Joshua David Campbell

This study investigates how trisomy 21 affects oligodendrocyte development and neuron-glia communication in human forebrain assembloids, finding a shift toward a pre-myelinating state and disrupted myelination.

This study benchmarks local ancestry inference across different genotyping assays and parameters, showing that ultra low-pass WGS with GLIMPSE2 achieves high accuracy, while SNP microarrays perform poorly.

The paper defines sub-phenotypes of pneumonia using histopathological features from human lung samples and validates them in mouse models.

The paper constructs a single-cell and spatial atlas of prostate cancer to reveal gene modules driving lineage plasticity and metastasis, identifying new biological insights and a transformer-based model for cell-state classification.

The paper identifies muscarinic receptor subtypes in primate prefrontal and cingulate cortices, revealing regional differences in receptor expression and functional properties.

This study uses in vitro exposure of human airway epithelial cells to genotoxic carcinogens to define mutational signatures associated with lung cancer.

The paper introduces GPAS to analyze gene co-expression modules in NSCLC, identifying lineage plasticity and aggressiveness patterns across different cancer subtypes.

The paper compares molecular programs in Drosophila nurse cell death and clearance under different conditions, identifying pathways and genes involved in apoptotic and non-apoptotic clearance mechanisms.

The paper shows that neutrophils in a murine pneumococcal pneumonia model transition through two distinct transcriptional trajectories with associated metabolic changes.

This study shows that repetitive head impacts in young athletes cause neuronal loss and neuroinflammation before CTE pathology, with specific cellular changes linked to disease progression.

This study identifies Myc dysregulation in macrophages as a driver of TB susceptibility by linking lipid peroxidation and IFN-I pathway hyperactivity.

The paper identifies and removes background noise in CITE-seq data using DecontPro, a Bayesian model that improves clustering specificity and reduces contamination from spongelets and ambient ADTs.

The paper identifies miRNAs and isomiRs associated with COPD and ILD through integrative network analysis of RNA-seq and SNP data from lung tissue samples.

SCTK2.0 provides an integrated toolkit for scRNA-seq analysis with a graphical interface, enabling non-programmers to perform end-to-end workflows and generate reproducible reports.

The paper develops contamination-focused metrics and software to optimize scRNA-seq experiments by reducing ambient contamination through experimental adjustments.

The paper introduces MAMS, a metadata standard for single-cell data matrices and analysis workflows, to improve reproducibility and interoperability across datasets.

Celda identifies transcriptional modules and cell subpopulations in scRNA-seq data, outperforming existing methods in detecting biological programs and cell types.

The paper introduces a pipeline for generating, visualizing, and reporting quality control metrics for scRNA-seq data, improving standardization across platforms.

The paper introduces musicatk, a toolkit for analyzing mutational signatures, enabling preprocessing, analysis, visualization, and comparison to COSMIC database.

DecontX is a Bayesian method to remove ambient RNA contamination in scRNA-seq data, improving cell cluster separation and marker gene accuracy.

This study uses single-cell RNA sequencing to analyze smoking effects on bronchial epithelial cell types, identifying molecular changes and a novel subpopulation linked to premalignant lesions.

Pipeliner provides a Nextflow-based framework for creating flexible and reproducible sequencing data processing pipelines, supporting bulk RNA-seq, scRNA-seq, and DGE data.

scruff is an R/Bioconductor package that preprocesses scRNA-seq data from CEL-Seq protocols, providing quality metrics and visualizations for reproducible analysis.

This study evaluates a highly multiplexed RNA sequencing platform (SFL) and compares its performance to existing techniques, finding it outperforms 3DGE in coverage and differential gene expression detection.

The paper introduces SCTK, an interactive scRNA-Seq analysis tool with command-line and GUI interfaces for handling complex single-cell data.