PEPE: scalable extraction of multi-modal protein language model representations.

Victor Greiff https://orcid.org/0000-0003-2622-5032 https://www.wikidata.org/entity/Q59683046 https://d-nb.info/gnd/103002183X

Jahn Zhong Niccolò Cardente Geir Kjetil Sandve Habib Bashour Maria Francesca Abbate Victor Greiff PEPE: scalable extraction of multi-modal protein language model representations. 2026 42 Bioinform. 6 https://doi.org/10.1093/bioinformatics/btag375 db/journals/bioinformatics/bioinformatics42.html#ZhongCSBAG26 streams/journals/bioinformatics

Koshlan Mayer-Blackwell Anastasia A. Minervina Mikhail Pogorelyy Puneet Rawat Melanie R. Shapiro Leeana D. Peters Emily S. Ford Amanda Posgai Kasi Vegesana Samuel Minot David M. Koelle Victor Greiff Philip Bradley Todd M. Brusko Paul G. Thomas Andrew Fiore-Gartland TCR2HLA: Calibrated inference of HLA genotypes from TCR repertoires enables identification of immunologically relevant metaclonotypes. 2026 1013767 22 PLoS Comput. Biol. 1 https://doi.org/10.1371/journal.pcbi.1013767 db/journals/ploscb/ploscb22.html#MayerBlackwellMPRSPFPVM26 streams/journals/ploscb

Robert Frank 0006 Michael Widrich Rahmad Akbar Günter Klambauer Geir Kjetil Sandve Philippe A. Robert Victor Greiff Attribution assignment for deep-generative sequence models enables interpretability analysis using positive-only data. 2025 June abs/2506.23182 CoRR https://doi.org/10.48550/arXiv.2506.23182 db/journals/corr/corr2506.html#abs-2506-23182 streams/journals/corr

Lonneke Scheffer Eric Emanuel Reber Brij Bhushan Mehta Milena Pavlovic Maria Chernigovskaya Eve Richardson Rahmad Akbar Fridtjof Lund-Johansen Victor Greiff Ingrid Hobæk Haff Geir Kjetil Sandve Predictability of antigen binding based on short motifs in the antibody CDRH3. 2024 November 25 Briefings Bioinform. 6 https://doi.org/10.1093/bib/bbae537 db/journals/bib/bib25.html#SchefferRMPCRALGHS24 streams/journals/bib

Milena Pavlovic Ghadi S. Al Hajj Chakravarthi Kanduri Johan Pensar Mollie Wood Ludvig Magne Sollid Victor Greiff Geir Kjetil Sandve Improving generalization of machine learning-identified biomarkers using causal modelling with examples from immune receptor diagnostics. 15-24 2024 6 Nat. Mac. Intell. 1 https://doi.org/10.1038/s42256-023-00781-8 https://www.wikidata.org/entity/Q129454407 db/journals/natmi/natmi6.html#PavlovicHKPWSGS24 streams/journals/natmi

Mai Ha Vu Philippe A. Robert Rahmad Akbar Bartlomiej Swiatczak Geir Kjetil Sandve Dag Trygve Truslew Haug Victor Greiff Linguistics-based formalization of the antibody language as a basis for antibody language models. 412-422 2024 June 4 Nat. Comput. Sci. 6 https://doi.org/10.1038/s43588-024-00642-3 db/journals/ncs/ncs4.html#VuRASSHG24

Ghadi S. Al Hajj Aliaksandr Hubin Chakravarthi Kanduri Milena Pavlovic Knut Dagestad Rand Michael Widrich Anne H. Schistad Solberg Victor Greiff Johan Pensar Günter Klambauer Geir Kjetil Sandve Incorporating probabilistic domain knowledge into deep multiple instance learning. 2024 ICML https://proceedings.mlr.press/v235/hajj24a.html https://openreview.net/forum?id=GfNyqrwECJ conf/icml/2024 db/conf/icml/icml2024.html#HajjHKPRWSGPKS24 17279-17297

Philippe A. Robert Victor Greiff Bridging the neutralization gap for unseen antibodies. 8-10 2023 January 5 Nat. Mac. Intell. 1 https://doi.org/10.1038/s42256-022-00594-1 db/journals/natmi/natmi5.html#RobertG23

Mai Ha Vu Rahmad Akbar Philippe A. Robert Bartlomiej Swiatczak Geir Kjetil Sandve Victor Greiff Dag Trygve Truslew Haug Linguistically inspired roadmap for building biologically reliable protein language models. 485-496 2023 May 5 Nat. Mac. Intell. 5 https://doi.org/10.1038/s42256-023-00637-1 db/journals/natmi/natmi5.html#VuARSSGH23

Leonard Wossnig Norbert Furtmann Andrew Buchanan Sandeep Kumar Victor Greiff Best practices for machine learning in antibody discovery and development. 2023 abs/2312.08470 CoRR https://doi.org/10.48550/arXiv.2312.08470 db/journals/corr/corr2312.html#abs-2312-08470

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 TCRpower: quantifying the detection power of T-cell receptor sequencing with a novel computational pipeline calibrated by spike-in sequences. 2022 23 Briefings Bioinform. 2 https://doi.org/10.1093/bib/bbab566 https://www.wikidata.org/entity/Q111508054 db/journals/bib/bib23.html#Dahal-KoiralaBN22

Wiktoria Wilman Sonia Wróbel Weronika Bielska Piotr Deszynski Pawel Dudzic Igor Jaszczyszyn Jedrzej Kaniewski Jakub Mlokosiewicz Anahita Rouyan Tadeusz Satlawa Sandeep Kumar Victor Greiff Konrad Krawczyk Machine-designed biotherapeutics: opportunities, feasibility and advantages of deep learning in computational antibody discovery. 2022 23 Briefings Bioinform. 4 https://doi.org/10.1093/bib/bbac267 db/journals/bib/bib23.html#WilmanWBDDJKMRS22

Torbjørn Rognes Lonneke Scheffer Victor Greiff Geir Kjetil Sandve CompAIRR: ultra-fast comparison of adaptive immune receptor repertoires by exact and approximate sequence matching. 4230-4232 2022 38 Bioinform. 17 https://doi.org/10.1093/bioinformatics/btac505 db/journals/bioinformatics/bioinformatics38.html#RognesSGS22

Geir Kjetil Sandve Victor Greiff Access to ground truth at unconstrained size makes simulated data as indispensable as experimental data for bioinformatics methods development and benchmarking. 4994-4996 2022 October 38 Bioinform. 21 https://doi.org/10.1093/bioinformatics/btac612 db/journals/bioinformatics/bioinformatics38.html#SandveG22

Philippe A. Robert Rahmad Akbar Robert Frank 0006 Milena Pavlovic Michael Widrich Igor Snapkov Andrei Slabodkin Maria Chernigovskaya Lonneke Scheffer Eva Smorodina Puneet Rawat Brij Bhushan Mehta Mai Ha Vu Ingvild Frøberg Mathisen Aurél Prósz Krzysztof Abram Alex Olar Enkelejda Miho Dag Trygve Truslew Haug Fridtjof Lund-Johansen Sepp Hochreiter Ingrid Hobæk Haff Günter Klambauer Geir Kjetil Sandve Victor Greiff Unconstrained generation of synthetic antibody-antigen structures to guide machine learning methodology for antibody specificity prediction. 845-865 2022 2 Nat. Comput. Sci. 12 https://doi.org/10.1038/s43588-022-00372-4 db/journals/ncs/ncs2.html#RobertAFPWSSCSS22

Mohammad Asif Khan 0001 Alexander I. Cowen-Rivers Derrick-Goh-Xin Deik Antoine Grosnit Kamil Dreczkowski Philippe A. Robert Victor Greiff Rasul Tutunov Dany Bou-Ammar Jun Wang 0012 Haitham Bou-Ammar AntBO: Towards Real-World Automated Antibody Design with Combinatorial Bayesian Optimisation. 2022 abs/2201.12570 CoRR https://arxiv.org/abs/2201.12570 db/journals/corr/corr2201.html#abs-2201-12570

Milena Pavlovic Ghadi S. Al Hajj Johan Pensar Mollie Wood Ludvig Magne Sollid Victor Greiff Geir Kjetil Sandve Improving generalization of machine learning-identified biomarkers with causal modeling: an investigation into immune receptor diagnostics. 2022 abs/2204.09291 CoRR https://doi.org/10.48550/arXiv.2204.09291 db/journals/corr/corr2204.html#abs-2204-09291

Mai Ha Vu Rahmad Akbar Philippe A. Robert Bartlomiej Swiatczak Victor Greiff Geir Kjetil Sandve Dag Trygve Truslew Haug Advancing protein language models with linguistics: a roadmap for improved interpretability. 2022 abs/2207.00982 CoRR https://doi.org/10.48550/arXiv.2207.00982 db/journals/corr/corr2207.html#abs-2207-00982

Mai Ha Vu Philippe A. Robert Rahmad Akbar Bartlomiej Swiatczak Geir Kjetil Sandve Dag Trygve Truslew Haug Victor Greiff ImmunoLingo: Linguistics-based formalization of the antibody language. 2022 abs/2209.12635 CoRR https://doi.org/10.48550/arXiv.2209.12635 db/journals/corr/corr2209.html#abs-2209-12635

Philippe A. Robert Heike Kunze-Schumacher Victor Greiff Andreas Krueger Modeling the Dynamics of T-Cell Development in the Thymus. 437 2021 23 Entropy 4 https://doi.org/10.3390/e23040437 db/journals/entropy/entropy23.html#RobertKGK21

Milena Pavlovic 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 0006 Ivar Grytten Sveinung Gundersen Ingrid Hobæk Haff Eivind Hovig Ping-Han Hsieh Günter Klambauer Marieke L. Kuijjer Christin Lund-Andersen Antonio Martini 0001 Thomas Minotto Johan Pensar Knut D. Rand Enrico Riccardi Philippe A. Robert Artur Rocha Andrei Slabodkin Igor Snapkov Ludvig Magne Sollid Dmytro Titov Cédric R. Weber Michael Widrich Gur Yaari Victor Greiff Geir Kjetil Sandve The immuneML ecosystem for machine learning analysis of adaptive immune receptor repertoires. 936-944 2021 3 Nat. Mach. Intell. 11 https://doi.org/10.1038/s42256-021-00413-z db/journals/natmi/natmi3.html#PavlovicSMKKVWB21

Erand Smakaj Lmar Babrak Mats Ohlin Mikhail Shugay Bryan S. Briney Deniz Tosoni Christopher Galli Vendi Grobelsek Igor D'Angelo Branden J. Olson Sai T. Reddy Victor Greiff Johannes Trück Susanna Marquez William D. Lees Enkelejda Miho Benchmarking immunoinformatic tools for the analysis of antibody repertoire sequences. 1731-1739 2020 36 Bioinform. 6 https://doi.org/10.1093/bioinformatics/btz845 https://www.wikidata.org/entity/Q92232205 db/journals/bioinformatics/bioinformatics36.html#SmakajBOSBTGGDO20

Cédric R. Weber Rahmad Akbar Alexander Yermanos Milena Pavlovic Igor Snapkov Geir Kjetil Sandve Sai T. Reddy Victor Greiff immuneSIM: tunable multi-feature simulation of B- and T-cell receptor repertoires for immunoinformatics benchmarking. 3594-3596 2020 36 Bioinform. 11 https://doi.org/10.1093/bioinformatics/btaa158 https://www.wikidata.org/entity/Q90184938 db/journals/bioinformatics/bioinformatics36.html#WeberAYPSSRG20

Michael Widrich Bernhard Schäfl Milena Pavlovic Hubert Ramsauer Lukas Gruber Markus Holzleitner Johannes Brandstetter Geir Kjetil Sandve Victor Greiff Sepp Hochreiter Günter Klambauer Modern Hopfield Networks and Attention for Immune Repertoire Classification. 2020 NeurIPS https://proceedings.neurips.cc/paper/2020/hash/da4902cb0bc38210839714ebdcf0efc3-Abstract.html conf/nips/2020 db/conf/nips/neurips2020.html#WidrichSPRGHBSG20

Michael Widrich Bernhard Schäfl Hubert Ramsauer Milena Pavlovic Lukas Gruber Markus Holzleitner Johannes Brandstetter Geir Kjetil Sandve Victor Greiff Sepp Hochreiter Günter Klambauer Modern Hopfield Networks and Attention for Immune Repertoire Classification. 2020 abs/2007.13505 CoRR https://arxiv.org/abs/2007.13505 db/journals/corr/corr2007.html#abs-2007-13505

Hubert Ramsauer Bernhard Schäfl Johannes Lehner Philipp Seidl Michael Widrich Lukas Gruber Markus Holzleitner Milena Pavlovic Geir Kjetil Sandve Victor Greiff David P. Kreil Michael Kopp 0001 Günter Klambauer Johannes Brandstetter Sepp Hochreiter Hopfield Networks is All You Need. 2020 abs/2008.02217 CoRR https://arxiv.org/abs/2008.02217 db/journals/corr/corr2008.html#abs-2008-02217

Alexander Yermanos Victor Greiff Nike Julia Krautler Ulrike Menzel Andreas Dounas Enkelejda Miho Annette Oxenius Tanja Stadler Sai T. Reddy Comparison of methods for phylogenetic B-cell lineage inference using time-resolved antibody repertoire simulations (AbSim). 3938-3946 2017 33 Bioinform. 24 https://doi.org/10.1093/bioinformatics/btx533 https://www.wikidata.org/entity/Q47316818 db/journals/bioinformatics/bioinformatics33.html#YermanosGKMDMOS17

Maria Francesca Abbate Krzysztof Abram Rahmad Akbar Lmar Babrak Gabriel Balaban Habib Bashour Fabian L. M. Bernal Weronika Bielska Dany Bou-Ammar Haitham Bou-Ammar Philip Bradley Johannes Brandstetter Bryan S. Briney Todd M. Brusko Andrew Buchanan Niccolò Cardente Maria Chernigovskaya Scott Christley Brian Corrie Alexandre Almeida Costa Lindsay G. Cowell Alexander I. Cowen-Rivers Shiva Dahal-Koirala Igor D'Angelo Derrick-Goh-Xin Deik Piotr Deszynski Andreas Dounas Kamil Dreczkowski Pawel Dudzic Andrew Fiore-Gartland Emily S. Ford Robert Frank 0006 Norbert Furtmann Christopher Galli Vendi Grobelsek Antoine Grosnit Lukas Gruber Ivar Grytten Sveinung Gundersen Ingrid Hobæk Haff Ghadi S. Al Hajj Dag Trygve Truslew Haug Sepp Hochreiter Markus Holzleitner Eivind Hovig Ping-Han Hsieh Aliaksandr Hubin Igor Jaszczyszyn Chakravarthi Kanduri Jedrzej Kaniewski Mohammad Asif Khan 0001 Günter Klambauer David M. Koelle Radmila Kompova Michael Kopp 0001 Nike Julia Krautler Konrad Krawczyk David P. Kreil Andreas Krueger Marieke L. Kuijjer Sandeep Kumar Heike Kunze-Schumacher William D. Lees Johannes Lehner Christin Lund-Andersen Fridtjof Lund-Johansen Knut Erik Aslaksen Lundin Susanna Marquez Antonio Martini 0001 Ingvild Frøberg Mathisen Koshlan Mayer-Blackwell Brij Bhushan Mehta Ulrike Menzel Enkelejda Miho Anastasia A. Minervina Samuel Minot Thomas Minotto Jakub Mlokosiewicz Keshav Motwani Ralf Stefan Neumann Mats Ohlin Alex Olar Branden J. Olson Annette Oxenius Milena Pavlovic Johan Pensar Leeana D. Peters Mikhail Pogorelyy Amanda Posgai Aurél Prósz Shuo-Wang Qiao Hubert Ramsauer Knut D. RandKnut Dagestad Rand Puneet Rawat Eric Emanuel Reber Sai T. Reddy Enrico Riccardi Eve Richardson Philippe A. Robert Artur Rocha Torbjørn Rognes Anahita Rouyan Geir Kjetil Sandve Tadeusz Satlawa Bernhard Schäfl Lonneke Scheffer Philipp Seidl Melanie R. Shapiro Mikhail Shugay Andrei Slabodkin Erand Smakaj Eva Smorodina Igor Snapkov Anne H. Schistad Solberg Ludvig Magne Sollid Tanja Stadler Bartlomiej Swiatczak Paul G. Thomas Dmytro Titov Deniz Tosoni Johannes Trück Rasul Tutunov Nikolay Vazov Kasi Vegesana Mai Ha Vu Knut Waagan Jun Wang 0012 Cédric R. Weber Michael Widrich Wiktoria Wilman Mollie Wood Leonard Wossnig Sonia Wróbel Gur Yaari Alexander Yermanos Jahn Zhong