MOTIVATION: B-cell receptor (BCR) repertoire profiling is an important tool for understanding the biology of diverse immunologic processes. Current methods for analyzing adaptive immune receptor repertoires depend upon PCR amplification of VDJ rearrangements followed by long read amplicon sequencing spanning the VDJ junctions. While this approach has proven to be effective, it is frequently not feasible due to cost or limited sample material. Additionally, there are many existing datasets where short-read RNA sequencing data are available but PCR amplified BCR data are not. RESULTS: We present here V'DJer, an assembly-based method that reconstructs adaptive immune receptor repertoires from short-read RNA sequencing data. This method captures expressed BCR loci from a standard RNA-seq assay. We applied this method to 473 Melanoma samples from The Cancer Genome Atlas and demonstrate V'DJer's ability to accurately reconstruct BCR repertoires from short read mRNA-seq data. AVAILABILITY AND IMPLEMENTATION: V'DJer is implemented in C/C ++, freely available for academic use and can be downloaded from Github: https://github.com/mozack/vdjer CONTACT: [email protected] or [email protected] information: Supplementary data are available at Bioinformatics online.

The shortest path problem is a well know routing problem which received a considerable amount of attention for several decades. This problem is the cornerstone of any real-world routing problem including the VRP or the Hub Location. The majority of efficient methods dedicated to these problems consist in computing first the matric of shortest path between nodes. Furthermore, there has been a renaissance of interest in the shortest path problem in recent year for use in various transportation engineering applications. This paper relates to the conception of efficient routing algorithms tuned for mobility. More precisely, it is targeted to the field of pedestrian mobility in an urban environment. In a mobile environment, specific constraints as the treatment of wireless network traffic disturbances must be taken into account. The architecture that we tune for the project is based on an active monitoring system, which dynamically required new shortest path calculation using the exposed web service API. The web service is performed when a specific constraint appears or a new part of the path is required. Using of such architecture offers a new approach in spreading operational research algorithms and our contribution stands at the crossroads of optimization research community and the web service community expectations.

The DNA recombination process known as V(D)J recombination is the central mechanism for generating diversity among antigen receptors such as T-cell receptors (TCRs). This diversity is crucial for the development of the adaptive immune system. However, modeling of all the α β TCR sequences is encumbered by the enormity of the potential repertoire, which has been predicted to exceed 1015sequences. Prior modeling efforts have, therefore, been limited to extrapolations based on the analysis of minor subsets of the overall TCRbeta repertoire. In this study, we map the recombination process completely onto the graphics processing unit (GPU) hardware architecture using the CUDA programming environment to circumvent prior limitations. For the first time, we present a model of the mouse TCRbeta repertoire to an extent which enabled us to evaluate the Convergent Recombination Hypothesis (CRH) comprehensively at peta-scale level on a single GPU.