Geoffrey J. Faulkner

The paper identifies DNA hexanucleotide sequences that determine DNA methylation maintenance across cell divisions, revealing their role in biological age and cancer progression.

This study shows that OGT inhibits TET activity, preventing DNA demethylation and transposable element expression in heterochromatin.

This study shows that mutant ASXL1 proteins disrupt heterochromatin integrity in clonal hematopoiesis and CMML by reducing H3K9me2/3 and H2AK119Ub, leading to increased transposable element expression.

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

The paper identifies cofactors required by different transcription factors and promoters using CRISPR-Cas9 screens and shows that unique cofactor combinations influence transcriptional steps.

The paper investigates how L1 retrotransposition potential declines with age through methylation changes and promoter shortening in mice.

The paper re-analyzes RNA-seq data from ataxia telangiectasia samples and finds a batch effect due to intronic L1 reads, challenging the conclusion of L1-driven pathogenesis.

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 study shows that synthetic mouse L1 retrotransposition efficiency is due to sequence changes and a 3UTR deletion, not just ORF GC content, and highlights the need to reconsider synthetic L1 constructs.

This study identifies HOPX as a molecular switch regulating cardiomyocyte progenitor and maturation gene programs, linking it to cardiac function and genetic variation.

The paper shows that SOX6 activates LINE-1 retrotransposons in PV+ interneurons, leading to increased morphological complexity through a novel CAPS2 isoform.

This study introduces Nanopore-DamID, a method to detect DNA methylation and DNA-protein interactions, revealing methylation's role in transcription factor activity.

The paper uses long-read sequencing to investigate SARS-CoV-2 integration into the human genome and finds no evidence of such integration in infected cells.

This study identifies hundreds of novel transcribed pseudogenes using long-read sequencing and shows their functional relevance through translation and perturbation experiments.

This study uses nanopore sequencing and the TLDR tool to profile CpG methylation of transposable elements in human tissues and tumors.

This study shows LINE-1 retrotransposition occurs in human pre-implantation embryos and extraembryonic tissues, impacting gene expression and potentially contributing to genomic variation.

The paper develops a graph-based visualization method for RNA-Seq data to better understand transcript diversity and assembly issues.

The paper identifies shared expression patterns of genetic variants across tissues and cell types, enabling fine mapping of disease-associated variants and revealing key cell types involved in disease pathogenesis.