Norma F Neff

The paper tracks lineage evolution and transmission of Bacteroides thetaiotaomicron across hosts and ecological scales using genomic barcoding and whole-genome sequencing.

The paper presents a single-cell long-read isoform atlas across 26 human tissues, revealing novel isoforms and their role in cellular identity and senescence.

This study identifies a conserved neural stem cell pool driving continuous CNS regeneration in Botryllus schlosseri, showing aging disrupts this process.

The paper presents a multimodal perturbation atlas using CRISPR knockouts in A549 cells, combining microscopy, phase imaging, and scRNA-seq to assess phenotypic resolution.

The paper investigates mobilized human HSC and finds they rapidly express G0-associated quiescence markers despite recent cell divisions.

The paper isolates and characterizes two postnatal human neural stem cell subsets, showing their fate biases and decline in frequency over time.

The study quantifies survival benefits and germline competition costs of chimerism in Botryllus schlosseri, finding survival advantages outweigh competition costs.

The paper uses cfDNA/cfRNA sequencing to identify molecular correlates of bNAb development in HIV patients, finding an MHC class I activation signature and microbial changes associated with bNAb production.

This study compares human and mouse ovarian biology across age using 3D-imaging, single-cell transcriptomics, and functional studies, identifying species-specific and age-related changes in follicle dynamics and gene expression.

This study investigates age-related changes in germline stem cells (GSCs) in the protochordate Botryllus schlosseri using single-cell RNA sequencing and transplantation assays, revealing that GSCs, not gametes, drive reproductive aging.

The paper tracks antibiotic resistance gene (ARG) dynamics in mice during long-term antibiotic treatment, finding that commensal bacteria reduce ARG burden by outcompeting resistant taxa.

This paper introduces a method to capture non-coding RNAs in single-cell RNA-seq, revealing new insights into gene regulation in immune cells, infected hepatocytes, and brain development.

RMC-113 inhibits PIP4K2C and PIKfyve, reversing SARS-CoV-2-induced autophagic flux impairment and showing antiviral effects.

The paper shows that pulsatile electrical current improves survival, regeneration, and reproduction in Botryllus schlosseri by altering stem cell and immune activity through transcriptomic changes.

This paper investigates how nitroxoline induces genomic instability, transcriptional collapse, and incomplete encystment in Balamuthia mandrillaris by chelating copper and iron.

This study investigates islet cell dysfunction in type 1 diabetes by integrating electrophysiological, transcriptomic, and machine learning analyses of human islet cells from T1D donors.

This study uses single-cell RNA sequencing to show that M. tuberculosis ESX-1 promotes the recruitment and differentiation of anti-inflammatory macrophages in infected mouse lungs.

The paper presents Zebrahub-Multiome, a single-cell multiomic atlas of zebrafish embryogenesis, revealing gene regulatory network dynamics and cis-regulatory elements across developmental stages.

This study uses single-nucleus RNA sequencing to analyze a mouse glioblastoma model, identifying potential therapeutic targets and similarities with human GBM subtypes.

The paper characterizes the transcriptional response to COVID-19 across multiple organs using single-nuclei RNA sequencing, identifying shared transcriptional signatures in endothelial cells and macrophages.

The paper provides a framework and interactive software tools for manually annotating cell types in single-cell multi-omics datasets, demonstrating how different modalities can be combined to improve annotation accuracy.

The paper uses metagenomic sequencing to investigate a wildlife mortality event in songbirds, finding no single pathogen but highlighting the utility of metagenomics in such investigations.

Zebrafish embryos sequenced individually across ten developmental stages, paired with light-sheet lineage reconstruction, form an atlas and browser for in silico fate mapping.

The paper compares MERFISH spatial transcriptomics with bulk and single-cell RNA sequencing in mouse liver and kidney, finding MERFISH provides comparable results and robust cell type identification without needing integration with scRNA-seq atlases.

The paper integrates multi-omic data to identify genetic and microbiome factors associated with severe COVID-19, independent of ancestry and social factors.

Portal integrates large-scale single-cell datasets efficiently and accurately by preserving biological variation across samples, platforms, and species.

DiMeLo-seq maps protein-DNA interactions genome-wide with single-molecule resolution by methylating DNA near binding sites and using long-read sequencing.

The paper creates a comprehensive cell atlas of mouse lemurs using single-cell RNA sequencing, identifying over 750 cell types and comparing their molecular profiles to humans, mice, and macaques.

The paper introduces uPIC-M, a method to efficiently create clonal single mutant libraries for high-throughput protein biochemistry, achieving high recovery rates and cost-effectiveness.

The paper studies neurodegeneration in the colonial chordate Botryllus schlosseri, finding conserved mechanisms between tunicates and humans.