@InProceedings{ HEFN01, author = {Falk H{\"u}ffner and Stefan Edelkamp and Henning Fernau and Rolf Niedermeier}, title = {Finding Optimal Solutions to {Atomix}}, booktitle = {Proceedings of the German Conference on Artificial Intelligence (KI~'01)}, pages = {229--243}, year = 2001, volume = 2174, series = {LNCS}, publisher = {Springer}, doi = {10.1007/3-540-45422-5_17} } @MastersThesis{ Huef02, author = {Falk H{\"u}ffner}, title = {Finding Optimal Solutions to {Atomix}}, school = {Wilhelm-Schickard-Institut f\"ur Informatik, Universit\"at T\"ubingen}, year = 2002, type = {Studienarbeit} } @Misc{ GHN02, author = {Jens Gramm and Falk H{\"u}ffner and Rolf Niedermeier}, title = {Closest Strings, Primer Design, and Motif Search}, howpublished = {Presented at \textit{6th Annual International Conference on Computational Molecular Biology (RECOMB~'02)}, poster session}, year = 2002 } @InProceedings{ GGHN03b, author = {Jens Gramm and Jiong Guo and Falk H{\"u}ffner and Rolf Niedermeier}, title = {Graph-modeled data clustering: fixed-parameter algorithms for clique generation.}, booktitle = {Proceedings of the 5th Italian Conference on Algorithms and Complexity (CIAC~'03)}, pages = {108--119}, year = 2003, volume = 2653, series = {LNCS}, publisher = {Springer}, doi = {10.1007/3-540-44849-7_17} } @Article{ GGHN05, author = {Jens Gramm and Jiong Guo and Falk H{\"u}ffner and Rolf Niedermeier}, title = {Graph-Modeled Data Clustering: Exact Algorithms for Clique Generation}, journal = {Theory of Computing Systems}, year = 2005, volume = 38, number = 4, pages = {373--392}, doi = {10.1007/s00224-004-1178-y} } @InProceedings{ GGHN03, author = {Jens Gramm and Jiong Guo and Falk H{\"u}ffner and Rolf Niedermeier}, title = {Automated generation of search tree algorithms for graph modification problems}, booktitle = {Proceedings of the 11th Annual European Symposium on Algorithms (ESA~'03)}, pages = {642--653}, year = 2003, volume = 2832, series = {LNCS}, publisher = {Springer} } @Article{ GGHN04, author = {Jens Gramm and Jiong Guo and Falk H{\"u}ffner and Rolf Niedermeier}, title = {Automated Generation of Search Tree Algorithms for Hard Graph Modification Problems}, journal = {Algorithmica}, year = 2004, volume = 39, number = 4, pages = {321--347}, doi = {10.1007/s00453-004-1090-5} } @MastersThesis{ Huef03, author = {Falk H{\"u}ffner}, title = {Graph Modification Problems and Automated Search Tree Generation}, school = {Wilhelm-Schickard-Institut f\"ur Informatik, Universit\"at T\"ubingen}, year = 2003, type = {Diplomarbeit} } @InProceedings{ GHN04, author = {Jiong Guo and Falk H{\"u}ffner and Rolf Niedermeier}, title = {A Structural View on Parameterizing Problems: Distance from Triviality}, booktitle = {Proceedings of the 1st International Workshop on Parameterized and Exact Computation (IWPEC~'04)}, pages = {162--173}, year = 2004, volume = 3162, series = {LNCS}, publisher = {Springer}, } @InProceedings{ DGHN04, author = {Michael Dom and Jiong Guo and Falk H{\"u}ffner and Rolf Niedermeier}, title = {Error compensation in leaf root problems}, booktitle = {Proceedings of the 15th Annual International Symposium on Algorithms and Computation (ISAAC~'04)}, pages = {389--401}, year = 2004, volume = 3341, series = {LNCS}, publisher = {Springer}, url = {http://springerlink.com/content/81lcymfngwjkh3gy} } @Article{ DGHN06, author = {Michael Dom and Jiong Guo and Falk H{\"u}ffner and Rolf Niedermeier}, title = {Error Compensation in Leaf Power Problems}, journal = {Algorithmica}, year = 2006, volume = 44, number = 4, pages = {363--381} } @InProceedings{ Huef05, author = {Falk H{\"u}ffner}, title = {Algorithm Engineering for Optimal Graph Bipartization}, booktitle = {Proceedings of the 4th International Workshop on Experimental and Efficient Algorithms (WEA~'05)}, pages = {240--252}, year = 2005, volume = 3503, series = {LNCS}, publisher = {Springer}, } @InProceedings{ DGHN05, author = {Michael Dom and Jiong Guo and Falk H{\"u}ffner and Rolf Niedermeier}, title = {Extending the Tractability Border for Closest Leaf Powers}, booktitle = {Proceedings of the 31st International Workshop on Graph-Theoretic Concepts in Computer Science (WG~'05)}, pages = {397--408}, year = 2005, volume = 3787, series = {LNCS}, publisher = {Springer}, } @InProceedings{ GGHNW05, author = {Jiong Guo and Jens Gramm and Falk H{\"u}ffner and Rolf Niedermeier and Sebastian Wernicke}, title = {Improved fixed-parameter algorithms for two feedback set problems}, booktitle = {Proceedings of the 9th Workshop on Algorithms and Data Structures (WADS~'05)}, pages = {158--168}, year = 2005, volume = 3503, series = {LNCS}, publisher = {Springer}, doi = {10.1007/11427186_22} } @Article{ GGHNW06, author = {Jiong Guo and Jens Gramm and Falk H{\"u}ffner and Rolf Niedermeier and Sebastian Wernicke}, title = {Compression-Based Fixed-Parameter Algorithms for Feedback Vertex Set and Edge Bipartization}, journal = {Journal of Computer and System Sciences}, year = 2006, volume = 72, number = 8, pages = {1386--1396} } @InProceedings{ GHKNU06, author = {Jiong Guo and Falk H{\"u}ffner and Erhan Kenar and Rolf Niedermeier and Johannes Uhlmann}, title = {Complexity and Exact Algorithms for Multicut}, booktitle = {Proceedings of the 32nd International Conference on Current Trends in Theory and Practice of Computer Science (SOFSEM~'06)}, pages = {137--147}, year = 2006, volume = 3831, series = {LNCS}, publisher = {Springer} } @Article{ GHKNU08, author = {Jiong Guo and Falk H{\"u}ffner and Erhan Kenar and Rolf Niedermeier and Johannes Uhlmann}, title = {Complexity and exact algorithms for vertex multicut in interval and bounded treewidth graphs}, journal = {European Journal of Operational Research}, year = 2008, volume = 186, number = 2, pages = {542--553}, doi = {10.1016/j.ejor.2007.02.014} } @InProceedings{ GGHN06, author = {Jens Gramm and Jiong Guo and Falk H{\"u}ffner and Rolf Niedermeier}, title = {Data Reduction, Exact, and Heuristic Algorithms for Clique Cover}, booktitle = {Proceedings of the 8th Workshop on Algorithm Engineering and Experiments (ALENEX~'06)}, pages = {86--94}, year = 2006, publisher = {SIAM} } @Article{ GGHN08, author = {Jens Gramm and Jiong Guo and Falk H{\"u}ffner and Rolf Niedermeier}, title = {Data reduction and exact algorithms for clique cover}, journal = {ACM Journal of Experimental Algorithmics}, year = 2008, volume = 13, pages = {2.2:1--2.2:15}, doi = {10.1145/1412228.1412236} } @InProceedings{ DGHNT06, author = {Michael Dom and Jiong Guo and Falk H{\"u}ffner and Rolf Niedermeier and Anke Tru{\ss}}, title = {Fixed-Parameter Tractability Results for Feedback Set Problems in Tournaments}, booktitle = {Proceedings of the 6th Conference on Algorithms and Complexity (CIAC~'06)}, pages = {320--331}, year = 2006, volume = 3998, series = {LNCS}, publisher = {Springer} } @InProceedings{ BAHN06, author = {Matthias Brosemann and Jochen Alber and Falk H{\"u}ffner and Rolf Niedermeier}, title = {Matrix Robustness, with an Application to Power System Observability}, booktitle = {Proceedings of the 2nd Algorithms and Complexity in Durham Workshop (ACiD~'06)}, pages = {37--48}, year = 2006, volume = 7, series = {Texts in Algorithmics}, publisher = {College Publications, London}, } @Article{ HNW08, author = {Falk H{\"u}ffner and Rolf Niedermeier and Sebastian Wernicke}, title = {Techniques for Practical Fixed-Parameter Algorithms}, journal = {The Computer Journal}, year = 2008, volume = 51, number = 1, pages = {7--25}, doi = {10.1093/comjnl/bxm040} } @InProceedings{ HWZ07, author = {Falk H{\"u}ffner and Sebastian Wernicke and Thomas Zichner}, title = {Algorithm Engineering for Color-Coding to Facilitate Signaling Pathway Detection}, booktitle = {Proceedings of the 5th Asia-Pacific Bioinformatics Conference (APBC~'07)}, pages = {277--286}, year = 2007, volume = 5, series = {Advances in Bioinformatics and Computational Biology}, publisher = {Imperial College Press} } @Article{ GGHNPS07, author = {Jens Gramm and Jiong Guo and Falk H{\"u}ffner and Rolf Niedermeier and Hans-Peter Piepho and Ramona Schmid}, title = {Algorithms for Compact Letter Displays: Comparison and Evaluation}, journal = {Computational Statistics\,\&\,Data Analysis}, year = 2007, volume = 52, number = 2, pages = {725--736}, doi = {10.1016/j.csda.2006.09.035} } @Article{ GHM07, author = {Jiong Guo and Falk H{\"u}ffner and Hannes Moser}, title = {Feedback Arc Set in Bipartite Tournaments is {NP}-Complete}, journal = {Information Processing Letters}, year = 2007, volume = 102, number = {2--3}, pages = {62--65} } @InProceedings{ HBN07, author = {Falk H{\"u}ffner and Nadja Betzler and Rolf Niedermeier}, title = {Optimal Edge Deletions for Signed Graph Balancing}, booktitle = {Proceedings of the 6th Workshop on Experimental Algorithms (WEA~'07)}, pages = {297--310}, year = 2007, volume = 4525, series = {LNCS}, publisher = {Springer}, doi = {10.1007/978-3-540-72845-0_23} } @InProceedings{ KHMN07, author = {Christian Komusiewicz and Falk H{\"u}ffner and Hannes Moser and Rolf Niedermeier}, title = {Isolation Concepts for Enumerating Dense Subgraphs}, booktitle = {Proceedings of the 13th International Computing and Combinatorics Conference (COCOON~'07)}, pages = {140--150}, year = 2007, volume = 4598, series = {LNCS}, publisher = {Springer}, doi = {10.1007/978-3-540-73545-8_16} } @Article{ HWZ07a, author = {Falk H{\"u}ffner and Sebastian Wernicke and Thomas Zichner}, title = {{FASPAD}: fast signaling pathway detection}, journal = {Bioinformatics}, year = 2007, volume = 23, number = 13, pages = {1708--1709}, doi = {10.1093/bioinformatics/btm160} } @InCollection{ HNW09, author = {Falk H{\"u}ffner and Rolf Niedermeier and Sebastian Wernicke}, title = {Fixed-parameter algorithms for graph-modeled data clustering}, booktitle = {Clustering Challenges in Biological Networks}, pages = {3--28}, publisher = {World Scientific}, year = 2009 } @Article{ HWZ08, author = {Falk H{\"u}ffner and Sebastian Wernicke and Thomas Zichner}, title = {Algorithm Engineering for Color-Coding with Applications to Signaling Pathway Detection}, journal = {Algorithmica}, year = 2008, volume = 52, number = 2, pages = {114--132}, doi = {10.1007/s00453-007-9008-7} } @InCollection{ DHN08, author = {Michael Dom and Falk H{\"u}ffner and Rolf Niedermeier}, title = {Tiefensuche ({Ariadne} und {Co}.)}, booktitle = {Taschenbuch der Algorithmen}, pages = {61--73}, publisher = {Springer}, year = 2008, chapter = 7, doi = {10.1007/978-3-540-76394-9_7} } @InCollection{ HNW07c, author = {Falk H{\"u}ffner and Rolf Niedermeier and Sebastian Wernicke}, title = {Developing Fixed-Parameter Algorithms to Solve Combinatorially Explosive Biological Problems}, booktitle = {Bioinformatics}, pages = {395--421}, publisher = {Humana Press}, year = 2007, volume = 453, series = {Methods in Molecular Biology Series}, doi = {10.1007/978-1-60327-429-6_21} } @InCollection{ HHRW10, author = {Sabine Helwig and Falk H{\"u}ffner and Ivo R{\"o}ssling and Maik Weinard}, title = {Selected Design Issues}, booktitle = {Algorithm Engineering}, pages = {58--126}, year = 2010, volume = 5971, series = {LNCS}, publisher = {Springer}, doi = {10.1007/978-3-642-14866-8_3} } @InCollection{ Huef08b, author = {Falk H{\"u}ffner}, title = {Automated Search Tree Generation}, booktitle = {Encyclopedia of Algorithms}, pages = {78--81}, publisher = {Springer}, year = 2008, doi = {10.1007/978-0-387-30162-4_44} } @InProceedings{ HKMN08, author = {Falk H{\"u}ffner and Christian Komusiewicz and Hannes Moser and Rolf Niedermeier}, title = {Fixed-Parameter Algorithms for Cluster Vertex Deletion}, booktitle = {Proceedings of the 8th Latin American Theoretical Informatics Symposium (LATIN~'08)}, pages = {711--722}, year = 2008, volume = 4598, series = {LNCS}, publisher = {Springer}, doi = {10.1007/978-3-540-78773-0_61} } @Article{ HKMN10, author = {Falk H{\"u}ffner and Christian Komusiewicz and Hannes Moser and Rolf Niedermeier}, title = {Fixed-Parameter Algorithms for Cluster Vertex Deletion}, journal = {Theory of Computing Systems}, year = 2010, volume = 47, number = 1, pages = {196--217}, doi = {10.1007/s00224-008-9150-x}, } @Article{ DGHN08, author = {Michael Dom and Jiong Guo and Falk H{\"u}ffner and Rolf Niedermeier}, title = {Closest 4-leaf power is fixed-parameter tractable}, journal = {Discrete Applied Mathematics}, year = 2008, volume = 156, number = 18, pages = {3345--3361}, doi = {10.1016/j.dam.2008.01.007} } @InProceedings{ GHKZ08, author = {Jiong Guo and Falk H{\"u}ffner and Christian Komusiewicz and Yong Zhang}, title = {Improved Algorithms for Bicluster Editing}, booktitle = {Proceedings of the 5th Annual Conference on Theory and Applications of Models of Computation (TAMC~'08)}, pages = {445--456}, year = 2008, volume = 4978, series = {LNCS}, publisher = {Springer}, doi = {10.1007/978-3-540-79228-4_39} } @InProceedings{ PHN08, author = {Oriana Ponta and Falk H{\"u}ffner and Rolf Niedermeier}, title = {Speeding up Dynamic Programming for Some {NP}-hard Graph Recoloring Problems}, booktitle = {Proceedings of the 5th Annual Conference on Theory and Applications of Models of Computation (TAMC~'08)}, pages = {490--501}, year = 2008, volume = 4978, series = {LNCS}, publisher = {Springer}, doi = {10.1007/978-3-540-79228-4_43} } @PhDThesis{ Huef07, author = {Falk H{\"u}ffner}, title = {Algorithms and Experiments for Parameterized Approaches to Hard Graph Problems}, school = {Institut f{\"u}r Informatik, Friedrich-Schiller-Universit{\"a}t Jena}, year = 2007, url = {http://theinf1.informatik.uni-jena.de/publications/diss-hueffner07.pdf} } @InCollection{ Huef08, author = {Falk H{\"u}ffner}, title = {{Parametrisierte Ans\"atze für schwere Graphprobleme: Algorithmen und Experimente}}, booktitle = {Ausgezeichnete Informatikdissertationen 2007}, pages = {151--160}, series = {GI Lecture Notes in Informatics}, publisher = {Gesellschaft für Informatik (GI)}, year = 2008, volume = {D-8} } @InProceedings{ HKMN08b, author = {Falk H{\"u}ffner and Christian Komusiewicz and Hannes Moser and Rolf Niedermeier}, title = {Enumerating Isolated Cliques in Synthetic and Financial Networks}, booktitle = {Proceedings of the 2nd Annual International Conference on Combinatorial Optimization and Applications (COCOA~'08)}, pages = {405--416}, year = 2008, volume = 5165, series = {LNCS}, publisher = {Springer}, doi = {10.1007/978-3-540-85097-7_38} } @Article{ Huef09, author = {Falk H{\"u}ffner}, title = {Algorithm Engineering for Optimal Graph Bipartization}, journal = {Journal of Graph Algorithms and Applications}, year = 2009, volume = 13, number = 2, pages = {77--98}, url = {http://www.cs.brown.edu/sites/jgaa/accepted/2009/Hueffner2009.13.2.pdf}, } @InProceedings{ BHKSS09, author = {Sharon Bruckner and Falk H{\"u}ffner and Richard M. Karp and Ron Shamir and Roded Sharan}, title = {Topology-Free Querying of Protein Interaction Networks}, booktitle = {Proceedings of the 13th Annual International Conference on Research in Computational Molecular Biology (RECOMB~'09)}, pages = {74--89}, year = 2009, volume = 5541, series = {Lecture Notes in Bioinformatics}, publisher = {Springer}, doi = {10.1007/978-3-642-02008-7_6} } @Article{ HBN10, author = {Falk H{\"u}ffner and Nadja Betzler and Rolf Niedermeier}, title = {Separator-Based Data Reduction for Signed Graph Balancing}, journal = {Journal of Combinatorial Optimization}, year = 2010, volume = 20, number = 4, pages = {335--360}, doi = {10.1007/s10878-009-9212-2} } @Article{ KHMN09, author = {Christian Komusiewicz and Falk H{\"u}ffner and Hannes Moser and Rolf Niedermeier}, title = {Isolation Concepts for Efficiently Enumerating Dense Subgraphs}, journal = {Theoretical Computer Science}, year = 2009, volume = 410, number = {38--40}, pages = {3640--3654}, doi = {10.1016/j.tcs.2009.04.021} } @Article{ HKMN09, author = {Falk H{\"u}ffner and Christian Komusiewicz and Hannes Moser and Rolf Niedermeier}, title = {Isolation Concepts for Clique Enumeration: Comparison and Computational Experiments}, journal = {Theoretical Computer Science}, year = 2009, volume = 410, number = {52}, pages = {5384--5397}, doi = {10.1016/j.tcs.2009.05.008} } @Article{ BHKSS09a, author = {Sharon Bruckner and Falk H{\"u}ffner and Richard M. Karp and Ron Shamir and Roded Sharan}, title = {Torque: Topology-free querying of protein interaction networks}, journal = {Nucleic Acids Research}, year = 2009, volume = 37, number = {suppl.~2}, pages = {W106--108}, doi = {10.1093/nar/gkp474} } @InCollection{ DHN11, author = {Michael Dom and Falk H{\"u}ffner and Rolf Niedermeier}, title = {Depth-First Search ({Ariadne}\,\&\,{Co}.)}, booktitle = {Algorithms Unplugged}, pages = {57--68}, publisher = {Springer}, year = 2011, chapter = 7, doi = {10.1007/978-3-642-15328-0_7} } @Article{ Huef09b, author = {Falk H{\"u}ffner}, title = {{Parametrisierte Ans\"atze für schwere Graphprobleme: Algorithmen und Experimente}}, journal = {it -- Information Technology}, year = 2009, volume = 51, number = 3, pages = {171--174}, doi = {10.1524/itit.2009.0538} } @Article{ DGHNT10, author = {Michael Dom and Jiong Guo and Falk H{\"u}ffner and Rolf Niedermeier and Anke Truss}, title = {Fixed-Parameter Tractability Results for Feedback Set Problems in Tournaments}, journal = {Journal of Discrete Algorithms}, year = 2010, volume = 8, number = 1, pages = {76--86}, doi = {10.1016/j.jda.2009.08.001} } @Article{ BHKSS10, author = {Sharon Bruckner and Falk H{\"u}ffner and Richard M. Karp and Ron Shamir and Roded Sharan}, title = {Topology-Free Querying of Protein Interaction Networks}, journal = {Journal of Computational Biology}, year = 2010, volume = 17, number = 3, pages = {237--252}, doi = {10.1089/cmb.2009.0170} } @InProceedings{ BHTW09, author = {Sebastian B{\"o}cker and Falk H{\"u}ffner and Anke Truss and Magnus Wahlstr{\"o}m}, title = {A Faster Fixed-Parameter Approach to Drawing Binary Tanglegrams}, booktitle = {Proceedings of the 4th International Workshop on Parameterized and Exact Computation (IWPEC~'09)}, pages = {38--49}, year = 2009, volume = 5917, series = {LNCS}, publisher = {Springer}, doi = {10.1007/978-3-642-11269-0_3} } @InProceedings{ AHLMS11, author = {Antonios Antoniadis and Falk H{\"u}ffner and Pascal Lenzner and Carsten Moldenhauer and Alexander Souza}, title = {Balanced Interval Coloring}, booktitle = {Proceedings of the 28th Symposium on Theoretical Aspects of Computer Science (STACS~'11)}, pages = {531--542}, year = 2011, volume = 9, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, publisher = {Schloss Dagstuhl--Leibniz-Zentrum f\"ur Informatik}, doi = {10.4230/LIPIcs.STACS.2011.531} } @InProceedings{ DHKNU11, author = {Britta Dorn and Falk H{\"u}ffner and Dominikus Kr{\"u}ger and Rolf Niedermeier and Johannes Uhlmann}, title = {Exploiting bounded signal flow for graph orientation based on cause--effect pairs}, booktitle = {Proceedings of the 1st International ICST Conference on Theory and Practice of Algorithms in (Computer) Systems (TAPAS~'11)}, pages = {104--115}, year = 2011, volume = 6595, series = {LNCS}, publisher = {Springer}, doi = {10.1007/978-3-642-19754-3_12} } @Article{ DHKNU11a, author = {Britta Dorn and Falk H{\"u}ffner and Dominikus Kr{\"u}ger and Rolf Niedermeier and Johannes Uhlmann}, title = {Exploiting bounded signal flow for graph orientation based on cause--effect pairs}, journal = {Algorithms for Molecular Biology}, year = 2011, volume = 6, number = 1, pages = {21}, doi = {10.1186/1748-7188-6-21} } @InProceedings{ EEHNR12, author = {Hartmut Ehrig and Claudia Ermel and Falk H{\"u}ffner and Rolf Niedermeier and Olga Runge}, title = {Confluent data reduction for edge clique cover: a bridge between graph transformation and kernelization}, booktitle = {Proceedings of the 8th Conference on Computability in Europe (CiE~'12)}, year = 2012, series = {LNCS}, publisher = {Springer}, note = {To appear.} } @InProceedings{ BHKNTU12, author = {Sharon Bruckner and Falk H{\"u}ffner and Christian Komusiewicz and Rolf Niedermeier and Sven Thiel and Johannes Uhlmann}, title = {Partitioning into Colorful Components by Minimum Edge Deletions}, booktitle = {Proceedings of the 23rd Annual Symposium on Combinatorial Pattern Matching (CPM~'12)}, year = 2012, series = {LNCS}, publisher = {Springer}, note = {To appear.} }