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Dan Gusfield - Publications

Affiliations: 
Computer Science University of California, Davis, Davis, CA 
Area:
Computer Science, Mathematics
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78 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2017 Matsieva J, Kelk S, Scornavacca C, Whidden C, Gusfield D. A Resolution of the Static Formulation Question for the Problem of Computing the History Bound. Ieee/Acm Transactions On Computational Biology and Bioinformatics. 14: 404-417. PMID 26887004 DOI: 10.1109/Tcbb.2016.2527645  0.391
2016 Frid Y, Gusfield D. An improved Four-Russians method and sparsified Four-Russians algorithm for RNA folding. Algorithms For Molecular Biology : Amb. 11: 22. PMID 27499801 DOI: 10.1186/S13015-016-0081-9  0.798
2015 Gusfield D. Persistent phylogeny: A galled-tree and integer linear programming approach Bcb 2015 - 6th Acm Conference On Bioinformatics, Computational Biology, and Health Informatics. 443-451. DOI: 10.1145/2808719.2808765  0.341
2015 Xu SJ, Gysel R, Gusfield D. Minimum average distance clique trees Siam Journal On Discrete Mathematics. 29: 1706-1734. DOI: 10.1137/15M1021052  0.369
2015 Coulombe M, Stevens K, Gusfield D. Construction, enumeration, and optimization of perfect phylogenies on multi-state data 2015 Ieee 5th International Conference On Computational Advances in Bio and Medical Sciences, Iccabs 2015. DOI: 10.1109/ICCABS.2015.7344709  0.377
2015 Frid Y, Gusfield D. A sparsified four-Russian algorithm for RNA folding Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 9289: 271-285. DOI: 10.1007/978-3-662-48221-6_20  0.812
2014 Venkatachalam B, Gusfield D, Frid Y. Faster algorithms for RNA-folding using the Four-Russians method. Algorithms For Molecular Biology : Amb. 9: 5. PMID 24602450 DOI: 10.1186/1748-7188-9-5  0.8
2013 Gysel R, Gusfield D, Stevens K. Triangulation heuristics for maximum character compatibility 2013 Ieee 3rd International Conference On Computational Advances in Bio and Medical Sciences, Iccabs 2013. DOI: 10.1109/ICCABS.2013.6629217  0.34
2012 Gysel R, Lam F, Gusfield D. Constructing perfect phylogenies and proper triangulations for three-state characters. Algorithms For Molecular Biology : Amb. 7: 26. PMID 23006612 DOI: 10.1186/1748-7188-7-26  0.37
2012 Gysel R, Stevens K, Gusfield D. Reducing problems in unrooted tree compatibility to restricted triangulations of intersection graphs Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 7534: 93-105. DOI: 10.1007/978-3-642-33122-0_8  0.344
2012 Frid Y, Gusfield D. Speedup of RNA pseudoknotted secondary structure recurrence computation with the four-Russians method Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 7402: 176-187. DOI: 10.1007/978-3-642-31770-5_16  0.798
2011 Gysel R, Gusfield D. Extensions and improvements to the chordal graph approach to the multistate perfect phylogeny problem. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 8: 912-7. PMID 21301033 DOI: 10.1109/Tcbb.2011.27  0.439
2011 Lam F, Gusfield D, Sridhar S. Generalizing the splits equivalence theorem and four gamete condition: Perfect phylogeny on three-state characters Siam Journal On Discrete Mathematics. 25: 1144-1175. DOI: 10.1137/090776305  0.329
2010 Venkatachalam B, Apple J, St John K, Gusfield D. Untangling tanglegrams: comparing trees by their drawings. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 7: 588-97. PMID 20530818 DOI: 10.1109/Tcbb.2010.57  0.552
2010 Gusfield D. The Multi-State Perfect Phylogeny Problem with missing and removable data: solutions via integer-programming and chordal graph theory. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 17: 383-99. PMID 20377452 DOI: 10.1089/Cmb.2009.0200  0.425
2010 Frid Y, Gusfield D. A simple, practical and complete O(n3/log n)-time algorithm for RNA folding using the Four-Russians speedup. Algorithms For Molecular Biology : Amb. 5: 13. PMID 20047670 DOI: 10.1186/1748-7188-5-13  0.798
2010 Frid Y, Gusfield D. A worst-case and practical speedup for the RNA co-folding problem using the Four-Russians idea Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 6293: 1-12. DOI: 10.1007/978-3-642-15294-8_1  0.813
2010 Gysel R, Gusfield D. Extensions and improvements to the chordal graph approach to the multi-state perfect phylogeny problem Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 6053: 52-60. DOI: 10.1007/978-3-642-13078-6_8  0.332
2009 Gusfield D, Wu Y. The Three-state Perfect Phylogeny Problem Reduces to 2-SAT Communications in Information and Systems. 9: 295-302. DOI: 10.4310/Cis.2009.V9.N4.A1  0.401
2009 Frid Y, Gusfield D. A Simple, Practical and Complete O(\frac{n3}{ \log n) -Time Algorithm for RNA Folding Using the Four-Russians Speedup Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 5724: 97-107. DOI: 10.1007/978-3-642-04241-6_9  0.808
2008 Wu Y, Gusfield D. A new recombination lower bound and the minimum perfect phylogenetic forest problem Journal of Combinatorial Optimization. 16: 229-247. DOI: 10.1007/S10878-007-9129-6  0.401
2007 Gusfield D, Bansal V, Bafna V, Song YS. A decomposition theory for phylogenetic networks and incompatible characters. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 14: 1247-72. PMID 18047426 DOI: 10.1089/Cmb.2006.0137  0.422
2007 Song YS, Ding Z, Gusfield D, Langley CH, Wu Y. Algorithms to distinguish the role of gene-conversion from single-crossover recombination in the derivation of SNP sequences in populations. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 14: 1273-86. PMID 18047424 DOI: 10.1089/Cmb.2007.0096  0.418
2007 Wu Y, Gusfield D. Efficient computation of minimum recombination with genotypes (not haplotypes). Journal of Bioinformatics and Computational Biology. 5: 181-200. PMID 17589959 DOI: 10.1142/S0219720007002631  0.361
2007 Gusfield D, Hickerson D, Eddhu S. An efficiently computed lower bound on the number of recombinations in phylogenetic networks: Theory and empirical study Discrete Applied Mathematics. 155: 806-830. DOI: 10.1016/J.Dam.2005.05.044  0.419
2007 Wu Y, Gusfield D. Improved algorithms for inferring the minimum mosaic of a set of recombinants Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4580: 150-161.  0.461
2007 Gusfield D, Frid Y, Brown D. Integer programming formulations and computations solving phylogenetic and population genetic problems with missing or genotypic data Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4598: 51-64.  0.76
2006 Ding Z, Filkov V, Gusfield D. A linear-time algorithm for the perfect phylogeny haplotyping (PPH) problem. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 13: 522-53. PMID 16597255 DOI: 10.1089/Cmb.2006.13.522  0.518
2005 Song YS, Wu Y, Gusfield D. Efficient computation of close lower and upper bounds on the minimum number of recombinations in biological sequence evolution. Bioinformatics (Oxford, England). 21: i413-22. PMID 15961486 DOI: 10.1093/Bioinformatics/Bti1033  0.419
2005 Gusfield D. Optimal, efficient reconstruction of root-unknown phylogenetic networks with constrained and structured recombination Journal of Computer and System Sciences. 70: 381-398. DOI: 10.1016/J.Jcss.2004.12.009  0.489
2004 Bafna V, Gusfield D, Hannenhalli S, Yooseph S. A note on efficient computation of haplotypes via perfect phylogeny. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 11: 858-66. PMID 15700406 DOI: 10.1089/Cmb.2004.11.858  0.411
2004 Gusfield D, Eddhu S, Langley C. Optimal, efficient reconstruction of phylogenetic networks with constrained recombination. Journal of Bioinformatics and Computational Biology. 2: 173-213. PMID 15272438 DOI: 10.1142/S0219720004000521  0.433
2004 Gusfield D, Eddhu S, Langley C. The fine structure of galls in phylogenetic networks Informs Journal On Computing. 16: 459-469. DOI: 10.1287/Ijoc.1040.0099  0.389
2004 Gusfield D, Stoye J. Linear time algorithms for finding and representing all the tandem repeats in a string Journal of Computer and System Sciences. 69: 525-546. DOI: 10.1016/J.Jcss.2004.03.004  0.389
2004 Gusfield D. Combinatorial approaches to haplotype inference Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2983: 136.  0.402
2003 Piccolboni A, Gusfield D. On the complexity of fundamental computational problems in pedigree analysis. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 10: 763-73. PMID 14633398 DOI: 10.1089/106652703322539088  0.384
2003 Bafna V, Gusfield D, Lancia G, Yooseph S. Haplotyping as perfect phylogeny: a direct approach. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 10: 323-40. PMID 12935331 DOI: 10.1089/10665270360688048  0.506
2002 Stoye J, Gusfield D. Simple and flexible detection of contiguous repeats using a suffix tree Theoretical Computer Science. 270: 843-856. DOI: 10.1016/S0304-3975(01)00121-9  0.471
2002 Gusfield D. Partition-distance: A problem and class of perfect graphs arising in clustering Information Processing Letters. 82: 159-164. DOI: 10.1016/S0020-0190(01)00263-0  0.328
2002 Gusfield D, Martel C. The structure and complexity of sports elimination numbers Algorithmica (New York). 32: 73-86. DOI: 10.1007/S00453-001-0074-Y  0.411
2001 Gusfield D. Inference of haplotypes from samples of diploid populations: Complexity and algorithms Journal of Computational Biology. 8: 305-323. PMID 11535178 DOI: 10.1089/10665270152530863  0.396
2000 Wang L, Jiang T, Gusfield D. A more efficient approximation scheme for tree alignment Siam Journal On Computing. 30: 283-299. DOI: 10.1137/S0097539796313507  0.477
1999 Holmes SP, Gusfield D. Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology Journal of the American Statistical Association. 94: 989. DOI: 10.2307/2670026  0.434
1998 Wang L, Gusfield D. Constructing additive trees when the error is small Journal of Computational Biology. 5: 127-133. PMID 9541876 DOI: 10.1089/Cmb.1998.5.127  0.339
1998 Kececioglu J, Gusfield D. Reconstructing a history of recombinations from a set of sequences Discrete Applied Mathematics. 88: 239-260. DOI: 10.1016/S0166-218X(98)00074-2  0.394
1998 Gusfield D, Karp R, Wang L, Stelling P. Graph traversals, genes and matroids: An efficient case of the travelling salesman problem Discrete Applied Mathematics. 88: 167-180. DOI: 10.1016/S0166-218X(98)00071-7  0.406
1998 Stoye J, Gusfield D. Simple and flexible detection of contiguous repeats using a suffix tree (preliminary version) Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 1448: 140-152.  0.371
1997 Naor D, Gusfield D, Martel C. A Fast Algorithm for Optimally Increasing the Edge Connectivity Siam Journal On Computing. 26: 1139-1165. DOI: 10.1137/S0097539792234226  0.478
1997 Wang L, Gusfield D. Improved Approximation Algorithms for Tree Alignment Journal of Algorithms. 25: 255-273. DOI: 10.1006/Jagm.1997.0882  0.477
1997 Naor D, Gusfield D, Martel C. A fast algorithm for optimally increasing the edge connectivity Siam Journal On Computing. 26: 1139-1165.  0.369
1994 Gusfield D. Faster implementation of a shortest superstring approximation Information Processing Letters. 51: 271-274. DOI: 10.1016/0020-0190(94)00097-2  0.454
1994 Gusfield D, Tardos E. A faster parametric minimum-cut algorithm Algorithmica. 11: 278-290. DOI: 10.1007/Bf01240737  0.484
1993 Gusfield D. Efficient methods for multiple sequence alignment with guaranteed error bounds Bulletin of Mathematical Biology. 55: 141-154. PMID 7680269 DOI: 10.1007/Bf02460299  0.409
1993 Kao M, Gusfield D. Efficient Detection and Protection of Information in Cross Tabulated Tables I: Linear Invariant Test Siam Journal On Discrete Mathematics. 6: 460-476. DOI: 10.1137/0406037  0.424
1993 Gusfield D, Naor D. Extracting maximal information about sets of minimum cuts Algorithmica. 10: 64-89. DOI: 10.1007/Bf01908632  0.385
1992 Gusfield D, M. Landau G, Schieber B. An efficient algorithm for the All Pairs Suffix-Prefix Problem Information Processing Letters. 41: 181-185. DOI: 10.1016/0020-0190(92)90176-V  0.402
1992 Gusfield D, Pitt L. A bounded approximation for the minimum cost 2-sat problem Algorithmica. 8: 103-117. DOI: 10.1007/Bf01758838  0.498
1992 Gusfield D, Martel C. A fast algorithm for the generalized parametric minimum cut problem and applications Algorithmica. 7: 499-519. DOI: 10.1007/Bf01758775  0.45
1991 Gusfield D. Computing the Strength of a Graph Siam Journal On Computing. 20: 639-654. DOI: 10.1137/0220040  0.386
1991 Gusfield D, Naor D. Efficient algorithms for generalized cut-trees Networks. 21: 505-520. DOI: 10.1002/Net.3230210503  0.383
1991 Gusfield D. Efficient algorithms for inferring evolutionary trees Networks. 21: 19-28. DOI: 10.1002/Net.3230210104  0.514
1990 Gusfield D. Very Simple Methods for All Pairs Network Flow Analysis Siam Journal On Computing. 19: 143-155. DOI: 10.1137/0219009  0.398
1989 Gusfield D. Efficient solution of the matroid product problem Operations Research Letters. 8: 257-259. DOI: 10.1016/0167-6377(89)90050-3  0.362
1989 Gusfield D, Irving RW. Parametric stable marriage and minimum cuts Information Processing Letters. 30: 255-259. DOI: 10.1016/0020-0190(89)90204-4  0.393
1989 Martel CU, Gusfield D. A fast parallel quicksort algorithm Information Processing Letters. 30: 97-102. DOI: 10.1016/0020-0190(89)90116-6  0.486
1988 Gusfield D. The Structure of the Stable Roommate Problem: Efficient Representation and Enumeration of All Stable Assignments Siam Journal On Computing. 17: 742-769. DOI: 10.1137/0217048  0.488
1988 Gusfield D. A Graph Theoretic Approach to Statistical Data Security Siam Journal On Computing. 17: 552-571. DOI: 10.1137/0217034  0.481
1987 Irving RW, Leather P, Gusfield D. An efficient algorithm for the “optimal” stable marriage Journal of the Acm (Jacm). 34: 532-543. DOI: 10.1145/28869.28871  0.491
1987 Gusfield D. Optimal Mixed Graph Augmentation Siam Journal On Computing. 16: 599-612. DOI: 10.1137/0216041  0.424
1987 Gusfield D, Martel C, Fernandez-Baca D. Fast Algorithms for Bipartite Network Flow Siam Journal On Computing. 16: 237-251. DOI: 10.1137/0216020  0.397
1987 Gusfield D. Three Fast Algorithms for Four Problems in Stable Marriage Siam Journal On Computing. 16: 111-128. DOI: 10.1137/0216010  0.545
1986 Gusfield D, Pitt L. Equivalent approximation algorithms for node cover Information Processing Letters. 22: 291-294. DOI: 10.1016/0020-0190(86)90068-2  0.364
1985 Gusfield D. Data structures and algorithms, by A. Aho, J. Hopcroft, and J. Ullman, Addison-Wesley, Reading, Mass., 1983, 427 pp. Price: $28.85 Networks. 15: 137-138. DOI: 10.1002/Net.3230150111  0.371
1984 Gusfield D. Bounds for naive multiple machine scheduling with release times and deadlines Journal of Algorithms. 5: 1-6. DOI: 10.1016/0196-6774(84)90035-X  0.382
1984 Gusfield D. Matroid optimization with the interleaving of two ordered sets Discrete Applied Mathematics. 8: 41-50. DOI: 10.1016/0166-218X(84)90077-5  0.343
1983 Gusfield D. Parametric Combinatorial Computing and a Problem of Program Module Distribution Journal of the Acm (Jacm). 30: 551-563. DOI: 10.1145/2402.322391  0.408
1983 Gusfield D. Simple Constructions for Multiterminal Network Flow Synthesis Siam Journal On Computing. 12: 157-165. DOI: 10.1137/0212010  0.387
1983 Gusfield D. A note on Arc tolerances in sparse shortest-path and network flow problems Networks. 13: 191-196. DOI: 10.1002/Net.3230130204  0.423
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