Nakhleh did his undergraduate studies in the Department of Computer Science at the Technion, Israel Institute of Technology, earning a bachelor's degree in 1996.
In addition to his duties as the Dean of Engineering at Rice University, Nakhleh currently teaches courses in discrete mathematics and computational biology.
[8] Later, his work started focusing on statistical approaches, in order to account for other evolutionary processes that could be at play in genomic data sets, most notably incomplete lineage sorting.
[citation needed] Additionally, Nakhleh has done research on biological networks (modeling and evolution) and, more recently, on computational questions arising in cancer genomics.
Nakhleh and his group have been developing PhyloNet,[9] an open-source software package, implemented in Java, for inference and analysis of (explicit) phylogenetic networks.