Journal Papers


    HW Yan, A. Gunawan, LX Zhang, S-Cluster++: A fast program for solving the cluster containment problem for phylogenetic networks, Special Issue of Bioinformatics for ECCB2018.

    W. Duchemin et al. RecPhyloXML - a format for reconciled gene trees. Bioinformatics, in press.

    P Gambette, AD Gunawan, A Labarre, S Vialette, LX Zhang.
    Solving the tree containment problem in linear time for nearly stable phylogenetic networks. Discrete Applied Mathematics, 246(2018): 62-79.


    Y Zheng, LX Zhang. Reconciliation with non-binary gene trees revisited, Journal of the ACM, 64 (4) (2017), 1--28. Also presented on RECOMB'14.

    L Wang, XZ Li, LX Zhang, Q Gao. Improved anticancer drug response prediction in cell lines using matrix factorization with similarity regularization, BMC Cancer 17(2017):513

    BX Lu, LX Zhang, HW Leong. A program to compute the soft Robinson-Foulds distance between phylogenetic networks. BMC Genomics. 2017 18(Suppl 2):111

    ADM Gunawan, B. Dasgupta, LX Zhang. A decomposition theorem and two algorithms for reticulation-visible networks, (arxiv version, IC version). Information and Computation 252 (2017): 161-175, presented on RECOMB'2016


    ADM Gunawan, BX Lu, LX Zhang. A program for verification of phylogenetic models. Bioinformatics 2016 32 (17): i503-i510. doi: 10.1093/bioinformatics/btw467. Presented on ECCB'2016. program code

    ADM Gunawan, LX Zhang. Bounding the size of a network defined by visibility property.

    LX Zhang. On tree-based phylogenetic networks (arxiv version, JCB version), J. Comput. Biology 23 (July 2016): 553--565.

    TTT Nguyen, et al. Predicting chemotherapeutic drug combinations through gene network profiling. Scientic Reports 6(2016), 18658.

    2011 — 2015

    TTT Nguyen, et al. Fitness Profiling Links Topoisomerase II Regulation of Centromeric Integrity to Doxorubicin Resistance in Fission Yeast. Scientific Reports 5 (2015), 8400.

    SH Zhang, DC Tian, NH Tran, KP Choi, LX Zhang. Profiling the Transcription Factor Regulatory Networks of Human Cell Types. Nucleic Acids Res., doi: 10.1093/nar/gku923, 2014.

    Y Zheng, LX Zhang. Are The Duplication Cost and The Robinson-Foulds Distance Equivalent? J. Comput Biol. 21(2014): 578-590.

    Y Zheng, LX Zhang. Effect of Incomplete Lineage Sorting on Tree-Reconciliation-Based Inference of Gene Duplication, IEEE-ACM TCBB 11(2014): 477-485. Also appeared in ISBRA'2013.

    N.H. Tran, KP Choi, LX Zhang. Counting Motifs in the Human Interactome. Nature Communications 4: Art. no. 2241. doi:10.1038/ncomms3241

    S Li, KP Choi, TY Wu, LX Zhang. Reconstruction of network evolutionary history from extant network topology and duplication history. IEEE-ACM TCBB 10 (2013): 1412-1421.

    X. Zhang et al. Toxicogenomic Analysis Suggests Chemical-Induced Sexual Dimorphism in the Expression of Metabolic Genes in Zebrafish Liver, PLoS ONE 7(12): e51971.

    X. Chen, Q. Wu, R. Sun, LX. Zhang. Two combinatorial optimization problems for SNP discovery using base-specific cleavage and mass spectrometry. BMC Systems Biol. 6(suppl)(2012): S5.

    G. Song et al., Revealing mammalian evolutionary relationships by comparative analysis of gene clusters. Genome Biology and Evolution 4 (2012): 586-601.

    CY Ung et al. Existence of Inverted Profile in Chemically Responsive Molecular Pathways in the Zebrafish Liver. PLoS ONE (Nov) 2011: e27819.

    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

    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 (2011): 1685-1691. ArXiv Id: 1003.1204

    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 Evol. Biology 11 (2011):226.

    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

    2006 — 2010

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

    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).

    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.

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

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

    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.

    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.

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

    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.

    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.

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

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

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

    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.

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

    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.

    2001 — 2005

    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.

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

    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.

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

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

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

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

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

    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.

    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.

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

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

    1997 — 2000

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

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

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

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

    Reviewed Conference Papers (no journal version)


    ADM Gunawan, B. DasGupta, LX Zhang. Locating a Tree in a Reticulation-Visible Network in Cubic Time. RECOMB'16, Los Angles, USA, 2016.

    ADM Gunawan, BX Lu, LX Zhang. A Program for Verification of Phylogenetic Models, ECCB'16, Netherlands, 2016.

    2011 — 2015

    P Gambette, ADM Gunawan, A Labarre, S Vialette, LX Zhang. Solving the Tree Containment Problem for Genetically Stable Networks in Quadratic Time. In Proc. IWOCA, Italy, 2015.

    P Gambette, ADM Gunawan, A Labarre, S Vialette, LX Zhang. Locating A Tree in A Phylogenetic Network in Quadratic Time , in Proc. RECOMB, 2015. full version

    NH Tran, KP Choi, LX Zhang. Counting Motifs in the Entire Biological Network from Noisy and Incomplete Data, in Proc. RECOMB, 2013.

    Y Zheng, LX Zhang. A Tool for Non-binary Tree Reconciliation, in ISBRA'2013, LBNI 7875, pp. 40-52. Springer-Verlag, Berlin Heidelberg, 2013.

    MM Hou, LX Zhang, R. Harris. Alignment seeding strategies using contiguous pyrimidine purine matches, in Proc. ACM-BCB, 2012, Orlando, USA.

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

    LX Zhang, YK Ng, T WU and Y ZHENG, Network model and efficient method for detecting relative duplications or horizontal gene transfers. in Proc. IEEE 1st Int'l Conference on Comput. Advances in Bio and Medical Sciences (2011): 214-219. New York: IEEE Computer Society. 3 - 5 Feb 2011, Holiday Inn, Orlando, United States

    2006 — 2010

    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)

    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).

    GL Li, J Ma, LX Zhang. Selecting Genomes for Reconstruction of Ancestral Genomes Proc. RECOMB CG, Sept, 2007.

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

    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.

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

    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.

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

    1997 — 2005

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

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

    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.

    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.

    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.

    Survey Papers

    LX Zhang. Clsuters, Trees and Phylogenetic Network Classes, 2018.

    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.

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

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

    Unpublished Works

    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

    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.