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ORCIDDan Gusfield
Daniel Gusfield
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- affiliation: University of California, Davis, USA
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2020 – today
- 2021
[c50]Dan Gusfield
, Hannah Brown:
Unified SAT-Solving for Hard Problems of Phylogenetic Network Construction. ICCABS 2021: 79-91- [i3]Thong Le, Dan Gusfield:
Matrix Chain Multiplication and Polygon Triangulation Revisited and Generalized. CoRR abs/2104.01777 (2021) - 2020
- [c49]Hannah Brown, Lei Zuo, Dan Gusfield:
Comparing Integer Linear Programming to SAT-Solving for Hard Problems in Computational and Systems Biology. AlCoB 2020: 63-76
2010 – 2019
- 2019
- [c48]Dan Gusfield:
Integer Linear Programming in Computational and Systems Biology: Tutorial. BCB 2019: 560 - [e4]Katharina T. Huber, Dan Gusfield:
19th International Workshop on Algorithms in Bioinformatics, WABI 2019, September 8-10, 2019, Niagara Falls, NY, USA. LIPIcs 143, Schloss Dagstuhl - Leibniz-Zentrum für Informatik 2019, ISBN 978-3-95977-123-8 [contents] - 2017
- [j80]Julia Matsieva, Steven Kelk, Céline Scornavacca, Chris Whidden, Dan Gusfield:
A Resolution of the Static Formulation Question for the Problem of Computing the History Bound. IEEE ACM Trans. Comput. Biol. Bioinform. 14(2): 404-417 (2017) - 2016
- [j79]Yelena Frid, Dan Gusfield:
An improved Four-Russians method and sparsified Four-Russians algorithm for RNA folding. Algorithms Mol. Biol. 11: 22 (2016) - 2015
- [j78]Shou-Jun Xu, Rob Gysel, Dan Gusfield:
Minimum Average Distance Clique Trees. SIAM J. Discret. Math. 29(3): 1706-1734 (2015) - [c47]Dan Gusfield:
Persistent phylogeny: a galled-tree and integer linear programming approach. BCB 2015: 443-451 - [c46]Michael J. Coulombe, Kristian Stevens, Dan Gusfield:
Construction, enumeration, and optimization of perfect phylogenies on multi-state data. ICCABS 2015: 1-6 - [c45]Dan Gusfield, Rasmus Nielsen:
Association Mapping for Compound Heterozygous Traits Using Phenotypic Distance and Integer Programming. WABI 2015: 136-147 - [c44]Yelena Frid, Dan Gusfield:
A Sparsified Four-Russian Algorithm for RNA Folding. WABI 2015: 271-285 - 2014
- [j77]Balaji Venkatachalam, Dan Gusfield, Yelena Frid:
Faster algorithms for RNA-folding using the Four-Russians method. Algorithms Mol. Biol. 9: 5 (2014) - [i2]Dan Gusfield:
Gödel for Goldilocks: A Rigorous, Streamlined Proof of Gödel's First Incompleteness Theorem, Requiring Minimal Background. CoRR abs/1409.5944 (2014) - 2013
- [c43]Rob Gysel, Dan Gusfield, Kristian Stevens:
Triangulation heuristics for maximum character compatibility. ICCABS 2013: 1-2 - [c42]Balaji Venkatachalam, Dan Gusfield, Yelena Frid:
Faster Algorithms for RNA-Folding Using the Four-Russians Method. WABI 2013: 126-140 - [i1]Balaji Venkatachalam, Dan Gusfield, Yelena Frid:
Faster Algorithms for RNA-folding using the Four-Russians method. CoRR abs/1307.7820 (2013) - 2012
- [j76]Rob Gysel, Fumei Lam, Dan Gusfield:
Constructing perfect phylogenies and proper triangulations for three-state characters. Algorithms Mol. Biol. 7: 26 (2012) - [c41]Yelena Frid, Dan Gusfield:
Speedup of RNA Pseudoknotted Secondary Structure Recurrence Computation with the Four-Russians Method. COCOA 2012: 176-187 - [c40]Rob Gysel, Kristian Stevens, Dan Gusfield:
Reducing Problems in Unrooted Tree Compatibility to Restricted Triangulations of Intersection Graphs. WABI 2012: 93-105 - 2011
- [j75]Fumei Lam, Dan Gusfield, Srinath Sridhar:
Generalizing the Splits Equivalence Theorem and Four Gamete Condition: Perfect Phylogeny on Three-State Characters. SIAM J. Discret. Math. 25(3): 1144-1175 (2011) - [j74]Rob Gysel, Dan Gusfield:
Extensions and Improvements to the Chordal Graph Approach to the Multistate Perfect Phylogeny Problem. IEEE ACM Trans. Comput. Biol. Bioinform. 8(4): 912-917 (2011) - [c39]Rob Gysel, Fumei Lam, Dan Gusfield:
Constructing Perfect Phylogenies and Proper Triangulations for Three-State Characters. WABI 2011: 104-115 - 2010
- [j73]Yelena Frid, Dan Gusfield:
A simple, practical and complete O-time Algorithm for RNA folding using the Four-Russians Speedup. Algorithms Mol. Biol. 5: 13 (2010) - [j72]Dan Gusfield:
The Multi-State Perfect Phylogeny Problem with Missing and Removable Data: Solutions via Integer-Programming and Chordal Graph Theory. J. Comput. Biol. 17(3): 383-399 (2010) - [j71]Balaji Venkatachalam, Jim Apple, Katherine St. John, Dan Gusfield:
Untangling Tanglegrams: Comparing Trees by Their Drawings. IEEE ACM Trans. Comput. Biol. Bioinform. 7(4): 588-597 (2010) - [c38]Rob Gysel, Dan Gusfield:
Extensions and Improvements to the Chordal Graph Approach to the Multi-state Perfect Phylogeny Problem. ISBRA 2010: 52-60 - [c37]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 - [c36]Kristian Stevens, Dan Gusfield:
Reducing Multi-state to Binary Perfect Phylogeny with Applications to Missing, Removable, Inserted, and Deleted Data. WABI 2010: 274-287
2000 – 2009
- 2009
- [j70]Dan Gusfield, Anna Tramontano:
Editorial. Bioinform. 25(12) (2009) - [j69]Dan Gusfield, Yufeng Wu:
The Three-state Perfect Phylogeny Problem Reduces to 2-SAT. Commun. Inf. Syst. 9(4): 295-302 (2009) - [j68]Dan Gusfield:
Final, Five-Year End, Editorial. IEEE ACM Trans. Comput. Biol. Bioinform. 6(1): 1-2 (2009) - [j67]Dan Gusfield:
Outgoing EIC Editorial for this Special Section of TCBB with the Theme of Phylogenetics. IEEE ACM Trans. Comput. Biol. Bioinform. 6(1): 96 (2009) - [c35]Balaji Venkatachalam, Jim Apple, Katherine St. John, Dan Gusfield:
Untangling Tanglegrams: Comparing Trees by Their Drawings. ISBRA 2009: 88-99 - [c34]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 - [c33]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 - [c32]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 - 2008
- [j66]Yufeng Wu, Dan Gusfield:
A new recombination lower bound and the minimum perfect phylogenetic forest problem. J. Comb. Optim. 16(3): 229-247 (2008) - [j65]Dan Gusfield:
EIC Editorial. IEEE ACM Trans. Comput. Biol. Bioinform. 5(4): 481 (2008) - [c31]Dan Gusfield:
ReCombinatorics: Combinatorial Algorithms for Studying the History of Recombination in Populations. CPM 2008: 1-2 - 2007
- [j64]Dan Gusfield, Dean Hickerson, Satish Eddhu:
An efficiently computed lower bound on the number of recombinations in phylogenetic networks: Theory and empirical study. Discret. Appl. Math. 155(6-7): 806-830 (2007) - [j63]Yufeng Wu, Dan Gusfield:
Efficient Computation of Minimum Recombination with genotypes (not Haplotypes). J. Bioinform. Comput. Biol. 5(2a): 181-200 (2007) - [j62]Dan Gusfield, Vikas Bansal, Vineet Bafna, Yun S. Song:
A Decomposition Theory for Phylogenetic Networks and Incompatible Characters. J. Comput. Biol. 14(10): 1247-1272 (2007) - [j61]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. J. Comput. Biol. 14(10): 1273-1286 (2007) - [j60]Dan Gusfield:
State of the Journal. IEEE ACM Trans. Comput. Biol. Bioinform. 4(1): 1 (2007) - [j59]Dan Gusfield:
Associate Editor Appreciation and Welcome. IEEE ACM Trans. Comput. Biol. Bioinform. 4(1): 2 (2007) - [j58]Dan Gusfield:
Associate Editor Appreciation and Welcome. IEEE ACM Trans. Comput. Biol. Bioinform. 4(3): 321 (2007) - [c30]Yufeng Wu, Dan Gusfield:
A New Recombination Lower Bound and the Minimum Perfect Phylogenetic Forest Problem. COCOON 2007: 16-26 - [c29]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 - [c28]Yufeng Wu, Dan Gusfield:
Improved Algorithms for Inferring the Minimum Mosaic of a Set of Recombinants. CPM 2007: 150-161 - 2006
- [j57]Zhihong Ding, Vladimir Filkov, Dan Gusfield:
A Linear-Time Algorithm for the Perfect Phylogeny Haplotyping (PPH) Problem. J. Comput. Biol. 13(2): 522-553 (2006) - [j56]Dan Gusfield:
State of the Journal. IEEE ACM Trans. Comput. Biol. Bioinform. 3(1): 1 (2006) - [j55]Dan Gusfield:
Introduction of New Associate Editors. IEEE ACM Trans. Comput. Biol. Bioinform. 3(2): 97 (2006) - [c27]Dan Gusfield:
Efficient and Practical Algorithms for Deducing the History of Recombination in Populations. International Conference on Computational Science (2) 2006: 618-619 - [c26]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 - 2005
- [j54]Dan Gusfield:
Preface: Special RECOMB 2004 Issue. J. Comput. Biol. 12(6): 567-568 (2005) - [j53]Dan Gusfield:
Optimal, efficient reconstruction of root-unknown phylogenetic networks with constrained and structured recombination. J. Comput. Syst. Sci. 70(3): 381-398 (2005) - [j52]Dan Gusfield:
Editorial-State of the Transaction. IEEE ACM Trans. Comput. Biol. Bioinform. 2(1): 39 (2005) - [c25]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 - [c24]Dan Gusfield, Vikas Bansal:
A Fundamental Decomposition Theory for Phylogenetic Networks and Incompatible Characters. RECOMB 2005: 217-232 - [c23]Zhihong Ding, Vladimir Filkov, Dan Gusfield:
A Linear-Time Algorithm for the Perfect Phylogeny Haplotyping (PPH) Problem. RECOMB 2005: 585-600 - [c22]Yun S. Song, Yufeng Wu, Dan Gusfield:
Algorithms for Imperfect Phylogeny Haplotyping (IPPH) with a Single Homoplasy or Recombination Event. WABI 2005: 152-164 - 2004
- [j51]Dan Gusfield, Satish Eddhu, Charles H. Langley:
The Fine Structure of Galls in Phylogenetic Networks. INFORMS J. Comput. 16(4): 459-469 (2004) - [j50]Dan Gusfield, Satish Eddhu, Charles H. Langley:
Optimal, Efficient Reconstruction of Phylogenetic Networks with Constrained Recombination. J. Bioinform. Comput. Biol. 2(1): 173-214 (2004) - [j49]Vineet Bafna, Dan Gusfield, Sridhar Hannenhalli, Shibu Yooseph:
A Note on Efficient Computation of Haplotypes via Perfect Phylogeny. J. Comput. Biol. 11(5): 858-866 (2004) - [j48]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) - [j47]Dan Gusfield:
Introduction of New Associate Editors. IEEE ACM Trans. Comput. Biol. Bioinform. 1(3): 97 (2004) - [c21]Dan Gusfield:
Invited Talk: Phylogenetic Networks with Constrained and Unconstrained Recombination. German Conference on Bioinformatics 2004: 1 - [e3]Philip E. Bourne, Dan Gusfield:
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 [contents] - 2003
- [j46]Ren Hua Chung, Dan Gusfield:
Perfect phylogeny haplotyper: haplotype inferral using a tree model. Bioinform. 19(6): 780-781 (2003) - [j45]Vineet Bafna, Dan Gusfield, Giuseppe Lancia, Shibu Yooseph:
Haplotyping as Perfect Phylogeny: A Direct Approach. J. Comput. Biol. 10(3/4): 323-340 (2003) - [j44]Antonio Piccolboni, Dan Gusfield:
On the Complexity of Fundamental Computational Problems in Pedigree Analysis. J. Comput. Biol. 10(5): 763-773 (2003) - [j43]Prashanti R. Srinivas, Daniel Gusfield, Oliver Mason, Michael Gertz, Michael A. Hogarth, James M. Stone, Edward G. Jones, Fredric Gorin:
Neuroanatomical term generation and comparison between two terminologies. Neuroinformatics 1(2): 177-192 (2003) - [c20]Ren Hua Chung, Dan Gusfield:
Empirical Exploration of Perfect Phylogeny Haplotyping and Haplotypers. COCOON 2003: 5-19 - [c19]Dan Gusfield:
Haplotype Inference by Pure Parsimony. CPM 2003: 144-155 - [c18]Dan Gusfield, Satish Eddhu, Charles H. Langley:
Efficient Reconstruction of Phylogenetic Networks with Constrained Recombination. CSB 2003: 363-374 - [c17]Dan Gusfield:
An Overview of Haplotyping via Perfect Phylogeny: Theory, Algorithms and Programs. ICTAI 2003 - 2002
- [j42]Dan Gusfield, Charles U. Martel:
The Structure and Complexity of Sports Elimination Numbers. Algorithmica 32(1): 73-86 (2002) - [j41]Dan Gusfield:
Partition-distance: A problem and class of perfect graphs arising in clustering. Inf. Process. Lett. 82(3): 159-164 (2002) - [j40]Jens Stoye, Dan Gusfield:
Simple and flexible detection of contiguous repeats using a suffix tree. Theor. Comput. Sci. 270(1-2): 843-856 (2002) - [c16]Dan Gusfield:
Suffix Trees (and Relatives) Come of Age in Bioinformatics. CSB 2002: 3 - [c15]Dan Gusfield:
An Overview of Combinatorial Methods for Haplotype Inference. Computational Methods for SNPs and Haplotype Inference 2002: 9-25 - [c14]Dan Gusfield:
Haplotyping as perfect phylogeny: conceptual framework and efficient solutions. RECOMB 2002: 166-175 - [c13]Sam Rash, Dan Gusfield:
String barcoding: uncovering optimal virus signatures. RECOMB 2002: 254-261 - [e2]Roderic Guigó, Dan Gusfield:
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 [contents] - 2001
- [j39]Dan Gusfield:
Inference of Haplotypes from Samples of Diploid Populations: Complexity and Algorithms. J. Comput. Biol. 8(3): 305-323 (2001) - 2000
- [j38]Lusheng Wang, Tao Jiang, Dan Gusfield:
A More Efficient Approximation Scheme for Tree Alignment. SIAM J. Comput. 30(1): 283-299 (2000) - [c12]Dan Gusfield:
A Practical Algorithm for Optimal Inference of Haplotypes from Diploid Populations. ISMB 2000: 183-189
1990 – 1999
- 1999
- [j37]Dan Gusfield, Ming-Yang Kao:
Guest Editors' Foreword. Algorithmica 25(2-3): 141 (1999) - [c11]Dan Gusfield, Charles U. Martel:
Tresholds for Sports Elimination Numbers Algorithms and Complexity. WADS 1999: 330-341 - 1998
- [j36]Dan Gusfield, Richard M. Karp, Lusheng Wang, Paul Stelling:
Graph Traversals, Genes and Matroids: An Efficient Case of the Travelling Salesman Problem. Discret. Appl. Math. 88(1-3): 167-180 (1998) - [j35]John D. Kececioglu, Dan Gusfield:
Reconstructing a History of Recombinations From a Set of Sequences. Discret. Appl. Math. 88(1-3): 239-260 (1998) - [j34]Lusheng Wang, Dan Gusfield:
Constructing Additive Trees When the Error Is Small. J. Comput. Biol. 5(1): 127-133 (1998) - [c10]Jens Stoye, Dan Gusfield:
Simple and Flexible Detection of Contiguous Repeats Using a Suffix Tree (Preliminary Version). CPM 1998: 140-152 - [c9]Dan Gusfield, Lusheng Wang:
New uses for uniform lifted alignments. Mathematical Support for Molecular Biology 1998: 33-51 - 1997
- [b2]Dan Gusfield:
Algorithms on Strings, Trees, and Sequences - Computer Science and Computational Biology. Cambridge University Press 1997, ISBN 0-521-58519-8 - [j33]Lusheng Wang, Dan Gusfield:
Improved Approximation Algorithms for Tree Alignment. J. Algorithms 25(2): 255-273 (1997) - [j32]Dalit Naor, Dan Gusfield, Charles U. Martel:
A Fast Algorithm for Optimally Increasing the Edge Connectivity. SIAM J. Comput. 26(4): 1139-1165 (1997) - [j31]Dan Gusfield:
Algorithms on Stings, Trees, and Sequences: Computer Science and Computational Biology. SIGACT News 28(4): 41-60 (1997) - [c8]Lusheng Wang, Tao Jiang, Dan Gusfield:
A more efficient approximation scheme for tree alignment. RECOMB 1997: 310-319 - 1996
- [c7]Lusheng Wang, Dan Gusfield:
Improved Approximation Algorithms for Tree Alignment. CPM 1996: 220-233 - [c6]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 - 1994
- [j30]Dan Gusfield, Éva Tardos:
A Faster Parametric Minimum-Cut Algorithm. Algorithmica 11(3): 278-290 (1994) - [j29]Dan Gusfield, K. Balasubramanian, Dalit Naor:
Parametric Optimization of Sequence Alignment. Algorithmica 12(4/5): 312-326 (1994) - [j28]Dan Gusfield:
Faster Implementation of a Shortest Superstring Approximation. Inf. Process. Lett. 51(5): 271-274 (1994) - [c5]John D. Kececioglu, Dan Gusfield:
Reconstructing a History of Recombinations from a Set of Sequences. SODA 1994: 471-480 - [e1]Maxime Crochemore, Dan Gusfield:
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 [contents] - 1993
- [j27]Dan Gusfield, Dalit Naor:
Extracting Maximal Information About Sets of Minimum Cuts. Algorithmica 10(1): 64-89 (1993) - [j26]Ming-Yang Kao, Dan Gusfield:
Efficient Detection and Protection of Information in Cross Tabulated Tables I: Linear Invariant Test. SIAM J. Discret. Math. 6(3): 460-476 (1993) - 1992
- [j25]Dan Gusfield, Charles U. Martel:
A Fast Algorithm for the Generalized Parametric Minimum Cut Problem and Applications. Algorithmica 7(5&6): 499-519 (1992) - [j24]Dan Gusfield, Leonard Pitt:
A Bounded Approximation for the Minimum Cost 2-Sat Problem. Algorithmica 8(2): 103-117 (1992) - [j23]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) - [c4]Dan Gusfield, K. Balasubramanian, Dalit Naor:
Parametric Optimization of Sequence Alignment. SODA 1992: 432-439 - 1991
- [j22]Dan Gusfield:
Efficient algorithms for inferring evolutionary trees. Networks 21(1): 19-28 (1991) - [j21]Dan Gusfield, Dalit Naor:
Efficient algorithms for generalized cut-trees. Networks 21(5): 505-520 (1991) - [j20]Dan Gusfield:
Computing the Strength of a Graph. SIAM J. Comput. 20(4): 639-654 (1991) - [j19]Andrew V. Goldberg, Dan Gusfield: