In addition to the traditional panels, this year the Call includes the following Special Sessions proposed by members of the Society:
- Algorithmic and statistical analysis of high throughput sequencing data
- Bioinformatics of protein-protein interactions
- Multicellular and Multi-scale Models of Biological Systems
Algorithmic and statistical analysis of high throughput sequencing data
Biomedical research is facing a real revolution with the advent of the new sequencing technologies of nucleic acids (High Throughput Sequencing, HTS), with the possibility of identifying genomic and transcriptomic variants with a resolution degree that was until very recently out of reach.
The introduction of these HTS platforms in basic research, in clinic research, and in diagnostics, has led to new open opportunities and problems that are mostly bioinformatics challenges.
The huge amount of data produced by HTS platforms needs sophisticated algorithmic methodologies for its storage, analysis, assembling of newly sequenced genomes, aligning data to a reference genome when this is available, as well as all consequent tasks of identification of variants such as Single Nucleotide Variants (SNV), insertions or deletions (InDel), Structural Variants (SV), or Copy Number Variations (CNV), that can all be carried out with or without assembling or alignment.
For algorithms and data structures theory these crucial tasks raise new specific bioinformatics problems of data indexing and analysis. For post alignment/assembly there are new challenges in the development of increasingly accurate and fast computational and statistical methods that allow the most possible benefit of the potential of HTS technologies in identifying the whole spectra of genetic variants and expression profiling of organisms.
We seek original research work, or work in progress on any bioinformatics issue raised by these challenges, as well as tool presentations and practical results.
Bioinformatics of protein-protein interactions
Recent technical advances in the fields of proteomics and structural biology have led to a dramatic increase in the amount of available data on protein-protein interactions (PPIs). This increase brings about many opportunities, like an unprecedented level of understanding of PPI-mediated processes or the development of new drugs acting as inhibitors or mediators of PPIs. However, new challenges have also arisen, for instance that of correctly identifying biologically relevant interfaces, i.e. genuine PPIs, in crystal structures.
This session will be open to contributions on all kinds of bioinformatics studies of PPIs. We invite in particular the submission of abstracts in the following areas: PPIs in human disease, integrative structure determination of protein complexes exploiting NMR and mass-spectrometry, all aspects of docking (methods to predict and simulate conformational changes, scoring functions, refinement and benchmarking procedures, use of non-structural information, protein docking in rational drug design, antibody-protein docking and DNA/RNA-protein docking, web servers), mapping and analysis of PPI networks. Abstracts on protein-ligand interaction studies will also be considered.
Multicellular and Multi-scale Models of Biological Systems
Systems Biology relies on computer modeling and simulation of complex biological systems. Most research in the field focuses on modeling metabolic and regulatory networks within a single cell using stochastic and differential equation-based simulation engines. This approach has been adopted by a large community and has led to a concerted effort to create effective standards for the specification, validation and sharing of subcellular models. As Systems Biology matured, many researchers started building models which operate at larger scales (multi- cell and organ level) in order to address phenomena such as organ development in animals and plants, tumor progression and invasion, tissue pathologies etc. This evolution of model scales requires either an increase in computational power or the development of efficient algorithms for simplified models that retain the most important features of the system but are more computationally tractable, and allow for compositionally and modularity. As the complexity and scale of models increases - from subcellular networks to cells to tissue to organ level scales and beyond, there is an increasing need for methods to describe the underlying biology, the computational models, and the linkages (and assumptions) between models at different scales.
The goal of this special session is to bring together researchers who build multicellular models of biological development, disease and homeostasis. We will focus on the following two issues that arise most often in the field: (1) multi-scale interaction with models at finer and coarser scales and (2) developing standards to share/exchange multicellular models or their components.
- Models of multicellular systems
- Biologically validated prediction results
- Models of multi-scale interactions
- Modeling languages and formalisms: geometry and dynamics
- Modularity and compositionality
- Exchange formats and ontologies for multicellular models
- Tools for multicellular systems simulation and analysis (numerical, qualitative)