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Publications de Stéphane Vialette


Article dans une revue38 documents

  • Both Neou, Romeo Rizzi, Stéphane Vialette. Permutation Pattern matching in (213, 231)-avoiding permutations. Discrete Mathematics and Theoretical Computer Science, DMTCS, 2017, Vol. 18 no. 2, Permutation Patterns 2015. 〈hal-01219299v6〉
  • Philippe Gambette, Andreas D.M. Gunawan, Anthony Labarre, Stéphane Vialette, Louxin Zhang. Solving the tree containment problem in linear time for nearly stable phylogenetic networks. Discrete Applied Mathematics, Elsevier, 2017, to appear, 〈10.1016/j.dam.2017.07.015〉. 〈hal-01575001〉
  • Paul Morel, Ryan Thomas Flynn, Edgar Gelover, Guillaume Blin, Stéphane Vialette, et al.. MSPT: An open-source motion simulator for proton therapy. Biomedical Physics & Engineering Express, 2015, 1 (3), 12 pp. 〈http://stacks.iop.org/2057-1976/1/037001〉. 〈hal-01171799〉
  • Paul Morel, Xiadong Wu, Guillaume Blin, Stéphane Vialette, Ryan Flynn, et al.. Spot Weight Adaptation for Moving Target in Spot Scanning Proton Therapy. Frontiers in Oncology, Frontiers, 2015, 5 (119), pp.1-7. 〈10.3389/fonc.2015.00119〉. 〈hal-01151923〉
  • Laurent Bulteau, Guillaume Fertin, Stéphane Vialette, Roméo Rizzi. Some algorithmic results for [2]-sumset covers. Information Processing Letters, Elsevier, 2015, 115 (1), pp.1-5. 〈hal-01044891〉
  • Riccardo Dondi, Guillaume Fertin, Stéphane Vialette. Finding Approximate and Constrained Motifs in Graphs. Theoretical Computer Science, Elsevier, 2013, 483 (-), pp.10-21. 〈10.1016/j.tcs.2012.08.023〉. 〈hal-00726556〉
  • Guillaume Blin, Romeo Rizzi, Florian Sikora, Stéphane Vialette. Minimum Mosaic Inference of a Set of Recombinants. International Journal of Foundations of Computer Science, World Scientific Publishing, 2013, 24 (1), pp.51-66. 〈10.1142/S0129054113400042〉. 〈hal-00679269〉
  • Gregory Kucherov, Lilla Tóthmérész, Stéphane Vialette. On the combinatorics of suffix arrays. Information Processing Letters, Elsevier, 2013, 113 (22-24), pp.915-920. 〈10.1016/j.ipl.2013.09.009〉. 〈hal-00864634〉
  • Guillaume Blin, Romeo Rizzi, Stéphane Vialette. A faster algorithm for finding minimum Tucker submatrices. Theory of Computing Systems, Springer Verlag, 2012, 51 (3), pp.270-281. 〈10.1007/s00224-012-9388-1〉. 〈hal-00657340〉
  • Guillaume Blin, Maxime Crochemore, Sylvie Hamel, Stéphane Vialette. Median of an odd number of permutations. Pure Mathematics and Applications, 2011, 21 (2), pp.161 - 175. 〈hal-00619773〉
  • Riccardo Dondi, Guillaume Fertin, Stéphane Vialette. Complexity issues in Vertex-Colored Graph Pattern Matching. Journal of Discrete Algorithms, Elsevier, 2011, 9 (1), pp.82-99. 〈10.1016/j.jda.2010.09.002〉. 〈hal-00606154〉
  • Michael R. Fellows, Guillaume Fertin, Danny Hermelin, Stéphane Vialette. Upper and lower bounds for finding connected motifs in vertex-colored graphs. Journal of Computer and System Sciences, Elsevier, 2011, 77 (4), pp.799-811. 〈10.1016/j.jcss.2010.07.003〉. 〈hal-00606148〉
  • Gaëlle Brevier, Romeo Rizzi, Stéphane Vialette. Complexity Issues in Color-Preserving Graph Embeddings. Theoretical Computer Science, Elsevier, 2010, 411 (4-5), pp.716-729. 〈hal-00619754〉
  • Guillaume Fertin, Danny Hermelin, Romeo Rizzi, Stéphane Vialette. Finding Common Structured Patterns in Linear Graphs. Theoretical Computer Science, Elsevier, 2010, 411 (26-28), pp.2475-2486. 〈10.1016/j.tcs.2010.02.017〉. 〈hal-00482850〉
  • Guillaume Blin, Florian Sikora, Stéphane Vialette. Querying Graphs in Protein-Protein Interactions Networks using Feedback Vertex Set. IEEE/ACM Transactions on Computational Biology and Bioinformatics, Institute of Electrical and Electronics Engineers, 2010, 7 (4), pp.628-635. 〈hal-00619763〉
  • Marcin Kubica, Romeo Rizzi, Thomas Waleń, Stéphane Vialette. Approximation of RNA Multiple Structural Alignment. Journal of Discrete Algorithms, Elsevier, 2010, ? (?). 〈hal-00619801〉
  • Danny Hermelin, Mike Fellows, Frances Rosamond, Stéphane Vialette. On the Parameterized Complexity of Multiple-Interval Graph Problems. Theoretical Computer Science, Elsevier, 2009, 410 (1), pp.53-61. 〈hal-00619739〉
  • Sébastien Angibaud, Guillaume Fertin, Irena Rusu, Annelyse Thévenin, Stéphane Vialette. On the Approximability of Comparing Genomes with Duplicates. Journal of Graph Algorithms and Applications (JGAA), Brown University, 2009, 13 (1), pp.19-53. 〈hal-00416440〉
  • Guillaume Fertin, Romeo Rizzi, Stéphane Vialette. Finding Occurrences of Protein Complexes in Protein-Protein Interaction Graphs. Journal of Discrete Algorithms, Elsevier, 2009, 7 (1), pp.90-101. 〈hal-00416394〉
  • Maxime Crochemore, Danny Hermelin, Gad Landau, Dror Rawitz, Stéphane Vialette. Approximating the 2-Interval Pattern problem. Theoretical Computer Science, Elsevier, 2008, 395 (2-3), pp.283-297. 〈hal-00619740〉
  • Sébastien Angibaud, Guillaume Fertin, Irena Rusu, Annelyse Thevenin, Stéphane Vialette. Efficient Tools for Computing the Number of Breakpoints and the Number of Adjacencies between two Genomes with Duplicate Genes. Journal of Computational Biology, Mary Ann Liebert, 2008, 15 (8), pp.1093-1115. 〈hal-00416446〉
  • Guillaume Blin, Guillaume Fertin, Danny Hermelin, Stéphane Vialette. Fixed-Parameter Algorithms For Protein Similarity Search Under mRNA Structure Constraints. Journal of Discrete Algorithms, Elsevier, 2008, 6 (4), pp.618-626. 〈hal-00416442〉
  • Isabelle Fagnot, Gaëlle Lelandais, Stéphane Vialette. Bounded List Injective Homomorphism for Comparative Analysis of Protein-Protein Interaction Graphs. Journal of Discrete Algorithms, Elsevier, 2008, 6 (2), pp.178-191. 〈hal-00619701〉
  • Danny Hermelin, Dror Rawitz, Romeo Rizzi, Stéphane Vialette. The Minimum Substring Cover Problem. Information and Computation, Elsevier, 2008, 206 (11), pp.1303-1312. 〈hal-00619729〉
  • Guillaume Blin, Guillaume Fertin, Stéphane Vialette. Extracting Constrained 2-Interval Subsets in 2-Interval Sets. Theoretical Computer Science, Elsevier, 2007, 385 (1-3), pp.241-263. 〈hal-00417717〉
  • Sébastien Angibaud, Guillaume Fertin, Irena Rusu, Stéphane Vialette. A General Framework for Computing Rearrangement Distances between Genomes with Duplicates. Journal of Computational Biology, Mary Ann Liebert, 2007, 14 (4), pp.379-393. 〈hal-00417735〉
  • Guillaume Blin, Cedric Chauve, Guillaume Fertin, Romeo Rizzi, Stéphane Vialette. Comparing Genomes with Duplications: a Computational Complexity Point of View. ACM Transactions on Computational Logic, Association for Computing Machinery, 2007, 4 (4), pp.523-534. 〈hal-00417720〉
  • Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Guillaume Fertin, Rafaella Rizzi, et al.. Exemplar Longest Common Subsequence. ACM Transactions on Computational Logic, Association for Computing Machinery, 2007, 4 (4), pp.535-543. 〈hal-00417728〉
  • G. Lelandais, P. Vincens, A. Badel-Chagnon, Stéphane Vialette, C. Jacq, et al.. Comparing gene expression networks in a multi-dimensional space to extract similarities and differences between organisms.. Bioinformatics, Oxford University Press (OUP), 2006, 22, pp.1359-1366. 〈hal-00091646〉
  • Gaëlle Lelandais, Pierre Vincens, Anne Badel-Chagnon, Stéphane Vialette, Claude Jacq, et al.. Comparing gene expression networks in multi-dimensional space to extract similarities and differences between organisms. Bioinformatics, Oxford University Press (OUP), 2006, 22 (11), pp.1359-1366. 〈hal-00619613〉
  • Stéphane Vialette. Packing of (0,1)-matrices. RAIRO - Theoretical Informatics and Applications (RAIRO: ITA), EDP Sciences, 2006, 40 (4), pp.519-536. 〈hal-00619759〉
  • Guillaume Blin, Guillaume Fertin, Romeo Rizzi, Stéphane Vialette. What makes the Arc-Preserving Subsequence problem hard ?. LNCS Transactions on Computational Systems Biology, 2005, 2, pp.1-36. 〈hal-00417738〉
  • Gaëlle Lelandais, Stephane Le Crom, Frédéric Devaux, Stéphane Vialette, George M. Church, et al.. yMGV: a cross-species expression data mining tool. Nucl. Acids. Res., 2004, 32 (1), pp.D323-D325. 〈hal-00619620〉
  • Stéphane Vialette. On the computational complexity of 2-interval pattern matching. Theoretical Computer Science, Elsevier, 2004, 312 (2-3), pp.223-249. 〈hal-00619682〉
  • Gaëlle Lelandais, Philippe Marc, Pierre Vincens, Claude Jacq, Stéphane Vialette. MiCoViTo: a tool for gene-centric comparison and visualization of yeast transcriptome states. BMC Bioinformatics, BioMed Central, 2004, 5 (20), 10pp. 〈hal-00619621〉
  • Gaëlle Lelandais, Philippe Marc, Pierre Vincens, Claude Jacq, Stéphane Vialette. MiCoViTo: a tool for gene-centric comparison and visualization of yeast transcriptome states.. BMC Bioinformatics, BioMed Central, 2004, 5, pp.20. 〈10.1186/1471-2105-5-20〉. 〈inserm-00112944〉
  • Julien Sylvestre, Stéphane Vialette, Marisol Corral-Debrinski, Claude Jacq. Long mRNA coding for yeast mitochondrial proteins of prokaryotic origin preferentially localize to the vicinity of mitochondria. Genome Biology, BioMed Central, 2003, 4 (7), pp.1-9. 〈hal-00619736〉
  • Antoine Margeot, Corinne Blugeon, Julien Sylvestre, Stéphane Vialette, Claude Jacq, et al.. In Saccharomyces cerevisae, ATP2 mRNA sorting to the vicinity of mitochondria is essential for respiratory function. EMBO Journal, EMBO Press, 2002, 21 (24), pp.6893-6904. 〈hal-00619675〉

Communication dans un congrès55 documents

  • Carlo Comin, Anthony Labarre, Romeo Rizzi, Stéphane Vialette. Sorting With Forbidden Intermediates. Third International Conference on Algorithms for Computational Biology (AlCoB 2016), Jun 2016, Trujillo, Spain. Proceedings of the Third International Conference on Algorithms for Computational Biology (AlCoB), 2016, 〈http://grammars.grlmc.com/AlCoB2016/〉. 〈hal-01287040〉
  • Samuele Giraudo, Stéphane Vialette. Unshuffling Permutations. Evangelos Kranakis; Gonzalo Navarro; Edgar Chávez. LATIN 2016, Apr 2016, Ensenada, Mexico. Proceedings of the 12th Latin American Symposium, 9644, pp.509-521, 2016, LNCS. 〈10.1007/978-3-662-49529-2_38〉. 〈hal-01260549v2〉
  • Guillaume Fertin, Irena Rusu, Stéphane Vialette. Obtaining a Triangular Matrix by Independent Row-Column Permutations. 26th International Symposium on Algorithms and Computation, Dec 2015, Nagoya, France. 〈hal-01189621〉
  • Philippe Gambette, Andreas D.M. Gunawan, Anthony Labarre, Stéphane Vialette, Louxin Zhang. Locating a Tree in a Phylogenetic Network in Quadratic Time. RECOMB 2015, Apr 2015, Varsovie, Poland. Springer, Proceedings of the 19th Annual International Conference on Research in Computational Molecular Biology, 9029, pp.96-107, 2015, LNCS. 〈10.1007/978-3-319-16706-0_12〉. 〈hal-01116231〉
  • Guillaume Fertin, Irena Rusu, Stéphane Vialette. Algorithmic aspects of the S-Labeling problem. 26th International Workshop on Combinatorial Algorithms (IWOCA 2015), Oct 2015, Verona, Italy. Springer-Verlag, pp.173-184, 2015, Lecture Notes in Computer Science. 〈hal-01311584〉
  • Philippe Gambette, Andreas D.M. Gunawan, Anthony Labarre, Stéphane Vialette, Louxin Zhang. Solving the Tree Containment Problem for Genetically Stable Networks in Quadratic Time. Zsuzsanna Lipták; William F. Smyth. IWOCA 2015, Oct 2015, Verona, Italy. Springer, Lecture Notes in Computer Science, 9538, pp.197-208, 2016, Proceedings of the 26th International Workshop on Combinatorial Algorithms. 〈10.1007/978-3-319-29516-9_17〉. 〈hal-01226035〉
  • Guillaume Blin, Paul Morel, Romeo Rizzi, Stéphane Vialette. Towards unlocking the full potential of Multileaf Collimators. 40th International Conference on Current Trends in Theory and Practice of Computer Science (SOFSEM), Jan 2014, High Tatras, Slovakia. 8327, pp.138-149, 2013, Lecture Notes in Computer Science. 〈hal-00859708〉
  • Djamal Belazzougui, Adeline Pierrot, Mathieu Raffinot, Stéphane Vialette. Single and multiple consecutive permutation motif search. ISAAC 2013, Dec 2013, Hong-Kong, Hong Kong SAR China. Proceedings of the 24th International Symposium on Algorithms and Computation, 8283, pp.66-77, 2013, LNCS. 〈10.1007/978-3-642-45030-3_7〉. 〈hal-00859363〉
  • Romeo Rizzi, Stéphane Vialette. On recognizing words that are squares for the shuffle product. Andrei A. Bulatov, Arseny M. Shur. The 8th International Computer Science Symposium in Russia, Jun 2013, Ekaterinburg, Russia. Springer, 7913, pp.235-245, 2013, Lecture Notes in Computer Science. 〈hal-00725429〉
  • Yu Zhou, Yann Ponty, Stéphane Vialette, Jérôme Waldispühl, Yi Zhang, et al.. Flexible RNA design under structure and sequence constraints using formal languages. ACM-BCB - ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics - 2013, Sep 2013, Bethesda, Washigton DC, United States. 2013. 〈hal-00823279v2〉
  • Guillaume Blin, Laurent Bulteau, Minghui Jiang, Pedro J. Tejada, Stéphane Vialette. Hardness of longest common subsequence for sequences with bounded run-lengths. Juha Kärkkäinen and Jens Stoye. 23rd Annual Symposium on Combinatorial Pattern Matching (CPM'12), Jul 2012, Helsinki, Finland. Springer-Verlag, 7354, pp.138-148, 2012, Lecture Notes in Computer Science. 〈10.1007/978-3-642-31265-6_11〉. 〈hal-00683311〉
  • Guillaume Blin, Minghui Jiang, Stéphane Vialette. The longest common subsequence problem with crossing-free arc-annotated sequences. L. Calderon-Benavides et al. 19th edition of the International Symposium on String Processing and Information Retrieval (SPIRE 2012), Oct 2012, Cartagena de Indias, Colombia. Springer, Heidelberg, 7608, pp. 130--142, 2012, LNCS. 〈hal-00713431〉
  • Danny Hermelin, Romeo Rizzi, Stéphane Vialette. Algorithmic Aspects of the Intersection and Overlap Numbers of a Graph. ISAAC 2012, Dec 2012, Taipei, Taiwan. Springer, 7676, pp.465-474, 2012, Lecture Notes in Computer Science. 〈10.1007/978-3-642-35261-4_49〉. 〈hal-01054925〉
  • Guillaume Blin, Romeo Rizzi, Florian Sikora, Stéphane Vialette. Minimum Mosaic Inference of a Set of Recombinants. Potanin Alex and Viglas Taso. 17th Computing: the Australasian Theory Symposium (CATS'11), Jan 2011, Perth, Australia. ACS, 119, pp.23-30, 2011, CRPIT. 〈hal-00620371〉
  • Guillaume Blin, Romeo Rizzi, Stéphane Vialette. A Polynomial-Time Algorithm for Finding a Minimal Conflicting Set Containing a Given Row. 6th International Computer Science Symposium in Russia (CSR'11), 2011, St Petersbourg, Russia. Computer Science – Theory and Applications, 6651, pp.373-384, 2011, Lecture Notes in Computer Science. 〈10.1007/978-3-642-20712-9_29〉. 〈hal-00620378〉
  • Riccardo Dondi, Guillaume Fertin, Stéphane Vialette. Finding Approximate and Constrained Motifs in Graphs. CPM 2011, 2011, Palermo, Italy. Springer, 6661, pp.388-401, 2011, Lecture Notes in Computer Science. 〈10.1007/978-3-642-21458-5_33〉. 〈hal-00606173〉
  • Guillaume Blin, Guillaume Fertin, Hafedh Mohamed-Babou, Irena Rusu, Florian Sikora, et al.. Algorithmic Aspects of Heterogeneous Biological Networks Comparison. COCOA 2011, 2011, Zhangjiajie, China. Springer, 6831, pp.272-286, 2011, Lecture Notes in Computer Science. 〈10.1007/978-3-642-22616-8_22〉. 〈hal-00606375〉
  • Guillaume Blin, Romeo Rizzi, Stéphane Vialette. A faster algorithm for finding minimum Tucker submatrices. 6th Computability in Europe (CiE'10), 2010, Portugal. Springer, 6158, pp.69-77, 2010, Lecture Notes in Computer Science. 〈hal-00620380〉
  • Guillaume Blin, Sylvie Hamel, Stéphane Vialette. Comparing RNA structures with biologically relevant operations cannot be done without strong combinatorial restrictions. Rahman Md. S. and Fujita S. 4th Workshop on Algorithms and Computation (WALCOM'10), Feb 2010, Dhaka, Bangladesh, Bangladesh. Springer-Verlag, 5942, pp.149-160, 2010, Lecture Notes in Computer Science. 〈hal-00620327〉
  • Guillaume Blin, Florian Sikora, Stéphane Vialette. GraMoFoNe: a Cytoscape plugin for querying motifs without topology in Protein-Protein Interactions networks. Hisham Al-Mubaid. Bioinformatics and Computational Biology (BICoB'10), Mar 2010, Honolulu, United States. pp.38-43, 2010, International Society for Computers and their Applications (ISCA). 〈hal-00425661〉
  • Guillaume Blin, Maxime Crochemore, Sylvie Hamel, Stéphane Vialette. Finding the median of three permutations under the Kendall-tau distance. Università degli Studi di Firenze. 7th annual international conference on Permutation Patterns, Jul 2009, Firenze, Italy. pp.6. 〈hal-00620459〉
  • Guillaume Fertin, Stéphane Vialette. On the S-labeling Problem. Eslevier. Proc. 5th Euroconference on Combinatorics, Graph Theory and Applications (EUROCOMB 2009), 2009, Bordeaux, France. Eslevier, 34, pp.273-277, 2009, Electronic Notes on Discrete Mathematics. 〈hal-00416570〉
  • Isabelle Fagnot, Guillaume Fertin, Stéphane Vialette. On Finding Small 2-Generating Sets. COCOON 2009, 2009, Niagara Falls, United States. Springer-Verlag, 5609, pp.378-387, 2009, Lecture Notes in Computer Science. 〈10.1007/978-3-642-02882-3_38〉. 〈hal-00416577〉
  • Sébastien Angibaud, Guillaume Fertin, Annelyse Thevenin, Stéphane Vialette. Pseudo-Boolean Programming for Partially Ordered Genomes. RECOMB-CG 2009, Sep 2009, Budapest, Hungary. Springer-Verlag, 5817, pp.126-137, 2009, Lecture Notes in BioInformatics. 〈10.1007/978-3-642-04744-2_11〉. 〈hal-00416458〉
  • Riccardo Dondi, Guillaume Fertin, Stéphane Vialette. Maximum Motif Problem in Vertex-Colored Graphs. 20th Annual Symposium on Combinatorial Pattern Matching (CPM 2009), 2009, Lille, France. Springer-Verlag, 5577, pp.221-235, 2009, Lecture Notes in Computer Science. 〈10.1007/978-3-642-02441-2_20〉. 〈hal-00416463〉
  • Guillaume Blin, Guillaume Fertin, Florian Sikora, Stéphane Vialette. The Exemplar Breakpoint Distance for non-trivial genomes cannot be approximated. Das S. and Uehara R. WALCOM 2009, 2009, Kolkata, India. Springer-Verlag, 5431, pp.357-368, 2009, Lecture Notes in Computer Science. 〈hal-00416491〉
  • Guillaume Blin, Florian Sikora, Stéphane Vialette. Querying Protein-Protein Interaction Networks. Mandoiu Ion and Narasimhan Giri and Zhang Yanqing. 5th International Symposium on Bioinformatics Research and Applications (ISBRA'09), May 2009, Fort Lauderdale, United States. Springer-Verlag, 5542, pp.52-62, 2009, LNBI. 〈hal-00620391〉
  • Sylvain Guillemot, Stéphane Vialette. Pattern matching for 321-avoiding permutations. Dong Yingfei and Du Ding-Zhu and Ibarra Oscar. 20th International Symposium on Algorithms and Computation (ISAAC'09), 2009, United States. Springer-Verlag, 5878, pp.1064-1073, 2009, Lecture Notes in Computer Science. 〈hal-00620322〉
  • Gaëlle Brevier, Romeo Rizzi, Stéphane Vialette. Pattern Matching in Protein-Protein Interaction Graphs. Csuhaj-Varjù Erzsébet and Ésik Zoltán. Proc. 16th International Symposium on Fundamentals of Computation Theory (FCT), 2007, Budapest, Hungary, Croatia. Springer, 4639, pp.125-136, 2007, LNCS. 〈hal-00620287〉
  • Danny Hermelin, Dror Rawitz, Romeo Rizzi, Stéphane Vialette. The Minimum Substring Cover Problem. Kaklamanis Christos and Skutella Martin. 5th Workshop on Approximation and Online Algorithms (WAOA'07), 2007, Eilat, Israel, Iceland. Springer, 4927, pp.170-183, 2007, Lecture Notes in Computer Science. 〈hal-00620289〉
  • Mathilde Bouvel, Dominique Rossin, Stéphane Vialette. Longest Common Separable Pattern between Permutations. Ma Bin and Zhang Kaizhong. Symposium on Combinatorial Pattern Matching (CPM'07), 2007, London, Ontario, Canada, Canada. Springer, 4580, pp.316-327, 2007, LNCS. 〈hal-00620293〉
  • Riccardo Dondi, Guillaume Fertin, Stéphane Vialette. Weak pattern matching in colored graphs: Minimizing the number of connected components. 10th Italian Conference on Theoretical Computer Science (ICTCS 2007), 2007, Rome, Italy. World-Scientific Conference Proceedings, pp.27-38, 2007, World-Scientific Conference Proceedings. 〈hal-00417910〉
  • Guillaume Blin, Guillaume Fertin, Gaël Herry, Stéphane Vialette. Comparing RNA Structures: Towards an Intermediate Model Between the EDIT and the LAPCS Problems. Sagot Marie-France and Telles Walter Maria Emilia. Brazilian Symposium on Bioinformatics (BSB 2007), Aug 2007, Angra dos Reis, Brazil. Springer-Verlag, Lecture Notes in BioInformatics (LNBI) (4643), pp.101-112, 2007, Lecture Notes in BioInformatics (LNBI). 〈hal-00417918〉
  • Sébastien Angibaud, Guillaume Fertin, Irena Rusu, Annelyse Thevenin, Stéphane Vialette. A Pseudo-Boolean programming approach for computing the breakpoint distance between two genomes with duplicate genes. 5th RECOMB Comparative Genomics Satellite Workshop (RECOMB-CG 2007), 2007, San Diego, United States. Springer-Verlag, Lecture Notes in BioInformatics (LNBI) (4751), pp.16-29, 2007, Lecture Notes in BioInformatics (LNBI). 〈hal-00417902〉
  • Sébastien Angibaud, Guillaume Fertin, Irena Rusu, Stéphane Vialette. How Pseudo-Boolean Programming can help Genome Rearrangement Distance Computation. 4th RECOMB Comparative Genomics Satellite Workshop (RECOMB-CG 2006), 2007, Montréal, Canada. Springer-Verlag, Lecture Notes in BioInformatics (LNBI) (4205), pp.75-86, 2006, Lecture Notes in BioInformatics (LNBI). 〈hal-00418258〉
  • Michael R. Fellows, Guillaume Fertin, Danny Hermelin, Stéphane Vialette. Sharp Tractability Borderlines for Finding Connected Motifs in Vertex-Colored Graphs. 34th International Colloquium on Automata, Languages and Programming (ICALP 2007), 2007, Wroclaw, Poland. Springer-Verlag, Lecture Notes in Computer Science (LNCS) (4596), pp.340-351, 2007, Lecture Notes in Computer Science (LNCS). 〈hal-00417928〉
  • Guillaume Fertin, Danny Hermelin, Romeo Rizzi, Stéphane Vialette. Common Structured Patterns in Linear Graphs: Approximations and Combinatorics. 18th Annual Symposium on Combinatorial Pattern Matching (CPM 2007), 2007, London, Canada. Springer-Verlag, Lecture Notes in Computer Science (LNCS) (4580), pp.214-252, 2007, Lecture Notes in Computer Science (LNCS). 〈hal-00418241〉
  • Philippe Gambette, Stéphane Vialette. On restrictions of balanced 2-interval graphs. 33rd International Workshop on Graph-Theoretic Concepts in Computer Science (WG'07), Jun 2007, Dornburg, Germany. 4769, pp.55-65, 2007, LNCS. 〈10.1007/978-3-540-74839-7_6〉. 〈hal-00141338v2〉
  • Mathilde Bouvel, Dominique Rossin, Stéphane Vialette. Longest Common Separable Pattern between Permutations. Bin Ma and Kaizhong Zhang. Combinatorial Pattern Matching, 18th Annual Symposium, CPM 2007, London, Canada, July 9-11, 2007, 2007, London, Canada. Springer, 4580, pp.316-327, 2007, Lecture Notes in Computer Science (LNCS). 〈hal-00128750〉
  • Gaëlle Brevier-Giberti, Roméo Rizzi, Stéphane Vialette. Pattern Matching in Protein-Protein Interaction Graphs. Erzsébet Csuhaj-Varjú; Zoltán Ésik. FCT 2007, Aug 2007, Budapest, Hungary. Springer Berlin / Heidelberg, Proceedings of the 16th International Symposium on Fundamentals of Computation Theory, 4639, pp.137-148, 2007, Lecture Notes in Computer Science. 〈10.1007/978-3-540-74240-1_13〉. 〈hal-00199009〉
  • Sébastien Angibaud, Guillaume Fertin, Irena Rusu, Stéphane Vialette. How Pseudo-boolean Programming Can Help Genome Rearrangement Distance Computation. 4thAnnual RECOMB Satellite Workshop on Comparative Genomics (RECOMB-CG'06), 2006, Montreal, Canada, Canada. Springer-Verlag, pp.75-86, 2006, LNBI. 〈hal-00619848〉
  • Marcin Kubica, Romeo Rizzi, Stéphane Vialette, Thomas Waleń. Approximation of RNA Multiple Structural Alignment. Lewenstein Moshe and Valiente Gabriel. 17th Symposium on Combinatorial Pattern Matching (CPM'06), 2006, Barcelona, Spain, Spain. Springer-Verlag, 4009, pp.211-222, 2006, LNCS. 〈hal-00620291〉
  • Cedric Chauve, Guillaume Fertin, Romeo Rizzi, Stéphane Vialette. Genomes containing duplicates are hard to compare. Mandoiu Ion. Proc Int. Workshop on Bioinformatics Research and Applications (IWBRA), 2006, Reading, UK, United Kingdom. Springer, 3992, pp.783-790, 2006, LNCS. 〈hal-00620297〉
  • Paola Bonizzoni, Gianuca Della Vedova, Riccardo Dondi, Guillaume Fertin, Stéphane Vialette. Exemplar Longest Common Subsequences. Mandoiu Ion. Int. Workshop on Bioinformatics Research and Applications (IWBRA), 2006, United States. Springer, 3992, pp.622-629, 2006, LNCS. 〈hal-00620296〉
  • Cedric Chauve, Guillaume Fertin, Romeo Rizzi, Stéphane Vialette. Genomes containing Duplicates are Hard to compare. International Workshop on Bioinformatics Research and Applications (IWBRA 2006), 2006, Reading, United Kingdom. Springer-Verlag, LNCS Vol. 3992, pp.783-790, 2006, Lecture Notes in Computer Science (LNCS). 〈hal-00418260〉
  • Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Guillaume Fertin, Stéphane Vialette. Exemplar Longest Common Subsequence (extended abstract). International Workshop on Bioinformatics Research and Applications (IWBRA 2006), May 2006, Reading, United Kingdom. Springer-Verlag, LNCS Vol. 3992, pp.622-629, 2006, Lecture Notes in Computer Science (LNCS). 〈hal-00461780〉
  • Maxime Crochemore, Danny Hermelin, Gad M. Landau, Stéphane Vialette. Approximating the 2-Interval Pattern Problem. Brodal G. S. and Leonardi S. 13th Annual European Symposium on Algorithms (ESA'05), 2005, Mallorca, Spain, Spain. Springer-Verlag, 3669, pp.426-437, 2005, LNCS. 〈hal-00619979〉
  • Claire Herrbach, Stéphane Vialette. Linear graph non-crossing structural alignment under the RNA stacking-pair scoring scheme. Guimaraes Katia and Sagot Marie-France. 2nd Conference on Algorithms and Computational Methods for biochemical and Evolutionary Networks (CompBioNets'05), 2005, Lyon, France, France. King's College London publications, 10pp., 2005. 〈hal-00620303〉
  • Guillaume Fertin, Romeo Rizzi, Stéphane Vialette. Finding Exact and Maximum Occurrences of Protein Complexes in Protein-Protein Interaction Graphs. Jedrzejowicz Joanna and Szepietowski Andrzej. 30th International Symposium on Mathematical Foundations of Computer Science (MFCS'05), 2005, Gdansk, Poland, Poland. Springer-Verlag, 3618, pp.328-339, 2005, LNCS. 〈hal-00620292〉
  • Guillaume Blin, Guillaume Fertin, Romeo Rizzi, Stéphane Vialette. What Makes the Arc-Preserving Subsequence Problem Hard?. S. Sunderam Vaidy and van Albada G. Dick and M. A. Sloot Peter and Dongarra Jack. 5th Int. Workshop on Bioinformatics Research and Applications (IWBRA'05), May 2005, Atlanta, GA, USA, United States. Springer-Verlag, 3515, pp.860-868, 2005, LNCS. 〈hal-00620359〉
  • Guillaume Blin, Guillaume Fertin, Danny Hermelin, Stéphane Vialette. Fixed-Parameter Algorithms for Protein Similarity Search Under mRNA Structure Constraints. Kratsch Dieter. 31st International Workshop on Graph-Theoretic Concepts in Computer Science (WG'05), Jun 2005, Metz, France, France. Springer-Verlag, 3787, pp.271-282, 2005, LNCS. 〈hal-00620363〉
  • Isabelle Fagnot, Gaëlle Lelandais, Stéphane Vialette. Bounded List Injective Homomorphism for Comparative Analysis of Protein-Protein Interaction Graphs. 1st International Conference on Algorithms and Computational Methods for Biochemical and Evolutionar, Dec 2004, Recife,Brazil, Brazil. KCL publications, King's College, London, 3, pp.45-70, 2004, Texts in Algorithms. 〈hal-00620023〉
  • Guillaume Blin, Guillaume Fertin, Roméo Rizzi, Stéphane Vialette. Pattern Matching in Arc-Annotated Sequences: New Results for the APS Problem. 5th Journées Ouvertes de Biologie, Informatique et Mathématiques (JOBIM'04), 2004, Montréal, Quebec, Canada. IEEE Computer Society, 12 pp., 2004. 〈hal-00620330〉
  • Guillaume Blin, Guillaume Fertin, Stéphane Vialette. New Results for the 2-Interval Pattern Problem. Sahinalp Suleyman Cenk and Muthukrishnan S. and Dogrusoz Ugur. 15th Symposium on Combinatorial Pattern Matching (CPM'04), Jul 2004, Istanbul, Turkey, Turkey. Springer-Verlag, 3109, pp.311-322, 2004, LNCS. 〈hal-00620366〉
  • Stéphane Vialette. Pattern Matching over 2-intervals sets. Apostolico Alberto and Tadeka Masayuki. Symposium on Combinatorial Pattern Matching (CPM'02), 2002, Fukuoka, Japan, Japan. Springer, 2373, pp.53-63, 2002, LNCS. 〈hal-00620286〉

Ouvrage (y compris édition critique et traduction)1 document

  • Guillaume Fertin, Anthony Labarre, Irena Rusu, Eric Tannier, Stéphane Vialette. Combinatorics of Genome Rearrangements. MIT Press, pp.312, 2009, Computational Molecular Biology. 〈hal-00416453〉

Chapitre d'ouvrage2 documents

  • Guillaume Blin, Maxime Crochemore, Stéphane Vialette. Algorithmic Aspects of Arc-Annotated Sequences. Elloumi Mourad, Zomaya Albert Y. Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications, Wiley, pp.113-126, 2011. 〈hal-00620821〉
  • Stéphane Vialette. Two-Interval Pattern Problems. Kao Ming-Yang. Encyclopedia of Algorithms, Springer-Verlag, pp.985-989, 2008. 〈hal-00620812〉

Direction d'ouvrage, Proceedings, Dossier2 documents

  • Craig Nelson, Stéphane Vialette. RECOMB - Comparative Genomics Special Issue. Mary Ann Liebert, Inc., pp.1285-1500, 2010. 〈hal-00620536〉
  • Craig Nelson, Stéphane Vialette. Comparative Genomics: International Workshop, RECOMB-CG 2008, Paris, France, October 13-15, 2008. Springer, 276pp., 2008. 〈hal-00620537〉

Pré-publication, Document de travail2 documents

  • Sébastien Angibaud, Guillaume Fertin, Irena Rusu, Annelyse Thevenin, Stéphane Vialette. On the Approximability of Comparing Genomes with Duplicates. 2008. 〈hal-00285511〉
  • Guillaume Blin, Sylvie Hamel, Stéphane Vialette. Comparing RNA structures using a full set of biologically relevant edit operations is intractable. 7 pages. 2008. 〈hal-00347464〉

Thèse1 document

  • Stéphane Vialette. Aspects algorithmiques de la prédiction des structures secondaires d'ARN. Informatique [cs]. Université Paris-Diderot - Paris VII, 2001. Français. 〈tel-00628623〉

HDR1 document

  • Stéphane Vialette. Algorithmic Contributions to Computational Molecular Biology. Data Structures and Algorithms [cs.DS]. Université Paris-Est, 2010. 〈tel-00862069〉