Chad Tomlinson

This study develops pangenome-based frameworks to analyze DNA methylome variation across diverse human genomes, identifying genetic factors influencing methylation patterns and their associations with complex traits.

The paper presents a human panepigenome map of DNA methylation, revealing epigenomic diversity across populations and highlighting the role of genetic variation in CpG presence and absence.

The paper investigates methylation patterns of polymorphic transposable elements using long-read sequencing and the Human Pangenome Reference, revealing distinct methylation profiles and context-dependent interactions.

The paper uses fully phased telomere-to-telomere assemblies and long-read epigenomes to study centromere genetic and epigenetic dynamics across inheritance and cell-fate transitions, finding positional stability of CDRs and dynamic epigenetic changes.

This paper presents a chromosome-level genome assembly and annotation for the degu, improving contiguity, completeness, and gene annotation compared to previous assemblies.

This study shows that using graph-based pangenomes and inferred donor-specific assemblies improves somatic variant detection compared to GRCh38.

The paper develops a pangenomic method to create a benchmark resource for somatic variant detection using HapMap mixtures, identifying millions of variants across different genomic regions.

The paper presents a draft human pangenome reference that improves variant discovery and structural variant detection compared to existing references.

The paper improves genomic inference by masking haplotigs in the eastern oyster genome, enhancing SNP discovery and diversity estimates.

The paper sequences and annotates the genomes of two sand fly species, identifying genes related to vector biology and population structure to aid in leishmaniasis control.

The paper presents a chromosome-level genome of surface fish Astyanax mexicanus and uses it to identify genetic factors contributing to trait evolution in cavefish populations.

The paper presents a new domestic cat genome assembly using long-read sequencing, identifies novel variants associated with cancer and dwarfism, and highlights the utility of feline genomics for biomedical research.

The paper presents a high-quality quail genome and uses it to study social behavior, photoperiodism, and immune response to H5N1 influenza.

The paper presents a comparative genomic analysis of six Glossina species, identifying genetic features related to their unique biology and vectorial capacity.