Creating reusable tools from scripts: the Galaxy Tool Factory. - Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team (Bioinform., 2012)

Gene name errors: Lessons not learned. - Mandhri Abeysooriya; Megan Soria; Mary Sravya Kasu; Mark Ziemann (PLoS Comput. Biol., 2021)

Urgent need for consistent standards in functional enrichment analysis. - Kaumadi Wijesooriya; Sameer A. Jadaan; Kaushalya L. Perera; Tanuveer Kaur; Mark Ziemann (PLoS Comput. Biol., 2022)

The five pillars of computational reproducibility: bioinformatics and beyond. - Mark Ziemann; Pierre Poulain; Anusuiya Bora (Briefings Bioinform., 2023)