Dan Gusfield

ORCID

Publication Activity (10 Years)

Years Active: 1983-2021
Publications (10 Years): 11

Top Venues

Publications

Dan Gusfield, Hannah Brown
Unified SAT-Solving for Hard Problems of Phylogenetic Network Construction. ICCABS (2021)
Thong Le, Dan Gusfield
Matrix Chain Multiplication and Polygon Triangulation Revisited and Generalized. CoRR (2021)
Hannah Brown, Lei Zuo, Dan Gusfield
Comparing Integer Linear Programming to SAT-Solving for Hard Problems in Computational and Systems Biology. AlCoB (2020)
Dan Gusfield
Integer Linear Programming in Computational and Systems Biology: Tutorial. BCB (2019)
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) (2017)
Yelena Frid, Dan Gusfield
An improved Four-Russians method and sparsified Four-Russians algorithm for RNA folding. Algorithms Mol. Biol. 11 (2016)
Yelena Frid, Dan Gusfield
A Sparsified Four-Russian Algorithm for RNA Folding. WABI (2015)
Shou-Jun Xu, Rob Gysel, Dan Gusfield
Minimum Average Distance Clique Trees. SIAM J. Discret. Math. 29 (3) (2015)
Michael J. Coulombe, Kristian Stevens, Dan Gusfield
Construction, enumeration, and optimization of perfect phylogenies on multi-state data. ICCABS (2015)
Dan Gusfield
Persistent phylogeny: a galled-tree and integer linear programming approach. BCB (2015)
Dan Gusfield, Rasmus Nielsen
Association Mapping for Compound Heterozygous Traits Using Phenotypic Distance and Integer Programming. WABI (2015)
Dan Gusfield
Gödel for Goldilocks: A Rigorous, Streamlined Proof of Gödel's First Incompleteness Theorem, Requiring Minimal Background. CoRR (2014)
Balaji Venkatachalam, Dan Gusfield, Yelena Frid
Faster algorithms for RNA-folding using the Four-Russians method. Algorithms Mol. Biol. 9 (2014)
Balaji Venkatachalam, Dan Gusfield, Yelena Frid
Faster Algorithms for RNA-Folding Using the Four-Russians Method. WABI (2013)
Rob Gysel, Dan Gusfield, Kristian Stevens
Triangulation heuristics for maximum character compatibility. ICCABS (2013)
Balaji Venkatachalam, Dan Gusfield, Yelena Frid
Faster Algorithms for RNA-folding using the Four-Russians method. CoRR (2013)
Yelena Frid, Dan Gusfield
Speedup of RNA Pseudoknotted Secondary Structure Recurrence Computation with the Four-Russians Method. COCOA (2012)
Rob Gysel, Fumei Lam, Dan Gusfield
Constructing perfect phylogenies and proper triangulations for three-state characters. Algorithms Mol. Biol. 7 (2012)
Rob Gysel, Kristian Stevens, Dan Gusfield
Reducing Problems in Unrooted Tree Compatibility to Restricted Triangulations of Intersection Graphs. WABI (2012)
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) (2011)
Rob Gysel, Fumei Lam, Dan Gusfield
Constructing Perfect Phylogenies and Proper Triangulations for Three-State Characters. WABI (2011)
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) (2011)
Kristian Stevens, Dan Gusfield
Reducing Multi-state to Binary Perfect Phylogeny with Applications to Missing, Removable, Inserted, and Deleted Data. WABI (2010)
Rob Gysel, Dan Gusfield
Extensions and Improvements to the Chordal Graph Approach to the Multi-state Perfect Phylogeny Problem. ISBRA (2010)
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) (2010)
Yelena Frid, Dan Gusfield
A simple, practical and complete O-time Algorithm for RNA folding using the Four-Russians Speedup. Algorithms Mol. Biol. 5 (2010)
Yelena Frid, Dan Gusfield
Idea. WABI (2010)
Balaji Venkatachalam, Jim Apple, Katherine St. John, Dan Gusfield
Untangling Tanglegrams: Comparing Trees by Their Drawings. IEEE ACM Trans. Comput. Biol. Bioinform. 7 (4) (2010)
Dan Gusfield
The Multi-State Perfect Phylogeny Problem with Missing and Removable Data: Solutions via Integer-Programming and Chordal Graph Theory. RECOMB (2009)
Dan Gusfield
Outgoing EIC Editorial for this Special Section of TCBB with the Theme of Phylogenetics. IEEE ACM Trans. Comput. Biol. Bioinform. 6 (1) (2009)
Dan Gusfield, Yufeng Wu
The Three-state Perfect Phylogeny Problem Reduces to 2-SAT. Commun. Inf. Syst. 9 (4) (2009)
Dan Gusfield, Anna Tramontano
Editorial. Bioinform. 25 (12) (2009)
Dan Gusfield
Final, Five-Year End, Editorial. IEEE ACM Trans. Comput. Biol. Bioinform. 6 (1) (2009)
Balaji Venkatachalam, Jim Apple, Katherine St. John, Dan Gusfield
Untangling Tanglegrams: Comparing Trees by Their Drawings. ISBRA (2009)
Fumei Lam, Dan Gusfield, Srinath Sridhar
Generalizing the Four Gamete Condition and Splits Equivalence Theorem: Perfect Phylogeny on Three State Characters. WABI (2009)
Yelena Frid, Dan Gusfield
Speedup. WABI (2009)
Dan Gusfield
ReCombinatorics: Combinatorial Algorithms for Studying the History of Recombination in Populations. CPM (2008)
Yufeng Wu, Dan Gusfield
A new recombination lower bound and the minimum perfect phylogenetic forest problem. J. Comb. Optim. 16 (3) (2008)
Dan Gusfield
EIC Editorial. IEEE ACM Trans. Comput. Biol. Bioinform. 5 (4) (2008)
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) (2007)
Dan Gusfield
State of the Journal. IEEE ACM Trans. Comput. Biol. Bioinform. 4 (1) (2007)
Dan Gusfield, Vikas Bansal, Vineet Bafna, Yun S. Song
A Decomposition Theory for Phylogenetic Networks and Incompatible Characters. J. Comput. Biol. 14 (10) (2007)
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)
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) (2007)
Yufeng Wu, Dan Gusfield
Improved Algorithms for Inferring the Minimum Mosaic of a Set of Recombinants. CPM (2007)
Dan Gusfield
Associate Editor Appreciation and Welcome. IEEE ACM Trans. Comput. Biol. Bioinform. 4 (1) (2007)
Dan Gusfield
Associate Editor Appreciation and Welcome. IEEE ACM Trans. Comput. Biol. Bioinform. 4 (3) (2007)
Yufeng Wu, Dan Gusfield
Efficient Computation of Minimum Recombination with genotypes (not Haplotypes). J. Bioinform. Comput. Biol. 5 (2a) (2007)
Yufeng Wu, Dan Gusfield
A New Recombination Lower Bound and the Minimum Perfect Phylogenetic Forest Problem. COCOON (2007)
Dan Gusfield
Efficient and Practical Algorithms for Deducing the History of Recombination in Populations. International Conference on Computational Science (2) (2006)
Zhihong Ding, Vladimir Filkov, Dan Gusfield
A Linear-Time Algorithm for the Perfect Phylogeny Haplotyping (PPH) Problem. J. Comput. Biol. 13 (2) (2006)
Dan Gusfield
Introduction of New Associate Editors. IEEE ACM Trans. Comput. Biol. Bioinform. 3 (2) (2006)
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)
Dan Gusfield
State of the Journal. IEEE ACM Trans. Comput. Biol. Bioinform. 3 (1) (2006)
Dan Gusfield, Vikas Bansal
A Fundamental Decomposition Theory for Phylogenetic Networks and Incompatible Characters. RECOMB (2005)
Zhihong Ding, Vladimir Filkov, Dan Gusfield
A Linear-Time Algorithm for the Perfect Phylogeny Haplotyping (PPH) Problem. RECOMB (2005)
Yun S. Song, Yufeng Wu, Dan Gusfield
Algorithms for Imperfect Phylogeny Haplotyping (IPPH) with a Single Homoplasy or Recombination Event. WABI (2005)
Dan Gusfield
Editorial-State of the Transaction. IEEE ACM Trans. Comput. Biol. Bioinform. 2 (1) (2005)
Dan Gusfield
Preface: Special RECOMB 2004 Issue. J. Comput. Biol. 12 (6) (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)
Dan Gusfield
Optimal, efficient reconstruction of root-unknown phylogenetic networks with constrained and structured recombination. J. Comput. Syst. Sci. 70 (3) (2005)
Dan Gusfield
Invited Talk: Phylogenetic Networks with Constrained and Unconstrained Recombination. German Conference on Bioinformatics (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) (2004)
Dan Gusfield
Introduction of New Associate Editors. IEEE ACM Trans. Comput. Biol. Bioinform. 1 (3) (2004)
Vineet Bafna, Dan Gusfield, Sridhar Hannenhalli, Shibu Yooseph
A Note on Efficient Computation of Haplotypes via Perfect Phylogeny. J. Comput. Biol. 11 (5) (2004)
Dan Gusfield, Satish Eddhu, Charles H. Langley
The Fine Structure of Galls in Phylogenetic Networks. INFORMS J. Comput. 16 (4) (2004)
Dan Gusfield, Satish Eddhu, Charles H. Langley
Optimal, Efficient Reconstruction of Phylogenetic Networks with Constrained Recombination. J. Bioinform. Comput. Biol. 2 (1) (2004)
Ren Hua Chung, Dan Gusfield
Perfect phylogeny haplotyper: haplotype inferral using a tree model. Bioinform. 19 (6) (2003)
Vineet Bafna, Dan Gusfield, Giuseppe Lancia, Shibu Yooseph
Haplotyping as Perfect Phylogeny: A Direct Approach. J. Comput. Biol. 10 (3/4) (2003)
Ren Hua Chung, Dan Gusfield
Empirical Exploration of Perfect Phylogeny Haplotyping and Haplotypers. COCOON (2003)
Dan Gusfield
Haplotype Inference by Pure Parsimony. CPM (2003)
Dan Gusfield
An Overview of Haplotyping via Perfect Phylogeny: Theory, Algorithms and Programs. ICTAI (2003)
Dan Gusfield, Satish Eddhu, Charles H. Langley
Efficient Reconstruction of Phylogenetic Networks with Constrained Recombination. CSB (2003)
Antonio Piccolboni, Dan Gusfield
On the Complexity of Fundamental Computational Problems in Pedigree Analysis. J. Comput. Biol. 10 (5) (2003)
Dan Gusfield
Partition-distance: A problem and class of perfect graphs arising in clustering. Inf. Process. Lett. 82 (3) (2002)
Sam Rash, Dan Gusfield
String barcoding: uncovering optimal virus signatures. RECOMB (2002)
Dan Gusfield, Charles U. Martel
The Structure and Complexity of Sports Elimination Numbers. Algorithmica 32 (1) (2002)
Dan Gusfield
Haplotyping as perfect phylogeny: conceptual framework and efficient solutions. RECOMB (2002)
Dan Gusfield
Suffix Trees (and Relatives) Come of Age in Bioinformatics. CSB (2002)
Jens Stoye, Dan Gusfield
Simple and flexible detection of contiguous repeats using a suffix tree. Theor. Comput. Sci. 270 (1-2) (2002)
Dan Gusfield
An Overview of Combinatorial Methods for Haplotype Inference. Computational Methods for SNPs and Haplotype Inference (2002)
Dan Gusfield
Inference of Haplotypes from Samples of Diploid Populations: Complexity and Algorithms. J. Comput. Biol. 8 (3) (2001)
Dan Gusfield
A Practical Algorithm for Optimal Inference of Haplotypes from Diploid Populations. ISMB (2000)
Lusheng Wang, Tao Jiang, Dan Gusfield
A More Efficient Approximation Scheme for Tree Alignment. SIAM J. Comput. 30 (1) (2000)
Dan Gusfield, Charles U. Martel
Tresholds for Sports Elimination Numbers Algorithms and Complexity. WADS (1999)
Dan Gusfield, Ming-Yang Kao
Guest Editors' Foreword. Algorithmica 25 (2-3) (1999)
Dan Gusfield, Lusheng Wang
New uses for uniform lifted alignments. Mathematical Support for Molecular Biology (1998)
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) (1998)
John D. Kececioglu, Dan Gusfield
Reconstructing a History of Recombinations From a Set of Sequences. Discret. Appl. Math. 88 (1-3) (1998)
Lusheng Wang, Dan Gusfield
Constructing Additive Trees When the Error Is Small. J. Comput. Biol. 5 (1) (1998)
Jens Stoye, Dan Gusfield
Simple and Flexible Detection of Contiguous Repeats Using a Suffix Tree (Preliminary Version). CPM (1998)
Dan Gusfield
Algorithms on Stings, Trees, and Sequences: Computer Science and Computational Biology. SIGACT News 28 (4) (1997)
Dalit Naor, Dan Gusfield, Charles U. Martel
A Fast Algorithm for Optimally Increasing the Edge Connectivity. SIAM J. Comput. 26 (4) (1997)
Lusheng Wang, Tao Jiang, Dan Gusfield
A more efficient approximation scheme for tree alignment. RECOMB (1997)
Lusheng Wang, Dan Gusfield
Improved Approximation Algorithms for Tree Alignment. J. Algorithms 25 (2) (1997)
Dan Gusfield, Richard M. Karp, Lusheng Wang, Paul Stelling
Graph Traversals, Genes, and Matroids: An Efficient Case of the Travelling Salesman Problem. CPM (1996)
Lusheng Wang, Dan Gusfield
Improved Approximation Algorithms for Tree Alignment. CPM (1996)
Dan Gusfield
Faster Implementation of a Shortest Superstring Approximation. Inf. Process. Lett. 51 (5) (1994)
John D. Kececioglu, Dan Gusfield
Reconstructing a History of Recombinations from a Set of Sequences. SODA (1994)
Dan Gusfield, Éva Tardos
A Faster Parametric Minimum-Cut Algorithm. Algorithmica 11 (3) (1994)

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Publication Activity (10 Years)

Top Topics

Top Venues

Dan Gusfield