Current Preprints
- Improving generalization of machine learning-identified biomarkers with causal modeling: an investigation into immune receptor diagnostics. Milena Pavlović, Ghadi S. Al Hajj, Johan Pensar, Mollie Wood, Ludvig M. Sollid, Victor Greiff, Geir Kjetil Sandve. arXiv
- Reference-based comparison of adaptive immune receptor repertoires.
- CompAIRR: ultra-fast comparison of adaptive immune receptor repertoires by exact and approximate sequence matching. Torbjørn Rognes, Lonneke Scheffer, Victor Greiff, Geir Kjetil Sandve. bioRxiv
- Echidna: integrated simulations of single-cell immune receptor repertoires and transcriptomes. Jiami Han, Raphael Kuhn, Chrysa Papadopoulou, Andreas Agrafiotis, Victor Kreiner, Danielle Shlesinger, Raphael Dizerens, Kai-Lin Hong, Cédric Weber, Victor Greiff, Annette Oxenius, Sai T. Reddy, Alexander Yermanos. bioRxiv
- One billion synthetic 3D-antibody-antigen complexes enable unconstrained machine-learning formalized investigation of antibody specificity prediction. Philippe Auguste Robert, Rahmad Akbar, Robert Frank, Milena Pavlović, Michael Widrich, Igor Snapkov, Maria Chernigovskaya, Lonneke Scheffer, Andrei Slabodkin, Brij Bhushan Mehta, Mai Ha Vu, Aurél Prósz, Krzysztof Abram, Alex Olar, Enkelejda Miho, Dag Trygve Tryslew Haug, Fridtjof Lund-Johansen, Sepp Hochreiter, Ingrid Hobæk Haff, Günter Klambauer, Geir Kjetil Sandve, Victor Greiff. bioRxiv
- The influence of the phylogenetic inference pipeline on murine antibody repertoire sequencing data following viral infection. Alexander Yermanos, Victor Greiff, Tanja Stadler, Annette Oxenius, Sai T Reddy. bioRxiv
2022
- Profiling the baseline performance and limits of machine learning models for adaptive immune receptor repertoire classification. Chakravarthi Kanduri, Milena Pavlović, Lonneke Scheffer, Keshav Motwani, Maria Chernigovskaya, Victor Greiff, Geir Kjetil Sandve. GigaScience
- In silico proof of principle of machine learning-based antibody design at unconstrained scale. Rahmad Akbar, Philippe A. Robert, Cédric R. Weber, Michael Widrich, Robert Frank, Milena Pavlović, Lonneke Scheffer, Maria Chernigovskaya, Igor Snapkov, Andrei Slabodkin, Brij Bhushan Mehta, Enkelejda Miho, Fridtjof Lund-Johansen, Jan Terje Andersen, Sepp Hochreiter, Ingrid Hobæk Haff, Günter Klambauer, Geir Kjetil Sandve & Victor Greiff. mAbs
- Progress and challenges for the machine learning-based design of fit-for-purpose monoclonal antibodies. Rahmad Akbar, Habib Bashour,Puneet Rawat,Philippe A. Robert,Eva Smorodina, Tudor-Stefan Cotet,Karine Flem-Karlsen, Robert Frank,Brij Bhushan Mehta, Mai Ha Vu, Talip Zengin, Jose Gutierrez-Marcos, Fridtjof Lund-Johansen,Jan Terje Andersen & Victor Greiff. mAbs
- A Nextflow pipeline for T-cell receptor repertoire reconstruction and analysis from RNA sequencing data. Teresa Rubio, Maria Chernigovskaya, Susanna Marquez, Cristina Marti, Paula Izquierdo-Altarejos, Amparo Urios, Carmina Montoliu, Vicente Felipo, Ana Conesa, Victor Greiff, Sonia Tarazona. Immunoinformatics
- TCRpower: quantifying the detection power of T-cell receptor sequencing with a novel computational pipeline calibrated by spike-in sequences. Shiva Dahal-Koirala, Gabriel Balaban, Ralf Stefan Neumann, Lonneke Scheffer, Knut Erik Aslaksen Lundin, Victor Greiff, Ludvig Magne Sollid, Shuo-Wang Qiao, Geir Kjetil Sandve. Briefings in Bioinformatics
- Antibody variable sequences have a pronounced effect on cellular transport and plasma half-life. Algirdas Grevys, Rahel Frick, Simone Mester, Karine Flem-Karlsen, Jeannette Nilsen, Stian Foss, Kine Marita Knudsen Sand, Thomas Emrich, Jens Andre Alexander Fischer, Victor Greiff, Inger Sandlie, Tilman Schlothauer, Jan Terje Andersen. iScience
2021
- Individualized VDJ recombination predisposes the available Ig sequence space. Andrei Slabodkin, Maria Chernigovskaya, Ivana Mikocziova, Rahmad Akbar, Lonneke Scheffer, Milena Pavlović, Habib Bashour, Igor Snapkov, Brij Bhushan Mehta, Cédric R. Weber, Jose Gutierrez-Marcos, Ludvig M. Sollid, Ingrid Hobæk Haff, Geir Kjetil Sandve, Philippe A. Robert, Victor Greiff. Genome Research
- The immuneML ecosystem for machine learning analysis of adaptive immune receptor repertoires. Milena Pavlović*, Lonneke Scheffer*, Keshav Motwani, Chakravarthi Kanduri, Radmila Kompova, Nikolay Vazov, Knut Waagan, Fabian L. M. Bernal, Alexandre Almeida Costa, Brian Corrie, Rahmad Akbar, Ghadi S. Al Hajj, Gabriel Balaban, Todd M. Brusko, Maria Chernigovskaya, Scott Christley, Lindsay G. Cowell, Robert Frank, Ivar Grytten, Sveinung Gundersen, Ingrid Hobæk Haff, Eivind Hovig, Ping-Han Hsieh, Günter Klambauer, Marieke L. Kuijjer, Christin Lund-Andersen, Antonio Martini, Thomas Minotto, Johan Pensar, Knut Rand, Enrico Riccardi, Philippe A. Robert, Artur Rocha, Andrei Slabodkin, Igor Snapkov, Ludvig M. Sollid, Dmytro Titov, Cédric R. Weber, Michael Widrich, Gur Yaari, Victor Greiff# & Geir Kjetil Sandve#. Nature Machine Intelligence
- Progress and challenges in mass spectrometry-based analysis of antibody repertoires. Igor Snapkov, Maria Chernigovskaya, Pavel Sinitcyn, Khang Lê Quý, Tuula A. Nyman, Victor Greiff. Trends in Biotechnology
- Profiling the specificity of clonally expanded plasma cells during chronic viral infection by single-cell analysis. Daniel Neumeier, Alessandro Pedrioli, Alessandro Genovese, Ioana Sandu, Roy Ehling, Kai-Lin Hong, Chrysa Papadopoulou, Andreas Agrafiotis, Raphael Kuhn, Danielle Shlesinger, Damiano Robbiani, Jiami Han, Laura Hauri, Lucia Csepregi, Victor Greiff, Doron Merkler, Sai T. Reddy, Annette Oxenius, Alexander Yermanos. European Journal of Immunology
- Ancestral diversity is limited in published T-cell receptor sequencing studies. Yu-Ning Huang, Kerui Peng, Alice B. Popejoy, Jieting Hu, Theodore Scott Nowicki, Stefan M. Gold, Lluis Quintana-Murci, Macarena Fuentes-Guajardo, Mikhail Shugay, Victor Greiff, Amanda M.Burkhardt, Houda Alachkar, Serghei Mangul.
- Germline polymorphisms and alternative splicing of human immunoglobulin light chain genes. Ivana Mikocziova, Ayelet Peres, Moriah Gidoni, Victor Greiff, Gur Yaari, Ludvig M Sollid. Iscience
- Dynamic changes in the T cell receptor repertoire during treatment with radiotherapy combined with an immune checkpoint inhibitor, Åsa Kristina Öjlert, Daniel Nebdal, Igor Snapkov, Vibeke Olsen, Joel Kidman, Victor Greiff, Jonathan Chee, Åslaug Helland, Molecular Oncology
- Coupled Antigen and BLIMP1 Asymmetric Division With a Large Segregation Between Daughter Cells Recapitulates the Temporal Transition From Memory B Cells to Plasma Cells and a DZ-to-LZ Ratio in the Germinal Center. Elena Merino Tejero, Danial Lashgari, Rodrigo García-Valiente, Jiaojiao He, Philippe A. Robert, Michael Meyer-Hermann, Jeroen E. J. Guikema, Huub Hoefsloot and Antoine H. C. van Kampen. Frontiers in Immunology
- Single-cell BCR and transcriptome analysis after influenza infection reveals spatiotemporal dynamics of antigen-specific B cells. Nimitha R. Mathew, Jayalal K. Jayanthan, Ilya V. Smirnov, Jonathan L. Robinson, Hannes Axelsson, Sravya S. Nakka, Aikaterini Emmanouilidi, Paulo Czarnewski, William T. Yewdell, Karin Schön, Cristina Lebrero-Fernández, Valentina Bernasconi, William Rodin, Ali M. Harandi, Nils Lycke, Nicholas Borcherding, Jonathan W. Yewdell, Victor Greiff, Mats Bemark, Davide Angeletti. Cell reports
- Immunoglobulin germline gene variation and its impact on human disease. Ivana Mikocziova, Victor Greiff & Ludvig M. Sollid. Genes & Immunity
- TCR repertoire diversity in Multiple Sclerosis: High-dimensional bioinformatics analysis of sequences from brain, cerebrospinal fluid and peripheral blood. Roberta Amoriello, Maria Chernigovskaya, Victor Greiff, Alberto Carnasciali, Luca Massacesi, Alessandro Barilaro, Anna M. Repice, Tiziana Biagioli, Alessandra Aldinucci, Paolo A. Muraro, David A. Laplaud, Andreas Lossius, Clara Ballerini. EBioMedicine
- Diversity in immunogenomics: the value and the challenge. Kerui Peng, Yana Safonova, Mikhail Shugay, Alice B. Popejoy, Oscar L. Rodriguez, Felix Breden, Petter Brodin, Amanda M. Burkhardt, Carlos Bustamante, Van-Mai Cao-Lormeau, Martin M. Corcoran, Darragh Duffy, Macarena Fuentes-Guajardo, Ricardo Fujita, Victor Greiff, Vanessa D. Jönsson, Xiao Liu, Lluis Quintana-Murci, Maura Rossetti, Jianming Xie, Gur Yaari, Wei Zhang, Malak S. Abedalthagafi, Khalid O. Adekoya, Rahaman A. Ahmed, Wei-Chiao Chang, Clive Gray, Yusuke Nakamura, William D. Lees, Purvesh Khatri, Houda Alachkar, Cathrine Scheepers, Corey T. Watson, Gunilla B. Karlsson Hedestam & Serghei Mangul. Nature Methods
- Modelling the Dynamics of T-Cell Development in the Thymus. Philippe Robert, Heike Kunze-Schumacher, Victor Greiff, Andreas Krueger. Entropy
- Animal Immunization, in Vitro Display Technologies, and Machine Learning for Antibody Discovery. Andreas H. Laustsen, Victor Greiff, Aneesh Karatt-Vellatt, Serge Muyldermans, Timothy P. Jenkins. Trends in Biotechnology.
- A compact vocabulary of paratope-epitope interactions enables predictability of antibody-antigen binding. Rahmad Akbar, Philippe A. Robert, Milena Pavlović, Jeliazko R. Jeliazkov, Igor Snapkov, Andrei Slabodkin, Cédric R. Weber, Lonneke Scheffer, , , , Yana Safonova, Geir K. Sandve, and Victor Greiff#. Cell Reports.
- Extended plasma half-life of albumin-binding domain fused human IgA upon pH-dependent albumin engagement of human FcRn in vitro and in vivo. Simone Mester, Mitchell Evers, Saskia Meyer, Jeannette Nilsen, Victor Greiff, Inger Sandlie, Jeanette Leusen & Jan Terje Andersen. mAbs
2020
- Mining adaptive immune receptor repertoires for biological and clinical information using machine learning.Victor Greiff, Gur Yaari, Lindsay Cowell. Current Opinion in Systems Biology.
- Hopfield Networks is All You Need. Hubert Ramsauer, Bernhard Schäfl, Johannes Lehner, Philipp Seidl, Michael Widrich, Lukas Gruber, Markus Holzleitner, Milena Pavlović, Geir Kjetil Sandve, Victor Greiff, David Kreil, Michael Kopp, Günter Klambauer, Johannes Brandstetter, Sepp Hochreiter. arXiv
- Modern Hopfield Networks and Attention for Immune Repertoire Classification. Michael Widrich, Bernhard Schäfl, Hubert Ramsauer, Milena Pavlović, Lukas Gruber, Markus Holzleitner, Johannes Brandstetter, Geir Kjetil Sandve, Victor Greiff, Sepp Hochreiter, Günter Klambauer. NeurIPS.
- Mucosal or systemic microbiota exposures shape the B cell repertoire. Hai Li, Julien P. Limenitakis, Victor Greiff, Bahtiyar Yilmaz, Olivier Schären, Camilla Urbaniak, Mirjam Zünd, Melissa A. E. Lawson, Ian D. Young, Sandra Rupp, Mathias Heikenwälder, Kathy D. McCoy, Siegfried Hapfelmeier, Stephanie C. Ganal-Vonarburg & Andrew J. Macpherson. Nature.
- Discrete populations of isotype-switched memory B lymphocytes are maintained in murine spleen and bone marrow. René Riedel, Richard Addo, Marta Ferreira-Gomes, Gitta Anne Heinz, Frederik Heinrich, Jannis Kummer, Victor Greiff, Daniel Schulz, Cora Klaeden, Rebecca Cornelis, Ulrike Menzel, Stefan Kröger, Ulrik Stervbo, Ralf Köhler, Claudia Haftmann, Silvia Kühnel, Katrin Lehmann, Patrick Maschmeyer, Mairi McGrath, Sandra Naundorf, Stefanie Hahne, Özen Sercan-Alp, Francesco Siracusa, Jonathan Stefanowski, Melanie Weber, Kerstin Westendorf, Jakob Zimmermann, Anja E. Hauser, Sai T. Reddy, Pawel Durek, Hyun-Dong Chang, Mir-Farzin Mashreghi & Andreas Radbruch. Nature communications.
- Mouse-specific but infection-unspecific IgM repertoire fingerprint following viral infection. Alexander Yermanos, Nike Julia Krautler, Alessandro Pedrioli, Ulrike Menzel, Victor Greiff, Tanja Stadler, Annette Oxenius, Sai T. Reddy. Frontiers in Immunology.
- Inter- and intraspecies comparison of phylogenetic fingerprints and sequence diversity of immunoglobulin variable genes. Alexander Yermanos, Andreas Dounas, Victor Greiff, Tanja Stadler, Annette Oxenius & Sai T. Reddy. Immunogenetics.
- The TCR Repertoire Reconstitution in Multiple Sclerosis: Comparing One-Shot and Continuous Immunosuppressive Therapies. Roberta Amoriello†, Victor Greiff†, Alessandra Aldinucci, Elena Bonechi, Alberto Carnasciali, Benedetta Peruzzi, Anna Maria Repice, Alice Mariottini, Riccardo Saccardi, Benedetta Mazzanti, Luca Massacesi and Clara Ballerini#. Frontiers in Immunology.
- immuneSIM: tunable multi-feature simulation of B- and T-cell receptor repertoires for immunoinformatics benchmarking. Cédric R. Weber, Rahmad Akbar, Alexander Yermanos, Milena Pavlović, Igor Snapkov, Geir K. Sandve, Sai T. Reddy#, Victor Greiff#. Bioinformatics
- Chronic Viral Infection Promotes Efficient Germinal Center B Cell Responses. Bénédict Fallet, Yi Hao, Marianna Florova , Karen Cornille, Alba Verge de los Aires, Giulia Girelli Zubani, Yusuf I. Ertuna, Victor Greiff, Ulrike Menzel, Karim Hammad, Doron Merkler, Sai T. Reddy, Jean-Claude Weill, Claude-Agnès Reynaud, Daniel D. Pinschewer. Cell Reports.
- Quantitative and Qualitative Analysis of Humoral Immunity Reveals Continued and Personalized Evolution in Chronic Viral Infection. Nike Julia Kräutler, Alexander Yermanos, Alessandro Pedrioli, Suzanne P.M. Welten, Dominique Lorgé, Ute Greczmiel, Ilka Bartsch, Jörg Scheuermann, Jonathan D. Kiefer, Klaus Eyer, Ulrike Menzel, Victor Greiff, Dario Neri, Tanja Stadler, Sai T. Reddy, Annette Oxenius. Cell Reports.
2019
- Benchmarking immunoinformatic tools for the analysis of antibody repertoire sequences. Erand Smakaj, Lmar Babrak, Mats Ohlin, Mikhail Shugay, Bryan Briney, Deniz Tosoni, Christopher Galli, Vendi Grobelsek, Igor D’Angelo, Branden Olson, Sai Reddy, Victor Greiff, Johannes Trück, Susanna Marquez, William Lees, Enkelejda Miho. Bioinformatics.
- Augmenting adaptive immunity: progress and challenges in the quantitative engineering and analysis of adaptive immune receptor repertoires. Alex J. Brown, Igor Snapkov, Rahmad Akbar, Milena Pavlović, Enkelejda Miho, Geir K. Sandve#, Victor Greiff#. Molecular Systems Design and Engineering.
- Resident memory CD8 T cells persist for years in human small intestine. Raquel Bartolome Casado, Ole J. B. Landsverk, Sudhir Kumar Chauhan, Lisa Richter, Danh Phung, Victor Greiff, Louise Fremgaard Risnes, Ying Yao, Ralf Stefan Neumann, Sheraz Yaqub, Ole Øyen, Rune Horneland, Einar Martin Aandahl, Vemund Paulsen, Ludvig M. Sollid, Shuo-Wang Qiao, Espen S. Baekkevold, Frode L. Jahnsen. Journal of Experimental Medicine.
- Persistence of intrathecal oligoclonal B cells and IgG in multiple sclerosis. Alina Tomescu-Baciua, Jorunn N. Johansena, Trygve Holmøy, Victor Greiff, Maria Stensland, Gustavo Antonio de Souzaa, Frode Vartdal, Andreas Lossius. Journal of Neuroimmunology.
- Large-scale network analysis reveals the sequence space architecture of antibody repertoires. Enkelejda Miho, Rok Roškar, Victor Greiff# & Sai T. Reddy#. Nature Communications.
- Inferred allelic variants of immunoglobulin receptor genes: a system for their evaluation, documentation and naming. Mats Ohlin, Cathrine Scheepers, Martin Corcoran, William D. Lees, Christian E. Busse, Davide Bagnara, Linnea Thörnqvist, Jean-Philippe Bürckert, Katherine J. Jackson, Duncan K. Ralph, Chaim A. Schramm, Nishanth Marthandan, Felix Breden, Jamie K. Scott, Frederick A. Matsen IV, Victor Greiff, Gur Yaari, Steven H. Kleinstein, Scott Christley, Jacob S. Sherkow, Sofia Kossida, Marie-Paule Lefranc, Menno C. van Zelm, Corey T. Watson and Andrew M. Collins. Frontiers in Immunology.
2018
- High-throughput antibody engineering in mammalian cells by CRISPR/Cas9-mediated homology-directed mutagenesis. Derek M Mason, Cédric R Weber, Cristina Parola, Simon M Meng, Victor Greiff, William J Kelton, Sai T Reddy. Nucleic Acids Research
- Computational Strategies for Dissecting the High-Dimensional Complexity of Adaptive Immune Repertoires. Enkelejda Miho , Alexander Yermanos, Cédric R. Weber, Christoph T. Berger, Sai T. Reddy#, Victor Greiff#. Frontiers in Immunology
2017
- Learning the High-Dimensional Immunogenomic Features that Predict Public and Private Antibody Repertoires. Victor Greiff*, Cédric R*. Weber, Johannes Palme, Ulrich Bodenhofer, Enkelejda Miho, Ulrike Menzel, Sai T Reddy. The Journal of Immunology
- Systems Analysis Reveals High Genetic and Antigen-Driven Predetermination of Antibody Repertoires throughout B Cell Development. Victor Greiff*, Ulrike Menzel*, Enkelejda Miho, Cédric Weber, René Riedel, Skylar Cook, Atijeh Valai, Telma Lopes, Andreas Radbruch, Thomas Winkler, Sai T Reddy. Cell Reports
- Comparison of methods for phylogenetic B-cell lineage inference using time-resolved antibody repertoire simulations (AbSim). Alexander Yermanos, Victor Greiff, Nike J Krautler, Ulrike Menzel, Andreas Dounas, Enkelejda Miho, Annette Oxenius, Tanja Stadler, Sai T Reddy. Bioinformatics
- Low immunoglobulin E flags two distinct types of immune dysregulation. Marius Elkuch,* Victor Greiff*, Christoph T Berger, M Bouchenaki, Thomas Daikeler, Andreas Bircher, Alexander A Navarini, Ingmar Heijnen, Mike Recher. Clinical and Experimental Immunology
- Adaptive Immune Receptor Repertoire Community recommendations for sharing immune-repertoire sequencing data. Florian Rubelt, Christian E Busse, Syed Ahmad Chan Bukhari, Jean-Philippe Bürckert, Encarnita Mariotti-Ferrandiz, Lindsay G Cowell, Corey T Watson, Nishanth Marthandan, William J Faison, Uri Hershberg, Uri Laserson, Brian D Corrie, Mark M Davis, Bjoern Peters, Marie-Paule Lefranc, Jamie K Scott, Felix Breden, The AIRR Community, Eline T Luning Prak, Steven H Kleinstein, Nature Immunology.
2015
- A bioinformatic framework for immune repertoire diversity profiling enables detection of immunological status. Victor Greiff, Pooja Bhat, Skylar C Cook, Ulrike Menzel, Wenjing Kang, Sai T Reddy. Genome Medicine
- Bioinformatic and statistical analysis of adaptive immune repertoires.Victor Greiff, Enkelejda Miho, Ulrike Menzel, Sai T Reddy. Trends in Immunology
- Influenza vaccine response profiles are affected by vaccine preparation and preexisting immunity, but not HIV infection. Christoph T Berger*, Victor Greiff*, Matthias Mehling, Stefanie Fritz, Marc A Meier, Gideon Hoenger, Anna Conen, Mike Recher, Manuel Battegay, Sai T Reddy, Christoph Hess, Human Vaccines & Immunotherapeutics
- Risk factors for pneumocystis pneumonia in giant cell arteritis: a single-centre cohort study. Christoph T Berger, Victor Greiff, S John, KF Koenig, Marc B Bigler, Mike Recher, Christoph Hess, Thomas Daikeler. Clinical and Experimental Rheumatology
2014
- Quantitative assessment of the robustness of next-generation sequencing of antibody variable gene repertoires from immunized mice. Victor Greiff*, Ulrike Menzel*, Ulrike Haessler, Skylar C Cook, Simon Friedensohn, Tarik A Khan, Mark Pogson, Ina Hellmann, Sai T Reddy. BMC Immunology
- Comprehensive evaluation and optimization of amplicon library preparation methods for high-throughput antibody sequencing. Ulrike Menzel*, Victor Greiff*, Tarik Khan, Ulrike Haessler, Ina Hellmann, Simon Friedensohn, Skyler C Cook, Mark Pogson, Sai T Reddy. PLoS One
2012
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