A. K. Chakraborty

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

This paper proposes a model where proximal lncRNAs regulate transcription by interacting with transcriptional condensates through charge-based heterotypic interactions, explaining gene expression patterns and genomic distance conservation.

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

The paper develops a computational model to study antibody evolution after vaccination with designed influenza immunogens, finding that a chimeric antigen outperforms a cocktail in eliciting RBS-directed antibodies due to T cell interactions.

This study develops a physics-based model to show how gene activity and genome organization shape nuclear condensate morphology and dynamics.

The paper shows that antigen presentation dynamics after multiple vaccinations influence the immune response to SARS-CoV-2 Omicron by shaping B cell responses and antibody targeting of epitopes.

This paper designs SARS-CoV-2 variant antigens using sequence analysis and machine learning, showing they are stable and bind ACE2, and suggests a pan-coronavirus vaccine target.

This paper simulates B cell receptor affinity maturation to model the evolution of HIV broadly neutralizing antibodies using real germline sequences and vaccine candidate antigens.

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.

The paper identifies a new saponin-polybromophenol compound (CU1) from Cassia fistula bark that inhibits RNA polymerase in MDR bacteria, showing potential as an alternative antibiotic.

This paper develops a minimal model to explore optimal vaccination strategies for eliciting broadly neutralizing antibodies against mutable pathogens by analyzing the dynamics of affinity maturation.

The paper examines how sedimentation rates and organic matter dynamics influence microbiome structure and function in different oxygen minimum zones along the Arabian Sea margin.

The paper presents a physics-based model predicting T cell epitope immunogenicity across pathogens, finding that only some SARS-CoV-2 epitopes are immunogenic and some are shared with low-pathogenicity coronaviruses.

This study uses computational models to show that sequential immunization protocols can optimize the evolution of broadly neutralizing antibodies against mutable pathogens.

The paper profiles the fitness landscape of HIV-1 protease resistance mutations and finds that positive epistasis is predominant, reducing the likelihood of reversing drug resistance mutations.