Andrew A. Farmer

Genotypic and multi-environment phenotypic evaluation of the lima bean USDA National Plant Germplasm System collection

The paper evaluates genotypic and phenotypic traits of lima bean accessions across environments to support breeding, identifying genomic associations and establishing a core collection.

A benchmarking study of copy number variation inference methods using single-cell RNA-sequencing data

This study benchmarks five scCNV inference methods across multiple scRNA-seq platforms and mixed samples, finding variations in performance based on data characteristics and batch effects.

SARS-CoV-2 Can Infect Human Embryos

This study shows SARS-CoV-2 can infect human embryos, specifically trophectoderm cells in blastocysts, with potential implications for reproductive health.

A Multi-center Cross-platform Single-cell RNA Sequencing Reference Dataset

The paper presents a multi-center cross-platform scRNA-seq reference dataset for benchmarking bioinformatics methods across different platforms and centers.

A Comprehensive Multi-Center Cross-platform Benchmarking Study of Single-cell RNA Sequencing Using Reference Samples

This study benchmarks scRNA-seq reproducibility across platforms and pipelines, finding that batch correction methods significantly affect results.

Systematic assessment of commercially available low-input miRNA library preparation kits

This study evaluates six commercial low-input miRNA library prep kits, finding differences in detection sensitivity and differential expression but no kit fully captures all expected miRNAs.

High-throughput chromatin accessibility profiling at single-cell resolution

The paper develops a high-throughput single-cell ATAC-seq method and applies it to cluster PBMCs by hematopoietic cell type.