26th IEEE International Symposium on
COMPUTER-BASED MEDICAL SYSTEMS

June 20-22,
University of Porto, Portugal

 

8th Special Track

Bioinformatics: towards personalized medicine from omics data

http://staff.icar.cnr.it/cannataro/cbms2013/

 

NEW EXTENDED SUBMISSION DEADLINE: FEBRUARY 21, 2013

 

CALL FOR PAPERS

 

The study of biological systems involves the basic biological elements (e.g., proteins, genes and metabolites) as well as the interactions among such components (e.g., protein interactions, genetic interactions). Such a study currently requires the integration of interdisciplinary approaches e.g., integrating computational methods and experiences with biological and life science knowledge.

 

This process starts from the production of experimental biological results, mostly reported in raw data, both from in vitro or in vivo wet� lab experiments. Results data need to be stored, preprocessed, integrated with semantic information and prior knowledge, e.g. through annotations or ontology data. Data analysis is performed by using computational methods which aim to extract behavior and information from biological systems. Computational methods lead also to building accurate models of such systems and that give feedback to the scientist to perform new experiments or to refine current ones.

 

Computational methods strongly depend on the analysis of the so-called omics data. For instance 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. More recently, Next Generation Sequencing (NGS) methods are accumulating large amounts of data that encode biologically meaningful knowledge. Proteomics is a rapidly 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. �Interactomics focuses on the modeling, storage, and retrieval of protein-to-protein interactions (PPI), as well as on algorithms for analyzing protein interaction networks (PIN) or for predicting interactions. Since the majority of protein functions are performed when proteins interact with each other, interactomics is a key discipline to explain and interpret protein functions. Finally, novel omics areas, such as metabolomics and trascriptomics are becoming more important due to the introduction of novel technologies producing raw data requiring additional computational methods and studies.

 

The maturity and experiences of the collaboration among biologists and computer scientists brings today to additional interests on integrating omics data with clinical data, e.g. through the integration of omics data into Electronic Patent Records. The combined use of genomics, proteomics, and clinical data will thus improve healthcare management. 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 aims to bring together computer scientists, biologists and clinicians for exploring the current state-of-the-art of computational methods for the analysis and management of omics data, including acquisition and preprocessing of omics data coming from biological laboratory experiments, annotation and analysis of data results, and finally integration into clinical data practices and applications. 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 of omics data

o   Pre-processing and analysis of omics data

o   Pre-processing and analysis for next generation sequencing data

o   Pattern extraction from omics data

o   Software environments for proteomics and genomics workflows

o   Exploration and visualization of omics data

o   Data models and integration for proteomics and genomics

o   Querying and retrieval of omics data

o   Knowledge management, text mining and ontologies for proteomics and genomics

o   Parallel and Grid-based methods for proteomics and genomics

o   Service Oriented approaches for Life Sciences applications

o   Standards in proteomics and genomics

o   Cloud computing in bioinformatics

 

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 omics and medical data for clinical applications

o   Data quality and provenance

o   Biomedical Images analysis

 

 

PAPER SUBMISSION

Papers should be submitted electronically using EasyChair online submission system. The papers must be prepared following the IEEE two-column format and should not exceed the length of 6 (six) Letter-sized pages. LaTeX or Microsoft Word templates can be used when preparing the papers. Please, note that only PDF format of submissions is allowed.

Submission through EasyChair requires that an account in the system be created by a prospective author first. In order to create a new account, select the "I have no EasyChair account" option and follow the instructions given. When submitting, please, select the Bioinformatics: towards personalized medicine from omics data special track.

 

 

JOURNAL SPECIAL ISSUE

After the workshop, selected papers may be invited for a special issue of an international journal or for an edited book. 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).

 

 

IMPORTANT DATES

Paper submission due: February 21, 2012 (EXTENDED)

Notification: March 31, 2012 (EXTENDED)

Camera-ready paper: April 24, 2012

CBMS symposium: June 20-22, 2012

 

 

TRACK CO-CHAIRS:

 

PROGRAM COMMITTEE (PROVISIONAL)