Mark D. Robinson

The paper introduces a junction coverage compatibility score to assess the reliability of transcript abundance estimates and annotation catalogs by comparing observed and predicted junction-spanning reads.

This study shows that covalently linking a DNA repair template to the CRISPR/Cas9 complex increases HDR efficiency 23-fold compared to NHEJ.

The paper introduces a bead-based compensation workflow for mass cytometry to correct channel crosstalk, improving data quality and panel development.

The paper evaluates 30 differential expression methods on scRNA-seq data, finding method-specific differences and the impact of pre-filtering on results.

The paper introduces a weighting strategy using a zero-inflated negative binomial model to improve bulk RNA-seq tools for single-cell RNA-seq data with zero inflation.

The paper develops an integrative proteogenomics strategy to improve prokaryotic genome annotation by combining multiple resources and experimental data, identifying novel ORFs and correcting errors.

This paper demonstrates efficient CRISPR-Cas9-based gene disruption in the medfly using RNPs, achieving high germline transmission and mutant phenotypes.

The paper introduces a stage-wise testing procedure for differential expression and transcript usage that provides gene-level FDR control while maintaining transcript-level resolution.

zingeR improves differential expression analysis in scRNA-seq by using a zero-inflated negative binomial model to address zero-inflation, matching performance of dedicated scRNA-seq tools.

The paper compares clustering methods for high-dimensional flow and mass cytometry data, finding several methods effective with FlowSOM being fast and suitable for large datasets.

benchmarkR evaluates and visualizes statistical methods' performance on genomic datasets with known truth, focusing on FDR control and calibration.