Jennifer K. Grenier

This paper evaluates three agentic coding systems for constructing bioinformatics pipelines and finds they produce plausible but incomplete implementations requiring expert review.

BLink-seq is a scalable Haplotagging method for generating phased haplotypes and detecting structural variants in non-model species using short-read sequencing.

This study uses single-nucleus RNA-seq to identify unique neuroepithelial features in canine acanthomatous ameloblastoma, revealing ERBB4 as a therapeutic target.

This study identifies metagenomic and transcriptomic signatures of periodontitis in companion dogs, revealing microbial and host gene expression changes associated with disease progression.

The paper analyzes replicate flower color hybrid zones in Antirrhinum to identify loci associated with gene flow barriers using haplotagging, FST scans, and genealogical methods.

This study uses longitudinal sequencing in Drosophila to show that genomic response to selection involves both polygenic shifts and epistatic interactions, with DEGs enriched for selected SNPs.

This paper develops a hybrid capture sequencing platform for tick-borne disease detection, identifying emerging pathogens and ecological transmission networks in New York.

This study uses a deep learning framework to analyze whole-genome data from ME/CFS patients, identifying risk genes and linking them to disease symptoms and other complex traits.

This study compares neonatal and adult CD8+ recent thymic emigrants using single-cell multiomics, finding distinct phenotypes and functions despite similar post-thymic maturation.

This study shows AGO3 and AGO4 regulate transcriptional silencing of XY-linked genes during meiosis in spermatogenesis, impacting fertility and sperm morphology.

This study uses single-nucleus multi-omics to analyze fibrolamellar carcinoma, revealing rewired cell communication and potential therapeutic targets.

The paper identifies gene regulatory programs distinguishing naive CD8+ T cell subsets using RNA-seq and ATAC-seq data, revealing novel regulators and transcriptional networks.

This study shows that male Padi2/Padi4 double knockout mice exhibit delayed puberty, reduced fertility, and lower testosterone levels, linking PADs to hormone signaling in vivo.

This study uses single-cell RNA sequencing to analyze transcriptional changes in spermatogonia and spermatocytes across developmental stages, revealing age-related gene expression differences and pathway utilization.

This study shows that CDK2 kinase activity regulates male germ cell fate by controlling the balance between stem cell renewal and differentiation, with loss of function leading to infertility.