Learning the High-Dimensional Immunogenomic Features That Predict Public and Private Antibody Repertoires von Greiff, Victor, Weber, Cédric R, Palme, Johannes, Bodenhofer, Ulrich, Miho, Enkelejda, Menzel, Ulrike, Reddy, Sai T

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Deep mutational learning predicts ACE2 binding and antibody escape to combinatorial mutations in the SARS-CoV-2 receptor-binding domain von Taft, Joseph M., Weber, Cédric R., Gao, Beichen, Ehling, Roy A., Han, Jiami, Frei, Lester, Metcalfe, Sean W., Overath, Max D., Yermanos, Alexander, Kelton, William, Reddy, Sai T.

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A compact vocabulary of paratope-epitope interactions enables predictability of antibody-antigen binding von Akbar, Rahmad, Robert, Philippe A., Pavlović, Milena, Jeliazkov, Jeliazko R., Snapkov, Igor, Slabodkin, Andrei, Weber, Cédric R., Scheffer, Lonneke, Miho, Enkelejda, Haff, Ingrid Hobæk, Haug, Dag Trygve Tryslew, Lund-Johansen, Fridtjof, Safonova, Yana, Sandve, Geir K., Greiff, Victor

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Computational Strategies for Dissecting the High-Dimensional Complexity of Adaptive Immune Repertoires von Miho, Enkelejda, Yermanos, Alexander, Weber, Cédric R, Berger, Christoph T, Reddy, Sai T, Greiff, Victor

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High-throughput antibody engineering in mammalian cells by CRISPR/Cas9-mediated homology-directed mutagenesis von Mason, Derek M, Weber, Cédric R, Parola, Cristina, Meng, Simon M, Greiff, Victor, Kelton, William J, Reddy, Sai T

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immuneSIM: tunable multi-feature simulation of B- and T-cell receptor repertoires for immunoinformatics benchmarking von Weber, Cédric R, Akbar, Rahmad, Yermanos, Alexander, Pavlović, Milena, Snapkov, Igor, Sandve, Geir K, Reddy, Sai T, Greiff, Victor

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Optimization of therapeutic antibodies by predicting antigen specificity from antibody sequence via deep learning von Mason, Derek M., Friedensohn, Simon, Weber, Cédric R., Jordi, Christian, Wagner, Bastian, Meng, Simon M., Ehling, Roy A., Bonati, Lucia, Dahinden, Jan, Gainza, Pablo, Correia, Bruno E., Reddy, Sai T.

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High-throughput T cell receptor engineering by functional screening identifies candidates with enhanced potency and specificity von Vazquez-Lombardi, Rodrigo, Jung, Johanna S., Schlatter, Fabrice S., Mei, Anna, Mantuano, Natalia Rodrigues, Bieberich, Florian, Hong, Kai-Lin, Kucharczyk, Jakub, Kapetanovic, Edo, Aznauryan, Erik, Weber, Cédric R., Zippelius, Alfred, Läubli, Heinz, Reddy, Sai T.

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Individualized VDJ recombination predisposes the available Ig sequence space von Slabodkin, Andrei, Chernigovskaya, Maria, Mikocziova, Ivana, Akbar, Rahmad, Scheffer, Lonneke, Pavlovic, Milena, Bashour, Habib, Snapkov, Igor, Mehta, Brij Bhushan, Weber, Cedric R., Gutierrez-Marcos, Jose, Sollid, Ludvig M., Haff, Ingrid Hobaek, Sandve, Geir Kjetil, Robert, Philippe A., Greiff, Victor

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In silico proof of principle of machine learning-based antibody design at unconstrained scale von Akbar, Rahmad, Robert, Philippe A, Weber, Cédric R, Widrich, Michael, Frank, Robert, Pavlović, Milena, Scheffer, Lonneke, Chernigovskaya, Maria, Snapkov, Igor, Slabodkin, Andrei, Mehta, Brij Bhushan, Miho, Enkelejda, Lund-Johansen, Fridtjof, Andersen, Jan Terje, Hochreiter, Sepp, Hobæk Haff, Ingrid, Klambauer, Günter, Sandve, Geir Kjetil, Greiff, Victor

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SARS-CoV-2 reactive and neutralizing antibodies discovered by single-cell sequencing of plasma cells and mammalian display von Ehling, Roy A., Weber, Cédric R., Mason, Derek M., Friedensohn, Simon, Wagner, Bastian, Bieberich, Florian, Kapetanovic, Edo, Vazquez-Lombardi, Rodrigo, Di Roberto, Raphaël B., Hong, Kai-Lin, Wagner, Camille, Pataia, Michele, Overath, Max D., Sheward, Daniel J., Murrell, Ben, Yermanos, Alexander, Cuny, Andreas P., Savic, Miodrag, Rudolf, Fabian, Reddy, Sai T.

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A Single-Cell Atlas of Lymphocyte Adaptive Immune Repertoires and Transcriptomes Reveals Age-Related Differences in Convalescent COVID-19 Patients von Bieberich, Florian, Vazquez-Lombardi, Rodrigo, Yermanos, Alexander, Ehling, Roy A., Mason, Derek M., Wagner, Bastian, Kapetanovic, Edo, Di Roberto, Raphael Brisset, Weber, Cédric R., Savic, Miodrag, Rudolf, Fabian, Reddy, Sai T.

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The immuneML ecosystem for machine learning analysis of adaptive immune receptor repertoires von Pavlović, Milena, Scheffer, Lonneke, Motwani, Keshav, Kanduri, Chakravarthi, Kompova, Radmila, Vazov, Nikolay, Waagan, Knut, Bernal, Fabian L. M., Costa, Alexandre Almeida, Corrie, Brian, Akbar, Rahmad, Al Hajj, Ghadi S., Balaban, Gabriel, Brusko, Todd M., Chernigovskaya, Maria, Christley, Scott, Cowell, Lindsay G., Frank, Robert, Grytten, Ivar, Gundersen, Sveinung, Haff, Ingrid Hobæk, Hovig, Eivind, Hsieh, Ping-Han, Klambauer, Günter, Kuijjer, Marieke L., Lund-Andersen, Christin, Martini, Antonio, Minotto, Thomas, Pensar, Johan, Rand, Knut, Riccardi, Enrico, Robert, Philippe A., Rocha, Artur, Slabodkin, Andrei, Snapkov, Igor, Sollid, Ludvig M., Titov, Dmytro, Weber, Cédric R., Widrich, Michael, Yaari, Gur, Greiff, Victor, Sandve, Geir Kjetil

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Reference-based comparison of adaptive immune receptor repertoires von Weber, Cédric R., Rubio, Teresa, Wang, Longlong, Zhang, Wei, Robert, Philippe A., Akbar, Rahmad, Snapkov, Igor, Wu, Jinghua, Kuijjer, Marieke L., Tarazona, Sonia, Conesa, Ana, Sandve, Geir K., Liu, Xiao, Reddy, Sai T., Greiff, Victor

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Engineered allogeneic T cells decoupling T-cell-receptor and CD3 signalling enhance the antitumour activity of bispecific antibodies von Kapetanovic, Edo, Weber, Cédric R, Bruand, Marine, Pöschl, Daniel, Kucharczyk, Jakub, Hirth, Elisabeth, Dietsche, Claudius, Khan, Riyaz, Wagner, Bastian, Belli, Olivier, Vazquez-Lombardi, Rodrigo, Castellanos-Rueda, Rocío, Di Roberto, Raphael B, Kalinka, Kevin, Raess, Luca, Ly, Kevin, Rai, Shivam, Dittrich, Petra S, Platt, Randall J, Oricchio, Elisa, Reddy, Sai T

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The Future of Blood Testing Is the Immunome von Arnaout, Ramy A., Prak, Eline T. Luning, Schwab, Nicholas, Rubelt, Florian

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A single-cell atlas of lymphocyte adaptive immune repertoires and transcriptomes reveals age-related differences in convalescent COVID-19 patients von Bieberich, Florian, Vazquez-Lombardi, Rodrigo, Yermanos, Alexander, Ehling, Roy A., Mason, Derek M., Wagner, Bastian, Kapetanovic, Edo, Di Roberto, Raphael Brisset, Weber, Cedric R., Savic, Miodrag, Rudolf, Fabian, Reddy, Sai T.

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Reference-based comparison of adaptive immune receptor repertoires von Weber, Cédric R, Rubio, Teresa, Wang, Longlong, Zhang, Wei, Robert, Philippe A, Akbar, Rahmad, Snapkov, Igor, Wu, Jinghua, Kuijjer, Marieke L, Tarazona, Sonia, Conesa, Ana, Sandve, Geir K, Liu, Xiao, Reddy, Sai T, Greiff, Victor

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Computational strategies for dissecting the high-dimensional complexity of adaptive immune repertoires von Enkelejda Miho, Yermanos, Alexander, Weber, Cédric R, Berger, Christoph T, Reddy, Sai T, Greiff, Victor

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In silico proof of principle of machine learning-based antibody design at unconstrained scale von Akbar, Rahmad, Robert, Philippe A., Weber, Cédric R., Widrich, Michael, Frank, Robert, Pavlović, Milena, Scheffer, Lonneke, Chernigovskaya, Maria, Snapkov, Igor, Slabodkin, Andrei, Mehta, Brij Bhushan, Miho, Enkelejda, Lund-Johansen, Fridtjof, Andersen, Jan Terje, Hochreiter, Sepp, Hobæk Haff, Ingrid, Klambauer, Günter, Sandve, Geir Kjetil, Greiff, Victor

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