M. Kardar

How persistent infection overcomes peripheral tolerance mechanisms to cause T cell-mediated autoimmune disease

The paper shows that persistent infections increase the likelihood of autoimmune T cell activation by exceeding a quorum threshold through molecular mimicry.

Polymer folding through active processes recreates features of genome organization

The paper investigates how active processes influence polymer folding, showing that activity patterns can lead to compartmentalization and long-range interactions in chromatin.

Inferring the intrinsic mutational fitness landscape of influenza-like evolving antigens from temporally ordered sequence data

The paper presents a computational method to infer the mutational fitness landscape of influenza-like viruses from sequence data, identifying vulnerable immune targets for vaccine design.

Mean-field computational approach to HIV dynamics on a fitness landscape

This paper introduces the evolutionary mean-field (EMF) method to simulate HIV dynamics using fitness landscapes, showing how fitness costs, epistasis, and immune responses influence mutation locations and timescales.