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

Computational Proteomics and Genomics

Management and Analysis of “omics” Data

http://staff.icar.cnr.it/cannataro/cbms2011

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. When conducting new research, all the necessary documents, explanatory and official notes, professional characteristics of scientific employees are written by https://writer-elite.com/memo-paper/ memo writing service specialists, because they have extensive experience in cooperation with research organizations. Therefore, if any of the bioengineering students have ideas for star taps, it is better to entrust their design to these partners.

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 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.

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.

TOPICS OF INTEREST

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

Data management and analysis in Computational Proteomics and Genomics

Computational methods for microarray
Computational methods for mass spectrometry
Pre-processing and analysis of microarray data
Pre-processing and analysis of mass-spectrometry data
Florescence-based methods and related image processing techniques
Peptide/protein identification
Protein structure prediction
Applications of Data Mining, Neural Networks, Soft Computing for proteomics
Software environments for proteomics and genomics workflows
Exploration and visualization of proteomic and genomics data
Data models and integration for proteomics and genomics
Querying and retrieval of proteomics and genomics data
Knowledge management, text mining and ontologies for proteomics and genomics
System biology ( protein-protein interactions, signalling networks)
Parallel and Grid-based methods for proteomics and genomics
Service Oriented approaches for Life Sciences applications
Standards in proteomics and genomics

Applications of Genomics and Proteomics in Translational Medicine and Clinical Practice

Biomarker discovery (identification of molecular targets for early detection, prognosis and treatment of diseases)
Technologies and data models for phenotype, genotype and proteotype data
Integration and analysis of genomics, proteomic, and clinical data for medical applications
Application of genomics and proteomics in translational medicine and clinical practice
Advanced Electronic Patient Records
Data quality and provenance
Medical Images

PAPER SUBMISSION, PUBLICATION AND DATES

Please see the CBMS 2011 call for papers and author kit.

JOURNAL SPECIAL ISSUE

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).

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, SystemsX.ch, 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

Computational Proteomics and Genomics

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