Kelly Street

This study uses single-cell RNA sequencing to trace the developmental trajectory of olfactory epithelium in mice, identifying Ascl1+ cells as multipotent progenitors that become transcriptionally primed over time.

This paper introduces an annotation-based gene-peak linkage method that improves gene expression prediction from chromatin accessibility in human kidney multi-omics data.

VDJdive and ECLIPSE resolve ambiguous clonotypes in scTCR-seq by improving chain pairing and clone size estimation, enhancing clonal tracking across conditions.

This study identifies a latent activated stem cell state in olfactory epithelium using single-cell transcriptomic and epigenomic profiling during injury-induced regeneration.

This study uses single-cell multiomic profiling to show radiation-induced transcriptional and chromatin remodeling in GBM, revealing dose-dependent and cluster-specific regulatory changes.

Dune improves replicability of cell type discovery in scRNA-Seq by optimizing the trade-off between cluster resolution and cross-dataset consistency.

The paper introduces a statistical method to assess the significance of clusters in single-cell RNA-seq data, improving accuracy by addressing variability and reducing false discoveries.

This paper explains trajectory inference and RNA velocity methods for analyzing single-cell RNA-seq data to study cellular dynamics.

The paper benchmarks ATAC-seq normalization methods and shows that GC-content effects must be accounted for to improve downstream analysis accuracy.

The paper creates a comprehensive atlas of mouse primary motor cortex cell types using integrated transcriptomic and epigenomic data from over 600,000 samples.

The paper introduces a method to infer and compare cell trajectories across multiple conditions, detecting differences in progression, population structure, and gene expression.

The paper identifies non-neuronal cell types in the olfactory system expressing SARS-CoV-2 entry genes, suggesting indirect mechanisms for COVID-19-associated anosmia.

The paper introduces a generalized additive model framework for trajectory-based differential expression analysis in single-cell RNA-seq data, enabling flexible inference of within and between lineage gene expression differences.

Slingshot builds a cluster-level minimum spanning tree to find branching lineages without fixing their number, then fits simultaneous principal curves for stable per-lineage pseudotimes.