[CPM-SPIRE-L] call for abstracts: "Algorithmic and statistical analysis of high throughput sequencing data"

[Matteo Comin]

Please distribute this call for paper.

In particular the following Special Session might be of interest for the SPIRE-CPM community:

"Algorithmic and statistical analysis of high throughput sequencing data"


Regards.

-----Messaggio originale-----
Da: BITS INFO [mailto:bits_info at bioinformatics.it] 
Inviato: venerdì 15 febbraio 2013 15:59
A: BITS INFO
Oggetto: BITS 2013 call for abstracts

BITS 2013 Call for Abstracts


Submissions are invited for poster and oral contributions to the annual 
meeting of the Bioinformatics Italian Society (BITS), which will be held 
in Udine on May 21-23, 2013.
Topics covered during the conference include (but are not limited to):

• Genomics
• Transcriptomics
• Next Generation Sequencing
• Metagenomics
• Molecular Evolution
• Comparative Genomics
• Pharmacogenomics
• Protein structure and function
• Proteomics
• Systems Biology
• Biological Databases
• Biobanks
• Algorithms for Bioinformatics
• Genomics of Disease

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

A detailed description of the Special Sessions is available at the end 
of this Call.
Contributions will be accepted for both traditional and special sessions 
and should address novel bioinformatics methods, algorithms, databases, 
tools and applications for research and development.
Abstracts will be reviewed by the Scientific Committee and accepted for 
oral communication and poster presentation or rejected in case they do 
not match the scientific standards of the conference. Two or three 
anonymous referees will evaluate each abstract. We encourage the authors 
to use the maximum space available in the submission form in order to 
describe at the best their work and results.
Accepted abstracts will be collected in the conference proceedings.
Negotiations are ongoing for the publication of a Supplement of BMC 
Bioinformatics (or other international journals) with full articles 
dedicated to the subjects presented at the conference as poster or oral 
communications.
Abstract submission requires early registration to the conference of the 
presenting author after the acceptance notification.

Important dates:
February 15, 2013: Opening of the Call for Abstracts
March 20, 2013: Deadline for Abstract submission for oral communications 
and posters
April 20, 2013: Abstract acceptance notification (Oral communications 
and posters)
April 24, 2013: Deadline for early registration to the conference 
(required for authors of accepted abstracts)
May 21-23, 2013: BITS2013 meeting
June 30, 2013: Deadline for manuscript submission for the BITS 
supplement of BMC Bioinformatics (or other international journals).




IMPORTANT NOTE:
Abstract submission form will be available soon. Please visit the BITS 
web site (www.bioinformatics.it) for updates and links to meeting web 
site and submission form.





Special Session

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.



Special Session

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.


Special Session

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.

RESEARCH TOPICS:
- 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)