He is an evolutionary biologist and botanist with broad interests in plant biodiversity — from the scale of global patterns and community assembly, to speciation and genetic variation within species. Deren's research is rooted in organismal biology and fieldwork, with projects focused in the Tibetan plateau and cloud forests of Central and South America. A common theme across his work is the development of new computational or statistical methods for analyzing comparative genomic data, and the implementation of, and support for reproducible science. This has included the development of genomic assembly software (ipyrad), evolutionary analysis tools (the ipyrad-analysis toolkit), and tree visualization software (toytree), all of which are designed to encourage reproducibility in evolutionary genomic analyses.