TITLE: "“Cross-tissue multiomics studies reveal gutbrain interactions mediating the effect of Akkermansia muciniphila in counteracting fructose-induced obesity” ABSTRACT: The gut bacterium Akkermansia muciniphila (A. muciniphila) has been implicated in anti-obesity effects, but a systems level understanding of the molecular mechanisms is lacking. We carried out multiomics studies to investigate the molecular cascades mediating the anti-obesity effect of A. muciniphila in a fructoseinduced obesity mouse model. […]

TITLE: "Comprehensive study of gene expression outliers and their regulation mechanisms in pan-cancer." ABSTRACT: Cancer is a disease characterized by remarkable heterogeneity. Gene expression varies drastically between tumours and within cells of a single. This variability can generate extreme outliers: transcripts that show atypically high gene expression in a small percentage of cancers. These outliers […]

TITLE: "Predicting Biological Aging from Epigenetics." ABSTRACT: Epigenetics are a proven measure of cellular health. Therefore, a field of research has emerged that utilizes epigenetics to measure, treat, and potentially reverse biological age in humans. Specifically, DNA methylation, responsible for cell differentiation and gene expression, has the potential to be a barcode for measuring biological […]

TITLE: "Universal annotation of the human genome through integration of over a thousand epigenomic datasets." ABSTRACT: Genome-wide maps of chromatin marks such as histone modifications and open chromatin sites provide valuable information for annotating the non-coding genome, including identifying regulatory elements. Computational approaches such as ChromHMM have been applied to discover and annotate chromatin states […]

TITLE: "Baseline MEthylation Patterns prior to flu vaccination." ABSTRACT: Influenza affects millions worldwide each year with responses varying from individual to individual. Influenza can be broken down into subtypes specifically H1N1, H3N2, Yamagata, and Victoria. One way to measure the immune response to influenza is to measure a person’s antibody response to influenza. To measure how […]

TITLE: "Tensor Factorization for Interpreting the Mechanisms of MRSA Persistence." ABSTRACT: Methicillin-resistant Staphylococcus aureus (MRSA) bacteria is an increasingly common and life-threatening infection. While some antibiotics resolve MRSA infections in vitro, these same antibiotics often fail to clear an infection when used to treat patients, suggesting that MRSA persistence is a confluence of both host […]

TITLE: "Stochastic Model and Optimization of SELEX." ABSTRACT: Systematic Evolution of Ligands by EXponential enrichment (SELEX) is a process to select the best aptamer sequence in a huge aptamer library that binds a specified target molecule with the highest affinity. There has been a deterministic model of SELEX, and we develop a fully discrete stochastic […]

TITLE: "PCA outperforms popular hidden variable inference methods for QTL mapping." ABSTRACT: Estimating and accounting for hidden variables is widely practiced as an important step in quantitative trait locus (QTL) analysis for improving the power of QTL identification. However, few benchmark studies have been performed to evaluate the efficacy of the various methods developed for […]