UMR CNRS 5558 Laboratoire de Biométrie et Biologie Évolutive

Bolivar P, Guéguen L, Duret L, Ellegren H, Mugal CF (2019)
GC-biased gene conversion conceals the prediction of the nearly neutral theory in avian genomes, Genome biology, vol. 20 pp.5-5.

de Vienne DM (2019)
Tanglegrams Are Misleading for Visual Evaluation of Tree Congruence, Molecular biology and evolution, vol. 36 pp.174-176.

Reiss D, Mialdea G, Miele V, de Vienne DM, Peccoud J, Gilbert C, Duret L, Charlat S (2019)
Global survey of mobile DNA horizontal transfer in arthropods reveals Lepidoptera as a prime hotspot, PLoS genetics, vol. 15 pp.e1007965-e1007965.

Anselmetti Y, Duchemin W, Tannier E, Chauve C, Bérard S (2018)
Phylogenetic signal from rearrangements in 18 Anopheles species by joint scaffolding extant and ancestral genomes, BMC Genomics, vol. 19 pp.96-96.

Anselmetti Y, Luhmann N, Bérard S, Tannier E, Chauve C (2018)
Comparative Methods for Reconstructing Ancient Genome Organization
in: Methods in Molecular Biology, , pp.343-362.

Branco S, Carpentier F, Rodriguez de la Vega RC, Badouin H, Snirc A, Le Prieur S, Coelho M A, de Vienne DM, Hartmann FE, Begerow D, Hood ME, Giraud T (2018)
Multiple convergent supergene evolution events in mating-type chromosomes, Nature communications, vol. 9 pp.2000-2000.

Davin AA, Tannier E, Williams TA, Boussau B, Daubin V, Szollosi GJ (2018)
Gene transfers can date the tree of life, Nature ecology & evolution, vol. 2 pp.904-909.

Duchemin W, Gence G, Arigon Chifolleau AM, Arvestad L, Bansal M S, Berry V, Boussau B, Chevenet F, Comte N, Davin AA, Dessimoz C, Dylus D, Hasic D, Mallo D, Planel R, Posada D, Scornavacca C, Szollosi G, Zhang L, Tannier E, Daubin V (2018)
RecPhyloXML - a format for reconciled gene trees, Bioinformatics, vol. 34 pp.3646-3652.

Dumas JG, Roch JA, Tannier E, Varrette S (2018) Théorie des codes, , 2018

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Filippi-Codaccioni O, Beugin MP, de Vienne DM, Portanier E, Fouchet D, Kaerle C, Muselet L, Queney G, Petit EJ, Régis C, Pons JB, Pontier D (2018)
Coexistence de deux espèces cryptiques de chauves-souris en Guyane française : apprentissages à partir de la génétique de l’acoustique et de l’écologie, Plume de naturalistes, vol. 2 pp.169-190.

Filippi-Codaccioni O, Beugin MP, de Vienne DM, Portanier E, Fouchet D, Kaerle C, Muselet L, Queney G, Petit EJ, Régis C, Pons JB, Pontier D (2018)
Coexistence of two sympatric cryptic bat species in French Guiana: insights from genetic acoustic and ecological data, BMC evolutionary biology, vol. 18 pp.175-175.

Guéguen L, Duret L (2018)
Unbiased estimate of synonymous and non-synonymous substitution rates with non-stationary base composition, Molecular biology and evolution, vol. 35 pp.734-742.

Rey C, Guéguen L, Semon M, Boussau B (2018)
Accurate detection of convergent amino-acid evolution with PCOC, Molecular biology and evolution, vol. 35 pp.2296-2306.

Saclier N, Francois CM, Konecny-Dupre L, Lartillot N, Guéguen L, Duret L, Malard F, Douady CJ, Lefebure T (2018)
Life History Traits Impact the Nuclear Rate of Substitution but Not the Mitochondrial Rate in Isopods, Molecular biology and evolution, vol. 35 pp.2900-2912.

Simao MC, Haudry A, Granzotto A, de Setta N, Carareto CMA (2018)
Helena and BS: Two Travellers between the Genera Drosophila and Zaprionus, Genome biology and evolution, vol. 10 pp.2671-2685.

Boutin H, de Vienne DM (2017)
Sonification of phylogenetic trees: listening to evolution, Journées d`Informatique Musicale 2017, pp.1-4.

Chauve C, Rafiey A, Davin AA, Scornavacca C, Veber P, Boussau B, Szollosi G, Daubin V, Tannier E (2017)
MaxTiC: Fast ranking of a phylogenetic tree by Maximum Time Consistency with lateral gene transfers, Peer Community In Evolutionary Biology, vol. pp.1-18.

Duchemin W, Anselmetti Y, Patterson M, Ponty Y, Berard S, Chauve C, Scornavacca C, Daubin V, Tannier E (2017)
DeCoSTAR: Reconstructing the Ancestral Organization of Genes or Genomes Using Reconciled Phylogenies, Genome Biology and Evolution, vol. 9 pp.1312-1319.

Fertin G, Jean G, Tannier E (2017)
Algorithms for computing the double cut and join distance on both gene order and intergenic sizes, Algorithms for Molecular Biology, vol. 12 pp.16-16.

Jacox E, Weller M, Tannier E, Scornavacca C (2017)
Resolution and reconciliation of non-binary gene trees with transfers duplications and losses, Bioinformatics, vol. 33 pp.980-987.

Lefebure T, Morvan C, Malard F, Francois C, Konecny-Dupre L, Guéguen L, Weiss-Gayet M, Seguin-Orlando A, Ermini L, Sarkissian C, Charrier N P, Eme D, Mermillod-Blondin F, Duret L, Vieira C, Orlando L, Douady CJ (2017)
Less effective selection leads to larger genomes, Genome research, vol. 27 pp.1016-1028.

Pantalacci S, Guéguen L, Petit C, Lambert A, Peterkova R, Sémon M (2017)
Transcriptomic signatures shaped by cell proportions shed light on comparative developmental biology, Genome biology, vol. 18 pp.29-29.

Philippe H, de Vienne DM, Ranwez V, Roure B, Baurain D, Delsuc F (2017)
Pitfalls in supermatrix phylogenomics, European Journal of Taxonomy, vol. 283 pp.1-25.

Siberchicot A, Bessy A, Guéguen L, Marais GAB (2017)
MareyMap Online: A User-Friendly Web Application and Database Service for Estimating Recombination Rates Using Physical and Genetic Maps, Genome biology and evolution, vol. 9 pp.2506-2509.

Venner S, Miele V, Terzian C, Biemont C, Daubin V, Feschotte C, Pontier D (2017)
Ecological networks to unravel the routes to horizontal transposon transfers, PLoS Biology, vol. 15 pp.e2001536-e2001536.

Williams TA, Szollosi GJ, Spang A, Foster PG, Heaps SE, Boussau B, Ettema TJG, Embley MT (2017)
Integrative modeling of gene and genome evolution roots the archaeal tree of life, Proceedings of the National Academy of Sciences of the United States of America, vol. 114 pp.E4602-E4602.

Biller P, Guéguen L, Knibbe C, Tannier E (2016)
Breaking Good: Accounting for Fragility of Genomic Regions in Rearrangement Distance Estimation, Genome Biology and Evolution, vol. 8 pp.1427-39.

Biller P, Knibbe C, Beslon G, Tannier E (2016)
Comparative Genomics on Artifical Life, Computability in Europe, pp.1-10.

Bulteau L, Fertin G, Tannier E (2016)
Genome rearrangements with indels in intergenes restrict the scenario space, BMC Bioinformatics, vol. 17 pp.225-231.

de Vienne DM (2016)
Lifemap: Exploring the Entire Tree of Life, PLoS Biology, vol. 14 pp.e2001624-e2001624.

Fertin G, Jean G, Tannier E (2016)
Genome Rearrangements on Both Gene Order and Intergenic Regions, WABI, , vol. 9838 pp.162-173.

Grégoire L, Haudry A, Lerat E (2016)
The transposable element environment of human genes is associated with histone and expression changes in cancer, BMC Genomics, vol. 17 pp.588-588.

Groussin M, Boussau B, Szollosi G, Eme L, Gouy M, Brochier-Armanet C, Daubin V (2016)
Gene Acquisitions from Bacteria at the Origins of Major Archaeal Clades Are Vastly Overestimated, Molecular Biology and Evolution, vol. 33 pp.305-10.

Groussin M, Daubin V, Gouy M, Tannier E (2016)
Ancestral Reconstruction: Theory and Practice
in: The Encyclopedia of Evolutionary Biology, , pp.70-77.

Hohna S, Landis MJ, Heath T A, Boussau B, Lartillot N, Moore BR, Huelsenbeck JP, Ronquist F (2016)
RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language, Systematic biology, vol. 65 pp.726-36.

Jauffrit F, Penel S, Delmotte S, Rey C, De Vienne DM, Gouy M, Charrier JP, Flandrois JP, Brochier-Armanet C (2016)
RiboDB Database: A Comprehensive Resource for Prokaryotic Systematics, Molecular Biology and Evolution, vol. 33 pp.2170-2172.

Lays C, Tannier E, Henry T (2016)
Francisella IglG protein and the DUF4280 proteins: PAAR-like proteins in non-canonical Type VI secretion systems?, Microbial Cell, vol. 3 pp.445-447.

Noutahi E, Semeria M, Lafond M, Seguin J, Boussau B, Guéguen L, El-Mabrouk N, Tannier E (2016)
Efficient Gene Tree Correction Guided by Genome Evolution, PLoS One, vol. 11 pp.e0159559-e0159559.

Pouyet F, Bailly-Bechet M, Mouchiroud D, Guéguen L (2016)
SENCA: A Multilayered Codon Model to Study the Origins and Dynamics of Codon Usage, Genome Biology and Evolution, vol. 8 pp.2427-41.

Sessegolo C, Burlet N, Haudry A (2016)
Strong phylogenetic inertia on genome size and transposable element content among 26 species of flies, Biology Letters, vol. 12 pp.20160407-20160407.

Anselmetti Y, Berry V, Chauve C, Chateau A, Tannier E, Berard S (2015)
Ancestral gene synteny reconstruction improves extant species scaffolding, BMC Genomics, vol. 16 Suppl 10 pp.S11-S11.

Biller P, Guéguen L, Tannier E (2015)
Moments of genome evolution by Double Cut-and-Join, BMC Bioinformatics, vol. 16 Suppl 14 pp.S7-S7.

Duchemin W, Daubin V, Tannier E (2015)
Reconstruction of an ancestral Yersinia pestis genome and comparison with an ancient sequence, BMC Genomics, vol. 16 Suppl 10 pp.S9-S9.

Dumas JG, Roch JL, Tannier E, Varrette S (2015) Foundations of coding. Compression Encryption Error Correction, Wiley, 2015

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Lassalle F, Perian S, Bataillon T, Nesme X, Duret L, Daubin V (2015)
GC-Content Evolution in Bacterial Genomes: The Biased Gene Conversion Hypothesis Expands, PLoS Genetics, vol. 11 pp.e1004941-e1004941.

Murat F, Zhang R, Guizard S, Gavranovic H, Flores R, Steinbach D, Quesneville H, Tannier E, Salse J (2015)
Karyotype and gene order evolution from reconstructed extinct ancestors highlight contrasts in genome plasticity of modern rosid crops, Genome Biology and Evolution, vol. 7 pp.735-49.

Semeria M, Tannier E, Guéguen L (2015)
Probabilistic modeling of the evolution of gene synteny within reconciled phylogenies, BMC Bioinformatics, vol. 16 Suppl 14 pp.S5-S5.

Szollosi GJ, Arellano Davin A, Tannier E, Daubin V, Boussau B (2015)
Genome-scale phylogenetic analysis finds extensive gene transfer among fungi, Philosophical Transactions of The Royal Society B-Biological Sciences, vol. 370 pp.201403335-201403335.

Szollosi G J, Tannier E, Daubin V, Boussau B (2015)
The Inference of Gene Trees with Species Trees, Systematic biology, vol. 64 pp.e42-e62.

Tannier E (2015)
Sorting Signed Permutations by Reversal (Reversal Sequence)
in: Encyclopedia of Algorithms, Springer Science+Business Media New York 2015, pp.1-5.

Aguileta G, de Vienne D M, Ross O N, Hood M E, Giraud T, Petit E, Gabaldon T (2014)
High variability of mitochondrial gene order among fungi, Genome Biology and Evolution, vol. 6 pp.451-465.

Bailly-Bechet M, Haudry A, Lerat E (2014)
“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files, Mobile DNA, vol. 5 pp.13-13.

Batut B, Knibbe C, Marais G, Daubin V (2014)
Reductive genome evolution at both ends of the bacterial population size spectrum, Nature reviews Microbiology, vol. 12 pp.841-50.

Boussau B, Walton Z, Delgado JA, Collantes F, Beani L, Stewart IJ, Cameron SA, Whitfield JB, Johnston JS, Holland P, Bachtrog D, Kathirithamby J, Huelsenbeck JP (2014)
Strepsiptera Phylogenomics and the Long Branch Attraction Problem, PLoS one, vol. 9 pp.e107709-e107709.

Fontanillas E, Hood M E, Badouin H, Petit E, Barbe V, Gouzy J, de Vienne DM, Aguileta G, Poulain J, Wincker P, Chen Z, Toh S S, Cuomo C A, Perlin M H, Gladieux P, Giraud T (2014)
Degeneration of the Nonrecombining Regions in the Mating-Type Chromosomes of the Anther-Smut Fungi, Molecular biology and evolution, vol. 32 pp.928-43.

Gladieux P, Ropars J, Badouin H, Branca A, Aguileta G, de Vienne DM, Rodriguez de la Vega RC, Branco S, Giraud T (2014)
Fungal evolutionary genomics provides insight into the mechanisms of adaptive divergence in eukaryotes, Molecular Ecology, vol. 23 pp.753-773.

Gouyon PH, de Vienne DM, Giraud T (2014)
Sex and Evolution
in: Handbook of Evolutionary Thinking in the Sciences, Springer, pp.499-507.

Höhna S, Heath TA, Boussau B (2014)
Probabilistic Graphical Model Representation in Phylogenetics, Systematic biology, vol. 63 pp.753-771.

Jarvis DE, Mirarab S, Aberer AJ, Houde P, Cai L, Ho S, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, Da Fonseca RR, Li J, Zhang F, Li H, Zhou L, Narula N, Liu L, Ganapathy G, Boussau B (2014)
Whole-genome analyses resolve early branches in the tree of life of modern birds, Science, vol. 346 pp.1230-1331.

Miklos I, Kiss SZ, Tannier E (2014)
Counting and sampling SCJ small parsimony solutions, Theoretical Computer Science, vol. 552 pp.83-98.

Mirarab S, Bayzid M S, Boussau B, Warnow T (2014)
Statistical binning enables an accurate coalescent-based estimation of the avian tree, Science, vol. 346 pp.1250463-1250463.

Ramirez-Bahena MH, Vial L, Lassalle F, Diel B, Chapulliot D, Daubin V, Nesme X, Muller D (2014)
, Molecular phylogenetics and evolution, vol. 73 pp.202-7.

Ramulu H G, Groussin M, Talla E, Planel R, Daubin V, Brochier-Armanet C (2014)
Ribosomal proteins: Toward a next generation standard for prokaryotic systematics?, Molecular phylogenetics and evolution, vol. 75C pp.103-117.

Ropars J, Aguileta G, de Vienne DM, Giraud T (2014)
Massive gene swamping among cheese-making Penicillium fungi, Microbial cell, vol. 1 pp.107-109.

Sen A, Daubin V, Abrouk D, Gifford I, Berry A M, Normand P (2014)
Phylogeny of the class Actinobacteria revisited in the light of complete genomes. The orders `Frankiales` and Micrococcales should be split into coherent entities: proposal of Frankiales ord. nov. Geodermatophilales ord. nov. Acidothermales ord. nov. and Nakamurellales ord. nov, International journal of systematic and evolutionary microbiology, vol. 64 pp.3821-32.

Sjöstrand J, Tofigh A, Daubin V, Arvestad L, Sennblad B, Lagersen J (2014)
A Bayesian Method for Analyzing Lateral Gene Transfer, Systematic Biology, vol. 63 pp.409-420.

Weber CC, Boussau B, Romiguier J, Jarvis ED, Ellegren H (2014)
Evidence for GC-biased gene conversion as a driver of between-lineage differences in avian base composition, Genome Biology, vol. 15 pp.549-549.

Williamson R J, Josephs E B, Platts A E, Hazzouri K M, Haudry A, Blanchette M, Wright S I (2014)
Evidence for Widespread Positive and Negative Selection in Coding and Conserved Noncoding Regions of Capsella grandiflora, PLoS genetics, vol. 10 pp.e1004622-e1004622.

Bigot T, Daubin V, Lassalle F, Perrière G (2013)
TPMS: a set of utilities for querying collections of gene trees, BMC Bioinformatics, vol. 14 pp.109-109.

Bourquard T, de Vienne D M, Azé J (2013)
Identification de complexes protéine-protéine par combinaison de classifieurs. Application à Escherichia Coli, EGC 2013 13e Conférence Francophone sur l`Extraction et la Gestion des Connaissances, pp.1-12.

Boussau B, Szollosi GJ, Duret L, Gouy M, Tannier E, Daubin V (2013)
Genome-scale coestimation of species and gene trees, Genome Research, vol. 23 pp.323-30.

Chauve C, El-Mabrouk N, Guéguen L, Semeria M, Tannier E (2013)
Duplication Rearrangement and Reconciliation: A Follow-Up 13 Years Later
in: Models and Algorithmes for Genome Evolution, Computentional BIology, pp.47-62.

Chauve C, El-Mabrouk N, Tannier E (2013) Models and Algorithms for Genome Evolution, Springer, 2013

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Daubin V, Penel S, Tannier E (2013)
L`ADN mémoire numérique du vivant, Pour la science, vol. 433 pp.103-108.

de Vienne DM, Giraud T, Gouyon PH (2013)
Lineage Selection and the Maintenance of Sex, PLoS one, vol. 8 pp.e66906-e66906.

de Vienne D M, Refregier G, Lopez-Villavicencio M, Tellier A, Hood M E, Giraud T (2013)
Cospeciation vs host-shift speciation: methods for testing evidence from natural associations and relation to coevolution, New phytologist, vol. 198 pp.347-385.

Dumas JG, Roch JL, Tannier E, Varrette S (2013) Théorie des codes, Dunod, 2013

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Groussin M, Boussau B, Charles S, Blanquart S, Gouy M (2013)
The molecular signal for the adaptation to cold temperature during early life on Earth, Biology Letters, vol. 9 pp.20130608-20130608.

Groussin M, Boussau B, Gouy M (2013)
A branch-heterogeneous model of protein evolution for efficient inference of ancestral sequences, Systematic biology, vol. 62 pp.523-38.

Guéguen L, Gaillard S, Boussau B, Gouy M, Groussin M, Rochette N, Bigot T, Fournier D, Pouyet F, Cahais V, Bernard A, Scornavacca C, Nabholz B, Haudry A, Dachary L, Galtier N, Belkhir K, Dutheil J Y (2013)
Bio++: Efficient Extensible Libraries and Tools for Computational Molecular Evolution, Molecular Biology and Evolution, vol. 30 pp.1745-1750.

Haudry A, Platts AE, Vello E, Hoen DR, Leclercq M, Williamson RJ, Forczek E, Joly-Lopez Z, Steffen JG, Hazzouri KM, Dewar K, Stinchcombe JR, Schoen DJ, Wang X, Schmutz J, Town CD, Edger PP, Pires JC, Schumaker KS, Jarvis DE, Mandakova T, Lysak MA, van den Bergh E, Schranz ME, Harrison PM, Moses AM, Bureau TE, Wright SI, Blanchette M (2013)
An atlas of over 90 000 conserved noncoding sequences provides insight into crucifer regulatory regions, Nature Genetics, vol. 45 pp.891-U228.

Kafer J, Talianova M, Bigot T, Michu E, Guéguen L, Widmer A, Zluvova J, Glemin S, Marais GA (2013)
Patterns of molecular evolution in dioecious and non-dioecious Silene, Journal of Evolutionary Biology, vol. 26 pp.335-46.

Lafond M, Semeria M, Swenson KM, Tannier E, El-Mabrouk N (2013)
Gene tree correction guided by orthology, BMC Bioinformatics, vol. 14 pp.S5-S5.

Patterson M, Szollosi GJ, Daubin V, Tannier E (2013)
Lateral gene transfer rearrangement reconciliation, BMC Bioinformatics, vol. 14 pp.S4-S4.

Pouyet F, Jacquemetton J, Bailly-Bechet M, Guéguen L (2013)
Codon usage in E. coli: an evolutionary approach, JOBIM 2013, pp.2427-41.

Rajaraman A, Tannier E, Chauve C (2013)
FPSAC: fast phylogenetic scaffolding of ancient contigs, Bioinformatics, vol. 29 pp.2987-2994.

Rajaraman A, Tannier E, Chauve C (2013)
The genome of the medieval Black Death agent (extended abstract), JOBIM 2013, pp.47-54.

Schumer M, Cui R, Boussau B, Walter R, Rosenthal G, Andolfatto P (2013)
An evaluation of the hybrid speciation hypothesis for Xiphophorus clemenciae based on whole genome sequences, Evolution, vol. 67 pp.1155-1168.

Szollosi GJ, Rosikiewicz W, Boussau B, Tannier E, Daubin V (2013)
Efficient exploration of the space of reconciled gene trees, Systematic biology, vol. 62 pp.901-12.

Szollosi GJ, Tannier E, Lartillot N, Daubin V (2013)
Lateral Gene Transfer from the Dead, Systematic Biology, vol. 62 pp.386-397.

Thakur S, Normand P, Daubin V, Tisa L S, Sen A (2013)
Contrasted evolutionary constraints on secreted and non-secreted proteomes of selected Actinobacteria, BMC Genomics, vol. 14 pp.474-474.

Abby S S, Tannier E, Gouy M, Daubin V (2012)
Lateral gene transfer as a support for the tree of life, Proceedings of the National Academy of Sciences of The United States of America, vol. 109 pp.4962-4967.

Bérard J, Guéguen L (2012)
Accurate Estimation of Substitution Rates with Neighbor-Dependent Modelsina Phylogenetic Context, Systematic Biology, vol. 61 pp.510-521.

Bérard S, Gallien C, Boussau B, Szollosi GJ, Daubin V, Tannier E (2012)
Evolution of gene neighborhoods within reconciled phylogenies, Bioinformatics, vol. 28 pp.I382-I388.

Bernt M, Chao K-M, Kao J-W, Middendorf M, Tannier E (2012)
Preserving Inversion Phylogeny Reconstruction, WABI 2012, Springer-Verlag, vol. 7534 pp.1-13.

Boussau B, Gouy M (2012)
What genomes have to say about the evolution of the Earth, Gondwana Research, vol. 21 pp.483-494.

Daubin V (2012)
HDR - Phylogénie Moléculaire 2.0 .

Daubin V, Abby S (2012)
Les transferts horizontaux de gènes et l’arbre de la vie, M S-Médecine Sciences, vol. 28 pp.695-698.

de Vienne D M, Azé J (2012)
Efficient Prediction of Co-Complexed Proteins Based on Coevolution, PLoS one, vol. 7 pp.e48728-e48728.

de Vienne D M, Ollier S, Aguileta G (2012)
Phylo-MCOA: a fast and efficient method to detect outlier genes and species in phylogenomics using multiple co-inertia analysis, Molecular biology and evolution, vol. 29 pp.1587-1598.

Dutheil J Y, Galtier N, Romiguier J, Douzery E J P, Ranwez V, Boussau B (2012)
Efficient Selection of Branch-Specific Models of Sequence Evolution, Molecular Biology and Evolution, vol. 29 pp.1861-1874.

Fong JJ, Brown JM, Fujita MK, Boussau B (2012)
A Phylogenomic Approach to Vertebrate Phylogeny Supports a Turtle-Archosaur Affinity and a Possible Paraphyletic Lissamphibia, PLoS one, vol. 7 pp.e48990-e48990.

Haudry A, Zha H G, Stift M, Mable B K (2012)
Disentangling the effects of breakdown of self-incompatibility and transition to selfing in North-American Arabidopsis lyrata, Molecular Ecology, vol. 21 pp.1130-1142.

Jones BR, Rajaraman A, Tannier E, Chauve C (2012)
ANGES: reconstructing ANcestral GEnomeS maps, Bioinformatics, vol. 28 pp.2388-90.

Manuch J, Patterson M, Wittler R, Chauve C, Tannier E (2012)
Linearization of ancestral multichromosomal genomes, BMC Bioinformatics, vol. 13 pp.11-11.

Miele V, Penel S, Daubin V, Picard F, Kahn D, Duret L (2012)
High-quality sequence clustering guided by network topology and multiple alignment likelihood, Bioinformatics, vol. 28 pp.1078-1085.

Miklos I, Tannier E (2012)
Approximating the number of Double Cut-and-Join scenarios, Theoretical Computer Science, vol. 439 pp.30-40.

Petit E, Giraud T, de Vienne D M, Coelho M A, Aguileta G, Amselem J, Kreplak J, Poulain J, Gavory F, Wincker P, Young S K, Cuomo C, Perlin M H, Hood M E (2012)
Linkage to the mating-type locus across the genus Microbotryum: insights into nonrecombining chromosomes, Evolution, vol. 66 pp.3519-3533.

Romiguier J, Figuet E, Galtier N, Douzery E J P, Boussau B, Dutheil J Y, Ranwez V (2012)
Fast and Robust Characterization of Time Heterogeneous Sequence Evolutionary Processes Using Substitution Mapping, PLos One, vol. 7 pp.e33852-e33852.

Szollosi GJ, Boussau B, Abby SS, Tannier E, Daubin V (2012)
Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations, Proceedings of the National Academy of Sciences of The United States of America, vol. 109 pp.17513-17518.

Szollosi GJ, Daubin V (2012)
Modeling Gene Family Evolution and Reconciling Phylogenetic Discord, Methods in Molecular Biology, vol. 856 pp.29-51.

Bigot T, Daubin V, Perrière G (2011)
Tpms: a Tree Pattern-matching Utility for Querying Gene Trees Collections, Journées Ouvertes Biologie Informatique Mathématiques (JOBIM), pp.111-112.

Boussau B, Brown J M, Fujita M K (2011)
Nonadaptive evolution of mitochondrial genome size, Evolution, vol. 65 pp.2706-2711.

de Vienne D M, Aguileta G, Ollier S (2011)
Euclidean Nature of Phylogenetic Distance Matrices, Systematic Biology, vol. 60 pp.826-832.

Doyon J-P, Ranwez V, Daubin V, Berry V (2011)
Models algorithms and programs for phylogeny reconciliation, Briefings in Bioinformatics, vol. 12 pp.392-400.

Gavranovic H, Chauve C, Salse J, Tannier E (2011)
Mapping ancestral genomes with massive gene loss: A matrix sandwich problem, Bioinformatics, vol. 27 pp.i257-i265.

Lassalle F, Campillo T, Vial L, Baude J, Costechareyre D, Chapulliot D, Shams M, Abrouk D, Lavire C, Oger C, Hommais F, Guéguen L, Daubin V, Muller D, Nesme X (2011)
Genomic Species Are Ecological Species as Revealed by Comparative Genomics in Agrobacterium tumefaciens, Genome Biology and Evolution, vol. 3 pp.762-781.

Marais G, Forrest A, Kamau E, Kafer J, Daubin V, Charlesworth D (2011)
Multiple Nuclear Gene Phylogenetic Analysis of the Evolution of Dioecy and Sex Chromosomes in the Genus Silene, PLoS One, vol. 6 pp.e21915-e21915.

Ouangraoua A, Tannier E, Chauve C (2011)
Reconstructing the architecture of the ancestral amniote genome, Bioinformatics, vol. 27 pp.2664-2671.

Tannier E (2011)
HDR - Evolution combinatoire Algorithmique des chromosomes .

Tannier E (2011) L`époque romantique contre la peine de mort, Editions Universitaires Europeennes, 2011

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Tannier E (2011)
Preface : Satellite Workshop on Comparative Genomics Research in Computational Molecular Biology (RECOMB-CG 2010), Journal of Computational Biology, vol. 18 pp.1019-1021.

Whitney K D, Boussau B, Baack J E, Garland T Jr (2011)
Drift and Genome Complexity Revisited, PLoS Genetics, vol. 7 pp.e1002092-e1002092.

Abby S, Tannier E, Gouy M, Daubin V (2010)
Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests, BMC Bioinformatics, vol. 11 pp.324-324.

Abrouk M, Murat F, Pont C, Messing J, Jackson S, Faraut T, Tannier E, Plomion C, Cooke R, Feuillet C, Salse J (2010)
Palaeogenomics of plants: syntenybased modelling of extinct ancestors, Trends in Plant Science, vol. 15 pp.479-487.

Baudet C, Lemaitre C, Dias Z, Gautier C, Tannier E, Sagot MF (2010)
Cassis: detection of genomic rearrangement breakpoints, Bioinformatics, vol. 26(15) pp.1897-1898.

Chauve C, Gavranovic H, Ouangraoua A, Tannier E (2010)
Yeast Ancestral Genome Reconstructions: The Possibilities of Computational Methods II, Journal of Computational Biology, vol. 17(9) pp.1097-1112.

de Vienne DM (2010) Spéciation chez les parasites: Importance des interactions avec les hôtes dans la formation de nouvelles espèces, Editions universitaires europeennes, 2010

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Duret L, Bataillon T, Bierne N, Daubin V, Dutheil J, Gautier C, Glémin S, Gouy M, Heyer E, Marais G, Mouchiroud D, Pontarroti P, Quintana-Murci L, Robinson-Rechavi M, Galtier N (2010)
Evolution Moléculaire
in: Biologie Evolutive, de Boeck, pp.114-173.

Escobar J S, Cenci A, Bolognini J, Haudry A, Laurent S, David J, Glémin S (2010)
An integrative test of the dead-end hypothesis of selfing evolution in Triticeae (Poaceae), Evolution, vol. 64 pp.2855-2872.

Foxe J P, Stift M, Tedder A, Haudry A, Wright S, Mable B K (2010)
Reconstructing origins of loss of self-incompatibility and selfing in North American Arabidopsis lyrata: a population genetic context, Evolution, vol. 64 pp.3495-3510.

Gavranovic H, Tannier E (2010)
Guided genome halving: provably optimal solutions provide good insights into the preduplication ancestral genome of Saccharomyces Cerevisiae, Pacific Symposium on Biocomputing, , vol. 15 pp.21-30.

Gribaldo S, Poole A, Daubin V, Forterre P, Brochier-Armanet C (2010)
The origin of eukaryotes and their relationship with the Archaea: are we at a phylogenomic impasse?, Nature Rewiews Microbiology, vol. 8 pp.743-752.

Lopez-Villavicencio M, Aguileta G, Giraud T, de Vienne D M, Lacoste S, Couloux A, Dupont J (2010)
Sex in Penicillium: combined phylogenetic and experimental approaches, Fungal genetics and biology, vol. 47 pp.693-706.

Miklos I, Tannier E (2010)
Bayesian sampling of genomic rearrangement scenarios via double cut and join, Bioinformatics, vol. 26 pp.3012-3019.

Murat F, Xu JH, Tannier E, Abrouk M, Guilhot N, Pont C, Messing J, Salse J (2010)
Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution, Genome Research, vol. 20 pp.1545-1557.

Tannier E (2010) Comparative Genomics, Springer, 2010

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Tannier E (2010)
Le génome aux ordres des mathématiciens, La Recherche, vol. 439 pp.54-56.

Barabote RD, Xie G, Leu DH, Normand P, Necsulea A, Daubin V, Médigue C, Adney WS, Xu XC, Lapidus A, Paralez RE, Detter C, Pujic P, Bruce D, Lavire C, Challacombe JF, Brettin TS, Berry AM (2009)
Complete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptations, Genome Research, vol. 19(6) pp.1033-1043.

Bérard A, Le Paslier M C, Dardevet M, Exbrayat-Vinson F, Bonnin I, Cenci A, Haudry A, Brunel D, Ravel C (2009)
High-throughput single nucleotide polymorphism genotyping in wheat (Triticum spp.), Plant Biotechnology journal, vol. 7 pp.364-374.

Bérard S, Chateau A, Chauve C, Paul C, Tannier E (2009)
Computation of Perfect DCJ Rearrangement Scenarios with Linear and Circular Chromosomes, Journal of Computational Biology, vol. 16(10) pp.1287-1309.

Boussau B (2009)
Phylogenetic Relationships Deduced from Whole Genome Comparisons, Encyclopedia of Life Sciences, vol. pp.1-8.

Boussau B, Daubin V (2009)
Genomes as documents of evolutionary history, Trends in Ecology & Evolution, vol. 1192 pp.1-9.

Boussau B, Guéguen L, Gouy M (2009)
A Mixture Model and a Hidden Markov Model to Simultaneously Detect Recombination Breakpoints and Reconstruct Phylogenies, Evolutionary Bioinformatics, vol. 5 pp.67-79.

de Vienne DM, Giraud T, Martin OC (2009)
In response to comment on ‘A congruence index for testing topological similarity between trees’, Bioinformatics, vol. 25 pp.150-151.

de Vienne D M, Hood M E, Giraud T (2009)
Phylogenetic determinants of potential host shifts in fungal pathogens, Journal of evolutionary biology, vol. 22 pp.2532-2541.

de Vienne D M, Refregier G, Hood M E, Guigue A, Devier B, Vercken E, Smadja C, Deseille A, Giraud T (2009)
Hybrid sterility and inviability in the parasitic fungal species complex Microbotryum, Journal of evolutionary biology, vol. 22 pp.683-698.

Fertin G, Labarre A, Rusu I, Tannier E, Vialette S (2009) Combinatorics of Genome Rearrangements, MIT press, 2009

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Lemaitre C, Braga Marilia D V , Gautier C, Sagot MF, Tannier E, Marais GAB (2009)
Footprints of Inversions at Present and Past Pseudoautosomal Boundaries in Human Sex Chromosomes, Genome Biology and Evolution, vol. 1(1) pp.56-66.

Lemaitre C, Zaghloul L, Sagot MF, Gautier C, Arneodo A, Tannier E, Audit B (2009)
Analysis of fine-scale mammalian evolutionary breakpoints provides new insight into their relation to genome organisation, BMC Genomics, vol. 10:335 pp.1-12.

Ouangraoua A, Boyer F, McPherson A, Tannier E, Chauve C (2009)
Prediction of Contiguous Regions in the Amniote Ancestral Genome, Proceedings of ISBRA`09, Springer, Lecture Notes in Bioinformatics, vol. 5542 pp.173-185.

Penel S, Arigon A-M, Dufayard J-F, Sertier A-S, Daubin V, Duret L, Gouy M, Perrière G (2009)
Databases of homologous gene families for comparative genomics, BMC Bioinformatics, vol. 10 pp.s3-s3.

Tannier E (2009)
Yeast Ancestral Genome Reconstructions: The Possibilities of Computational Methods, Proceedings of RECOMB Comparative Genomics, Springer, Lecture notes in Bioinformatics, vol. 5817 pp.1-12.

Tannier E, Zheng C, Sankoff D (2009)
Multichromosomal median and halving problems under different genomic distances, BMC Bioinformatics, vol. 10 pp.120-120.

Teillier A, de Vienne DM, Giraud T, Hood M E, Refrégier G (2009)
Theory and examples of reciprocal influence between hosts and pathogens from short-term to long term interactions: coevolution cospeciation and pathogen speciation following host shifts.
in: Host-Pathogen Interactions: Genetics Immunology and Physiology., , pp.161-161.

Bérard S, Chateau A, Chauve C, Paul C, Tannier E (2008)
Perfect DCJ Rearrangement, Proceedings of RECOMB-CG` 2008, Springer-Verlag, Lecture Notes in Bioinformatics, vol. 5267 pp.510-521.

Boussau B (2008)
Early Evolution and Phylogeny .

Boussau B, Blanquart S, Necsulea A, Lartillot N, Gouy M (2008)
Parallel adaptations to high temperatures in the Archaean eon, Nature, vol. 456 pp.942-945.

Boussau B, Guéguen L, Gouy M (2008)
Accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of aquificales in the phylogeny of Bacteria, BMC Evolutionary Biology, vol. 8 pp.272-272.

Boyer F, Chauve C, Tannier E (2008)
Prédiction de synténies dans le génome ancestral des amniotes, Actes des Journée Ouvertes de Biologie Informatique et Mathématiques JOBIM 2008, pp.141-148.

Braga MDV, Sagot M-F, Scornavacca C, Tannier E (2008)
Exploring the Solution Space of Sorting by Reversals with Experiments and an Application to Evolution, IEEE-ACM Transactions on Computational Biology and Bioinformatics, vol. 5 - n°3 pp.348-356.

Brochier-Armanet C, Boussau B, Gribaldo S, Forterre P (2008)
Mesophilic crenarchaeota: proposal for a third archaeal phylum the Thaumarchaeota, Nature Reviews Microbiology, vol. 6 pp.245-252.

Chauve C, Tannier E (2008)
A Methodological Framework for the Reconstruction of Contiguous Regions of Ancestral Genomes and Its Application to Mammalian Genomes, PLoS Computational Biology, vol. 4 pp.1-18.

Dutheil J, Boussau B (2008)
Non-homogeneous models of sequence evolution in the Bio++ suite of libraries and programs, BMC Evolutionary Biology, vol. 8:255 pp.e1004892-e1004892.

Galtier N, Daubin V (2008)
Dealing with incongruence in phylogenomic analyses, Philosophical Transactions of The Royal Society B-Biological Sciences, vol. pp.1233-1241.

Giraud T, Refregier G, Le Gac M, de Vienne D M, Hood M E (2008)
Speciation in fungi, Fungal genetics and biology, vol. 45 pp.791-802.

Giraud T, Yockteng R, Marthey S, Chiapello H, Jonot O, Lopez-Villavicencio M, de Vienne D M, Hood M E, Refregier G, Gendrault-Jacquemard A, Wincker P, Dossat C (2008)
Isolation of 60 polymorphic microsatellite loci in EST libraries of four sibling species of the phytopathogenic fungal complex Microbotryum, Molecular ecology resources, vol. 8 pp.387-392.

Haudry A, Cenci A, Guilhaumon C, Paux E, Poirier S, Santoni S, David J, Glémin S (2008)
Mating system and recombination affect molecular evolution in four Triticeae species, Genetics research, vol. 90 pp.97-109.

Lemaitre C, Tannier E, Gautier C, Sagot MF (2008)
Precise detection of rearrangement breakpoints in mammalian chromosomes, BMC Bioinformatics, vol. 9 pp.286-322.

Lenne R, Solnon C, Stützle T, Tannier E, Birattari M (2008)
Reactive Stochastic Local Search Algorithms for the Genomic Median Problem, EvoCOP 2008, Springer Verlag, Lecture Notes in Computer Science, vol. 4972 pp.266-276.

Mugnier N, Guéguen L, Vieira C, Biémont C (2008)
The heterochromatic copies of the LTR retrotransposons as a record of the genomic events that have shaped the Drosophila melanogaster genome, Gene, vol. 411 pp.87-93.

Tannier E (2008)
Sorting Signed Permutations by Reversal (Reversal Sequence) 2004; Tannier Sagot
in: Encyclopedia of algorithms, Springer, pp.860-863.

Tannier E, Zheng C, Sankoff D (2008)
Multichromosomal Genome Median and Halving Problems, Proceedings of WABI`08, Springer-Verlag, Lecture notes in Bioinformatics, vol. 5251 pp.1-13.

Abby S, Daubin V (2007)
Comparative genomics and the evolution of prokaryotes, Trends in Microbiology, vol. 15 pp.135-141.

Braga MDV, Sagot M-F, Scornavacca C, Tannier E (2007)
The solution space of sorting by reversals, Proceedings of ISBRA`07, Lecture Notes in Bioinformatics, vol. 4463 pp.293-304.

de Vienne D M, Giraud T, Martin O C (2007)
A congruence index for testing topological similarity between trees, Bioinformatics, vol. 23 pp.3119-24.

de Vienne D M, Giraud T, Shykoff J A (2007)
When can host shifts produce congruent host and parasite phylogenies? A simulation approach, Journal of evolutionary biology, vol. 20 pp.1428-38.

Diekmann Y, Sagot M-F, Tannier E (2007)
Evolution under Reversals: Parsimony and Conservation of Common Intervals, IEEE-ACM Transactions on Computational Biology and Bioinformatics, vol. 4 pp.301-309.

Dumas J-G, Roch J-L, Tannier E, Varrette S (2007) Théorie des codes: compression cryptage correction, Dunod, 2007

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Fall S, Mercier A, Bertolla F, Calteau A, Guéguen L, Perrière G, Vogel TM , Simonet P (2007)
Horizontal Gene Transfer Regulation in Bacteria as a "Spandrel" of DNA Repair Mechanisms, PLoS One, vol. 2 pp.e1055-e1055.

Haudry A, Cenci A, Ravel C, Bataillon T, Brunel D, Poncet C, Hochu I, Poirier S, Santoni S, Glémin S, David J (2007)
Grinding up wheat: a massive loss of nucleotide diversity since domestication, Molecular Biology Evolution, vol. 24 pp.1506-1517.

Normand P, Lapierre P, Tisa LS, Gogarten JP, Alloisio N, Bagnarol E, Bassi CA, Berry AM, Bickhart DM, Choisne N, Couloux A, Cournoyer B, Cruveiller S, Daubin V, Demange N, Francino MP, Goltsman E, Huang Y, Kopp OR, Labarre L, Lapidus A, Lavire C, Marechal J, Martinez M, Mastronunzio JE, Mullin BC, Niemann J, Pujic P, Rawnsley T, Rouy Z, Schenowitz C, Sellstedt A, Tavares F, Tomkins JP, Vallenet D, Valverde C, Wall LG, Wang Y, Medigue C, Benson DR (2007)
Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography, Genome Research, vol. pp.7-15.

Rezvoy C, Charif D, Guéguen L , Marais GAB (2007)
MareyMap: an R-based tool with graphical interface for estimating recombination rates, Bioinformatics, vol. 23 pp.2188-2189.

Tannier E, Bergeron A, Sagot M-F (2007)
Advances on sorting by reversals, Discrete Applied Mathematics, vol. 155 pp.881-888.

Aury J-M, Jaillon O, Duret L, Noel B, Jubin C, Porcel BM, Segurens B, Daubin V, Anthouard V, Aiach N, Arnaiz O, Billaut A, Beisson J, Blanc I, Bouhouche K, Camara F, Duharcourt S, Guigo R, Gogendeau D, Katinka M, Keller AM, Kissmehl R, Klotz C, Koll F, Le Mouel A, Lepere G, Malinsky S, Nowacki M, Nowak JK, Plattner H, Poulain J, Ruiz F, Serrano V, Zagulski M, Dessen P, Betermier M, Weissenbach J, Scarpelli C, Schachter V, Sperling L, Meyer E, Cohen J, Wincker P (2006)
Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia, Nature, vol. 444 pp.171-178.

Boussau B, Gouy M (2006)
Efficient Likelihood Computations with Nonreversible Models of Evolution, Systematic Biology, vol. 55 pp.756-768.

Melodelima C, Guéguen L, Gautier C, Piau D (2006)
A Markovian Approach for the Analysis of the Gene Structure, Proceedings of the Prague Stringology Conference, , vol. 19(1) pp.19-35.

Melodelima C, Guéguen L, Piau D, Gautier C (2006)
A computational prediction of isochores based on hidden Markov models, Gene, vol. 385 pp.41-49.

Palmeira L, Guéguen L, Lobry JR (2006)
UV-Targeted Dinucleotides Are Not Depleted in Light-Exposed Prokaryotic Genomes, Molecular Biology and Evolution, vol. 23 pp.2214-2219.

Guéguen L (2005)
Sarment: Python modules for HMM analysis and partitioning of sequences, Bioinformatics, vol. 21 pp.3427-3428.

Lerat E, Daubin V, Ochman H, Moran NA (2005)
Evolutionary origins of genomic repertoires in bacteria, PLoS Biology, vol. 3 pp.0807-0814.

Ochman H, Daubin V, Lerat E (2005)
A bunch of fun-guys: the whole-genome view of yeast evolution, Trends in Genetics, vol. 21 pp.1-3.

Ochman H, Lerat E, Daubin V (2005)
Examining bacterial species under the specter of gene transfer and exchange, Proceedings of The National Academy of Sciences of The United States of America, vol. 102 pp.6595-6599.

Sagot MF, Tannier E (2005)
Perfect sorting by reversals, Proceedings of COCOON`05, Springer-Verlag, Lecture Notes in Computer Science, vol. 3595 pp.42-51.

Boussau B, Karlberg EO, Frank AC, Legault BA, Andersson SG (2004)
Computational inference of scenarios for alpha-proteobacterial genome evolution, Proceedings of The National Academy of Sciences of The United States of America, vol. 101 pp.9722-9727.

Daubin V, Moran NA (2004)
Comment on "The origins of genome complexity", Science, vol. 306 pp.978a-978a.

Daubin V, Ochman H (2004)
Bacterial genomes as new gene homes: the genealogy of ORFans in E. coli, Genome Research, vol. 14 pp.1036-1042.

Daubin V, Ochman H (2004)
Quartet mapping and the extent of lateral transfer in bacterial genomes, Molecular Biology and Evolution, vol. 21 pp.86-89.

Daubin V, Ochman H (2004)
Start-up entities in the origin of new genes, Current Opinion in Genetics and Development, vol. 14 pp.616-619.

Robinson-Rechavi M, Boussau B, Laudet V (2004)
Phylogenetic dating and characterization of gene duplications in vertebrates: the cartilaginous fish reference, Molecular Biology and Evolution, vol. 21 pp.580-586.

Sebo A, Tannier E (2004)
On Metric Generators of Graphs, Mathematics of Operations Research, vol. 29 pp.383-393.

Tannier E, Sagot M-F (2004)
Sorting by reversals in subquadratic time, Proceedings of CPM`04, Springer Verlag, Lecture Notes in Computer Science, vol. 3109 pp.1-13.

Zelwer M, Daubin V (2004)
Detecting phylogenetic incongruence using BIONJ: an improvement of the ILD test, Molecular Phylogenetics and Evolution, vol. 33 pp.687-693.

Daubin V, Lerat E, Perrière G (2003)
The source of laterally transferred genes in bacterial genomes, Genome Biology, vol. 4 pp.R57.1-R57.12.

Daubin V, Moran NA, Ochman H (2003)
Phylogenetics and the cohesion of bacterial genomes, Science, vol. 301 pp.829-832.

Daubin V, Perrière G (2003)
G+C3 structuring along the genome: a common feature in prokaryotes, Molecular Biology and Evolution, vol. 20 pp.471-483.

Gravier S, Mhalla M, Tannier E (2003)
On a modular domination game, Theoretical Computer Science, vol. 306 pp.291-303.

Lerat E, Daubin V, Moran NA (2003)
From gene trees to organismal phylogeny in prokaryotes: the case of the gamma-Proteobacteria, PLoS Biology, vol. 1 pp.101-109.

Daubin V, Gouy M, Perrière G (2002)
A phylogenomic approach to bacterial phylogeny: evidence of a core of genes sharing a common history, Genome Research, vol. 12 pp.1080-1090.

Tannier E (2002)
Sur quelques problèmes de recouvrement et empilement dans les graphes et les matroïdes .

Cariou ML, Silvain J F, Daubin V, Da Lage J L, Lachaise D (2001)
Divergence between Drosophila santomea and allopatric or sympatric populations of D. yakuba using paralogous amylase genes and migration scenarios along the Cameroon volcanic line, Molecular Ecology, vol. 10 pp.649-660.

Sebo A, Tannier E (2001)
Connected Joins in Graphs, Proceedings of IPCO`01, Springer Verlag, Lecture Notes in Computer Science, vol. 2081 pp.383-391.