Research

Publications

Diffusion t-SNE for manifold learning. L.H. Nguyen, S. Holmes. Machine Learning in Computational Biology (MLCB) 2019 Proceedings [link].
Ten quick tips for effective dimensionality reduction. L.H. Nguyen, S. Holmes. PLOS Computationa Biology (2019) [link].
Bayesian Unidimensional Scaling for visualizing uncertainty in high dimensional datasets with latent ordering of observations L.H. Nguyen., S. Holmes. BMC Bioinformatics (2017) 18 (Suppl 10) :394 [link]
Chromosome-level de novo assembly of the pig-tailed macaque genome using linked-read sequencing and HiC proximity scaffolding. M. Roodgar, A. Babveyh, L. H. Nguyen, et al. (under review) [preprint]
Gut microbiota plasticity correlated with sustained weight loss after a low-carb or low-fat dietary intervention. J.A. Grembi, L.H. Nguyen, T.D. Haggerty, C.D. Gardner, S.P. Holmes and J. Parsonnet. (under review) [preprint]
Optimal uncertainty quantification with model uncertainty and legacy data. P.H.T. Kamga, B. Li, M. McKerns, L.H. Nguyen, M. Ortiz, H. Owhadi, and T.J. Sullivan. Journal of the Mechanics and Physics of Solids, 72 (2014) [link]

TimeSeriesExperiment. R package for analysis and visualization of short time course data. L.H. Nguyen [Bioconductor]
BUDS Stan based package for Bayesian Unidimensional Scaling. L.H.Nguyen. [github]
visTrajectory Shiny app for discovering the ordering of the data points. L.H. Nguyen [github]
mvarVis R package that generates interactive plots of standard multivariate analysis methods, via the FactoMineR, ade4, and vegan packages. K. Sankaran, L.H. Nguyen [github]