B.S. Computer Science (1996) Technion - Israel Institute of Technology
M.S. Computer Science (1998) Texas A&M
Ph.D. Computer Science (2004) University of Texas
Department of Biochemistry and Cell Biology
Email: nakhleh@rice.edu
Phone: 713-348-3959
Office: Duncan Hall, 3119
http://www.cs.rice.edu/~nakhleh/
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Luay K. Nakhleh
Assistant Professor of Computer Science and Biochemistry and Cell Biology
Computational biology and bioinformatics, particularly phylogenetics and its applications, computational phylogenetics in historical linguistics, algorithm design and analysis, and experimental and empirical performance studies
Selected Publications
Articles
"Rapidly Exploring Structural and Dynamic Properties of Signaling Networks Using PathwayOracle." BMC Systems Biology, 2 (2008).(Published)
"The Compatibility of Binary Characters on Phylogenetic Networks: Complexity and Parameterized Algorithms." Algorithmica, 51 (2008).(Published)
C. Than, D. Ruths and L. Nakhleh "PhyloNet: A Software Package for Analyzing and Reconstructing Reticulate Evolutionary Relationships." BMC Bioformatics, 9 (2008).(Published)
G. Jin, L. Nakhleh, S. Snir, and T. Tuller "Parsimony Score of Phyogenetic Networks: Hardness Results and a Linear-time Heuristic." .(In Press)
I. Kanj, L. Nakhleh, C. Than and G. Xia "Seeing the Trees and Their Branches in the Network is Hard." Theoretical Computer Science (TCS), 401 (2008).(Published)
I. Kanj, L. Nakhleh and G. Xia "The Compatibility of Binary Characters on Phylogenetic Networks:Complexity and Parameterized Algorithms." Algorithmica (2008).(Published)
Book chapters
L. Nakleh, D. Ruths and H. Innan "Gene Trees, Species Trees and Species Networks." Meta-analysis and Combining Information in Genetics (2007).(In Press)
Refereed Conference Papers
D. Ruths and L. Nakhleh "RECOMP: A Parsimony-based Method for Detecting Recombination." Proceedings of The Fourth Asia-Pacific Bioinformatics Conference (2006).(In Press)
D. Ruths and L. Nakhleh "Techniques for Assessing Phylogenetic Branch Support: A Performance Study." Proceedings of The Fourth Asia-Pacific Bioinformatics Conference (2006).(In Press)
Theses
Derek Ruths, Doctor of Philosophy. "Deriving Executable Models of Biochemical Network Dynamics from Qualitative Data." (2009).(Thesis or Dissertation Director)
Amarda Shehu, Doctor of Philosophy. "Molecules in Motion:Computing Structural Flexibility." (2008).(Committee Member)
Cuong Than, Master of Science. "Reconstruction of Phylogenetic Networks and Their Relationships with Trees and Branches." (2008).(Thesis or Dissertation Director)
Konstantinos Tsianos, Master of Science. "Replanning: A Powerful Planning Strategy for Systems with Differential Constraints." (2008).(Committee Member)
Seth Fogarty, Master of Science. "Buchi Containment and Size-Change Termination." (2008).(Committee Member)
Hernan Stamati, Master of Science. "Analysis of Molecular Motion using Non-Linear Dimensionality Reduction." (2007).(Committee Member)
Samah Abu-Mahmeed, Master of Science. "In-Place Updating of Variables in LabVIEW." (2007).(Committee Member)
, Master of Science. "Sara Kalla." (2006).(Committee Member)
Allison Heath, Master of Science. "Towards Multiscale Protein Simulations: Moving from Coarse-Grain to All-Atom Models." (2006).(Committee Member)
Amarda Shehu, Master of Science. "Sampling Biomecular Conformations with Spatial and Energetic Constraints." (2005).(Committee Member)
Deian Tabakov, Master of Science. "Experimental Evaluation of Explicit and Symbolic Automata-Theoretic Algorithms." (2005).(Committee Member)
Derek Ruths, Master of Science. "Detection and Reconstruction of Horizontal Gene Transfer." (2005).(Thesis or Dissertation Director)
Derek Ruths, Master of Science. "Applications of Phylogenetic Incongruence to Detecting and Reconstructing Interspecific Recombination and Horizontal Gene Transfer." (2005).(Thesis or Dissertation Director)
Martin Schwarz, Master of Science. "Local Conformational Search of Proteins Using the Expansive Spaces Search." (2005).(Committee Member)
Wendee Holtcamp, Master of Science. "Species Boundaries as a Key to Understanding Hybridization." (2005).(Committee Member)
, Doctor of Philosophy. "Xiaoyun "Sean" Liao." (Committee Member)
, "Niv Sabath." (Committee Member)
, "Ching-Hua Shih." (Committee Member)
, "Christopher A. Miller." (Committee Member)
, Doctor of Philosophy. "Shuwei Li." (Committee Member)
, "Alan R. Harris." (Committee Member)
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