PPID 2010 - WORKSHOP ON PROTEIN PROTEIN INTERACTION DATA: MANAGEMENT, QUERYING AND ANALYSIS PPID 2010

Biological macromolecules, such as proteins, play their role by interacting among them. Nowadays, many biochemical interactions among biological macromolecules are known, thanks to the application of different experimental platforms using different technologies, such as Yeast2Hybrid, Mass Spectrometry, etc. Results of such interactions may be stored in databases originating a knowledge base for biochemical reactions among known macromolecules.
A key area in such field is the study of the interactions among proteins, especially within a cell. Currently, different experiments have lead to the accumulation of a large amount of data about proteins, also referred as Protein-Protein Interaction (PPI) data. Nevertheless, as the analysis of single protein structure requires large computational efforts, also analysing protein to protein interactions requires algorithms and software platforms for the modeling, management and analysis of PPI data.
Moreover, thanks to such an interest in interactions, representing a large base of protein to protein interactions may generate a very large network, referred to as Protein Interaction Network (PIN), that codes biochemical and spatial relations among proteins. The analysis of such networks allows to discover new knowledge about biological functionalities.
PINs can be represented by using (direct) graphs where nodes are associated to proteins, and edges represent interactions among proteins. Once that an interaction network is modeled by using a graph, the study of biological properties can be done using graph-based algorithms and associating biological properties of the modeled PPI to the topological properties of the underlying graph.
In recent years many research efforts have produced different databases for storing interactions (PPI databases), as well as many algorithms for analyzing PINs and software tool for their visualization. Analysis algorithms can be grouped in three main classes: (i) algorithms that predict protein complexes, (ii) algorithms used for the extraction of functional modules (e.g. pathways), and (iii) algorithms for the alignment of PPI networks (e.g. belonging to different organisms).
Nevertheless, many research problems are still open such as: the integration of existing databases in a large map of interaction, the introduction of semantic technologies to manage, query and analyze data, the introduction of novel models able to represent the spatio-temporal variation of interactome, the integration of PPI information with biochemical pathways, gene (regulatory) pathways, and transcriptomics.
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 interactomics, from basic science to clinical practice. The workshop intends to provide a forum for the presentation oforiginal research, valuable software tools (basic algorithms, modelling, analysis, and visualization tools, databases), and clinical fallouts, on topics of importance to interactomics.
TOPICS OF INTEREST
The topics of interest will include but will be not limited to:
Data management and querying in Interactomics
Data management and analysis in Interactomics
Data models and integration for interactomics
Querying and retrieval of PPI data
Semantic web technologies for Interactomics
Parallel and Grid-based methods for interactomics
Algorithms and software tools for Interactomics
Computational methods for Interactomics
Novel interaction identification
Protein interaction prediction
Alignment of PINs
Applications of Data Mining, Neural Networks, Soft Computing for interactomics
Exploration and visualization of PPI data
Interactomics and biomedical research
Biomarker discovery (identification of molecular targets for early detection, prognosis and treatment of diseases
Integration and analysis of genomics, proteomic, and interactomics data for medical applications
PAPER SUBMISSION
ACM-BCB invites authors to submit papers using the Easychair system [SUBMIT A PAPER]. By submitting your paper to ACM-BCB, you implicitly state that the paper is based on your own original research and that it was not and will not be submitted elsewhere. Papers should not exceed 8 pages in ACM template on 8.5 x 11 inch paper (see ACM templates). All submitted papers should be written in English. Submission implies the willingness of at least one of the authors to register and present the work associated with the paper submitted.
All submitted papers will be reviewed by ACM-BCB’s technical program committee. All accepted papers of registered authors will be included in the proceedings published by ACM digital libraries. Selected papers will be invited to adapt their papers for their publication in several journals.