Publications des unités MIA-Jouy, MIG, MaIAGE

Sélection : $type!="TOTO"&(year >= 2018);  Critères de tri / (Sorted on) : $type, author, year

Article

[1] N. Abdollahi, A. Albani, E. Anthony, A. Baud, M. Cardon, R. Clerc, D. Czernecki, R. Conte, L. David, A. Delaune, S. Djerroud, P. Fourgoux, N. Guiglielmoni, J. Laurentie, N. Lehmann, C. Lochard, R. Montagne, V. Myrodia, V. Opuu, E. Parey, L. Polit, S. Privé, C. Quignot, M. Ruiz-Cuevas, M. Sissoko, N. Sompairac, A. Vallerix, V. Verrecchia, M. Delarue, M. Guérois, Y. Ponty, S. Sacquin-Mora, A. carbone, C. Froidevaux, S. Le Crom, O. Lespinet, M. Weigt, S. Abboud, J. Bernardes, G. Bouvier, C. Dequeker, A. Ferré, P. Fuchs, G. Lelandais, P. Poulain, H. Richard, H. Schweke, E. Laine, and A. Lopes. Meet-U: Educating through research immersion. Plos Computational Biology, 14(3): 1-10, 2018.

[2] P. Bastide, C. Ané, S. Robin, and M. Mariadassou. Inference of adaptive shifts for multivariate correlated traits. Systematic Biology, 67, 2018.

[3] P. Bastide, C. Solís-Lemus, R. Kriebel, K. W. Sparks, and C. Ané. Phylogenetic comparative methods on phylogenetic networks with reticulations. Systematic Biology, 67(5): 800-820, 2018.

[4] L. Campillos, L. Deleger, C. Grouin, T. Hamon, A.-L. Ligozat, and A. Neveol. A french clinical corpus with comprehensive semantic annotations: development of the Medical Entity and Relation LIMSI annOtated text corpus -MERLOT. Language Resources and Evaluation, 52(2): 571-601, 2018.

[5] E. Chaix, L. Deleger, R. Bossy, and C. Nédellec. Text-mining tools for extracting information about microbial biodiversity in food. Food Microbiology, 13 p., 2018. Available online 21 April 2018 In Press, Corrected Proof.

[6] M. Chaves and L. Tournier. Analysis tools for interconnected Boolean networks with biological applications. Frontiers Physiology, 9(586): 1-18, 2018.

[7] J. Chiquet, M. Mariadassou, and S. Robin. Variational inference for probabilistic poisson pca. Annals of Applied Statistics, 12: 2674-2698, 2018.

[8] J. Cornuault, M. A. Petit, M. Mariadassou, L. De Jesus Benevides, E. Moncaut, P. Langella, H. Sokol, and M. Paepe. Phages infecting faecalibacterium prausnitzii belong to novel viral genera that help to decipher intestinal viromes. Microbiome, 6(1): 14 p., 2018.

[9] B. Couvigny, S. Kulakauskas, N. Pons, B. Quinquis, A.-L. Abraham, T. Meylheuc, C. Delorme, P. Renault, R. Briandet, N. Lapaque, and E. Guedon. Identification of new factors modulating adhesion abilities of the pioneer commensal bacterium streptococcus salivariu. Frontiers in Microbiology, 9: 14 p., 2018.

[10] L. Crouzet, M. Derrien, C. Cherbuy, S. Plancade, M. Foulon, B. Chalin, J. van Hylckama Vlieg, G. Grompone, L. Rigottier-Gois, and P. Serror. Lactobacillus paracasei cncm i-3689 reduces vancomycin-resistant enterococcus persistence and promotes bacteroidetes resilience in the gut following antibiotic challenge. Scientific Reports, 8(1): 11 p., 2018.

[11] M. Delattre, V. Genon-Catalo, and C. Laredo. Parametric inference for discrete observations of diffusion processes with mixed effects. Stochastic Processes and their Applications, 126(6): 1929-1957, 2018.

[12] M. Delattre, V. Genon-Catalot, and C. Laredo. Approximate maximum likelihood estimation for stochastic differential equations with random effects in the drift and the diffusion. Metrika, 81(8), 2018.

[13] T. P. Delforno, T. Z. Macedo, C. Midoux, Lacerda, O. Rué, M. Mariadassou, V. Loux, Varesche, Bouchez, A. Bize, and V. Oliveira. Comparative metatranscriptomic analysis of anaerobic digesters treating anionic surfactant contaminated wastewater. Science of The Total Environment, 2019, 2019.

[14] R. Dessalles, M. D'Orsogna, and T. Chou. Exact steady-state distributions of multispecies birth–death–immigration processes: Effects of mutations and carrying capacity on diversity. Journal of statistical physics, 173: 182-221, 2018.

[15] V. Dominguez Del Angel, E. Hjerde, L. Sterck, S. Capella-Gutierrez, C. Notredame, O. Vinnere Pettersson, J. Amselem, L. Bouri, S. Bocs, C. Klopp, J.-F. Gibrat, A. Vlasova, B. L. Leskosek, L. Soler, M. Binzer-Panchal, and H. Lantz. Ten steps to get started in genome assembly and annotation. F1000Research, 7: 148-149, 2018.

[16] E. Duchaud, T. Rochat, C. Habib, P. Barbier, V. Loux, C. Guerin, I. Dalsgaard, L. Madsen, H. Nilsen, K. Sundell, T. Wiklund, N. Strepparava, T. Wahli, G. Caburlotto, A. Manfrin, G. D. Wiens, E. Fujiwara-Nagata, R. Avendano-Herrera, J.-F. Bernarde, and P. Nicolas. Genomic diversity and evolution of the fish pathogen flavobacterium psychrophilum. Frontiers in Microbiology, 9: 1-20, 2018.

[17] F. Escudie, L. Auer, M. Bernard, M. Mariadassou, L. Cauquil, K. Vidal, S. Maman Haddad, G. Hernandez-Raquet, S. Combes, and G. Pascal. FROGS: Find, rapidly, OTUs with galaxy solution. Bioinformatics, 34(8): 1287-1294, 2018.

[18] K. Faust, F. Bauchinger, B. Laroche, S. de Buyl, L. Lahti, A. D. Washburne, D. Gonze, and S. Widder. Signatures of ecological processes in microbial community time series. Microbiome, 6(article n° 120), 2018.

[19] J. Ferrer Savall, D. Franqueville, P. Barbillon, C. Benhamou, P. Durand, M.-L. Taupin, H. Monod, and J.-L. Drouet. Sensitivity analysis of spatio-temporal models describing nitrogen transfers, transformations and losses at the landscape scale. Environmental Modelling and Software, 2018.

[20] J.-F. Gibrat. A short note on dynamic programming in a band. BMC Bioinformatics, 19(1), 2018.

[21] J. Giguelay and S. Huet. Testing k-monotonicity of a discrete distribution. application to the estimation of the number of classes in a population. Computational Statistics & Data Analysis, 2018. online.

[22] B. Glasset, S. Herbin, S. Granier, L. Cavalié, E. Lafeuille, C. Guerin, R. Ruimy, F. Casagrande-Magne, M. Levast, N. Chautemps, J.-W. Decousser, L. Belotti, I. Pelloux, J. Robert, A. Brisabois, and N. Rama Rao. Bacillus cereus, a serious cause of nosocomial infections: Epidemiologic and genetic survey. Plos One, 13(5): 1-19, 2018. article numéro: e0194346.

[23] N. Go, C. Belloc, C. Bidot, and S. Touzeau. Why, when and how should exposure be considered at the within-host scale? a modelling contribution to PRRSv infection. Mathematical Medicine and Biology, 2018.

[24] P. Hoscheit and O. Pybus. The multifurcating skyline plot. bioRxiv, 2018. preprint online.

[25] S. Labarthe, B. Polizzi, T. Phan, M. Goudon, T. Ribot, and B. Laroche. Thermodynamic constraints for identifying elementary flux modes. Journal of Theoretical Biology, 2018. article accepté- préprint.

[26] B. Laflaquière, G. Leclercq, C. Choey, J. Chen, S. Peres, C. Ito, and M. Jolicoeur. Identifying Biomarkers of Wharton's Jelly Mesenchymal Stromal Cells Using a Dynamic Metabolic Model: The Cell Passage Effect. Metabolites, 8(1): 18 p., 2018.

[27] V. Loux, G. Coeuret, M. Zagorec, M.-C. Champomier-Verges, and S. Chaillou. Complete and draft genome sequences of nine lactobacillus sakei strains selected from the three known phylogenetic lineages and their main clonal complexes. Genome Announcements, 6(16): 3 p., 2018.

[28] D. Ly, S. Huet, A. Gauffreteau, R. Rincent, G. Touzy, A. Mini, J.-L. Jannink, F. Cormier, E. Paux, S. Lafarge, J. Le Gouis, and G. Charmet. whole-genome prediction of reaction norms to environmental stress in bread wheat (titicum aestivum l.) by genomic random regression. Field Crops Research, 216: 32-41, 2018.

[29] R. Malek, P. Bonnarme, F. Irlinger, P. Frey-Klett, D. Onesime, J. Aubert, V. Loux, and J.-M. Beckerich. Transcriptomic response of debaryomyces hansenii during mixed culture in a liquid model cheese medium with yarrowia lipolytica. International Journal of Food Microbiology, 264: 53-62, 2018. on line novembre 2017 - paper : janvier 2018.

[30] L. Noda-Garcia, W. Liebermeister, and D. Tawfik. Metabolite–enzyme coevolution: From single enzymes to metabolic pathways and networks. Annual Review of Biochemistry, 19(1): 187-216, 2018.

[31] S. Peres, S. Schuster, and P. Dague. Thermodynamic constraints for identifying elementary flux modes. Biochemical Society Transactions, 46: 641-647, 2018.

[32] S. Poirier, O. Rué, R. Peguilhan, G. Coeuret, M. Zagorec, M.-C. Champomier-Verges, V. Loux, and S. Chaillou. Deciphering intra-species bacterial diversity of meat and seafood spoilage microbiota using gyrb amplicon sequencing: A comparative analysis with 16s rdna v3-v4 amplicon sequencing. Plos One, 13(9), 2018. article n° e0204629.

[33] M. T. Wortel, E. Noor, M. Ferris, Bruggeman, and W. Liebermeister. Metabolic enzyme cost explains variable trade-offs between microbial growth rate and yield. Plos Computational Biology, 14(2): 21 p., 2018.

Inbook

[34] L. Noda-Garcia, W. Liebermeister, and D. S. Tawfik. book : Annual Reviews. Annual Reviews, Palo Alto (Etats-Unis), 2018, ch. title: Metabolite-Enzyme coevolution: from single enzymes to metabolic pathways and networks, pp. 187-216.

Inproceedings

[35] J. Amselem, N. Francillonne, C. Michotey, T. Letellier, J.-M. Aury, C. Da Silva, S. Duplessis, F. EHRENMANN, S. Faye, C. Gaspin, C. Klopp, K. Labadie, I. Lesur Kupin, T. Leroy, F. Murat, O. Rué, C. Bodenes-Brezard, J.-C. Leplé, G. Le Provost, P. Faivre-Rampant, A. Kremer, F. Martin, and H. Quesneville. An integrated information system dedicated to Oak genomics and genetics. In Plant and Animal Genome (San Diego - Etats-Unis), janvier 2018. Présentation orale.

[36] M. Ba, C. Nédellec, and R. Bossy. Data Exchange Solution between PubAnnotation and alvisAE. In BLAH4 symposium (Tokyo, Japon), janvier 2018. Short paper.

[37] G. Beaunée, P. Ezanno, A. Joly, P. Nicolas, and E. Vergu. Inference in a metapopulation model via a composite-likelihood approximation. In 11th. European Conference on Mathematical and Theoretical Biology (ECMTB) (Lisbonne, Portugal), Juillet 2018. Présentation orale.

[38] G. Beaunée, P. Ezanno, A. Joly, P. Nicolas, and E. Vergu. Inférence, modélisation et compréhension des pathosystèmes : cas d'étude de la paratuberculose bovine. In book of abstracts of Journées d'Animation Scientifique du Département Santé Animale (JSA DSA) (La Chapelle-sur-Erdre, France), octobre 2018. Poster.

[39] E. Chaix, R. Bossy, and C. Nédellec. Reconstruction and visualisation of gene regulatory networks from different provenances : application at arabidopsis thaliana. In BLAH4 symposium (Tokyo, Japon), 2018. Short paper.

[40] E. Chaix, S. Derozier, L. Deleger, H. Falentin, J.-B. Bohuon, M. Ba, R. Bossy, D. Sicard, and C. Loux, V. ; Nédellec. FLORILEGE: an integrative database using text mining and ontologies. In JOBIM 2018 (Marseille - FR). JOBIM éditions, Juillet 2018, p. 563. Poster.

[41] H. Chiapello. Evolution et co-évolution des petits arns régulateurs et des gènes codants chez les bactéries. In ANSES, Séminaire DEBUG (Toulouse, France), juin 2018. Présentation orale - conférence invitée.

[42] A. De Paula Reis, M. Belghiti, B. Marquant Le Guienne, L. Laffont, S. Ruffini, E. Canon, P. Adenot, V. Le Brusq, M. Duranthon, and A. Trubuil. Identification and mathematical prediction of different morphokinetic profiles of in vitro developed bovine embryos. In Proceedings of the 34rd Meeting of the Association of Embryo Transfer in Europe (AETE) (Nantes, FR). AET, septembre 2018. Présentation Orale.

[43] A. De Paula Reis, M. Belghiti, B. Marquant Le Guienne, L. Laffont, S. Ruffini, E. Canon, P. Adenot, V. Duranthon, and A. Trubuil. Mise en place d’un outil prédictif de la qualité embryonnaire grâce à des paramètres morphocinétiques. In Journées d'Animation Scientifique (Rennes- FR). INRA Book of abstrats, avril 2018. Présentation Orale.

[44] S. Derozier, M. V., J.-M. Chantel, R. Rao, V. Loux, and G. André-Leroux. MetaFoldScan: a pipeline to scan metagenomes and identify structural homologs using HMM. In JOBIM 2018 (Marseille - FR). JOBIM éditions, Juillet 2018, p. 470. Poster.

[45] A. Frouin, E. Le Flocch, and C. Ambroise. Quantify genomic heritability through a prediction measure. In Human Heredity : book of meetings abstracts of 46th European Mathematical Genetics Meeting (EMGM) (Caglianri, Italie), vol. 83. anger - basel - Switzerland, Basel (Suisse), 2018, pp. 7-8. doi:10.1159/000488519 - abstract.

[46] V. Gagnaire, F. Canon, M. Mariadassou, H. Falentin, S. Parayre, M.-B. Maillard, G. Henry, M.-N. Madec, F. Valence-Bertel, O. Ménard, V. Laroute, M.-L. Daveran Mingot, M. Bousquet, and A. Thierry. Design de communautés bactériennes pour fermenter un nouvel aliment associant lait et légumineuse. In Book of abstracts of RFL2, 2e Rencontres Francophones sur les Légumineuses (Toulouse, France), 2018. présentation orale.

[47] M. Garnaut, G. Couleaud, P. Leroux, C. Duplaix, O. David, F. Carpentier, and A.-S. Walker. Contrasted spatiotemporal dynamics of resistance and its drivers in the pathogenic fungus zymoseptoria tritici in france revealed by statistical analysis. In Journées Jean Chevauchon JJC2018 - 12èmes Rencontres de Phytopathologie & Mycologie (Aussois - FR), 2018. short paper.

[48] P. Hoscheit, E. Anthony, and E. Vergu. Using TempoRank to identify central nodes in cattle trace networks. In ECMTB - 11ème European Conference on Mathematical and Theoretical Biology (Lisbonne, Portugal), juillet 2018, p. 20 diapo. Présentation orale.

[49] P. Hoscheit, E. Anthony, and E. Vergu. Using TempoRank to identify central nodes in cattle trace networks. In NetSci conference, LMNID satellite meeting (Paris, France), juin 2018, p. 20 diapo. Présentation orale.

[50] G. Jeanne, A. Goelzer, S. Tebbani, D. Dumur, and V. Fromion. Dynamical resource allocation models for bioreactor optimization. In proceeding of 7th. International FOSBE 2018 Foundations of Systems Biology in Engineering (Chicago, EUA), vol. 51. Elsevier-Science BV- Amsterdam, PB, 2018, pp. 20-23. doi:10.1016/j.ifacol.2018.09.020 + présentation orale.

[51] G. Jeanne, A. Goelzer, S. Tebbani, D. Dumur, and V. Fromion. Towards a realistic and integrated strain design in batch bioreactor. In Proceeding of 57th IEEE Conference on Decision and Control (Miami, EUA), 2018. présentation orale + full paper.

[52] G. Jeanne, A. Goelzer, S. Tebbani, D. Dumur, and V. Fromion. Towards a realistic and integrated strain design in batch bioreactor. In Proceeding of 57th IEEE Conference on Decision and Control (Miami,EUA), 2018, p. 6p. Présentation orale + full paper -papier accepté.

[53] F. Kettani, S. Schneider, S. Aubin, R. Bossy, C. François, C. Jonquet, A. Tchechmedijiev, A. Toulet, and C. Nédellec. Projet visatm : l'interconnexion openminted – agroportal – istex, un exemple de service de text et data mining pour les scientifiques français. In Proceedings of 29es Journées Francophones d'Ingénierie des Connaissances (Nancy, FR), 2018. abstract - acte non publié.

[54] E. Kuhn and M. Delattre. Un nouvel estimateur pour l'information de fisher dans les modèles à variables latentes. In acte of SFdS- 50ème Journées de Statistique de la SFdS (JdS'2018) (Pallaiseau, France). online, 2018, p. 6 p. Presentation oral.

[55] E. Kuhn and A. Oodally. Estimation dans des modèles de fragilité à partir d'une vraisemblance partielle. In acte of SFdS- 50ème Journées de Statistique de la SFdS (JdS'2018) (Palaiseau, France). on line, 2018, p. 6 p. Presentation oral.

[56] T. Lacroix, V. Loux, J. Lorenzo, B. Brancotte, C. Blanchet, and J.-F. Gibrat. Insyght : Analyse evolutionary conserved CDS, orthologs, syntenies, pan-genome, fusion, etc., for your bacteria of interest​. In Research in Computational Molecular Biology (RECOMB) (Paris, France). Springer, avril 2018, p. numéro 106. Poster.

[57] V. Marcon, L. Quintric, P. Durand, O. Inizan, C. Dussart, V. Loux, M. Bernard, and G. Pascal. The journey of a team of engineers in learning packaging technology. In Jobim (Journées Ouvertes Biologie Informatique Mathématiques) - 2018 (Marseille, France). edition JOBIM, 2018, pp. 612-613. Presentation oral et Poster.

[58] C. Nédellec, E. Chaix, R. Bossy, L. Deléger, S. Derozier, J.-B. Bohuonn, and V. Loux. L'ontologie OntoBiotope pour l'étude de la biodiversité microbienne. In EGC'2018: 18èmes Conférence Internationale sur l'Extraction et la Gestion des Connaissances (Paris, France). RNTI, janvier 2018, p. 253... Short paper.

[59] L. Quintric, P. Durand, O. Inizan, V. Marcon, v. Loux, , M. Bernard, and G. Pascal. The journey of a team of engineers in learning packaging technology. In Abstracts of Galaxy Community Conference - GCC2018 (Portland, Etats-Unis). online, 2018, p. 1 p. Presentation oral.

[60] S. Schbath and v. Loux. Des microbes dans mon fromage ? In Journées Nationales de la Science Ouverte (Paris, FR), 2018. Présentation Orale.

[61] S. Schbath. À la recherche de mots exceptionnels dans les génomes. In K'fêt des sciences du collège de La Gyonnerie (Bures-sur-Yvette, FR), 2018. Présentation Orale.

[62] J. Yon, N. Bareille, B. Bed'Hom, X. Berthelot, S. Combes, O. Dameron, G. Foucras, A. Journaux, F. Launay, P.-Y. Le Bail, N. Le Floc'h, M. Martignon, C. Nédellec, M.-H. Pinard Van Der Laan, E. Quillet, and M.-C. Meunier-Salaün. Ontologie ATOL : amélioration de l'outil par l'intégration des caractères de santé. In Journées d'Animation Scientifique du département Phase (JAS Phase 2018 (Rennes -FR). INRA- book of abstracts, avril 2018, p. 68. présentation orale.

Mastersthesis

[63] M. Kassa. Mod�lisation de parcellaires agricoles. M�moire de stage, G�nie Math�matique - INSA de Rennes (INRA, UR1404- MaIAGE, 78350 Jouy en Josas, France), 2018. encadr� par Katarzyna Adamczyk.

 

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