RepSeq-2016 Workshop on Immune Repertoire Sequencing

Dear colleagues,

I’m pleased to announce an upcoming workshop on immune repertoire sequencing RepSeq-2016 that will be held during ECCB2016 conference on 3rd of September 2016 in The Hague, Netherlands.

High-throughput sequencing of antigen receptor genes (RepSeq) is a promising and versatile method for adaptive immunity studies. RepSeq-2016 will cover various aspects of the emerging RepSeq technology ranging from library preparation and sequencing protocols to best practices of data storage and analysis, as well as novel algorithms helping to unravel the state and dynamics of adaptive immunity in health and disease.

The workshop is targeted both to bioinformaticians developing RepSeq methods and software and hematologists or immunologists using RepSeq software for research and clinical applications.

UPDATE Application submission is now open (deadline: 1st of May, with a possible extension to May 8).

Please find additional information by following this link and below:

RepSeq 2016

Immune Repertoire Sequencing : Bioinformatics and Applications in Hematology and Immunology

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

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

Key dates

  • 5 April 2016 Submission server opens
  • 1 May 2016 Paper submission deadline
  • 27 May 2016 Paper acceptance notification
  • 1 June 2016 Detailed program
  • 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 Fronkova, Charles University Prague, Czech Republic
  • Mathieu Giraud, CNRS, Lille, France (program co-chair)
  • Peter N. Robinson, Charite Berlin, Germany
  • Mikael Salson, Universite 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


The paper submission deadline is approaching (with possible extension to May 8th). The papers, in .pdf, should be submitted through EasyChair. Papers should be between 4 and 12 pages. LaTeX template and the Word/LibreOffice templates are available at

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UPD: Submission deadline is extended to May 23 (there will be no further extensions).