Luay K. Nakhleh, Ph.D.
Assistant Professor
Department of Computer Science
Rice University
About :: Research :: Teaching :: Students :: Publications :: Miscellaneous :: Contact

About

Luay (an Arabic name pronounced "Lo-I", where the "I" is pronouned like the pronoun "I") received the PhD degree from UT Austin in May 2004, under the supervision of Prof. Tandy Warnow. He joined the Computer Science department at Rice University as an assistant professor in July 2004.

Prior to joing Rice, Luay received two outstanding dissertation awards from UT Austin (department- and university-wide), and two outstanding teaching awards (department- and college-wide). Since joining Rice, Luay has received the DOE CAREER award in 2006, the NSF CAREER award in 2009, and the Phi Beta Kappa Teaching award in 2009.

In addition to the two CAREER awards, Luay's work has been funded by two NIH R01 grants, two NSF grants (including a SGER award), and internal funding from Rice University.

Luay is very proud of his students' research work and achievements, which include: Derek Ruths' PhD graduation and assistant professor position in CS at McGill University (2009), Cuong Than's Vietnamese Education Foundation fellowship (2005) and PhD graduation and postdoc position with Prof. Noah Rosenberg at U Michigan (2009), Jeff Kilpatrick's DOE/Krell graduate fellowship (2008), Troy Ruths' DOE/Krell and NSF graduate fellowships (2009).

Luay and his Japanese wife, Mika, have two beautiful children, Brooke Amal (born on January 25, 2006) and Dylan Karim (born on October 15, 2008). Here's their picture (taken around June 2009).

Luay's affiliations include:

  1. Assistant Professor, Department of Computer Science, Rice University.
  2. Assistant Professor, Department of Biochemistry and Cell Biology, Rice University.
  3. Adjunct Assistant Professor, Department of Systems Biology, MD Anderson Cancer Center.
  4. Faculty member, The PhD Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine.

For Luay's somehow up-to-date CV, please click here (PDF).


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Research

Luay's research falls into the general areas of computational biology and bioinformatics, with focus on computational evolutionary biology, particularly "networks of evolution and evolution of networks," as well as other topics related to biological networks.

  1. For Luay's research group website, click here.
  2. For the website Luay maintains on research in computational phylogenetics for historical linguistics, click here.

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Teaching

Luay regularly teaches three courses:

  1. COMP 481 - Automata, Formal Languages, and Computability. (Homepage)
  2. COMP 571 - Bioinformatics: Sequence Analysis. (Homepage)
  3. COMP 572 - Bioinformatics: Network Analysis. (Homepage)


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Students

Alumni

  1. Derek Ruths. PhD 2009. First position: Assistant Professor of Computer Science, McGill University. (Homepage).
  2. Cuong V. Than. PhD 2009. First position: Postdoctoral Fellow with Prof. Noah Rosenberg at the University of Michigan. (Homepage)

Current PhD Students

  1. Jeff Kilpatrick. (Homepage)
  2. Hyun Jung (Justin) Park. (Homepage)
  3. Troy Ruths. (Homepage)
  4. Natalie Yudin. (Homepage)
  5. Wanding Zhou. (Homepage)
  6. Yun Yu. (Homepage)
Current Undergraduate Students

  1. Skyler Johnson.
  2. Rick Manning.

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Publications

Copyright Notice: The documents accessible through these links are included by the author as a means to ensure convenient electronic dissemination of technical work on a non-commercial basis. Copyright and all rights therein are maintained by the copyright holders (the authors or the publishers), notwithstanding that they have offered their works here electronically. It is understood that all persons copying this information will adhere to the terms and constraints invoked by each author's and publisher's copyright. In particular, these works may not be re-posted without permission of the copyright holders.


In the list below, Luay's students are marked with a &Dagger superscript.


58 S. Takuno, T. Kado, R.P. Sugino, L. Nakhleh, and H. Innan, "Evolutionary advantages of homologous recombination in a bacterial population." Under review, 2009.
57 C-H. Shih, S. Li, H.J. Park&Dagger, L. Nakhleh, and M.H. Kohn, "Gene-gene network interactions as predictors of intra-chromosomal linkage disequilibrium in the human haplotype map." Under review, 2009.
56 H.J. Park&Dagger, G. Jin, and L. Nakhleh, "Algorithmic strategies for estimating the amount of reticulation from a collection of gene trees." Under review, 2009.
55 H.J. Park&Dagger, G. Jin, and L. Nakhleh, "On the significance of phylogenetic networks inferred by maximum parsimony." Under review, 2009.
54 C. Than&Dagger and L. Nakhleh, "Coalescent histories on phylogenetic networks and detection of hybridization despite lineage sorting." Under review, 2009.
53 D. Ruths&Dagger and L. Nakhleh, "Deriving predictive models of signaling network dynamics from qualitative experimental data." Under review, 2009.
52 Y. Lu, M. Muller, D. Smith, D. Ruths&Dagger, B. Dutta, J.T. Tseng, K. Kumorov, S. Yu, Q. Yu, L. Nakhleh, G. Balazsi, J. Donnelly, M. Schurdak, S. Morgan-Lappe, S. Fesik, P.T. Ram, and G.B. Mills, "A kinome-wide siRNA functional proteomics screen demonstrates bidirectional homeostatic balance between the AKT and MAPK pathways in breast cancer." Science Signaling, To appear (under minor revision) 2009.
51 C. Than&Dagger and L. Nakhleh, "Inference of parsimonious species phylogenies from multi-locus data by minimizing deep coalescences." In: Estimating Species Trees: Practical and Theoretical Aspects, L.L. Knowles and L.S. Kubatko (eds.), Wiley-VCH, to appear 2009.
50 C. Than&Dagger and L. Nakhleh, "Species tree inference by minimizing deep coalescences." PLoS Computational Biology, 5(9): e1000501, 2009.
49 L. Nakhleh, "Evolutionary phylogenetic networks: models and issues." In: The Problem Solving Handbook for Computational Biology and Bioinformatics, L. Heath and N. Ramakrishnan (editors). Springer, In press, 2009.
48 L. Nakhleh, D. Ruths&Dagger, and H. Innan, "Gene Trees, Species Trees, and Species Networks." In: Meta-analysis and Combining Information in Genetics, R. Guerra and D. Goldstein (editors). CRC Press, 275-293, 2009.
47 T. Ruths&Dagger, D. Ruths&Dagger, and L. Nakhleh, "GS2: An efficiently computable measure of GO-based similarity of gene sets." Bioinformatics, 25(9): 1178-1184, 2009.
46 L. Nakhleh, "A Metric on the Space of Reduced Phylogenetic Networks." IEEE/ACM Transactions on Computational Biology and Bioinformatics. To appear, 2009.
45 F. Barbancon, T. Warnow, D. Ringe, S. Evans, and L. Nakhleh, "An experimental study comparing linguistic phylogenetic reconstruction methods." Proceedings of the conference Languages and Genes, held at UC Santa Barbara (Cambridge University Press). To appear, 2009.
44 G. Jin, L. Nakhleh, S. Snir, and T. Tuller, "Parsimony Score of Phylogenetic Networks: Hardness Results and a Linear-time Heuristic." IEEE/ACM Transactions on Computational Biology and Bioinformatics, 6(3): 495-505, 2009.
43 C. Than&Dagger, G. Jin, and L. Nakhleh, "Integrating Sequence and Topology for Efficient and Accurate Detection of Horizontal Gene Transfer." Proceedings of the Sixth RECOMB Comparative Genomics Satellite Workshop. Lecture Notes in Bioinformatics (LNBI #5267), 113-127, 2008.
42 C. Than&Dagger, D. Ruths&Dagger, and L. Nakhleh, "PhyloNet: A Software Package for Analyzing and Reconstructing Reticulate Evolutionary Relationships." BMC Bioinformatics, 9:322, 2008.
41 D. Ruths&Dagger, L. Nakhleh, and P.T. Ram, "Rapidly Exploring Structural and Dynamic Properties of Signaling Networks Using PathwayOracle." BMC Systems Biology, 2:76, 2008.
40 I. Kanj, L. Nakhleh, C. Than&Dagger, and G. Xia, "Seeing the Trees and Their Branches in the Network is Hard." Theoretical Computer Science (TCS), 401: 153-164, 2008.
39 C. Than&Dagger, R. Sugino, H. Innan, and L. Nakhleh, "Efficient Inference of Bacterial Strain Trees From Genome-scale Multi-locus Data." The 16th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB). Bioinformatics, 24: i123-i131, 2008.
38 D. Ruths&Dagger, M. Muller, J.T. Tseng, L. Nakhleh, and P.T. Ram, "The Signaling Petri Net-based Simulator: A Non-parametric Strategy for Characterizing the Dynamics of Cell-specific Signaling Networks." PLoS Computational Biology, 4(2): e1000005, 2008.
37 I. Kanj, L. Nakhleh, and G. Xia, "The Compatibility of Binary Characters on Phylogenetic Networks: Complexity and Parameterized Algorithms." Algorithmica, 51: 99-128, 2008.
36 C. Than&Dagger and L. Nakhleh, "SPR-based Tree Reconciliation: Non-binary Trees and Multiple Solutions." Proceedings of the Sixth Asia Pacific Bioinformatics Conference (APBC), 251-260, 2008.
35 I. Kanj, L. Nakhleh, C. Than&Dagger, and G. Xia, "Seeing the Trees and Their Branches in the Network is Hard." Proceedings of the Tenth Italian Conference on Theoretical Computer Science (ICTCS), 82-93, 2007.
34 C. Than&Dagger, D. Ruths&Dagger, H. Innan, and L. Nakhleh, "Confounding Factors in HGT Detection: Statistical Error, Coalescent Effects, and Multiple Solutions." Journal of Computational Biology, 14(4): 517-535, 2007.
33 G. Jin, L. Nakhleh, S. Snir, and T. Tuller, "A New Linear-time Heuristic Algorithm for Computing the Parsimony Score of Phylogenetic Networks: Theoretical Bounds and Empirical Performance." Proceedings of the International Symposium on Bioinformatics Research and Applications (ISBRA). Lecture Notes in Bioinformatics (LNBI #4463), 61-72, 2007.
32 D. Ruths&Dagger, J.T. Tseng, L. Nakhleh, and P.T. Ram, "De novo Signaling Pathway Predictions based on Protein-Protein Interaction, Targeted Therapy and Protein Microarray Analysis." Proceedings of the RECOMB Satellite Workshop on Systems Biology and Proteomics. Lecture Notes in Bioinformatics (LNBI #4205), 108-118, 2007.
31 G. Jin, L. Nakhleh, S. Snir, and T. Tuller, "Inferring Phylogenetic Networks by the Maximum Parsimony Criterion: A Case Study." Molecular Biology and Evolution, 24(1): 324-337, 2007.
30 G. Jin, L. Nakhleh, S. Snir, and T. Tuller, "Maximum Likelihood of Phylogenetic Networks." Bioinformatics, 22(21): 2604-2611, 2006. (The supplementary material contains the proofs and more technical details.)
29 C. Than&Dagger, D. Ruths&Dagger, H. Innan, and L. Nakhleh, "Identifiability Issues in Phylogeny-based Detection of Horizontal Gene Transfer." Proceedings of the Fourth RECOMB Comparative Genomics Satellite Workshop. Lecture Notes in Bioinformatics (LNBI 4205), 215-229, 2006. [Typo in formula (1) on page 223: the summation should be a product.]
28 D. Ruths&Dagger, L. Nakhleh, M.S. Iyengar, S.A.G. Reddy, and P.T. Ram, "Graph-theoretic Hypothesis Generation in Biological Signaling Networks." Journal of Computational Biology, 13(9): 1546-1557, 2006.
27 G. Jin, L. Nakhleh, S. Snir, and T. Tuller, "Efficient Parsimony-based Methods for Phylogenetic Network Reconstruction." Bioinformatics, 23:e123-e128, 2006. (Proceedings of the European Conference on Computational Biology (ECCB 2006)).
26 T. Shigaki, I. Rees, L. Nakhleh, and K. Hirschi, "Identification of Three Distinct Phylogenetic Groups of CAX Cation/Proton Antiporters." Journal of Molecular Evolution, 63:815-825, 2006.
25 I. Kanj, L. Nakhleh, and G. Xia, "Reconstructing Evolution of Natural Languages: Complexity and Parameterized Algorithms." Proceedings of the 12th Annual International Computing and Combinatorics Conference (COCOON 2006). Lecture Notes in Computer Science (LNCS #4112), 299-308, 2006.
24 Y. Dotsenko, C. Coarfa, L. Nakhleh, J. Mellor-Crummey, and U. Roshan, "PRec-I-DCM3: A Parallel Framework for Fast and Accurate Large Scale Phylogeny Reconstruction." International Journal on Bioinformatics Research and Applications (IJBRA), 2(4): 407-419, 2006.
23 D. Ruths&Dagger and L. Nakhleh, "Techniques for Assessing Phylogenetic Branch Support: A Performance Study." Proceedings of the Forth Asia-Pacific Bioinformatics Conference, (APBC2006), 187-196, 2006.
22 D. Ruths&Dagger and L. Nakhleh, "RECOMP: A Parsimony-based Method for Detecting Recombination." Proceedings of the Forth Asia-Pacific Bioinformatics Conference, (APBC2006), 59-68, 2006.
21 Z. Du, A. Stamatakis, F. Lin, U. Roshan, and L. Nakhleh, "Parallel divide-and-conquer phylogeny reconstruction by maximum likelihood." Proceedings of the 2005 International Conference on High Performance Computing and Communications (HPCC 05), 2:346-350, 2005.
20 L. Nakhleh, G. Jin, F. Zhao, and J. Mellor-Crummey, "Reconstructing Phylogenetic Networks Using Maximum Parsimony." Proceedings of the 2005 IEEE Computational Systems Bioinformatics Conference (CSB2005), 93-102, 2005.
19 L. Nakhleh and L.S. Wang, "Phylogenetic Networks: Properties and Relationship to Trees and Clusters." LNCS Transactions on Computational Systems Biology, II, LNBI 3680, 82-99, 2005.
18 L. Nakhleh, D. Ruths&Dagger, and L.S. Wang, "RIATA-HGT: A Fast and Accurate Heuristic for Reconstructing Horizontal Gene Transfer." Proceedings of the Eleventh International Computing and Combinatorics Conference (COCOON 05). LNCS #3595 (L. Wang, editor), 84-93, 2005.
17 C. Coarfa, Y. Dotsenko, J. Mellor-Crummey, L. Nakhleh, and U. Roshan, "PRec-I-DCM3: A Parallel Framework for Fast and Accurate Large Scale Phylogeny Reconstruction." Proceedigns of the First IEEE Workshop on High Performance Computing in Medicine and Biology (HiPCoMP 2005), 2:346-350, 2005. (Best paper award.)
16 D. Ruths&Dagger and L. Nakhleh, "Recombination and Phylogeny: Effects and Detection." The International Journal of Bioinformatics Research and Applications (IJBRA), 1(2): 202-212, 2005.
15 L. Nakhleh, T. Warnow, D. Ringe, and S.N. Evans, "A Comparison of Phylogenetic Reconstruction Methods on an IE Dataset." Transactions of the Philological Society, 3(2): 171-192, 2005.
14 L. Nakhleh and L.S. Wang, "Phylogenetic Networks, Trees, and Clusters." Proceedings of the 2005 International Workshop on Bioinformatics Research and Applications (IWBRA 05). Lecture Notes in Computer Science, LNCS #3515, pp. 919-926, 2005.
13 L. Nakhleh, T. Warnow, C.R. Linder, and K. St. John, "Reconstructing Reticulate Evolution in Species -- Theory and Practice." Journal of Computational Biology, 12(6-7), 796-811, 2005.
12 L. Nakhleh, D. Ringe, and T. Warnow, "Perfect Phylogenetic Networks: A New Methodology for Reconstructing the Evolutionary History of Natural Languages." LANGUAGE, Journal of the Linguistic Society of America. 81(2):382-420, 2005.
11 B.M.E. Moret, L. Nakhleh, T. Warnow, C.R. Linder, A. Tholse, A. Padolina, J. Sun, and R. Timme, "Phylogenetic networks: modeling, reconstructibility, and accuracy." The IEEE/ACM Transactions on Computational Biology and Bioinformatics, 1(1):13-23, 2004. [Lemma 1 is incorrect (and, consequently, Theorem 3 is incorrect). m^{tri} is a dissimilarity measure, but not a metric on the space of reduced networks. Further, the reduction procedure does not accurately capture the "indistinguishability" part. See Publication #46 above for a metric on the space of reduced phylogenetic networks, and for a revised version of the reduction procedure.]
10 T. Warnow, S.N. Evans, D. Ringe, and L. Nakhleh, "A Stochastic model of language evolution that incorporates homoplasy and borrowing." Phylogenetic Methods and the Prehistory of Languages. Cambridge, UK, July 2004.
9 L. Nakhleh, T. Warnow, and C.R. Linder, "Reconstructing Reticulate Evolution in Species -- Theory and Practice." Proceedings of the Eighth Annual International Conference on Research in Computational Molecular Biology (RECOMB 2004), 337-346.
8 C.R. Linder, B.M.E. Moret, L. Nakhleh, and T. Warnow, "Network (Reticulate) Evolution: Biology, Models, and Algorithms." A tutorial presented at The Ninth Pacific Symposium on Biocomputing (PSB 2004).
7 L. Nakhleh, D. Miranker, F. Barbancon, W.H. Piel, and M.J. Donoghue, "Requirements of Phylogenetic Databases." Proceedings of the Third IEEE Symposium on Bioinformatics and Bioengineering (BIBE 2003), IEEE Press, 2003, 141-148. (Full technical report version of the paper: PDF.)
6 E. Erdem, V. Lifschitz, L. Nakhleh, and D. Ringe, "Reconstructing the Evolutionary History of Indo-European Languages using Answer Set Programming." Proceedings of the Fifth International Symposium on Practical Aspects of Declarative Languages (PADL 2003). Lecture Notes in Computer Science (LNCS #2562).
5 L. Nakhleh, J. Sun, T. Warnow, C.R. Linder, B.M.E. Moret, and Anna Tholse, "Towards the Development of Computational Tools for Evaluating Phylogenetic Network Reconstruction Methods." Proceedings of the Eighth Pacific Symposium on Biocomputing (PSB 03), January 2003.
4 L. Nakhleh, U. Roshan, L. Vawter, and T. Warnow, "Estimating the Deviation from a Molecular Clock." Proceedings of the Second International Workshop on Algorithms in Bioinformatics (WABI 02), Rome, Italy, Lecture Notes in Computer Science (LNCS #2452).
3 L. Nakhleh, B.M.E. Moret, U. Roshan, K. St. John, J. Sun, and T. Warnow, "The Accuracy of Phylogenetic Methods for Large Datasets." Proceedings of the Seventh Pacific Symposium on Biocomputing (PSB 02), 7:211-222, January 2002.
2 L. Nakhleh, U. Roshan, K. St. John, J. Sun, and T. Warnow, "The Performance of Phylogenetic Methods on Trees of Bounded Diameter." Proceedings of the First International Workshop on Algorithms in Bioinformatics (WABI 01), Aarhus, Denmark, Lecture Notes in Computer Science (LNCS #2149). Pages 214-226.
1 L. Nakhleh, U. Roshan, K. St. John, J. Sun, and T. Warnow, "Designing Fast Converging Phylogenetic Methods." Bioinformatics, 17(90001), pp S190-S198, 2001. Proceedings of the Ninth International Conference on Intelligent Systems for Molecular Biology (ISMB 01), Copenhagen, Denmark.

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Miscellaneous


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Contact

Department of Computer Science
Rice University
6100 Main Street, MS 132
Houston, TX 77005

Email: "lastname" @ "cs" . "rice" . "edu"
Work phone: (713) 348 3959.
Work fax: (713) 348 5930.

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