Publications Dan Gusfield 1. 1979 D. Gusfield. MATROID OPTIMIZATION WITH THE INTERLEAVING OF TWO ORDERED SETS. In Proceedings of the Humboldt Conference on Graph Theory, Combinatorics and Computing, Utilitus Mathematica, 9 pages. 2. 1979 D. Gusfield. BOUNDS FOR THE PARAMETRIC MINIMUM SPANNING TREE PROBLEM. In Proceedings of the Humboldt Conference on Graph Theory, Combinatorics and Computing, Utilitus Mathematica, 9 pages. 3. 1983 D. Gusfield. CONNECTIVITY AND EDGE-DISJOINT SPANNING TREES. In Information Processing Letters, Vol. 16, 87-89. 4. 1983 D. Gusfield. SIMPLE CONSTRUCTIONS FOR MULTI-TERMINAL NETWORK FLOW SYNTHESIS. In SIAM Journal on Computing, Vol. 12, No. 1, 157-165. 5. 1983 D. Gusfield. PARAMETRIC COMBINATORIAL COMPUTING AND A PROBLEM OF PROGRAM MODULE DISTRIBUTION. In Journal of the Association for Computing Machinery, Vol. 30, No. 3, 551-563. 6. 1983 D. Gusfield. A NOTE ON ARC TOLERANCES IN SPARSE SHORTEST PATH AND NETWORK FLOW PROBLEMS. Networks, Vol. 13, 191-196. 7. 1984 D. Gusfield. MATROID OPTIMIZATION WITH THE INTERLEAVING OF TWO ORDERED SETS. Discrete Applied Mathematics, Vol. 8, 41-50. (Significantly revised journal version of paper 1). 8. 1984 D. Gusfield. BOUNDS FOR NAIVE MULTIPLE MACHINE SCHEDULING WITH RELEASE TIMES AND DEADLINES. Journal of Algorithms, Vol. 5, 1-6. 9. 1986 D. Gusfield, and L. Pitt. EQUIVALENT APPROXIMATION ALGORITHMS FOR NODE. In Information Processing Letters, Vol. 22, No. 6, 291-294. 10. 1987 D. Gusfield. THREE FAST ALGORITHMS FOR FOUR PROBLEMS IN STABLE MARRIAGE. SIAM Journal on Computing, Vol. 16, No. 1, 111-128. 11. 1987 D. Gusfield, C. Martel, and D. Fernández-Baca. FAST ALGORITHMS FOR BIPARTITE NETWORK FLOW. SIAM Journal on Computing, Vol. 16, No. 2, 237-251. 12. 1987 D. Gusfield. OPTIMAL MIXED GRAPH AUGMENTATION. SIAM Journal on Computing, Vol. 16, No. 4, 599-612. 13. 1987 R. W. Irving, P. Leather, and D. Gusfield. AN EFFICIENT ALGORITHM FOR THE "OPTIMAL" STABLE MARRIAGE. Journal of the Association for Computing Machinery, Vol. 34, No. 3, 532-543. 14. 1987 D. Gusfield, R. Irving, P. Leather, and M. Saks. EVERY FINITE DISTRIBUTIVE LATTICE IS A SET OF STABLE MATCHINGS FOR A SMALL STABLE MARRIAGE INSTANCE. In Journal of Combinatorial Theory, Series A, Vol. 44, No. 2, 304-309. 15. 1988 D. Gusfield. THE STRUCTURE OF THE STABLE ROOMMATE PROBLEM: EFFICIENT REPRESENTATION AND ENUMERATION OF ALL STABLE ASSIGNMENTS. SIAM Journal on Computing, Vol. 17, No. 4, 742-769. 16. 1988 D. Gusfield. A GRAPH THEORETIC APPROACH TO STATISTICAL DATA SECURITY. SIAM Journal on Computing, Vol. 17, No. 3, 552-571. 17. 1989 D. Gusfield, and R. W. Irving. PARAMETRIC STABLE MARRIAGE AND MINIMUM CUTS. Information Processing Letters, Vol. 30, 255-259. 18. 1989 C. U. Martel, and D. Gusfield. A FAST PARALLEL QUICKSORT ALGORITHM. Information Processing Letters, Vol. 30, 97-102. 19. 1989 D. Gusfield, and R. W. Irving. THE STABLE MARRIAGE PROBLEM: STRUCTURE AND ALGORITHMS. (A Book) Series on Foundations of Computing. The MIT Press, 240 pages. 20. 1989 D. Gusfield. EFFICIENT SOLUTION OF THE MATROID PRODUCT PROBLEM. Operations Research Letters, Vol. 8, 257-259. 21. 1990 D. Gusfield. VERY SIMPLE METHODS FOR ALL PAIRS NETWORK FLOW ANALYSIS. SIAM Journal on Computing, 143-155. 22. 1990 D. Gusfield, and D. Naor. EFFICIENT ALGORITHMS FOR GENERALIZED CUT TREES. Proceedings of the First Annual ACM-SIAM Joint Symposium on Discrete Algorithm, 422-433. Also in Networks, Vol. 21, pp. 505-520, 1991. 23. 1990 D. Gusfield. A LITTLE KNOWLEDGE GOES A LONG WAY: FAST DETECTION OF COMPROMISED DATA IN 2-D TABLES. Proceedings of The IEEE Symposium on Research in Security and Privacy, p. 86-94. 24. 1990 D. Naor, D. Gusfield, and C. Martel. A FAST ALGORITHM FOR OPTIMALLY INCREASING THE EDGE-CONNECTIVITY. Proceedings of the 31st Annual Symposium on Foundations of Computer Science (FOCS), 698-707. 25. 1991 D. Gusfield. COMPUTING THE STRENGTH OF A GRAPH. SIAM Journal on Computing, Vol. 20, No. 4, 639-654. 26. 1991 D. Gusfield. EFFICIENT ALGORITHMS FOR INFERRING EVOLUTIONARY TREES. Networks, Vol. 21, 19-28. 27. 1991 A. Goldberg, and D. Gusfield. FLOW ALGORITHMS -REVIEW OF POTOKOVYE ALGORITHMY (Review of the Russian Book). SIAM Review, 306-314. 28. 1991 D. Gusfield, G. M. Landau, and B. Schieber. AN EFFICIENT ALGORITHM FOR SUFFIX-PREFIX MATCHING. Proceedings of SEQUENCES 91, 7 pages. 29. 1992 D. Gusfield, K. Balasubramanian, and D. Naor. PARAMETRIC OPTIMIZATION OF SEQUENCE ALIGNMENT. Proceedings of the Third Annual ACM-SIAM Symposium on Discrete Algorithms, 432-439. 30. 1992 D. Gusfield. DESIGN (WITH ANALYSIS) OF EFFICIENT ALGORITHMS. Handbooks on Operations Research and Management Science: Computation, E. G. Coffman, J. K. Lenstra, and A. H. G. Rinooy Kan, eds., Elsevier North Holland Press, 375-453. 31. 1992 D. Gusfield, and L. Pitt. A BOUNDED APPROXIMATION FOR THE MINIMUM COST 2-SAT PROBLEM. Journal of Algorithmica, Vol. 8, No. 2, 103-117. 32. 1992 D. Gusfield, and C. U. Martel. A FAST ALGORITHM FOR THE GENERALIZED PARAMETRIC MINIMUM CUT PROBLEM AND APPLICATIONS. Journal of Algorithmica, Vol. 7, 499-519. 33. 1992 D. Gusfield. EFFICIENT METHODS FOR MULTIPLE SEQUENCE ALIGNMENT WITH GUARANTEED ERROR BOUNDS. Bulletin on Mathematical Biology, Vol. 55, No. 1, 141-154. 34. 1992 D. Gusfield, G. M. Landau, and B. Schieber. AN EFFICIENT ALGORITHM FOR SUFFIX-PREFIX MATCHING. Information Processing Letters, 181-185. (See also 28). 35. 1993 M. Y. Kao, and D. Gusfield. DETECTION AND PROTECTION OF LINEAR INFORMATION IN CROSS TABULATION. SIAM Journal on Discrete Math, Vol. 6, No. 3, 460-476. 36. 1993 D. Gusfield, and D. Naor. EXTRACTING MAXIMAL INFORMATION ABOUT THE MINIMUM CUTS IN A GRAPH. Journal of Algorithmica, Vol. 10, 64-89. 37. 1994 J. Kececioglu, and D. Gusfield. RECONSTRUCTING A HISTORY OF RECOMBINATIONS FROM A SET OF SEQUENCES. Proceedings of the Fifth Annual ACM-SIAM Symposium of Discrete Algorithms, Arlington, VA, 10 pages. 38. 1994 D. Gusfield, K. Balasubramanian, and D. Naor. PARAMETRIC OPTIMIZATION OF SEQUENCE ALIGNMENT. Journal of Algorithmica, Special Issue on String Algorithms, Vol. 12, 312-326. (See also A29). 39. 1994 D. Gusfield, and M. Crochemore, eds. COMBINATORIAL PATTERN MATCHING. Springer-Verlag. 40. 1994 D. Gusfield, and E. Tardos. A FASTER PARAMETRIC MINIMUM CUT ALGORITHM. Algorithmica, Vol. 11, 278-290. 41. 1994 D. Gusfield. FASTER IMPLEMENTATION OF A SHORTEST SUPERSTRING APPROXIMATION. Information Processing Letters, Vol. 51, 271-274. 42. 1994 D. Naor, D. Gusfield, and C. Martel. A FAST ALGORITHM FOR OPTIMALLY INCREASING THE EDGE-CONNECTIVITY. SIAM Journal on Computing, Vol. 26, No. 4, 1139-1165. (See also A24). 43. 1996 D. Gusfield, R. Karp, L. Wang, and P. Stelling. GRAPH TRAVERSALS, GENES AND MATROIDS: AN EFFICIENT CASE OF THE TRAVELLING SALESMAN PROBLEM. Proceedings of the Seventh Annual Combinatorial Pattern Matching Conference, Lecture Notes in Computer Science 1075, Springer-Verlag, 304-319. 44. 1996 L. Wang, and D. Gusfield. IMPROVED APPROXIMATION ALGORITHMS FOR TREE ALIGNMENT. Proceedings of the Seventh Annual Combinatorial Pattern Matching Conference, Lecture Notes in Computer Science 1075, Springer-Verlag, 220-233. 45. Journal version of 44 is in Journal of Algorithms, Vol. 25, 255-273, 1997. 46. 1997 L. Wang, T. Jiang, and D. Gusfield. A MORE EFFICIENT APPROXIMATION SCHEME FOR TREE ALIGNMENT. In RECOMB: The First Annual International Conference on Computational Molecular Biology, 310-319. 47. 1997 D. Gusfield. ALGORITHMS ON STRINGS, TREES AND SEQUENCES: COMPUTER SCIENCE AND COMPUTATIONAL BIOLOGY. (A book). Cambridge University Press, 534 pages. 48. 1998 D. Gusfield, R. Karp, L. Wang, and P. Stelling. GRAPH TRAVERSALS, GENES AND MATROIDS: AN EFFICIENT SPECIAL CASE OF THE TRAVELING SALESMAN PROBLEM. Discrete Applied Math, Vol. 88, pp. 167-180. (See also A44) Also published in 1999 on the Editor's Choice list of best papers of 1998. 49. 1998 D. Gusfield, and L. Wang. NEW USES FOR UNIFORM LISTED ALIGNMENTS. DIMACS Series 47, American Mathematical Society, Papers on the special year on Mathematical Support for Molecular Biology, pp. 33-52. 50. 1998 L. Wang, and D. Gusfield. CONSTRUCTING ADDITIVE TREES WHEN THE ERROR IS SMALL. Journal of Computational Molecular Biology, Vol. 5, No. 1, pp. 127-134. 51. 1998 J. Kececioglu, and D. Gusfield. RECONSTRUCTING A HISTORY OF RECOMBINATIONS FROM A SET OF SEQUENCES. Discrete Applied Math 98, special issue on Computational Molecular Biology, pp. 239-260. (See also A37). 52. 1998 J. Stoye, and D. Gusfield. SIMPLE AND FLEXIBLE REPEAT DETECTION USING SUFFIX TREES. Proceedings of the Ninth Annual Symposium on Combinatorial Pattern Matching (CPM '98), M. Farach- Colton, ed., Piscataway, NJ, July 1998, Springer, Vol. 1448, pp. 140-152. 53. 1999 D. Gusfield, and M. Y. Kao, eds.. GUEST EDITOR'S FOREWORD. In Algorithmica, Vol. 25, No. 2-3, p. 141. 54. 1999 D. Gusfield, and C. Martel. THRESHOLDS FOR SPORTS ELIMINATION NUMBERS: ALGORITHMS AND COMPLEXITY. Proceedings of the 6th International Workshop on Algorithms and Data Structures (WADS '99), F. Dehne, A. Gupta, J.-R. Sack, and R. Tamassia, eds., Vancouver, Canada, August 1999, Springer, Vol. 1663, pp. 330-341. 55. 2000 D. Gusfield. A PRACTICAL ALGORITHM FOR OPTIMAL INFERENCE OF HAPLOTYPES FROM DIPLOID POPULATIONS. Proceedings of the 8th Annual Conference on Intelligent Systems in Molecular Biology (ISMB 2000), AAAI Press, pp. 183-189. 56. 2000 L. Wang, T. Jiang, and D. Gusfield. A MORE EFFICIENT APPROXIMATION SCHEME FOR TREE ALIGNMENT. SIAM Journal on Computing, Vol. 30, No. 1, pp. 283-299. (See also A46). 57. 2002 J. Stoye, and D. Gusfield. SIMPLE AND FLEXIBLE REPEAT DETECTION USING A SUFFIX TREE. Theoretical Computer Science, Vol. 270, pp. 843-856. (See also A52). 58. 2002 D. Gusfield, and C. Martel. THE STRUCTURE AND COMPLEXITY OF SPORTS ELIMINATION NUMBERS. Algorithmica, Vol. 32, pp. 73-86. (See also A54). 59. 2002 D. Gusfield. INFERENCE OF HAPLOTYPES FROM SAMPLES OF DIPLOID POPULATIONS: COMPLEXITY AND ALGORITHMS. Journal of Computational Biology, Vol. 8, No. 3, pp. 305-323. 60. 2002 D. Gusfield. HAPLOTYPING AS PERFECT PHYLOGENY: CONCEPTUAL FRAMEWORK AND EFFICIENT SOLUTIONS. Proceedings of the Sixth Annual International Conference on Computational Biology (RECOMB 2002), G. Myers, S. Hannenhalli, S. Istrail, P. Pevzner, and M. Waterman, eds., Washington, DC, April 18-21, ACM Press, pp. 166-175. 61. 2002 S. Rash, and D. Gusfield. STRING BARCODING: UNCOVERING OPTIMAL VIRUS SIGNATURES. Proceedings of the Sixth Annual International Conference on Computational Biology (RECOMB 2002), G. Myers, S. Hannenhalli, S. Istrail, P. Pevzner, and M. Waterman, eds., Washington, DC, April 18-21, ACM Press, pp. 254-261. 62. 2002 D. Gusfield. PARTITION-DISTANCE: A PROBLEM AND CLASS OF PERFECT GRAPHS ARISING IN CLUSTERING. Information Processing Letters, Vol. 82, No. 3, pp. 150-164. 63. 2002 R. Guigo, and D. Gusfield, eds. ALGORITHMS IN BIOINFORMATICS. Proceedings of the Second International Workshop, WABI 2002, Lecture Notes in Computer Science, Vol. 2452, Springer, Rome, Italy, 551 pages. 64. 2002 R.-H. Chung, and D. Gusfield. PERFECT PHYLOGENY HAPLOTYPER: HAPLOTYPE INFERRAL USING A TREE MODEL. Bioinformatics, Vol.19, No. 6, pp. 780-781. 65. 2003 A. Piccolboni, and D. Gusfield. ON THE COMPLEXITY OF FUNDAMENTAL COMPUTATIONAL PROBLEMS IN PEDIGREE ANALYSIS. Journal of Computational Biology, Vol. 10, pp. 763-774. 66. 2003 V. Bafna, D. Gusfield, G. Lancia, and S. Yooseph. HAPLOTYPING AS PERFECT PHYLOGENY: A DIRECT APPROACH. Journal of Computational Biology, Vol 10. pp. 323-340. 67. 2003 S. H. Orzack, D. Gusfield, J. Olson, S. Nesbitt, and V. P. Stanton Jr.. ANALYSIS AND EXPLORATION OF THE USE OF RULE-BASED ALGORITHMS AND CONSENSUS METHODS FOR THE INFERRAL OF HAPLOTYPES. Genetics, Vol. 165 pp. 915-928. 68. 2003 P. R. Srinivasas, D. Gusfield, O. Mason, M. Gertz, M. Hogarth, J. Stone, E. G. Jones, and F. Gorin. NEUROANATOMICAL TERM GENERATION AND COMPARISON BETWEEN TWO TERMINOLOGIES. Neuroinformatics, Vol 1, pp 177-192. 69. 2003 D. Gusfield. HAPLOTYPE INFERENCE BY PURE PARSIMONY. Proceedings of the 14th Annual Symposium on Combinatorial Pattern Matching, Lecture Notes in Computer Science, Springer, Vol 2676, Morelia, Mexico, pp. 144-155. 70. 2003 R.H. Chung and D. Gusfield. EMPIRICAL EXPLORATION OF PERFECT PHYLOGENY HAPLOTYPING AND HAPLOTYPERS. Proceedings of the 9th Annual Conference on Computing and Combinatorics, Lecture Notes in Computer Science, Springer. Vol. 2697, pp. 5-19. 71. 2003 D. Gusfield, S. Eddhu, and C. Langley. EFFICIENT RECONSTRUCTION OF PHYLOGENETIC NETWORKS WITH CONSTRAINED RECOMBINATION. Proceedings of the 2nd Annual IEEE Computer Society Conference on Bioinformatics, pp. 3663-374. 72. 2004 D. Gusfield, P. Bourne, S. Istrail, P. Pevzner, M. Waterman, editors. PROCEEDINGS OF THE EIGHTH INTERNATIONAL CONFERENCE ON COMPUTATIONAL MOLECULAR BIOLOGY (RECOMB 2004). ACM Press. 73. 2004 D. Gusfield, and J. Stoye. LINEAR TIME ALGORITHMS FOR FINDING AND REPRESENTING ALL THE TANDEM REPEATS IN A STRING. Journal of Computer and System Sciences, Vol 69 pp. 525-546. 74. 2004 D. Gusfield, S. Eddhu, C. Langley. OPTIMAL, EFFICIENT RECONSTRUCTION OF PHYLOGENETIC NETWORKS WITH CONSTRAINED RECOMBINATION. Journal of Bioinformatics and Computational Biology, Vol. 2, pp. 173-213. (Expanded journal version of A71). 75. 2004 V. Bafna, D. Gusfield, S. Hannenhalli, and S. Yooseph. A NOTE ON EFFICIENT COMPUTATION OF HAPLOTYPES VIA PERFECT PHYLOGENY. Journal of Computational Biology, Vol. 11, no. 5, p. 858-866. 76. 2004 D. Gusfield, S. Eddhu, and C. Langley. THE FINE STRUCTURE OF GALLS IN PHYLOGENETIC NETWORKS. INFORMS Journal on Computing special issue on Computational Biology, Vol 16, no. 4, p.459-469. 77. 2004 D. Gusfield. AN OVERVIEW OF COMBINATORIAL METHODS FOR HAPLOTYPE INFERENCE. Computational Methods for SNPs and Haplotype Inference, S. Istrail, M. Waterman, and A. Clark (eds). Lecture Notes in Computer Science, vol. 2983, Springer, p. 9-25. 78. 2004 D. Gusfield. OPTIMAL, EFFICIENT RECONSTRUCTION OF ROOT- UNKNOWN PHYLOGENETIC NETWORKS WITH CONSTRAINED RECOMBINATION. Journal of Computer and Systems Sciences, Special issue on Computational Biology. Vol. 70 p. 381-398. 79. 2005 D. Gusfield and V. Bansal. A FUNDAMENTAL DECOMPOSITION THEORY FOR PHYLOGENETIC NETWORKS AND INCOMPATIBLE CHARACTERS. Proceedings of the Ninth Annual International Conference on Computational Biology (RECOMB 2005), S. Miyano, J. Mesirov, S. Kasif, S. Istrail, P. Pevzner, and M. Waterman (eds). Springer, LNBI 3500 pp. 217-232. 80. 2005 . Ding, V. Filkov and D. Gusfield. A LINEAR-TIME ALGORITHM FOR THE PERFECT PHYLOGENY HAPLOTYPING (PPH) PROBLEM. Proceedings of the Ninth Annual International Conference on Computational Biology (RECOMB 2005), S. Miyano, J. Mesirov, S. Kasif, S. Istrail, P. Pevzner, and M. Waterman (eds). Springer, LNBI 3500 p. 585-600. 81. 2005 Y. Song, Y. Wu and D. Gusfield. EFFICIENT COMPUTATION OF CLOSE LOWER AND UPPER BOUNDS ON THE MINIMUM NUMBER OF NEEDED RECOMBINATIONS IN THE EVOLUTION OF BIOLOGICAL SEQUENCES. In Bioinformatics Vol. 21 Supplement 1, Proceedings of the ISMB 2005 Conference. p. 413-422. 82. 2005 D. Gusfield. Guest Editor. JOURNAL OF COMPUTATIONAL BIOLOGY. Vol. 12, No. 6 July/Aug. Selected journal version of papers from RECOMB 2004. 83. 2005 Y. Song, Y. Wu and D. Gusfield. ALGORITHMS FOR IMPERFECT PHYLOGENY (IPPH) WITH A SINGLE HOMOPLASY OR RECOMBINATION EVENT. Proceedings of The Workshop on Algorithms in Bioinformatics (WABI) 2005, Mollorca Spain, October 2005, pp.152-164. 84. 2005 D. Gusfield, D. Hickerson and S. Eddhu. AN EFFICIENTLY COMPUTED LOWER BOUND ON THE NUMBER OF RECOMBINATIONS IN PHYLOGENETIC NETWORKS: THEORY AND EMPIRICAL STUDY. Discrete Applied Mathematics, Special issue on ComputationalBiology, Vol. 155, pg. 806-830. 85. 2006 D. Gusfield and S. Orzack. HAPLOTYPE INFERENCE. In CRC Handbook on Bioinformatics 2006 (S. Aluru Editor), p. 18-25. 86. 2006 Orzack, D. Gusfield, L. Subrahmanyan, L. Essioux, S. Lissarrague. ANALYTICAL AND ALGORITHMIC METHODS FOR HAPLOTYPE FREQUENCY INFERENCE: WHAT DO THEY TELL US? Bioinformatics Algorithms: Techniques and Applications, I. Mandoiu and A. Zelikovsky (eds.), Wiley 2008 p. 373-394. 87. 2006 Z. Ding, V. Filkov, D. Gusfield. LINEAR-TIME ALGORITHM FOR PERFECT PHYLOGENY HAPLOTYPING. Journal of Computational Biology, Vol. 13, No. 2, pg. 522-553, 2006. 88. 2006 Dan Gusfield, Vikas Bansal, Vineet Bafna, Yun S. Song. A DECOMPOSITION THEORY FOR PHYLOGENETIC NETWORKS AND INCOMPATIBLE CHARACTERS. Journal of Computational Biology Dec 2007, Vol. 14, No. 10: 1247-1272. 89. 2006 Y.S. Song, Z. Ding, D. Gusfield, C. Langley, Y. Wu. ALGORITHMS TO DISTINGUISH THE ROLE OF GENE-CONVERSION FROM SINGLE•CROSSOVER RECOMBINATION IN THE DERIVATIONS OF SNP SEQUENCES IN POPULATIONS. Proceedings of RECOMB 2006. Springer LNBI 3909, p. 231-245. 90. 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. Journal of Computational Biology Dec 2007, Vol. 14, No. 10: 1273-1286. 91. 2006 Y.Wu and D. Gusfield. EFFICIENT COMPUTATION OF MINIMUM RECOMBINATION WITH GENOTYPES (NOT HAPLOTYPES). Proceedings of The CSB Conference, Stanford CA., August 2006. 92. 2007 Y. Wu and D. Gusfield. A NEW RECOMBINATION LOWER BOUND AND THE MINIMUM PERFECT PHYLOGENETIC FOREST PROBLEM. Springer LNCS, vol. 4598, Proceedings of the 13th Annual International Conference on Combinatorics and Computing, 2007, p. 16-26. 93. 2007 Y. Wu and D. Gusfield. IMPROVED ALGORITHMS FOR INFERRING THE MINIMUM MOSAIC OF A SET OF RECOMBINANTS. Springer LNCS, vol. 4580, Proceedings of the 18'th Annual Symposium on Combinatorial Pattern Matching, 2007, p. 150-161. 94. 2007 Y.Wu and D. Gusfield. EFFICIENT COMPUTATION OF MINIMUM RECOMBINATION WITH GENOTYPES (NOT HAPLOTYPES). J. Bioinformatics and Computational Biology, Vol. 5 No. 2(a), 2007, p. 181-200. 95. 2007 D. Gusfield and Y. Frid and D. Brown. . INTEGER PROGRAMMING FORMULATIONS AND COMPUTATIONS SOLVING PHYLOGENETIC AND POPULATION GENETIC PROBLEMS WITH MISSING OR GENOTYPIC DATA. Springer LNCS, vol. 4598, Proceedings of the 13th Annual International Conference on Combinatorics and Computing, 2007, p. 51-64. 96. 2009 Dan Gusfield and Yufeng Wu. THE THREE-STATE PERFECT PHYLOGENY PROBLEM REDUCES TO 2-SAT Communications and Information Systems, Special Issue Dedicated to Michael Waterman, 9(4): 195-301. 97. 2009 Dan Gusfield. THE MULTI-STATE PERFECT PHYLOGENY PROBLEM WITH MISSING AND REMOVABLE DATA; SOLUTIONS VIA INTEGER LINEAR PROGRAMMING AND CHORDAL GRAPH THEORY. Proceedings of the 2009 RECOMB Conference, May 2009. 98. 2009 F. Lam, D. Gusfield, S. Sridhar. GENERALIZING THE SPLITS EQUIVALENCE THEOREM AND FOUR GAMETE CONDITION: PERFECT PHYLOGENY ON THREE STATE CHARACTERS. Proceedings of the WABI 2009 conference, Springer LNCS Volume 5724, 2009, p. 206-219. 99. 2009 B. Venkatachalam, J. Apple, K. St John, D. Gusfield. UNTANGLING TANGLEGRAMS: COMPARING TREES BY THEIR DRAWINGS. In Proceedings of Bioinformatics Research and Applications, 5542: 88-99 May 13-16, 2009. 100. 2009 Y. Frid, D. Gusfield. A SIMPLE, PRACTICAL AND COMPLETE O(n^3/ log n)-TIME ALGORITHM FOR RNA FOLDING USING THE FOUR•RUSSIANS SPEEDUP. Proceedings of the WABI 2009 conference, Springer LNCS Volume 5724, 2009, p. 97-107 September 2009. 101. 2010 Kristian Stevens and Dan Gusfield. REDUCING MULTI-STATE TO BINARY PERFECT PHYLOGENY WITH APPLICATIONS TO MISSING, REMOVABLE, INSERTED AND DELETED DATA. Proceedings of WABI 2010, Springer LNCS Vol. 6293 2010, p. 274-287. 102. 2010 R. Gysel and D. Gusfield. EXTENSIONS AND IMPROVEMENTS TO THE CHORDAL GRAPH APPROACH TO THE MULTI-STATE PERFECT PHYLOGENY PROBLEM. In Proceedings of the ISBRA Conference, 2010, Springer LNBI Vol. 6054, p. 52-60. 103. 2010 Dan Gusfield. THE MULTI-STATE PERFECT PHYLOGENY PROBLEM WITH MISSING AND REMOVABLE DATA; SOLUTIONS VIA INTEGER LINEAR PROGRAMMING AND CHORDAL GRAPH THEORY. J. of Computational Biology, Vol. 17, no. 3, 2010, p. 383-399. 104. 2010 Yelena Frid and Dan Gusfield. WORST-CASE AND PRACTICAL SPEEDUP FOR THE RNA CO-FOLDING PROBLEM USING THE 4-RUSSIANS IDEA. Proceedings of WABI 2010, Springer LNCS Vol. 6293, 2010, p. 1-12. 105. 2010 B. Venkatachalam, J. Apple, K. St John, D. Gusfield. UNTANGLING TANGLEGRAMS: COMPARING TREES BY THEIR DRAWINGS. IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 7, 2010, p. 588-597. 106. 2010 Y. Frid, D. Gusfield. A SIMPLE, PRACTICAL AND COMPLETE O(n^3/ log n)-TIME ALGORITHM FOR RNA FOLDING USING THE FOUR-RUSSIANS SPEEDUP. Algorithms for Molecular Biology 2010, 5:13. (See also 100.) 107. 2011 Rob Gysel, Fumei Lam and Dan Gusfield. CONSTRUCTING PERFECT PHYLOGENIES AND PROPER TRIANGULATIONS FOR THREE-STATE CHARACTERS. Proceedings of WABI 2011, Springer LNCS Vol. 6833, pages 104-115. 108. 2011 R. Gysel and D. Gusfield. EXTENSIONS AND IMPROVEMENTS TO THE CHORDAL GRAPH APPROACH TO THE MULTI-STATE PERFECT PHYLOGENY PROBLEM. IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 8, 2011, pages 912-917. 109. 2011 F. Lam, D. Gusfield, S. Sridhar. GENERALIZING THE SPLITS EQUIVALENCE THEOREM AND FOUR GAMETE CONDITION: PERFECT PHYLOGENY ON THREE STATE CHARACTERS. SIAM J. Discrete Math. 25, Volume 25, Issue 3 pp. 1144-1175. (This is a much expanded journal version of 98.)