Publications

  • Shagin DA, Turchaninova MA, Shagina IA, Shugay M, Zaretsky AR, Zueva OI, Bolotin DA, Lukyanov S, Chudakov DM. Application of nonsense-mediated primer exclusion (NOPE) for preparation of unique molecular barcoded libraries. BMC Genomics. 2017 Jun 5. full text
  • Shugay M, Zaretsky AR, Shagin DA, Shagina IA, Volchenkov IA, Shelenkov AA, Lebedin MY, Bagaev DV, Lukyanov S, Chudakov DM. MAGERI: Computational pipeline for molecular-barcoded targeted resequencing. PLoS Comput Biol. 2017 May5. full text
  • Tappeiner E, Finotello F, Charoentong P, Mayer C, Rieder D, Trajanoski Z. TIminer: NGS data mining pipeline for cancer immunology and immunotherapy. Bioinformatics. 2017 Jun 15. full text
  • Finotello F, Trajanoski Z. New strategies for cancer immunotherapy: targeting regulatory T cells. Genome Med. 2017 Jan 27. full text
  • Schubert B, de la Garza L, Mohr C, Walzer M, Kohlbacher O: ImmunoNodes – graphical development of complex immunoinformatics workflows, BMC Bioinformatics, 2017 May 8, full text
  • Poster: Carlos Torroja, Francesca Finotello, Zlatko Trajanoski, Fátima Sánchez-Cabo: Deconvolution-based Approaches to Quantify TILs from Bulk RNA-Seq, Quantitative Approaches in Immuno-Oncology, The New York Academy of Sciences, 2017 March 1
  • Charoentong P, Finotello F, Angelova M, Mayer C, Efremova M, Rieder D, Hackl H, Trajanoski Z: Pan-cancer Immunogenomic Analyses Reveal Genotype-Immunophenotype Relationships and Predictors of Response to Checkpoint Blockade. Cell Rep. 2017 Jan 3, full text
  • Hackl H, Charoentong P, Finotello F, Trajanoski Z. Computational genomics tools for dissecting tumour-immune cell interactions. Nat Rev Genet. 2016 Jul 4, full text
  • Strønen E, Toebes M, Kelderman S, van Buuren MM, Yang W, van Rooij N, Donia M, Böschen ML, Lund-Johansen F, Olweus J, Schumacher TN: Targeting of cancer neoantigens with donor-derived T cell receptor repertoires. Science 2016 May 19. full text
  • Bernhard Mlecnik,, Gabriela Bindea , Helen K. Angell, Pauline Maby, Mihaela Angelova, David Tougeron, Sarah E. Church, Lucie Lafontaine, Maria Fischer, Tessa Fredriksen, Maristella Sasso, Amélie M. Bilocq, Amos Kirilovsky, Anna C. Obenauf, Mohamad Hamieh, Anne Berger, Patrick Bruneval, Jean-Jacques Tuech, Jean-Christophe Sabourin, Florence Le Pessot, Jacques Mauillon, Arash Rafii, Pierre Laurent-Puig, Michael R. Speicher, Zlatko Trajanoski, Pierre Michel, Richard Sesboüe, Thierry Frebourg, Franck Pagès, Viia Valge-Archer, Jean-Baptiste Latouche, Jérôme Galon, . Integrative analyses of colorectal cancer show Immunoscore is a stronger predictor of patient survival than microsatellite instability, Immunity, 44, 1–14, March 15, 2016 full text
  • Mlecnik B, Bindea G, Kirilovsky A, Angell HK, Obenauf AC, Tosolini M, Church SE, Maby P, Vasaturo A, Angelova M, Fredriksen T, Mauger S, Berger A, Speicher MR, Pagès F, Valge-Archer V, Galon J* The tumor microenvironment and Immunoscore are critical determinants of dissemination to distant metastasis. Science Transl. Med. 24;8(327):327ra26 Feb 2016 full text
  • Benjamin Schubert; Mathias Walzer; Hans-Philipp Brachvogel; Andras Szolek; Christopher Mohr; Oliver Kohlbacher: FRED 2 – An Immunoinformatics Framework for Python. Bioinformatics 2016; doi: 10.1093/bioinformatics/btw113 full text
  • Schubert B, Kohlbacher O: Designing string-of-beads vaccines with optimal spacers, Genome Medicine 2016, 8:9 full text