David M. Rocke

This study shows adult killifish exposure to crude oil causes developmental and gene expression changes in first- and second-generation offspring.

The paper shows that urban killifish populations resistant to PCBs are also resilient to crude oil toxicity due to shared molecular mechanisms.

This paper demonstrates that deep semi-supervised learning improves peptide identification in shotgun proteomics by recalibrating peptide-spectrum matches more effectively than existing methods.

The paper evaluates differential gene expression methods using RNA-Seq data and finds that methods relying on negative binomial models show high false positive rates, while variance-based methods do not.

The paper evaluates differential gene expression methods using RNA-Seq data, finding that many produce false positives and recommends limma-voom and simple methods for better performance.