A. M. Walczak

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.

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.

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.

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.

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.

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.

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.

hunchback promoters can readout morphogenetic positional information in less than a minute

The paper shows that hunchback promoters can make accurate cell fate decisions within minutes by dynamically updating likelihoods of anterior/posterior positions based on Bicoid morphogen concentration.

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.

Genesis of the αβ T-cell receptor

The paper quantitatively characterizes the β T-cell receptor generation process using high-throughput sequencing and computational experiments, revealing correlations and diversity properties.

How a well-adapting immune system remembers

The paper models the adaptive immune system as a Bayesian framework that balances new pathogen observations with prior experience to predict future threats and optimize memory repertoire updates.

Precision in a rush: trade-offs between reproducibility and steepness of the hunchback expression pattern

The paper examines how short developmental cycles affect the precision and reproducibility of hunchback gene expression patterns in flies.

Detecting T-cell receptors involved in immune responses from single repertoire snapshots

This paper introduces ALICE, a method to identify TCRs involved in immune responses from single RepSeq samples, showing its effectiveness across various disease conditions.

Predicting the spectrum of TCR repertoire sharing with a data-driven model of recombination

The paper develops a model to predict TCR repertoire sharing by accounting for recombination biases and thymic selection, introducing a classifier that performs well across cohort sizes.

Method for identification of condition-associated public antigen receptor sequences

The paper develops a statistical framework to associate antigen receptor sequences with diseases using a small patient cohort, successfully identifying validated receptors for Cytomegalovirus and type 1 diabetes.