2. G. Song et al.,     Revealing mammalian evolutionary relationships by comparative analysis of gene clusters. Genome Biology and Evolution (March) 2012; doi: 10.1093/gbe/evs032.

  2. CY Ung et al. Existence of Inverted Profile in Chemically Responsive Molecular Pathways in the Zebrafish Liver. PLoS ONE (Nov) 2011: e27819. doi:10.1371/journal.pone.0027819


  3. TY Wu, LX Zhang. Structural properties of the reconciliation space and their applications in enumerating nearly-optimal reconciliations between a gene tree and a species tree. BMC Bioinformatics (Oct.) 2011, 12(Suppl 9):S7 doi:10.1186/1471-2105-12-S9-S7


  4. LX Zhang, From gene trees to species trees II: species tree inference in the deep coalescence model. IEEE/ACM Trans. on Comput Biol and Bioinformatics 8: 1685-1691, Nov/Dec 2011. Also in ArXiv Id: 1003.1204


  5. G Song, C-H Hsu, C Riemer, Y Zhang, HL Kim, F Hoffmann, LX Zhang, R Hardison, Nisc Comparative Sequencing Prog., E Green, W Miller, Conversion events in gene clusters. BMC Evolutionary Biology 11:226, July 2011


  6. B Ma, LX Zhang. Efficient Estimation of the Accuracy of the Maximum Likelihood Method for Ancestral State Reconstruction. J Combin. Optimization 21(4)(2011): 409-422


  7. G Song, LX Zhang, T Vinar, W Miller, CAGE: Combinatorial Analysis of Gene-cluster Evolution. J. Comput. Biology 17:1227-1242 2010


  8. GL Li, J. Ma, LX Zhang, Greedy selection of species for ancestral state reconstruction: Elimination is better than insertion . PLoS ONE (to appear in 2010).


  9. LX Zhang, J Shen, JL Yang, GL Li, Analyzing the Fitch method for reconstructing ancestral states on ultrametric phylogenetic trees. Bulletin of Math Biology 72:1760-1782, 2010.


  10. YK Ng, W Wu, LX Zhang. Positive correlation between gene coexpression and positional clustering in the zebrafish genome. BMC Genomics, 2009


  11. M Xu, M Zhu, LX Zhang. A stable iterative method for refining discriminative gene clusters. BMC Genomics, 2008


  12. HH Do, KP Choi, FP Preparata, WK Sung, LX Zhang.Spectrum-based de novo repeat detection in genomic sequences.J. Comput. Biol. 15(2008), 469-487.

  13. J Ma, A Ratan, BJ Raney, BB Suh, LX Zhang, W Miller, and D Haussler. DUPCAR: Reconstructing contiguous ancestral regions with duplications. J. Comput. Biol. 15(2008), 1007-1027.

  14. JL Yang, LX Zhang. Run Probabilities of Seed-Like Patternsand Identifying Good Transition Seeds. J. Comput. Biol. 15 (2008), 1295-1313

  15. GL Li, M Steel, LX Zhang. More Taxa Are Not Necessarily Better for the Reconstruction of Ancestral Character States. Systematic Biol. 57(2008): 647-653, Supplementary document.

  16. CT Nguyen, J Shen, MM Hou, Li Sheng, Webb Miller, LX Zhang. Approximating the Spanning Star Forest Problem and Its Applications to Genomic Sequence Alignment SIAM J Comput. 38(2008), 946-962. Extended abstract appeared in Proc. SODA'07.

  17. CT Ngyuen, NB Nguyen, WK Sung and LX Zhang.Reconstructing Recombination Network from Sequence Data: The Small Parsimony Problem IEEE/ACM Trans. Comput. Biol. Bioinfor 4 (2007): 394-402.

  18. LX Zhang. Superiority of Spaced Seeds for Homology Search IEEE/ACM Trans. Comput. Biol. Bioinfor. 4(2007): 496-505. Extended abstract appeared in SODA'06.

  19. LP Yang, MQ Wang, W Wu and LX Zhang. Transcriptome Analysis of Cold Syndrome Using Microarray.Am. J Chinese Med. 35(2007): 609-620.

  20. JS Tan, KS Chua, LX Zhang and S. Zhu. Algorithmic and Complexity Issues of the Three Clustering Methods in Microarray Data Analysis,Algorithmica 48(2007): 203-219. Extended abstract appeared in COCOON'05.

  21. JS Tan, LX Zhang. The Consecutive Ones Submatrix Problem for SparseMatrices ,Algorithmica 48(2007): 287-299.

  22. J Ma, LX Zhang, B. Suh, BJ Raney, WJ Kent, M Blanchette, D Haussler and W Miller. Reconstructing Contiguous Regions of An Ancestral Genome,Genome Research 16 (2006): 1557-1565.

  23. K Ning, KP Choi, HW Leong, LX Zhang.A post processing method for optimizing synthesis strategy for oligonucleotide microarray. Nucleic Acids Research 33(2005): e144.


  24. FP Preparata, LX Zhang, KP Choi. Quick, practical selection of effective seeds for homology search. Journal of Comput. Biol. 12 (2005):1137-1152.


  25. GL Li, T-Y Leong, LX Zhang. Translation Initiation Sites Prediction with mixture Gaussian models, IEEE Transactions on Knowledge and Data Engineering 17 (8): 1152-1160 2005 Also appeared in Proc. of WABI04, Norway, 2004.


  26. Q Li, BTK Lee, LX Zhang. Genome-scale analysis of positional clustering of mouse testis-specific genes, BMC genomics 6:7(2005)


  27. CT Nguyen, YC Tay, LX Zhang. Divide-and-conquer approach for the exemplar breakpoint distance, Bioinformatics 21(2005), 2171-2176. Source code


  28. JL Yang, LX Zhang.On Counting Tandem Duplication Trees,Molecular Biology and Evolution 21(2004):1160-1163.


  29. KP Choi, FF Zeng, LX Zhang. Good Spaced Seeds for Homology Search,Bioinformatics 20(2004), 1053-59.


  30. KP Choi, LX Zhang. Sensitivity Analysis and Efficient Methodfor Identifying Optimal Spaced Seeds.Journal of Computer and System Sciences, 68 (2004), 22-40.


  31. JK Lanctot, B Ma, M Li, SJ Wang, LX Zhang.Distinguishing String Selection Problems.Information and Computation, 185(2003), 41-55. Extended abstract alsoappeared on SODA'99, 633-642, Baltimore, USA, 1999.


  32. LX Zhang, B Ma, LS Wang, Y Xu.Greedy Method for Inferring TandemDuplication History. Bioinformatics 19(2003), 1497-1504.Abstract also appeared on WABI'2002.

  33. LX Zhang, C-K Heng, TW Tan. Cladogramer: Incorporating haplotype frequency intocladogram analysis.Bioinformatics 17(2001), 481-482.


  34. LS Wang, KZ Zhang, LX Zhang. Perfect phylogeny with recombination.Journal of Comput. Bio. 8(2001), 69-78.


  35. B Ma, M Li, LX Zhang.From gene trees to species trees, SIAM Journal on Comput. 30(2000), 729-752.


  36. A Lim, LX Zhang.WebPHYLIP: A Web Interface to PHYLIP,Bioinformatics 15 (1999), 1068-69.


  37. LX Zhang. On Mirkin-Muchnik-Smith conjecture for comparing molecularphylogenies, J. Comput. Biology, 4 (1997), 177-187.


  38. M Li, J Tromp, LX Zhang. On nni distances on evolutionary trees,J. of Theoretical Biology 182 (1996), 463-467.




  39. KH Heng, JC Tong, LX Zhang. Recent Applications of Hidden Markov Models in Computational Biology: A Review, Genomics, Proteomics and Bioinformatics 2(2)(2004), 84-96.


  40. G Bourque, LX Zhang, Models and Methods in Comparative Genomics, Advances in Computers (vol 68): Computational Biology and Bioinformatics, pp59-104, 2006.


  41. J. Ma, LX Zhang, Modern BLAST Porgrams, LS Heath and N. Ramakrishnan (eds.) Problem Solving Handbook for Comput Biol. and Bioinformatics, pp.3-19, Springer, 2010.


  42. B Fu, LX Zhang. A polynomial algebra method for computing exemplar breakpoint distance, In Prof. of ISBRA'2011, J. Chen, J. Wang, A. Zelikovsky (eds): LNBI 6674, pp. 297--305, Springer, Heidelberg (2011)


  43. Zhang*, L, YK Ng, T WU and Y ZHENG, "Network model and efficient method for detecting relative duplications or horizontal gene transfers". Proceedings of IEEE First International Conference on Computational Advances in Bio and Medical Sciences (2011): 214-219. New York: IEEE Computer Society. 3 - 5 Feb 2011, Holiday Inn, Orlando, United States


  44. LX Zhang, Y Cui. An Efficient Method for DNA-Based Species Assignment. In Proc. of WABI'10, V. Moulton and M. Singh (Eds.): LNBI 6293, pp. 300--311. Springer, Heidelberg (2010)


  45. G Song, LX Zhang, T Vinar, W Miller. Inferring the recent duplication history of a gene cluster. In Proc. of RECOMB CG09, F.D. Ciccarelli and I. Miklos (Eds.): LNBI 5817, pp. 111-125 Springer, Heideberg (2009).


  46. GL Li, J Ma, LX Zhang. Selecting Genomes for Reconstruction of Ancestral Genomes Proceedings of Recomb Comparative Genomics Workshop , Sept, 2007.


  47. M Xu, LX Zhang. A robust method for generating discriminative gene clusters Proceedings of IEEE 7th Symposium on Bioinformatics and Bioengineering(BIBE'07) , Boston, October, 2007.


  48. C.T. Nguyen, J Shen, MM Hou, Li Sheng, Webb Miller, LX Zhang. Approximating the Spanning Star Forest Problem and Its Applications to Genomic Sequence Alignment Proc. of SIAM-ACM Symposium on Discrete Algorithms (SODA'07), 645-654, Jan, 2007.

  49. MM Hou, P. Berman, LX Zhang, W. Miller. Controlling size when aligning multiple genomic sequences with duplications. Proc. of WABI'06, Zurich, 2006.

  50. AE Darling, TJ Treangen, LX Zhang, C Kuiken, X. Messeguer and NT Perna. Procrastination leads to efficient filtration for local multiple alignment. Proc. of WABI'06, Zurich, 2006.

  51. M Li, B Ma, LX Zhang. Superiority and Complexity of Spaced Seeds. Proc. of SIAM-ACM Symposium on Discrete Algorithms, pp444-453, 2006.

  52. LX Zhang, S Zhu. An Approach to Clustering Gene Expression Data,Proceedings of IEEE Symposium on Bioinformatics, USA, 2002, 268-275.

  53. LX Zhang, S Zhu. Complexity Study on Two Clustering Problems. Proceedings of the Annual International Symposium on Algorithms andComputation, Christchurch, 2001, 660-669.

  54. B Ma, M Li, LX Zhang.On reconstructing species trees from gene trees in terms of duplications and losses,Proccedings of the 2nd Inter.Confer. on Computational MolecularBiology (Recomb'98), New York, 182-191, 1998.


  55. J Chen, LS Wong, LX Zhang. A protein patent query system powered by Kleisli (demo session), Proceedings of ACM SIGMOD International Conference onManagement of Data, 593-595, 1998.


  56. B DasGupta, X He, T Jiang, M Li, J Tromp, LX Zhang. On distances between phylogenetic trees,Proc. of the 8th Annual ACM-SIAM Symposium on Discrete Algorithms(SODA'97), 427-436, 1997.




  57. LX Zhang, Inferring a Species Tree from Gene Trees under the Deep Coalescence Cost, Current in Computatioal Molecular Biology (ed. by S. Miyanoet al.), 192-193, 2000. full version


  58. Craig A Stewart, TW Tan, M Buchhorn, D Hart, D Berry, LX Zhang, E Wernert, M Sakharkar, W Fisher, D McMullen, Evolutionary biology and computational grids , IBM CASCON 1999Computational Biology Workshop:Software Tools for Computational Biology.




  59. B DasGupta, X He, T Jiang, M Li, J Tromp, LS Wang, LX Zhang. Computing distances between evolutionary trees. Handbook of Combinatorial Optimization (eds. by D.-Z. Du and P. M. Pardalos), Kluwer Academic Publishers, 1998.

  60. B DasGupta, X He, T Jiang, M Li, J Tromp, LX Zhang. Nearest Neighbor Interchange and Related Distances Encyclopedia of Algorithms, Ming-Yang Kao (editor), Springer-Verlag, 2008.