John Ngai

Neocortical long-range inhibition promotes cortical synchrony and sleep

This study identifies Sst-Chodl inhibitory neurons that promote cortical synchrony and sleep by exerting long-range inhibition during low-arousal states.

Evolving stem cell fate capacities and transcriptional priming in the developing olfactory epithelium

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.

A Latent Activated Olfactory Stem Cell State Revealed by Single Cell Transcriptomic and Epigenomic Profiling

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

Improving replicability in single-cell RNA-Seq cell type discovery with Dune

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

Normalization benchmark of ATAC-seq datasets shows the importance of accounting for GC-content effects

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

A multimodal cell census and atlas of the mammalian primary motor cortex

The paper generates a multimodal cell census and atlas of the mammalian primary motor cortex, revealing a unified molecular genetic landscape and cross-species taxonomy of cell types.

An integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell types

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

Generation of a DAT-Flp mouse line for intersectional genetic targeting of dopamine neuron subpopulations

The paper introduces a DAT-Flp mouse line to selectively label dopaminergic subpopulations using intersectional genetic strategies.

Non-neuronal expression of SARS-CoV-2 entry genes in the olfactory system suggests mechanisms underlying COVID-19-associated anosmia

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.

Transcriptome analysis of the zebrafish atoh7-/- mutant, lakritz, highlights Atoh7-dependent genetic networks with potential implications for human eye diseases

The paper analyzes transcriptomes of zebrafish atoh7 mutant embryos to identify Atoh7-dependent genetic networks linked to retinal development and human eye diseases.

Performance Assessment and Selection of Normalization Procedures for Single-Cell RNA-seq

This paper evaluates normalization methods for scRNA-seq using a framework called scone, showing that top methods improve agreement with validation data.

Complementary networks of cortical somatostatin interneurons enforce layer specific control

The paper identifies distinct somatostatin interneuron circuits that specifically control activity in different cortical layers through complementary inhibitory mechanisms.

clusterExperiment and RSEC: A Bioconductor package and framework for clustering of single-cell and other large gene expression datasets

The paper introduces clusterExperiment, a Bioconductor package for clustering large gene expression datasets using Resampling-based Sequential Ensemble Clustering (RSEC) to identify biologically meaningful subtypes.

Slingshot: Cell lineage and pseudotime inference for single-cell transcriptomics

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.