Darryl K. Shibata

Fluctuating DNA methylation sites encode colorectal tumour growth history

This paper introduces a computational model to infer colorectal tumour growth history from DNA methylation data, finding that growth is driven by gland fission rather than cell turnover.

Annotation-Based Gene-Peak Links Improve Regulatory Network Prediction of Gene Expression in Human Kidney Multi-Omics

This paper introduces an annotation-based gene-peak linkage method that improves gene expression prediction from chromatin accessibility in human kidney multi-omics data.

PHYFUM: Phylogenetic Reconstruction of Normal and Pre-malignant Tissue Evolution Using Fluctuating Methylation

PHYFUM reconstructs the evolutionary history of normal and pre-malignant tissues using methylation data, revealing early gland divergence in the gut and later divergence in the endometrium.

Aggressive Neuroblastomas Start Growing after Infancy

This study estimates tumor mitotic ages in neuroblastoma patients to show aggressive tumors start growing after infancy, making them undetectable by infant screening.

Mapping the Temporal Landscape of Breast Cancer Using Epigenetic Entropy

This paper estimates the age of breast cancers using an epigenetic clock based on methylation data, finding that younger tumors are more aggressive while older tumors show higher immune infiltration.

Developmental hematopoietic stem cell variation explains clonal hematopoiesis later in life

The paper shows that clonal hematopoiesis later in life is driven by stem cell variation established before birth, using CpG methylation patterns in twins.

Human Brain Ancestral Barcodes

The paper uses CpG methylation barcodes from single human cells to infer ancestry and developmental relationships, finding that barcodes reflect mitotic age and cell type differences.

Reconstruction of Contemporary Human Stem Cell Dynamics with Oscillatory Molecular Clocks

The paper introduces rapidly oscillating molecular clocks to quantify human stem cell dynamics and finds differences in stem cell replacement rates between small intestine and colon, as well as effects of germline mutations.

Functional Human Genes Typically Exhibit Epigenetic Conservation

The paper shows that epigenetic conservation of genes correlates with their functional importance in human cells and drug sensitivity.

HiLDA: a statistical approach to investigate differences in mutational signatures

HiLDA identifies mutational patterns and their frequencies in cancer data, showing significant associations with mutation timing in colon cancer.