Olivier Gascuel

发表

Efficiently Analysing Large Viral Data Sets in Computational Phylogenomics

Anna Zhukova, Olivier Gascuel, Sebastián Duchêne, 2020 .

Evolution of Tandemly Repeated Sequences Through Duplication and Inversion

Olivier Gascuel, Denis Bertrand, Mathieu Lajoie, 2006, Comparative Genomics.

COVID-Align: accurate online alignment of hCoV-19 genomes using a profile HMM

Olivier Gascuel, Frédéric Lemoine, Luc Blassel, 2020, bioRxiv.

Performance Analysis of Hierarchical Clustering Algorithms

Olivier Gascuel, Andy McKenzie, O. Gascuel, 2004, J. Classif..

Fitting hidden Markov models of protein domains to a target species: application to Plasmodium falciparum

Olivier Gascuel, Laurent Bréhélin, Nicolas Terrapon, 2011, BMC Bioinformatics.

Markov Models in Molecular Evolution

Olivier Gascuel, Alain Jean-Marie, Nicolas Galtier, 2005 .

Concerning the NJ algorithm and its unweighted version, UNJ

Olivier Gascuel, O. Gascuel, 1996, Mathematical Hierarchies and Biology.

A simple method for predicting the secondary structure of globular proteins: implications and accuracy

Olivier Gascuel, J. L. Golmard, O. Gascuel, 1988, Comput. Appl. Biosci..

Fast NJ-like algorithms to deal with incomplete distance matrices

Olivier Gascuel, Alexis Criscuolo, O. Gascuel, 2008, BMC Bioinformatics.

Control of a 3-DOF Over-Actuated Parallel Mechansim

Olivier Gascuel, Franc¸ois Pierrot, Fre´de´ric Marquet, 2002 .

SPECIAL SECTION ON THE WORKSHOP ON ALGORITHMS IN BIOINFORMATICS 1 Guest Editorial: WABI Special Section Part II

Ying Liu, Olivier Gascuel, Ashwin Ram, 2005 .

Data Model and Classification by Trees: The Minimum Variance Reduction (MVR) Method

Olivier Gascuel, O. Gascuel, 2000, J. Classif..

Hidden Markov and independence models with patterns for sequential BIST

Patrick Girard, Christian Landrault, Olivier Gascuel, 2000, Proceedings 18th IEEE VLSI Test Symposium.

Fast and Accurate Phylogeny Reconstruction Algorithms Based on the Minimum-Evolution Principle

Olivier Gascuel, Richard Desper, 2002, J. Comput. Biol..

Distance-based methods in phylogenetics

Olivier Gascuel, Fabio Pardi, O. Gascuel, 2015, FOCS 2015.

Distance-Based Phylogeny Reconstruction: Safety and Edge Radius

Olivier Gascuel, Jakub Truszkowski, Fabio Pardi, 2016, Encyclopedia of Algorithms.

Topological rearrangements and local search method for tandem duplication trees

Olivier Gascuel, Denis Bertrand, O. Gascuel, 2004, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

PlasmoDraft: a database of Plasmodium falciparum gene function predictions based on postgenomic data

Olivier Gascuel, Laurent Bréhélin, Jean-François Dufayard, 2008, BMC Bioinformatics.

FastME 2.0: A Comprehensive, Accurate, and Fast Distance-Based Phylogeny Inference Program

Olivier Gascuel, Vincent Lefort, Richard Desper, 2015, Molecular biology and evolution.

Detection of new protein domains using co-occurrence: application to Plasmodium falciparum

Olivier Gascuel, Laurent Bréhélin, Nicolas Terrapon, 2009, Bioinform..

Statistical Methods in Molecular Evolution

Olivier Gascuel, Alain Jean-Marie, Nicolas Galtier, 2005 .

Getting a Tree Fast: Neighbor Joining and Distance‐Based Methods

Olivier Gascuel, O. Gascuel, 2002 .

A ‘Stochastic Safety Radius’ for Distance-Based Tree Reconstruction

Olivier Gascuel, Mike A. Steel, O. Gascuel, 2014, Algorithmica.

An efficient and accurate distance based algorithm to reconstruct tandem duplication trees

Olivier Gascuel, Olivier Elemento, O. Elemento, 2002, ECCB.

An exact and polynomial distance-based algorithm to reconstruct single copy tandem duplication trees

Olivier Gascuel, Olivier Elemento, 2005, J. Discrete Algorithms.

Negative Robust Learning Results from Horn Claus Programs

Richard Nock, Olivier Gascuel, Pascal Jappy, 1996, ICML.

Searching for virus phylotypes

Olivier Gascuel, Tulio de Oliveira, François Chevenet, 2013, Bioinform..

FastMG: a simple, fast, and accurate maximum likelihood procedure to estimate amino acid replacement rate matrices from large data sets

Olivier Gascuel, Si Quang Le, Le Sy Vinh, 2014, BMC Bioinformatics.

Duplication and Inversion History of a Tandemly Repeated Genes Family

Olivier Gascuel, Denis Bertrand, Nadia El-Mabrouk, 2007, J. Comput. Biol..

Final Report of the ModSysC2020 Working Group - Data, Models and Theories for Complex Systems: new challenges and opportunities

Patrick Valduriez, Pascal Neveu, Olivier Gascuel, 2012 .

Fast and Accurate Phylogeny Reconstruction Algorithms Based on the Minimum-Evolution Principle

Olivier Gascuel, Richard Desper, O. Gascuel, 2002, WABI.

Phylogenetic Reconstruction Algorithms Based on Weighted 4-Trees

Olivier Gascuel, Vincent Ranwez, O. Gascuel, 2000, JOBIM.

Using repeated measurements to validate hierarchical gene clusters

Olivier Martin, Olivier Gascuel, Laurent Bréhélin, 2008, Bioinform..

Getting a tree fast: Neighbor Joining, FastME, and distance-based methods.

Olivier Gascuel, Richard Desper, O. Gascuel, 2003, Current protocols in bioinformatics.

ReplacementMatrix: a web server for maximum-likelihood estimation of amino acid replacement rate matrices

Olivier Gascuel, Vincent Lefort, Si Quang Le, 2011, Bioinform..

Distance-Based Phylogeny Reconstruction (Optimal Radius)

Olivier Gascuel, Richard Desper, O. Gascuel, 2008, Encyclopedia of Algorithms.

Improving the efficiency of SPR moves in phylogenetic tree search methods based on maximum likelihood

Olivier Gascuel, Wim Hordijk, O. Gascuel, 2005, Bioinform..

GONNA: a Gene Ontology Nearest Neighbor Approach for the Functional Prediction of P.falciparum Orphan Genes

Olivier Gascuel, Laurent Bréhélin, 2007 .

Inferring evolutionary trees with strong combinatorial evidence

Olivier Gascuel, Vincent Berry, 2000, Theor. Comput. Sci..

Assessing the accuracy of Approximate Bayesian Computation approaches to infer epidemiological parameters from phylogenies

Olivier Gascuel, Samuel Alizon, E Saulnier, 2016, bioRxiv.

Hypertension Management : Connection of an Expert System to the Artemis Patient Database

Patrice Degoulet, Olivier Gascuel, Patrick Ferrand, 1986 .

Models and Algorithms in Phylogenetics

Olivier Gascuel, 2014 .

A Fast and Accurate Distance Algorithm to Reconstruct Tandem Duplication Trees

Olivier Gascuel, Olivier Elemento, O. Elemento, 2001 .

PHYML Online: A Web Server for Fast Maximum Likelihood-Based Phylogenetic Inference

Olivier Gascuel, Patrice Duroux, Stéphane Guindon, 2018 .

Renewing Felsenstein’s Phylogenetic Bootstrap in the Era of Big Data

Olivier Gascuel, Tulio de Oliveira, Jean-Baka Domelevo Entfellner, 2018, Nature.

On the consistency of the minimum evolution principle of phylogenetic inference

Olivier Gascuel, François Denis, O. Gascuel, 2003, Discret. Appl. Math..

Computational Biology: First International Conference on Biology, Informatics, and Mathematics, JOBIM 2000 Montpellier, France, May 3-5, 2000 Selected Papers

Olivier Gascuel, Marie-France Sagot, 2001 .

COVID-Align: Accurate online alignment of hCoV-19 genomes using a profile HMM

Olivier Gascuel, Frédéric Lemoine, Luc Blassel, 2020, Bioinformatics.

Selected papers from the First International Conference on Computational Biology, Biology, Informatics, and Mathematics

Olivier Gascuel, Marie-France Sagot, 2000 .

A ring architecture strategy for BIST test pattern generation

Patrick Girard, Christian Landrault, Olivier Gascuel, 1998, Proceedings Seventh Asian Test Symposium (ATS'98) (Cat. No.98TB100259).

Phylogenetic reconstruction: models, methods, and algorithms

Olivier Gascuel, 2014 .

Distribution-free performance bounds with the resubstitution error estimate

Olivier Gascuel, Gilles Caraux, O. Gascuel, 1992, Pattern Recognit. Lett..

Practical Use of PhyML

Olivier Gascuel, 2008 .

Empirical profile mixture models for phylogenetic reconstruction

Olivier Gascuel, Si Quang Le, Nicolas Lartillot, 2008, Bioinform..

Hidden Markov Models with Patterns to Learn Boolean Vector Sequences and Application to the Built-In Self-Test for Integrated Circuits

Olivier Gascuel, Laurent Bréhélin, Gilles Caraux, 2001, IEEE Trans. Pattern Anal. Mach. Intell..

An exact and polynomial distance-based algorithm to reconstruct single copy tandem duplication trees

Olivier Gascuel, Olivier Elemento, O. Elemento, 2003, J. Discrete Algorithms.

Modelling the Variability of Evolutionary Processes

Olivier Gascuel, Stéphane Guindon, O. Gascuel, 2007 .

A Ring Architecture Strategy for BIST Test Pattern Generation

Patrick Girard, Christian Landrault, Olivier Gascuel, 2003, J. Electron. Test..

Learning from Recursive, Tree Structured Examples

Olivier Gascuel, Colin de la Higuera, Marie-Catherine Daniel-Vatonne, 1994, ECML.

Topological Rearrangements and Local Search Method for Tandem Duplication Trees

Olivier Gascuel, Denis Bertrand, 2004, WABI.

Fast and accurate branch lengths estimation for phylogenomic trees

Olivier Gascuel, Céline Scornavacca, Fabio Pardi, 2015, BMC Bioinformatics.

Discrimination of yeast genes involved in methionine and phosphate metabolism on the basis of upstream motifs

Olivier Gascuel, Jacques van Helden, Didier Gonze, 2005, Bioinform..

Inferring evolutionary trees with strong combinatorial evidence

Olivier Gascuel, Vincent Berry, O. Gascuel, 1997, Theor. Comput. Sci..

Topological rearrangements and local search method for tandem duplication trees

Olivier Gascuel, Denis Bertrand, 2005, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

PastView: a user-friendly interface to explore evolutionary scenarios

Olivier Gascuel, François Chevenet, Guillaume Castel, 2019, bioRxiv.

Simulating trajectories and phylogenies from population dynamics models with TiPS

Olivier Gascuel, Samuel Alizon, Marc Choisy, 2020 .

Statistical Significance in Inductive Learning

Olivier Gascuel, Gilles Caraux, O. Gascuel, 1992, ECAI.

Phylogeny.fr: robust phylogenetic analysis for the non-specialist

Jean-Michel Claverie, Olivier Gascuel, Vincent Lefort, 2008, Nucleic Acids Res..

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics): Preface

Gad M. Landau, Steven Skiena, Roded Sharan, 2006, WABI 2012.

SDL, a stochastic algorithm for learning decision lists with limited complexity

Olivier Gascuel, Fernando de Carvalho Gomes, 2005, Annals of Mathematics and Artificial Intelligence.

Implementation and assessment of an hypertension expert system

Patrice Degoulet, Olivier Gascuel, J F Boisvieux, 1987 .

Reconstructing the duplication history of tandemly repeated sequences

Olivier Gascuel, Denis Bertrand, Olivier Elemento, 2007, Mathematics of Evolution and Phylogeny.

Mathematics of Evolution and Phylogeny

Olivier Gascuel, O. Gascuel, 2005 .

The minimum evolution distance-based approach of phylogenetic inference

Olivier Gascuel, Richard Desper, O. Gascuel, 2007, Mathematics of Evolution and Phylogeny.

Hidden Markov Models with Patterns and Their Application to Integrated Circuit Testing

Olivier Gascuel, Laurent Bréhélin, Gilles Caraux, 2000, ECML.

Consistency of Topological Moves Based on the Balanced Minimum Evolution Principle of Phylogenetic Inference

Olivier Gascuel, Katharina T. Huber, Vincent Moulton, 2009, IEEE/ACM Transactions on Computational Biology & Bioinformatics.

Improving pairwise comparison of protein sequences with domain co-occurrence

Olivier Gascuel, Laurent Bréhélin, Christophe Menichelli, 2018, PLoS Comput. Biol..

Rapidly Computing the Phylogenetic Transfer Index

Olivier Gascuel, Krister M. Swenson, Jakub Truszkowski, 2019, bioRxiv.

Fast dating using least squares

Olivier Gascuel, 2015 .

Inferring epidemiological parameters from phylogenies using regression-ABC: A comparative study

Olivier Gascuel, Samuel Alizon, Emma Saulnier, 2017, PLoS Comput. Biol..

A simple method to predict protein-binding from aligned sequences - application to MHC superfamily and ß2-microglobulin

Olivier Gascuel, Marie-Paule Lefranc, Elodie Duprat, 2006, Bioinform..

Proceedings of the First International Workshop on Algorithms in Bioinformatics

Olivier Gascuel, Bernard M. E. Moret, O. Gascuel, 2001 .

Incorporating alignment uncertainty into Felsenstein’s phylogenetic bootstrap to improve its reliability

Olivier Gascuel, Paolo Di Tommaso, Jia-Ming Chang, 2019, Bioinform..

The Behavior of Admixed Populations in Neighbor-Joining Inference of Population Trees

Olivier Gascuel, Noah A. Rosenberg, Lewi Stone, 2012, Pacific Symposium on Biocomputing.

Data Analysis Using a Learning Program, a Case Study: An Application of PLAGE to a Biological Sequence Analysis

Olivier Gascuel, Antoine Danchin, 1988, ECAI.

Commentaires sur une histoire de discrétisation

Olivier Gascuel, 1993, Monde des Util. Anal. Données.

Enhancing Protein Domain Detection Using Domain Co-occurrence and Domain Exclusion

Olivier Gascuel, Sadok Ben Yahia, Amel Ghouila, 2012, 2012 23rd International Workshop on Database and Expert Systems Applications.

Twelve Numerical, Symbolic and Hybrid Supervised Classification Methods

Richard Nock, Bernadette Bouchon-Meunier, Christophe Marsala, 1998, Int. J. Pattern Recognit. Artif. Intell..

Descriptions structurelles. Discrimination et apprentissage sur ces descriptions

Olivier Gascuel, O. Gascuel, 1985 .

Phylogeny Reconstruction Methods

Olivier Gascuel, 2013 .

A Fast Likelihood Method to Reconstruct and Visualize Ancestral Scenarios

Olivier Gascuel, Wataru Iwasaki, Sohta A. Ishikawa, 2018, bioRxiv.

TCS: a web server for multiple sequence alignment evaluation and phylogenetic reconstruction

Olivier Gascuel, Vincent Lefort, Cédric Notredame, 2015, Nucleic Acids Res..

Computational Biology

J. van Leeuwen, Jan van Leeuwen, Olivier Gascuel, 2001, Lecture Notes in Computer Science.

On Learning Decision Committees

Richard Nock, Olivier Gascuel, 1995, ICML.

Advances and Limitations of Maximum Likelihood Phylogenetics

Olivier Gascuel, 2007 .

LSD (Least-Squares Dating) Software: Fast dating using least-squares criteria and algorithms (C++ code)

Olivier Gascuel, Matthieu Jung, Samantha J. Lycett, 2015 .

Algorithms in Bioinformatics

Olivier Gascuel, Bernard M. E. Moret, O. Gascuel, 2001, Lecture Notes in Computer Science.

A tutorial on the balanced minimum evolution problem

Olivier Gascuel, Raffaele Pesenti, Daniele Catanzaro, 2021, Eur. J. Oper. Res..

Using machine learning and big data to explore the drug resistance landscape in HIV

Olivier Gascuel, Luc Blassel, Stéphane Hué, 2021, PLoS Comput. Biol..

Identification of novel peptide hormones in the human proteome by hidden Markov model screening.

Olivier Gascuel, Ewan Birney, Cornelius Gross, 2007, Genome research.

Reconstructing evolution : new mathematical and computational advances

Olivier Gascuel, Mike Steel, O. Gascuel, 2007 .

Inferring ancestral sequences in taxon-rich phylogenies.

Olivier Gascuel, Mike Steel, O. Gascuel, 2010, Mathematical biosciences.

Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable

Christina Boucher, Olivier Gascuel, Guy Baele, 2020, Proceedings of the National Academy of Sciences.

Combinatorics of distance-based tree inference

Olivier Gascuel, Fabio Pardi, O. Gascuel, 2012, Proceedings of the National Academy of Sciences.

The Origin and Evolutionary History of HIV-1 Subtype C in Senegal

Olivier Gascuel, Matthieu Jung, Martine Peeters, 2012, PloS one.

Robustness of Phylogenetic Inference Based on Minimum Evolution

Olivier Gascuel, Sylvain Guillemot, Fabio Pardi, 2010, Bulletin of mathematical biology.

Distribution and asymptotic behavior of the phylogenetic transfer distance

Olivier Gascuel, Jakub Truszkowski, Frédéric Lemoine, 2018 .

SDM: a fast distance-based approach for (super) tree building in phylogenomics.

Olivier Gascuel, Vincent Berry, Alexis Criscuolo, 2006, Systematic biology.

Genomics, biogeography, and the diversification of placental mammals

Olivier Gascuel, Derek E. Wildman, Vincent Lefort, 2007, Proceedings of the National Academy of Sciences.

Modeling protein evolution with several amino acid replacement matrices depending on site rates.

Olivier Gascuel, Si Quang Le, Cuong Cao Dang, 2012, Molecular biology and evolution.

NGPhylogeny.fr: new generation phylogenetic services for non-specialists

Olivier Gascuel, Frédéric Lemoine, Vincent Lefort, 2019, Nucleic Acids Res..

Data Model and Classification by Trees

Olivier Gascuel, O. Gascuel, 1999 .

Fast Dating Using Least-Squares Criteria and Algorithms

Olivier Gascuel, Matthieu Jung, Thu-Hien To, 2015, Systematic biology.

Mathematical and computational evolutionary biology (2013).

Olivier Gascuel, Tanja Stadler, O. Gascuel, 2015, Systematic biology.

Machine learning of strategic knowledge in organic synthesis from reaction databases

Olivier Gascuel, Jean-Charles Régin, Claude Laurenço, 2008 .

Concomitant emergence of the antisense protein gene of HIV-1 and of the pandemic

Olivier Gascuel, O. Gascuel, E. Cassan, 2016, Proceedings of the National Academy of Sciences.

Generalized Bootstrap Supports for Phylogenetic Analyses of Protein Sequences Incorporating Alignment Uncertainty

Olivier Gascuel, Paolo Di Tommaso, Maria Chatzou, 2018, Systematic biology.

A Fast and Specific Alignment Method for Minisatellite Maps

Olivier Gascuel, François Nicolas, Eric Rivals, 2006 .

Sexually-Transmitted/Founder HIV-1 Cannot Be Directly Predicted from Plasma or PBMC-Derived Viral Quasispecies in the Transmitting Partner

Olivier Gascuel, Laurence Meyer, Sylvie Abel, 2013, PloS one.

Computational discovery of regulatory elements in a continuous expression space

Olivier Gascuel, Vincent Lefort, Laurent Bréhélin, 2012, Genome Biology.

On the Interpretation of Bootstrap Trees: Appropriate Threshold of Clade Selection and Induced Gain

Olivier Gascuel, Vincent Berry, O. Gascuel, 1996 .

Choosing the tree which actually best explains the data: another look at the bootstrap in phylogenetic reconstruction

Olivier Gascuel, G. Caraux, O. Gascuel, 2000 .

EuPathDomains: the divergent domain database for eukaryotic pathogens.

Olivier Gascuel, Amel Ghouila, Laurent Bréhélin, 2011, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

Bamako 2009 conference on the bioinformatics of infectious diseases.

Olivier Gascuel, Manuel Corpas, Nicola Mulder, 2011, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

FLU, an amino acid substitution model for influenza proteins

Olivier Gascuel, Cuong Cao Dang, O. Gascuel, 2010, BMC Evolutionary Biology.

A Fast and Specific Alignment Method for Minisatellite Maps

Olivier Gascuel, François Nicolas, Eric Rivals, 2006, Evolutionary bioinformatics online.

Assessing functional annotation transfers with inter-species conserved coexpression: application to Plasmodium falciparum

Olivier Gascuel, Laurent Bréhélin, O. Gascuel, 2010, BMC Genomics.

The Role of Phylogenetics as a Tool to Predict the Spread of Resistance

Olivier Gascuel, Anna Zhukova, Deenan Pillay, 2017, The Journal of infectious diseases.

Predicting the ancestral character changes in a tree is typically easier than predicting the root state.

Olivier Gascuel, Mike Steel, O. Gascuel, 2013, Systematic biology.

A Plasmodium falciparum FcB1-schizont-EST collection providing clues to schizont specific gene structure and polymorphism

Olivier Gascuel, Laurent Bréhélin, Patrick Wincker, 2009, BMC Genomics.