Simultaneous enumeration of cancer and immune cell types from bulk tumor gene expression data von Racle, Julien, de Jonge, Kaat, Baumgaertner, Petra, Speiser, Daniel E, Gfeller, David

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Robust prediction of HLA class II epitopes by deep motif deconvolution of immunopeptidomes von Racle, Julien, Michaux, Justine, Rockinger, Georg Alexander, Arnaud, Marion, Bobisse, Sara, Chong, Chloe, Guillaume, Philippe, Coukos, George, Harari, Alexandre, Jandus, Camilla, Bassani-Sternberg, Michal, Gfeller, David

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High-throughput and Sensitive Immunopeptidomics Platform Reveals Profound Interferonγ-Mediated Remodeling of the Human Leukocyte Antigen (HLA) Ligandome von Chong, Chloe, Marino, Fabio, Pak, HuiSong, Racle, Julien, Daniel, Roy T., Müller, Markus, Gfeller, David, Coukos, George, Bassani-Sternberg, Michal

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The Length Distribution and Multiple Specificity of Naturally Presented HLA-I Ligands von Gfeller, David, Guillaume, Philippe, Michaux, Justine, Pak, Hui-Song, Daniel, Roy T, Racle, Julien, Coukos, George, Bassani-Sternberg, Michal

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EPIC: A Tool to Estimate the Proportions of Different Cell Types from Bulk Gene Expression Data von Racle, Julien, Gfeller, David

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Robust estimation of cancer and immune cell-type proportions from bulk tumor ATAC-Seq data von Gabriel, Aurélie Anne-Gaëlle, Racle, Julien, Falquet, Maryline, Jandus, Camilla, Gfeller, David

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Sensitive and frequent identification of high avidity neo-epitope specific CD8+ T cells in immunotherapy-naive ovarian cancer von Bobisse, Sara, Genolet, Raphael, Roberti, Annalisa, Tanyi, Janos L., Racle, Julien, Stevenson, Brian J., Iseli, Christian, Michel, Alexandra, Le Bitoux, Marie-Aude, Guillaume, Philippe, Schmidt, Julien, Bianchi, Valentina, Dangaj, Denarda, Fenwick, Craig, Derré, Laurent, Xenarios, Ioannis, Michielin, Olivier, Romero, Pedro, Monos, Dimitri S., Zoete, Vincent, Gfeller, David, Kandalaft, Lana E., Coukos, George, Harari, Alexandre

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A Phase Ib Study of the Combination of Personalized Autologous Dendritic Cell Vaccine, Aspirin, and Standard of Care Adjuvant Chemotherapy Followed by Nivolumab for Resected Pancre... von Bassani-Sternberg, Michal, Digklia, Antonia, Huber, Florian, Wagner, Dorothea, Sempoux, Christine, Stevenson, Brian J, Thierry, Anne-Christine, Michaux, Justine, Pak, HuiSong, Racle, Julien, Boudousquie, Caroline, Balint, Klara, Coukos, George, Gfeller, David, Martin Lluesma, Silvia, Harari, Alexandre, Demartines, Nicolas, Kandalaft, Lana E

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Immunopeptidomics of colorectal cancer organoids reveals a sparse HLA class I neoantigen landscape and no increase in neoantigens with interferon or MEK-inhibitor treatment von Newey, Alice, Griffiths, Beatrice, Michaux, Justine, Pak, Hui Song, Stevenson, Brian J., Woolston, Andrew, Semiannikova, Maria, Spain, Georgia, Barber, Louise J., Matthews, Nik, Rao, Sheela, Watkins, David, Chau, Ian, Coukos, George, Racle, Julien, Gfeller, David, Starling, Naureen, Cunningham, David, Bassani-Sternberg, Michal, Gerlinger, Marco

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A novel pulse-chase SILAC strategy measures changes in protein decay and synthesis rates induced by perturbation of proteostasis with an Hsp90 inhibitor von Fierro-Monti, Ivo, Racle, Julien, Hernandez, Celine, Waridel, Patrice, Hatzimanikatis, Vassily, Quadroni, Manfredo

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Dynamic impacts of the inhibition of the molecular chaperone Hsp90 on the T-cell proteome have implications for anti-cancer therapy von Fierro-Monti, Ivo, Echeverria, Pablo, Racle, Julien, Hernandez, Celine, Picard, Didier, Quadroni, Manfredo

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Inflammatory B cells correlate with failure to checkpoint blockade in melanoma patients von de Jonge, Kaat, Tillé, Laure, Lourenco, Joao, Maby-El Hajjami, Hélène, Nassiri, Sina, Racle, Julien, Gfeller, David, Delorenzi, Mauro, Verdeil, Grégory, Baumgaertner, Petra, Speiser, Daniel E.

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Deciphering the landscape of phosphorylated HLA-II ligands von Solleder, Marthe, Racle, Julien, Guillaume, Philippe, Coukos, George, Bassani-Sternberg, Michal, Gfeller, David

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A genome-scale integration and analysis of Lactococcus lactis translation data von Racle, Julien, Picard, Flora, Girbal, Laurence, Cocaign-Bousquet, Muriel, Hatzimanikatis, Vassily

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Contemplating immunopeptidomes to better predict them von Gfeller, David, Liu, Yan, Racle, Julien

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How to Predict Binding Specificity and Ligands for New MHC-II Alleles with MixMHC2pred von Racle, Julien, Gfeller, David

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The MHC Motif Atlas: a database of MHC binding specificities and ligands von Tadros, Daniel M, Eggenschwiler, Simon, Racle, Julien, Gfeller, David

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Improved predictions of antigen presentation and TCR recognition with MixMHCpred2.2 and PRIME2.0 reveal potent SARS-CoV-2 CD8+ T-cell epitopes von Gfeller, David, Schmidt, Julien, Croce, Giancarlo, Guillaume, Philippe, Bobisse, Sara, Genolet, Raphael, Queiroz, Lise, Cesbron, Julien, Racle, Julien, Harari, Alexandre

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ILC2-modulated T cell-to-MDSC balance is associated with bladder cancer recurrence von Chevalier, Mathieu F, Trabanelli, Sara, Racle, Julien, Salomé, Bérengère, Cesson, Valérie, Gharbi, Dalila, Bohner, Perrine, Domingos-Pereira, Sonia, Dartiguenave, Florence, Fritschi, Anne-Sophie, Speiser, Daniel E, Rentsch, Cyrill A, Gfeller, David, Jichlinski, Patrice, Nardelli-Haefliger, Denise, Jandus, Camilla, Derré, Laurent

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Machine learning predictions of MHC-II specificities reveal alternative binding mode of class II epitopes von Racle, Julien, Guillaume, Philippe, Schmidt, Julien, Michaux, Justine, Larabi, Amédé, Lau, Kelvin, Perez, Marta A.S., Croce, Giancarlo, Genolet, Raphaël, Coukos, George, Zoete, Vincent, Pojer, Florence, Bassani-Sternberg, Michal, Harari, Alexandre, Gfeller, David

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