Kimberly Roche

TL;DR: In this article, a conceptual framework outlining four types of processes that may give rise to zero values in sequence count data was developed and compared with different zero-handling models to identify the most differentially expressed sequences.

TL;DR: It is demonstrated that parasites have low cell-to-cell variance in cycle period, on par with a circadian oscillator, and concluded that an intrinsic oscillator maintains Plasmodium’s rhythmic life cycle.

TL;DR: The results demonstrate that zero-inflated models can have substantial biases in both simulated and real data settings and find that zeros due to biological absences can, for many applications, be approximated as originating from under sampling.

TL;DR: Inference schemes for Marginally LTP models are developed and, through application to MLN models, it is demonstrated that their inference schemes are both highly accurate and often 4-5 orders of magnitude faster than MCMC.

TL;DR: The Pediatric Metabolism and Microbiome Study (POMMS) is available as a shared resource as discussed by the authors for clinical, metabolomic, and microbiome samples from adolescents with obesity as they undergo lifestyle modification.