Amol Carl Shetty

This study uses scRNA-seq on PBMCs to identify cell-type and sex-specific immune signatures associated with alcohol misuse and its dose-dependent effects.

This study identifies regenerative and fibrotic cell programs in human kidney transplants that determine outcomes of acute kidney injury.

This study uses snRNA-seq to analyze kidney transplant biopsies and identifies molecular and cellular mechanisms of recurrent FSGS, including podocyte loss and PEC dedifferentiation.

The paper identifies altered huntingtin-chromatin interactions in HD mouse models, linking them to transcriptional and epigenetic changes in striatal tissue.

This study identifies Treg-mediated lymphotoxin signaling that promotes tumor growth and metastasis by activating nonclassical NFκB pathways in tumor and endothelial cells, and shows that targeting this pathway can suppress tumor progression.

The paper analyzes single neuron transcriptomic changes in aging Aplysia to show progressive impairments in transcriptional plasticity during learning.

The paper identifies transcriptional and epigenetic programs driving hair cell differentiation from supporting cells in cochlear organoids and predicts novel regulatory factors.

This study uses dual-species RNA-seq to analyze the transcriptional responses of Neisseria gonorrhoeae and human neutrophils during infection, revealing shared metabolic and immunologic processes.

Over 400 million variants, 97% below 1% frequency, emerge from deep whole-genome sequencing of 53,831 diverse TOPMed participants; TOPMed haplotypes enable imputation down to ~0.01% frequency.

The paper introduces a method to detect short IBD segments using rare variant sharing, improving the identification of distant relatedness and older population divergence.

This study evaluates the impact of read length and pairing on differential expression analysis in host-pathogen interactions, finding 54-bp paired reads most robust and 36-bp single reads suitable for bacterial samples.

This study compares enrichment techniques for multi-species RNA-Seq, finding that targeted enrichment with Agilent SureSelect improves read mapping to target organisms.

This study sequenced and analyzed genomes from Native American and mestizo populations in Peru to reconstruct their demographic history and genetic admixture patterns.

FADU improves RNA-Seq quantification for prokaryotes by better detecting genes missed by HTSeq and featurecounts, especially in organisms with overlapping transcriptional units and polycistronic transcripts.

This paper introduces a method to simultaneously analyze host and bacterial transcriptomes in infected cells and provides a protocol for its implementation.