Medicine and
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 genomics and proteomics in translational medicine and
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
contribution must be prepared following the IEEE 2-column format format,
and should not exceed the length of 6 (six) Letter-sized pages; the
authors may use LaTeX or Microsoft Word templates when preparing their
drafts. The papers should be submitted electronically before the paper
submission deadline using the EasyChair online submission system. Papers
must be submitted in PDF format, with fonts embedded. Authors of accepted
papers should refer to the full IEEE Xplore® PDF Specification.

All submissions will be peer-reviewed by at least three reviewers. All
accepted papers will be included in the conference proceedings published
by the IEEE CS Press. At least one author must pay the registration fee
before May 30th for each accepted paper. Please refer to the IEEE IPR
guidelines concerning copyright. Authors of accepted papers must include a
completed IEEE Copyright Form with the submission of their final
camera-ready paper. Please contact cannataro AT unicz DOT it for any

Paper submission deadline: 20 April 2011
Notification of acceptance for papers: 20 May 2011
Final camera ready due: 30 May 2011
Author registration: 30 May 2011

After the workshop, selected papers may be invited for a special issue of
an international journal. Selected papers (extended and revised versions)
accepted on the previous editions of the workshop have been published on a
special section of Briefings in Bioinformatics (Oxford University Press).


    * 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, SystemsX.ch, ETHZ, Switzerland
    * Maria Mirto, University of Salento, Italy
    * Stephen Pennington, Conway Institute, University College Dublin,
    * 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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