Selected publications

(reprints are available on request)

• Applied Mathematics, Algorithmic, Theoretical Computer Science
• Statistics, Probability, Classification, Data Analysis
• Machine Learning, Pattern Recognition
• Biological sequence analysis, Phylogenetic reconstruction
• Microelectronics

Applied Mathematics, Algorithmic, Theoretical Computer Science

• HORDIJK W., KAUFFMAN S. A.,
  "Correlation Analysis of Coupled Fitness Landscapes"
  Complexity 10(6), 42-49, 2005. download
• BERRY V., NICOLAS F.,
  "Improved parametrized complexity of the maximum agreement subtree and maximum compatible tree problems",
  IEEE/ACM Transactions on Computational Biology and Bioinfomatics, 2005, in press. download
• NICOLAS F., RIVALS E.,
  "Hardness of Optimal Spaced Seed Design",
  Proc. of the 16th Annual Symposium on Combinatorial Pattern Matching (CPM’05),
  LNCS 3537, 144-155, 2005. download
• DELGRANGE O., RIVALS E.,
  "Modular Data Compression to Optimally Locate Regular Segments in Sequences. Application to DNA Sequence Analysis",
  26th Symposium on Information Theory in the Benelux (IT05), pp. 105-112,  2005. download
• NICOLAS F., RIVALS E.,
  "Hardness Results for the Center and Median String Problems under the Weighted and Unweighted Edit Distances",
  Journal of Discrete Algorithms, 3(2-4), 390-415, 2005. download
  (improved version of CPM’03,  LNCS 2676)
• ELEMENTO, O., GASCUEL, O
  "An Exact and Polynomial Distance-Based Algorithm to Reconstruct Single Copy Tandem Duplication Trees"
  Journal of Discrete Algorithms 3(2-4), 362-374, 2005. download
  (improved version of CPM’03, LNCS 2676, 96-108)
• BERTRAND, D., GASCUEL, O.,
  "Topological Rearrangements and Local Search Method for Tandem Duplication Trees"
  IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2(1), 15-28, 2005. download
  (improved version of WABI’04, LNCS 3240, 374-387)
• RIVALS E.,
  "A Survey on Algorithmic Aspects of Tandem Repeats Evolution",
  International Journal of Foundations of Computer Science, Vol. 15(2), 225-257, 2004. download
• BERRY, V., NICOLAS, F.
  " Maximum Agreement and Compatible Supertrees"
  in Proc. 15th Annual Symposium on Combinatorial Pattern Matching (CPM’04),
  Lecture Notes in Computer Science (Springer) 3109, 205-219, 2004. download
• RIVALS, E., RAHMANN, S.
  "Combinatorics of Periods in Strings"
  Journal of Combinatorial Theory - Series A, 104(1), 95-113, 2003. download
• DENIS, F., GASCUEL, O.,
  "On the consistency of the minimum evolution principle",
  Discrete Applied Mathematics 127(1) :63-77, Computational Molecular Biology Series - Issue IV, 2003. download
• GASCUEL, O., HENDY, M., JEAN-MARIE, A., McLACHLAN, R.,
  " The Combinatorics of Tandem Duplication Trees"
  Systematic Biology 52 :110-118, 2003. download
• BRYANT, D., BERRY, V.,
  "A structured family of clustering and tree construction methods"
  Advance in Applied Mathematics, 27(4):705 –732, 2001. download
• RIVALS, E., RAHMANN, S.,
  "Combinatorics of Periods in Strings"
  Proc. 28th International Colloquium on Automata, Languages, and Programming,
  Lecture Notes in Computer Science (Springer) 2076, 615-626, 2001. download
• BOECKER, S., BRYANT, D., DRESS, A., and STEEL, M.
  "Algorithmic aspects of tree amalgamation"
  Journal of Algorithms, 37, 522-537. 2000. download
• RAHMANN, S., RIVALS, E.,
  "Exact and Efficient Computation of the Expected Number of Missing and Common Words in Random Texts"
  11th Annual Symposium on Combinatorial Pattern Matching,
  Lecture Notes in Computer Science, 1848, 375-387, 2000. download
• BERRY V., BRYANT D., JIANG T., KEARNEY P., LI M., WAREHAM T., ZHANG H.,
  "A Practical Algorithm for Recovering the Best Supported Edges of an Evolutionary Tree",
  Symposium on Discrete Algorithms, San-Francisco, 287-296, 2000. download
• BERRY V., GASCUEL O.,
  "Inferring Evolutionary Trees with Strong Combinatorial Evidence",
  Theoretical Computer Science 240(2), 271-298, 2000. download
• BERRY V., JIANG T., KEARNEY P., LI M., WAREHAM T.,
  "Quartet cleaning: improved algorithms and simulation",
  European Symposium on Algorithms, Prague, LNCS 1643, 313-324, 1999. download
• DE LA HIGUERA C., DANIEL-VATONNE M.C.,
  "On sets of terms a study of a generalisation relation and of its algorithmic properties",
  Fundamenta Informaticae 25(2), 99-122, 1996. download

Statistics, Probability, Classification and Data Analysis

• CELEUX, G., MARTIN, O., LAVERGNE, C.,
  "Mixture of linear mixed models for clustering gene expression profiles from repeated microarray experiments",
  Statistical Modelling, 5(3), 2005, in press. download
• GASCUEL, O., McKENZIE, A.,
  "Performance Analysis of Hierarchical Clustering Algorithms"
  Journal of Classification 21, 3-18, 2004. download
• RAHMANN, S., RIVALS, E.,
  "The Number of Missing Words in Random Texts"
  Combinatorics, Probability and Computing 12, 73-87, 2003. download
• BERRY V., GASCUEL O., CARAUX G.,
  "Chosing the tree which actually best explains the data: another look at the bootstrap in phylogenetic reconstruction",
  Computational Statistics and Data Analysis 38, 273-283, 2000. download
• GASCUEL O.,
  "Evidence for a relationship between algorithmic scheme and shape of inferred trees",
  in Data Analysis, Scientific Modeling and Practical Applications,
  W. Gaul, O. Opitz and M. Schader (Eds.), Springer, Berlin, 157-168, 2000. download
• GASCUEL O.,
  "Data model and classification by trees: the minimum variance reduction (MVR) method",
  Journal of Classification, 17(1), 67-99, 2000. download
• GASCUEL O.,
  "Concerning the NJ algorithm and its unweighted version, UNJ",
  in Mathematical Hierarchies and Biology, B. Mirkin, F.R. McMorris, F.S. Roberts and A. Rzetsky (eds.),
  American Mathematical Society, Providence, 149-170, 1997. download
• GASCUEL O.,
  "Dimension de Vapnik-Chervonenkis et validité de l'approche neuronale",
  in "Statistique et Réseaux de Neurones", S. Thiria, Y. Lechevallier, O. Gascuel et S. Canu (Editeurs scientifiques), Dunod, 1997. download
• GASCUEL O., LEVY D.,
  "A reduction algorithm for approximating a (non-metric) dissimilarity by a tree distance",
  Journal of Classification 13, 129-155, 1996. download
• GASCUEL O., CARAUX G.,
  "Bounds on the expectation of order statistics via extremal dependence".
  Statistics & Probability Letters 15, 143-148, 1992. download
• CARAUX G., GASCUEL O.,
  "Bounds on distribution function of order statistics for dependent variates".
  Statistics & Probability Letters 14, 103-105, 1992. download
• GASCUEL O., CARAUX G.,
  "Distribution-free performance bounds with the resubstitution error estimate",
  Pattern Recognition Letters 13, 757-764, 1992. download
• GASCUEL O., CARAUX G.,
  "Statistical significance in inductive learning",
  European Conference on Artificial Intelligence, Vienne, 435-439, 1992. download

Machine Learning, Pattern Recognition

• BREHELIN L., GASCUEL O., CARAUX G.,
  "Hidden Markov Models with Patterns to Learn Boolean Vector Sequences,
  and Application to the Built-in Self-Test for Integrated Circuits,"
  IEEE-Transactions on Pattern Analysis and Machine Intelligence, 23(9), 978-997, 2001. download
• BREHELIN L., GASCUEL O., CARAUX G.,
  "Hidden Markov Models with Patterns and their application to integrated circuit testing"
  European Conference on Machine Learning, Barcelona, 75-87, 2000. download
• NOCK R., JAPPY P.,
  "On the power of decision lists",
  International Conference on Machine Learning, Madison, 413-420, 1998.
• GASCUEL O. et al. (groupe SYMENU),
  "Twelve numerical, symbolic and hybrid supervised classification methods",
  International Journal of Pattern Recognition and Artificial Intelligence 12(5), 517-572, 1998. download
• DE LA HIGUERA C.,
  "Characteristic sets for polynomial grammatical inference",
  Machine Learning 27(2), 125-138, 1997.
• JAPPY P., NOCK R., GASCUEL O.,
  "Negative Robust Learnability results for Horn Clause Programs",
  International Conference on Machine Learning, Barri,  258-265, 1996. download
• NOCK R., GASCUEL O.,
  "On learning decision commitees",
  International Conference on Machine Learning, Tahoe city, 413-420, 1995. download
• CIBAS T., GALLINARI P., GASCUEL O.,
  "Experimental investigations on the complexity-performance relations in multilayer perceptrons",
  International Conference on Artificial Neural Networks (ICANN), Paris, 569-574, 1995. download
• CARVALHO F., GASCUEL O.,
  "SDL : a stochastic algorithm for learning decision lists with limited complexity",
  Annals of Mathematics and Artificial Intelligence 10 (3), 281-302, 1994. download
• GASCUEL O.,
  "A conceptual regression method",
  European Conference on Machine Learning, Montpellier, Pitman Publishing, 81-90, 1989. download
• GASCUEL O., DANCHIN A.,
  "Data analysis using a learning program, a case study : an application of PLAGE to a biological sequence analysis",
  European Conference on Artificial Intelligence, Munich, 390-395, 1988. download

Biological Sequence Analysis, Phylogenetic Reconstruction, Expression Data

• BRÉHÉLIN, L.,
  "Clustering Gene Expression Series with Prior Knowledge,"
  5th Workshop on Algorithms in Bioinformatics (WABI'05),
  Lecture Notes in Bioinformatics (Springer), 2005, in press. download
• GONZE D., PINLOCHE S., GASCUEL O., VAN HELDEN J.,
  "Discrimination of yeast genes involved in methionine and phosphate metabolism on the basis of upstream motifs"
  Bioinformatics, 21(17), 3490-3500, 2005. download Bioinformatics
• PHILIPPE, H. , LARTILLOT,  N., BRINKMANN, H.,
  "Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa and Protostomia."
  Molecular Biology and  Evolution , 22, 1246-1253, 2005. download
• RODRIGUE, N., LARTILLOT, N., BRYANT, D. and PHILIPPE, H.,
  "Site interdependence attributed to tertiary structure in amino acid sequence evolution."
  Gene 347, 207-217, 2005. download
• GUINDON, S., LE THIEC, F., DUROUX, P., GASCUEL, O.,
  "PHYML Online: a web server for fast maximum likelihood-based phylogenetic inference"
  Nucleic Acid Research 33, 557-559, 2005. download NAR
• CARAUX, G., and PINLOCHE, S.
  "Permutmatrix: A Graphical Environment to Arrange Gene Expression Profiles in Optimal Linear Order,"
  Bioinformatics 21: 1280-1281, 2005. download
• GASCUEL, O., ed,
  "Mathematics of Evolution and Phylogeny"
  Oxford University Press, 2005. contents
• CHEVALIER, F., MARTIN, O., ROFIDAL, V., DEVAUCHELLE, A.-D., BARTEAU, S., SOMMERER, N., ROSSIGNOL, M.,
  "Proteomic investigation of natural variation between Arabidopsis ecotypes", Proteomics, 4(5):1372-1381, 2004. download
• DELGRANGE O., RIVALS E.,
  "STAR: an algorithm to Search for Tandem Approximate Repeats",
  Bioinformatics, Vol. 20(16), 2812-2820, 2004. download
• WEILLER, G. F., CARAUX, G., SYLVESTER, N.,
  "The Modal Distribution of Protein Isoelectric Points Reflects Amino Acid Properties Rather Than Sequence Evolution"
  Proteomics 4: 943-949, 2004. download
• BERARD, S., BERGERON, A., CHAUVE, C
  "Conservation of Combinatorial Structures in Evolution Scenarios,"
  2nd RECOMB ComparativeGenomics Satellite Workshop, Bologna, Lecture Notes in Bioinformatics 338 (Springer), 1-14, 2004. download
• LARTILLOT, N., PHILIPPE, H.,
  "A Bayesian Mixture Model for Across-Site Heterogeneities in the Amino-Acid Replacement Process," Molecular Biology and Evolution 21(6):1095-1109, 2004. download
• DESPER, R., GASCUEL, O.,
  "Theoretical Foundation of the Balanced Minimum Evolution Method of Phylogenetic Inference and its Relationship to Weighted Least-squares Tree Fitting"
  Molecular Biology and Evolution 21(3):587-598, 2004. download MBE
• GUINDON, S., GASCUEL, O.,
  "A simple, fast and accurate method to estimate large phylogenies by maximum-likelihood"
  Systematic Biology 52(5), 696-704, 2003. download
• BERARD, S., RIVALS, E.
  "Comparison of Minisatellites"
  Journal of Computational Biology, 10(3-4), p. 357-372, 2003. download
• GASCUEL O.,
  " Getting a Tree Fast: Neighbor Joining and Distance Based Methods”, in Current Protocols in Bioinformatics,
  A. Baxevanis, D. Davison, C. Hogue, R. Page, L. Stein, G. Stormo (Eds), Wiley, 6.3.1-6.3.18, 2003. download
• DESPER, R., GASCUEL, O.,
  " Fast and Accurate Phylogeny Reconstruction Algorithms Based on the Minimum-Evolution Principle"
  Journal of Computational Biology 9(5), 687-705, 2002. download
• RANWEZ, V., GASCUEL, O.,
  "Improvement of distance-based phylogenetic methods by a local maximum likelihood approach using triplets"
  Molecular Biology and Evolution, 19(11), 1952-1963, 2002. download
• ELEMENTO, O., GASCUEL, O.,
  "A fast and accurate distance algorithm to reconstruct tandem duplication trees"
  Bioinformatics 18(Suppl. 2, Proceedings of ECCB’2002), 92-99, 2002. download
• GUINDON, S., GASCUEL, O.,
  "Efficient biased estimation of evolutionary distances when substitution rates vary across sites"
  Molecular Biology and Evolution, 19(4), 534-543, 2002. download
• ELEMENTO, O., GASCUEL, O., LEFRANC M.-P.,
  "Reconstructing the duplication history of tandemly repeated genes",
  Molecular Biology and Evolution, 19(3), 278-288, 2002. download
• WEILLER, G. F., DJORDJEVIC, M. J., CARAUX, G., CHEN, H., and WEINMAN, J. J.,
  "A Specialized Proteomic Database for Comparing Matrix-Assisted Laser Desorption/Ionization-Time
  of Flight Mass Spectrometry Data of Tryptic Peptides with Corresponding Sequence Database Segments,"
  Proteomics 1, 1489-1494, 2001. download
• GUINDON, S., PERRIERE, G.,
  "Intragenomic base content variation is a potential source of biases when searching for horizontally transferred genes",
  Molecular Biology and Evolution, 18, 1838-1840, 2001. download
• GASCUEL, O, BRYANT, D. and DENIS, F.,
  "Strengths and limitations of the minimum evolution principle",
  Systematic Biology, 50(5), 621-627, 2001. download
• RANWEZ, V., GASCUEL, O.,
  "Quartet based phylogenetic inference: improvements and limits,"
  Molecular Biology and Evolution, 18(6), 1103-1116, 2001. download
• BRYANT, D.,
  "The complexity of calculating exemplar distances"
  in Comparative Genomics, Sankoff, D. and Nadeau, J.H. (eds),
  Kluwer, 207-212, 2000. download
• GASCUEL O.,
  "On the optimization principle in phylogenetic analysis and the minimum evolution criterion",
  Molecular Biology and Evolution 17(3), 401-405, 2000. download
• HAAS, S., BEISSBARTH, T., RIVALS, E., KRAUSE, A., VINGRON, M.,
  "GeneNest: automated generation and visualization of gene indices"
  Trends in Genetics 16(11), 521-2, 2000. download
• BERRY V., BRYANT D.,
  "Faster reliable phylogenetic analysis",
  International Computational Biology Conference (RECOMB), Lyon, 1999. download
  (Young investigator award).
• VAREE J.S., DELAHAYE J.P., RIVALS E.,
  "The Transformation Distance: a Dissimilarity Measure Based on Movements of Segments"
  Bioinformatics 15(3), 194-202, 1999. download
• BURKHART S., CRAUSER A., FERRAGINA P., LENHOF H.P., RIVALS E., VINGRON E.,
  "q-gram Based Database Searching Using a Suffix Array (QUASAR)"
  International Computational Biology Conference (RECOMB), Lyon, 1999. download
• GASCUEL O.,
  "BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data",
  Molecular Biology and Evolution 14(7), 685-695, 1997.
  (First paper in the issue). download
• ANDRIEU G., CARAUX G., GASCUEL O.,
  "Confidence intervals of evolutionary distances between sequences and comparison with usual approaches including the bootstrap method",
  Molecular Biology and Evolution 14(8), 875-882, 1997. download
• BERRY V., GASCUEL O.,
  "Interpretation of bootstrap trees : threeshold of clade selection and induced gain",
  Molecular Biology and Evolution 13(7), 999-1011, 1996. download
• CARAUX G., GASCUEL O., ANDRIEU G. et LEVY D.,
  "Méthodes informatiques pour la reconstruction phylogenetique",
  Technique et Science Informatiques 14(2), 113-139, 1995. download
• GASCUEL O.,
  "A note on Sattath and Tversky's, Saittou and Nei's and Studier and Keppler's algorithms for inferring phylogenies from evolutionary distances",
  Molecular Biology and Evolution 11(6), 961-963, 1994. download
• GASCUEL O., GOLMARD J. L.,
  "A simple method for predicting the secondary structure of globular proteins : Implications and Accuracy",
  Computer Applications in the Biosciences 4 (3), 357-365, 1988. download
• GASCUEL O., DANCHIN A.,
  "Protein export in prokaryotes and eukaryotes : indications for a difference in the mechanism of exportation",
  Journal of Molecular Evolution 24, 130-142, 1986. download

Microelectronics

• FAGOT C., GASCUEL O., GIRARD P., LANDRAULT C.,
  "A ring architecture strategy for BIST test pattern generation",
  Journal of Electronic Testing: Theory and Applications (JETTA) 19, 223-231, 2003. download
• BREHELIN L., GASCUEL O., CARAUX G., GIRARD P., LANDRAULT C.,
  Hidden Markov and Independence Models with Patterns for Sequential BIST",
  IEEE VLSI Test Symposium, Montréal, 359-367, 2000. download
• FAGOT C., GASCUEL O., GIRARD P., LANDRAULT C.,
  "On calculating Efficient LFSR Seeds for Built-In Self Test",
  IEEE European Test Workshop (ETW), Germany, 7-14, 1999. download
• FAGOT C., GIRARD P., LANDRAULT C.,
  "On using machine learning for logic BIST",
  International Test Conference, Washington, 338-346, 1997. download