Zuguang Gu

This study shows that Magel2 deficiency in a mouse model of Prader-Willi syndrome causes microglial structural changes and increased synaptic engulfment, altering neuron-microglia interactions and hypothalamic circuit function.

This paper introduces a citation enrichment metric to analyze global scientific influence and finds two separated worlds of scientific exchange based on citation patterns.

The paper introduces simona, an R package for semantic similarity analysis on bio-ontologies, benchmarking methods and showing topology-based approaches are effective for less-studied organisms.

rGREAT is an R/Bioconductor package that provides local implementation of the GREAT algorithm for functional enrichment on genomic regions, supporting over 500 organisms and user-provided gene sets.

This study shows that Dnmt3a regulates placental vascularization and fetal growth by controlling DNA methylation in endothelial cells, identifying it as a key factor in placental function.

The paper introduces a method to cluster and visualize functional enrichment results, showing improved consistency and exclusivity in term grouping.

The paper introduces a tool to analyze dependency heaviness in R packages and performs a global analysis of dependencies in CRAN and Bioconductor ecosystems.

This paper introduces hierarchical consensus partitioning to improve subgroup identification in high-throughput data, demonstrating its effectiveness on a DNA methylation dataset.

The paper introduces an R package that adds interactivity to static heatmaps, enabling deeper exploration through Shiny web applications.

The paper introduces an R package called spiralize for visualizing data on spirals, demonstrating its flexibility and power through real-world examples.

The paper maps DNA methylation changes during differentiation of HL-60/S4 cells, showing enhancer and CTCF site methylation drives transcriptional reprogramming.

The paper links cancer mutational signatures to changes in transcription factor binding site motifs, showing correlations between motif alteration and signature information content.

The paper introduces pheno-seq, a method that links morphological features to gene expression in 3D cell cultures, showing its ability to identify morphology-specific genes and regulatory states not captured by scRNA-seq.

ACEseq estimates allele-specific copy numbers, tumor purity, ploidy, and homologous recombination deficiency scores from tumor whole-genome sequencing by combining GC-bias correction, replication-timing correction, and structural variant breakpoints.