V. Upadhyay

A diet-dependent host metabolite shapes the gut microbiota to protect from autoimmunity

This study shows that a ketogenic diet reduces autoimmune disease in mice by altering host metabolism and shaping gut microbiota, specifically through β-hydroxybutyrate and Lactobacillus species.

Biophysical evolution of the receptor binding domains of SARS-CoVs

This study compares the biophysical properties of SARS-CoV and SARS-CoV-2 receptor binding domains, finding differences in stability, aggregation, and ACE2 binding affinity.

Mild SARS-CoV-2 infection results in long-lasting microbiota instability

This study shows that mild SARS-CoV-2 infection causes long-term gut microbiota instability in both humans and mice, with Omicron variant also disrupting microbial communities despite causing milder symptoms.

Biophysical fitness landscape of the SARS-CoV-2 Delta variant receptor binding domain

This study examines how biophysical properties of the Delta variant's RBD correlate with clinical outcomes, finding that L452R mutation drives immune escape rather than receptor binding.

Convergent evolution of multiple mutations improves the viral fitness of SARS-CoV-2 variants by balancing positive and negative selection

The paper examines how convergent mutations in SARS-CoV-2 variants balance positive and negative selection to enhance viral fitness.

Interplay between receptor binding, immune escape and protein stability determines the natural selection of SARS-CoV-2 variants

The paper evaluates how mutations in SARS-CoV-2's receptor binding domain affect protein stability, ACE2 binding, and antibody escape, showing multiple factors influence variant selection.

Differences in the gut microbiomes of distinct ethnicities within the same geographic area are linked to host metabolic health

The paper compares gut microbiomes of East Asian and White individuals in the same geographic area, finding ethnic differences linked to metabolic health and independent of diet.

A diet-dependent enzyme from the human gut microbiome promotes Th17 cell accumulation and colitis

Diet induces reproducible alterations in the mouse and human gut microbiome

This study identifies reproducible gut microbiome changes induced by a high-fat diet in mice and shows that a machine learning model can predict dietary intake in mice and humans.