| 2015 | WABI | A Sparsified Four-Russian Algorithm for RNA Folding. | Yelena Frid, Dan Gusfield |
| 2015 | WABI | Association Mapping for Compound Heterozygous Traits Using Phenotypic Distance and Integer Programming. | Dan Gusfield, Rasmus Nielsen |
| 2013 | WABI | Faster Algorithms for RNA-Folding Using the Four-Russians Method. | Balaji Venkatachalam, Dan Gusfield, Yelena Frid |
| 2012 | COCOA | Speedup of RNA Pseudoknotted Secondary Structure Recurrence Computation with the Four-Russians Method. | Yelena Frid, Dan Gusfield |
| 2012 | WABI | Reducing Problems in Unrooted Tree Compatibility to Restricted Triangulations of Intersection Graphs. | Rob Gysel, Kristian Stevens, Dan Gusfield |
| 2011 | WABI | Constructing Perfect Phylogenies and Proper Triangulations for Three-State Characters. | Rob Gysel, Fumei Lam, Dan Gusfield |
| 2010 | WABI | A Worst-Case and Practical Speedup for the RNA Co-folding Problem Using the | Yelena Frid, Dan Gusfield |
| 2010 | WABI | Reducing Multi-state to Binary Perfect Phylogeny with Applications to Missing, Removable, Inserted, and Deleted Data. | Kristian Stevens, Dan Gusfield |
| 2009 | RECOMB | The Multi-State Perfect Phylogeny Problem with Missing and Removable Data: Solutions via Integer-Programming and Chordal Graph Theory. | Dan Gusfield |
| 2009 | WABI | A Simple, Practical and Complete | Yelena Frid, Dan Gusfield |
| 2009 | WABI | Generalizing the Four Gamete Condition and Splits Equivalence Theorem: Perfect Phylogeny on Three State Characters. | Fumei Lam, Dan Gusfield, Srinath Sridhar |
| 2008 | CPM | ReCombinatorics: Combinatorial Algorithms for Studying the History of Recombination in Populations. | Dan Gusfield |
| 2007 | COCOON | Integer Programming Formulations and Computations Solving Phylogenetic and Population Genetic Problems with Missing or Genotypic Data. | Dan Gusfield, Yelena Frid, Daniel G. Brown |
| 2007 | COCOON | A New Recombination Lower Bound and the Minimum Perfect Phylogenetic Forest Problem. | Yufeng Wu, Dan Gusfield |
| 2007 | CPM | Improved Algorithms for Inferring the Minimum Mosaic of a Set of Recombinants. | Yufeng Wu, Dan Gusfield |
| 2006 | ICCS | Efficient and Practical Algorithms for Deducing the History of Recombination in Populations. | Dan Gusfield |
| 2006 | RECOMB | 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, Dan Gusfield, Charles H. Langley, Yufeng Wu |
| 2005 | ISMB | Efficient computation of close lower and upper bounds on the minimum number of recombinations in biological sequence evolution. | Yun S. Song, Yufeng Wu, Dan Gusfield |
| 2005 | RECOMB | A Linear-Time Algorithm for the Perfect Phylogeny Haplotyping (PPH) Problem. | Zhihong Ding, Vladimir Filkov, Dan Gusfield |
| 2005 | RECOMB | A Fundamental Decomposition Theory for Phylogenetic Networks and Incompatible Characters. | Dan Gusfield, Vikas Bansal |
| 2005 | WABI | Algorithms for Imperfect Phylogeny Haplotyping (IPPH) with a Single Homoplasy or Recombination Event. | Yun S. Song, Yufeng Wu, Dan Gusfield |
| 2003 | COCOON | Empirical Exploration of Perfect Phylogeny Haplotyping and Haplotypers. | Ren Hua Chung, Dan Gusfield |
| 2003 | CPM | Haplotype Inference by Pure Parsimony. | Dan Gusfield |
| 2003 | ICTAI | An Overview of Haplotyping via Perfect Phylogeny: Theory, Algorithms and Programs. | Dan Gusfield |
| 2002 | RECOMB | Haplotyping as perfect phylogeny: conceptual framework and efficient solutions. | Dan Gusfield |
| 2002 | RECOMB | An Overview of Combinatorial Methods for Haplotype Inference. | Dan Gusfield |
| 2002 | RECOMB | String barcoding: uncovering optimal virus signatures. | Sam Rash, Dan Gusfield |
| 2000 | ISMB | A Practical Algorithm for Optimal Inference of Haplotypes from Diploid Populations. | Dan Gusfield |
| 1999 | WADS | Tresholds for Sports Elimination Numbers Algorithms and Complexity. | Dan Gusfield, Charles U. Martel |
| 1998 | CPM | Simple and Flexible Detection of Contiguous Repeats Using a Suffix Tree (Preliminary Version). | Jens Stoye, Dan Gusfield |
| 1997 | RECOMB | A more efficient approximation scheme for tree alignment. | Lusheng Wang, Tao Jiang, Dan Gusfield |
| 1996 | CPM | Graph Traversals, Genes, and Matroids: An Efficient Case of the Travelling Salesman Problem. | Dan Gusfield, Richard M. Karp, Lusheng Wang, Paul Stelling |
| 1996 | CPM | Improved Approximation Algorithms for Tree Alignment. | Lusheng Wang, Dan Gusfield |
| 1994 | SODA | Reconstructing a History of Recombinations from a Set of Sequences. | John D. Kececioglu, Dan Gusfield |
| 1992 | SODA | Parametric Optimization of Sequence Alignment. | Dan Gusfield, K. Balasubramanian, Dalit Naor |
| 1990 | FOCS | A Fast Algorithm for Optimally Increasing the Edge-Connectivity | Dalit Naor, Dan Gusfield, Charles U. Martel |
| 1990 | SODA | Efficient Algorithms for Generalized Cut Trees. | Dan Gusfield, Dalit Naor |
| 1990 | SP | A Little Knowledge Goes a Long Way: Faster Detection of Compromised Data in 2-D Tables. | Dan Gusfield |