Peter F. Hickey

This study identifies γδ T cell infiltration in SCLC and shows their anti-tumor activity, suggesting they could be therapeutic targets.

SpatialBench evaluates spatial transcriptomics platforms using a mouse spleen model, finding consistent biological signals but varying resolution across technologies.

The paper shows iron deficiency reduces Plasmodium parasitemia in pregnant women and mice, and iron supplementation does not increase parasitemia when combined with malaria prevention.

TIRE-seq streamlines RNA-seq workflows by integrating mRNA purification into library preparation, improving efficiency and data quality in perturbation studies.

The paper benchmarks spatial transcriptomics technologies using a multi-sample dataset from mouse spleen tissue, finding improved data quality with probe-based capture methods and CytAssist.

This study evaluates sample multiplexing reagents and protocols for scRNA-Seq, finding that workflow improvements and reagent choice impact data quality and cost-effectiveness.

This study benchmarks seven HTO demultiplexing tools using datasets with genetic variant-based ground truth, finding similar performance on high-quality data but poor performance on lower quality data for bimodal distribution methods.

The paper introduces two methods to handle group heteroscedasticity in pseudo-bulk single-cell RNA-seq data, showing improved error control and power compared to existing methods.

The paper uses scRNA-seq and flow cytometry to identify novel immune and epithelial cell populations in preschool CF patients' bronchoalveolar lavage.

The paper evaluates genetic demultiplexing tools for pooled single-cell RNA-seq in cancer, showing they work effectively despite challenges from ambient RNA.

This study benchmarks 9 scRNA-seq preprocessing workflows, finding that while they vary in gene detection and quantification, downstream analysis with effective normalization and clustering methods leads to consistent clustering results.

The paper identifies brain region-specific variably methylated regions (VMRs) enriched for schizophrenia heritability using DNA methylation data from neuronal nuclei across multiple brain regions.

NanoMethViz provides an R/Bioconductor package for visualizing long-read methylation data, offering tools to explore methylation patterns at multiple resolutions.

Tximeta automatically identifies reference transcriptomes and gathers metadata for RNA-seq analysis using checksums, improving reproducibility and reducing errors.

The paper identifies 103 novel epigenetic regulator disease candidates by analyzing co-expression patterns and loss-of-function intolerance in human epigenetic machinery genes.

This study identifies Smchd1 as a regulator of long-range chromatin interactions, showing context-dependent effects on transcription and chromatin structure.

The paper identifies brain region-specific DNA methylation and chromatin accessibility differences and links them to heritability of neuropsychiatric disorders.