Duncan T. Odom

This study tracks somatic mutation evolution in hair follicles to forecast early skin cancer development non-invasively.

The paper shows that aged female CD8 memory T cells exhibit erosion of Xi transcriptional fidelity, linked to immune activation and clonal expansion, with similar findings in humans.

This paper uses machine learning to predict genomic alterations from H&E images of liver tumors, revealing genotype-phenotype links and highlighting genetic background limitations.

The paper quantifies enhancer activation frequency in response to TF perturbations and identifies H3K27Ac as a chromatin mark required for enhancer activation.

This study shows that genetic background and environmental factors determine the trajectory of cancer evolution in mice, with distinct mutational paths despite similar final tumor states.

The paper presents a high-quality de novo genome assembly of Ansells mole-rat using long-read, short-read, and Hi-C data, enabling genetic and phylogenetic studies.

This study investigates how germline and somatic genetic variations affect mitochondrial DNA content, mutation patterns, and gene expression in liver tumors across four mouse strains.

This study shows that SRSF2 mutations cause DNA damage and cell cycle arrest, highlighting its role in transcription regulation during cell division.

The paper identifies an X-Y translocation in Four-Core Genotypes mice that increases Tlr7 expression and affects genetic interpretation.

The paper investigates how strand-asymmetric processes like replication and transcription influence DNA damage, repair, and mutagenesis, revealing mechanisms that shape cancer genome evolution.

This study shows Xist RNA modulates X-chromosome inactivation beyond early development, reversibly silencing escapee genes and altering topological domain structures in mouse embryos.

This study maps the single-cell transcriptional and morphological changes in the mouse female reproductive tract across the estrus cycle, decidualization, and aging, revealing age-related fibrosis and inflammation.

This study shows that aged intestinal epithelial cells exhibit a persistent inflammation signature, marked by MHC class II upregulation and increased chromatin accessibility of inflammation-associated loci.

This study investigates how superovulation and aging affect oocyte-granulosa cell communication in mice, finding that both disrupt similar gene sets and impair oocyte quality.

This study maps the transcriptional and regulatory changes during mouse somitogenesis, showing accelerated differentiation and lineage-specific programs.

The paper identifies DNA methylation patterns at TF binding sites across species, linking them to functional roles and evolutionary changes.

The paper investigates evolutionarily young CTCF binding sites in two Mus subspecies, finding some functional signatures and a novel immune locus formed by tandem duplication.

The paper investigates how LINE elements contribute to the evolution of tissue-specific and shared regulatory regions across mammalian genomes.

The paper investigates how CTCF binding patterns across species contribute to the stability and evolution of TAD boundaries through clustered binding sites.

The paper creates a single-cell transcriptomic atlas of mouse spermatogenesis, identifying key developmental stages and X chromosome transcriptional dynamics.

This study shows that ageing alters the composition of γδ T cells in lymph nodes, promoting tumour growth in mice.

The paper introduces Ragout, a reference-assisted assembly tool that improves chromosome assembly for large and complex genomes, achieving high accuracy with less than 5% unlocalized sequence.

This paper presents an integrative framework to detect structural variants in cancer genomes using multiple methods and finds that non-coding structural variation significantly impacts genome function in cancer cells.

The paper annotates pseudogenes in the mouse genome and strains, finding similar overall characteristics to humans but distinct age distributions and transcriptional patterns.

This study compares the off-target effects of RNAi, antisense oligonucleotides, and CRISPRi in transcriptomic analyses, showing that all methods have non-negligible off-target effects and recommend using multiple LOF methods for functional validation.

The paper compares genome assemblies of Mus caroli and Mus pahari with Mus musculus and Rattus norvegicus to reveal lineage-specific evolutionary mechanisms, particularly repeat-associated processes.

The paper presents full-length de novo genome assemblies for 16 inbred mouse strains, identifying strain-specific haplotypes and novel functional loci, including a large unannotated gene with potential developmental roles.

The paper examines how regulatory landscapes influence gene expression stability across mammals, finding that conserved elements and element number are key to expression resilience.

The paper investigates cis and trans mechanisms influencing transcription factor binding and gene expression evolution in mice by analyzing allele-specific occupancy in crosses of two inbred strains.