Browsing Institutt for informatikk by Author "Greiff, Victor"

Now showing items 1-12 of 12

  • A compact vocabulary of paratope-epitope interactions enables predictability of antibody-antigen binding 
    Akbar, Rahmad; Robert, Philippe Paul Auguste; Pavlović, Milena; Jeliazkov, Jeliazko R.; Snapkov, Igor; Slabodkin, Andrei; Weber, Cédric R.; Scheffer, Lonneke; Miho, Enkelejda; Haff, Ingrid Hobæk; Haug, Dag Trygve Truslew; Lund-Johansen, Fridtjof; Safonova, Yana; Sandve, Geir Kjetil Ferkingstad; Greiff, Victor (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2021)
    Antibody-antigen binding relies on the specific interaction of amino acids at the paratope-epitope interface. The predictability of antibody-antigen binding is a prerequisite for de novo antibody and (neo-)epitope design. ...
  • Access to ground truth at unconstrained size makes simulated data as indispensable as experimental data for bioinformatics methods development and benchmarking 
    Sandve, Geir Kjetil Ferkingstad; Greiff, Victor (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2022)
  • CompAIRR: ultra-fast comparison of adaptive immune receptor repertoires by exact and approximate sequence matching 
    Rognes, Torbjørn; Scheffer, Lonneke; Greiff, Victor; Sandve, Geir Kjetil Ferkingstad (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2022)
    Abstract Motivation Adaptive immune receptor (AIR) repertoires (AIRRs) record past immune encounters with exquisite specificity. Therefore, identifying identical or similar AIR sequences ...
  • immuneSIM: tunable multi-feature simulation of B- and T-cell receptor repertoires for immunoinformatics benchmarking 
    Weber, Cédric R.; Akbar, Rahmad; Yermanos, Alexander; Pavlovic, Milena; Snapkov, Igor; Sandve, Geir Kjetil; Reddy, Sai T.; Greiff, Victor (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2020)
    Abstract Summary B- and T-cell receptor repertoires of the adaptive immune system have become a key target for diagnostics and therapeutics research. Consequently, there is a rapidly growing ...
  • In silico proof of principle of machine learning-based antibody design at unconstrained scale 
    Akbar, Rahmad; Robert, Philippe Paul Auguste; Weber, Cédric R.; Widrich, Michael; Frank, Robert; Pavlovic, Milena; Scheffer, Lonneke; Chernigovskaia, Maria; Snapkow, Igor; Slabodkin, Andrei; Mehta, Brij Bhushan; Miho, Enkelejda; Lund-Johansen, Fridtjof; Andersen, Jan Terje; Hochreiter, Sepp; Haff, Ingrid Hobæk; Klambauer, Günter; Sandve, Geir Kjetil Ferkingstad; Greiff, Victor (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2022)
    Generative machine learning (ML) has been postulated to become a major driver in the computational design of antigen-specific monoclonal antibodies (mAb). However, efforts to confirm this hypothesis have been hindered by ...
  • Individualized VDJ recombination predisposes the available Ig sequence space 
    Slabodkin, Andrei; Chernigovskaia, Maria; Mikocziova, Ivana; Akbar, Rahmad; Scheffer, Lonneke; Pavlović, Milena; Bashour, Habib; Snapkov, Igor; Mehta, Brij Bhushan; Weber, Cédric R.; Gutierrez-Marcos, Jose; Sollid, Ludvig Magne; Haff, Ingrid Hobæk; Sandve, Geir Kjetil Ferkingstad; Robert, Philippe Paul Auguste; Greiff, Victor (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2021)
    The process of recombination between variable (V), diversity (D), and joining (J) immunoglobulin (Ig) gene segments determines an individual's naive Ig repertoire and, consequently, (auto)antigen recognition. VDJ recombination ...
  • Profiling the baseline performance and limits of machine learning models for adaptive immune receptor repertoire classification 
    Kanduri, Chakravarthi; Pavlović, Milena; Scheffer, Lonneke; Motwani, Keshav; Chernigovskaya, Maria; Greiff, Victor; Sandve, Geir Kjetil Ferkingstad (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2022)
    Background Machine learning (ML) methodology development for the classification of immune states in adaptive immune receptor repertoires (AIRRs) has seen a recent surge of interest. However, so far, there does not exist ...
  • Reference-based comparison of adaptive immune receptor repertoires 
    Weber, Cédric R.; Rubio, Teresa; Wang, Longlong; Zhang, Wei; Robert, Philippe Paul Auguste; Akbar, Rahmad; Snapkov, Igor; Wu, Jinghua; Kuijjer, Marieke; Tarazona, Sonia; Conesa, Ana; Sandve, Geir Kjetil Ferkingstad; Liu, Xiao; Reddy, Sai T.; Greiff, Victor (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2022)
    B and T cell receptor (immune) repertoires can represent an individual’s immune history. While current repertoire analysis methods aim to discriminate between health and disease states, they are typically based on only a ...
  • simAIRR: simulation of adaptive immune repertoires with realistic receptor sequence sharing for benchmarking of immune state prediction methods 
    Kanduri, Chakravarthi; Scheffer, Lonneke; Pavlović, Milena; Rand, Knut Dagestad; Chernigovskaia, Maria; Pirvandy, Oz; Yaari, Gur; Greiff, Victor; Sandve, Geir Kjetil Ferkingstad (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2023)
    Abstract Background Machine learning (ML) has gained significant attention for classifying immune states in adaptive immune receptor repertoires (AIRRs) to support the advancement of ...
  • T cell receptor repertoire sequencing reveals chemotherapy-driven clonal expansion in colorectal liver metastases 
    Høye, Eirik; Dagenborg, Vegar Johansen; Kristensen, Annette Torgunrud; Lund-Andersen, Christin; Fretland, Åsmund Avdem; Lorenz, Susanne; Edwin, Bjørn von Gohren; Hovig, Eivind; Fromm, Bastian; Inderberg, Else Marit; Greiff, Victor; Ree, Anne Hansen; Flatmark, Kjersti (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2023)
    Abstract Background Colorectal liver metastasis (CLM) is a leading cause of colorectal cancer mortality, and the response to immune checkpoint inhibition (ICI) in microsatellite-stable CRC ...
  • TCRpower: quantifying the detection power of T-cell receptor sequencing with a novel computational pipeline calibrated by spike-in sequences 
    Dahal-Koirala, Shiva; Balaban, Gabriel; Neumann, Ralf Stefan; Scheffer, Lonneke; Lundin, Knut; Greiff, Victor; Sollid, Ludvig Magne; Qiao, Shuo-Wang; Sandve, Geir Kjetil Ferkingstad (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2022)
    Abstract T-cell receptor (TCR) sequencing has enabled the development of innovative diagnostic tests for cancers, autoimmune diseases and other applications. However, the rarity of many T-cell clonotypes presents ...
  • The Future of Blood Testing Is the Immunome 
    Arnaout, Ramy A.; Luning Prak, Eline T.; Schwab, Nicholas; Rubelt, Florian; Greiff, Victor; Pavlović, Milena; Sandve, Geir Kjetil Ferkingstad; Snapkov, Igor; Arora, Rohit; Bashford-Rogers, Rachael; Breden, Felix; Bukhari, Syed Ahmad Chan; Corrie, Brian; Cowell, Lindsay G.; Efroni, Sol; Gooley, Christopher; Heiden, Jason Vander; Koguchi, Yoshinobu; Langerak, Ton; Soon Lim, Thean; Mariotti-Ferrandiz, Encarnita; Marquez, Susanna; Meysman, Pieter; Miho, Enkelejda; Motwani, Keshav; Nouri, Nima; Soto, Cinque; Stervbo, Ulrik; Trück, Johannes; van den Ham, Henk-Jan; Watson, Corey; Weber, Cédric R. (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2021)
    It is increasingly clear that an extraordinarily diverse range of clinically important conditions—including infections, vaccinations, autoimmune diseases, transplants, transfusion reactions, aging, and cancers—leave telltale ...