T. Mora

Learning predictive signatures of HLA type from T-cell repertoires

The paper develops a model to predict HLA types from TCR repertoires using associations inferred from HLA-typed donors.

Computational detection of antigen specific B cell receptors following immunization

This study presents a computational method to identify antigen-specific BCRs from immune repertoires using sequence similarity and validates it with human data post-vaccination and infection.

Modelling collective behavior in groups of mice housed under semi-naturalistic conditions

This study uses an automated system to analyze social behavior in groups of mice, revealing social rules and the impact of neuronal plasticity on social interactions.

Variability in the local and global composition of human T-cell receptor repertoires during thymic development across cell types and individuals

The paper analyzes human TCR repertoires across thymic development stages and individuals, finding that inter-individual variability persists through maturation and that local sequence similarity correlates with cell type information.

Combining mutation and recombination statistics to infer clonal families in antibody repertoires

The paper introduces HILARy, a method to identify clonal families in antibody repertoires by combining mutation and recombination statistics, finding evolutionary properties are independent of junction length and revealing broad selection pressures.

DRAG in situ barcoding reveals an increased number of HSPCs contributing to myelopoiesis with age

This study uses an in situ lineage tracing method to show that aging increases the number of HSPCs contributing to myelopoiesis, not their individual output.

Inspecting the interaction between HIV and the immune system through genetic turnover

The paper analyzes HIV-infected patient data to study viral and immune system turnover, finding an anti-correlation between viral composition changes and B-cell receptor repertoire changes.

Probabilities of HIV-1 bNAb development in healthy and chronically infected individuals

The paper uses sequence analysis to predict the likelihood of HIV-1 broadly neutralizing antibody (bNAb) development in healthy and infected individuals, finding that chronic infection is not required for bNAb generation.

Inferring the T-cells repertoire dynamics of healthy individuals

This study infers T-cell repertoire dynamics in healthy individuals using Bayesian inference on longitudinal RepSeq data, finding clone sizes follow geometric Brownian motion and turnover time scales increase with age.

Population based selection shapes the T cell receptor repertoire during thymic development

The paper studies how thymic selection shapes the TCR repertoire during T cell development and finds that selection acts statistically rather than through specific sequence suppression.

Modeling and predicting the overlap of B- and T-cell receptor repertoires in healthy and SARS-CoV-2 infected individuals

The paper develops a statistical model to predict B- and T-cell receptor repertoire overlap in healthy and SARS-CoV-2 infected individuals, identifying COVID-associated receptors and designing a diagnostic tool.

Affinity maturation for an optimal balance between long-term immune coverage and short-term resource constraints

The paper models the trade-off between immune protection and metabolic costs during affinity maturation, predicting power-law distributions of clonotype sizes and antigenic imprinting.

Binding affinity landscapes constrain the evolution of broadly neutralizing anti-influenza antibodies

This study measures binding affinity landscapes of two influenza bnAbs to understand their evolutionary pathways and how they acquire breadth.

Deep generative selection models of T and B cell receptor repertoires with soNNia

The paper uses machine learning to analyze T and B cell receptor sequences and identifies features distinguishing functional lymphocyte subsets and their selection processes.

Physical observables to determine the nature of membrane-less cellular sub-compartments

The paper proposes a theoretical framework to distinguish between liquid-liquid phase separation and binding site models for membrane-less cellular sub-compartments using single molecule tracking experiments.

Antigenic waves of virus-immune co-evolution

This paper develops a mathematical framework to model antigenic waves in virus-immune co-evolution, showing how cross-reactivity shapes the dynamics of pathogen and immune adaptation.

Single molecule microscopy reveals key physical features of repair foci in living cells

The paper uses single molecule microscopy to study the physical properties of repair foci in living cells, revealing differences in diffusion behavior between Rad52 and Rfa1 proteins.

Contribution of resident and circulating precursors to tumor-infiltrating CD8+ T cell populations in non-small cell lung cancer patients

The paper identifies two CD8+ TIL subpopulations in NSCLC, one circulating and one resident, which transition into terminally differentiated cells through a unique state.

Learning the heterogeneous hypermutation landscape of immunoglobulins from high-throughput repertoire data

The paper develops a model to quantify hypermutation biases in Ig genes, revealing sequence context and position effects, and identifies co-localization of mutations in B-cell lineages.

Longitudinal high-throughput TCR repertoire profiling reveals the dynamics of T cell memory formation after mild COVID-19 infection

This study tracks T cell memory formation after mild COVID-19 infection using longitudinal TCR sequencing, showing clonal expansion and memory phenotype acquisition in infected individuals.

Optimal prediction with resource constraints using the information bottleneck

The paper investigates optimal prediction under resource constraints by analyzing trade-offs between encoding past information and predicting future inputs in different dynamic systems.

On generative models of T-cell receptor sequences

This study compares two models for predicting TCR sequence probabilities, finding that a knowledge-guided approach outperforms a deep learning model in accuracy, interpretability, and efficiency.

Population variability in the generation and thymic selection of T-cell repertoires

The paper introduces SONIA, a tool to analyze TCR repertoire variability, finding that most variability stems from VDJ generation and that inter-individual variance is small compared to intra-individual variance.

Inferring the immune response from repertoire sequencing

This paper develops a Bayesian method to quantify immune repertoire changes by accounting for technical noise, applying it to yellow fever vaccination data to identify response clones.

Comprehensive analysis of antiviral adaptive immunity formation and reactivation down to single-cell level

The paper tracks T-cell clone dynamics and TCR repertoire changes after primary and secondary yellow fever vaccination using single-cell RNAseq and TCRseq.

Physical limit to concentration sensing in a changing environment

The paper derives a new physical bound on concentration sensing accuracy in fluctuating environments and shows how it can be achieved with a biochemical network.

Quantitative Immunology for Physicists

This paper reviews recent theoretical and experimental contributions from physicists to quantitative immunology, focusing on methodologies to predict immune system behavior.

How many different clonotypes do immune repertoires contain?

The paper estimates the number of distinct clonotypes in immune repertoires and highlights limitations in current methods.

Fierce selection and interference in B-cell repertoire response to chronic HIV-1

The paper analyzes B-cell repertoire evolution in chronic HIV-1 infection, finding that beneficial mutations are frequently outcompeted by new mutants due to clonal interference.

Size and structure of the sequence space of repeat proteins

The paper estimates the sequence space size of repeat protein families using maximum entropy models and finds that correlations between amino acid positions significantly affect diversity.