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Publications

Published or Accepted Peer-Reviewed Papers

  1. Steve G. Hershman, Qijun Chen, Julia Y. Lee, Marina L. Kozak, Peng Yue, Li-San Wang, and F. Brad Johnson.
    Genomic distribution and functional analyses of potential G-quadruplex-forming sequences in Saccharomyces cerevisiae.
    Nucleic Acids Research, in press.
  2. Larry Singh, Li-San Wang, and Sridhar Hannenhalli.
    TREMOR -- a tool for retrieving transcriptional modules by incorporating motif covariance."
    Nucleic Acids Research, in press.
  3. Lauren M.F. Merlo, Li-San Wang, John W. Pepper, Peter S. Rabinovitch and Carlo C. Maley.
    Polyploidy, Aneuploidy and the Evolution of Cancer.
    In Poon RYC, ed., Polyploidization and Cancer, Austin/New York: Landes Bioscience, Inc. and Springer Science+Business Media, 2008, in press.
  4. Li-San Wang, Shane T. Jensen, and Sridhar Hannenhalli.
    "An Interaction-dependent model for transcription factor binding."
    LNCS: Second Annual RECOMB Satellite Workshop on Regulatory Genomics, Volume 4023, pp. 225-234, 2006.
  5. Li-San Wang, Doris Wagner, Chang Seob Kwon, Yanhui Su, and Junhyong Kim.
    "Transcriptional Target Prediction Using Qualitative Reasoning."
    Proceedings of the 28th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC'06), pp. 3138-3141, 2006.
  6. Logan Everett, Li-San Wang, and Sridhar Hannenhalli.
    "Dense subgraph computation via stochastic search: application to detect transcriptional modules."
    Bioinformatics 2006 22(14): Proceedings of The Twelfth International Conference on Intelligent Systems and Molecular Biology (ISMB'06), pp. e117-e123. (PDF) (PubMed)
  7. Liying Cui, Jim Leebens-Mack, Li-San Wang, Jijun Tang, Linda Rymarquis, David Stern, and Claude W. dePamphilis.
    "Adaptive Evolution of Chloroplast Genome Structure Inferred Using a Parametric Bootstrap Approach."
    BMC Evolutionary Biology, 6:13, 2006. (PubMed)
  8. Li-San Wang and Tandy Warnow.
    "Reconstructing Chromosomal Evolution."
    SIAM Journal on Computing, 36: 99-131, 2006.
  9. Li-San Wang, Tandy Warnow, Bernard M.E. Moret, Robert K. Jansen, and Linda A. Raubeson.
    "Distance-based Genome Rearrangement Phylogeny."
    Journal of Molecular Evolution, 63(4):473-83, 2006. (PubMed)
  10. Stanislav Angelov, Boulos Harb, Sampath Kannan, and Li-San Wang.
    "Weighted Isotonic Regression under L1 Norm."
    Proceedings of the Seventeenth Annual ACM-SIAM Symposium on Discrete Algorithms (SODA'06), pp. 783-791, 2006 (PDF)
  11. Jijun Tang and Li-San Wang.
    "Improving Genome Rearrangement Phylogeny Using Sequence-Style Parsimony."
    Proceedings of the IEEE Fifth Symposium on Bioinformatics and Bioengineering (BIBE'05), pages 137--144. (PDF)
  12. Fan Ge, Li-San Wang, and Junhyong Kim.
    "The Cobweb of Life Revealed by Genome-Scale Estimates of Horizontal Gene Transfer.
    Public Library of Science (PLoS) Biology, 3(10):e316, 2005. (PubMed)
  13. Luay Nakhleh and Li-San Wang.
    "Phylogenetic Networks: Properties and Relationship to Trees and Clusters."
    LNCS Transactions on Computational Systems Biology 3680, special issue for IWBRA'05 (special invitation), pp. 82-99, 2005 (PDF)
  14. Luay Nakhleh, Derek Ruths, and Li-San Wang.
    "RIATA-HGT: A Fast and Accurate Heuristic for Reconstructing Horizontal Gene Transfer."
    Lecture Notes of Computer Science No. 3595: The Eleventh International Computing and Combinatorics Conference (COCOON'05), pp. 84-93. (PDF)
  15. Sridhar Hannenhalli and Li-San Wang.
    "Enhanced position weight matrices using mixture models."
    Bioinformatics 2005 21(suppl1): Proceedings of The Eleventh International Conference on Intelligent Systems and Molecular Biology (ISMB'05), pp. i204-i212. (PDF) (PubMed)
  16. Luay Nakhleh and Li-San Wang.
    "Phylogenetic Networks, Trees, and Clusters."
    Lecture Notes in Computer Science No. 3515: 2005 International Workshop on Bioinformatics Research and Applications (IWBRA'05), pp. 919-926. (PDF)
  17. Li-San Wang and Tandy Warnow.
    "Distance-Based Genome Rearrangement Phylogeny."
    In Mathematics of Evolution and Phylogeny,, O. Gascuel ed., pp. 353-380, Oxford Univ. Press, 2005. (PDF)
  18. Stanislav Angelov, Boulos Harb, Sampath Kannan, Sanjeev Khanna, Junhyong Kim, and Li-San Wang.
    "Genome Identification and Classification by Short Oligo Arrays."
    Lecture Notes for Computer Science No. 3240: Proc. 4th Workshop on Algorithms in Bioinformatics (WABI'04), pp. 400-411. (PDF)
  19. Matthew Spencer, Barbara Bordalejo, Li-San Wang, Adrian C. Barbrook, Linne R. Mooney, Peter Robinson, Tandy Warnow, and Christopher J. Howe.
    "Analyzing the Order of Items in Manuscripts of The Canterbury Tales."
    Computers and the Humanities, 37(1):97-109, February 2003, Kluwer Academic Pub.
  20. Li-San Wang.
    "Genome Rearrangement Phylogeny Using Weighbor."
    Lecture Notes for Computer Sciences No. 2452: Proceedings for the Second Workshop on Algorithms in BioInformatics (WABI'02), Rome, Italy, pp. 112-125, September, 2002. (PDF)
  21. Bernard M.E. Moret, Li-San Wang, and Tandy Warnow.
    "New Software for Computational Phylogenetics."
    IEEE Computer: Special Issue on Bioinformatics, 35(7): 55-64, July 2002. (PS)
  22. Cara Stockham, Li-San Wang, and Tandy Warnow.
    "Statistically Based Postprocessing of Phylogenetic Analysis by Clustering."
    Proceedings of 10th Int'l Conf. on Intelligent Systems for Molecular Biology (ISMB'02), Edmonton, Canada, pp. 285--293, August 2002. (PS) (PubMed)
  23. Bernard M.E. Moret, Jijun Tang, Li-San Wang, and Tandy Warnow.
    "Steps Toward Accurate Reconstructions of Phylogenies from Gene-Order Data."
    Journal of Computer and Systems Sciences: Special Issue of Computational Biology, 65(3):508-525, 2002 (Invited article). (PS)
  24. Li-San Wang, Robert Jansen, Bernard Moret, Linda Raubeson, and Tandy Warnow.
    "Fast Phylogenetic Methods For Genome Rearrangement Evolution: An Empirical Study."
    Proceedings of Fifth Pacific Symp. of Biocomputing (PSB'02), Hawaii, USA, pp. 524-535, 2002. (PS) (PubMed)
  25. Li-San Wang.
    "Exact-IEBP: A New Technique For Estimating Evolutionary Distances Between Whole Genomes."
    Lecture Notes for Computer Sciences No. 2149: Proceedings for the First Workshop on Algorithms in BioInformatics (WABI'01), BRICS, University of Aarhus, Denmark, pp. 175-188, 2001. (PS)
  26. Li-San Wang and Tandy Warnow.
    "Estimating true evolutionary distances between genomes."
    Proceedings of the Thirty-Third Annual ACM Symposium on the Theory of Computing (STOC'01), Crete, Greece, pp. 637-646, 2001. (PS)
  27. Bernard M.E. Moret, Li-San Wang, Tandy Warnow, and Stacia Wyman.
    "New approaches for reconstructing phylogenies based on gene order."
    Proceedings of 9th Int'l Conf. on Intelligent Systems for Molecular Biology (ISMB'01), Copenhagen, Denmark, pp. 165-173, 2001. (This paper is elected by the conference as one of the five best papers in ISMB'01.) (PDF) (PubMed)
  28. Mary E. Cosner, Robert K. Jansen, Bernard M.E. Moret, Linda A. Raubeson, Li-San Wang, Tandy Warnow, and Stacia Wyman.
    "An empirical comparison of phylogenetic methods on chloroplast gene order data in Campanulaceae."
    Proc. Gene Order Dynamics, Comparative Maps, and Multigene Families," DCAF-2000, Montreal (2000) in Comparative Genomics: Empirical and Analytical Approaches to Gene Order Dynamics, Map Alignment, and the Evolution of Gene Families, D. Sankoff and J. Nadeau, eds., Kluwer Academic Pub., Dordrecht, pp. 99-121, 2000. (PDF)
  29. Mary E. Cosner, Robert K. Jansen, Bernard M.E. Moret, Linda A. Raubeson, Li-San Wang, Tandy Warnow, and Stacia Wyman.
    "A new fast heuristic for computing the breakpoint phylogeny and a phylogenetic analysis of a group of highly rearranged chloroplast genomes."
    Proc. 8th Int'l Conf. on Intelligent Systems for Molecular Biology (ISMB'00), San Diego, pp. 104-115, 2000. (PDF) (PubMed)

Abstracts in Conference Proceedings

  1. Liying Cui, Jude E. Maul, Li-San Wang, David B. Stern, and Claude W. dePamphilis.
    "Unusual Gene Clustering in a Highly Rearranged Chloroplast Genome."
    In the Society for Molecular Biology and Evolution Annual Conference (SMBE), June 26-29, 2003.
  2. Linda Raubeson, David Bader, Bernard M. E. Moret, Li-San Wang, Tandy Warnow, and Stacia K. Wyman.
    "Inferring phylogenies of photosynthetic organisms from chloroplast gene orders."
    In Botany 2001, August 12 - 16, 2001.

Other Publications

  1. Li-San Wang.
    "Large-Scale Phylogenetic Analysis."
    Ph.D. Dissertation, University of Texas, May 2003.
  2. Li-San Wang.
    "Design and Implementation of an Adaptive Modeling Unit for Multialphabet Arithmetic Compression."
    Master's Thesis, National Taiwan University, 1996.