Noah Simon

Constructing microbiome co-occurrence networks with confidence: A conditional, nonparametric, inference-based approach

The paper introduces a nonparametric method to construct microbiome co-occurrence networks with confidence, improving network recovery by accounting for conditional associations and providing statistical inference.

Thrifty wide-context models of B cell receptor somatic hypermutation

The paper develops 'thrifty' models of somatic hypermutation using convolutions on 3-mer embeddings, showing they outperform 5-mer models with fewer parameters.

Differential Expression Analysis for Spatially Correlated Data

The paper addresses challenges in differential expression analysis of spatial transcriptomics data by mitigating segmentation errors and accounting for spatial correlation, reducing false discoveries.

Multidimensional analysis and detection of informative features in diffusion MRI measurements of human white matter

This paper introduces a sparse group lasso method to analyze diffusion MRI data, identifying informative white matter features for ALS classification and brain age prediction.

Estimation of cell lineage trees by maximum-likelihood phylogenetics

This paper introduces a statistical model and method for estimating cell lineage trees using maximum-likelihood phylogenetics, showing improved accuracy over existing methods in simulations and zebrafish development.

seagull: lasso, group lasso and sparse-group lasso regularisation for linear regression models via proximal gradient descent

The paper introduces an R package implementing lasso, group lasso, and sparse-group lasso regularization via proximal gradient descent for high-dimensional linear regression.

Epigenetic memory via concordant DNA methylation is inversely correlated to developmental potential of mammalian cells

The paper introduces a framework to quantify DNA methylation stability and flexibility in mammalian cells, finding that differentiated cells have higher stability than stem cells.