Pramod S. Shinde

An Open Benchmark for Systems Vaccinology: Insights from the CMI-PB Challenges

The paper benchmarks computational models predicting B. pertussis booster vaccine responses using multi-omics data from three cohorts, identifying key predictors of immunity and establishing a community resource for systems vaccinology.

Th1 polarization in Bordetella pertussis vaccine responses is maintained through a positive feedback loop

This study compares immune responses to whole-cell and acellular pertussis vaccines, finding that Th1 polarization is maintained through an early interferon response in whole-cell vaccine recipients.

Putting computational models of immunity to the test - an invited challenge to predict B. pertussis vaccination outcomes

The paper benchmarks 49 algorithms for predicting B. pertussis vaccination outcomes, finding that purpose-built models outperform literature-based ones due to better handling of nonlinearities and data preprocessing.

Brain rewiring during developmental transitions: A Comparative Analysis of Larva and Adult Drosophila melanogaster

This study compares brain network rewiring in larval and adult Drosophila melanogaster, finding differences in degree distribution and core neuron composition.

Higher-order co-mutation interactions in mitochondrial genomes

The paper introduces a method to analyze higher-order co-mutation interactions in mitochondrial genomes using 3-uniform hypergraphs and identifies altitude-specific genes based on hyperedge weights.

A systems vaccinology resource to develop and test computational models of immunity

The paper evaluates computational models predicting immune responses to Pertussis Booster vaccinations using a new community resource, finding that existing models perform poorly and new models show variable performance based on features and strategies.

Impact of modular mitochondrial epistatic interactions on the evolution of human subpopulations

The paper analyzes mitochondrial genome variation across human populations to identify co-mutation patterns and epistatic interactions, finding subpopulation-specific biases in mutation clustering.

Analysis of human mitochondrial genome co-occurrence networks of Asian population at varying altitudes

The paper analyzes mitochondrial genome co-occurrence networks in Asian populations at different altitudes to understand high altitude adaptation mechanisms.