Department of Computer Science
Luay Nakhleh
  • 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 BioSciences



  • Email: nakhleh@rice.edu
    Phone:  713-348-3959
    Office: Duncan Hall, 3119

    http://www.cs.rice.edu/~nakhleh/
    Homepage

    Luay Nakhleh

    Associate 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


    "Evolutionary Analysis of Bacterial Genomes: High-throughput Computational Tools.”
    Principal Investigator. $1,325,790 (R01 mechanism). National Library of Medicine,
    National Institutes of Health, USA. (subcontractor: Hideki Innan)


    Theses

    Sonali Dutta, PhD.  "Assertion-based Flow Monitoring of SystemC models."  (2016).(Committee Member)

    Anna Drummond, PhD.  "Extension of Topic Models in Text Analysis."  (2014).(Committee Member)

    Troy Ruths, PhD.  "Population Regulomics: Applying population genetics to the cis-regulome."  (2014).(Thesis or Dissertation Director)

    Drew Bryant, Doctoral.  "Redundancy-aware learning of protein structure-function relationships."  (2013).(Committee Member)

    Natalie Berestovsky, Doctoral.  "Toward Integrated Computational Models of Cellular Networks."  (2013).(Thesis or Dissertation Director)

    Seth Fogarty, Doctoral.  "Biichi Automata as Specifications for Reactive Systems."  (2013).(Committee Member)

    Hyun Park, Doctoral.  "Towards Accurate Reconstruction of Phylogentic Networks."  (2012).(Thesis or Dissertation Director)

    Deian Tabakov, Doctor of Philosophy.  "Dynamic Assertion-Based Verification for SystemsC."  (2011).(Committee Member)

    Natalie Berestovsky, Master of Science.  "On the Modeling of Signaling Networks with Petri Nets."  (2011).(Thesis or Dissertation Director)

    Troy Ruths, Master of Science.  "A Sequence-Based, Population Genetic Model of Regulatory Pathway Evolution."  (2011).(Thesis or Dissertation Director)

    Allison Heath, Doctor of Philosophy.  "Computational Discovery and Analysis of Metabolic Pathway."  (2010).(Committee Member)

    Cuong Than, PhD.  "Inference of Parsimonious Species Phylogenies from Multi-locus Data."  (2010).(Thesis or Dissertation Director)

    Drew Bryant, Master of Science.  "Mapping the Structural Landscape of Protein Families with Geometric Feature Vectors."  (2010).(Committee Member)

    Jeffrey Kilpatrick, Master of Science.  "Methods for detecting multi-locus genotype-phenotype association."  (2010).(Thesis or Dissertation Director)

    Powei Feng, Master of Science.  "Segmentation and Visualization of Volume Maps."  (2010).(Committee Member)

    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.  "Shuwei Li."  (Committee Member)

    , Doctor of Philosophy.  "Xiaoyun "Sean" Liao."  (Committee Member)

    , "Christopher A. Miller."  (Committee Member)

    , "Niv Sabath."  (Committee Member)

    , "Ching-Hua Shih."  (Committee Member)

    , "Alan R. Harris."  (Committee Member)

    Yun Yu, Master's.  "From Gene Trees to Species Trees: Algorithms for Parsimonious Reconciliation."  (Thesis or Dissertation Director)




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