Melanie R. Neeland

Order Matters: Ambient RNA correction confounds doublet detection in single-cell RNA sequencing

This study shows that ambient RNA correction can reduce doublet detection accuracy and recommends detecting doublets before correction, except when using CellBender.

Single-cell CRISPR activation screens in primary B cells discover gene regulatory mechanisms for hundreds of autoimmune risk loci.

The paper uses single-cell CRISPR activation screens in human B cells to link non-coding autoimmune risk loci to their cis-regulatory target genes, revealing shared genetic mechanisms across diseases.

Antibody responses against bacterial glycans affinity mature and diversify in germinal centers.

The paper shows that glycan-specific B cells undergo class-switching and diversification in germinal centers with age and infection, influencing vaccine design.

Macrophages Mediate Antiviral Immunity and Repair of Type 2 Alveolar Epithelial Cells in a Human Stem Cell Model

This study develops an iPSC-derived air-liquid interface platform to study AT2-macrophage interactions in homeostasis, infection, and repair, revealing their roles in antiviral immunity and epithelial repair.

A genome catalog of the early-life human skin microbiome

The paper presents a genome catalog of the early-life human skin microbiome, expanding diversity and improving classification rates using metagenomic data from infants and their mothers.

Benchmarking single-cell hashtag oligo demultiplexing methods

This study benchmarks seven HTO demultiplexing tools using datasets with genetic variant-based ground truth, finding similar performance on high-quality data but poor performance on lower quality data for bimodal distribution methods.

Single-cell atlas of bronchoalveolar lavage from preschool cystic fibrosis reveals new cell phenotypes

The paper uses scRNA-seq and flow cytometry to identify novel immune and epithelial cell populations in preschool CF patients' bronchoalveolar lavage.