Ryan Lister

PICARD-seq enables rapid, affordable whole-plasmid sequencing using nanopore technology, improving accuracy and resolving repetitive regions in synthetic constructs.

This study profiles root cells from five Brassicaceae species under stress treatments, revealing cell-type-specific gene expression divergence and stress response variation across species.

The paper identifies context-specific failures of the Cre recombinase in plant gene circuits and develops improved recombinase systems for stable memory functions.

The paper introduces a method to track coral individuals and their offspring over time using CRISPR-Cas9 genetic barcodes and eDNA metabarcoding.

The paper refutes claims that Sendai virus expression undermines the TNT reprogramming method, showing no detectable Sendai virus gene expression in TNT iPS cells.

This study shows early moderate prenatal alcohol exposure affects DNA methylation in offspring, with some effects replicated in humans, and maternal diet can mitigate these effects.

The paper introduces a modular dCas9-based platform for combinatorial epigenome editing, demonstrating its ability to control effector recruitment and spatial organization for improved transcriptional regulation.

The paper examines DNA methylation patterns in neurons derived from mouse ES-cells and cultured primary neurons, finding similarities and differences in mCH deposition compared to in vivo conditions.

The paper identifies retrotransposon insertions as the main source of mutations in mouse induced pluripotent stem cells, showing hypomethylation of LINE-1 elements and their impact on gene regulation.

This paper develops CRISPRi-based gene circuits in Arabidopsis for implementing logic gates and modular control of gene expression.

This study evaluates deconvolution methods for human brain transcriptome data, finding that cell-type signatures impact accuracy more than methods, and partial methods outperform complete ones.

The paper introduces synthetic gene circuits in plants that enable programmable reconfiguration of transcriptional activity through logic gates and genetic recombination.

The paper compares single-cell and single-nucleus RNA-seq workflows in adult mouse kidneys to identify protocol-specific biases in cell type recovery and transcriptional profiles.

This study identifies that amyloid plaque phagocytosis through Hif1α controls microglial phenotypes in Alzheimer’s disease in both mice and humans.

HOME identifies differentially methylated regions with higher accuracy and broader applicability across organisms and contexts.

This paper creates a single-cell brain atlas of Alzheimer’s disease, identifying cell-type specific gene expression patterns and regulatory networks associated with disease.

This paper develops a modular dCas9-SunTag DNMT3A system to improve DNA methylation editing specificity and reduce off-target effects compared to direct fusion constructs.

Forcing DNA methylation onto thousands of human promoters with a zinc finger-DNMT3A fusion often fails to repress them, and the mark is quickly erased at H3K4me3-marked promoters.

The paper examines DNA methylation variation in Brachypodium distachyon, showing correlations with genetic diversity and transposable element polymorphisms.

The paper identifies TE presence/absence variants in Arabidopsis and links them to gene expression and DNA methylation differences.