Algorithmic Challenges in Analysis of Immune Repertoires

Rapid development of DNA sequencing opened new avenues for analyzing immune system through interrogation of antibody repertoires and further applications of immunogenomics to cancer immunotherapy and vaccine development. We recently developed IgRepertoireConstructor algorithm for constructing antibody repertoires from Ig-seq reads combined with immunoproteogenomics analysis. IgRepertoireConstructor enabled further studies of the process of antibody diversification  using new AntEvolo algorithm that constructs evolutionary trees of antibodies. We will discuss the link between biological and computational problems in immunogenomics and the emerging challenging in this rapidly developing field.
This is a joint work with Sergey Bankevich (Center for Algorithmic Biology (CAB) at Saint Petersburg State University), Stefano Bonissone (Digital Proteomics, La Jolla), Andrey Bzikadze (CAB), Dmitry Chudakov (Moscow Institute for Bioorganic Chemistry), Jennie Lill (Genentech), Yana Safonova (CAB), Wendy Sandoval (Genentech), and Alexander Shlemov (CAB).