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Louxin Zhang
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2020 – today
- 2024
- [j70]Elahe Khayatian
, Gabriel Valiente
The k-Robinson-Foulds Dissimilarity Measures for Comparison of Labeled Trees. J. Comput. Biol. 31(4): 328-344 (2024) - [j69]Yufeng Wu
Computing the Bounds of the Number of Reticulations in a Tree-Child Network That Displays a Set of Trees. J. Comput. Biol. 31(4): 345-359 (2024) - [j68]Laurent Bulteau, Louxin Zhang:
The tree-child network inference problem for line trees and the shortest common supersequence problem for permutation strings. J. Comput. Syst. Sci. 144: 103546 (2024) - [i9]Cédric Chauve, Caroline Colijn, Louxin Zhang:
A Vector Representation for Phylogenetic Trees. CoRR abs/2405.07110 (2024) - 2023
- [c48]Elahe Khayatian
The K-Robinson Foulds Measures for Labeled Trees. RECOMB-CG 2023: 146-161 - [c47]Yufeng Wu, Louxin Zhang:
Bounding the Number of Reticulations in a Tree-Child Network that Displays a Set of Trees. RECOMB-CG 2023: 162-178 - 2022
- [j67]Yurui Chen
How much can deep learning improve prediction of the responses to drugs in cancer cell lines? Briefings Bioinform. 23(1) (2022) - [j66]Michael Fuchs
Asymptotic enumeration and distributional properties of galled networks. J. Comb. Theory A 189: 105599 (2022) - [c46]Louxin Zhang
The Sackin Index of Simplex Networks. RECOMB-CG 2022: 52-67 - 2021
- [j65]Katharina Jahn, Niko Beerenwinkel, Louxin Zhang
The Bourque distances for mutation trees of cancers. Algorithms Mol. Biol. 16(1): 9 (2021) - [j64]Jinyu Chen, Louxin Zhang:
A survey and systematic assessment of computational methods for drug response prediction. Briefings Bioinform. 22(1): 232-246 (2021) - [j63]Michael Fuchs
On the asymptotic growth of the number of tree-child networks. Eur. J. Comb. 93: 103278 (2021) - [j62]Rohan B. H. Williams, Louxin Zhang:
Introduction to the Special Issue of the 18th Annual International RECOMB Satellite Workshop on Comparative Genomics. J. Bioinform. Comput. Biol. 19(6): 2102003:1-2102003:4 (2021) - [j61]Louxin Zhang
Guest Editorial for the 17th Asia Pacific Bioinformatics Conference. IEEE ACM Trans. Comput. Biol. Bioinform. 18(6): 2123-2124 (2021) - 2020
- [j60]Andreas D. M. Gunawan, Jeyaram Rathin
Counting and enumerating galled networks. Discret. Appl. Math. 283: 644-654 (2020) - [j59]Gabriel Cardona
Counting and enumerating tree-child networks and their subclasses. J. Comput. Syst. Sci. 114: 84-104 (2020) - [c45]Katharina Jahn, Niko Beerenwinkel, Louxin Zhang:
The Bourque Distances for Mutation Trees of Cancers. WABI 2020: 14:1-14:22 - [c44]Louxin Zhang:
Recent Progresses in the Combinatorial and Algorithmic Study of Rooted Phylogenetic Networks. WALCOM 2020: 22-27
2010 – 2019
- 2019
- [j58]Rudi Alberts
ZDOG: zooming in on dominating genes with mutations in cancer pathways. BMC Bioinform. 20(1): 740 (2019) - [j57]Louxin Zhang:
Generating normal networks via leaf insertion and nearest neighbor interchange. BMC Bioinform. 20-S(20): 642 (2019) - [j56]Andreas D. M. Gunawan, Hongwei Yan, Louxin Zhang:
Compression of Phylogenetic Networks and Algorithm for the Tree Containment Problem. J. Comput. Biol. 26(3): 285-294 (2019) - [i8]Louxin Zhang:
Generating Normal Networks via Leaf Insertion and Nearest Neighbor Interchange. CoRR abs/1906.12053 (2019) - 2018
- [j55]Hongwei Yan, Andreas D. M. Gunawan, Louxin Zhang:
S-Cluster++: a fast program for solving the cluster containment problem for phylogenetic networks. Bioinform. 34(17): i680-i686 (2018) - [j54]Wandrille Duchemin
RecPhyloXML: a format for reconciled gene trees. Bioinform. 34(21): 3646-3652 (2018) - [j53]Philippe Gambette
Solving the tree containment problem in linear time for nearly stable phylogenetic networks. Discret. Appl. Math. 246: 62-79 (2018) - [j52]Yi-Hua Yang, Chung-Shou Liao, Xin Han, Louxin Zhang:
Online buffer management for transmitting packets with processing cycles. Theor. Comput. Sci. 723: 73-83 (2018) - [i7]Andreas D. M. Gunawan, Bingxin Lu, Louxin Zhang:
Fast Methods for Solving the Cluster Containment Problem for Phylogenetic Networks. CoRR abs/1801.04498 (2018) - [i6]Andreas D. M. Gunawan, Hongwei Yan, Louxin Zhang:
The compressions of reticulation-visible networks are tree-child. CoRR abs/1806.07625 (2018) - 2017
- [j51]Bingxin Lu
A program to compute the soft Robinson-Foulds distance between phylogenetic networks. BMC Genom. 18(S2) (2017) - [j50]Andreas D. M. Gunawan, Bhaskar DasGupta, Louxin Zhang:
A decomposition theorem and two algorithms for reticulation-visible networks. Inf. Comput. 252: 161-175 (2017) - [j49]Yu Zheng, Louxin Zhang:
Reconciliation With Nonbinary Gene Trees Revisited. J. ACM 64(4): 24:1-24:28 (2017) - 2016
- [j48]Andreas D. M. Gunawan, Bingxin Lu
A program for verification of phylogenetic network models. Bioinform. 32(17): 503-510 (2016) - [j47]Louxin Zhang:
On Tree-Based Phylogenetic Networks. J. Comput. Biol. 23(7): 553-565 (2016) - [c43]Andreas D. M. Gunawan, Bhaskar DasGupta, Louxin Zhang:
Locating a Tree in a Reticulation-Visible Network in Cubic Time. RECOMB 2016: 266 - [r3]Bhaskar DasGupta, Xin He, Ming Li, John Tromp, Louxin Zhang:
Nearest Neighbor Interchange and Related Distances. Encyclopedia of Algorithms 2016: 1402-1405 - [r2]Louxin Zhang:
Superiority and Complexity of the Spaced Seeds. Encyclopedia of Algorithms 2016: 2166-2170 - [i5]Andreas D. M. Gunawan, Bhaskar DasGupta, Louxin Zhang:
Locating a Phylogenetic Tree in a Reticulation-Visible Network in Quadratic Time. CoRR abs/1603.08655 (2016) - 2015
- [c42]Philippe Gambette
Solving the Tree Containment Problem for Genetically Stable Networks in Quadratic Time. IWOCA 2015: 197-208 - [c41]Philippe Gambette
Locating a Tree in a Phylogenetic Network in Quadratic Time. RECOMB 2015: 96-107 - [i4]Philippe Gambette, Andreas D. M. Gunawan, Anthony Labarre, Stéphane Vialette, Louxin Zhang:
Locating a Tree in a Phylogenetic Network in Quadratic Time. CoRR abs/1502.03379 (2015) - [i3]Andreas D. M. Gunawan, Bhaskar DasGupta, Louxin Zhang:
Stability Implies Computational Tractability: Locating a Tree in a Stable Network is Easy. CoRR abs/1507.02119 (2015) - [i2]Andreas D. M. Gunawan, Louxin Zhang:
Bounding the Size of a Network Defined By Visibility Property. CoRR abs/1510.00115 (2015) - 2014
- [j46]Yu Zheng, Louxin Zhang:
Are the Duplication Cost and Robinson-Foulds Distance Equivalent? J. Comput. Biol. 21(8): 578-590 (2014) - [j45]Yu Zheng, Louxin Zhang:
Effect of Incomplete Lineage SortingOn Tree-Reconciliation-Based Inferenceof Gene Duplication. IEEE ACM Trans. Comput. Biol. Bioinform. 11(3): 477-485 (2014) - [c40]Yu Zheng, Louxin Zhang:
Reconciliation with Non-binary Gene Trees Revisited. RECOMB 2014: 418-432 - 2013
- [j44]Sebastian Maurer-Stroh
Motif Discovery with Data Mining in 3D protein Structure Databases: Discovery, Validation and Prediction of the U-Shape zinc binding ("Huf-zinc") Motif. J. Bioinform. Comput. Biol. 11(1) (2013) - [j43]Si Li, Kwok Pui Choi, Taoyang Wu
Maximum Likelihood Inference of the Evolutionary History of a PPI Network from the Duplication History of Its Proteins. IEEE ACM Trans. Comput. Biol. Bioinform. 10(6): 1412-1421 (2013) - [c39]Yu Zheng, Taoyang Wu
A Linear-Time Algorithm for Reconciliation of Non-binary Gene Tree and Binary Species Tree. COCOA 2013: 190-201 - [c38]Yu Zheng, Louxin Zhang:
A Tool for Non-binary Tree Reconciliation. ISBRA 2013: 40-51 - [c37]Yu Zheng, Louxin Zhang:
Effect of Incomplete Lineage Sorting on Tree-Reconciliation-Based Inference of Gene Duplication. ISBRA 2013: 261-272 - [c36]Ngoc Hieu Tran, Kwok Pui Choi, Louxin Zhang:
Counting Motifs in the Entire Biological Network from Noisy and Incomplete Data - (Extended Abstract). RECOMB 2013: 269-270 - 2012
- [j42]Xin Chen, Qiong Wu, Ruimin Sun, Louxin Zhang:
Two combinatorial optimization problems for SNP discovery using base-specific cleavage and mass spectrometry. BMC Syst. Biol. 6(S-2): S5 (2012) - [j41]Chung-Shou Liao, Louxin Zhang:
Approximating the Spanning k-Tree forest Problem. Int. J. Found. Comput. Sci. 23(7): 1543-1554 (2012) - [c35]Minmei Hou, Louxin Zhang, Robert S. Harris:
Alignment seeding strategies using contiguous pyrimidine purine matches. BCB 2012: 384-391 - [c34]Si Li, Kwok Pui Choi, Taoyang Wu
Reconstruction of Network Evolutionary History from Extant Network Topology and Duplication History. ISBRA 2012: 165-176 - 2011
- [j40]Taoyang Wu
Structural properties of the reconciliation space and their applications in enumerating nearly-optimal reconciliations between a gene tree and a species tree. BMC Bioinform. 12(S-9): S7 (2011) - [j39]Bin Ma, Louxin Zhang:
Efficient estimation of the accuracy of the maximum likelihood method for ancestral state reconstruction. J. Comb. Optim. 21(4): 409-422 (2011) - [j38]Louxin Zhang:
From Gene Trees to Species Trees II: Species Tree Inference by Minimizing Deep Coalescence Events. IEEE ACM Trans. Comput. Biol. Bioinform. 8(6): 1685-1691 (2011) - [c33]Louxin Zhang, Yen Kaow Ng
Network model and efficient method for detecting relative duplications or horizontal gene transfers. ICCABS 2011: 214-219 - [c32]Bin Fu, Louxin Zhang:
A Polynomial Algebra Method for Computing Exemplar Breakpoint Distance. ISBRA 2011: 297-305 - 2010
- [j37]Giltae Song
CAGE: Combinatorial Analysis of Gene-Cluster Evolution. J. Comput. Biol. 17(9): 1227-1242 (2010) - [c31]Louxin Zhang, Yun Cui:
An Efficient Method for DNA-Based Species Assignment via Gene Tree and Species Tree Reconciliation. WABI 2010: 300-311
2000 – 2009
- 2009
- [b1]Kun-Mao Chao, Louxin Zhang:
Sequence Comparison - Theory and Methods. Computational Biology 7, Springer 2009, ISBN 978-1-84800-319-4, pp. i-xx, 1-209 - [c30]Chung-Shou Liao, Louxin Zhang:
Approximating the Spanning k-Tree Forest Problem. FAW 2009: 293-301 - [c29]Giltae Song
Inferring the Recent Duplication History of a Gene Cluster. RECOMB-CG 2009: 111-125 - 2008
- [j36]Shuai Cheng Li
A PTAS For The k-Consensus Structures Problem Under Squared Euclidean Distance. Algorithms 1(2): 43-51 (2008) - [j35]Huy Hoang Do, Kwok Pui Choi, Franco P. Preparata, Wing-Kin Sung
Spectrum-Based De Novo Repeat Detection in Genomic Sequences. J. Comput. Biol. 15(5): 469-488 (2008) - [j34]Jian Ma
DUPCAR: Reconstructing Contiguous Ancestral Regions with Duplications. J. Comput. Biol. 15(8): 1007-1027 (2008) - [j33]Jialiang Yang
Run Probabilities of Seed-Like Patterns and Identifying Good Transition Seeds. J. Comput. Biol. 15(10): 1295-1313 (2008) - [j32]C. Thach Nguyen, Jian Shen, Minmei Hou, Li Sheng, Webb Miller, Louxin Zhang:
Approximating the Spanning Star Forest Problem and Its Application to Genomic Sequence Alignment. SIAM J. Comput. 38(3): 946-962 (2008) - [c28]Jialiang Yang, Louxin Zhang:
Run Probability of High-Order Seed Patterns and its Applications to Finding Good Transition Seeds. APBC 2008: 123-132 - [c27]Shuai Cheng Li
A PTAS for the k-Consensus Structures Problem Under Euclidean Squared Distance. FAW 2008: 35-44 - [r1]Bhaskar DasGupta, Xin He, Tao Jiang, Ming Li, John Tromp, Louxin Zhang:
Nearest Neighbor Interchange and Related Distances. Encyclopedia of Algorithms 2008 - 2007
- [j31]Jinsong Tan, Kok Seng Chua, Louxin Zhang, Song Zhu:
Algorithmic and Complexity Issues of Three Clustering Methods in Microarray Data Analysis. Algorithmica 48(2): 203-219 (2007) - [j30]Jinsong Tan, Louxin Zhang:
The Consecutive Ones Submatrix Problem for Sparse Matrices. Algorithmica 48(3): 287-299 (2007) - [j29]C. Thach Nguyen, Nguyen Bao Nguyen, Wing-Kin Sung
Reconstructing Recombination Network from Sequence Data: The Small Parsimony Problem. IEEE ACM Trans. Comput. Biol. Bioinform. 4(3): 394-402 (2007) - [j28]Louxin Zhang:
Superiority of Spaced Seeds for Homology Search. IEEE ACM Trans. Comput. Biol. Bioinform. 4(3): 496-505 (2007) - [c26]Min Xu, Louxin Zhang, Pei Li Joe Zhou:
A Robust Method for Generating Discriminative Gene Clusters. BIBE 2007: 538-545 - [c25]Guoliang Li, Jian Ma, Louxin Zhang:
Selecting Genomes for Reconstruction of Ancestral Genomes. RECOMB-CG 2007: 110-121 - [c24]Jian Ma, Aakrosh Ratan, Louxin Zhang, Webb Miller, David Haussler:
A Heuristic Algorithm for Reconstructing Ancestral Gene Orders with Duplications. RECOMB-CG 2007: 122-135 - [c23]C. Thach Nguyen, Jian Shen, Minmei Hou, Li Sheng, Webb Miller, Louxin Zhang:
Approximating the spanning star forest problem and its applications to genomic sequence alignment. SODA 2007: 645-654 - 2006
- [j27]Guillaume Bourque, Louxin Zhang:
Models and Methods in Comparative Genomics. Adv. Comput. 68: 60-105 (2006) - [c22]Ming Li, Bin Ma, Louxin Zhang:
Superiority and complexity of the spaced seeds. SODA 2006: 444-453 - [c21]Aaron E. Darling, Todd J. Treangen, Louxin Zhang, Carla Kuiken, Xavier Messeguer, Nicole T. Perna:
Procrastination Leads to Efficient Filtration for Local Multiple Alignment. WABI 2006: 126-137 - [c20]Minmei Hou, Piotr Berman, Louxin Zhang, Webb Miller:
Controlling Size When Aligning Multiple Genomic Sequences with Duplications. WABI 2006: 138-149 - 2005
- [j26]C. Thach Nguyen, Y. C. Tay, Louxin Zhang:
Divide-and-conquer approach for the exemplar breakpoint distance. Bioinform. 21(10): 2171-2176 (2005) - [j25]Franco P. Preparata, Louxin Zhang, Kwok Pui Choi:
Quick, Practical Selection of Effective Seeds for Homology Search. J. Comput. Biol. 12(9): 1137-1152 (2005) - [j24]Guoliang Li
Translation Initiation Sites Prediction with Mixture Gaussian Models in Human cDNA Sequences. IEEE Trans. Knowl. Data Eng. 17(8): 1152-1160 (2005) - [c19]Jinsong Tan, Kok Seng Chua, Louxin Zhang:
Algorithmic and Complexity Issues of Three Clustering Methods in Microarray Data Analysis. COCOON 2005: 74-83 - 2004
- [j23]Kwok Pui Choi, Fanfan Zeng, Louxin Zhang:
Good spaced seeds for homology search. Bioinform. 20(7): 1053-1059 (2004) - [j22]Oscar H. Ibarra, Louxin Zhang:
Computing And Combinatorics Conference -- Cocoon'02. Int. J. Found. Comput. Sci. 15(1): 1 (2004) - [j21]Kwok Pui Choi, Louxin Zhang:
Sensitivity analysis and efficient method for identifying optimal spaced seeds. J. Comput. Syst. Sci. 68(1): 22-40 (2004) - [c18]Kwok Pui Choi, Fanfan Zeng, Louxin Zhang:
Good Spaced Seeds For Homology Search. BIBE 2004: 379-386 - [c17]Jinsong Tan, Louxin Zhang:
Approximation Algorithms for the Consecutive Ones Submatrix Problem on Sparse Matrices. ISAAC 2004: 835-846 - [c16]Guoliang Li, Tze-Yun Leong, Louxin Zhang:
Translation Initiation Sites Prediction with Mixture Gaussian Models. WABI 2004: 338-349 - 2003
- [j20]Louxin Zhang, Bin Ma, Lusheng Wang
Greedy method for inferring tandem duplication history. Bioinform. 19(12): 1497-1504 (2003) - [j19]J. Kevin Lanctôt, Ming Li, Bin Ma, Shaojiu Wang, Louxin Zhang:
Distinguishing string selection problems. Inf. Comput. 185(1): 41-55 (2003) - 2002
- [c15]Louxin Zhang, Song Zhu:
A New Clustering Method for Microarray Data Analysis. CSB 2002: 268-275 - [c14]Louxin Zhang, Bin Ma, Lusheng Wang:
Efficient Methods for Inferring Tandem Duplication History. WABI 2002: 97-111 - [e1]Oscar H. Ibarra, Louxin Zhang:
Computing and Combinatorics, 8th Annual International Conference, COCOON 2002, Singapore, August 15-17, 2002, Proceedings. Lecture Notes in Computer Science 2387, Springer 2002, ISBN 3-540-43996-X [contents] - 2001
- [j18]Louxin Zhang, Chew-Kiat Heng
Cladogramer: incorporating haplotype frequency into cladogram analysis. Bioinform. 17(5): 481-482 (2001) - [j17]Lusheng Wang
Perfect Phylogenetic Networks with Recombination. J. Comput. Biol. 8(1): 69-78 (2001) - [c13]Louxin Zhang, Song Zhu:
Complexity Study on Two Clustering Problems. ISAAC 2001: 660-669 - [c12]Lusheng Wang, Kaizhong Zhang, Louxin Zhang:
Perfect phylogenetic networks with recombination. SAC 2001: 46-50 - 2000
- [j16]Guozhu Dong, Louxin Zhang:
Separating Auxiliary Arity Hierarchy of First-Order Incremental Evaluation Systems Using (3k+1)-ary Input Relations. Int. J. Found. Comput. Sci. 11(4): 573-578 (2000) - [j15]Bin Ma, Ming Li, Louxin Zhang:
From Gene Trees to Species Trees. SIAM J. Comput. 30(3): 729-752 (2000)
1990 – 1999
- 1999
- [j14]Allison Lim, Louxin Zhang:
WebPHYLIP: a web interface to PHYLIP. Bioinform. 15(12): 1068-1069 (1999) - [j13]Ming Li, Louxin Zhang:
Twist-Rotation Transformations of Binary Trees and Arithmetic Expressions. J. Algorithms 32(2): 155-166 (1999) - [j12]Bin Ma, Lusheng Wang, Louxin Zhang:
Fitting Distances by Tree Metrics with Increment Error. J. Comb. Optim. 3(2-3): 213-225 (1999) - [j11]Louxin Zhang:
Optimal Bounds for Matching Routing on Trees. SIAM J. Discret. Math. 12(1): 64-77 (1999) - [c11]Bhaskar DasGupta, Xin He, Tao Jiang, Ming Li, John Tromp, Louxin Zhang:
On computing the nearest neighbor interchange distance. Discrete Mathematical Problems with Medical Applications 1999: 125-143 - [c10]J. Kevin Lanctôt, Ming Li, Bin Ma, Shaojiu Wang, Louxin Zhang:
Distinguishing String Selection Problems. SODA 1999: 633-642 - 1998
- [j10]Richard Beigel, William I. Gasarch, Ming Li, Louxin Zhang:
Addition in log2n + O(1) Steps on Average: A Simple Analysis. Theor. Comput. Sci. 191(1-2): 245-248 (1998) - [c9]Ming Li, Louxin Zhang:
Better Approximation of Diagonal-Flip Transformation and Rotation Transformation. COCOON 1998: 85-94 - [c8]Bin Ma, Ming Li, Louxin Zhang:
On reconstructing species trees from gene trees in term of duplications and losses. RECOMB 1998: 182-191 - [c7]Jing Chen, Limsoon Wong, Louxin Zhang:
A Protein Patent Query System Powered By Kleisli. SIGMOD Conference 1998: 593-595 - 1997
- [j9]Louxin Zhang:
On a Mirkin-Muchnik-Smith Conjecture for Comparing Molecular Phylogenies. J. Comput. Biol. 4(2): 177-187 (1997) - [j8]John Tromp
Small Weight Bases for Hamming Codes. Theor. Comput. Sci. 181(2): 337-345 (1997) - [c6]Danny Krizanc, Louxin Zhang:
Many-to-One Packed Routing via Matchings. COCOON 1997: 11-17 - [c5]Bhaskar DasGupta, Xin He, Tao Jiang, Ming Li, John Tromp, Louxin Zhang:
On Distances between Phylogenetic Trees (Extended Abstract). SODA 1997: 427-436 - [c4]Louxin Zhang:
Optimal Bounds for Matching Routing on Trees. SODA 1997: 445-453 - 1996
- [j7]Louxin Zhang, Lian Li, Jinzhao Wu:
On the descriptive power of special Thue systems. Discret. Math. 160(1-3): 291-297 (1996) - [c3]Ming Li, John Tromp, Louxin Zhang:
Some Notes on the Nearest Neighbour Interchange Distance. COCOON 1996: 343-351 - [i1]Richard Beigel, William I. Gasarch, Ming Li, Louxin Zhang:
Addition in log2n + O(1) Steps on Average: A Simple Analysis. Electron. Colloquium Comput. Complex. TR96 (1996) - 1995
- [j6]Louxin Zhang:
On the Approximation of Longest Common Nonsupersequences and Shortest Common Nonsubsequences. Theor. Comput. Sci. 143(2): 353-362 (1995) - [c2]John Tromp, Louxin Zhang, Ying Zhao:
Small Weight Bases for Hamming Codes. COCOON 1995: 235-243 - [c1]Alan Roberts, Antonios Symvonis
Routing on Trees via Matchings. WADS 1995: 251-262 - 1993
- [j5]Klaus Madlener, Paliath Narendran, Friedrich Otto, Louxin Zhang:
On Weakly Confluent Monadic String-Rewriting Systems. Theor. Comput. Sci. 113(1): 119-165 (1993) - 1992
- [j4]Louxin Zhang:
On the Conjugacy Problem for One-Relator Monoids with Elements of Finite Order. Int. J. Algebra Comput. 2(2): 209-220 (1992) - [j3]Louxin Zhang:
The Pre-NTS Property is Undecidable for Context-Free Grammars. Inf. Process. Lett. 44(4): 181-184 (1992) - [j2]Louxin Zhang:
Some Properties of Finite Special String-Rewriting Systems. J. Symb. Comput. 14(4): 359-370 (1992) - 1991
- [j1]Friedrich Otto, Louxin Zhang:
Decision Problems for Finite Special String-Rewriting Systems that are Confluent on Some Congruence Class. Acta Informatica 28(5): 477-510 (1991)
Coauthor Index
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