1. K Ng, W Wu, LX Zhang. Positive correlation between gene coexpression and positional clustering in the zebrafish genome. to appear in 2009


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


  3. 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.

  4. 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.

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

  6. 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.

  7. 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.

  8. 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.

  9. 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.

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

  11. 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.

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

  13. 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.

  14. 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.


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


  16. 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.


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


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


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


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


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


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


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

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


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


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


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


  28. LX Zhang. On Mirkin-Muchnik-Smith conjecture for comparing molecular phylogenies, J. Comput. Biology, 4 (1997), 177-188.


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




  30. 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.


  31. G Bourque, LX Zhang, Models and Methods in Comparative Genomics, Advances in Computers (vol 68): Computational Biology and Bioinformatics, 59-104.


  32. J. Ma, LX Zhang, Modern BLAST Porgrams, Problem Solving Handbook in Bioinformatics, Springer, 2009.


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


  34. 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.


  35. 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.

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

  37. 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.

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

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

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

  41. 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 Molecular Biology (Recomb'98), New York, 182-191, 1998.


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


  43. 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.




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


  45. 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 1999 Computational Biology Workshop: Software Tools for Computational Biology.




  46. 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.

  47. 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.