Timothy Durham

Himito is a graph-based toolkit for analyzing mitochondrial genomes using long reads, achieving superior performance in assembly and variant calling and revealing age-related patterns in the All of Us dataset.

This study shows hydrogen sulfide increases copper uptake and localization in cells, with copper primarily in the Cu2+ state, using the ZNT1 transporter for import and ATP7A for export.

The paper investigates the mechanism of age-related mtDNA mutation accumulation in human blood using whole genome sequences, revealing a two-step process involving cryptic mutations and clonal expansion.

Blood whole genomes from 274,832 people yield 92 independent nuclear signals for mtDNA copy number and 42 for inherited heteroplasmy levels, implicating mtDNA replication machinery.

The paper introduces a matrix prior for latent Dirichlet allocation to improve cell type detection in small scATAC-seq datasets by leveraging information from existing data.

The paper presents the first single cell ATAC-seq study in C. elegans, identifying tissue-specific chromatin accessibility patterns aligned with existing RNA-seq data.

The paper introduces Avocado, a deep tensor factorization method that learns a latent representation of the human epigenome, improving imputation and performance on genomics tasks.

This paper introduces Scribe, a toolkit for causal gene regulatory network inference from single-cell data, showing that pseudotime data performs worse than true time series data.

The paper characterizes the evolutionary-functional trajectories of liver enhancers in primates by analyzing sequence mutations and their impact on regulatory activity.

PREDICTD imputes missing epigenomics experiments using tensor decomposition, improving accuracy over existing methods and enabling analysis of enhancer biology in non-coding human regions.