| 2020 | WABI | The Bourque Distances for Mutation Trees of Cancers. | Katharina Jahn, Niko Beerenwinkel, Louxin Zhang |
| 2020 | WALCOM | Recent Progresses in the Combinatorial and Algorithmic Study of Rooted Phylogenetic Networks. | Louxin Zhang |
| 2016 | RECOMB | Locating a Tree in a Reticulation-Visible Network in Cubic Time. | Andreas D. M. Gunawan, Bhaskar DasGupta, Louxin Zhang |
| 2015 | IWOCA | Solving the Tree Containment Problem for Genetically Stable Networks in Quadratic Time. | Philippe Gambette, Andreas D. M. Gunawan, Anthony Labarre, Stphane Vialette, Louxin Zhang |
| 2015 | RECOMB | Locating a Tree in a Phylogenetic Network in Quadratic Time. | Philippe Gambette, Andreas D. M. Gunawan, Anthony Labarre, Stphane Vialette, Louxin Zhang |
| 2014 | RECOMB | Reconciliation with Non-binary Gene Trees Revisited. | Yu Zheng, Louxin Zhang |
| 2013 | COCOA | A Linear-Time Algorithm for Reconciliation of Non-binary Gene Tree and Binary Species Tree. | Yu Zheng, Taoyang Wu, Louxin Zhang |
| 2013 | RECOMB | Counting Motifs in the Entire Biological Network from Noisy and Incomplete Data - (Extended Abstract). | Ngoc Hieu Tran, Kwok Pui Choi, Louxin Zhang |
| 2010 | WABI | An Efficient Method for DNA-Based Species Assignment via Gene Tree and Species Tree Reconciliation. | Louxin Zhang, Yun Cui |
| 2009 | FAW | Approximating the Spanning k-Tree Forest Problem. | Chung-Shou Liao, Louxin Zhang |
| 2009 | RECOMB | Inferring the Recent Duplication History of a Gene Cluster. | Giltae Song, Louxin Zhang, Toms Vinar, Webb Miller |
| 2008 | APBC | Run Probability of High-Order Seed Patterns and its Applications to Finding Good Transition Seeds. | Jialiang Yang, Louxin Zhang |
| 2008 | FAW | A PTAS for the k-Consensus Structures Problem Under Euclidean Squared Distance. | Shuai Cheng Li, Yen Kaow Ng, Louxin Zhang |
| 2007 | BIBE | A Robust Method for Generating Discriminative Gene Clusters. | Min Xu, Louxin Zhang, Pei Li Joe Zhou |
| 2007 | RECOMB | Selecting Genomes for Reconstruction of Ancestral Genomes. | Guoliang Li, Jian Ma, Louxin Zhang |
| 2007 | RECOMB | A Heuristic Algorithm for Reconstructing Ancestral Gene Orders with Duplications. | Jian Ma, Aakrosh Ratan, Louxin Zhang, Webb Miller, David Haussler |
| 2007 | SODA | Approximating the spanning star forest problem and its applications to genomic sequence alignment. | C. Thach Nguyen, Jian Shen, Minmei Hou, Li Sheng, Webb Miller, Louxin Zhang |
| 2006 | SODA | Superiority and complexity of the spaced seeds. | Ming Li, Bin Ma, Louxin Zhang |
| 2006 | WABI | Procrastination Leads to Efficient Filtration for Local Multiple Alignment. | Aaron E. Darling, Todd J. Treangen, Louxin Zhang, Carla Kuiken, Xavier Messeguer, Nicole T. Perna |
| 2006 | WABI | Controlling Size When Aligning Multiple Genomic Sequences with Duplications. | Minmei Hou, Piotr Berman, Louxin Zhang, Webb Miller |
| 2005 | COCOON | Algorithmic and Complexity Issues of Three Clustering Methods in Microarray Data Analysis. | Jinsong Tan, Kok Seng Chua, Louxin Zhang |
| 2004 | BIBE | Good Spaced Seeds For Homology Search. | Kwok Pui Choi, Fanfan Zeng, Louxin Zhang |
| 2004 | ISAAC | Approximation Algorithms for the Consecutive Ones Submatrix Problem on Sparse Matrices. | Jinsong Tan, Louxin Zhang |
| 2004 | WABI | Translation Initiation Sites Prediction with Mixture Gaussian Models. | Guoliang Li, Tze-Yun Leong, Louxin Zhang |
| 2002 | WABI | Efficient Methods for Inferring Tandem Duplication History. | Louxin Zhang, Bin Ma, Lusheng Wang |
| 2001 | ISAAC | Complexity Study on Two Clustering Problems. | Louxin Zhang, Song Zhu |
| 2001 | SAC | Perfect phylogenetic networks with recombination. | Lusheng Wang, Kaizhong Zhang, Louxin Zhang |
| 1999 | SODA | Distinguishing String Selection Problems. | J. Kevin Lanctt, Ming Li, Bin Ma, Shaojiu Wang, Louxin Zhang |
| 1998 | COCOON | Better Approximation of Diagonal-Flip Transformation and Rotation Transformation. | Ming Li, Louxin Zhang |
| 1998 | RECOMB | On reconstructing species trees from gene trees in term of duplications and losses. | Bin Ma, Ming Li, Louxin Zhang |
| 1998 | SIGMOD | A Protein Patent Query System Powered By Kleisli. | Jing Chen, Limsoon Wong, Louxin Zhang |
| 1997 | COCOON | Many-to-One Packed Routing via Matchings. | Danny Krizanc, Louxin Zhang |
| 1997 | SODA | On Distances between Phylogenetic Trees (Extended Abstract). | Bhaskar DasGupta, Xin He, Tao Jiang, Ming Li, John Tromp, Louxin Zhang |
| 1997 | SODA | Optimal Bounds for Matching Routing on Trees. | Louxin Zhang |
| 1996 | COCOON | Some Notes on the Nearest Neighbour Interchange Distance. | Ming Li, John Tromp, Louxin Zhang |
| 1995 | COCOON | Small Weight Bases for Hamming Codes. | John Tromp, Louxin Zhang, Ying Zhao |
| 1995 | WADS | Routing on Trees via Matchings. | Alan Roberts, Antonios Symvonis, Louxin Zhang |