=== RepSeq 2016
=== Immune Repertoire Sequencing : Bioinformatics and Applications in Hematology and Immunology
=== http://www.repseq.net/2016
=== Workshop at ECCB 2016, The Hague, Netherlands, 3 september 2016

Adaptive immunity is a process by which lymphocytes are able to mount effective and
specific immune responses. The striking diversity required to withstand multiple pathogens
is generated by several processes including V(D)J recombination, thymic selection of
T-cells and affinity maturation of B-cells. With the advent of high-throughput sequencing,
it is now possible to sequence millions of T- and B-cell receptors using techniques called
Immune Repertoire Sequencing (RepSeq). These studies already provided us with a much better
understanding of the structure and dynamics of adaptive immune system.

On the bioinformatics side, even the basic task of mapping V(D)J junctions is a challenge
for alignment algorithms. The first dedicated RepSeq software and algorithms started to
emerge around 2011. Currently, there are more than a dozen tools able to manage, process,
visualize and perform statistical analysis of RepSeq data, using string matching techniques
such as optimized dynamic programming, spaced seeds, statistical models, clustering or text
indexing.

The RepSeq 2016 workshop is targeted both to bioinformaticians developing RepSeq methods
and hematologists or immunologists using RepSeq software for research and clinical
applications. The workshop will feature keynote talks by Anton Langerak and Thierry Mora,
selected contributions and a round table discussion on immune repertoire sequencing.

=== Call for contributions

We welcome both methodological and algorithmic contributions in bioinformatics as well as
contributions in fundamental or applied immunology and hematology on the following themes:
- Library preparation and sequencing protocols for RepSeq
- Bioinformatic methods to manage and analyze RepSeq data: reads pre-processing,
V(D)J mapping, clone clustering, statistics, visualization
- Fundamental and applied RepSeq studies in immunology and hematology
- Expected developments in RepSeq methodology: paired-chain sequencing, functional
annotation of repertoires

=== Submission

Papers should be between 8 and 12 pages, formatted in 12pt single-column.
LaTeX and Word/LibreOffice templates will be provided at the opening of the submission server.

The proceedings of the workshop will be published in open access for authors willing to
distribute their contribution. We are in the process of contacting editors to publish
selected papers from the workshop in a special issue of a journal.

=== Key dates

21 March 2016 Submission server opens
23 May 2016 Paper submission deadline
30 May 2016 Paper acceptance notification
20 June 2016 Final version of accepted papers
3 September 2016 Workshop at ECCB 2016

=== Organizing and program committee

- Jack Bartram, University College London, UK
- Eva Froňková, Charles University Prague, Czech Republic
- Mathieu Giraud, CNRS, Lille, France (program co-chair)
- Peter N. Robinson, Charité Berlin, Germany
- Mikaël Salson, Université de Lille, France (proceedings chair)
- Mikhail Shugay, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia (program co-chair)
- Andrew P. Stubbs, Erasmus MC, Rotterdam, The Netherlands