Will Macnair

Unique transcriptional profiles of adult human immature neurons in healthy aging, Alzheimer's disease, and cognitive resilience

The paper identifies unique transcriptional profiles of immature neurons in aged human hippocampus across healthy, Alzheimer's disease, and resilient conditions, linking them to homeostasis and cognitive resilience.

scprocess: a pipeline for processing, integrating and visualising atlas-scale single cell data

scprocess is a Snakemake pipeline that automates and integrates single cell RNA sequencing data processing, enabling reproducible and scalable analysis of large datasets.

Foamy microglia link oxylipins to disease progression in multiple sclerosis

The paper identifies foamy microglia as contributors to disease progression in secondary progressive MS, linking oxylipins to lesion expansion and proposing monoacylglycerol lipase as a therapeutic target.

Single nuclei RNAseq stratifies multiple sclerosis patients into distinct white matter glia responses

The paper uses single nuclei RNAseq to identify distinct glial gene expression patterns in MS patients, revealing subgroup-specific pathological processes and suggesting precision medicine approaches.

SampleQC: robust multivariate, multi-celltype, multi-sample quality control for single cell data

SampleQC improves single-cell RNA-seq quality control by robustly fitting a Gaussian mixture model across multiple samples, reducing bias against rare celltypes.

Dynamic Distribution Decomposition for Single-Cell Snapshot Time Series Identifies Subpopulations and Trajectories during iPSC Reprogramming

DDD identifies dynamically important cell states and trajectories during iPSC reprogramming by modeling single-cell time series as a continuous Markov process.

psupertime: supervised pseudotime inference for single cell RNA-seq data with sequential labels

psupertime improves pseudotime inference in single-cell RNA-seq by using sequential labels to identify genes relevant to biological processes rather than other sources of variation.

Tree-ensemble analysis tests for presence of multifurcations in single cell data

TreeTop identifies and assesses branch points in single-cell data, showing shallow differentiation hierarchies in hematopoiesis.