A. K. Chakraborty

Designed mosaic nanoparticles enhance cross-reactive immune responses in mice

The paper designs mosaic nanoparticles with SARS-like betacoronavirus RBDs to enhance cross-reactive immune responses in mice, finding that mosaic-7COM elicits stronger responses against zoonotic sarbecoviruses and Omicrons.

Two-dose "extended priming" immunization amplifies humoral immune responses by synchronizing vaccine delivery with the germinal center response

This study shows that a two-dose extended priming vaccine regimen enhances humoral immune responses by synchronizing antigen delivery with germinal center dynamics.

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.

A model for cis-regulation of transcriptional condensates and gene expression by proximal lncRNAs

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.

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.

Mechanisms that promote the evolution of cross-reactive antibodies upon vaccination with designed influenza immunogens

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.

Organization and regulation of nuclear condensates by gene activity

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

Antigen presentation dynamics shape the response to emergent variants like SARS-CoV-2 Omicron strain after multiple vaccinations with wild type strain

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.

Design of immunogens for eliciting antibody responses that may protect against SARS-CoV-2 variants

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.

Multiscale affinity maturation simulations to elicit HIV broadly neutralizing antibodies

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.

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.

An Abundant New Saponin-Polybromophenol Antibiotic (CU1) from Cassia fistula Bark Against Multi-Drug Resistant Bacteria Targeting RNA Polymerase

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.

Mechanisms underlying vaccination protocols that may optimally elicit broadly neutralizing antibodies against highly mutable pathogens

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.

Sedimentation rate and organic matter dynamics shape microbiomes across a continental margin

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.

Predicting the Immunogenicity of T cell epitopes: From HIV to SARS-CoV-2

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.

Optimizing immunization protocols to elicit broadly neutralizing antibodies

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

Predominance of positive epistasis among drug resistance-associated mutations in HIV-1 protease

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.