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Found 21 papers, 9 papers with code
Computational detection of antigen specific B cell receptors following immunization
B cell receptors (BCRs) play a crucial role in recognizing and fighting foreign antigens.
Variability in the local and global composition of human T-cell receptor repertoires during thymic development across cell types and individuals
The adaptive immune response relies on T cells that combine phenotypic specialization with diversity of T cell receptors (TCRs) to recognize a wide range of pathogens.
Evolutionary stability of antigenically escaping viruses
The immune-virus system behaves like a Fisher wave at low cross-reactivities, and like a fitness wave at high cross-reactivities.
Towards a quantitative theory of tolerance
A cornerstone of the classical view of tolerance is the elimination of self-reactive T cells during negative selection in the thymus.
Dynamical information synergy in biochemical signaling networks
Biological cells encode information about their environment through biochemical signaling networks that control their internal state and response.
Combining mutation and recombination statistics to infer clonal families in antibody repertoires
B-cell repertoires are characterized by a diverse set of receptors of distinct specificities generated through two processes of somatic diversification: V(D)J recombination and somatic hypermutations.
From evolution to folding of repeat proteins
Here, we propose a scheme to map evolutionary information at the sequence level to a coarse-grained model for repeat-protein folding and use it to investigate the folding of thousands of repeat-proteins.
Learning the statistics and landscape of somatic mutation-induced insertions and deletions in antibodies
The model includes antibody-specific maturation ages to account for variable mutational loads in the repertoire.
Affinity maturation for an optimal balance between long-term immune coverage and short-term resource constraints
This plasticity of the repertoire drives the emergence of distinct regimes for the size and diversity of the memory pool, depending on the density of naive cells and on the mutation rate of the strain.
MINIMALIST: Mutual INformatIon Maximization for Amortized Likelihood Inference from Sampled Trajectories
One class of methods uses data simulated with different parameters to infer models of the likelihood-to-evidence ratio, or equivalently the posterior function.
Antigenic waves of virus-immune co-evolution
Here we present a mathematical theory of co-evolution between immune systems and viruses in a finite-dimensional antigenic space, which describes the cross-reactivity of viral strains and immune systems primed by previous infections.
NoisET: Noise learning and Expansion detection of T-cell receptors
High-throughput sequencing of T- and B-cell receptors makes it possible to track immune repertoires across time, in different tissues, in acute and chronic diseases and in healthy individuals.
Learning the heterogeneous hypermutation landscape of immunoglobulins from high-throughput repertoire data
Somatic hypermutations of immunoglobulin (Ig) genes occuring during affinity maturation drive B-cell receptors' ability to evolve strong binding to their antigenic targets.
Immune Fingerprinting through Repertoire Similarity
Immune repertoires provide a unique fingerprint reflecting the immune history of individuals, with potential applications in precision medicine.
Longitudinal high-throughput TCR repertoire profiling reveals the dynamics of T cell memory formation after mild COVID-19 infection
Certain T cell clones were detected in the memory fraction at the pre-infection timepoint, suggesting participation of pre-existing cross-reactive memory T cells in the immune response to SARS-CoV-2.
SOS: Online probability estimation and generation of T and B cell receptors
Recent advances in modelling VDJ recombination and subsequent selection of T and B cell receptors provide useful tools to analyze and compare immune repertoires across time, individuals, and tissues.
Inferring the immune response from repertoire sequencing
High-throughput sequencing of B- and T-cell receptors makes it possible to track immune repertoires across time, in different tissues, and in acute and chronic diseases or in healthy individuals.
Quantitative Methods
On generative models of T-cell receptor sequences
T-cell receptors (TCR) are key proteins of the adaptive immune system, generated randomly in each individual, whose diversity underlies our ability to recognize infections and malignancies.
Quantitative Methods
Primary and secondary anti-viral response captured by the dynamics and phenotype of individual T cell clones
The diverse repertoire of T-cell receptors (TCR) plays a key role in the adaptive immune response to infections.
Quantitative Immunology for Physicists
The adaptive immune system is a dynamical, self-organized multiscale system that protects vertebrates from both pathogens and internal irregularities, such as tumours.
Inferring processes underlying B-cell repertoire diversity
We quantify the VDJ recombination and somatic hypermutation processes in human B-cells using probabilistic inference methods on high-throughput DNA sequence repertoires of human B-cell receptor heavy chains.
Populations and Evolution Genomics
