Progress and challenges for the machine learning-based design of fit-for-purpose monoclonal antibodies
Although the therapeutic efficacy and commercial success of monoclonal antibodies (mAbs)
are tremendous, the design and discovery of new candidates remain a time and cost …
are tremendous, the design and discovery of new candidates remain a time and cost …
Adaptive immune receptor repertoire analysis
B cell and T cell receptor repertoires compose the adaptive immune receptor repertoire
(AIRR) of an individual. The AIRR is a unique collection of antigen-specific receptors that …
(AIRR) of an individual. The AIRR is a unique collection of antigen-specific receptors that …
In silico proof of principle of machine learning-based antibody design at unconstrained scale
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 …
computational design of antigen-specific monoclonal antibodies (mAb). However, efforts to …
A compact vocabulary of paratope-epitope interactions enables predictability of antibody-antigen binding
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 …
epitope interface. The predictability of antibody-antigen binding is a prerequisite for de novo …
The immuneML ecosystem for machine learning analysis of adaptive immune receptor repertoires
Adaptive immune receptor repertoires (AIRR) are key targets for biomedical research as
they record past and ongoing adaptive immune responses. The capacity of machine …
they record past and ongoing adaptive immune responses. The capacity of machine …
Genetic variation in the immunoglobulin heavy chain locus shapes the human antibody repertoire
OL Rodriguez, Y Safonova, CA Silver, K Shields… - Nature …, 2023 - nature.com
Variation in the antibody response has been linked to differential outcomes in disease, and
suboptimal vaccine and therapeutic responsiveness, the determinants of which have not …
suboptimal vaccine and therapeutic responsiveness, the determinants of which have not …
The evolutionary and functional significance of germline immunoglobulin gene variation
The recombination between immunoglobulin (IG) gene segments determines an individual's
naïve antibody repertoire and, consequently,(auto) antigen recognition. Emerging evidence …
naïve antibody repertoire and, consequently,(auto) antigen recognition. Emerging evidence …
Single-cell analysis of immune recognition in chronic myeloid leukemia patients following tyrosine kinase inhibitor discontinuation
J Huuhtanen, S Adnan-Awad, J Theodoropoulos… - Leukemia, 2024 - nature.com
Immunological control of residual leukemia cells is thought to occur in patients with chronic
myeloid leukemia (CML) that maintain treatment-free remission (TFR) following tyrosine …
myeloid leukemia (CML) that maintain treatment-free remission (TFR) following tyrosine …
Evolution and modulation of antigen-specific T cell responses in melanoma patients
J Huuhtanen, L Chen, E Jokinen, H Kasanen… - Nature …, 2022 - nature.com
Analyzing antigen-specific T cell responses at scale has been challenging. Here, we
analyze three types of T cell receptor (TCR) repertoire data (antigen-specific TCRs, TCR …
analyze three types of T cell receptor (TCR) repertoire data (antigen-specific TCRs, TCR …
Unconstrained generation of synthetic antibody–antigen structures to guide machine learning methodology for antibody specificity prediction
Abstract Machine learning (ML) is a key technology for accurate prediction of antibody–
antigen binding. Two orthogonal problems hinder the application of ML to antibody …
antigen binding. Two orthogonal problems hinder the application of ML to antibody …