ImmunExplorer (IMEX): a software framework for diversity and clonality analyses of immunoglobulins and T cell receptors on the basis of IMGT/HighV-QUEST preprocessed NGS data

[1]  Patrice Duroux,et al.  IMGT®, the international ImMunoGeneTics information system® 25 years on , 2014, Nucleic Acids Res..

[2]  Stephan M. Winkler,et al.  Mathematical modeling of the diversity in human B and T cell receptors using machine learning , 2014 .

[3]  Marie-Paule Lefranc,et al.  Immunoglobulin and T Cell Receptor Genes: IMGT® and the Birth and Rise of Immunoinformatics , 2014, Front. Immunol..

[4]  Stephan M. Winkler,et al.  Architecture and Design of the HeuristicLab Optimization Environment , 2014 .

[5]  O. Filipe-Santos,et al.  ImmunTraCkeR® as a reliable TCR repertoire profiling tool to understand immune response and to explore immunotherapy biomarkers , 2013, Journal of Immunotherapy for Cancer.

[6]  Patrice Duroux,et al.  IMGT/HighV QUEST paradigm for T cell receptor IMGT clonotype diversity and next generation repertoire immunoprofiling , 2013, Nature Communications.

[7]  Mikhail Shugay,et al.  MiTCR: software for T-cell receptor sequencing data analysis , 2013, Nature Methods.

[8]  E. Mardis Next-generation sequencing platforms. , 2013, Annual review of analytical chemistry.

[9]  Ning Ma,et al.  IgBLAST: an immunoglobulin variable domain sequence analysis tool , 2013, Nucleic Acids Res..

[10]  John Shawe-Taylor,et al.  Decombinator: a tool for fast, efficient gene assignment in T-cell receptor sequences using a finite state machine , 2013, Bioinform..

[11]  Patrice Duroux,et al.  IMGT/HIGHV-QUEST: THE IMGT® WEB PORTAL FOR IMMUNOGLOBULIN (IG) OR ANTIBODY AND T CELL RECEPTOR (TR) ANALYSIS FROM NGS HIGH THROUGHPUT AND DEEP SEQUENCING , 2012 .

[12]  V. Giudicelli,et al.  IMGT(®) tools for the nucleotide analysis of immunoglobulin (IG) and T cell receptor (TR) V-(D)-J repertoires, polymorphisms, and IG mutations: IMGT/V-QUEST and IMGT/HighV-QUEST for NGS. , 2012, Methods in molecular biology.

[13]  C. Nusbaum,et al.  High-Resolution Description of Antibody Heavy-Chain Repertoires in Humans , 2011, PloS one.

[14]  Marie-Paule Lefranc,et al.  IMGT/V-QUEST: the highly customized and integrated system for IG and TR standardized V-J and V-D-J sequence analysis , 2008, Nucleic Acids Res..

[15]  Walter Daelemans,et al.  IGTree: Using Trees for Compression and Classification in Lazy Learning Algorithms , 1997, Artificial Intelligence Review.

[16]  Marie-Paule Lefranc,et al.  IMGT/JunctionAnalysis: the first tool for the analysis of the immunoglobulin and T cell receptor complex V-J and V-D-J JUNCTIONs , 2004, ISMB/ECCB.

[17]  M Hummel,et al.  Design and standardization of PCR primers and protocols for detection of clonal immunoglobulin and T-cell receptor gene recombinations in suspect lymphoproliferations: Report of the BIOMED-2 Concerted Action BMH4-CT98-3936 , 2003, Leukemia.

[18]  Gérard Lefranc,et al.  The Immunoglobulin FactsBook , 2001 .

[19]  Ingo Rechenberg,et al.  Evolution Strategy: Nature’s Way of Optimization , 1989 .