Systematic benchmarking of omics computational tools

Serghei Mangul*, Lana S. Martin, Brian L. Hill, Angela Ka Mei Lam, Margaret G. Distler, Alex Zelikovsky, Eleazar Eskin, Jonathan Flint

*Corresponding author for this work

Research output: Contribution to journalReview article

13 Scopus citations

Abstract

Computational omics methods packaged as software have become essential to modern biological research. The increasing dependence of scientists on these powerful software tools creates a need for systematic assessment of these methods, known as benchmarking. Adopting a standardized benchmarking practice could help researchers who use omics data to better leverage recent technological innovations. Our review summarizes benchmarking practices from 25 recent studies and discusses the challenges, advantages, and limitations of benchmarking across various domains of biology. We also propose principles that can make computational biology benchmarking studies more sustainable and reproducible, ultimately increasing the transparency of biomedical data and results.

Original languageEnglish (US)
Article number1393
JournalNature communications
Volume10
Issue number1
DOIs
StatePublished - Dec 1 2019

ASJC Scopus subject areas

  • Chemistry(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Physics and Astronomy(all)

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    Mangul, S., Martin, L. S., Hill, B. L., Lam, A. K. M., Distler, M. G., Zelikovsky, A., Eskin, E., & Flint, J. (2019). Systematic benchmarking of omics computational tools. Nature communications, 10(1), [1393]. https://doi.org/10.1038/s41467-019-09406-4