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Rechercher
UMR CNRS 5558 - LBBE "Biométrie et Biologie Évolutive" UCB Lyon 1 - Bât. Grégor Mendel 43 bd du 11 novembre 1918 69622 VILLEURBANNE cedex
- +Thèmes de recherche -Thèmes de recherche
I have two main research interests today (2019) :
1/ The first and historical one is to construct mathematical models and computational methods for the reconstruction of the history of life, by comparison of DNA molecules.
In particular my focus is on large mutations of chromosomes : duplications, transfers, losses, inversions, translocations. These mutations, while highly informative for the biology and evolution of living organisms, are not yet included in the standard phylogenetic toolbox because of the mathematical difficulty of their integration in evolutionary models.
I have applied the design of statistical and combinatorial methods to the construction or phylogenetic trees, the dating of phylogenetic trees, or the reconstruction of ancestral genomes. My project is to expand these methods to account for muti-scale interactions inside genes, between genes in a single species or genes in different species sharing an environment, for example for co-evolving species, host-parasite associations, microbiome. Hugo Menet just started his Ph-D on this subject.
I am also involved in validation issues, with the Evoluthon project, just funded by ANR. Its goal is to use bioinspired computer science to test bioinformatics models and methods.
2/ I am also involved in the reflexion on the social and environmental responsibilities of researchers. This is a rather ancient interest but it is all the more acute today as all our activities can be thought in the light of the anthropocene.
I participate to activist groups at Inria, LBBE, Labo1.5, and associations promoting polyculture and citizen science. I have the project to develop the algorithmics of permacultural design.
- +Enseignements -Enseignements
Cours en ligne :
Cours/TD MADG Master Bioinfo UCBL M1 Bioinfo UCBL
Ethique et intégrité scientifique M2 Bioinfo UCBL : supports de cours Environnement et IntégritéAutres interventions :
Université Populaire de Lyon
Ethique scientifique, Inria
MOOC on research ethics from Université de Lyon
- +Papers to appear -Papers to appear
Gene tree reconciliation including transfers with replacement is hard and FPT
D Hasic, E Tannier
Accepted by Journal of Combinatorial Optimization
https://link.springer.com/article/10.1007/s10878-019-00396-z
arXiv preprint arXiv:1709.04459
Gene tree species tree reconciliation with gene conversion
D Hasic, E Tannier
Accepted by Journal of Mathematical Biology
https://link.springer.com/article/10.1007/s00285-019-01331-w
arXiv preprint arXiv:1703.08950
Zombi : A simulator of species, genes and genomes that
accounts for extinct lineages
Davin A, Tricoud T, Tannier E, de Vienne D, Szollosi G,
https://www.biorxiv.org/content/10.1101/339473v1
Leveraging evolutionary relationships to improve Anopheles genome assemblies
Robert M. Waterhouse, Sergey Aganezov, Yoann Anselmetti, Jiyoung Lee, Sèverine Bérard, Phillip George, Matthew W. Hahn, Paul I. Howell, Maryam Kamali, Marcia Kern, Sergey Koren, Ashley Peery, Adam M. Phillippy, Maarten J.M.F. Reijnders, Livio Ruzzante, Maria V. Sharakhova, Eric Tannier, Maria F. Unger, Max A. Alekseyev, Nora J. Be-
sansky, Cedric Chauve, Scott J. Emrich, Igor V. Sharakhov,
https://www.biorxiv.org/content/10.1101/434670v2
+Publications -Publications
article :
Hasic D, Tannier E (2019)
Gene tree species tree reconciliation with gene conversion, Journal of mathematical biology, vol. 78 pp.1981-2014.
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.
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.
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.
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.
Bulteau L, Fertin G, Tannier E (2016)
Genome rearrangements with indels in intergenes restrict the scenario space, BMC Bioinformatics, vol. 17 pp.225-231.
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.
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.
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.
Miklos I, Kiss SZ, Tannier E (2014)
Counting and sampling SCJ small parsimony solutions, Theoretical Computer Science, vol. 552 pp.83-98.
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.
Daubin V, Penel S, Tannier E (2013)
L`ADN mémoire numérique du vivant, Pour la science, vol. 433 pp.103-108.
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.
Rajaraman A, Tannier E, Chauve C (2013)
FPSAC: fast phylogenetic scaffolding of ancient contigs, Bioinformatics, vol. 29 pp.2987-2994.
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.
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 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.
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.
Miklos I, Tannier E (2012)
Approximating the number of Double Cut-and-Join scenarios, Theoretical Computer Science, vol. 439 pp.30-40.
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.
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.
Ouangraoua A, Tannier E, Chauve C (2011)
Reconstructing the architecture of the ancestral amniote genome, Bioinformatics, vol. 27 pp.2664-2671.
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.
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.
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)
Le génome aux ordres des mathématiciens, La Recherche, vol. 439 pp.54-56.
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.
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.
Tannier E, Zheng C, Sankoff D (2009)
Multichromosomal median and halving problems under different genomic distances, BMC Bioinformatics, vol. 10 pp.120-120.
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.
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.
Lemaitre C, Tannier E, Gautier C, Sagot MF (2008)
Precise detection of rearrangement breakpoints in mammalian chromosomes, BMC Bioinformatics, vol. 9 pp.286-322.
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.
Tannier E, Bergeron A, Sagot M-F (2007)
Advances on sorting by reversals, Discrete Applied Mathematics, vol. 155 pp.881-888.
Sebo A, Tannier E (2004)
On Metric Generators of Graphs, Mathematics of Operations Research, vol. 29 pp.383-393.
Gravier S, Mhalla M, Tannier E (2003)
On a modular domination game, Theoretical Computer Science, vol. 306 pp.291-303.
book :
 | Dumas JG, Roch JA, Tannier E, Varrette S (2018) Théorie des codes, , 2018 |
 | Dumas JG, Roch JL, Tannier E, Varrette S (2015) Foundations of coding. Compression Encryption Error Correction, Wiley, 2015 |
 | Chauve C, El-Mabrouk N, Tannier E (2013) Models and Algorithms for Genome Evolution, Springer, 2013 |
 | Dumas JG, Roch JL, Tannier E, Varrette S (2013) Théorie des codes, Dunod, 2013 |
 | Tannier E (2011) L`époque romantique contre la peine de mort, Editions Universitaires Europeennes, 2011 |
 | Tannier E (2010) Comparative Genomics, Springer, 2010 |
 | Fertin G, Labarre A, Rusu I, Tannier E, Vialette S (2009) Combinatorics of Genome Rearrangements, MIT press, 2009 |
 | Dumas J-G, Roch J-L, Tannier E, Varrette S (2007) Théorie des codes: compression cryptage correction, Dunod, 2007 |
inbook :
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.
Groussin M, Daubin V, Gouy M, Tannier E (2016)
Ancestral Reconstruction: Theory and Practice
in: The Encyclopedia of Evolutionary Biology, , pp.70-77.
Tannier E (2015)
Sorting Signed Permutations by Reversal (Reversal Sequence)
in: Encyclopedia of Algorithms, Springer Science+Business Media New York 2015, pp.1-5.
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.
Tannier E (2008)
Sorting Signed Permutations by Reversal (Reversal Sequence) 2004; Tannier Sagot
in: Encyclopedia of algorithms, Springer, pp.860-863.
inproceedings :
Biller P, Knibbe C, Beslon G, Tannier E (2016)
Comparative Genomics on Artifical Life, Computability in Europe, pp.1-10.
Fertin G, Jean G, Tannier E (2016)
Genome Rearrangements on Both Gene Order and Intergenic Regions, WABI, , vol. 9838 pp.162-173.
Rajaraman A, Tannier E, Chauve C (2013)
The genome of the medieval Black Death agent (extended abstract), JOBIM 2013, pp.47-54.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
phdthesis :
Tannier E (2011)
HDR - Evolution combinatoire Algorithmique des chromosomes .
Tannier E (2002)
Sur quelques problèmes de recouvrement et empilement dans les graphes et les matroïdes .
