Ayshwarya Subramanian

An Integrated Atlas of the Human Kidney Spanning Health and Diseases

The paper integrates multiple single-cell and single-nucleus RNA-sequencing datasets to create a comprehensive Human Kidney Cell Atlas, identifying cell types, states, and disease-associated populations.

Nanobody immunolabelling and three-dimensional imaging reveals spatially restricted LYVE1 expression by kidney lymphatic vessels in mice

The paper develops a nanobody-based method to label kidney lymphatic vessels in mice, revealing spatially restricted LYVE1 expression unique to the kidney.

A single-nucleus and spatial transcriptomic atlas of the COVID-19 liver reveals topological, functional, and regenerative organ disruption in patients

This study creates a single-nucleus and spatial transcriptomic atlas of the COVID-19 liver, revealing cellular and functional disruptions associated with organ damage.

Biology-inspired data-driven quality control for scientific discovery in single-cell transcriptomics

This paper introduces a data-driven quality control framework for single-cell transcriptomics that improves cell retention and biological insight compared to conventional methods.

High Resolution Slide-seqV2 Spatial Transcriptomics Enables Discovery of Disease-Specific Cell Neighborhoods and Pathways

This study uses Slide-seqV2 to identify disease-specific cell neighborhoods and pathways in human and mouse kidneys.

Deep learning and alignment of spatially-resolved whole transcriptomes of single cells in the mouse brain with Tangram

The paper introduces Tangram, a method that aligns single-nucleus RNA-seq data with spatial data to create an anatomically integrated spatial map of the mouse brain.

Obesity-instructed TREM2high macrophages identified by comparative analysis of diabetic mouse and human kidney at single cell resolution

The paper identifies obesity-related TREM2high macrophages in diabetic mouse and human kidney through single-cell transcriptomics and cross-species comparison.

A single-cell and spatial atlas of autopsy tissues reveals pathology and cellular targets of SARS-CoV-2

This study creates a single-cell and spatial atlas of autopsy tissues from COVID-19 patients, revealing altered cellular responses and potential therapeutic targets.

RAAS blockade, kidney disease, and expression of ACE2, the entry receptor for SARS-CoV-2, in kidney epithelial and endothelial cells

The paper examines ACE2 expression in kidney cells in relation to RAAS blockers and age/sex, finding age-related differences and associations with drug use.

Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells

Across 1,176,683 airway and lung cells from 22 datasets, ACE2 rises with age, in males and in smokers' multiciliated cells, and is lowest in young children.

Kidney organoid reproducibility across multiple human iPSC lines and diminished off target cells after transplantation revealed by single cell transcriptomics

The paper uses single-cell RNA-Seq to assess kidney organoid reproducibility across iPSC lines and shows transplantation reduces off-target cells.

A practical guide to methods controlling false discoveries in computational biology

This paper benchmarks classic and modern false discovery rate methods in computational biology, finding modern methods with informative covariates offer modest power gains without sacrificing FDR control.