D. Gusfield

Most-cited papers

Haplotyping as perfect phylogeny: conceptual framework and efficient solutions
D. Gusfield
2002Annual International Conference on Research in Computational Molecular Biology227 citations
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Haplotype Inference by Pure Parsimony
D. Gusfield
2003Annual Symposium on Combinatorial Pattern Matching221 citations
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Optimal, Efficient Reconstruction of Phylogenetic Networks with Constrained Recombination
D. Gusfield, Satish Eddhu, C. Langley
2004J. Bioinform. Comput. Biol.197 citations
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Partition-distance: A problem and class of perfect graphs arising in clustering
D. Gusfield
2002Information Processing Letters182 citations
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Linear time algorithms for finding and representing all the tandem repeats in a string
D. Gusfield, J. Stoye
2004Journal of computer and system sciences (Print)166 citations Open access
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Haplotyping as Perfect Phylogeny: A Direct Approach
V. Bafna, D. Gusfield, G. Lancia, S. Yooseph
2003J. Comput. Biol.134 citations
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ReCombinatorics: The Algorithmics of Ancestral Recombination Graphs and Explicit Phylogenetic Networks
D. Gusfield
2014121 citations
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Efficient reconstruction of phylogenetic networks with constrained recombination
D. Gusfield, Satish Eddhu, C. Langley
2003Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB200397 citations
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A Linear-Time Algorithm for the Perfect Phylogeny Haplotyping (PPH) Problem
Zhihong Ding, V. Filkov, D. Gusfield
2005Annual International Conference on Research in Computational Molecular Biology82 citations Open access
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The Fine Structure of Galls in Phylogenetic Networks
D. Gusfield, Satish Eddhu, C. Langley
2004INFORMS journal on computing79 citations
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A Fundamental Decomposition Theory for Phylogenetic Networks and Incompatible Characters
D. Gusfield, V. Bansal
2005Annual International Conference on Research in Computational Molecular Biology75 citations
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Integer Programming Formulations and Computations Solving Phylogenetic and Population Genetic Problems with Missing or Genotypic Data
D. Gusfield, Yelena Frid, Daniel G. Brown
2007International Computing and Combinatorics Conference61 citations
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A Decomposition Theory for Phylogenetic Networks and Incompatible Characters
D. Gusfield, V. Bansal, V. Bafna, Yun S. Song
2007J. Comput. Biol.61 citations Open access
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An Overview of Combinatorial Methods for Haplotype Inference
D. Gusfield
2002Computational Methods for SNPs and Haplotype Inference61 citations
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Optimal, efficient reconstruction of root-unknown phylogenetic networks with constrained and structured recombination
D. Gusfield
2005Journal of computer and system sciences (Print)57 citations Open access
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Efficient computation of close lower and upper bounds on the minimum number of recombinations in biological sequence evolution
Yun S. Song, Y. Wu, D. Gusfield
2005Intelligent Systems in Molecular Biology55 citations
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Untangling Tanglegrams: Comparing Trees by Their Drawings
B. Venkatachalam, Jim Apple, K. St. John, D. Gusfield
2009IEEE/ACM Transactions on Computational Biology & Bioinformatics46 citations
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String barcoding: uncovering optimal virus signatures
S. Rash, D. Gusfield
2002Annual International Conference on Research in Computational Molecular Biology44 citations
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The Multi-State Perfect Phylogeny Problem with Missing and Removable Data: Solutions via Integer-Programming and Chordal Graph Theory
D. Gusfield
2009Annual International Conference on Research in Computational Molecular Biology43 citations
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Analysis and exploration of the use of rule-based algorithms and consensus methods for the inferral of haplotypes.
S. Orzack, D. Gusfield, Jeffrey Olson, S. Nesbitt +2 more
2003Genetics42 citations
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A Note on Efficient Computation of Haplotypes via Perfect Phylogeny
V. Bafna, D. Gusfield, S. Hannenhalli, S. Yooseph
2004J. Comput. Biol.38 citations
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Perfect phylogeny haplotyper: haplotype inferral using a tree model
Hua-Chung Ren, D. Gusfield
2003Bioinform.36 citations Open access
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An efficiently computed lower bound on the number of recombinations in phylogenetic networks: Theory and empirical study
D. Gusfield, Dean R. Hickerson, Satish Eddhu
2007Discrete Applied Mathematics35 citations Open access
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On the Complexity of Fundamental Computational Problems in Pedigree Analysis
A. Piccolboni, D. Gusfield
2003J. Comput. Biol.34 citations
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Faster algorithms for RNA-folding using the Four-Russians method
B. Venkatachalam, D. Gusfield, Yelena Frid
2013Algorithms for Molecular Biology30 citations Open access
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A simple, practical and complete O-time Algorithm for RNA folding using the Four-Russians Speedup
Yelena Frid, D. Gusfield
2010Algorithms for Molecular Biology30 citations Open access
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Algorithms to Distinguish the Role of Gene-Conversion from Single-Crossover Recombination in the Derivation of SNP Sequences in Populations
Yun S. Song, Zhihong Ding, D. Gusfield, C. Langley +1 more
2006Annual International Conference on Research in Computational Molecular Biology28 citations Open access
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Algorithms for Imperfect Phylogeny Haplotyping (IPPH) with a Single Homoplasy or Recombination Event
Yun S. Song, Y. Wu, D. Gusfield
2005Workshop on Algorithms in Bioinformatics28 citations
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Empirical Exploration of Perfect Phylogeny Haplotyping and Haplotypers
Hua-Chung Ren, D. Gusfield
2003International Computing and Combinatorics Conference23 citations
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Simple and flexible detection of contiguous repeats using a suffix tree
Jens Stoye, D. Gusfield
2002Theoretical Computer Science23 citations Open access
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Improved Algorithms for Inferring the Minimum Mosaic of a Set of Recombinants
Y. Wu, D. Gusfield
2007Annual Symposium on Combinatorial Pattern Matching22 citations
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A simple, practical and complete O(n³/log n)-time algorithm for RNA folding using the four-Russians speedup
Yelena Frid, D. Gusfield
2009Workshop on Algorithms in Bioinformatics20 citations
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Generalizing the Splits Equivalence Theorem and Four Gamete Condition: Perfect Phylogeny on Three-State Characters
Fumei Lam, D. Gusfield, S. Sridhar
2009SIAM Journal on Discrete Mathematics17 citations Open access
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Persistent phylogeny: a galled-tree and integer linear programming approach
D. Gusfield
2015ACM International Conference on Bioinformatics, Computational Biology and Biomedicine15 citations
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Extensions and Improvements to the Chordal Graph Approach to the Multistate Perfect Phylogeny Problem
Rob Gysel, D. Gusfield
2011IEEE/ACM Transactions on Computational Biology & Bioinformatics14 citations
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A new recombination lower bound and the minimum perfect phylogenetic forest problem
Y. Wu, D. Gusfield
2007Journal of combinatorial optimization12 citations
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Suffix trees (and relatives) come of age in bioinformatics
D. Gusfield
2002Proceedings. IEEE Computer Society Bioinformatics Conference12 citations
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Integer Linear Programming in Computational and Systems Biology: Tutorial
D. Gusfield
2019ACM International Conference on Bioinformatics, Computational Biology and Biomedicine10 citations Open access
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An improved Four-Russians method and sparsified Four-Russians algorithm for RNA folding
Yelena Frid, D. Gusfield
2016Algorithms for Molecular Biology9 citations Open access
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Reducing Problems in Unrooted Tree Compatibility to Restricted Triangulations of Intersection Graphs
Rob Gysel, Kristian Stevens, D. Gusfield
2012Workshop on Algorithms in Bioinformatics9 citations
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Constructing perfect phylogenies and proper triangulations for three-state characters
Rob Gysel, Fumei Lam, D. Gusfield
2011Algorithms for Molecular Biology9 citations Open access
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A Simple, Practical and Complete O(\fracn3 logn)O(\frac{n^3}{ \log n})-Time Algorithm for RNA Folding Using the Four-Russians Speedup
Yelena Frid, D. Gusfield
2009Workshop on Algorithms in Bioinformatics8 citations
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Generalizing the Four Gamete Condition and Splits Equivalence Theorem: Perfect Phylogeny on Three State Characters
Fumei Lam, D. Gusfield, S. Sridhar
2009Workshop on Algorithms in Bioinformatics8 citations
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Proceedings of the eighth annual international conference on Research in computational molecular biology
P. Bourne, D. Gusfield
2004Annual International Conference on Research in Computational Molecular Biology8 citations
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Minimum Average Distance Clique Trees
Shoujun Xu, Rob Gysel, D. Gusfield
2015SIAM Journal on Discrete Mathematics7 citations
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A Worst-Case and Practical Speedup for the RNA Co-folding Problem Using the Four-Russians Idea
Yelena Frid, D. Gusfield
2010Workshop on Algorithms in Bioinformatics7 citations
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Extensions and Improvements to the Chordal Graph Approach to the Multi-state Perfect Phylogeny Problem
Rob Gysel, D. Gusfield
2010International Symposium on Bioinformatics Research and Applications7 citations
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Comparing Integer Linear Programming to SAT-Solving for Hard Problems in Computational and Systems Biology
Hannah Brown, L. Zuo, D. Gusfield
2020International Conference on Algorithms for Computational Biology6 citations
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Reducing Multi-state to Binary Perfect Phylogeny with Applications to Missing, Removable, Inserted, and Deleted Data
Kristian Stevens, D. Gusfield
2010Workshop on Algorithms in Bioinformatics6 citations
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The Three-state Perfect Phylogeny Problem Reduces to 2-SAT
D. Gusfield, Y. Wu
2009Communications in Information and Systems6 citations Open access
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