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Divisions: Bioinformatics Group

Number of items at this level: 64.

Mann, Martin and Hamra, Mohamed A. and Backofen, Rolf and Steinhöfel, Kathleen (2009) Constraint-based local move definitions for lattice protein models including side chains. In: Workshop on Constraint Based Methods for Bioinformatics, (WCB 2009), 20 Septemeber 2009, Lisbon, Portugal.

Kapsokalivas, Leonidas and Gan, Xiangchao and Steinhöfel, Kathleen and Albrecht, Andreas Alexander (2009) Population-based local search for protein folding simulation in the MJ energy model and cubic lattices. Computational Biology and Chemistry, 33 (4). 283 - 294.

Ullah, Abu Z. Dayem and Kapsokalivas, Leonidas and Mann, Martin and Steinhöfel, Kathleen (2009) Protein Folding Simulation by Two-Stage Optimization. In: 4th International Symposium on Intelligence Computation and Applications, (ISICA 2009), 23-25 October 2009, Wuhan, China.

Kapsokalivas, Leonidas and Albrecht, Andreas A. and Steinhöfel, Kathleen (2009) Uphill Unfolding of Native Protein Conformations. In: Poster Abstracts of German Conference in Bioinformatics, (GCB 2009), 28-30 September 2009, Halle (Saale), Germany.

Ullah, Abu Z. Dayem and Steinhöfel, Kathleen (2009) Upper Bounds for Foldings in the FCC-HP Protein Model. In: IEEE International Conference on Bioinformatics and Biomedicine Workshop, (BIBMW 2009), 1-4 Nov 2009, Washington D.C., USA.

Gan, Xiangchao and Liew, Alan and Yan, Hong (2008) Discovering biclusters in gene expression data based on high-dimensional linear geometries. BMC Bioinformatics, 9 (1). 209.

Albrecht, Andreas Alexander and Skaliotis, Alexandros and Steinhöfel, Kathleen (2008) Stochastic protein folding simulation in the three-dimensional HP-model. Computational Biology and Chemistry, 32 (4). pp. 248-255.

Rahman, M. Sohel and Iliopoulos, Costas S. and Mouchard, Laurent (2007) Pattern Matching in Degenerate DNA/RNA Sequences. In: Proceedings of the Workshop on Algorithms and Computation.

Crochemore, Maxime and Hancart, Christophe and Lecroq, Thierry (2007) Algorithms on Strings. Cambridge University Press.

Antoniou, Pavlos and Crochemore, Maxime and Iliopoulos, Costas and Peterlongo, Pierre (2007) Application of suffix trees for the acquisition of common motifs with gaps in a set of strings. In: Proceedings of the 1st International Conference on Language and Automata Theory and Applications, March 2007, Tarragona, Spain.

Christodoulakis, Manolis and Golding, G. B. and Iliopoulos, Costas S. and Pinzon, Yoan J. and Smyth, William F. (2007) Efficient Algorithms for Counting and Reporting Segregating Sites in Genomic Sequences. Journal of Computational Biology, 14 (7). 1001 - 1010.

Lee, Inbok and Iliopoulos, Costas S. and Park, Kunsoo (2007) Linear time algorithm for the longest common repeat problem. Journal of Discrete Algorithms, 5 (2). pp. 243-249.

Bakalis, A. and Iliopoulos, Costas S. and Makris, C. and Sioutas, S. and Theodoridis, E. and Tsakalidis, A. and Tsichlas, K. (2007) Locating Maximal Multirepeats in Multiple Strings Under Various Constraints. The Computer Journal, 50 (2). pp. 178-185.

Steinhofel, K. and Skaliotis, A. and Albrecht, A. (2007) Logarithmic Simulated Annealing for Protein Folding. In: Abstracts British Colloquium for Theoretical Computer Science.

Steinhofel, Kathleen and Skaliotis, Alexandros and Albrecht, Andreas Alexander (2007) Relating Time Complexity of Protein Folding Simulation to Approximations of Folding Time. Computer Physics Communications, 176 (7). pp. 465-470.

Steinhofel, Kathleen and Skaliotis, Alexandros and Albrecht, Andreas Alexander (2007) Stochastic Protein Folding Simulation in the d-Dimensional HP-Model. In: Bioinformatics Research and Development, First International Conference, BIRD 2007, Berlin, Germany, March 12-14, 2007, Proceedings.

Crochemore, Maxime and Ilie, Lucian and Seid-Hilmi, Emine (2007) The structure of Factor Oracles. International Journal of Foundations of Computer Science, 18 (4). pp. 781-797.

Iliopoulos, Costas S. and Jayasekara, I. and Mouchard, Laurent (2006) Fast practical exact and approximate pattern matching in protein sequences. In: Proceedings of the 17th Australasian Workshop on Combinatorial Algorithms. (Unpublished)

Crochemore, Maxime and Iliopoulos, Costas S. and Park, Kunsoo and Roh, Kangho (2006) External memory algorithms for string problems. In: Proceedings of the Seventeenth Australasian Workshop on Combinatorial Algorithms.

Crochemore, Maxime and Ilie, Lucian and Seid-Hilmi, Emine (2006) Factor Oracles. In: Implementation and Application of Automata.

Steinhofel, Kathleen and Skaliotis, Alexandros and Albrecht, Andreas Alexander (2006) Landscape Analysis for Protein-Folding Simulation in the H-P Model. In: Algorithms in Bioinformatics, 6th International Workshop, WABI 2006, Zurich, Switzerland, September 11-13, 2006, Proceedings.

Crochemore, Maxime and Iliopoulos, Costas S. and Mohamed, Manal and Sagot, Marie-France (2006) Longest Repeats with a Block of k Don't Cares. Theoretical Computer Science, 362 (1-3). pp. 248-254.

Lappas, G. and Steinhofel, K. and Albrecht, A.A. (2006) Splice-junction Gene Sequences by a Special Type of Threshold Circuits. In: Algorithms in Bioinformatics.

Crochemore, Maxime and Lecroq, Thierry (2006) Text Searching and Indexing. In: Recent Advances in Formal Languages and Applications. Springer-Verlag, pp. 43-80.

Iliopoulos, Costas S. and Makris, C. and Panagis, Y. and Perdikuri, Katerina and Theodoridis, E. and Tsakalidis, A. (2006) The Weighted Suffix Tree: An Efficient Data Structure for Handling Molecular Weighted Sequences and its Applications. Fundamenta Informaticae, 71 (2-3). pp. 259-277.

Iliopoulos, Costas S. and Perdikuri, Katerina and Tsakalidis, A. and Tsichlas, K. (2005) Algorithms for extracting structured motifs from biologically weighted sequences. In: Proceedings of the 16th Australasian Workshop on Combinatorial Algorithms (AWOCA). (Unpublished)

Pisanti, Nadia and Crochemore, Maxime and Grossi, Roberto and Sagot, Marie-France (2005) A Comparative Study of Bases for Motif Inference. In: String Algorithmics.

Crochemore, Maxime and Hermelin, Danny and Landau, Gad M. and Vialette, Stéphane (2005) Approximating the 2-Interval Pattern Problem. In: ESA 2005: 13th Annual European Symposium.

Pisanti, Nadia and Crochemore, Maxime and Grossi, Roberto and Sagot, Marie-France (2005) Bases of Motifs for Generating Repeated Patterns with Wild Cards. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2 (1). pp. 40-50.

Crochemore, Maxime and Iliopoulos, Costas and Navarro, Gonzalo and Pinzon, Yoan and Salinger, Alejandro (2005) Bit-parallel (delta,gamma)-matching and suffix automata. Journal of Discrete Algorithms, 3 (2-4). pp. 198-214.

Apostolico, Alberto and Crochemore, Maxime and Park, Kunsoo, eds. (2005) Combinatorial Pattern Matching. LNCS, 3537 . Springer-Verlag.

Hein, E. and Albrecht, A. and Melzer, D. and Steinhofel, K. and Rogalla, P. and Hamm, B. and Taupitz, M. (2005) Computer-assisted diagnosis of focal liver lesions on CT images. Academic Radiology, 12 (9). pp. 1205-1210.

Baeza-Yates, Ricardo and Crochemore, Maxime, eds. (2005) Indexing and Matching Strings. Elsevier.

Crochemore, Maxime and Landau, Gad M. and Schieber, Baruch and Ziv-Ukelson, Michal (2005) Re-Use Dynamic Programming for Sequence Alignment: An Algorithmic Toolkit. In: String Algorithmics.

Crochemore, Maxime (2005) Structures for indexes. In: Applied Combinatorics on Words. Cambridge University Press, pp. 106-163.

Iliopoulos, Costas S. and Perdikuri, Katerina and Theodoridis, E. and Tsakalidis, A. and Tsichlas, K. (2004) Motif Extraction from Weighted Sequences. In: Proceedings of the Eleventh Symposium on String Processing and Information Retrieval (SPIRE'04).

Iliopoulos, Costas S. and McHugh, J. A. M. and Peterlongo, Pierre and Pisanti, Nadia and Rytter, Wojciech and Sagot, Marie-France (2004) A First Approach to Finding Common Motifs with Gaps. International Journal of Foundations of Computer Science, 16 (6). pp. 1145-1154.

Iliopoulos, Costas S. and McHugh, J. A. M. and Peterlongo, Pierre and Pisanti, Nadia and Rytter, Wojciech and Sagot, Marie-France (2004) A First Approach to Finding Common Motifs with Gaps. In: Proceedings of the 2004 Prague Stringology Conference (PSC'04).

Iliopoulos, Costas S. and Makris, C. and Panagis, Y. and Theodoridis, E. and Tsakalidis, A. (2004) Efficient Algorithms for Handling Molecular Weighted Sequences. Exploring New Frontiers of Theoretical Informatics, IFIP 18th World Computer Congress, TC1 3rd International Conference on Theoretical Computer Science (TCS2004) .

Gabbay, D. M. and d'AvilaGarcez, A. S. (2004) Fibring neural networks. In: Proceedings of 19th National Conference on Artificial Intelligence (AAA'04).

Crochemore, Maxime and Giancarlo, Raffaele and Sagot, Marie-France (2004) Longest Motifs with a Functionally Equivalent Block. In: Proc. 11th International Symposium on String Processing and Information Retrieval (SPIRE'2004).

Crochemore, Maxime and Iliopoulos, Costas~S. and Mohamed, Manal and Sagot, Marie-France (2004) Longest repeated motif with a block of don't cares. In: LATIN 2004: Theoretical Informatics.

Christodoulakis, M. and Iliopoulos, Costas S. and Mouchard, Laurent and Tsichlas, K. (2004) Pattern Matching on Weighted Sequences. In: Proceedings of the Algorithms and Computational Methods for Biochemical and Evolutionary Networks 2004 (CompBioNets'04).

Iliopoulos, Costas S. and Perdikuri, Katerina and Tsichlas, K. (2004) The Pattern Matching Problem in Biological Weighted Sequences. In: Proceedings of the Third International Conference on FUN WITH ALGORITHMS (FUN 2004).

Pisanti, Nadia and Crochemore, Maxime and Grossi, Roberto and Sagot, Marie-France (2003) A basis of tiling motifs for generating repeated patterns and its complexity for higher quorum. In: Mathematical Foundations of Computer Science (MFCS).

Crochemore, Maxime and Landau, Gad M. and Ziv-Ukelson, Michal (2003) A Sub-quadratic Sequence Alignment Algorithm for Unrestricted Cost Matrices. SIAM Journal of Computing, 32 (6). pp. 1654-1673.

Crochemore, Maxime and Hancart, Christophe and Lecroq, Thierry (2003) A unifying look at the Apostolico-Giancarlo string-matching algorithm. Journal of Discrete Algorithms, 1 (1). pp. 37-52.

Iliopoulos, Costas S. and Makris, C. and Panagis, I. and Perdikuri, Katerina and Theodoridis, E. and Tsakalidis, A. (2003) Computing the Repetitions in a Weighted Sequence using Weighted Suffix Trees. In: European Conference on Computational Biology.

Crochemore, Maxime and Melichar, Bovrivoj and Tron'ivcek, Zdenvek (2003) Directed Acyclic Subsequence Graph - Overview. Journal of Discrete Algorithms, 1 (3-4). pp. 255-280.

Béal, Marie-Pierre and Crochemore, Maxime and Mignosi, Filippo and Restivo, Antonio and Sciortino, Marinella (2003) Forbidden words of regular languages. Fundamenta Informaticae, 56 (1,2). pp. 121-135.

Cole, Richard and Iliopoulos, Costas S. and Lecroq, Thierry and Plandowski, Wojciech and Rytter, Wojciech (2003) On Special Families of Morphisms Related to delta-Matching and Don't Care Symbols. Information Processing Letters, 85 (5). pp. 227-233.

Holub, Jan and Crochemore, Maxime (2003) On the implementation of compact DAWG's. In: Implementation and Application of Automata.

Crochemore, Maxime (2003) Reducing space for index implementation. Theoretical Computer Science, 292 (1). pp. 185-197.

Crochemore, Maxime and Iliopoulos, Costas S. and Pinzon, Yoan J. (2003) Speeding-up Hirschberg and Hunt-Szymanski LCS algorithms. Fundamenta Informaticae, 56 (1,2). pp. 89-103.

Pisanti, Nadia and Crochemore, Maxime and Grossi, Roberto and Sagot, Marie-France (2002) A Basis for Repeated Motifs in Pattern Discovery and Text Mining. Technical Report. Institut Gaspard-Monge.

Crochemore, Maxime and Landau, Gad M. and Ziv-Ukelson, Michal (2002) A Sub-quadratic Sequence Alignment Algorithm for Unrestricted Cost Matrices. In: Proceedings of the Thirteen Annual ACM-SIAM Symposium on Discrete Algorithms.

Crochemore, Maxime and Iliopoulos, Costas S. and Makris, C. and Rytter, Wojciech and Tsakalidis, A. and Tsichlas, K. (2002) Approximate string matching with gaps. Nordic Journal of Computing, 9 (1). pp. 54-65.

Risler, Jean-Loup and Crochemore, Maxime and Konopka, Andrzej K. and Prum, Bernard and Rouzé, Pierre, eds. (2002) Genome and Informatics. Elsevier Science.

Crochemore, Maxime and Rytter, Wojciech (2002) Jewels of Stringology. World Scientific Publishing, Hong-Kong.

Crochemore, Maxime and Tron'ivcek, Zdenvek (2002) On the size of DASG for multiple texts. In: String Processing and Information Retrieval, SPIRE'2002.

Crochemore, Maxime and Iliopoulos, Costas S. and Pinzon, Yoan J. (2002) Recovering an LCS in O(n<sup>2</sup>/w) time and space. Colombian Journal of Computation, 3 (1). pp. 41-52.

Apostolico, Alberto and Crochemore, Maxime (2002) String pattern matching for a deluge survival kit. In: Handbook of Massive Data Sets. Kluwer Academic Publishers, pp. 151-194.

Crochemore, Maxime and Iliopoulos, Costas S. and Pinzon, Yoan J. and Reid, J. F. (2001) A Fast and Practical Bit-Vector Algorithm for the Longest Common Subsequence Problem. Information Processing Letters, 80 (6). pp. 279-285.

Albrecht, Andreas Alexander and Hein, Eike and Melzer, Daniela and Steinhofel, Kathleen and Taupitz, Matthias and Wong, Chak-Kuen (2001) Liver tissue classification by bounded-depth threshold circuits. In: CARS 2001. Computer Assisted Radiology and Surgery. Proceedings.

This list was generated on Sat Apr 19 08:04:12 2014 BST.