Stephen R. Williams

This paper introduces a service for automated cell type annotation in scRNA-seq data using reverse search against a curated database, providing both fine-grained and coarse annotations without relying on predefined markers.

This study uses Visium HD spatial transcriptomics to map immune cell populations in colorectal cancer tumor microenvironments, identifying spatially distinct macrophage and T cell subpopulations.

The paper uses spatial proteogenomics to analyze gene expression changes in Alzheimer's disease brains linked to amyloid-beta and tau pathology.

This paper develops a spatial multi-omics platform to analyze immune responses in SARS-CoV-2-infected lung tissues, revealing macrophage infiltration and spatial heterogeneity in cytokine and interferon signaling.

This paper introduces SpaceMarkers, a method to infer molecular changes from cell-cell interactions in spatial transcriptomics data, applied to tumor-immune interactions in metastasis and immunotherapy.

BayesSpace enhances spatial transcriptomics resolution and clustering, revealing tissue structures undetectable at lower resolutions.

The paper maps spatial gene expression in the human dorsolateral prefrontal cortex using spatial transcriptomics and identifies layer-specific gene expression patterns linked to neuropsychiatric disorders.

The paper identifies brain-region specific splicing patterns at single-cell and spatial resolution in postnatal mice, revealing cell-type specific and region-specific isoform expression.

This paper introduces Linked-Reads as a method to comprehensively analyze genome variation, showing it can detect both small and large variants and reconstruct haplotypes more effectively than short-read sequencing.

The paper introduces Novel-X, a method using Linked-Read data to detect novel sequence insertions without whole-genome de novo assembly, outperforming short-read tools and enabling cost-effective large-scale screening.

This paper links subclonal mutations to transcriptional profiles in AML using integrated single-cell RNA-sequencing and whole genome sequencing.

This study uses Linked-Read sequencing to assemble a high-quality, contiguous reference genome for Capsicum annuum, demonstrating its utility for complex plant genomes.

This study identifies the causal mechanism of X-linked Dystonia-Parkinsonism (XDP) by integrating genome and transcriptome assembly, revealing a SVA insertion causing intron retention and TAF1 dysfunction.

This study evaluates Linked-Read sequencing for detecting structural variants, finding it can identify most known events with low sequencing depth and provides breakpoint resolution.