jens gramm
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| Journal Articles |
J. Gramm, E.A. Hirsch, R. Niedermeier and P. Rossmanith. Worst-case upper bounds for MAX-2-SAT with application to MAX-CUT. Discrete Applied Mathematics 130(2):139--155, 2003. J. Gramm and R. Niedermeier. A fixed-parameter algorithm for Minimum Quartet Inconsistency. Journal of Computer and System Sciences 67(4):723--741, 2003. J. Gramm, R. Niedermeier, and P. Rossmanith. Fixed-parameter algorithms for Closest String and related problems. Algorithmica 37(1):25--42, 2003, Springer. J. Alber, J. Gramm, J. Guo and R. Niedermeier. Computing the similarity of two sequences with nested arc annotations. Theoretical Computer Science 312(2-3):337--358. 2004. J. Gramm, J. Guo, F. Hüffner and R. Niedermeier. Automated generation of search tree algorithms for hard graph modification problems. Algorithmica, 39(4):321--347, 2004. [J. Gramm. A Polynomial-Time Algorithm for the Matching of Crossing Contact-Map Patterns. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 4(1):171--180, 2004.] There is a bug in the algorithm presented in this paper, for a proper treatment of the problem refer to: Shuai-Cheng Li and Ming Li. On the Complexity of the Crossing Contact Map Pattern Matching Problem. To appear in Proceedings of 6th Workshop on Algorithms in Bioinformatics (WABI 2006). R. Sharan, J. Gramm, A. Ben-Dor, Z. Yakhini. Multiplexing schemes for generic SNP genotyping assays. Journal of Computational Biology 12(5):514--533, 2005. J. Gramm, J. Guo, F. Hüffner and R. Niedermeier. Graph-modeled data clustering: fixed-parameter algorithms for clique generation. Theory of Computing Systems 38(4):373--392, 2005. J. Gramm, J. Guo, and R. Niedermeier. Pattern matching for arc-annotated sequences. ACM Transactions on Algorithms 2(1):44--65, 2006. J. Gramm, J. Guo and R. Niedermeier. Parameterized intractability of Distinguishing Substring Selection. Theory of Computing Systems 39(4):545--560, 2006. M.R. Fellows, J. Gramm, and R. Niedermeier. On the parameterized intractability of motif search problems. Combinatorica 26(2):141--167, 2006. J. Guo, J. Gramm, F. Hüffner, R. Niedermeier, and S. Wernicke. Compression-based fixed-parameter algorithms for Feedback Vertex Set and Edge Bipartization. Journal of Computer and System Sciences 72(8):1386--1396, 2006. S. Wernicke, J. Alber, J. Gramm, J. Guo, and R. Niedermeier: The computational complexity of avoiding forbidden submatrices by row deletions.. International Journal of Foundations of Computer Science. 17(6):1467--1484, 2006. J. Gramm, T. Nierhoff, T. Tantau, and R. Sharan. Haplotyping with missing data via perfect path phylogenies. Accepted for publication in Discrete Applied Mathemaics 155(6-7, Special issue on computational biology):788--805, 2007. J. Gramm, J. Guo, F. Hüffner, R. Niedermeier, H.-P. Piepho, and R. Schmid: Algorithms for compact letters displays: comparison and evaluation. Accepted for publication in Computational Statistics and Data Analysis, in press. J. Gramm, J. Guo, F. Hüffner, and R. Niedermeier: Data reduction and exact algorithms for clique cover. Accepted for publication in ACM Journal of Experimental Algorithmics, in press. J. Gramm, A. Nickelsen, and T. Tantau: Fixed-parameter algorithms in phylogenetics. Accepted for publication in The Computer Journal, in press. |
| Conference Articles |
J. Gramm and R. Niedermeier.
Faster exact solutions for Max2Sat.
In G. Bongiovanni, G. Gambosi, R. Petreschi (Eds.):
Proceedings of the 4th Italian Conference on Algorithms and
Complexity (CIAC
2000), Lecture Notes in Computer Science, volume number
1767, 174-186, Rome, Italy, March 2000, Springer. (.ps.gz) J. Gramm and R. Niedermeier. Minimum Quartet Inconsistency is fixed parameter tractable. In A. Amir, G.M. Landau (Eds.): Proceedings of the 12th Annual Symposium on Combinatorial Pattern Matching (CPM 2001), Lecture Notes in Computer Science, volume number 2089, 241-256, Jerusalem, Israel, July 2001, Springer. (.ps.gz) J. Gramm, R. Niedermeier and Peter Rossmanith. Exact solutions for Closest String and related problems. In P. Eades, T. Takaoka (Eds.): Proceedings of the 12th Annual Symposium on Algorithms and Computation (ISAAC 2001), Lecture Notes in Computer Science, volume number 2223, 441-453, Christchurch, New Zealand, December 2001, Springer. (.ps.gz). M.R. Fellows, J. Gramm and R. Niedermeier. On the parameterized intractability of Closest Substring and related problems. In H. Alt, A. Ferreira (Eds.): Proceedings of the 19th International Symposium on Theoretical Aspects of Computer Science (STACS 2002), Lecture Notes in Computer Science, volume number 2285, 262-273, Antibes/Juan-Les-Pins, France, March 2002, Springer. (.ps.gz). J. Alber, J. Gramm, J. Guo and R. Niedermeier. Towards optimally solving the Longest Common Subsequence problem for sequences with nested arc annotations in linear time. In A. Apostolico, M. Takeda (Eds.): Proceedings of the 13th Annual Symposium on Combinatorial Pattern Matching (CPM 2002), Lecture Notes in Computer Science, volume number 2373, 99-114, Fukuoka, Japan, July 2002, Springer. (.ps.gz) J. Gramm and R. Niedermeier. Breakpoint medians and breakpoint phylogenies - a fixed-parameter approach. In T. Lengauer, H.-P. Lenhof (Eds.): Proceedings of the 1st European Conference on Computational Biology (ECCB 2002), Bioinformatics 18 (Supplement 2):S128-S139. Oxford University Press. (.ps.gz) J. Gramm, J. Guo and R. Niedermeier. Pattern matching for arc-annotated sequences. In M. Agrawal, A. Seth (Eds.): Proceedings of the 22nd Conference on Foundations of Software Technology and Theoretical Computer Science (FST TCS 2002), Lecture Notes in Computer Science, volume number 2556, 182-193, Kanpur, India, December 2002, Springer. (.ps.gz) J. Gramm, J. Guo, F. Hüffner and R. Niedermeier. Graph-modeled data clustering: fixed-parameter algorithms for clique generation. Proceedings of the 5th Italian Conference on Algorithms and Complexity (CIAC 2003), Lecture Notes in Computer Science, volume number 2653, 108-119, Rome, Italy, May 2003, Springer. (.ps.gz) J. Gramm, J. Guo and R. Niedermeier. On exact and approximation algorithms for distinguishing substring selection. Proceedings of the 14th International Symposium on Fundamentals of Computation Theory (FCT 2003), Lecture Notes in Computer Science, volume number 2751, pages 195--209, Malmö, Sweden, August 2003, Springer. (.ps.gz) J. Gramm, J. Guo, F. Hüffner and R. Niedermeier. Automated generation of search tree algorithms for graph modification problems. Proceedings of the 11th Annual European Symposium on Algorithms (ESA 2003), Lecture Notes in Computer Science, volume number 2832, pages 642--653, Budapest, Hungary, September 2003. (.ps.gz) S. Wernicke, J. Alber, J. Gramm, J. Guo, and R. Niedermeier. Avoiding forbidden submatrices by row deletions. In Proceedings of the 30th International Conference on Current Trends in Theory and Practice of Informatics (SOFSEM 2004), Lecture Notes in Computer Science, volume number 2832, pages 349--360, Springer, 2004. J. Gramm, T. Nierhoff, T. Tantau, and R. Sharan. On the complexity of haplotyping via perfect phylogeny. Presented at the Second RECOMB Satellite Workshop on Computational Methods for SNPs and Haplotypes, February 20-21, Pittsburgh, USA. Proceedings to appear in LNBI, Springer, 2004. [J. Gramm. A polynomial-time algorithm for the matching of crossing contact-map patterns. In Proceedings of the 4th International Workshop on Algorithms in Bioinformatics (WABI 2004), Lecture Notes in Bioinformatics, volume number 3240, pages 38--49, Springer, 2004.] There is a bug in the algorithm presented in this paper, for a proper treatment of the problem refer to: Shuai-Cheng Li and Ming Li. On the Complexity of the Crossing Contact Map Pattern Matching Problem. To appear in Proceedings of 6th Workshop on Algorithms in Bioinformatics (WABI 2006). J. Gramm, T. Nierhoff, and T. Tantau. Perfect path phylogeny haplotyping with missing data is fixed-parameter tractable. In Proceedings of the First International Workshop on Parametrized and Exact Computation (IWPEC 2004), Lecture Notes in Computer Science, volume number 3162, pages 174--186, Springer, 2004. Jiong Guo, Jens Gramm, Falk Hüffner, Rolf Niedermeier, and Sebastian Wernicke. Improved fixed-parameter algorithms for two feedback set problems. In Proceedings of the 9th Workshop on Algorithms and Data Structures (WADS 2005), volume 3608 in LNCS, pages 158-168, Springer, 2005. Jiong Guo, Jens Gramm, Falk Hüffner, and Rolf Niedermeier. Data reduction, exact, and heuristic algorithms for clique cover. In Proceedings of the 8th Workshop on Algorithm Engineering and Experiments (ALENEX 2006), pages 86--94, SIAM Press, 2006. J. Gramm, T. Hartman, T. Nierhoff, R. Sharan, and T. Tantau. On the Complexity of SNP Block Partitioning Under the Perfect Phylogeny Model. In Proceedings of the 6th Workshop on Algorithms in Bioinformatics (WABI 2006), volume 4175 in LNCS, pages 92--102, Springer, 2006. |
| Reports |
J. Gramm, E.A. Hirsch, R. Niedermeier and P. Rossmanith.
New worst-case upper bounds for MAX-2-SAT with application to
MAX-CUT. ECCC Technical Report TR00-037, Trier, Fed. Rep. of Germany. Presented at SAT 2000, Renesse, The Netherlands, May 2000. J. Gramm and R. Niedermeier. Minimum Quartet Inconsistency is fixed parameter tractable. Technical Report WSI-2001-3, Wilhelm-Schickard Institut für Informatik, Universität Tübingen, 2001 (29 pages, postscript , gzipped ). M. R. Fellows, J. Gramm and R. Niedermeier. Parameterized intractability of motif search problems.. Technical Report WSI-2001-2, Wilhelm-Schickard Institut für Informatik, Universität Tübingen, May 2002. |
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