Luay Nakhleh

Luay Nakhleh^[1] is a Professor of Computer Science^[2] and of BioSciences^[3] at Rice University in Houston, Texas.

Biography

Luay was born on May 8, 1974 to a Christian, Palestinian family in Israel. He currently lives with his Japanese wife and two children in Texas, and holds a U.S. citizenship (in addition to the Israeli citizenship).

Luay did his undergraduate studies in the Department of Computer Science at the Technion, Israel Institute of Technology, earning a Bachelor's degree in 1996. He earned a Master's degree in Computer Science from Texas A&M University in 1998, and a PhD degree in Computer Science from the University of Texas at Austin, under the supervision of Prof. Tandy Warnow, in 2004. Luay started his academic position at Rice University in July 2004, where he has been an Assistant Professor (2004-2010), Associate Professor (2010-2016), and a Full Professor (2016-current). As for August 2016, he also serves as the Associate Chair of the Computer Science Department.

Research

Luay's research has been focused mainly on computational and statistical approaches to phylogenomics and comparative genomics under scenarios where the evolutionary history of the genomes is not treelike. His earlier work in this area focused on parsimonious phylogenetic networks: Networks that embed a given set of trees with the fewest number of reticulations, assuming all gene tree incongruence is due to reticulate evolution. He and his colleagues also applied similar approaches to language data to elucidate the (reticulate) evolutionary history of the Indo-European languages. 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. These approaches could be viewed as approximations of the multispecies coalescent with gene flow.

Additionally, Luay has done research on biological networks (modeling and evolution) and, more recently, on computational questions arising in cancer genomics.

Luay and his group have been developing PhyloNet,^[4] an open-source software package, implemented in Java, for inference and analysis of (explicit) phylogenetic networks.

Honors and awards

Luay's honors and awards include:

• The Computer Sciences Bert Kay Outstanding Dissertation Award,^[5] Department of Computer Sciences, UT Austin, 2005.
• The Outstanding Dissertation Award^[6] in the Mathematics, Engineering, Physical Sciences, and Biological and Life Sciences category, UT Austin, 2005.
• The Department of Energy Early Career Award,^[7] 2006.
• The National Science Foundation CAREER Award, 2009.
• The Phi Beta Kappa Teaching Award,^[8] Rice University, 2009.
• The Sloan Fellowship in the Molecular Biology category, 2010.
• The Guggenheim Fellowship in the Organismic Biology and Ecology category, 2012.
• The Teaching and Research Excellence Award,^[9] School of Engineering, Rice University, 2015.

Selected publications

• Wen, D.; Yu, Y.; Nakhleh, L. (2016), "Bayesian inference of species phylogenies under the multispecies network coalescent", PLoS Genetics, 12(5): e1006006.
• Zafar, H.; Wang, Y.; Nakhleh, L.; Navin, N.; Chen, K. (2016), "Monovar: single nucleotide variant detection in single cells", Nature Methods,13(6): 505-507.
• Wen, D.; Yu, Y.; Hahn, M.W.; Nakhleh, L. (2016), "Reticulate evolutionary history and extensive introgression in mosquito species revealed by phylogenetic network analysis", Molecular Ecology, 25: 2361-2372.
• Liu, K.J; Steinberg, E.; Yozzo, A.; Song, Y.; Kohn, M.H.; Nakhleh, L. (2015), "Interspecific introgressive origin of genomic diversity in the house mouse", PNAS, 112(1): 196-201.
• Yu, Y.; Dong, J.; Liu, K.J.; Nakhleh, L. (2014), "Maximum likelihood inference of reticulate evolutionary histories", PNAS, 111(46): 16448-16453.
• Nakhleh, L. (2013), "Computational approaches to species phylogeny inference and gene tree reconciliation", Trends in Ecology and Evolution, 28(12): 719-728.
• Ruths, T.; Nakhleh, L. (2013), "Neutral forces acting on intragenomic variability shape the Escherichia coli regulatory network topology", PNAS, 110(19): 7754-7759.
• Nakhleh, L.; Ringe, D.; Warnow, T. (2005), "Perfect phylogenetic networks: a new methodology for reconstructing the evolutionary history of natural languages" (PDF), Language, 81 (2): 382–420.

References