Manu N. Setty

This study identifies molecular and architectural changes in normal-adjacent field tissue in HNSCC that disrupt epithelial differentiation and may promote cancer development.

AnnZarro enables interactive exploration of cell-by-cell and gene-by-gene relationships in single-cell data through a browser-based viewer linked to AnnData objects.

The paper examines how T cell-tissue cell communication changes in human placental tissue during acute inflammation, finding that tissue-resident CD8 T cells support trophoblast homeostasis in both healthy and inflamed states.

Echo identifies desynchronized cell states and their drivers from paired single-cell RNA and ATAC data, revealing structured desynchronization in human fetal retina and hematopoiesis.

SCOPE identifies fate-decision states and regulatory drivers in single-cell differentiation by localizing branchpoints and epigenetic priming across developmental processes.

This study identifies distinct olfactory pathways to appetite-regulating neurons in the hypothalamus, showing differential input to AgRP and POMC neurons.

Kompot enables cluster-free differential expression analysis in single-cell data, identifying phenotypic shifts and transcriptional changes across conditions.

The paper introduces Mellon, a method to estimate cell-state densities in single-cell data, revealing high-density regions for major cell types and low-density regions for rare transitory states.

The paper uses single-cell RNA and ATAC-seq to study bidirectional reprogramming between embryonic states, revealing differences in lineage plasticity.

The paper identifies molecular subcategories of C. elegans glia across sexes using single nuclear RNA-seq and machine learning, revealing sex-specific heterogeneity and alternative neuromodulator processing mechanisms.

SEACells identifies metacells from single-cell data, improving gene-peak associations and revealing chromatin dynamics in hematopoiesis and COVID-19.

CellRank maps cell fates in single-cell RNA sequencing data by integrating RNA velocity and trajectory inference, revealing novel regeneration trajectories in lung injury.

The paper describes a modified CUT&Tag protocol that profiles both active and repressive regulatory elements in single cells using computational signal deconvolution.

Palantir models cell fate as a probabilistic process using entropy to analyze differentiation trajectories in human hematopoiesis, identifying key transcription factors and terminal states.

The paper maps the developmental trajectories of endoderm cells in the mouse embryo to reveal lineage relationships and spatial organization during gut formation.