Publications

Current Preprints

• Revealing the hidden sequence distribution of epitope-specific TCR repertoires and its influence on machine learning model performance. Sofie Gielis, Maria Chernigovskaya , Milena Pavlovic, Vincent Van Deuren, Romi Vandoren, Sebastiaan Valkiers, Kris Laukens, Victor Greiff, Pieter Meysman. bioRxiv.
• Baselining the Buzz; Trastuzumab-HER2 Affinity, and Beyond. Lewis Chinery, Alissa M. Hummer, Brij Bhushan Mehta, Rahmad Akbar, Puneet Rawat, Andrei Slabodkin, Khang Le Quy, Fridtjof Lund-Johansen, Victor Greif, Jeliazko R. Jeliazkov, Charlotte M. Deane. bioRxiv.

• Quantitative mapping of antigen specificity in adaptive immune repertoire embedding spaces. Marina Frolenkova, Niccolò Cardente, Jahn Zhong, Evgenii Egorov, Giulio Isacchini, Julien Limenitakis, Philipp Fleig, Puneet Rawat, Milena Pavlović, Caterina Sanetti, Jose Gutierrez-Marcos, Geir Kjetil Sandve, Habib Bashour, Maria Francesca Abbate and Victor Greiff. bioRxiv
• Improving nanobody structure prediction with self-distillation. Montader Ali, Matthew Greenig, Mateusz Jaskolowski, Mia Crnogaj, Eva Smorodina, Haowen Zhao, Victor Greiff, Pietro Sormanni. bioRxiv
• PEPE: Scalable extraction of multi-modal protein language model representations. Jahn Zhong, Niccolò Cardente, Geir Kjetil Sandve, Habib Bashour, Maria Francesca Abbate, Victor Greiff. bioRxiv

2026

• IgD from atypical-like memory B cells and plasma cells targets commensal and environmental antigens. Roser Tachó-Piñot, Habib Bashour, Martyna Filipska, Sonia Tejedor-Vaquero, Leire de Campos-Mata, Alba Sáez-Gordón, Júlia Perera-Bel, Mauricio Guzman, Xavi Marcos-Fa, Pablo Canales-Herrerias, Jorge Domínguez-Barragán, Berta Arcós-Ribas, Andrei Slabodkin, Maria Chernigovskaya, María Luisa Rodríguez de la Concepción, osé Gutierrez-Marcos, Ana García-García, Andrés Nascimento-Osorio, Mariona Pascal, Laia Alsina, Juan I. Aróstegui, Saurabh Mehandru, Charlotte Cunningham-Rundles, Jorge Carrillo, Giuliana Magri, Victor Greiff, Andrea Cerutti. Journal of Experimental Medicine
• ASD: Antigen-Specific Antibody Database. Arkadiusz Czerwinski, Pawel Dudzic, Konrad Wojtowicz, Igor Jaszczyszyn, Weronika Bielska, Sonia Wrobel, Samuel Demharter, Roberto Spreafico, Victor Greiff, Konrad Krawczyk. mAbs
• TCR2HLA: Calibrated inference of HLA genotypes from TCR repertoires enables identification of immunologically relevant metaclonotypes. Koshlan Mayer-Blackwell, Anastasia Minervina, Mikhail Pogorelyy, Puneet Rawat, Melanie R. Shapiro, Leeana D. Peters, Emily S. Ford, Amanda L. Posgai, Kasi Vengesana, Samuel Minot, David M. Koelle, Victor Greiff, Philip Bradley, Todd M. Brusko, Paul G. Thomas, Andrew Fiore-Gartland. PLoS Computational Biology
• Active learning for improving out-of-distribution lab-in-the-loop experimental design. Daria Balashova, Robert Frank, Svetlana Kuzyakina, Dominique Weltevreden, Philippe A. Robert, Geir Kjetil Sandve, Victor Greiff. ImmunoInformatics
• Idiotype-specific CD4+ T cells chronically stimulate autoreactive B cells to develop into B lymphomas in mice. Ramakrishna Prabhu Gopalakrishnan, Jerrold M. Ward, Victor Greiff, Ranveig Braathen, Xian Hu, Livia Bajelan, Khang Lê Quý, Ludvig Munthe, Peter Csaba Huszthy and Bjarne Bogen. Nature Communications
• Identification of a type 1 diabetes–associated T cell receptor repertoire signature from the human peripheral blood. Puneet Rawat, Melanie R. Shapiro, Leeana D. Peters, Michael Widrich, Koshlan Mayer-Blackwell, Keshav Motwani, Milena Pavlović, Ghadi al Hajj, Amanda L. Posgai, Chakravarthi Kanduri, Giulio Isacchini, Maria Chernigovskaya, Lonneke Scheffer, Kartik Motwani, Leandro Octavio Balzano-Nogueira, Camryn M. Pettenger-Willey, Sebastiaan Valkiers, Laura M. Jacobsen, Michael J. Haller, Desmond A. Schatz, Clive H. Wasserfall, Ryan O. Emerson, Andrew J. Fiore-Gartland, Mark A. Atkinson, Günter Klambauer, Geir Kjetil Sandve, Victor Greiff and Todd M. Brusko. Science Advances

2025

• Computational Biophysical Analyses of Antibody Structure-Function Relationships with Emphasis on Therapeutic Antibody-Based Biologics. Puneet Rawat, Eva Smorodina, Divya Sharma, R Prabakaran, Jack Wade, Rahmad Akbar, Amrinder Singh, Sandeep Kumar, Victor Greiff, M Michael Gromiha. Biopharmaceutical Informatics
• Dissecting the tumor immune microenvironment by single cell transcriptomics and immune repertoire analysis in breast tumors treated with the aromatase inhibitor letrozole and the CDK4/6 inhibitor ribociclib. Xavier Tekpli, Villads Winton, Marie Fongaard, Pal Marius Bjornstad, Tatjana Bosnjak-Olsen, Knut Selsas, Stephanie Beate Geisler, Kamilla Fjermeros, Manouchehr Seyedzadeh, Unn-Cathrin Buvarp, Nam Thi Nguyen, Torben Lueders, Diether Lambrechts, Marianne Lyngra, Arnoldo Frigessi, Victor Greiff, Vessela Kristensen, Juergen Geisler. Clinical Cancer Research
• Challenges and future directions of AIRR-seq-based diagnostics. Ulrik Stervbo, Paraskevas Filippidis, Felix Breden, Lindsay G Cowell, Frederic Davi, Victor Greiff, Anton W Langerak, Eline T Luning Prak, Alexandra Francesca Sharland, Enkelejda Miho, Pieter Meysman. ImmunoInformatics
• Systematic benchmarking of mass spectrometry-based antibody sequencing reveals methodological biases. Maria Chernigovskaya, Khang Lê Quý, Maria Stensland, Sachin Singh, Rowan Nelson, Melih Yilmaz, Konstantinos Kalogeropoulos, Pavel Sinitcyn, Anand Patel, Natalie Castellana, Stefano Bonissone, Stian Foss,Jan Terje Andersen, Geir Kjetil Sandve, Timothy Patrick Jenkins, William S. Noble, Tuula A. Nyman,Igor Snapkow, Victor Greiff. Cell Systems.

• Pan-carcinoma sialyl-Tn-targeting expands CAR therapy to solid tumors. Rafaela Abrantes, Christopher Forcados, David J. Warren, Liliana Santos-Ferreira, Karianne Giller Fleten, Emanuel Senra, Ana Filipa Costa, Klara Krpina, Rui Henrique, Ann Magritt Liberg, Puneet Rawat, Pascal Gelebart, Emmet McCormack, Line Bjørge, Ben Davidson, Victor Greiff, Daniela Elena Costea, Filipe Pinto, Kjersti Flatmark, Catarina Gomes, Else Marit Inderberg, Celso A. Reis, Sébastien Wälchli. Cell Reports Medicine.

• Training data composition determines machine learning generalization and biological rule discovery. Eugen Ursu, Aygul Minnegalieva, Puneet Rawat, Maria Chernigovskaya, Robi Tacutu, Geir Kjetil Sandve,
Philippe A. Robert & Victor Greiff. Nature Machine Intelligence.
• Applying computational protein design to therapeutic antibody discovery – current state and perspectives. Weronika Bielska, Igor Jaszczyszyn, Pawel Dudzic, Bartosz Janusz, Dawid Chomicz, Sonia Wrobel, Victor Greiff, Ryan Feehan, Jared Adolf-Bryfogle, Konrad Krawczyk. Frontiers in Immunology
• YAbS: The Antibody Society’s antibody therapeutics database. Puneet Rawat, Silvia Crescioli,  Prabakaran Ramakrishnan, Divya Sharma, Victor Greiff, Janice Reichert. mAbs
• Simulation of adaptive immune receptors and repertoires with complex immune information to guide the development and benchmarking of AIRR machine learning. Maria Chernigovskaya, Milena Pavlović, Chakravarthi Kanduri, Sofie Gielis, Philippe A. Robert, Lonneke Scheffer, Andrei Slabodkin, Ingrid Hobæk Haff, Pieter Meysman, Gur Yaari, Geir Kjetil Sandve, and Victor Greiff . Nucleic Acids Research
• High-resolution mapping of cell cycle dynamics during steady-state T cell development and regeneration in vivo. Heike Kunze-Schumacher, Nikita A. Verheyden, Zoe Grewers, Michael Meyer-Hermann, Victor Greiff, Philippe A. Robert, Andreas Krueger. Cell Reports.
• Investigating Local Sequence-Structural Attributes of Amyloidogenic Light Chain Variable Domains. Puneet Rawat, R. Prabakaran, Divya Sharma, Vasanth Mandala, Victor Greiff, Sandeep Kumar, M. Michael Gromiha. Proteins. 

2024

• Reading the repertoire: Progress in adaptive immune receptor analysis using machine learning. Timothy J. O’Donnell, Chakravarthi Kanduri, Giulio Isacchini, Julien P. Limenitakis, Rebecca A. Brachman, Raymond A. Alvarez, Ingrid H. Haff, Geir K. Sandve, and Victor Greiff
• Predictability of antigen binding based on short motifs in the antibody CDRH3. Lonneke Scheffer, Eric Emanuel Reber, Brij Bhushan Mehta, Milena Pavlović, Maria Chernigovskaya, Eve Richardson, Rahmad Akbar, Fridtjof Lund-Johansen, Victor Greiff, Ingrid Hobæk Haff, Geir Kjetil Sandve. Briefings in Bioinformatics
• Lessons learned from the IMMREP23 TCR-epitope prediction challenge. Morten Nielsen, Anne Eugster, Mathias Fynbo Jensen, Manisha Goel, Andreas Tiffeau-Mayer, Aurelien Pelissier, Sebastiaan Valkiers, María Rodríguez Martínez, Barthélémy Meynard-Piganeeau, Victor Greiff, Thierry Mora, Aleksandra M. Walczak, Giancarlo Croce, Dana L Moreno, David Gfeller, Pieter Meysman, Justin Barton. ImmunoInformatics
• Assessing AF2’s ability to predict structural ensembles of proteins. Jakob R. Riccabona, Fabian C. Spoendlin, Anna-Lena M. Fischer, Johannes R. Loeffler, Patrick K. Quoika, Timothy P. Jenkins, James A. Ferguson, Eva Smorodina, Andreas H. Laustsen, Victor Greiff, Stefano Forli, Andrew B. Ward, Charlotte M. Deane, Monica L. Fernández-Quintero.  Structure.
• Biophysical cartography of the native and human-engineered antibody landscapes quantifies the plasticity of antibody developability Habib Bashour, Eva Smorodina, Matteo Pariset, Jahn Zhong, Rahmad Akbar, Maria Chernigovskaya, Khang Lê Quý, Igor Snapkov, Puneet Rawat, Konrad Krawczyk, Geir Kjetil Sandve, Jose Gutierrez-Marcos, Daniel Nakhaee-Zadeh Gutierrez, Jan Terje Andersen, and Victor Greiff. Communications Biology.
• MHC heterozygosity limits T cell receptor variability in CD4 T cells. Alexander J. Brown, Janice White, Laura Shaw, Jimmy Gross, Andrei Slabodkin, Ella Kushner, Victor Greiff, Jennifer Matsuda, Laurent Gapin, James Scott-Browne ,John Kappler, Philippa Marrack. Science Immunology. 
• Benchmarking and integrating human B-cell receptor genomic and antibody proteomic profiling. Khang Lê Quý, Maria Chernigovskaya, Maria Stensland, Sachin Singh, Jinwoo Leem, Santiago Revale, David A. Yadin, Francesca L. Nice, Chelsea Povall, Danielle H. Minns, Jacob D. Galson, Tuula A. Nyman, Igor Snapkow & Victor Greiff. npj Systems Biology and Applications.
• Linguistics-based formalization of the antibody language as a basis for antibody language models. Mai Ha Vu, Philippe A. Robert, Rahmad Akbar, Bartlomiej Swiatczak, Geir Kjetil Sandve, Dag Trygve Truslew Haug & Victor Greiff. Nature Computational Science.
• Best practices for machine learning in antibody discovery and development. Leonard Wossnig, Norbert Furtmann, Andrew Buchanan, Sandeep Kumar, Victor Greiff. Drug Discovery Today.
• ExpoSeq: Simplified analysis of high-throughput sequencing data from antibody discovery campaigns.  Christoffer V. Sørensen, Nils Hofmann, Puneet Rawat, Frederik V. Sørensen, Anne Ljungars, Victor Greiff, Andreas H. Laustsen, Timothy P. Jenkins. Bioinformatics Advances.
• Systematic evaluation of B-cell clonal family inference approaches. Daria Balashova, Barbera D. C. van Schaik, Maria Stratigopoulou, Jeroen E. J. Guikema, Tom G. Caniels, Mathieu Claireaux, Marit J. van Gils, Anne Musters, Dornatien C. Anang, Niek de Vries, Victor Greiff  & Antoine H. C. van Kampen. BMC Immunology. 
• Adaptive immune receptor repertoire analysis. Vanessa Mhanna, Habib Bashour, Khang Lê Quý, Pierre Barennes, Puneet Rawat, Victor Greiff & Encarnita Mariotti-Ferrandiz. Nature Reviews Methods Primers.  
• Improving generalization of machine learning-identified biomarkers using causal modelling with examples from immune receptor diagnostics. Milena Pavlović, Ghadi S. Al Hajj, Chakravarthi Kanduri, Johan Pensar, Mollie E. Wood, Ludvig M. Sollid, Victor Greiff & Geir K. Sandve. Nature Machine Intelligence.  
• The dengue-specific immune response and antibody identification with machine learning. Eriberto Noel Natali, Alexander Horst, Patrick Meier, Victor Greiff, Mario Nuvolone, Lmar Marie Babrak, Katja Fink & Enkelejda Miho. npj Vaccines.

2023

• Predicting the immune escape of SARS-CoV-2 neutralizing antibodies upon mutation. Divya Sharma, Puneet Rawat, Victor Greiff, Vani Janakiraman, M. Michael Gromiha. Biochimica et Biophysica Acta (BBA)-Molecular Basis of Disease.
• Experimental validation of immunogenic SARS-CoV-2 T cell epitopes identified by artificial intelligence. Lorenzo Federico, Brandon Malone, Simen Tennøe, Viktoriia Chaban, Julie R. Osen, Murat Gainullin, Eva Smorodina, Hassen Kared, Rahmad Akbar, Victor Greiff, Richard Stratford, Trevor Clancy, Ludvig A. Munthe. Front. Immunol. Sec. Vaccines and Molecular Therapeutics.
• Using TCR and BCR sequencing to unravel the role of T and B cells in abdominal aortic aneurysm. Christin Elster, Miriam Ommer-Bläsius, Alexander Lang, Tanja Vajen, Susanne Pfeiler, Milena Feige, Khang Lê Quý, Maria Chernigovskaya, Malte Kelm, Holger Winkels, Susanne Schmidt, Victor Greiff#, Norbert Gerdes#. Front. Cardiovasc. Med. 
• Insights into next generation sequencing guided antibody selection strategies. M. Frank Erasmus, Fortunato Ferrara, Sara D’Angelo, Laura Spector, Camila Leal-Lopes, André A. Teixeira, Jesper Sørensen, Suhani Nagpal, Kathryn Perea-Schmittle, Alok Choudhary, William Honnen, David Calianese, Luis Antonio Rodriguez Carnero, Simon Cocklin, Victor Greiff, Abraham Pinter & Andrew R. M. Bradbury. Scientific Reports
• simAIRR: simulation of adaptive immune repertoires with realistic receptor sequence sharing for benchmarking of immune state prediction methods. Chakravarthi Kanduri, Lonneke Scheffer, Milena Pavlović, Knut Dagestad Rand, Maria Chernigovskaya, Oz Pirvandy, Gur Yaari, Victor Greiff, Geir K Sandve. GigaScience
• Human thymic putative CD8αα precursors exhibit a biased TCR repertoire in single cell AIRR‑seq. Marte Heimli, Siri Tennebø Flåm, Hanne Sagsveen Hjorthaug, Pål Marius Bjørnstad, Maria Chernigovskaya, Quy Khang Le, Xavier Tekpli, Victor Greiff & Benedicte Alexandra Lie. Scientific Reports
• Defining and Studying B Cell Receptor and TCR Interactions. C Garrett Rappazzo, Monica L Fernández-Quintero, Andreas Mayer, Nicholas C Wu, Victor Greiff, Jenna J Guthmiller. Journal of Immunology
• T cell receptor repertoire sequencing reveals chemotherapy-driven clonal expansion in colorectal liver metastases. Eirik Høye, Vegar J Dagenborg, Annette Torgunrud, Christin Lund-Andersen, Åsmund A Fretland, Susanne Lorenz, Bjørn Edwin, Eivind Hovig, Bastian Fromm, Else M Inderberg, Victor Greiff, Anne H Ree, Kjersti Flatmark. GigaScience
• Linguistically inspired roadmap for building biologically reliable protein language models. Mai Ha Vu, Rahmad Akbar, Philippe A. Robert, Bartlomiej Swiatczak, Geir Kjetil Sandve, Victor Greiff & Dag Trygve Truslew Haug. Nature Machine Intelligence
• Assessing developability early in the discovery process for novel biologics. Monica L. Fernández-Quintero, Anne Ljungars, Franz Waibl, Victor Greiff, Jan Terje Andersen, Torelif T. Gjølberg, Timothy P. Jenkins, Bjørn Gunnar Voldborg, Lise Marie Grav, Sandeep Kumar, Guy Georges, Hubert Kettenberger, Klaus R. Liedl, Peter M. Tessier, John McCafferty & Andreas H. Laustsen. mAbs
• Toward real-world automated antibody design with combinatorial Bayesian optimization. Asif Khan, Alexander I. Cowen-Rivers, Antoine Grosnit, Derrick-Goh-Xin Deik, Philippe A. Robert, Victor Greiff, Eva Smorodina, Puneet Rawat, Rahmad Akbar, Kamil Dreczkowski, Rasul Tutunov, Dany Bou-Ammar, Jun Wang, Amos Storkey, Haitham Bou-Ammar. Cell Reports Methods

2022

• 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, Enkelejda Miho, Ingrid Hobæk Haff, Dag Trygve Tryslew Haug, Fridtjof Lund-Johansen, 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

2017

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

• A minimal model of peptide binding predicts ensemble properties of serum antibodies. Victor Greiff, Henning Redestig, Juliane Lück, Nicole Bruni, Atijeh Valai, Susanne Hartmann, Sebastian Rausch, Johannes Schuchhardt, Michal Or-Guil, BMC Genomics