Publications HAL de Guillaume,FERTIN de la collection LINA

auteur: Guillaume Fertin, Christian Komusiewicz, Hafedh Mohamed-Babou, Irena Rusu
titre: Finding Supported Paths in Heterogeneous Networks
article: Algorithms, 2015, ⟨10.3390/a8040810⟩
Resume_court: Subnetwork mining is an essential issue in the analysis of biological, social and communication netw .....
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auteur: Guillaume Fertin, Géraldine Jean, Andreea Radulescu, Irena Rusu
titre: Hybrid de novo tandem repeat detection using short and long reads
article: BMC Medical Genomics, 2015, 8 (Suppl 3), pp.S5. ⟨10.1186/1755-8794-8-S3-S5⟩
Resume_court: BackgroundAs one of the most studied genome rearrangements, tandem repeats have a considerable impac .....
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auteur: Guillaume Fertin, Riccardo Dondi, Giancarlo Mauri
titre: Algorithmic Aspects in Information and Management 11th International Conference, AAIM 2016, Bergamo, Italy, July 18-20, 2016, Proceedings
article: 2016
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auteur: Matthieu David, Guillaume Fertin, Dominique Tessier
titre: SpecTrees: An efficient without a priori data structure for MS/MS spectra identification
article: 16th International Workshop on Algorithms in Bioinformatics (WABI), Aug 2016, Aarhus, Denmark. 12 p., ⟨10.1007/978-3-319-43681-4_6⟩
Resume_court: Tandem Mass Spectrometry (or MS/MS) is the most common strategy used to identify unknown proteins pr .....
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auteur: Guillaume Fertin, Géraldine Jean, Eric Tannier
titre: Genome Rearrangements on both Gene Order and Intergenic Regions
article: WABI 2016, 2016, Aarhus, Denmark. pp.162-173
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auteur: Laurent Bulteau, Guillaume Fertin, Christian Komusiewicz
titre: (Prefix) reversal distance for (signed) strings with few blocks or small alphabets
article: Journal of Discrete Algorithms, 2016, 37, pp.44-55. ⟨10.1016/j.jda.2016.05.002⟩
Resume_court: We study the String Reversal Distance problem, an extension of the well-known Sorting by Reversals p .....
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auteur: Guillaume Fertin, Irena Rusu, Stéphane Vialette
titre: Algorithmic aspects of the S-Labeling problem
article: 26th International Workshop on Combinatorial Algorithms (IWOCA 2015), Oct 2015, Verona, Italy. pp.173-184
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auteur: Guillaume Fertin, Christian Komusiewicz
titre: Graph Motif Problems Parameterized by Dual
article: 27th Annual Symposium on Combinatorial Pattern Matching, Jun 2016, Tel-Aviv, France
Resume_court: Let $G=(V,E)$ be a vertex-colored graph, where $C$ is the set of colors used to color $V$. The \GM ( .....
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auteur: Laurent Bulteau, Guillaume Fertin, Anthony Labarre, Romeo Rizzi, Irena Rusu
titre: Decomposing Cubic Graphs into Connected Subgraphs of Size Three
article: The 22nd International Computing and Combinatorics Conference (COCOON), Aug 2016, Ho Chi Minh City, Vietnam. ⟨10.1007/978-3-319-42634-1_32⟩
Resume_court: Let S = {K_1,3, K₃, P₄} be the set of connected graphs of size 3. We .....
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auteur: Guillaume Fertin, Loïc Jankowiak, Géraldine Jean
titre: Prefix and Suffix Reversals on Strings
article: 22nd International Symposiumon String Processing and Information Retrieval (SPIRE 2015), Sep 2015, London, United Kingdom. pp.1-12, ⟨10.1007/978-3-319-23826-5_17⟩
Resume_court: The Sorting by Prefix Reversals problem consists in sorting the elements of a given permutation π w .....
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auteur: Guillaume Fertin, Irena Rusu, Stéphane Vialette
titre: Obtaining a Triangular Matrix by Independent Row-Column Permutations
article: 26th International Symposium on Algorithms and Computation, Dec 2015, Nagoya, France. ⟨10.1007/978-3-662-48971-0_15⟩
Resume_court: Given a square (0, 1)-matrix A, we consider the problem of deciding whether there exists a permutati .....
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auteur: Guillaume Fertin, André Raspaud
titre: Acyclic Coloring of Graphs of Maximum Degree $\Delta$
article: 2005 European Conference on Combinatorics, Graph Theory and Applications (EuroComb '05), 2005, Berlin, Germany. pp.389-396, ⟨10.46298/dmtcs.3450⟩
Resume_court: An acyclic coloring of a graph $G$ is a coloring of its vertices such that: (i) no two neighbors in .....
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auteur: Carla Negri Lintzmayer, Zanoni Dias, Guillaume Fertin
titre: Approximation algorithms for sorting by length-weighted prefix and suffix operations
article: Theoretical Computer Science, 2015, 593, pp.26-41. ⟨10.1016/j.tcs.2015.05.039⟩
Resume_court: The traditional approach for the problems of sorting permutations by rearrangements is to consider t .....
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auteur: Guillaume Fertin, Shahrad Jamshidi, Christian Komusiewicz
titre: Towards an Algorithmic Guide to Spiral Galaxies
article: Theoretical Computer Science, 2015, pp.26-39. ⟨10.1016/j.tcs.2015.01.051⟩
Resume_court: We study the one-player game Spiral Galaxies from an algorithmic viewpoint. Spiral Galaxies has been .....
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auteur: Guillaume Fertin, Géraldine Jean, Andreea Radulescu, Irena Rusu
titre: DExTaR: Detection of Exact Tandem Repeats based on the de Bruijn graph
article: IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2014), Nov 2014, Belfast, Ireland. pp.90-93, ⟨10.1109/BIBM.2014.6999134⟩
Resume_court: Genomes present various types of repeated structures having important roles in the mechanism of evol .....
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auteur: Freddy Cliquet, Guillaume Fertin, Irena Rusu, Dominique Tessier
titre: Proper Alignment of MS/MS Spectra from Unsequenced Species
article: 11th International Conference on Bioinformatics and Computational Biology (BIOCOMP 2010), Sep 2010, Las Vegas, United States. pp.766-772, ⟨10.1007/978-3-642-03223-3_3⟩
Resume_court: Correct interpretation of tandem mass spectrom- etry (MS/MS) data is a critical step in the protein .....
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auteur: Laurent Bulteau, Guillaume Fertin, Irena Rusu
titre: Pancake Flipping Is Hard
article: Journal of Computer and System Sciences, 2015, 81 (8), pp.1556-1574. ⟨10.1016/j.jcss.2015.02.003⟩
Resume_court: Pancake Flipping is the problem of sorting a stack of pancakes of di erent sizes (that is, a permuta .....
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auteur: Guillaume Fertin, Hafedh Mohamed-Babou, Irena Rusu
titre: Path-Driven Orientation of Mixed Graphs
article: Discrete Applied Mathematics, 2015, 181, pp.98-108. ⟨10.1016/j.dam.2014.10.016⟩
Resume_court: We consider in this paper two graph orientation problems. The input of both problems is (i) a mixed .....
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auteur: Laurent Bulteau, Guillaume Fertin, Christian Komusiewicz
titre: Reversal Distances for Strings with Few Blocks or Small Alphabets
article: 25th Annual Symposium on Combinatorial Pattern Matching (CPM 2014), Jun 2014, Moscou, Russia. pp.50-59, ⟨10.1007/978-3-319-07566-2_6⟩
Resume_court: We study the String Reversal Distance problem, an extension of the well-known Sorting by Reversals p .....
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auteur: Guillaume Fertin, Shahrad Jamshidi, Christian Komusiewicz
titre: Towards an Algorithmic Guide to Spiral Galaxies
article: Seventh International Conference on FUN WITH ALGORITHMS (FUN 2014), Jul 2014, Lipari, Italy. pp.171-182, ⟨10.1007/978-3-319-07890-8_15⟩
Resume_court: In this paper, we are interested in the one-player game Spiral Galaxies, and study it from an algori .....
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auteur: Laurent Bulteau, Guillaume Fertin, Stéphane Vialette, Roméo Rizzi
titre: Some algorithmic results for [2]-sumset covers
article: Information Processing Letters, 2015, 115 (1), pp.1-5
Resume_court: Let X={xi:1≤i≤n}⊂N+X={xi:1≤i≤n}⊂N+, and h∈N+h∈N+. The h-iterated sumset of X , denot .....
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auteur: Laurent Bulteau, Guillaume Fertin, Christian Komusiewicz, Irena Rusu
titre: A Fixed-Parameter Algorithm for Minimum Common String Partition with Few Duplications
article: 13th Workshop on Algorithms in Bioinformatics (WABI2013), Sep 2013, Nice, France. pp.244-258, ⟨10.1007/978-3-642-40453-5_19⟩
Resume_court: Motivated by the study of genome rearrangements, the NP-hard Minimum Common String Partition problem .....
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auteur: Laurent Bulteau, Guillaume Fertin, Irena Rusu
titre: Revisiting the Minimum Breakpoint Linearization Problem Theoretical Computer Science
article: Theoretical Computer Science, 2013, 494, pp.122-133
Resume_court: The gene order on a chromosome is a necessary data for most comparative genomics studies, but in man .....
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auteur: Laurent Bulteau, Guillaume Fertin, Irena Rusu
titre: Maximal Strip Recovery Problem with Gaps: Hardness and Approximation Algorithms
article: Journal of Discrete Algorithms, 2013, 19, pp.1-22
Resume_court: Given two comparative maps, that is two sequences of markers each representing a genome, the Maximal .....
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auteur: Laurent Bulteau, Guillaume Fertin, Irena Rusu
titre: Sorting by Transpositions is Difficult
article: SIAM Journal on Discrete Mathematics, 2012, 26 (3), pp.1148-1180. ⟨10.1137/110851390⟩
Resume_court: In comparative genomics, a transposition is an operation that exchanges two consecutive sequences of .....
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auteur: Guillaume Fertin, Hafedh Mohamed-Babou, Irena Rusu
titre: On the Complexity of two Problems on Orientations of Mixed Graphs
article: In Proc. 5èmes Journées Ouvertes Biologie Informatique Mathématiques (JOBIM 2012), Jul 2012, Rennes, France. pp.161-170
Resume_court: Interactions between biomolecules within the cell can be modeled by biological networks, i.e. graphs .....
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auteur: Riccardo Dondi, Guillaume Fertin, Stéphane Vialette
titre: Finding Approximate and Constrained Motifs in Graphs
article: Theoretical Computer Science, 2013, 483 (-), pp.10-21. ⟨10.1016/j.tcs.2012.08.023⟩
Resume_court: One of the most relevant topics in the analysis of biological networks is the identification of func .....
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auteur: Laurent Bulteau, Guillaume Fertin, Irena Rusu
titre: Pancake Flipping is Hard
article: 37th International Symposium on Mathematical Foundations of Computer Science (MFCS 2012), Aug 2012, Bratislava, Slovakia. pp.247-258
Resume_court: Pancake Flipping is the problem of sorting a stack of pancakes of different sizes (that is, a permut .....
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auteur: Laurent Bulteau, Guillaume Fertin, Minghui Jiang, Irena Rusu
titre: Tractability and approximability of maximal strip recovery
article: Theoretical Computer Science, 2012, 440-441, pp.14-28. ⟨10.1016/j.tcs.2012.04.034⟩
Resume_court: An essential task in comparative genomics is to decompose two or more genomes into synteny blocks th .....
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auteur: Guillaume Fertin, Hafedh Mohamed-Babou, Irena Rusu
titre: Algorithms for subnetwork mining in heterogeneous networks
article: 11th Symposium on Experimental Algorithms (SEA 2012), Jun 2012, Bordeaux, France. pp.184-194
Resume_court: Subnetwork mining is an essential issue in network analysis, with specific applications e.g. in biol .....
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auteur: Olivier Baudon, Guillaume Fertin, Ivan Havel
titre: Routing permutations in the hypercube
article: International Workshop on Graph-Theoretic Concepts in Computer Science WG'99, Jun 1999, Ascona, Switzerland. pp.179-190
Resume_court: We study an n-dimensional directed symmetric hypercube Hn, in which every pair of adjacent vertices .....
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auteur: Olivier Baudon, Guillaume Fertin, Ivan Havel
titre: Routing permutations and 2-1 routing requests in the hypercube
article: Discrete Applied Mathematics, 2001, 113, pp.43-58
Resume_court: Let Hn be the directed symmetric n-dimensional hypercube. Using the computer, we show that for any p .....
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auteur: Guillaume Blin, Guillaume Fertin, Cedric Chauve
titre: The breakpoint distance for signed sequences
article: 1st Conference on Algorithms and Computational Methods for biochemical and Evolutionary Networks (CompBioNets'04), Dec 2004, Recife, Brazil, Brazil. pp.3-16
Resume_court: We consider the problem of estimating the rearrangement distance in terms of reversals, insertion an .....
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auteur: Guillaume Blin, Guillaume Fertin, Romeo Rizzi, Stéphane Vialette
titre: What Makes the Arc-Preserving Subsequence Problem Hard?
article: 5th Int. Workshop on Bioinformatics Research and Applications (IWBRA'05), May 2005, Atlanta, GA, USA, United States. pp.860-868
Resume_court: Given two arc-annotated sequences (S, P ) and (T, Q) representing RNA structures, the Arc-Preserving .....
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auteur: Guillaume Blin, Guillaume Fertin, Danny Hermelin, Stéphane Vialette
titre: Fixed-Parameter Algorithms for Protein Similarity Search Under mRNA Structure Constraints
article: 31st International Workshop on Graph-Theoretic Concepts in Computer Science (WG'05), Jun 2005, Metz, France, France. pp.271-282
Resume_court: In the context of protein engineering, we consider the problem of computing an mRNA sequence of maxi .....
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auteur: Guillaume Blin, Cedric Chauve, Guillaume Fertin
titre: Genes Order and Phylogenetic Reconstruction: Application to $\gamma$-Proteobacteria
article: 3rd Annual RECOMB Satellite Workshop on Comparative Genomics (RECOMB-CG'05), Sep 2005, Dublin, Ireland, Ireland. pp.11-20
Resume_court: We study the problem of phylogenetic reconstruction based on gene order for whole genomes. We define .....
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auteur: Guillaume Blin, Guillaume Fertin, Stéphane Vialette
titre: New Results for the 2-Interval Pattern Problem
article: 15th Symposium on Combinatorial Pattern Matching (CPM'04), Jul 2004, Istanbul, Turkey, Turkey. pp.311-322
Resume_court: We present new results concerning the problem of finding a constrained pattern in a set of 2-interva .....
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auteur: Guillaume Blin, Guillaume Fertin, Roméo Rizzi, Stéphane Vialette
titre: Pattern Matching in Arc-Annotated Sequences: New Results for the APS Problem
article: 5th Journées Ouvertes de Biologie, Informatique et Mathématiques (JOBIM'04), 2004, Montréal, Quebec, Canada. 12 pp
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auteur: Cedric Chauve, Guillaume Fertin, Romeo Rizzi, Stéphane Vialette
titre: Genomes containing duplicates are hard to compare
article: Proc Int. Workshop on Bioinformatics Research and Applications (IWBRA), 2006, Reading, UK, United Kingdom. pp.783-790
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auteur: Paola Bonizzoni, Gianuca Della Vedova, Riccardo Dondi, Guillaume Fertin, Stéphane Vialette
titre: Exemplar Longest Common Subsequences
article: Int. Workshop on Bioinformatics Research and Applications (IWBRA), 2006, United States. pp.622-629
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auteur: Guillaume Fertin, Romeo Rizzi, Stéphane Vialette
titre: Finding Exact and Maximum Occurrences of Protein Complexes in Protein-Protein Interaction Graphs
article: 30th International Symposium on Mathematical Foundations of Computer Science (MFCS'05), 2005, Gdansk, Poland, Poland. pp.328-339
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auteur: Sébastien Angibaud, Guillaume Fertin, Irena Rusu, Stéphane Vialette
titre: How Pseudo-boolean Programming Can Help Genome Rearrangement Distance Computation
article: 4thAnnual RECOMB Satellite Workshop on Comparative Genomics (RECOMB-CG'06), 2006, Montreal, Canada, Canada. pp.75-86
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auteur: Guillaume Blin, Guillaume Fertin, Hafedh Mohamed-Babou, Irena Rusu, Florian Sikora, Stéphane Vialette
titre: Algorithmic Aspects of Heterogeneous Biological Networks Comparison
article: COCOA 2011, 2011, Zhangjiajie, China. pp.272-286, ⟨10.1007/978-3-642-22616-8_22⟩
Resume_court: Biological networks are commonly used to model molecular activity within the cell. Recent experiment .....
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auteur: Sébastien Angibaud, Philippe Bordron, Damien Eveillard, Guillaume Fertin, Irena Rusu
titre: Integration of omics data to investigate common intervals
article: 1st International Conference on Bioscience, Biochemistry and Bioinformatics (ICBBB 2011), 2011, Singapore, Singapore. pp.101-105
Resume_court: During the last decade, we witnessed the huge impact of the comparative genomics for understanding g .....
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auteur: Laurent Bulteau, Guillaume Fertin, Irena Rusu
titre: Sorting by Transpositions is Difficult
article: 38th International Colloquium on Automata, Languages and Programming (ICALP 2011), 2011, Zürich, Switzerland. pp.654-665
Resume_court: In comparative genomics, a transposition is an operation that ex- changes two consecutive sequences .....
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auteur: Riccardo Dondi, Guillaume Fertin, Stéphane Vialette
titre: Finding Approximate and Constrained Motifs in Graphs
article: CPM 2011, 2011, Palermo, Italy. pp.388-401, ⟨10.1007/978-3-642-21458-5_33⟩
Resume_court: One of the emerging topics in the analysis of biological networks is the inference of motifs inside .....
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auteur: Laurent Bulteau, Guillaume Fertin, Minghui Jiang, Irena Rusu
titre: Tractability and Approximability of Maximal Strip Recovery
article: 22nd Annual Symposium on Combinatorial Pattern Matching (CPM 2011), 2011, Palermo, Italy. pp.336-349
Resume_court: An essential task in comparative genomics is usually to de- compose two or more genomes into synteny .....
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auteur: Riccardo Dondi, Guillaume Fertin, Stéphane Vialette
titre: Complexity issues in Vertex-Colored Graph Pattern Matching
article: Journal of Discrete Algorithms, 2011, 9 (1), pp.82-99. ⟨10.1016/j.jda.2010.09.002⟩
Resume_court: Searching for motifs in graphs has become a crucial problem in the analysis of biological networks. .....
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auteur: Michael R. Fellows, Guillaume Fertin, Danny Hermelin, Stéphane Vialette
titre: Upper and lower bounds for finding connected motifs in vertex-colored graphs
article: Journal of Computer and System Sciences, 2011, 77 (4), pp.799-811. ⟨10.1016/j.jcss.2010.07.003⟩
Resume_court: We study the problem of finding occurrences of motifs in vertex-colored graphs, where a motif is a m .....
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auteur: Guillaume Fertin, Irena Rusu
titre: Computing Genomic Distances: An Algorihtmic Viewpoint
article: Wiley Science. Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications, Wiley Science, pp.773-798, 2011, ⟨10.1002/9780470892107.ch34⟩
Resume_court: Comparative genomics is a field of bioinformatics in which the goal is to compare several species by .....
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auteur: Laurent Bulteau, Guillaume Fertin, Irena Rusu
titre: Revisiting the Minimum Breakpoint Linearization Problem
article: 7th Annual Conference on Theory and Applications of Models of Computation (TAMC 2010), Jun 2010, Prague, France. pp.163-174
Resume_court: The gene order on a chromosome is a necessary data for most comparative genomics studies, but in man .....
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auteur: Guillaume Fertin, Danny Hermelin, Romeo Rizzi, Stéphane Vialette
titre: Finding Common Structured Patterns in Linear Graphs
article: Theoretical Computer Science, 2010, 411 (26-28), pp.2475-2486. ⟨10.1016/j.tcs.2010.02.017⟩
Resume_court: A linear graph is a graph whose vertices are linearly ordered. This linear ordering allows pairs of .....
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auteur: Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Guillaume Fertin, Stéphane Vialette
titre: Exemplar Longest Common Subsequence (extended abstract)
article: International Workshop on Bioinformatics Research and Applications (IWBRA 2006), May 2006, Reading, United Kingdom. pp.622-629
Resume_court: In the paper we investigate the computational and approximation complexity of the Exemplar Longest C .....
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auteur: Zhongzhi Zhang, Francesc Comellas, Guillaume Fertin, Lili Rong
titre: High dimensional Apollonian networks
article: Journal of Physics A: Mathematical and Theoretical, 2006, 39, pp.1811-1818
Resume_court: We propose a simple algorithm which produces high dimensional Apollonian networks with both small-wo .....
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auteur: Tiziana Calamoneri, Saverio Caminiti, Guillaume Fertin
titre: New Bounds for the L(h,k) Number of Regular Grids
article: International Journal of Mobile Network Design and Innovation, 2006, 1 (2), pp.92-101
Resume_court: For any non negative real values h and k, an L(h; k)-labeling of a graph G = (V;E) is a function L : .....
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auteur: Guillaume Fertin, André Raspaud
titre: A Survey on Knödel Graphs
article: Discrete Applied Mathematics, 2003, 137 (2), pp.173--195
Resume_court: no abstract
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auteur: Guillaume Fertin, Roger Labahn
titre: Compounding of Gossip Graphs
article: Networks, 2000, 36 (2), pp.126--137
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auteur: Guillaume Fertin
titre: On the Structure of Minimum Broadcast Digraphs
article: Theoretical Computer Science, 2000, 245 (2), pp.203--216
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auteur: Guillaume Fertin
titre: A Study of Minimum Gossip Graphs
article: Discrete Mathematics, 2000, 215 (1--3), pp.33--57
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auteur: Olivier Baudon, Guillaume Fertin, Ivan Havel
titre: Routing Permutations and 2-1 Routing Requests in the Hypercube
article: Discrete Applied Mathematics, 2001, 113 (1), pp.43--58
Resume_court: no abstract
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auteur: Noga Alon, Guillaume Fertin, Arthur L. Liestman, Thomas C. Shermer, Ladislav Stacho
titre: Factor d-Domatic Colorings of Graphs
article: Discrete Mathematics, 2003, 262 (1--3), pp.17--25
Resume_court: no abstract
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auteur: Laurent Bulteau, Guillaume Fertin, Irena Rusu
titre: Maximal Strip Recovery Problem with Gaps: Hardness and Approximation Algorithms
article: ISAAC 2009 (20th International Symposium on Algorithms and Computation), 2009, Hawaii, United States. pp.710-719
Resume_court: Given two comparative maps, that is two sequences of markers each representing a genome, the Maximal .....
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auteur: Cedric Chauve, Guillaume Fertin, Romeo Rizzi, Stéphane Vialette
titre: Genomes containing Duplicates are Hard to compare
article: International Workshop on Bioinformatics Research and Applications (IWBRA 2006), 2006, Reading, United Kingdom. pp.783-790
Resume_court: In this paper, we are interested in the algorithmic complexity of computing (dis)similarity measures .....
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auteur: Sébastien Angibaud, Guillaume Fertin, Irena Rusu, Stéphane Vialette
titre: How Pseudo-Boolean Programming can help Genome Rearrangement Distance Computation
article: 4th RECOMB Comparative Genomics Satellite Workshop (RECOMB-CG 2006), 2007, Montréal, Canada. pp.75-86
Resume_court: Computing genomic distances between whole genomes is a fundamental problem in comparative genomics. .....
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auteur: Guillaume Blin, Guillaume Fertin, Irena Rusu, Christine Sinoquet
titre: Extending the Hardness of RNA Secondary Structure Comparison
article: 1st International Symposium on Combinatorics, Algorithms, Probabilistic and Experimental Methodologies (ESCAPE 2007), Apr 2007, Hangzhou, China. pp.140-151
Resume_court: In molecular biology, RNA structure comparison is of great interest to help solving problems as diff .....
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auteur: Guillaume Fertin, Danny Hermelin, Romeo Rizzi, Stéphane Vialette
titre: Common Structured Patterns in Linear Graphs: Approximations and Combinatorics
article: 18th Annual Symposium on Combinatorial Pattern Matching (CPM 2007), 2007, London, Canada. pp.214-252
Resume_court: A linear graph is a graph whose vertices are linearly ordered. This linear ordering allows pairs of .....
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auteur: Michael R. Fellows, Guillaume Fertin, Danny Hermelin, Stéphane Vialette
titre: Sharp Tractability Borderlines for Finding Connected Motifs in Vertex-Colored Graphs
article: 34th International Colloquium on Automata, Languages and Programming (ICALP 2007), 2007, Wroclaw, Poland. pp.340-351
Resume_court: We study the problem of finding occurrences of motifs in vertex-colored graphs, where a motif is a m .....
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auteur: Guillaume Blin, Guillaume Fertin, Gaël Herry, Stéphane Vialette
titre: Comparing RNA Structures: Towards an Intermediate Model Between the EDIT and the LAPCS Problems
article: Brazilian Symposium on Bioinformatics (BSB 2007), Aug 2007, Angra dos Reis, Brazil. pp.101-112
Resume_court: In the recent past, RNA structure comparison has appeared as an important field of bioinformatics. I .....
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auteur: Riccardo Dondi, Guillaume Fertin, Stéphane Vialette
titre: Weak pattern matching in colored graphs: Minimizing the number of connected components
article: 10th Italian Conference on Theoretical Computer Science (ICTCS 2007), 2007, Rome, Italy. pp.27-38
Resume_court: In the context of metabolic network analysis, Lacroix et al.11 introduced the problem of finding occ .....
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auteur: Sébastien Angibaud, Guillaume Fertin, Irena Rusu, Annelyse Thevenin, Stéphane Vialette
titre: A Pseudo-Boolean programming approach for computing the breakpoint distance between two genomes with duplicate genes
article: 5th RECOMB Comparative Genomics Satellite Workshop (RECOMB-CG 2007), 2007, San Diego, United States. pp.16-29
Resume_court: Comparing genomes of different species has become a crucial problem in comparative genomics. Recent .....
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auteur: Cedric Chauve, Guillaume Fertin
titre: On Maximal Instances for the Original Syntenic Distance
article: Theoretical Computer Science, 2004, 326, pp.29-43
Resume_court: The syntenic distance between two genomes has been introduced by Ferretti, Nadeau and Sankoff as an .....
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auteur: Guillaume Blin, Guillaume Fertin, Romeo Rizzi, Stéphane Vialette
titre: What makes the Arc-Preserving Subsequence problem hard ?
article: LNCS Transactions on Computational Systems Biology, 2005, 2, pp.1-36
Resume_court: In molecular biology, RNA structure comparison and motif search are of great interest for solving ma .....
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auteur: Sébastien Angibaud, Guillaume Fertin, Irena Rusu, Stéphane Vialette
titre: A General Framework for Computing Rearrangement Distances between Genomes with Duplicates
article: Journal of Computational Biology, 2007, 14 (4), pp.379-393. ⟨10.1089/cmb.2007.A001⟩
Resume_court: Computing genomic distances between whole genomes is a fundamental problem in comparative genomics. .....
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auteur: Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Guillaume Fertin, Rafaella Rizzi, Stéphane Vialette
titre: Exemplar Longest Common Subsequence
article: ACM Transactions on Computational Logic, 2007, 4 (4), pp.535-543
Resume_court: In this paper, we investigate the computational and approximation complexity of the Exemplar Longest .....
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auteur: Guillaume Blin, Cedric Chauve, Guillaume Fertin, Romeo Rizzi, Stéphane Vialette
titre: Comparing Genomes with Duplications: a Computational Complexity Point of View
article: ACM Transactions on Computational Logic, 2007, 4 (4), pp.523-534. ⟨10.1109/TCBB.2007.1069⟩
Resume_court: In this paper, we are interested in the computational complexity of computing (dis)similarity measur .....
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auteur: Guillaume Blin, Guillaume Fertin, Stéphane Vialette
titre: Extracting Constrained 2-Interval Subsets in 2-Interval Sets
article: Theoretical Computer Science, 2007, 385 (1-3), pp.241-263
Resume_court: 2-interval sets were used in [S. Vialette, Pattern matching over 2-intervals sets, in: Proc. 13th An .....
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auteur: Guillaume Blin, Guillaume Fertin, Danny Hermelin, Stéphane Vialette
titre: Fixed-Parameter Algorithms For Protein Similarity Search Under mRNA Structure Constraints
article: Journal of Discrete Algorithms, 2008, 6 (4), pp.618-626
Resume_court: In the context of protein engineering, we consider the problem of computing an mRNA sequence of maxi .....
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auteur: Sébastien Angibaud, Guillaume Fertin, Irena Rusu, Annelyse Thevenin, Stéphane Vialette
titre: Efficient Tools for Computing the Number of Breakpoints and the Number of Adjacencies between two Genomes with Duplicate Genes
article: Journal of Computational Biology, 2008, 15 (8), pp.1093-1115. ⟨10.1089/cmb.2008.0061⟩
Resume_court: Comparing genomes of different species is a fundamental problem in comparative genomics. Recent rese .....
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auteur: Sébastien Angibaud, Damien Eveillard, Guillaume Fertin, Irena Rusu
titre: Comparing Bacterial Genomes by Searching their Common Intervals
article: 1st International Conference on Bioinformatics and Computational Biology (BICoB 2009), 2009, New Orleans, United States. pp.102-113, ⟨10.1007/978-3-642-00727-9_12⟩
Resume_court: Comparing bacterial genomes implies the use of a dedicated measure. It relies on comparing circular .....
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auteur: Guillaume Blin, Guillaume Fertin, Florian Sikora, Stéphane Vialette
titre: The Exemplar Breakpoint Distance for non-trivial genomes cannot be approximated
article: WALCOM 2009, 2009, Kolkata, India. pp.357-368
Resume_court: A promising and active field of comparative genomics con- sists in comparing two genomes by establis .....
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auteur: Sébastien Angibaud, Guillaume Fertin, Irena Rusu
titre: On the Approximability of Comparing Genomes with Duplicates
article: 2nd Workshop on Algorithms and Computation (WALCOM 2008), 2008, Dhaka, Bangladesh. pp.34-45
Resume_court: A central problem in comparative genomics consists in computing a (dis-)simi- larity measure between .....
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auteur: Guillaume Fertin, André Raspaud
titre: Acyclic Coloring of Graphs of Maximum Degree Five: Nine Colors are Enough
article: Information Processing Letters, 2008, 105 (2), pp.65-72
Resume_court: An acyclic coloring of a graph G is a coloring of its vertices such that: (i) no two neighbors in G .....
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auteur: Guillaume Fertin, Stéphane Vialette
titre: On the S-labeling Problem
article: Proc. 5th Euroconference on Combinatorics, Graph Theory and Applications (EUROCOMB 2009), 2009, Bordeaux, France. pp.273-277
Resume_court: Let G be a graph of order n and size m. A labeling of G is a bijective mapping theta : V(G) --> 1, 2 .....
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auteur: Zhongzhi Zhang, Francesc Comellas, Guillaume Fertin, André Raspaud, Lili Rong, Shuigeng Zhou
titre: Vertex labeling and routing in expanded Apollonian networks
article: Journal of Physics A: Mathematical and Theoretical, 2008, 41 (3), pp.035004
Resume_court: We present a family of networks, expanded deterministic Apollonian networks, which are a generalizat .....
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auteur: Isabelle Fagnot, Guillaume Fertin, Stéphane Vialette
titre: On Finding Small 2-Generating Sets
article: COCOON 2009, 2009, Niagara Falls, United States. pp.378-387, ⟨10.1007/978-3-642-02882-3_38⟩
Resume_court: Given a set of positive integers S, we consider the problem of finding a minimum cardinality set of .....
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auteur: Guillaume Fertin, André Raspaud, Bruce Reed
titre: Star Coloring of Graphs
article: Journal of Graph Theory, 2004, 47 (3), pp.163-182
Resume_court: A star coloring of an undirected graph G is a proper vertex coloring of G (i.e., no two neighbors ar .....
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auteur: Guillaume Fertin, André Raspaud
titre: A Survey of Knödel Graphs
article: Discrete Applied Mathematics, 2004, 137 (2), pp.173-195
Resume_court: Knödel graphs of even order n and degree 1\leq Delta \leq \lfloor log2(n)\rfloor, W(Delta,n), are g .....
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auteur: Guillaume Fertin, Emmanuel Godard, André Raspaud
titre: Minimum feedback vertex set and acyclic coloring
article: Information Processing Letters, 2002, 84 (3), pp.131-139
Resume_court: In the feedback vertex set problem, the aim is to minimize, in a connected graph G =(V,E), the cardi .....
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auteur: Guillaume Fertin, André Raspaud, Arup Roychowdhury
titre: On the oriented chromatic number of grids
article: Information Processing Letters, 2003, 85 (5), pp.261-266
Resume_court: In this paper, we focus on the oriented coloring of graphs. Oriented coloring is a coloring of the v .....
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auteur: Guillaume Fertin, André Raspaud
titre: L(p,q) labeling of d-Dimensional Grids
article: Discrete Mathematics, 2007, 307 (16), pp.2132-2140
Resume_court: In this paper, we address the problem of lambda labelings, that was introduced in the context of fre .....
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auteur: Guillaume Fertin, André Raspaud, Ondrej Sykora
titre: No-Hole L(p,0)-Labelling of Cycles, Grids and Hypercubes
article: 11th International Colloquium on Structural Information & Communication Complexity (SIROCCO 2004), Jun 2004, Smolenice, Slovakia. pp.138-148
Resume_court: In this paper, we address a particular case of the general problem of $\lambda$ labellings, concerni .....
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auteur: Riccardo Dondi, Guillaume Fertin, Stéphane Vialette
titre: Maximum Motif Problem in Vertex-Colored Graphs
article: 20th Annual Symposium on Combinatorial Pattern Matching (CPM 2009), 2009, Lille, France. pp.221-235, ⟨10.1007/978-3-642-02441-2_20⟩
Resume_court: Searching for motifs in graphs has become a crucial problem in the analysis of biological networks. .....
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auteur: Freddy Cliquet, Guillaume Fertin, Irena Rusu, Dominique Tessier
titre: Comparison of Spectra in Unsequenced Species
article: 4th Brazilian Symposium on Bioinformatics (BSB 2009), 2009, Porto Alegre, Brazil. pp.24-35, ⟨10.1007/978-3-642-03223-3_3⟩
Resume_court: We introduce a new algorithm for the mass spectromet- ric identication of proteins. Experimental spe .....
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auteur: Sébastien Angibaud, Guillaume Fertin, Annelyse Thevenin, Stéphane Vialette
titre: Pseudo-Boolean Programming for Partially Ordered Genomes
article: RECOMB-CG 2009, Sep 2009, Budapest, Hungary. pp.126-137, ⟨10.1007/978-3-642-04744-2_11⟩
Resume_court: Comparing genomes of different species is a crucial problem in comparative genomics. Different measu .....
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auteur: Guillaume Fertin, Anthony Labarre, Irena Rusu, Eric Tannier, Stéphane Vialette
titre: Combinatorics of Genome Rearrangements
article: MIT Press, pp.312, 2009, Computational Molecular Biology, 978-0-262-06282-4
Resume_court: From one cell to another, from one individual to another, and from one species to another, the conte .....
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auteur: Sébastien Angibaud, Guillaume Fertin, Irena Rusu, Annelyse Thévenin, Stéphane Vialette
titre: On the Approximability of Comparing Genomes with Duplicates
article: Journal of Graph Algorithms and Applications, 2009, 13 (1), pp.19-53
Resume_court: A central problem in comparative genomics consists in computing a (dis-)similarity measure between t .....
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auteur: Guillaume Fertin, Romeo Rizzi, Stéphane Vialette
titre: Finding Occurrences of Protein Complexes in Protein-Protein Interaction Graphs
article: Journal of Discrete Algorithms, 2009, 7 (1), pp.90-101
Resume_court: In the context of comparative analysis of protein-protein interaction graphs, we use a graph-based f .....
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auteur: Guillaume Fertin, André Raspaud
titre: L(p,q) labeling of d-dimensional grids
article: Discrete Mathematics, 2007, 307 (16), pp.2132-2140
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auteur: Sébastien Angibaud, Guillaume Fertin, Irena Rusu, Annelyse Thevenin, Stéphane Vialette
titre: On the Approximability of Comparing Genomes with Duplicates
article: 2008
Resume_court: A central problem in comparative genomics consists in computing a (dis-)similarity measure between t .....
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auteur: Sébastien Angibaud, Guillaume Fertin, Irena Rusu
titre: On the Approximability of Comparing Genomes with Duplicates
article: 2007
Resume_court: A central problem in comparative genomics consists in computing a (dis-)similarity measure between t .....
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auteur: Tiziana Calamoneri, Saverio Caminiti, Guillaume Fertin
titre: New Bounds for the L(h, k) Number of Regular Grids
article: 2006
Resume_court: For any non negative real values h and k, an L(h; k)-labeling of a graph G = (V;E) is a function L : .....
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