Dan Gusfield

Rob Gysel, Fumei Lam, Dan Gusfield: Constructing perfect phylogenies and proper triangulations for three-state characters. Algorithms for Molecular Biology 7: 26 (2012)

Yelena Frid, Dan Gusfield: Speedup of RNA Pseudoknotted Secondary Structure Recurrence Computation with the Four-Russians Method. COCOA 2012: 176-187

Rob Gysel, Kristian Stevens, Dan Gusfield: Reducing Problems in Unrooted Tree Compatibility to Restricted Triangulations of Intersection Graphs. WABI 2012: 93-105

Fumei Lam, Dan Gusfield, Srinath Sridhar: Generalizing the Splits Equivalence Theorem and Four Gamete Condition: Perfect Phylogeny on Three-State Characters. SIAM J. Discrete Math. 25(3): 1144-1175 (2011)

Rob Gysel, Dan Gusfield: Extensions and Improvements to the Chordal Graph Approach to the Multistate Perfect Phylogeny Problem. IEEE/ACM Trans. Comput. Biology Bioinform. 8(4): 912-917 (2011)

Rob Gysel, Fumei Lam, Dan Gusfield: Constructing Perfect Phylogenies and Proper Triangulations for Three-State Characters. WABI 2011: 104-115

Yelena Frid, Dan Gusfield: A simple, practical and complete O-time Algorithm for RNA folding using the Four-Russians Speedup. Algorithms for Molecular Biology 5: 13 (2010)

Dan Gusfield: The Multi-State Perfect Phylogeny Problem with Missing and Removable Data: Solutions via Integer-Programming and Chordal Graph Theory. Journal of Computational Biology 17(3): 383-399 (2010)

Balaji Venkatachalam, Jim Apple, Katherine St. John, Dan Gusfield: Untangling Tanglegrams: Comparing Trees by Their Drawings. IEEE/ACM Trans. Comput. Biology Bioinform. 7(4): 588-597 (2010)

Rob Gysel, Dan Gusfield: Extensions and Improvements to the Chordal Graph Approach to the Multi-state Perfect Phylogeny Problem. ISBRA 2010: 52-60

Yelena Frid, Dan Gusfield: A Worst-Case and Practical Speedup for the RNA Co-folding Problem Using the Four-Russians Idea. WABI 2010: 1-12

Kristian Stevens, Dan Gusfield: Reducing Multi-state to Binary Perfect Phylogeny with Applications to Missing, Removable, Inserted, and Deleted Data. WABI 2010: 274-287

Dan Gusfield, Anna Tramontano: Editorial. Bioinformatics 25(12) (2009)

Dan Gusfield: Final, Five-Year End, Editorial. IEEE/ACM Trans. Comput. Biology Bioinform. 6(1): 1-2 (2009)

Dan Gusfield: Outgoing EIC Editorial for this Special Section of TCBB with the Theme of Phylogenetics. IEEE/ACM Trans. Comput. Biology Bioinform. 6(1): 96 (2009)

Balaji Venkatachalam, Jim Apple, Katherine St. John, Dan Gusfield: Untangling Tanglegrams: Comparing Trees by Their Drawings. ISBRA 2009: 88-99

Dan Gusfield: The Multi-State Perfect Phylogeny Problem with Missing and Removable Data: Solutions via Integer-Programming and Chordal Graph Theory. RECOMB 2009: 236-252

Yelena Frid, Dan Gusfield: A Simple, Practical and Complete O(\fracn³ logn)O(\frac{n^3}{ \log n})-Time Algorithm for RNA Folding Using the Four-Russians Speedup. WABI 2009: 97-107

Fumei Lam, Dan Gusfield, Srinath Sridhar: Generalizing the Four Gamete Condition and Splits Equivalence Theorem: Perfect Phylogeny on Three State Characters. WABI 2009: 206-219

Yufeng Wu, Dan Gusfield: A new recombination lower bound and the minimum perfect phylogenetic forest problem. J. Comb. Optim. 16(3): 229-247 (2008)

Dan Gusfield: EIC Editorial. IEEE/ACM Trans. Comput. Biology Bioinform. 5(4): 481 (2008)

Dan Gusfield: ReCombinatorics: Combinatorial Algorithms for Studying the History of Recombination in Populations. CPM 2008: 1-2

Dan Gusfield, Dean Hickerson, Satish Eddhu: An efficiently computed lower bound on the number of recombinations in phylogenetic networks: Theory and empirical study. Discrete Applied Mathematics 155(6-7): 806-830 (2007)

Yufeng Wu, Dan Gusfield: Efficient Computation of Minimum Recombination with genotypes (not Haplotypes). J. Bioinformatics and Computational Biology 5(2a): 181-200 (2007)

Dan Gusfield, Vikas Bansal, Vineet Bafna, Yun S. Song: A Decomposition Theory for Phylogenetic Networks and Incompatible Characters. Journal of Computational Biology 14(10): 1247-1272 (2007)

Yun S. Song, Zhihong Ding, Dan Gusfield, Charles H. Langley, Yufeng Wu: Algorithms to Distinguish the Role of Gene-Conversion from Single-Crossover Recombination in the Derivation of SNP Sequences in Populations. Journal of Computational Biology 14(10): 1273-1286 (2007)

Dan Gusfield: State of the Journal. IEEE/ACM Trans. Comput. Biology Bioinform. 4(1): 1 (2007)

Dan Gusfield: Associate Editor Appreciation and Welcome. IEEE/ACM Trans. Comput. Biology Bioinform. 4(1): 2 (2007)

Dan Gusfield: Associate Editor Appreciation and Welcome. IEEE/ACM Trans. Comput. Biology Bioinform. 4(3): 321 (2007)

Yufeng Wu, Dan Gusfield: A New Recombination Lower Bound and the Minimum Perfect Phylogenetic Forest Problem. COCOON 2007: 16-26

Dan Gusfield, Yelena Frid, Daniel G. Brown: Integer Programming Formulations and Computations Solving Phylogenetic and Population Genetic Problems with Missing or Genotypic Data. COCOON 2007: 51-64

Yufeng Wu, Dan Gusfield: Improved Algorithms for Inferring the Minimum Mosaic of a Set of Recombinants. CPM 2007: 150-161

Zhihong Ding, Vladimir Filkov, Dan Gusfield: A Linear-Time Algorithm for the Perfect Phylogeny Haplotyping (PPH) Problem. Journal of Computational Biology 13(2): 522-553 (2006)

Dan Gusfield: State of the Journal. IEEE/ACM Trans. Comput. Biology Bioinform. 3(1): 1 (2006)

Dan Gusfield: Introduction of New Associate Editors. IEEE/ACM Trans. Comput. Biology Bioinform. 3(2): 97 (2006)

Dan Gusfield: Efficient and Practical Algorithms for Deducing the History of Recombination in Populations. International Conference on Computational Science (2) 2006: 618-619

Yun S. Song, Zhihong Ding, Dan Gusfield, Charles H. Langley, Yufeng Wu: Algorithms to Distinguish the Role of Gene-Conversion from Single-Crossover Recombination in the Derivation of SNP Sequences in Populations. RECOMB 2006: 231-245

Dan Gusfield: Preface: Special RECOMB 2004 Issue. Journal of Computational Biology 12(6): 567-568 (2005)

Dan Gusfield: Optimal, efficient reconstruction of root-unknown phylogenetic networks with constrained and structured recombination. J. Comput. Syst. Sci. 70(3): 381-398 (2005)

Dan Gusfield: Editorial-State of the Transaction. IEEE/ACM Trans. Comput. Biology Bioinform. 2(1): 39 (2005)

Yun S. Song, Yufeng Wu, Dan Gusfield: Efficient computation of close lower and upper bounds on the minimum number of recombinations in biological sequence evolution. ISMB (Supplement of Bioinformatics) 2005: 413-422

Dan Gusfield, Vikas Bansal: A Fundamental Decomposition Theory for Phylogenetic Networks and Incompatible Characters. RECOMB 2005: 217-232

Zhihong Ding, Vladimir Filkov, Dan Gusfield: A Linear-Time Algorithm for the Perfect Phylogeny Haplotyping (PPH) Problem. RECOMB 2005: 585-600

Yun S. Song, Yufeng Wu, Dan Gusfield: Algorithms for Imperfect Phylogeny Haplotyping (IPPH) with a Single Homoplasy or Recombination Event. WABI 2005: 152-164

Dan Gusfield, Satish Eddhu, Charles H. Langley: The Fine Structure of Galls in Phylogenetic Networks. INFORMS Journal on Computing 16(4): 459-469 (2004)

Dan Gusfield, Satish Eddhu, Charles H. Langley: Optimal, Efficient Reconstruction of Phylogenetic Networks with Constrained Recombination. J. Bioinformatics and Computational Biology 2(1): 173-214 (2004)

Vineet Bafna, Dan Gusfield, Sridhar Hannenhalli, Shibu Yooseph: A Note on Efficient Computation of Haplotypes via Perfect Phylogeny. Journal of Computational Biology 11(5): 858-866 (2004)

Dan Gusfield, Jens Stoye: Linear time algorithms for finding and representing all the tandem repeats in a string. J. Comput. Syst. Sci. 69(4): 525-546 (2004)

Dan Gusfield: Introduction of New Associate Editors. IEEE/ACM Trans. Comput. Biology Bioinform. 1(3): 97 (2004)

Dan Gusfield: Invited Talk: Phylogenetic Networks with Constrained and Unconstrained Recombination. German Conference on Bioinformatics 2004: 1-2

Philip E. Bourne, Dan Gusfield (Eds.): Proceedings of the Eighth Annual International Conference on Computational Molecular Biology, 2004, San Diego, California, USA, March 27-31, 2004. ACM 2004, isbn 1-58113-755-9

Ren Hua Chung, Dan Gusfield: Perfect phylogeny haplotyper: haplotype inferral using a tree model. Bioinformatics 19(6): 780-781 (2003)

Vineet Bafna, Dan Gusfield, Giuseppe Lancia, Shibu Yooseph: Haplotyping as Perfect Phylogeny: A Direct Approach. Journal of Computational Biology 10(3/4): 323-340 (2003)

Antonio Piccolboni, Dan Gusfield: On the Complexity of Fundamental Computational Problems in Pedigree Analysis. Journal of Computational Biology 10(5): 763-773 (2003)

Ren Hua Chung, Dan Gusfield: Empirical Exploration of Perfect Phylogeny Haplotyping and Haplotypers. COCOON 2003: 5-19

Dan Gusfield: Haplotype Inference by Pure Parsimony. CPM 2003: 144-155

Dan Gusfield, Satish Eddhu, Charles H. Langley: Efficient Reconstruction of Phylogenetic Networks with Constrained Recombination. CSB 2003: 363-374

Dan Gusfield: An Overview of Haplotyping via Perfect Phylogeny: Theory, Algorithms and Programs. ICTAI 2003

Dan Gusfield, Charles U. Martel: The Structure and Complexity of Sports Elimination Numbers. Algorithmica 32(1): 73-86 (2002)

Dan Gusfield: Partition-distance: A problem and class of perfect graphs arising in clustering. Inf. Process. Lett. 82(3): 159-164 (2002)

Jens Stoye, Dan Gusfield: Simple and flexible detection of contiguous repeats using a suffix tree. Theor. Comput. Sci. 270(1-2): 843-856 (2002)

Dan Gusfield: Suffix Trees (and Relatives) Come of Age in Bioinformatics. CSB 2002: 3

Dan Gusfield: An Overview of Combinatorial Methods for Haplotype Inference. Computational Methods for SNPs and Haplotype Inference 2002: 9-25

Dan Gusfield: Haplotyping as perfect phylogeny: conceptual framework and efficient solutions. RECOMB 2002: 166-175

Sam Rash, Dan Gusfield: String barcoding: uncovering optimal virus signatures. RECOMB 2002: 254-261

Roderic Guigó, Dan Gusfield (Eds.): Algorithms in Bioinformatics, Second International Workshop, WABI 2002, Rome, Italy, September 17-21, 2002, Proceedings. Lecture Notes in Computer Science 2452, Springer 2002, isbn 3-540-44211-1

Dan Gusfield: Inference of Haplotypes from Samples of Diploid Populations: Complexity and Algorithms. Journal of Computational Biology 8(3): 305-323 (2001)

Lusheng Wang, Tao Jiang, Dan Gusfield: A More Efficient Approximation Scheme for Tree Alignment. SIAM J. Comput. 30(1): 283-299 (2000)

Dan Gusfield: A Practical Algorithm for Optimal Inference of Haplotypes from Diploid Populations. ISMB 2000: 183-189

Dan Gusfield, Ming-Yang Kao: Guest Editors' Foreword. Algorithmica 25(2-3): 141 (1999)

Dan Gusfield, Charles U. Martel: Tresholds for Sports Elimination Numbers Algorithms and Complexity. WADS 1999: 330-341

Dan Gusfield, Richard M. Karp, Lusheng Wang, Paul Stelling: Graph Traversals, Genes and Matroids: An Efficient Case of the Travelling Salesman Problem. Discrete Applied Mathematics 88(1-3): 167-180 (1998)

John D. Kececioglu, Dan Gusfield: Reconstructing a History of Recombinations From a Set of Sequences. Discrete Applied Mathematics 88(1-3): 239-260 (1998)

Lusheng Wang, Dan Gusfield: Constructing Additive Trees When the Error Is Small. Journal of Computational Biology 5(1): 127-133 (1998)

Jens Stoye, Dan Gusfield: Simple and Flexible Detection of Contiguous Repeats Using a Suffix Tree (Preliminary Version). CPM 1998: 140-152

Dan Gusfield: Algorithms on Strings, Trees, and Sequences - Computer Science and Computational Biology. Cambridge University Press 1997, isbn 0-521-58519-8

Lusheng Wang, Dan Gusfield: Improved Approximation Algorithms for Tree Alignment. J. Algorithms 25(2): 255-273 (1997)

Dalit Naor, Dan Gusfield, Charles U. Martel: A Fast Algorithm for Optimally Increasing the Edge Connectivity. SIAM J. Comput. 26(4): 1139-1165 (1997)

Dan Gusfield: Algorithms on Stings, Trees, and Sequences: Computer Science and Computational Biology. SIGACT News 28(4): 41-60 (1997)

Lusheng Wang, Tao Jiang, Dan Gusfield: A more efficient approximation scheme for tree alignment. RECOMB 1997: 310-319

Lusheng Wang, Dan Gusfield: Improved Approximation Algorithms for Tree Alignment. CPM 1996: 220-233

Dan Gusfield, Richard M. Karp, Lusheng Wang, Paul Stelling: Graph Traversals, Genes, and Matroids: An Efficient Case of the Travelling Salesman Problem. CPM 1996: 304-319

Dan Gusfield, Éva Tardos: A Faster Parametric Minimum-Cut Algorithm. Algorithmica 11(3): 278-290 (1994)

Dan Gusfield, K. Balasubramanian, Dalit Naor: Parametric Optimization of Sequence Alignment. Algorithmica 12(4/5): 312-326 (1994)

Dan Gusfield: Faster Implementation of a Shortest Superstring Approximation. Inf. Process. Lett. 51(5): 271-274 (1994)

John D. Kececioglu, Dan Gusfield: Reconstructing a History of Recombinations from a Set of Sequences. SODA 1994: 471-480

Maxime Crochemore, Dan Gusfield (Eds.): Combinatorial Pattern Matching, 5th Annual Symposium, CPM 94, Asilomar, California, USA, June 5-8, 1994, Proceedings. Lecture Notes in Computer Science 807, Springer 1994, isbn 3-540-58094-8

Dan Gusfield, Dalit Naor: Extracting Maximal Information About Sets of Minimum Cuts. Algorithmica 10(1): 64-89 (1993)

Ming-Yang Kao, Dan Gusfield: Efficient Detection and Protection of Information in Cross Tabulated Tables I: Linear Invariant Test. SIAM J. Discrete Math. 6(3): 460-476 (1993)

Dan Gusfield, Charles U. Martel: A Fast Algorithm for the Generalized Parametric Minimum Cut Problem and Applications. Algorithmica 7(5&6): 499-519 (1992)

Dan Gusfield, Leonard Pitt: A Bounded Approximation for the Minimum Cost 2-Sat Problem. Algorithmica 8(2): 103-117 (1992)

Dan Gusfield, Gad M. Landau, Baruch Schieber: An Efficient Algorithm for the All Pairs Suffix-Prefix Problem. Inf. Process. Lett. 41(4): 181-185 (1992)

Dan Gusfield, K. Balasubramanian, Dalit Naor: Parametric Optimization of Sequence Alignment. SODA 1992: 432-439

Dan Gusfield: Efficient algorithms for inferring evolutionary trees. Networks 21(1): 19-28 (1991)

Dan Gusfield, Dalit Naor: Efficient algorithms for generalized cut-trees. Networks 21(5): 505-520 (1991)

Dan Gusfield: Computing the Strength of a Graph. SIAM J. Comput. 20(4): 639-654 (1991)

Dan Gusfield: Very Simple Methods for All Pairs Network Flow Analysis. SIAM J. Comput. 19(1): 143-155 (1990)

Dalit Naor, Dan Gusfield, Charles U. Martel: A Fast Algorithm for Optimally Increasing the Edge-Connectivity. FOCS 1990: 698-707

Dan Gusfield, Dalit Naor: Efficient Algorithms for Generalized Cut Trees. SODA 1990: 422-433

Dan Gusfield: A Little Knowledge Goes a Long Way: Faster Detection of Compromised Data in 2-D Tables. IEEE Symposium on Security and Privacy 1990: 86-94

Dan Gusfield, Robert W. Irving: The Stable marriage problem - structure and algorithms. Foundations of computing series, MIT Press 1989, isbn 978-0-262-07118-5, pp. I-XVII, 1-240

Charles U. Martel, Dan Gusfield: A Fast Parallel Quicksort Algorithm. Inf. Process. Lett. 30(2): 97-102 (1989)

Dan Gusfield, Robert W. Irving: Parametric Stable Marriage and Minimum Cuts. Inf. Process. Lett. 30(5): 255-259 (1989)

Dan Gusfield: A Graph Theoretic Approach to Statistical Data Security. SIAM J. Comput. 17(3): 552-571 (1988)

Dan Gusfield: The Structure of the Stable Roommate Problem: Efficient Representation and Enumeration of All Stable Assignments. SIAM J. Comput. 17(4): 742-769 (1988)

Robert W. Irving, Paul Leather, Dan Gusfield: An efficient algorithm for the ``optimal'' stable marriage. J. ACM 34(3): 532-543 (1987)

Dan Gusfield, Robert W. Irving, Paul Leather, Michael E. Saks: Every finite distributive lattice is a set of stable matchings for a small stable marriage instance. J. Comb. Theory, Ser. A 44(2): 304-309 (1987)

Dan Gusfield: Three Fast Algorithms for Four Problems in Stable Marriage. SIAM J. Comput. 16(1): 111-128 (1987)

Dan Gusfield, Charles U. Martel, David Fernández-Baca: Fast Algorithms for Bipartite Network Flow. SIAM J. Comput. 16(2): 237-251 (1987)

Dan Gusfield: Optimal Mixed Graph Augmentation. SIAM J. Comput. 16(4): 599-612 (1987)

Dan Gusfield, Leonard Pitt: Equivalent Approximation Algorithms for Node Cover. Inf. Process. Lett. 22(6): 291-294 (1986)

Dan Gusfield: Data structures and algorithms, by A. Aho, J. Hopcroft, and J. Ullman, Addison-Wesley, Reading, Mass., 1983, 427 pp. Price: $28.85. Networks 15(1): 137-138 (1985)

Dan Gusfield: Bounds for Naive Multiple Machine Scheduling with Release Times and Deadlines. J. Algorithms 5(1): 1-6 (1984)

Dan Gusfield: Connectivity and Edge-Disjoint Spanning Trees. Inf. Process. Lett. 16(2): 87-89 (1983)

Dan Gusfield: Parametric Combinatorial Computing and a Problem of Program Module Distribution. J. ACM 30(3): 551-563 (1983)

Dan Gusfield: A note on Arc tolerances in sparse shortest-path and network flow problems. Networks 13(2): 191-196 (1983)

Dan Gusfield: Simple Construction for Multi-Terminal Network Flow Synthesis. SIAM J. Comput. 12(1): 157-165 (1983)