Decision Problems for Finite Special String-Rewriting Systems that are Confluent on Some Congruence Class. - Friedrich Otto; Louxin Zhang (Acta Informatica, 1991)

On the Conjugacy Problem for One-Relator Monoids with Elements of Finite Order. - Louxin Zhang (Int. J. Algebra Comput., 1992)

The Pre-NTS Property is Undecidable for Context-Free Grammars. - Louxin Zhang (Inf. Process. Lett., 1992)

Some Properties of Finite Special String-Rewriting Systems. - Louxin Zhang (J. Symb. Comput., 1992)

On Weakly Confluent Monadic String-Rewriting Systems. - Klaus Madlener; Paliath Narendran; Friedrich Otto; Louxin Zhang (Theor. Comput. Sci., 1993)

Routing on Trees via Matchings. - Alan Roberts; Antonios Symvonis; Louxin Zhang (WADS, 1995)

On the Approximation of Longest Common Nonsupersequences and Shortest Common Nonsubsequences. - Louxin Zhang (Theor. Comput. Sci., 1995)

Some Notes on the Nearest Neighbour Interchange Distance. - Ming Li 001; John Tromp; Louxin Zhang (COCOON, 1996)

On the descriptive power of special Thue systems. - Louxin Zhang; Lian Li; Jinzhao Wu (Discret. Math., 1996)

Many-to-One Packed Routing via Matchings. - Danny Krizanc; Louxin Zhang (COCOON, 1997)

On Distances between Phylogenetic Trees (Extended Abstract). - Bhaskar DasGupta; Xin He 005; Tao Jiang 001; Ming Li 001; John Tromp; Louxin Zhang (SODA, 1997)

On a Mirkin-Muchnik-Smith Conjecture for Comparing Molecular Phylogenies. - Louxin Zhang (J. Comput. Biol., 1997)

Small Weight Bases for Hamming Codes. - John Tromp; Louxin Zhang; Ying Zhao (Theor. Comput. Sci., 1997)

Better Approximation of Diagonal-Flip Transformation and Rotation Transformation. - Ming Li 001; Louxin Zhang (COCOON, 1998)

On reconstructing species trees from gene trees in term of duplications and losses. - Bin Ma 002; Ming Li 001; Louxin Zhang (RECOMB, 1998)

A Protein Patent Query System Powered By Kleisli. - Jing Chen; Limsoon Wong; Louxin Zhang (SIGMOD Conference, 1998)

Addition in log2n + O(1) Steps on Average: A Simple Analysis. - Richard Beigel; William I. Gasarch; Ming Li 001; Louxin Zhang (Theor. Comput. Sci., 1998)

On computing the nearest neighbor interchange distance. - Bhaskar DasGupta; Xin He 005; Tao Jiang 001; Ming Li 001; John Tromp; Louxin Zhang (Discrete Mathematical Problems with Medical Applications, 1999)

WebPHYLIP: a web interface to PHYLIP. - Allison Lim; Louxin Zhang (Bioinform., 1999)

Twist-Rotation Transformations of Binary Trees and Arithmetic Expressions. - Ming Li 001; Louxin Zhang (J. Algorithms, 1999)

Fitting Distances by Tree Metrics with Increment Error. - Bin Ma 002; Lusheng Wang 001; Louxin Zhang (J. Comb. Optim., 1999)

Optimal Bounds for Matching Routing on Trees. - Louxin Zhang (SIAM J. Discret. Math., 1999)

Separating Auxiliary Arity Hierarchy of First-Order Incremental Evaluation Systems Using (3k+1)-ary Input Relations. - Guozhu Dong; Louxin Zhang (Int. J. Found. Comput. Sci., 2000)

From Gene Trees to Species Trees. - Bin Ma 002; Ming Li 001; Louxin Zhang (SIAM J. Comput., 2000)

Complexity Study on Two Clustering Problems. - Louxin Zhang; Song Zhu (ISAAC, 2001)

Cladogramer: incorporating haplotype frequency into cladogram analysis. - Louxin Zhang; Chew-Kiat Heng; Tin Wee Tan (Bioinform., 2001)

Perfect Phylogenetic Networks with Recombination. - Lusheng Wang 001; Kaizhong Zhang; Louxin Zhang (J. Comput. Biol., 2001)

A New Clustering Method for Microarray Data Analysis. - Louxin Zhang; Song Zhu (CSB, 2002)

Efficient Methods for Inferring Tandem Duplication History. - Louxin Zhang; Bin Ma 002; Lusheng Wang 001 (WABI, 2002)

Greedy method for inferring tandem duplication history. - Louxin Zhang; Bin Ma 002; Lusheng Wang 001; Ying Xu 002 (Bioinform., 2003)

Distinguishing string selection problems. - J. Kevin Lanctôt; Ming Li 001; Bin Ma 002; Shaojiu Wang; Louxin Zhang (Inf. Comput., 2003)

Approximation Algorithms for the Consecutive Ones Submatrix Problem on Sparse Matrices. - Jinsong Tan; Louxin Zhang (ISAAC, 2004)

Translation Initiation Sites Prediction with Mixture Gaussian Models. - Guoliang Li 002; Tze-Yun Leong; Louxin Zhang (WABI, 2004)

Good spaced seeds for homology search. - Kwok Pui Choi; Fanfan Zeng; Louxin Zhang (Bioinform., 2004)

Computing And Combinatorics Conference – Cocoon'02. - Oscar H. Ibarra; Louxin Zhang (Int. J. Found. Comput. Sci., 2004)

Sensitivity analysis and efficient method for identifying optimal spaced seeds. - Kwok Pui Choi; Louxin Zhang (J. Comput. Syst. Sci., 2004)

Algorithmic and Complexity Issues of Three Clustering Methods in Microarray Data Analysis. - Jinsong Tan; Kok Seng Chua; Louxin Zhang (COCOON, 2005)

Divide-and-conquer approach for the exemplar breakpoint distance. - C. Thach Nguyen; Y. C. Tay; Louxin Zhang (Bioinform., 2005)

Quick, Practical Selection of Effective Seeds for Homology Search. - Franco P. Preparata; Louxin Zhang; Kwok Pui Choi (J. Comput. Biol., 2005)

Translation Initiation Sites Prediction with Mixture Gaussian Models in Human cDNA Sequences. - Guoliang Li 002; Tze-Yun Leong; Louxin Zhang (IEEE Trans. Knowl. Data Eng., 2005)

Superiority and complexity of the spaced seeds. - Ming Li 001; Bin Ma 002; Louxin Zhang (SODA, 2006)

Procrastination Leads to Efficient Filtration for Local Multiple Alignment. - Aaron E. Darling; Todd J. Treangen; Louxin Zhang; Carla Kuiken; Xavier Messeguer; Nicole T. Perna (WABI, 2006)

Controlling Size When Aligning Multiple Genomic Sequences with Duplications. - Minmei Hou; Piotr Berman; Louxin Zhang; Webb Miller (WABI, 2006)

Models and Methods in Comparative Genomics. - Guillaume Bourque; Louxin Zhang (Adv. Comput., 2006)

A Robust Method for Generating Discriminative Gene Clusters. - Min Xu; Louxin Zhang; Pei Li Joe Zhou (BIBE, 2007)

Selecting Genomes for Reconstruction of Ancestral Genomes. - Guoliang Li 002; Jian Ma 004; Louxin Zhang (RECOMB-CG, 2007)

A Heuristic Algorithm for Reconstructing Ancestral Gene Orders with Duplications. - Jian Ma 004; Aakrosh Ratan; Louxin Zhang; Webb Miller; David Haussler (RECOMB-CG, 2007)

Approximating the spanning star forest problem and its applications to genomic sequence alignment. - C. Thach Nguyen; Jian Shen; Minmei Hou; Li Sheng 001; Webb Miller; Louxin Zhang (SODA, 2007)

Algorithmic and Complexity Issues of Three Clustering Methods in Microarray Data Analysis. - Jinsong Tan; Kok Seng Chua; Louxin Zhang; Song Zhu (Algorithmica, 2007)

The Consecutive Ones Submatrix Problem for Sparse Matrices. - Jinsong Tan; Louxin Zhang (Algorithmica, 2007)

Reconstructing Recombination Network from Sequence Data: The Small Parsimony Problem. - C. Thach Nguyen; Nguyen Bao Nguyen; Wing-Kin Sung; Louxin Zhang (IEEE ACM Trans. Comput. Biol. Bioinform., 2007)

Superiority of Spaced Seeds for Homology Search. - Louxin Zhang (IEEE ACM Trans. Comput. Biol. Bioinform., 2007)

Run Probability of High-Order Seed Patterns and its Applications to Finding Good Transition Seeds. - Jialiang Yang; Louxin Zhang (APBC, 2008)

A PTAS for the k-Consensus Structures Problem Under Euclidean Squared Distance. - Shuai Cheng Li 001; Yen Kaow Ng; Louxin Zhang (FAW, 2008)

A PTAS For The k-Consensus Structures Problem Under Squared Euclidean Distance. - Shuai Cheng Li 001; Yen Kaow Ng; Louxin Zhang (Algorithms, 2008)

Spectrum-Based De Novo Repeat Detection in Genomic Sequences. - Huy Hoang Do; Kwok Pui Choi; Franco P. Preparata; Wing-Kin Sung; Louxin Zhang (J. Comput. Biol., 2008)

DUPCAR: Reconstructing Contiguous Ancestral Regions with Duplications. - Jian Ma 004; Aakrosh Ratan; Brian J. Raney; Bernard B. Suh; Louxin Zhang; Webb Miller; David Haussler (J. Comput. Biol., 2008)

Run Probabilities of Seed-Like Patterns and Identifying Good Transition Seeds. - Jialiang Yang; Louxin Zhang (J. Comput. Biol., 2008)

Approximating the Spanning Star Forest Problem and Its Application to Genomic Sequence Alignment. - C. Thach Nguyen; Jian Shen; Minmei Hou; Li Sheng 001; Webb Miller; Louxin Zhang (SIAM J. Comput., 2008)

Nearest Neighbor Interchange and Related Distances. - Bhaskar DasGupta; Xin He 005; Tao Jiang 001; Ming Li 001; John Tromp; Louxin Zhang (Encyclopedia of Algorithms, 2008)

Inferring the Recent Duplication History of a Gene Cluster. - Giltae Song; Louxin Zhang; Tomás Vinar; Webb Miller (RECOMB-CG, 2009)

Sequence Comparison - Theory and Methods - Kun-Mao Chao; Louxin Zhang (Springer, 2009)

An Efficient Method for DNA-Based Species Assignment via Gene Tree and Species Tree Reconciliation. - Louxin Zhang; Yun Cui (WABI, 2010)

CAGE: Combinatorial Analysis of Gene-Cluster Evolution. - Giltae Song; Louxin Zhang; Tomás Vinar; Webb Miller (J. Comput. Biol., 2010)

Network model and efficient method for detecting relative duplications or horizontal gene transfers. - Louxin Zhang; Yen Kaow Ng; Taoyang Wu; Yu Zheng 018 (ICCABS, 2011)

A Polynomial Algebra Method for Computing Exemplar Breakpoint Distance. - Bin Fu; Louxin Zhang (ISBRA, 2011)

Structural properties of the reconciliation space and their applications in enumerating nearly-optimal reconciliations between a gene tree and a species tree. - Taoyang Wu; Louxin Zhang (BMC Bioinform., 2011)

Efficient estimation of the accuracy of the maximum likelihood method for ancestral state reconstruction. - Bin Ma 002; Louxin Zhang (J. Comb. Optim., 2011)

From Gene Trees to Species Trees II: Species Tree Inference by Minimizing Deep Coalescence Events. - Louxin Zhang (IEEE ACM Trans. Comput. Biol. Bioinform., 2011)

Alignment seeding strategies using contiguous pyrimidine purine matches. - Minmei Hou; Louxin Zhang; Robert S. Harris (BCB, 2012)

Reconstruction of Network Evolutionary History from Extant Network Topology and Duplication History. - Si Li 003; Kwok Pui Choi; Taoyang Wu; Louxin Zhang (ISBRA, 2012)

Two combinatorial optimization problems for SNP discovery using base-specific cleavage and mass spectrometry. - Xin Chen; Qiong Wu; Ruimin Sun; Louxin Zhang (BMC Syst. Biol., 2012)

Approximating the Spanning k-Tree forest Problem. - Chung-Shou Liao; Louxin Zhang (Int. J. Found. Comput. Sci., 2012)

A Linear-Time Algorithm for Reconciliation of Non-binary Gene Tree and Binary Species Tree. - Yu Zheng 018; Taoyang Wu; Louxin Zhang (COCOA, 2013)

A Tool for Non-binary Tree Reconciliation. - Yu Zheng 018; Louxin Zhang (ISBRA, 2013)

Effect of Incomplete Lineage Sorting on Tree-Reconciliation-Based Inference of Gene Duplication. - Yu Zheng 018; Louxin Zhang (ISBRA, 2013)

Counting Motifs in the Entire Biological Network from Noisy and Incomplete Data - (Extended Abstract). - Ngoc Hieu Tran; Kwok Pui Choi; Louxin Zhang (RECOMB, 2013)

Motif Discovery with Data Mining in 3D protein Structure Databases: Discovery, Validation and Prediction of the U-Shape zinc binding ("Huf-zinc") Motif. - Sebastian Maurer-Stroh; He Gao; Hao Han; Lies Baeten; Joost Schymkowitz; Frederic Rousseau 001; Louxin Zhang; Frank Eisenhaber (J. Bioinform. Comput. Biol., 2013)

Maximum Likelihood Inference of the Evolutionary History of a PPI Network from the Duplication History of Its Proteins. - Si Li 003; Kwok Pui Choi; Taoyang Wu; Louxin Zhang (IEEE ACM Trans. Comput. Biol. Bioinform., 2013)

Reconciliation with Non-binary Gene Trees Revisited. - Yu Zheng 018; Louxin Zhang (RECOMB, 2014)

Are the Duplication Cost and Robinson-Foulds Distance Equivalent? - Yu Zheng 018; Louxin Zhang (J. Comput. Biol., 2014)

Effect of Incomplete Lineage SortingOn Tree-Reconciliation-Based Inferenceof Gene Duplication. - Yu Zheng 018; Louxin Zhang (IEEE ACM Trans. Comput. Biol. Bioinform., 2014)

Solving the Tree Containment Problem for Genetically Stable Networks in Quadratic Time. - Philippe Gambette; Andreas D. M. Gunawan; Anthony Labarre; Stéphane Vialette; Louxin Zhang (IWOCA, 2015)

Locating a Tree in a Phylogenetic Network in Quadratic Time. - Philippe Gambette; Andreas D. M. Gunawan; Anthony Labarre; Stéphane Vialette; Louxin Zhang (RECOMB, 2015)

Stability Implies Computational Tractability: Locating a Tree in a Stable Network is Easy. - Andreas D. M. Gunawan; Bhaskar DasGupta; Louxin Zhang (CoRR, 2015)

Bounding the Size of a Network Defined By Visibility Property. - Andreas D. M. Gunawan; Louxin Zhang (CoRR, 2015)

Locating a Tree in a Reticulation-Visible Network in Cubic Time. - Andreas D. M. Gunawan; Bhaskar DasGupta; Louxin Zhang (RECOMB, 2016)

A program for verification of phylogenetic network models. - Andreas D. M. Gunawan; Bingxin Lu; Louxin Zhang (Bioinform., 2016)

Locating a Phylogenetic Tree in a Reticulation-Visible Network in Quadratic Time. - Andreas D. M. Gunawan; Bhaskar DasGupta; Louxin Zhang (CoRR, 2016)

On Tree-Based Phylogenetic Networks. - Louxin Zhang (J. Comput. Biol., 2016)

Nearest Neighbor Interchange and Related Distances. - Bhaskar DasGupta; Xin He 005; Ming Li 001; John Tromp; Louxin Zhang (Encyclopedia of Algorithms, 2016)

Superiority and Complexity of the Spaced Seeds. - Louxin Zhang (Encyclopedia of Algorithms, 2016)

A program to compute the soft Robinson-Foulds distance between phylogenetic networks. - Bingxin Lu; Louxin Zhang; Hon Wai Leong (BMC Genom., 2017)

A decomposition theorem and two algorithms for reticulation-visible networks. - Andreas D. M. Gunawan; Bhaskar DasGupta; Louxin Zhang (Inf. Comput., 2017)

Reconciliation With Nonbinary Gene Trees Revisited. - Yu Zheng 018; Louxin Zhang (J. ACM, 2017)

RecPhyloXML: a format for reconciled gene trees. - Wandrille Duchemin; Guillaume Gence; Anne-Muriel Arigon Chifolleau; Lars Arvestad; Mukul S. Bansal; Vincent Berry; Bastien Boussau; François Chevenet; Nicolas Comte; Adrián A. Davín; Christophe Dessimoz; David Dylus; et al. (Bioinform., 2018)

S-Cluster++: a fast program for solving the cluster containment problem for phylogenetic networks. - Hongwei Yan; Andreas D. M. Gunawan; Louxin Zhang (Bioinform., 2018)

Fast Methods for Solving the Cluster Containment Problem for Phylogenetic Networks. - Andreas D. M. Gunawan; Bingxin Lu; Louxin Zhang (CoRR, 2018)

The compressions of reticulation-visible networks are tree-child. - Andreas D. M. Gunawan; Hongwei Yan; Louxin Zhang (CoRR, 2018)

Solving the tree containment problem in linear time for nearly stable phylogenetic networks. - Philippe Gambette; Andreas D. M. Gunawan; Anthony Labarre; Stéphane Vialette; Louxin Zhang (Discret. Appl. Math., 2018)

Online buffer management for transmitting packets with processing cycles. - Yi-Hua Yang; Chung-Shou Liao; Xin Han; Louxin Zhang (Theor. Comput. Sci., 2018)

ZDOG: zooming in on dominating genes with mutations in cancer pathways. - Rudi Alberts; Jinyu Chen; Louxin Zhang (BMC Bioinform., 2019)

Generating normal networks via leaf insertion and nearest neighbor interchange. - Louxin Zhang (BMC Bioinform., 2019)

Compression of Phylogenetic Networks and Algorithm for the Tree Containment Problem. - Andreas D. M. Gunawan; Hongwei Yan; Louxin Zhang (J. Comput. Biol., 2019)

Recent Progresses in the Combinatorial and Algorithmic Study of Rooted Phylogenetic Networks. - Louxin Zhang (WALCOM, 2020)

Counting and enumerating galled networks. - Andreas D. M. Gunawan; Rathin Jeyaram; Louxin Zhang (Discret. Appl. Math., 2020)

Counting and enumerating tree-child networks and their subclasses. - Gabriel Cardona; Louxin Zhang (J. Comput. Syst. Sci., 2020)

The Bourque distances for mutation trees of cancers. - Katharina Jahn 001; Niko Beerenwinkel; Louxin Zhang (Algorithms Mol. Biol., 2021)

A survey and systematic assessment of computational methods for drug response prediction. - Jinyu Chen; Louxin Zhang (Briefings Bioinform., 2021)

On the asymptotic growth of the number of tree-child networks. - Michael Fuchs 001; Guan-Ru Yu; Louxin Zhang (Eur. J. Comb., 2021)

Introduction to the Special Issue of the 18th Annual International RECOMB Satellite Workshop on Comparative Genomics. - Rohan B. H. Williams; Louxin Zhang (J. Bioinform. Comput. Biol., 2021)

Guest Editorial for the 17th Asia Pacific Bioinformatics Conference. - Louxin Zhang; Shaoliang Peng; Yi-Ping Phoebe Chen; David Sankoff; Guoliang Li 002; Hong-Yu Zhang (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

The Sackin Index of Simplex Networks. - Louxin Zhang (RECOMB-CG, 2022)

How much can deep learning improve prediction of the responses to drugs in cancer cell lines? - Yurui Chen; Louxin Zhang (Briefings Bioinform., 2022)

Asymptotic enumeration and distributional properties of galled networks. - Michael Fuchs 001; Guan-Ru Yu; Louxin Zhang (J. Comb. Theory A, 2022)

The K-Robinson Foulds Measures for Labeled Trees. - Elahe Khayatian; Gabriel Valiente; Louxin Zhang (RECOMB-CG, 2023)

Bounding the Number of Reticulations in a Tree-Child Network that Displays a Set of Trees. - Yufeng Wu; Louxin Zhang (RECOMB-CG, 2023)

A Vector Representation for Phylogenetic Trees. - Cédric Chauve; Caroline Colijn; Louxin Zhang (CoRR, 2024)

The k-Robinson-Foulds Dissimilarity Measures for Comparison of Labeled Trees. - Elahe Khayatian; Gabriel Valiente; Louxin Zhang (J. Comput. Biol., 2024)

Computing the Bounds of the Number of Reticulations in a Tree-Child Network That Displays a Set of Trees. - Yufeng Wu; Louxin Zhang (J. Comput. Biol., 2024)

The tree-child network inference problem for line trees and the shortest common supersequence problem for permutation strings. - Laurent Bulteau; Louxin Zhang (J. Comput. Syst. Sci., 2024)

Exact Counts of Binary Phylogenetic Networks with Two and Three Reticulation Events (Extended Abstract). - Hao Yu; Louxin Zhang (RECOMB-CG, 2025)

Bounding the number of reticulation events for displaying multiple trees in a phylogenetic network. - Yufeng Wu; Louxin Zhang (J. Comput. Syst. Sci., 2025)

On the size of the neighborhoods of a word. - Cédric Chauve; Louxin Zhang (CoRR, 2025)