Amy L. Olex

The paper evaluates exclusion set generation strategies in short-read sequencing, finding that pre-generated Blacklists are hard to reproduce and proposes sponge sequences as an alternative to reduce artifacts.

The paper identifies an ETR1-dependent gene regulatory network in Arabidopsis roots that modulates ethylene signaling, synthesis, and root development through transcriptomic analysis of gain- and loss-of-function mutants.

The paper determines sample size requirements for ML classification in bulk RNA-seq data and finds that ML methods generally need larger samples than differential analysis power analysis.

This study shows Treg cells remodel the tumor ECM to promote metastasis, with matrisome signatures linked to poor survival in breast cancer.

The paper shows that anti-tumor immunity in HCC relies on monocyte-driven tissue homeostasis rather than direct tumor cytotoxicity, highlighting the importance of restoring liver integrity.

This study identifies YY1's role in regulating cerebellar astrocyte maturation and maintenance in adult mice through single-cell RNA-seq analysis.

This study evaluates the impact of mouse read removal and library preparation on Hi-C data quality in patient-derived xenografts, finding that library strategy has the largest effect.