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Scholarly Interest Report
         
Luay Nakhleh
Professor
Professor of Computer Science and Biochemistry and Cell Biology
 
e-mail:nakhleh@rice.edu
 
  • B.S. Computer Science (1996) Technion - Israel Institute of Technology, Israel
  • M.S. Computer Science (1998) Texas A&M, College Station, Texas
  • Ph.D. Computer Science (2004) University of Texas, Austin, Texas
 
Primary Department
   Department of Computer Science
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Department Affiliations
 
  • Department of BioSciences
  •  
    Other Affiliations
     
  • Baylor College of Medicine
  • MD Anderson
  •  
    Co-chair of Phylogenomics and Population Genomics sessin at the Pacific Symposium on Biocomputing, 2013.
     
     
    Websites
     Homepage
     
    Research Areas
     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.”

     

    "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)

     
    Teaching Areas
     Bioinformatics-Sequence Analysis; Automata, Formal Languages, and Computability
     
    Selected Publications
     Refereed articles
     

    K. Liu, E. Steinberg, A. Yozzo, MH Kohn, L. Nakhleh, ""Interspecific Introgressive origin of genomic diversity in the house mouse." Proceedings of he National Academy of Sciences. ." 

     
     

    H.J. Park and L. Nakhleh, “Inference of reticulate evolutionary histories by maximum likelihood: The performance of information criteria.” BMC Bioinformatics, 13(Suppl 19): S12, 2012. (Special issue on accepted papers to RECOMB Comparative Genomics 2012).

     
     

    S. Takuno, T. Kado, R.P. Sugino, L. Nakhleh, and H. Innan, “Population genomics in bacteria: A case study of Staphylococcus aureus.” Molecular Biology and Evolution, 29(2): 797-809, 2012.

     
     

    T. Ruths  and L. Nakhleh, “ncDNA and drift drive binding site accumulation.” BMC Evolutionary

    Biology, 12: 159, 2012

     
     

    W. Zhou and L. Nakhleh, “Convergent evolution of modularity in metabolic networks through differ- ent community structures.” BMC Evolutionary Biology, 12: 181, 2012.

     
     

    Y. Yu , J.H. Degnan, and L. Nakhleh, Y. Yu , J.H. Degnan, and L. Nakhleh,  “The probability of a gene tree topology within a phylogenetic network with applications to hybridization detection.” PLoS Genetics, 8(4): e1002660, 2012.

     
     

    Y. Zhu, P. Du, and L. Nakhleh, “Gene duplicability-connectivity-complexity across organisms and a neutral evolutionary explanation.” PLoS One, 7(9): e44491, 2012.

     
     

    Y. Zhu, P. Du, and L. Nakhleh, “Gene duplicability-connectivity-complexity across organisms and a neutral evolutionary explanation.” PLoS One, 7(9): e44491, 2012.

     
     

    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 (2006) Submitted

     
     

    Derek Ruths and Luay Nakhleh "Recombination and Phylogeny: Effects and Detection." International Journal of Bioinformatics Research and Applications, 1(2) (2005) : 202-212.

     
     

    I. Kanj, L. Nakhleh, and G. Xia "Reconstructing Evolution of Natural Languages: Complexity and Parameterized Algorithms."  (2005) Submitted

     
     

    L. Nakhleh and L.S. Wang "Phylogenetic Networks: Properties and Relationship to Trees and Clusters." LNCS Transactions on Computational Systems Biology, LNBI 3680 (2005) : 82-99.

     
     

    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) (2005) : 382-420.

     
     

    Luay Nakhleh, Tandy Warnow, C. Randal Linder, and Katherine St. John "Reconstructing Reticulate Evolution in Species -- Theory and Practice." Journal of Computational Biology, 12(6-7) (2005) : 796-811.

     
     

    Luay Nakhleh, Tandy Warnow, Don Ringe, and Steven N. Evans "A Comparison of Phylogenetic Reconstruction Methods on an IE Dataset." Transactions of the Philological Society, 3(2) (2005) : 171-192.

     
     

    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." IEEE/ACM Transactions on Computational Biology and Bioinformatics, 1(1) (2004) : 13-23.

     
     

    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) (2004)

     
     

    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 (July 2004)

     
     

    E. Erdam, 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) (2003) : 160-176.

     
     

    L. Nakhleh, D. Miranker, F. Barbancon, W.H. Piel, and M.J. Donoghue "Requirements of Phylogenitic Databases." Proceedings of the Third IEEE Symposium on Bioinformatics and Bioengineering (BIBE 2003) (2003) : 141-148.

     
     

    L. Nakhleh, J. sun, T. Warnow, C.R. Linder, B.M.E. Moret, and A. Tholse "Towards the Development of Computational Tools for Evaluating Phylogenetic Network Reconstruction Methods." Proceedings of the Eighth Pacific Symposium on Biocomputing (PSB 2003), 8 (2003) : 315-326.

     
     

    L. Nakhleh, B.M.E. Moret, Ul 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 2002), 7 (2002) : 211-222.

     
     

    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 2002) (2002) : 287-299.

     
     

    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 2001) (2001) : 214-226.

     
     

    L. Naklheh, U. Roshan, K. St. John, J. Sun, and T. Warnow "Designing Fast Converging Phylogenetic Methods." proceedings of the Ningh International Conference on Intelligent systems for Molecular Biology (ISMB 2001) (2001) : 190-198.

     
     Articles
     

    Y.Yu, R.M. Barnett, and L. Nakhleh ""Parsimonious inference of hybridization in the presence of incomplete lineage sorting." Systematic Biology. To appear, 2013.." 

     
     

    W. Zhou and L. Nakhleh, “Quantifying and assessing the effect of chemical symmetry in metabolic pathways.” Journal of Chemical Information and Modeling, 52(10): 2684-96, 2012.

     
     

    W. Zhou and L. Nakhleh, "Properties of matabolic graphs: Biological organization or representation artifacts?" BMC Bioinformatics, 12: 132, 2011.

     
     

    W. Zhou and L. Nakhleh, "The strength of chemical linkage as a criterion for pruning metabolic graphs." Bioinformatics, 27(14): 1957-1963, 2011.

     
     

    Y. Lu, M. Muller, D. Smith, K. Kuomurov, S. Iadevaia, D. Ruths, J.T. Tseng, S. Yu, Q. Yu, L. Nakhleh, G. Balazsi, J. Donnelly, M. Schurdak, S. Morgan-Lappe, S. Fesik, P.T. Ram, and G.B. Mills, "Kinome siRNA-phosphoproteomic screen identifies networks regulating AKT singaling." Oncogene, 30(45): 4567-4577, 2011.

     
     

    Y. Yu, C. Than, J.H. Degnan, and L. Nakhleh, "Coalescent histories on phylogenetic networks and detection of hybridization despite lineage sorting." Systematic Biology, 60(2): 138-149, 2011.

     
     

    Y. Yu, T. Warnow, and L. Nakhleh, "Algorithms for MDC-based multi-locus phlogeny inference: Beyond rooted binary gene trees on single allels." Journal of Computational Biology, 18(11): 1543-1559, 2011.

     
     

    Y. Yun,T.Warnow, and L.Nakhleh "Algorithms for MDC-based multi-locus phylogeny inference.." In Revision

     
     

    J. Kilpatrick and l. Nakhleh "Classifying and evaluating methods for detecting multi-locus genotypephenotype association.." In Press

     
     

    W. Zhou and L. Nakhleh "Revisting topological properties of metabolic networks under hypergraph represenation." 

     
     

    Y. Yun and L. Nakhleh "The performance of methods for inferring species despite lineage sorting ." In Revision

     
     

    C. Than, D. Ruths and L. Nakhleh "PhyloNet: A Software Package for Analyzing and Reconstructing Reticulate Evolutionary Relationships." BMC Bioformatics, 9 (2008)

     
     

    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)

     
     

    "Rapidly Exploring Structural and Dynamic Properties of Signaling Networks Using PathwayOracle." BMC Systems Biology, 2 (2008)

     
     

    "The Compatibility of Binary Characters on Phylogenetic Networks: Complexity and Parameterized Algorithms." Algorithmica, 51 (2008)

     
     

    "The Signaling Petri Net-based Simulator: A Non-parametric Strategy for Characterizinf the Dynamics of Cell-specific Signaling Networks.." PLoS Computational Biology, 4 (2) (2008) Submitted

     
     

    C. Than, D. Ruths, H. Innan and L. Nakhleh "Confounding Factors in HGT Detection: Statistical Error, Coalescent Effects, and Multiple Solutions.." Journal of Computational Biology, 14(4) (2007) : 517-535.

     
     

    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) (2007) : 324-337.

     
     

    I. Kanj, L. Nakhleh and G. Xia "The Compatibility of Binary Characters on Phylogenetic Networks:Complexity and Parameterized Algorithms." Algorithmica (2008)

     
     Book chapters
     

    C. Than 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 (editors). Wiley-VCH, 79-98, 2010." 

     
     

    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, 125-158, 2010." 

     
     

    L. Nakhleh, D. Ruths, and H. Innan ""Gene Trees, Species Trees, and Species Networks." In Metaanalysis and Combining Informations in Genetics." , 275 (2009) : 293.In Press

     
     

    L. Nakleh, D. Ruths and H. Innan "Gene Trees, Species Trees and Species Networks." Meta-analysis and Combining Information in Genetics (2007) In Press

     
     

    L. Nakhleh, D. Ruths, and H. Innan "Gene trees, species trees, and species networks." Meta-analysis and combining information in genetics (2005) In Press

     
     Refereed conference papers
     

    G. Saxer, M.D. Krepps, E.D. Merkley, C.K. Ansong, B.L.D. Kaiser, M-T Valovska, N. Ristic, T. Yeh, V. Prakash, O.P. Leiser, L. Nakhleh, H.S. Gibbons, H.W. Kreuzer, and Y. Shamoo ""Adaptation to complex environments consistently leads to metabolic selection via global regulators" PLoS Genetics, 10 (12): e1004872, 2014." 

     
     

    K. Liu, J. Dai, K. Truong, Y. Song, M.H. Kohn, and L. Nakhleh ""An HMM-based comparative genomic framework for detecting introgression in eukaryotes." PLoS Computational Biology, 10(6): e1003649, 2014." 

     
     

    N. Berestovsky, L. Nakhleh, R. Azencott, and P.T. Ram ""Mapping motif tunability and robustness in the design of synthetic signaling networks." PLoS One, 9(3):e91743, 2014." 

     
     

    X. Fan, W. Zhou, Z. Chong, L. Nakhleh, and K. Chen ""Towards accurate characterization of clonal heterogeneity based on structural variation." BMC Bioinformatics, 15: 299, 2014." 

     
     

    Y. Yu, J. Dong, K. Liu and L. Nakhleh. ""Maximum likelihood inference of reticulate evolutionary histories." Proceedings of the National Academy of Sciences, 111 (46): 16448-16453, 2014." 

     
     

    E. Bapteste, L. van Iersel, A. Janke, S. Kelchner, S. Kelk, J.O. McInerney, D.A. Morrison, L. Nakhleh, M. Steel, L. Stougie, J. Whitfield, “Networks: Expanding evolutionary thinking.” Trends in Genetics, 29(8): 439-441, 2013.

     
     

    F. Barbancon, S.N. Evans, L. Nakhleh, D. Ringe, and T. Warnow, “An experimental study comparing linguistic phylogenetic reconstruction methods.” Diachronica, 30(2): 143-170, 2013.

     
     

    L. Nakhleh, “Computational approaches to species phylogeny inference and gene tree reconciliation.”
    Trends in Ecology and Evolution, 28(12): 719-728, 2013

     
     

    N. Berestovskyz and L. Nakhleh, “An evaluation of methods for inferring Boolean networks from timeseries data.” PLoS One, 8(6): e66031, 2013.

     
     

    T. Ruthsz and L. Nakhleh, “Quantifying neutral trends in the E. coli regulatory network.” Proceedings of the National Academy of Sciences, 110(19): 7754-7759, 2013.

     
     

    T. Ruthsz and L. Nakhleh, “Boosting forward-time population genetic simulators through genotype compression.” BMC Bioinformatics, 14: 192, 2013.

     
     

    Y. Yuz, N. Risticz, and L. Nakhleh, “Fast algorithms and heuristics for phylogenomics under ILS and hybridization.” BMC Bioinformatics, 14(Suppl 16): S6, 2013.

     
     

    Y. Zhuz, Z. Lin, and L. Nakhleh, “Evolution after whole-genome duplication: A network perspective.” G3: Genes j Genomes j Genetics, 3(11): 2049-2057, 2013.

     
     

    H.J. Park and L. Nakhleh, “MURPAR: A fast heuristic for inferring parsimonious phylogenetic net- works from multiple gene trees.” Proceedings of the 8th International Symposium on Bioinformatics Research and Applications. Lecture Notes in Bioinformatics (LNBI #7292), pp. 213-224, 2012.

     
     

    N. Berestovsky, R. Fukui and L. Nakhleh, “On the performance of particle swarm optimization for parameterizing kinetic models of cellular networks.” Proceedings of the IEEE Symposium on Compu- tational Intelligence in Bioinformatics and Computational Biology, 184-191, 2012.

     
     

    Y. Zhu and L. Nakhleh, “Reconstructing the evolution of molecular interaction networks under the DMC and link dynamics models.” Proceedings of the Workshop on Algorithms in Bioinformatics (WABI), LNBI 7534, 57-68, 2012.

     
     

    Y. Yun, T. Warnow, and L. Nakhleh, "Algorithms for MDC-based multi-locus phylogeny inference." Proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology (RECOMB), LNBI 6577, 114-123, 2011.

     
     

    C. Than, 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 (2008) : 113-127.

     
     

    C. Than, R. Sugino, H. Innan, and L. Nakhleh "Efficient Inference of Bacterial Strain Trees From Genome-scale Multi-locus Data." Bioinformatics, 24 (2008) : i123.

     
     

    "SPR-based Tree Reconciliation: Non-binary Trees and Multiple Solutions." Proceeding of the Sixth Asia Pacific Bioinformatics Conference (APBC 08) (2008) : 251-260.

     
     

    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

     
     

    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." Proceedings of the First IEEE Workshop on High Performance Computing in Medicine and Biology, 2 (2005) : 346-350.

     
     

    D. Ruths, L. Nakhleh, M.S. Iyengar, S.A.G. Reddy, and P.T. Ram "Graph-theoretic Hypothesis Generation in Biological Signaling Networks."  (2005) Submitted

     
     

    G. Jin, L. Nakhleh, S. Snir, and T. Tuller "Parsimony of Phylogenetic Networks: Hardness Results and Efficient Algorithms and Heuristics."  (2005) Submitted

     
     

    L. Nakhleh, G. Jin, F. Zhao, J. Mellor-Crummey "Reconstructing Phylogenetic Networks Using Maximum Parsimony." The IEEE Computational Systems Bioinformatics Conference (CSB 05) (2005) : 93-102.

     
     

    Luay Nakhleh and Li-San Wang "Phylogenetic Networks, Trees, and Clusters." The International Workshop on Bioinformatics Research and Applications, LNCS 3515 (2005) : 919-926.

     
     

    Luay Nakhleh, Derek Ruths, and Li-San Wang "RIATA-HGT: A Fast and Accurate Heuristic for Reconstructing Horizontal Gene Transfer." International Computing and Combinatorics Conference (COCOON 05), LNCS 3595 (2005) : 84-93.

     
     

    Z. Du, A. Stamatakis, F. Lin, U. Roshan, and L. Nakhleh "Parallel Divide-and-conquer Phylogeny Reconstruction by Maximum Likelihood." Proceedings of the International Conference on High Performance Computing and Communications, 2 (2005) : 346-350.

     
     Conference papers
     

    N. Berestovskyz, W. Zhouz, D. Nagrath, and L. Nakhleh, “Modeling integrated cellular machinery
    using hybrid Petri-Boolean networks.” PLoS Computational Biology, 9(11): e1003306, 2013.

     
     

    D. Ruths and L. Nakhleh, " “Deriving predictive models of signaling network dynamics from qualitative experimental data.” Proceedings of the Ninth Annual International Conference on Computational Systems Biology, 136-145, 2010." Submitted

     
     

    H.J. Park,G. Jin, and L. Nakhleh " “Algorithmic strategies for estimating the amount of reticulation from a collection of gene trees.” Proceedings of the Ninth Annual International Conference on Computational Systems Biology, 114-123, 2010." 

     
     

    D. Ruths, J.T. Tseng, L. Nakhleh and P.T. Ram "De novo Signaling Pathway Predictions based on Protein-Protein Interaction, Targeted Therapy and Protein Micoarray Analysis.."  (2007) : 109-119.

     
     

    G. Jin, L. Nakhleh, S. Snir and T. Tuller "A New Linear-time Heuristic Algorithm for Computing the Parsimony Score of Phylogenetic Networks: Theoretical Bonds and Empirical Performance.."  (ISBRA '07) : 61-72.

     
     

    I. Kanj, L. Nakhleh, C. Than and G. Xia "Seeing the Trees and Their Branches in the Network is Hard.."  (2007) : 82-93.

     
     Other
     

    H.J. Park, G. Jin, and L. Nakhleh " “Bootstrap-based support of HGT inferred by maximum parsimony.” BMC Evolutionary Biology, 10: 131, 2010." 

     
     

    L. Nakhleh " “A Metric on the Space of Reduced Phylogenetic Networks”. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 7(2): 218-222, 2010." 

     
     

    Y. Yu, C. Than, J.H. Degnan and L. Nakhleh, " “Coalescent histories on phylogenetic networks and detection of hybridization despite lineage sorting.” Systematic Biology. To appear, 2010." In Press

     
     

    L. Nakhleh "Phylogenetic Networks."  (2004)

     
     

    L. Nakhleh, A. Clement, T. Warnow, C.R. Linder, and B.M.E. Moret "Quality Measures for Phylogenetic Networks." Technical Report (2004)

     
     

    T. Warnow, S.N. Evans, D. Ringe, and L. Nakhleh "Stochastic Models of Language Evolution and an Application to the Indo-European Family of Languages."  (2004)

     
    Presentations
     Conference Committee Member
     

    "PC member, The Ninth European Conference on Computational Biology (ECCB 2010)."

     
     Invited Talks
     

    “Complexities in the Inference of Phylogenetic Networks.” The “Utilizing Genealogical Phylogenetic
    Networks in Evolutionary Biology: Touching the Data” Workshop, The Lorentz Center, Leiden University, The Netherlands, July 2014.

     
     

    “Genomic Underpinnings for Network Patterns and Evolution.” The Highlights Track at ISMB 2014,
    Boston, July 2014.

     
     

    “Inference of Reticulate Evolutionary Histories from Multi-locus and Whole-genome Data.” The Frontiers in Phylogenetics Symposium, National Museum of Natural History, Smithsonian Institution,
    Washington D.C., September 2014.

     
     

    “Inference of Reticulate Evolutionary Histories.” The Phylogenomics Symposium, Evolution 2014,
    Raleigh, North Carolina, June 2014.

     
     

    “New Methods for Inferring Reticulate Evolutionary Relationships.” Department of Botany and Plant
    Pathology, Oregon State University, November 2014.

     
     

    “On the Interplay Between Genome and Interactome Evolution.” The 2014 PhyloLab Conference on
    Computational Biology, Department of Computer Science, University of Texas, Austin, May 2014

     
     

    “Elucidating Properties of Molecular Interaction Networks via Evolutionary Genomics.” Mathematical
    and Computational Evolutionary Biology Conference, Hameau de l’Etoile, France, May 2013.

     
     

    “Hybridization Detection in the Presence of Incomplete Lineage Sorting.” Botany 2013, New Orleans,
    July 2013.

     
     

    “PhyloNet: A Software Package for Reconstructing Trees and Networks.” iEvoBio 2013, Snowbird,
    Utah, June 2013.

     
     

    “Phylogeny Inference in the Presence of Hybridization and Incomplete Lineage Sorting.” Symposium
    on New Methods for Phylogenomics and Metagenomics, The University of Texas at Austin, Feb 2013.

     
     

    “From Gene Trees to Species Trees.” The Millican Colloquium, The Department of Mathematics, TheUniversity of North Texas, Denton, Nov 2012.

     
     

    “Quantifying Homologous Recombination in Staphylococcus aureus Using Whole-genome Data.” The Center for Computational and Integrative Biomedical Research (CIBR) Seminar Series, Baylor College of Medicine, Houston, Nov 2012.

     
     

    “The Probability of Gene Trees in the Presence of Hybridization.” The Annual Meeting of the Society for Molecular Biology and Evolution, Dublin, Ireland, June 2012.

     
     

    Modeling With Fewer Parameters: Petri Nets and Boolean Networks.” The 28th Southern BiomedicalEngineering Conference, MD Anderson Cancer Center, Houston, May 2012.

     
     

    Phylogenetic Networks and the Trees Within: A Probabilistic Framework.” The Future of Phyloge- netic Networks Workshop, The Lorentz Center, Leiden University, The Netherlands, Oct 2012.

     
     

    "Disentangling Vertical and Horizontal Evolution in Phylogenomic Studies," The Human Genetics Center Seminar, The University of Texas at Houston, Oct 2011.

     
     

    "Disentangling Vertical and Horizontal Evolution in Phylogenomic Studies," The Workshop on Evolutionary Genomics, UCLA Institute for Pure and Applied Mathematics, Nov. 2011.

     
     

    "Inferring Species Phlogenies from Multi-Iocus Data: New Algorithmic Techniques," Department of Biology, University of British Columbia, Vancouver, Canada, Mar 2011.

     
     

    "Reconciling Gene Trees in the Presence of Incomplete Lineage Sorting and Hybridization," The Isaac Newton Institute for Mathematical Sciences (the Phlogenetics Workshop), The University of Cambridge, UK, Jun 2011.

     
     

    ""Accurate Inference of Phylogentic Relationship from Multi-locus Data."." Penn Bioinformatics Forum, University of Pennsylvania, Philadelphia, PA . (Jan 2010)

     
     

    "“Inference of ParsimoniousMulti-locus Phylogenies.” Symposiumon Integrative Phylogenomics: From Genes to Organismal History.

    ." The AnnualMeeting of the Society forMolecular Biology and Evolution, Lyon, France. (Jul 2010)

     
     

    "Accurate Inference of Phylogenetic Relationships from Multi-locus Data.." Penn Bioinformatics Forum University of Pennsylvania, Philadelphia, PA. (Jan 2010)

     
     

    "Accurate Inference of Phylogenetic Relationships from Multi-locus Data.." Department of Computer Science, McGill University, Montreal, Canada. (Mar 2010)

     
     

    "Accurate Inference of Phylogenetic Relationships from Multi-locus Data.  ." Bertinoro Computational Biology meeting., Bertinoro, Italy.. (May 2010)

     
     

    "Algorithmic strategies for estimating the amount of reticulation from a collection of gene trees.." CSB Conference, Stanford, . (Aug 2010)

     
     

    "Evolution and Networks.." Department of Ecology and Evolutionary Biology, Rice University, . (Feb 2010)

     
     

    "Inference of Phylogenetic Relationships from Multi-locus Data.." Department of Computer Science and Engineering, Texas A&M University. (Oct 2010)

     
     

    "Simulating Cellular Networks Using Petri Nets.." The Institutional Grand Grounds Series, MD Anderson Cancer Center. (Sep 2010)

     
     

    "Species Tree Inference by Minimizing Deep Coalescences.

    ." The ISMB Highlights Track, Boston, MA,. (Jul 2010)

     
     

    ""Accurate Inference of Phylogentic Relationship from Multi-locus Data."." Penn Bioinformatics Forum, University of Pennsylvania, Philadelphia, PA . (Jan 2010)

     
     

    ""Accurate Inference of Phylogentic Relationship from Multi-locus Data."." University of Washington Computer science Department, Seattle, WA. (Nov 2009)

     
     

    ""Computational Techniques for Inferring Phylogenetic Relationships Using Multiple Loci."." Department of Computer Science, University of texas at Austin. (Oct 2009)

     
     

    ""Computational Techniques for Inferring Phylogenetic Relationships Using Multiple Loci."." Uiversity of California Berkeley Mathematical and Computational Biology Seminar, Berkeley, CA. (Vov 2009)

     
     

    ""Computational Techniques for Inferring Phylogenetic Relationships Using Multiple Loci."." University of California Los Angeles Bioinformatics Program, Los Angeles, CA. (Oct 2009)

     
     

    ""Computational Techniques for Inferring Phylogenetic Relationships Using Multiple Loci."." University of Maryland Center for Bioinformatics and Computational Biology, College Park, MD . (Oct 2009)

     
     

    ""Interdisciplinary Research." ." The Graduate Student Advising Day, Dept. of CS, , The University of Texas at Austin. (Feb 2009)

     
     

    "Computational Techniques for Inferring Phylogenetic Relationship Using Multiple Loci."." Univesity of California San Diego, Los Angeles, CA. (Oct 2009)

     
     

    ""Efficient Search for the Species Three in the Compatibility Graph of Gene Threes."." The Estimating Species Tree Workshop, The University of Michigan, Ann Arbor. (Jan 2009)

     
     

    ""Exploiting Biological Networks for Identifying Drug Targets and Understanding Genetic Causes of Disease."." Pathways to Personalized Medicine: Rate-limiting Factors in Delivering the Promise, Rice Univesity and the Texas Medical Center. (June 2008)

     
     

    ""Networks-guided Search for Biological Hypotheses."." The Keck Annual Research Conference, The Gulf Coast Consortia. (October 2008)

     
     

    ""Novel algorithmic techniques for gene tree reconciliation in bacterial genomes.." The Evolution 2008 Conference, The University of Minnesota. (June 2008)

     
     

    ""Phylogenetic Networks: Reconstruction and Evaluation."." The ITES Networks Cluster Seminar, The University of Houston. (April 2008)

     
     

    "Network-guided Search for Biological Hypotheses in Large Data Sets.." The High Throughput Screening Large Scale Data Sets Workshop, The Gulf Coast Consortium for Bioformatics and the Gulf Coast Consortium for Chemical Genomics. (October 2008)

     
     

    "Petri Net Modeling of Signal Transduction Networks: Qualitative Characterizations Based on the Networks Connectivity."." The Graduate Program in Structural and Computational Aspect of Biology and Molecular Biophysics, Baylor College of Medicine. (May 2008)

     
     

    "Efficient Reconstruction of Species Trees from Genome-scale Multi-locus Data Under the Coalescent." Department of Computational and Applied Mathematics, RIce University, Houston. (November 2007)

     
     

    "From Gene Trees to Species Phylogenies." Microsoft Research, (December 2007)

     
     

    "Graph-Theoretic Techniques for Analyzing Signaling Networks." The 24th Annual Houston Conference on Biomedical Engineering Research, Houston, Tx. (February 2007)

     
     

    "Graph-theoretic Modeling and Reasoning about Signaling Networks." Oklahoma Medical Research Foundation, (August 2007)

     
     

    "Horizontal Gene Transfer Detection: Issues and Algorithums." The 5th Bertinoro Computational Biology Meeting, Bertinoro, Italy. (May 2007)

     
     

    "Petri Net Modeling of Signal Transduction Networks: Predicting Dynamics Without Prior Knowledge of Kinetics." Department of Biochemistry and Cell Biology, Rice University, Houston, TX. (November 2007)

     
     

    Speaker.  "Alien Genes, Complex Diseases, and Targeted Drugs." Rice Alliance, Rice University, (October 2005)

     
     

    Speaker.  "Alien Genes, Complex Diseases, and Targeted Drugs." CITI, Rice University, (December 2005)

     
     

    Speaker.  "Alien Genes, Complex Diseases, and Targeted Drugs: Computational Approaches." Department of Computer Science, UT Austin, (December 2005)

     
     

    Invited Speaker.  "Computational phylogenetics in historical linguistics." Chinese-American Frontiers of Sciences (CAFOS), China. (November 2005)

     
     

    Speaker.  "Phylogenetic Networks: Reconstructing methods and Quality measures." Missouri Botanical Gardens Symposium on Complex Evolutionary Relationships, St. Louis, Missouri. (October 2005)

     
     

    Speaker.  "The Gene Tree / Species Network Problem." Ecology and Evolutionary Biology, Rice University, (November 2005)

     
     

    "Reconstructing Phylogenies: Accuracy of Methods and Appropriateness of Models." School of Informatics, Indiana University, Bloomington, Indiana. (March 2004)

     
     

    "Reconstructing Phylogenies: Accuracy of Methods and Appropriateness of Models." Department of Computer Science, The University of Texas at Dallas, Richland, Texas. (February 2004)

     
     

    "Reconstructing Phylogenies: Accuracy of Methods and Appropriateness of Models." Department of Computer Science, Tufts University, Medford, Massachusetts. (March 2004)

     
     

    "Reconstructing Phylogenies: Accuracy of Methods and Appropriateness of Models." Department of Computer Science, The University of Toronto, Toronto, Canada. (April 2004)

     
     

    "Reconstructing Phylogenies: Accuracy of Methods and Appropriateness of Models." Department of Computer Science, University of Maryland, College Park, Maryland. (March 2004)

     
     

    "Reconstructing Phylogenies: Accuracy of Methods and Appropriateness of Models." Department of Computer Science, George Washington University, Washington, D.c.. (February 2004)

     
     

    "Reconstructing Phylogenies: Accuracy of Methods and Appropriateness of Models." Department of Computer Science, Rice University, Houston, Texas. (April 2004)

     
     Other
     

    “Phylogenomics and Population Genomics: Models, Algorithms, and Analytical Tools.” Tutorial given
    at the Pacific Symposium on Biocomputing, The Big Island of Hawaii, Jan 2013

     
     

    Speaker.  "PRec-I-DCM3: A Parallel Framework for Fast and Accurate Large Scale Phylogeny Reconstruction." The First IEEE Workshop on High Performance Computing in Medicine and Biology (HiPCoMP 2005), Fukuoka, Japan. (July 2005) With C. Coarfa, Y. Dotsenko, J. Mellor-Crummey, and U. Roshan

     
     

    Speaker.  "Phylogenetic Networks, Trees, and Clusters." International Workshop on Bioinformatics Research and Applications, Atlanta, GA. (May 2005) With Li-San Wang

     
     

    Speaker.  "Reconstructing Phylogenetic Networks Using Maximum Parsimony." The 2005 IEEE Computational Systems Bioinformatics Conference, Stanford, CA. (August 2005) With G. Jin, F. Zhao, and J. Mellor-Crummey

     
     

    "Network (Reticulate) Evolution: Biology, Models, and Algorithms." PSB '04, The Big Island, Hawaii. (January 2004) With C.R. Linder, B.M.E. Moret, and T. Warnow

     
     

    "Reconstructing Reticulate Evolution in Species - Theory and Practice." RECOMB '04, San Diego, CA. (March 2004) With T. Warnow, L. Nakhleh, C.R. Linder

     
     Posters
     

    "Network (Reticulate) Evolution: Biology, Models, and Algorithms." The Ninth Pacific Symposium on Biocomputing (PSB 2004), (2004) With C.R. Linder, B.M.E. Moret, L. Nakhleh, and T. Warner

     
     

    "Applications of Clustering and Visualization to Phylogeny." European Conference on Computational Biology (ECCB 2003), (2003) With R. Kalra, K. St. John, L. Nakhleh, and T. Warnow

     
     

    "Reconstructing Reticulate Evolution in Species." The IMA Workshop on Comparative Genomics, Minneapolis, MN. (October 2003) With L. Nakhleh, T. Warnow,, and C.R. Linder

     
     Seminar Speaker
     

    "" From Gene Trees to Species Phylogenies: Computational Techniques."." The Integrative Biology Seminar Series/School of Biological Science, The University of Texas. (Feb 2009)

     
     

    ""Accurate Inference of Phylogentic Relationship from Multi-locus Data."." Stanford University Computational Biology Seminar, Stanford, CA. (Nov 2009)

     
     

    ""Computational Techniques for inferring Phylogenetic Relationships Using Multiple Loci."." University of Southern California Computational Biology Seminar, Los Angeles, CA. (Oct 2009)

     
     Workshops
     

    ""Efficient Search for the Species Tree in the Compatibility Graph of Gene Tree."." The Estimating Species Trees Workshop, The University of Michigan, Ann Arbor. (Jan 2009)

     
     

    ""From Gene Trees to Phyogenetic Networks: Computational Approaches."." Symposium on Biological Networks from Genes to Populations, The 17th Annual Meeting of the Society for Molocular Biology and Evolution (SMBE 2009), Iowa City IA. (Jun 2009)

     
     

    "Phylogenetic Networks: Generation, Reconstructibility and Comparison." DIMACS Workshop on Reticulated Evolution, Rutgers University, New Jersey. (September 2004) With C.R. Linder, B.M.E. Moret, T. Warnow, A. Tholse, A. Padolina, J. Sun, and R. Timme

     
    Supervised Theses & Dissertations
     Martin David Schwarz, Master of Science Local Conformational Search of Proteins Using the Expansive Spaces Search. (2005) (Thesis Committee Member)

     Wendee Holtcamp, Master of Science Species Boundaries as a Key to Understanding Hybridization. (2005) (Thesis Committee Member)

     Derek Ruths, Master of Science Detection and Reconstruction of Horizontal Gene Transfer. (2005) (Thesis Director)

     Amarda Shehu, Master of Science Sampling Biomecular Conformations with Spatial and Energetic Constraints. (2005) (Thesis Committee Member)

     Deian Tabakov, Master of Science Experimental Evaluation of Explicit and Symbolic Automata-Theoretic Algorithms. (2005) (Thesis Committee Member)

     Derek A. Ruths, Master of Science Applications of Phylogenetic Incongruence to Detecting and Reconstructing Interspecific Recombination and Horizontal Gene Transfer. (2005) (Thesis Director)

     Allison Heath, Master of Science Towards Multiscale Protein Simulations: Moving from Coarse-Grain to All-Atom Models. (2006) (Thesis Committee Member)

     Master of Science Sara Kalla. (2006) (Thesis Committee Member)

     Samah Abu-Mahmeed, Master of Science In-Place Updating of Variables in LabVIEW. (2007) (Thesis Committee Member)

     Hernan Stamati, Master of Science Analysis of Molecular Motion using Non-Linear Dimensionality Reduction. (2007) (Thesis Committee Member)

     Cuong V. Than, Master of Science Reconstruction of Phylogenetic Networks and Their Relationships with Trees and Branches. (2008) (Thesis Director)

     Konstantinos Tsianos, Master of Science Replanning: A Powerful Planning Strategy for Systems with Differential Constraints. (2008) (Thesis Committee Member)

     Amarda Shehu, Doctor of Philosophy Molecules in Motion:Computing Structural Flexibility. (2008) (Thesis Committee Member)

     Seth Fogarty, Master of Science Buchi Containment and Size-Change Termination. (2008) (Thesis Committee Member)

     Derek Ruths, Doctor of Philosophy Deriving Executable Models of Biochemical Network Dynamics from Qualitative Data. (2009) (Thesis Director)

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

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

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

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

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

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

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

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

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

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

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

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

     Kuldeep Meel, Masters Sampling Techniques for Boolean Satisfiability. (2014) (Thesis Committee Member)

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

     Zhuhua Cai, PhD Very Large Scale Bayesian Machine Learning. (2014) (Thesis Committee Member)

     Yun Zhu, PhD Computational Analysis of Gene Duplication and Network Evolution. (2014) (Thesis Director)

     Yun Yu, Doctoral Models and Methods for Evolutionary Histories Involving Hybridization and Incomplete Lineage Sorting. (2014) (Thesis Director)

     Zekai Gao, Masters Distributed Algorithms for Computing Very Large Thresholded Covariance Matrices. (2014) (Thesis Committee Member)

     Anna Drummond, PhD Statistical Machine Lerning for Text Mining with Markov Chain Monte Carlo Inference. (2014) (Thesis Committee Member)

     Xian Fan, MS Calculating Variant Allele Fraction of Structural Variation in Next Generation Sequencing by Maximum Likelihood. (2014) (Thesis Director)

     Ye Fang, MS Computer Aided Mechanism. (2014) (Thesis Committee Member)

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

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

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

     Christopher A. Miller. (Thesis Committee Member)

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

     Alan R. Harris. (Thesis Committee Member)

     Doctor of Philosophy Shuwei Li. (Thesis Committee Member)

     Niv Sabath. (Thesis Committee Member)

     Ching-Hua Shih. (Thesis Committee Member)

    Awards, Prizes, & Fellowships
     The (T+R)2 Excellence inTeaching and Research Award., School of Engineering, Rice University (04/2015)

     Best Paper Award. RECOMB Comparative Genomics, Lyon, France., (10/2013)

     Guggenheim Fellowship, The John Simon Guggenheim Memorial Foundation (April 2012)

      Alfred P. Sloan Research Fellowship, (09/2012)

     “Network-guided Integration of Omics Data for Predicting Therapeutic Combinations.” Principal Investigator. $100,000. , The Gulf Coast Center for Computational Cancer Research (GC4R), Rice University. (01/2010)

     The Phi Beta Kappa Rice Teaching Price, Rice University (04/2009)

     Faculty Early Career Development (Career) Award, The National Science Foundation, USA (01/2009)

     Sloan Fellow,

     Early Career Award, The Department of Energy, USA (08/2006)

     Outstanding Dissertation Award, The University of Texas at Austin (May 2005)

     Computer Sciences Bert Kay Outstanding Dissertation Award, Department of Computer Science, UT Austin (April 2005)

     Best Paper Award, The First IEEE Workshop on High Performance Computing in Medicine and Biology (July 2005)

     Travel Fellowship, The University of Texas at Austin (03/2004)

     James C. Brown Graduate Fellowship, The University of Texas at Austin (02/2004)

     Graduate Award for Research, The George H. Mitchell/University Co-op, The University of Texas at Austin (04/2003)

     Invited Speaker, College of Natural Sciences, The University of Texas at Austin (05/2003)

     Travel Fellowship, Department of Computer Science, The University of Texas at Austin (01/2002)

     Travel Fellowship, National Library of medicine (01/2002)

     Texas Excellence Teaching Award, College of Natural Sciences, The University of Texas at Austin (2/2001)

     outstanding Teaching Assistant Award, Dept. of Computer Science, The University of Texas at Austin (12/2000)